Gene Literature Dashboard

Suicidality is a significant public health concern, with neuroimaging studies revealing abnormalities in the brains of suicidal individuals and post-mortem samples. However, the genetic architecture between suicidality and subcortical brain volumes remains poorly characterized. Using genome-wide association studies (GWAS), we investigated the genetic overlap between suicidality and subcortical brain volume. GWAS summary statistics for suicidal behaviours, including Suicide Attempts, Ever Self-Harmed, and Thoughts of Life Not Worth Living, from the UK Biobank, Suicide from the FinnGen Biobank, and data on seven subcortical brain volumes and Intracranial Volume from the ENIGMA2 study, were used to investigate the genetic correlation between phenotypes as well as potential genetic factors. A common genetic factor was identified, comprising two categories: Suicide Attempt, Ever Self-Harmed, and Thoughts of Life Not Worth Living from the UK Biobank, and Suicide from FinnGen, Intracranial Volume, and subcortical brain volumes. Cross-phenotype GWAS meta-analysis of each category at variant, gene and subnetwork levels unveils a list of significant variants (P-value <5 × 10^-8), and potential hub genes (P-value <0.05) of consideration. Network, pathway, and Gene Ontology analyses of these joint categories highlighted enriched pathways and biological processes related to blood-brain barrier permeability suggesting that the presence and severity of suicidality are associated with an inflammatory signature detectable in both blood and brain tissues. This study underscores the role of brain and peripheral blood inflammation in suicide risk and holds promise for developing targeted interventions and personalized treatment strategies to reduce suicidality in at-risk populations.

Activation of the innate immune response is essential for host cells to restrict the dissemination of invading viruses and other pathogens. Proteins belonging to the tripartite motif (TRIM) family are key effectors in antiviral innate immunity. Among these, TRIM22, a RING-type E3 ubiquitin ligase, has been recognized as a significant regulator in the pathogenesis of various diseases. In the present study, we identified TRIM22 as a critical modulator of mitochondrial antiviral signaling protein (MAVS) activation. Loss of TRIM22 function led to reduced production of type I interferons (IFNs) in response to viral infection such as influenza A virus (IAV) or vesicular stomatitis virus (VSV), thereby facilitating viral replication. Mechanistically, TRIM22 was found to enhance retinoic acid-inducible gene I (RIG-I)-mediated signaling through the catalysis of Lys63-linked polyubiquitination of MAVS, which, in turn, activated the TANK-binding kinase 1 (TBK1)/interferon regulatory factor 3 (IRF3) pathway, driving IFN-β production. Additionally, TRIM22 was shown to inhibit the assembly of the MAVS-NLRX1 inhibitory complex, further amplifying innate immune responses. Our findings also demonstrated that RNA virus infection upregulated TRIM22 expression via the nuclear translocation of ELF3, a transcription factor that activates TRIM22 gene expression. This regulatory loop underscores the role of TRIM22 in modulating the type I IFN pathway, providing critical insights into the host's antiviral defense mechanisms. Our research highlights the potential of targeting the ELF3-TRIM22-MAVS axis as a therapeutic strategy for enhancing antiviral immunity and preventing RNA virus infections.IMPORTANCEInterferon (IFN)-mediated antiviral responses are crucial for the host's defense against foreign pathogens and are regulated by various signaling pathways. The tripartite motif (TRIM) family, recognized for its multifaceted roles in immune regulation and antiviral defense, plays a significant part in this process. In our study, we explored the important role of TRIM22, a protein that helped regulate the host's immune response to viral infections. We found that TRIM22 enhances the Lys63-linked polyubiquitination of mitochondrial antiviral signaling protein (MAVS), which was essential for producing type I interferons. Interestingly, we discovered that the expression of TRIM22 increases after an RNA virus infection, due to a transcription factor ELF3, which moved into the nucleus of cells to activate TRIM22 transcription. This created a feedback loop that strengthens the role of TRIM22 in modulating the type I IFN pathway. By uncovering these mechanisms, we aimed to enhance our understanding of how the immune system works and provide insights that could lead to innovative antiviral therapies.

<h4>Background</h4>Tumor-associated antigens (TAAs) lead to the production of tumor-specific autoantibodies (anti-TAA autoantibodies) by triggering the humoral immune system which can be used as candidate biomarkers. This study aims to investigate TAAs proteins eliciting humoral responses in different stages of urothelial bladder carcinoma (UBC) using an immunoproteomics approach to find novel biomarkers for the clinical management of the disease.<h4>Methods</h4>Total proteins were obtained from the newly established UBC cell line, JAM-ICR, and separated by two-dimensional gel electrophoresis (2DE). These proteins were then immobilized using pooled serum samples from healthy individuals, autoimmune and UBC patients at different stages. The immunoreactive spots in UBC patient samples were identified by mass spectrometry and verified with several databases such as GEPIA and Enrichr databases.<h4>Results</h4>Through the comparison of the immunoreactivity pattern of serums, we were able to identify eight specific proteins using LC-MS. Patients with muscle invasion showed increased expression of ENO1, VDAC2, AKR1B1, SDF2L1, PRDX6, PSME1, HSPB1 and PHB1 compared to controls. In addition, non-muscle invasive patients showed overexpression of ENO1, VDAC2, AKR1B1, and PRDX6 compared to controls. In addition to their diagnostic function, PRDX6, ENO1, VDAC2, and PHB1 have been demonstrated to possess prognostic capabilities in patients with UBC. Interestingly, these proteins were mainly associated with cellular growth and anti-apoptotic activity.<h4>Conclusion</h4>In this study, eight anti-TAA autoantibodies were identified that have the potential to serve as diagnostic and prognostic biomarkers. These could represent a valuable panel of biomarkers for the management of UBC.

Gamma Secretase Inhibitors (GSIs) effectively block oncogenic Notch homolog-1 (NOTCH1), a characteristic feature of T cell acute lymphoblastic leukemias (T-ALL). However, their clinical application has been stalled by the induction of severe gastrointestinal toxicity resulting from the inhibition of NOTCH signaling in the gut, which translates into increased goblet cell differentiation. Genome-wide CRISPR loss-of-function screen in the colon cancer cell line LS174T identified the neddylation pathway as a main regulator of goblet cell differentiation upon NOTCH1 inhibition. Consistently, pharmacologic inhibition of the neddylation pathway with the small molecule inhibitor MLN4924, rescued GSI-induced differentiation in LS174T cells. Mechanistically, neddylation inhibition by MLN4924 increases the protein stability of Hairy and enhancer of split-1, a direct NOTCH1 transcriptional target and key regulator of absorptive and secretory cell fate decisions. Combined treatment with GSI and MLN4924 in a murine <i>Notch1</i>-dependent model of T-ALL led to leukemia regression and improved overall survival in the absence of gut toxicity. Overall, these results support the combined targeting of the NOTCH1 and neddylation pathways for the treatment of NOTCH1-induced T-ALL.

Hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA) represent the most prevalent primary liver cancers and pose significant challenges in oncology. While their etiology and incidence vary globally, the molecular landscape of these tumors is increasingly understood, offering new opportunities for precision medicine. In this joint multinational review, we present a comprehensive analysis of the key molecular pathways involved in the pathogenesis of HCC and CCA, highlighting actionable targets for emerging therapies. Recent advances in molecular diagnostics have significantly influenced treatment paradigms for both cancers. In HCC, while genetic alterations have not yet led to established diagnostic or therapeutic applications, targeting vascular endothelial growth factor (VEGF), immune checkpoints, and tyrosine kinase pathways has demonstrated considerable therapeutic potential. In CCA, genetic profiling has uncovered actionable alterations, such as FGFR2 fusions and IDH1 mutations, driving the development of targeted therapies. The growing complexity of precision oncology underscores the need for standardized molecular testing and streamlined diagnostic workflows to ensure timely and effective treatment. This review also emphasizes the importance of collaborative efforts between clinicians, pathologists, and oncologists to optimize outcomes. By synthesizing the latest molecular insights and treatment trends, this review provides a valuable resource to guide the personalized management of HCC and CCA.

New antifungals are urgently needed to treat deadly fungal infections. Targeting the fungal inositol polyphosphate kinases IP_3-4K (Arg1) and IP₆K (Kcs1) is a promising strategy as it has been validated genetically to be crucial for fungal virulence but never pharmacologically. We now report the synthesis of <b>DT-23</b>, an analogue of <i>N</i>2-(<i>m</i>-trifluorobenzylamino)-<i>N</i>6-(<i>p</i>-nitrobenzylamino)purine (<b>TNP</b>), and demonstrate that it more potently inhibits recombinant Arg1 from the priority pathogen <i>Cryptococcus neoformans</i> (<i>Cn</i>) (IC₅₀ = 0.6 μM) than previous analogues (IC₅₀ = 10-30 μM). <b>DT-23</b> also inhibits recombinant Kcs1 with similar potency (IC₅₀ = 0.68 μM) and Arg1 and Kcs1 activity <i>in vivo</i>. Unlike previous analogues, <b>DT-23</b> inhibits fungal growth (MIC₅₀ = 15 μg/mL) and only 1.5 μg/mL synergizes with Amphotericin B to kill <i>Cn in vitro</i>. <b>DT-23</b>/Amphotericin B is also more protective against <i>Cn</i> infection in an insect model compared to each drug alone. Transcription profiling shows that <b>DT-23</b> impacts early stages in IP synthesis and cellular functions impacted by IPK gene deletion, consistent with its targeted effect. This study establishes the first pharmacological link between inhibiting IPK activity and antifungal activity, providing tools for studying IPK function and a foundation to potentially develop a new class of antifungal drug.

<h4>Purpose</h4>Changing sperm donors after unsuccessful intrauterine insemination (IUI) cycles is a common yet understudied practice. This study evaluates whether switching sperm donors impacts the number of IUI cycles required to achieve pregnancy.<h4>Methods</h4>This retrospective cohort study analyzed 312 women undergoing donor sperm IUI at Lis Maternity Hospital, Tel Aviv Sourasky Medical Center, from 1992 to 2020. Participants were divided into two groups: Group A (conceived using only one donor) and Group B (switched donors after initial unsuccessful attempts). The primary outcome was the number of IUI cycles until pregnancy. Statistical analyses included t-tests, ANOVA, and multivariate analysis of covariance (MANCOVA).<h4>Results</h4>Women in Group A required fewer cycles (mean 3.78 ± 1.90) to achieve pregnancy compared to Group B (mean 6.07 ± 2.95, P < .001). However, after switching donors, the mean number of cycles needed in Group B (2.23 ± 1.61) was significantly lower than the total cycles required by Group A (P < .001). Cumulative live birth rates were higher in Group A (50.5% after three cycles; 81.5% after six cycles) compared to Group B (26.0% after three cycles; 61.9% after six cycles).<h4>Conclusion</h4>Switching sperm donors after repeated unsuccessful IUI attempts significantly reduces the additional number of cycles needed to achieve pregnancy. These findings suggest that sperm-oocyte compatibility may influence IUI success. Clinicians should consider donor replacement after multiple failures. Prospective studies are required to confirm these results and investigate underlying biological mechanisms.

Data from the first phase of the Human Tumor Atlas Network (HTAN) are now available, comprising 8,425 biospecimens from 2,042 research participants profiled with more than 20 molecular assays. The data were generated to study the evolution from precancerous to advanced disease. The HTAN Data Coordinating Center (DCC) has enabled their dissemination and effective reuse. We describe the diverse datasets, how to access them, data standards, underlying infrastructure and governance approaches, and our methods to sustain community engagement. HTAN data can be accessed through the HTAN Portal, explored in visualization tools-including CellxGene, Minerva and cBioPortal-and analyzed in the cloud through the NCI Cancer Research Data Commons. Infrastructure was developed to enable data ingestion and dissemination through the Synapse platform. The HTAN DCC's flexible and modular approach to sharing complex cancer research data offers valuable insights to other data-coordination efforts and researchers looking to leverage HTAN data.

In the domestic cat (Felis catus), the corpus luteum (CL) is the main source of progestogen during pregnancy. Here, we studied gene expression changes in different life cycle stages of the CL of pseudopregnant cats to identify potential regulatory factors. Results revealed no support for different regression substages, which were previously defined on the basis of morphological examination analysis and intraluteal hormone content, as only a very low number of differentially expressed genes and no subclusters in PCA plot were detected. By comparing the regression stage with the developmental/maintenance stage, we detected a total of 6174 differentially expressed genes in the sample set, of which 2882 were upregulated and 3292 were downregulated. The large changes in the expression levels of some genes indicate that the endocrine function of the CL may not be restricted to progesterone (P4) secretion. The findings suggest that domestic cat CLs could also be a source of adipokines such as adiponectin or APELA. The expression of these genes is highly variable and reversed between stages. The life cycle and activity of CLs seem to be regulated by different factors, as genes encoding for the hormone receptors LHCGR and PAQR5 were more highly expressed in the development/maintenance stage, in contrast to this encoding for LEPR, which is higher expressed in regression stage. For regression stage, we identified different potential ways to modulate the cholesterol level and/or P4 concentration. Furthermore, we found differences from previous studies in other species for many genes that were studied in more detail, as well as when analysing functions and pathways. Our findings support the hypothesis that different stages of the CL life cycle in domestic cats can be characterized by changes in gene regulation and that CL life cycles are partly differentially regulated between species.

<h4>Background</h4>Pseudomonas aeruginosa infections in the lungs affect millions of children and adults worldwide. To our knowledge, no clinically validated prognostic biomarkers for chronic pulmonary P. aeruginosa infections exist. Therefore, this study aims to identify potential prognostic markers for chronic P. aeruginosa biofilm lung infections.<h4>Methods</h4>Here, we screened the expression of 11 P. aeruginosa regulatory genes (tesG, algD, lasR, lasA, lasB, pelB, phzF, rhlA, rsmY, rsmZ, and sagS) to identify associations between clinical status and chronic biofilm infection.<h4>Results</h4>RNA was extracted from 210 sputum samples from patients (n = 70) with chronic P. aeruginosa lung infections (mean age; 29.3-56.2 years; 33 female). Strong biofilm formation was correlated with prolonged hospital stays (212.2 days vs. 44.4 days) and increased mortality (46.2% (18)). Strong biofilm formation is associated with increased tesG expression (P = 0.001), influencing extended intensive care unit (P = 0.002) or hospitalisation stays (P = 0.001), pneumonia risk (P = 0.006), and mortality (P = 0.001). Notably, tesG expression is linked to the modulation of systemic and sputum inflammatory responses and predicts biofilm biomass.<h4>Conclusions</h4>This study provides the first clinical dataset of tesG expression levels as a predictive biomarker for chronic P. aeruginosa pulmonary infections.

<h4>Background</h4>Osteoporosis and kidney stones share several common pathophysiological risk factors, and their association is well-established. However, previous studies have primarily focused on environmental mediators, such as diet, and the precise mechanism linking these two conditions remains unclear.<h4>Methods</h4>The relationship between osteoporosis and kidney stones was analyzed using weighted multivariate logistic regression, employing data from five cycles of the National Health and Nutrition Examination Survey (NHANES) from 2007-2010, 2013-2014, and 2017-2020. Gene expression data from the Gene Expression Omnibus (GEO) microarray database were integrated with machine learning techniques to identify key genes involved in both osteoporosis and kidney stones. Common targets were then identified through the Comparative Toxicogenomics Database (CTD) and GeneCards. GMFA enrichment analysis was performed to identify shared biological pathways. Additionally, drug prediction and molecular docking were employed to further investigate the pharmacological relevance of these targets.<h4>Results</h4>Analysis of the NHANES database confirmed a strong association between osteoporosis and kidney stones. Weighted multivariate logistic regression showed that osteoporosis (OR: 1.41; 95% CI 1.11-1.79; P < 0.001) and bone loss (OR: 1.24; 95% CI 1.08-1.43; P < 0.001) were significantly correlated with an increased risk of kidney stones. Three hub genes-WNT1, AKT1, and TNF-were identified through various analytical methods. GMFA revealed that the mTOR signaling pathway is a key shared pathway. Molecular docking studies further confirmed the pharmacological relevance of these targets, demonstrating strong binding affinity between drugs and the proteins involved, consistent with previous findings.<h4>Conclusion</h4>Bone loss is associated with an increased risk of kidney stones. Targeting the mTOR signaling pathway may offer a potential therapeutic approach for treating both osteoporosis and kidney stones.

<h4>Background</h4>Crohn's disease (CD) is a chronic inflammatory bowel disease (IBD) and is considered a Th1-mediated disease, supported by the over-expression of interferon-gamma (IFN-γ) in the intestinal lamina propria. IFN-γ has a pleiotropic effect on the intestinal epithelial cells (IECs), suggesting that IFN-γ-induced responses may differ between epithelial cell types.<h4>Methods</h4>We established human small intestinal organoids (enteroids) derived from non-IBD controls and CD patients. Using human enteroids, the major response of IECs induced by IFN-γ was evaluated, focusing on the IFN-γ-induced programmed cell death (PCD) pathway. Identified IFN-γ-induced responses were validated in surgically resected intestinal samples and publicly available single-cell RNA-sequencing datasets.<h4>Results</h4>IFN-γ stimulated programmed cell death (PCD) of IECs in both control and CD enteroids in a dose-dependent manner. Pyroptosis, apoptosis. and necroptosis were activated in enteroids, suggesting that PANoptosis was the main process of IFN-γ-induced PCD in IECs. The response to IFN-γ depends on the cell type of the IECs. IFN-γ induced depletion of enterocytes with upregulation of PANoptosis-associated genes, while leading to expansion of goblet cells without significant change in PANoptosis-associated gene expression. Individual PCD inhibitors were insufficient to block IFN-γ-induced cytotoxicity, whereas the selective JAK1 inhibitor (upadacitinib) effectively blocked IFN-γ-induced cytotoxicity and PANoptosis. Furthermore, PANoptosis was significantly activated in surgically resected tissues and in publicly available single-cell RNA-sequencing datasets of intestinal tissues from patients with CD.<h4>Conclusion</h4>IFN-γ induces PANoptosis in enterocytes, which can be treated with a selective JAK1 inhibitor in patients with CD.

<h4>Objective</h4>To explore the role of transketolase (TKT) in the immunotherapy and prognosis of hepatocellular carcinoma (HCC).<h4>Materials and methods</h4>TKT expression across various cancers and its associations with tumor immunity and prognosis were analyzed using nomogram models. A multi-omics approach was employed, including bulk RNA-seq analysis, methylation profiling, single-cell analysis, and spatial transcriptomics. Experimental methods included RT-qPCR, siRNA transfection, luciferase reporter assay, and chromatin immunoprecipitation.<h4>Results</h4>TKT was significantly upregulated in multiple cancers and correlated with immune cell infiltration, particularly in HCC. Elevated TKT expression was associated with poor overall survival (OS) in HCC and was an independent prognostic factor (p < 0.05). Drug sensitivity analysis suggested that higher TKT expression was associated with reduced sensitivity to several chemotherapeutic agents, including sorafenib (p < 0.01). Furthermore, hypermethylation of the TKT promoter and low TKT expression were linked to improved OS in HCC (log-rank test p = 0.005). Single-cell analysis revealed that TKT was predominantly expressed in the monocyte/macrophage cluster associated with HCC, and pseudo-time series analysis highlighted TKT's role in cell differentiation within this cluster. Spatial transcriptomics confirmed the close association between TKT and macrophage distribution in HCC. Moreover, STAT3 was found to directly regulate TKT expression by binding to its promoter region.<h4>Conclusion</h4>Our findings suggest that TKT may play a role in tumor immunity and prognosis in HCC. Although these results provide insights into the potential involvement of TKT in immune cell infiltration and survival outcomes, further studies are required to fully elucidate its role in immunotherapy.

<h4>Background</h4>Achieving survival free from physical disability or neurocognitive impairment, known as disability-free survival (DFS), is a key public health goal. This study aimed to (1) determine the long-term interactive effects of depression and cardiometabolic diseases (CMDs) on DFS, and (2) explore any associated antidepressant treatment effect on improvements in DFS among older adults.<h4>Methods</h4>We used data from the ASPREE trial and its observational follow-ups (2010-2019), involving community-dwelling adults aged ≥ 70 years (≥65 for U.S. minorities). Time-updated Cox models were used to estimate the combined effect of depression and CMDs (type 2 diabetes, dyslipidemia, hypertension, chronic kidney disease, metabolic-associated steatotic liver disease, and major adverse cardiovascular events) as well as cardiometabolic multimorbidity (≥2 CMDs) on DFS. To evaluate the improvement in DFS associated with antidepressant treatment in individuals with depression, we estimated the number needed to treat (NNT) to achieve a one-year increase in DFS through antidepressant therapy.<h4>Findings</h4>18,739 participants (mean [SD] age, 75.1 [4.6] years; 56.0% female) were included, with a median follow-up of seven years; individuals with both depression and CMDs demonstrated a significantly lower DFS compared to those without either condition. In individuals with depressive symptoms, antidepressant use was associated with a median increase in DFS of 2.95 years (95% CI, 2.12-3.04), with an estimated NNT of 8.05 (95% CI, 5.63-14.86) associated with a one-year increase in DFS.<h4>Interpretation</h4>Integrating depression treatment into chronic disease management, when appropriate, is associated with an improvement in DFS among older adults.<h4>Funding</h4>Deakin University Postgraduate Research Scholarship.

Focal cortical dysplasia type III (FCDIII) is a rare and complex condition associated with drug-resistant epilepsy and often characterized by cortical lamination abnormalities, along with a variety of neoplasms and vascular abnormalities.<h4>Objectives</h4>This study aimed to elucidate the genetic architecture underlying FCDIII through the use of whole-exome sequencing (WES) of brain and peripheral blood samples from 19 patients who had been diagnosed with FCDIII.<h4>Methods</h4>Variants were identified through a series of machine-learning-based detection and functional prediction methods and were not previously associated with FCDIII. Mosaic fraction scores of these variants validated the variants' pathogenicity, and in silico and gene ontology enrichment analyses demonstrated that these variants had severe destabilizing effects on protein structure.<h4>Results</h4>We reported ten novel pathogenic somatic missense and loss of function variants across eight genes, including <i>CNTNAP2</i>, <i>ACY1</i>, <i>SERAC1</i>, and <i>BRAF</i>. Genetic alterations were linked to clinical manifestations, such as encephalopathies and intellectual disabilities, thereby emphasizing their role as molecular drivers of FCDIII.<h4>Conclusions</h4>We demonstrated that next-generation sequencing-based mosaic variant-calling pipelines are useful for the genetic diagnosis of FCDIII, opening up avenues for targeted therapies, yet further research is required to validate these findings and examine their therapeutic implications.

<b>Background/Objectives:</b> The purpose of this research was to investigate the effects of bisphenol A (BPA) exposure on neurobehavioral testing in young Wistar rats and to evaluate the therapeutic potential of <i>Thymus ciliatus</i> (TEO) essential oil to attenuate the damage induced by this chemical toxin. <b>Methods</b>: The essential oil was extracted by hydro-distillation (yield of 2.26%), and the characterization by GC-MS indicates that the major components of <i>Thymus ciliatus</i> oil are thymol (63.33%), p-cymene (13.4%), and σ-terpinene (6.69%). Acute BPA intoxication was induced with a dose of 50 mg/kg orally for 60 days. The neurobehavioral evaluation, performed using a comprehensive set of tests including the forced swim test, dark/light box, Morris water maze, open field test, and sucrose preference test, clearly demonstrated that bisphenol A (BPA) exposure induced significant neurobehavioral impairments. <b>Results</b>: These impairments included reduced exploratory behavior indicative of heightened stress, anxiety, and depressive-like states, as well as deficits in memory and learning. Furthermore, BPA intoxication was associated with metabolic disturbances such as hyperglycemia along with histopathological evidence of brain tissue damage. However, TEO treatment attenuated these adverse effects by restoring neurobehavioral function. Molecular docking analysis revealed an affinity between the major essential oils identified in <i>T. ciliatus</i>, BPA, and the 5HT2C receptor and the MAO, AChE, and BChE enzymes, suggesting a potential mechanism underlying BPA's effects on behavior and memory. In addition, TEO also showed an interaction with these molecules, suggesting a therapeutic potential against BPA. These findings underscore the promising role of TEO in mitigating the poisonous effects of BPA and pave the way for additional research into the molecular mechanisms and therapeutic uses of natural bioactive compounds for the prevention and treatment of toxic diseases. Thymol, the major compound in TEO, exhibited activity related to the dopamine and serotonin pathways, so it could have potential antidepressant properties. <b>Conclusions</b>: Thymol might be a promising candidate for the treatment of neurodegenerative and neurological disorders such as depression, Parkinson's disease, and Alzheimer's disease while also preventing histological damage in the brain.

Pancreatic cancer is one of the most lethal neoplasms. Despite considerable research conducted in recent decades, not much has been achieved to improve its survival rate. That may stem from the lack of effective screening strategies in increased pancreatic cancer risk groups. One population that may be appropriate for screening is new-onset diabetes (NOD) patients. Such a conclusion stems from the fact that pancreatic cancer can cause diabetes several months before diagnosis. The most widely used screening tool for this population, the ENDPAC (Enriching New-Onset Diabetes for Pancreatic Cancer) model, has not achieved satisfactory results in validation trials. This provoked the first attempts at using artificial intelligence (AI) to create larger, multi-parameter models that could better identify the at-risk population, which would be suitable for screening. The results shown by the authors of these trials seem promising. Nonetheless, the number of publications is limited, and the downfalls of using AI are not well highlighted. This narrative review presents a summary of previous publications, recent advancements and feasible solutions for effective screening of patients with NOD for pancreatic cancer.

The pathogenesis of tumors involves various abnormalities at both the cellular and genetic levels. Chimeric antigen receptor (CAR)-T cell immunotherapy has emerged as a transformative treatment strategy that effectively addresses these challenges. While CAR-T therapy has shown remarkable success in treating hematological malignancies, limitations have been identified, particularly in single antigen-targeting CAR-T therapies. These limitations include antigenic mutation or loss, reduced efficacy against leukemia, and poor results in solid tumors due to factors like low CAR-T cell persistence, limited tumor infiltration, rapid cell exhaustion, the suppressive tumor microenvironment, and heterogeneous tumor antigen expression. In recent years, multi-antigen targeted CAR-T therapies have garnered significant attention for their potential to prevent tumor relapse and progression. This review outlines the fundamental design of dual CAR structures and summarizes the major advancements in both preclinical studies and clinical trials of dual-targeted CAR-T cell therapy, categorized by cancer type. Additionally, it discusses the challenges associated with dual-targeted CAR-T therapy and the strategies to enhance its efficacy and applicability in treating both hematologic and solid tumors. In conclusion, the progress in dual-targeted CAR-T cell therapy presents a promising therapeutic avenue for multiple malignancies, offering insights into future modifications of immunotherapy to advance the field.

<b>Rationale:</b> Spinal cord injury (SCI) leads to limited regenerative capacity and severe energy deficiency in the injury microenvironment. This study aimed to develop a biomimetic piezoelectric hydrogel system that could recapitulate the native tissue microenvironment while enabling wireless physical regulation for SCI repair. <b>Methods:</b> A piezoelectric hydrogel was fabricated by integrating K_0.5Na_0.5NbO₃ (KNN) nanoparticles with porous decellularized spinal cord matrix gel (pDG). The hydrogel's effects on vascular endothelial cell migration, neural stem cell differentiation, and ATP synthesis were evaluated <i>in vitro</i>. RNA sequencing was performed to identify key regulatory pathways. The therapeutic efficacy was assessed in a rat model of spinal cord hemisection, examining motor function and angiogenesis. <b>Results:</b> The piezoelectric hydrogel demonstrated excellent biocompatibility and significantly enhanced vascular endothelial cell and neural cell migration. Under ultrasonic stimulation, the hydrogel promoted neural stem cell differentiation into neurons more effectively than control hydrogels. The piezoelectric stimulation increased ATP synthesis and calcium ion flux, activating the Ca2+/Camk2b/PGC-1α signaling axis. <i>In vivo</i> studies showed that implantation of the piezoelectric hydrogel combined with ultrasound stimulation significantly improved motor function recovery and promoted angiogenesis. <b>Conclusion:</b> The piezoelectric hydrogel system presents an effective strategy for SCI repair through energy metabolism reprogramming and demonstrates promising potential in neural tissue engineering applications.

The peroxiredoxin (PRDX) family, also known as the peroxidase family, consists of six members that participate in a variety of essential bio-processes in carcinogenesis. However, their molecular role in lung adenocarcinoma (LUAD) has not been systematically explored. Using bioinformatic tools, we systematically analyzed the expression, prognostic value and drug sensitivity of the PRDX gene family members in LUAD. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to verify the expression of PRDX1 in both LUAD tissues and cells. Cell Counting Kit-8 (CCK-8) assay was applied to detect the half-maximal inhibitory concentration (IC₅₀) of osimertinib in LUAD. A series of cellular drug assays, including 5-Ethynyl-2'-deoxyuridine (EdU), colony formation, and apoptosis assays, were performed to explore the correlation of PRDX1 with epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI) sensitivity by using EGFR-mutant and wild-type LUAD cell lines. Among all the PRDX family members, PRDX1 has a promising prognostic value and is associated with EGFR mutations, as verified by experiments conducted on collected LUAD specimens. In addition, pathway enrichment analysis suggested that PRDX1 expression positively correlated with DNA repair, which is often considered to be inextricably linked to drug resistance in tumor cells. Thus, we validated the correlation between PRDX1 and EGFR-TKI sensitivity through a series of <i>in vitro</i> experiments and found that PRDX1 inhibition along with osimertinib treatment resulted in synergistic inhibition of tumor growth. Moreover, we found that PRDX1 was negatively correlated with the immune infiltration of dendritic cells (DCs) in the tumor microenvironment (TME) of LUAD, further suggesting an oncogenic role of PRDX1. This study demonstrates that high PRDX1 expression could be a potential diagnostic and prognostic marker of LUAD, and the strategy of PRDX1 knockdown provides new insights into improving the therapeutic sensitivity of EGFR-TKI in patients with LUAD.

Myeloid sarcoma (MS) is a solid mass of myeloid blasts outside the bone marrow (BM). Most cases occur in the setting of intramedullary acute myeloid leukemia (AML), but it can also present in the absence of overt BM disease, as a presentation of newly diagnosed or relapsed AML, or as a progression of myeloproliferative neoplasms or myelodysplastic syndromes. There are a few reports of spinal cord compression due to MS, and there is no consensus regarding its management. Here, we present a case of relapsed AML in the form of MS resulting in spinal cord compression and provide a comprehensive literature review of previously reported cases of MS causing cord compression. An 18-year-old male was diagnosed with AML with poor-risk cytogenetics in September 2023. He received induction chemotherapy (CTX) with 7+3, followed by consolidation with high-dose cytarabine, achieving remission. He was referred for BM transplant evaluation but opted against it. One year later, he presented with a four-month history of bilateral motor and sensory deficits along with bladder dysfunction. A magnetic resonance imaging (MRI) of the spine showed multilevel nerve root thickening and enhancement and multiple extramedullary masses. Spinal radiation therapy and corticosteroids were given; a biopsy was deferred due to high procedural risks. Given his prior history of AML, the findings were highly suspicious for MS. A complete blood count (CBC) and smear did not show circulating blasts, and a BM exam was inconclusive. Induction CTX with MEC regimen (mitoxantrone, etoposide, cytarabine) was started. A lumbar puncture with CSF flow cytometry confirmed central nervous system involvement with myeloid blasts, and a brain MRI revealed leptomeningeal disease. Intrathecal CTX was given. A spine MRI on day 15 post-induction showed partial improvement in spinal disease. The patient was discharged 30 days after receiving induction CTX, and he planned to continue his care at a local cancer institute in his home state.

<h4>Purpose</h4>Tuberculosis (TB) claims around 1.5 million lives annually. The M72/AS01E vaccine candidate is an innovative effort demonstrating a 50% reduction in the incidence of active TB in adults. However, optimization and effective immunization strategies against TB depends heavily on precise identification of specific molecular signatures active in vaccine protection.<h4>Materials and methods</h4>In this study, we employed weighted gene co-expression network analysis, machine learning, and network biology to investigate the gene expression patterns of peripheral blood mononuclear cells, identifying transcriptomic markers of vaccine protection.<h4>Results</h4>Our comprehensive exploration of publicly available gene expression dataset comprising samples from subjects vaccinated twice with 10 μg of M72/AS01E vaccine one day post-second dose (D31) and one week post-second dose (D37) in a phase IIA clinical trial revealed intense induction of multiple gene modules, indicative of acute/immediate immune response at D31 that subsided by D37. Thirty-one hub genes with significant elevation/correlation with immune protection were identified significantly mediating key events in immunity to TB. The more selective profile at D37 involved additional adaptive immunity pathways including T helper (Th) 1/Th2/Th17 differentiation, T cell receptor and cytokine signaling. The functional relevance of these biomarkers in predicting vaccine response was further analyzed using the Random Forest classifier demonstrating high accuracy in distinguishing between vaccinated and non-vaccinated samples. Additionally, the study pinpointed a miRNAs-transcription factors (TF)-target regulatory network excavating key TF, miRNA, mRNAs mediating vaccine protection.<h4>Conclusion</h4>Our results provided new insights into M72/AS01E immunity, warranting further study to optimize and guide future TB vaccine development.

<h4>Purpose</h4>Bioprinting is an additive manufacturing technique used to print living cells within a three-dimensional scaffold that mimics natural tissue microenvironments. There are several disadvantages to using hydrogel-based biomaterials for bioprinting including limited cell adhesion and functionality. To address this, we have developed a library of Janus base Nano-Matrices (JBNms) which are novel nanoscale scaffolds self-assembled from DNA-inspired Janus base nanotubes (JBNts) and ECM molecules. In this study, JBNms are incorporated in bioprinting by printing a cartilage-specific JBNm with human mesenchymal stem cells (hMSCs) into a 3D alginate scaffold to selectively improve chondro-lineage cell adhesion and differentiation.<h4>Methods</h4>Human mesenchymal stem cells (hMSCs) were combined with a cartilage-specific JBNm and printed within an alginate-based bioink. They were maintained in chondrogenic media and were characterized at 7 and 28 days. Reverse transcription quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) and histological staining were used to determine the presence of cartilage-specific genes and proteins.<h4>Results</h4>The bioprinted structures with the cartilage-specific JBNm showed significantly greater expression of chondrogenic-related marker genes and glycosaminoglycan (GAG) expression after 28 days compared to the negative control group, indicating successful chondrogenesis. The cells were viable within the structures and showed significant proliferation after 28 days.<h4>Conclusion</h4>Cartilage-specific JBNm scaffolds successfully promote enhanced hMSC adhesion, growth, and chondrogenic differentiation within bioprinted constructs.

A major challenge in human evolutionary biology is to pinpoint genetic differences that underlie human-specific traits, such as increased neuron number and differences in cognitive behaviors. We used human-chimpanzee tetraploid cells to distinguish gene expression changes due to cis -acting sequence variants that change local gene regulation, from trans expression changes due to species differences in the cellular environment. In neural progenitor cells, examination of both cis and trans changes — combined with CRISPR inhibition and transcription factor motif analyses — identified cis -acting, species-specific gene regulatory changes, including to TNIK, FOSL2 , and MAZ , with widespread trans effects on neurogenesis-related gene programs. In excitatory neurons, we identified POU3F2 as a key cis -regulated gene with trans effects on synaptic gene expression and neuronal firing. This study identifies cis -acting genomic changes that cause cascading trans gene regulatory effects to contribute to human neural specializations, and provides a general framework for discovering genetic differences underlying human traits.

Curcumin, a major phytochemical derived from Curcuma longa, has been shown to enhance the efficacy of chemotherapeutic agents such as doxorubicin, 5-fluorouracil, and cisplatin by overcoming drug resistance, making it a promising adjunct in the treatment of glioblastoma. However, the global gene expression changes triggered by curcumin in glioblastoma remain underexplored. In this study, we investigated the effects of curcumin on human glioblastoma (U87 MG) cells, where it significantly reduced cell viability and proliferation in a dose- and time-dependent manner and induced apoptosis without affecting senescence. Transcriptomic analysis revealed 5,036 differentially expressed genes, with pathway enrichment identifying 13 dysregulated cancer-associated pathways. Notably, curcumin modulated several key regulators involved in MAPK, Ras, TGF-&beta;, Wnt, Cytokine, and TNF signalling pathways. Several apoptosis and cell cycle-associated genes, including PRKCG, GDF7, GDF9, GDF15, GDF5, FZD1, FZD2, FZD8, AIFM3, TP53AIP1, CRD14, NIBAN3, BOK, BCL2L10, BCL2L14, BNIPL, FASLG, GZMM, TNFSF10, TNFSF11, and TNFSF4, were significantly altered. Importantly, RUNX3, a key tumour suppressor, was markedly upregulated following curcumin treatment, emphasizing its potential role in curcumin-mediated anti-tumour effects. This study provides insight into the molecular mechanisms underlying curcumin's action against glioblastoma.

<h4>Background</h4>The high heterogeneity of hepatocellular carcinoma (HCC) poses challenges for precision treatment strategies. This study aims to use multi-omics methodologies to better understand its pathogenesis and discover biomarkers.<h4>Methods</h4>Quantitative proteomics was used to investigate hepatocellular carcinoma tissues (HCT) and their corresponding adjacent non-tumor tissues (DNT), obtained from six HCC patients. Untargeted metabolomics was applied to analyze the metabolic profiles of HCT and DNT of ten HCC patients. Statistical analyses, such as the Student's t-test, were performed to identify differentially expressed proteins (DEPs) and metabolites (DEMs) between the two groups. The functions and metabolic pathways involving DEPs and DEMs were annotated and enriched using the gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) databases. Bioinformatics methods were then utilized to analyze consistency between proteomics and metabolomics results, leading to identification of potential biomarkers along with key altered pathways associated with HCC.<h4>Results</h4>This study identified 1556 DEPs between HCT and DNT samples. These DEPs were primarily enriched in crucial biological pathways such as amino acid degradation, fatty acid metabolism, and DNA replication. Subsequently, the analysis of metabolomics identified 500 DEMs that mainly participated in glycerophospholipid metabolism, the phospholipase D signaling pathway, and choline metabolism related to cancer. Integrated analysis of proteomics and metabolomics data unveiled significant dysfunctions in bile secretion, multiple amino acid and fatty acid metabolic pathways among HCC patients. Further investigation revealed that five proteins (PTP4A3, B4GALT5, GAB1, ME2, and PKM) along with seven metabolites (PI(6 keto-PGF1alpha/16:0), 13, 16, 19-docosatrienoic acid, PA(18:2(9Z, 12Z)/20:1(11Z)), Citric Acid, PG(20:3(6, 8, 11)-OH(5)/18:2(9Z, 12Z)), Spermidine, and N2-Acetylornithine) exhibited excellent diagnostic efficiency for HCC and could serve as its potential biomarkers.<h4>Conclusion</h4>Our integrated proteome and metabolome analysis revealed 10 key HCC-related pathways and proposed 12 potential biomarkers, which may enhance our understanding of HCC pathophysiology and be helpful in facilitating early diagnosis and treatment strategies.

Methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) represents a major global health threat due to its resistance to conventional antibiotics. The commensal microbiota maintains a symbiotic relationship with the host, playing essential roles in metabolism, energy regulation, immune modulation, and pathogen control. Mammals harbor a wide range of commensal bacteria capable of producing unique metabolites with potential therapeutic properties. This study demonstrated that M28 family peptidase (M28), derived from commensal bacteria <i>Peribacillus frigoritolerans</i> (<i>P. f</i>), provided protective effects against MRSA-induced pneumonia. M28 enhanced the phagocytosis and bactericidal activity of macrophages by inducing trained immunity. RNA sequencing and metabolomic analyses identified the CFB-C3a-C3aR-HIF-1α axis-mediated phosphatidylcholine accumulation as the key mechanism for M28-induced trained immunity. Phosphatidylcholine, like M28, also induced trained immunity. To enhance M28-mediated therapeutic potential, it was encapsulated in liposomes (M28-LNPs), which exhibited superior immune-stimulating properties compared to M28 alone. In vivo experiments revealed that M28-LNPs significantly reduced bacterial loads and lung damage following MRSA infection, which also provided enhanced protection against <i>Klebsiella pneumoniae</i> and <i>Candida albicans</i>. We first confirmed a link between complement activation and trained immunity, offering valuable insights into the treatment and prevention of complement-related autoimmune diseases.

Fitting mechanistic models, such as the Farquhar-von-Caemmerer-Berry model, to experimentally measured photosynthetic CO₂ response curves (A-C_i curves) is a widely used technique for estimating the values of key leaf biochemical parameters and determining limitations to photosynthesis in vivo. Here, we present PhotoGEA, an R package with tools for C₃ A-C_i, C₃ Variable J and C₄ A-C_i curve fitting. In contrast to existing software, these automated tools use derivative-free optimizers to ensure close fits and they calculate non-Gaussian confidence intervals to indicate which parameter values are most reliable. Results from PhotoGEA's C₃ A-C_i curve fitting tool are compared against other available tools, where it is found to achieve the closest fits and most reasonable parameter estimates across a range of curves with different characteristics. PhotoGEA's C₃ Variable J and C₄ A-C_i fitting tools are also presented, demonstrating how they can provide insights into mesophyll conductance and the processes limiting C₄ photosynthesis at high CO₂ concentrations. PhotoGEA enables users to develop data analysis pipelines for efficiently reading, processing, fitting and analysing photosynthetic gas exchange measurements. It includes extensive documentation and example scripts to help new users become proficient as quickly as possible.

<h4>Introduction</h4>Little is known about the role of transition metals in glioblastoma progression. Here we investigated whether transition metal content is associated with glioblastoma outcomes.<h4>Methods</h4>Tumor samples were obtained from 37 newly diagnosed patients with glioblastoma, 21 of which had matched plasma. Iron, zinc, manganese, and copper content in those samples was quantified via inductively-coupled mass spectrometry or atomic emission spectrometry, and subsequently analyzed for associations with overall survival. Multiplexed immune profiling was performed to determine whether transition metal content was associated with altered cytokine profiles.<h4>Results</h4>Higher plasma iron levels were strongly associated with prolonged survival (Kaplan-Meier analysis: 30.15 months vs. 12.43 months, P = 0.0036; Multivariate Cox regression analysis: HR: 0.79 [0.64 - 0.97], P = 0.03). Zinc, manganese, and copper concentration in plasma or tumor and iron in tumor were not significantly associated with overall survival. Immune profiling of plasma and tumor samples revealed that plasma iron correlated with plasma IFN-β concentration (R = 0.63, P = 0.0057) in patients with glioblastoma. No correlation of plasma iron and IFN-β was observed in age- and sex- matched healthy individuals (R = -0.15, P = 0.153). Plasma transition metal concentration did not correlate with tumor transition metal concentration. Within tumors, manganese and zinc were correlated (R = 0.52, P = 0.0048) as well as copper and zinc (R = 0.36, P = 0.038).<h4>Conclusions</h4>Plasma iron is associated with survival in glioblastoma patients and may serve as a prognostic marker. The mechanisms underlying this association require further study.

Short tandem repeat (STR) sequences are highly variable DNA segments that significantly contribute to human neurodegenerative disorders, highlighting their crucial role in neuropsychiatric conditions. This article examines the pathogenicity of abnormal STRs and classifies tandem repeat expansion disorders(TREDs), emphasizing their genetic characteristics, mechanisms of action, detection methods, and associated animal models. STR expansions exhibit complex genetic patterns that affect the age of onset and symptom severity. These expansions disrupt gene function through mechanisms such as gene silencing, toxic gain-of-function mutations leading to RNA and protein toxicity, and the generation of toxic peptides via repeat-associated non-AUG (RAN) translation. Advances in sequencing technologies-from traditional PCR and Southern blotting to next-generation and long-read sequencing-have enhanced the accuracy of STR variation detection. Research utilizing these technologies has linked STR expansions to a range of neuropsychiatric disorders, including autism spectrum disorders and schizophrenia, highlighting their contribution to disease risk and phenotypic expression through effects on genes involved in neurodevelopment, synaptic function, and neuronal signaling. Therefore, further investigation is essential to elucidate the intricate interplay between STRs and neuropsychiatric diseases, paving the way for improved diagnostic and therapeutic strategies.

Inflammasomes are multi-protein complexes that detect pathogenic and damage-associated molecular patterns, activating caspase-1, pyroptosis, and the maturation of pro-inflammatory cytokines such as IL-1β and IL-18Within the tumor microenvironment, inflammasomes like NLRP3 play critical roles in cancer initiation, promotion, and progression. Their activation influences the crosstalk between innate and adaptive immunity by modulating immune cell recruitment, cytokine secretion, and T-cell differentiation. While inflammasomes can contribute to tumor growth and metastasis through chronic inflammation, their components also present novel therapeutic targets. Several inhibitors targeting inflammasome components- such as sensor proteins (e.g., NLRP3, AIM2), adaptor proteins (e.g., ASC), caspase-1, and downstream cytokines- are being explored to modulate inflammasome activity. These therapeutic strategies aim to modulate inflammasome activity to enhance anti-tumor immune responses and improve clinical outcomes. Understanding the role of inflammasomes in cancer immunity is crucial for developing interventions that effectively bridge innate and adaptive immune responses for better therapeutic outcomes.

Antibodies play a crucial role in defending the human body against diseases, including life-threatening conditions like cancer. They mediate immune responses against foreign antigens and, in some cases, self-antigens. Over time, antibody-based technologies have evolved from monoclonal antibodies (mAbs) to chimeric antigen receptor T cells (CAR-T cells), significantly impacting biotechnology, diagnostics, and therapeutics. Although these advancements have enhanced therapeutic interventions, the integration of artificial intelligence (AI) is revolutionizing antibody design and optimization. This review explores recent AI advancements, including large language models (LLMs), diffusion models, and generative AI-based applications, which have transformed antibody discovery by accelerating de novo generation, enhancing immune response precision, and optimizing therapeutic efficacy. Through advanced data analysis, AI enables the prediction and design of antibody sequences, 3D structures, complementarity-determining regions (CDRs), paratopes, epitopes, and antigen-antibody interactions. These AI-powered innovations address longstanding challenges in antibody development, significantly improving speed, specificity, and accuracy in therapeutic design. By integrating computational advancements with biomedical applications, AI is driving next-generation cancer therapies, transforming precision medicine, and enhancing patient outcomes.

<h4>Purpose</h4>The clinical relevance of the red blood cell distribution width (RDW) in patients with distal cholangiocarcinoma (DCC) undergoing pancreaticoduodenectomy (PD) has not been clearly investigated.<h4>Methods</h4>The relationship between the preoperatively measured RDW and prognosis for the recurrence/survival was evaluated in patients with DCC undergoing PD. A subgroup analysis was also performed in patients with pathological stage I DCC.<h4>Results</h4>A total of 77 patients were included in the analysis. The cutoff value of the preoperatively measured RDW was set at 14%, and the normal reference range at our center was ≤ 14%. The patient group with an RDW > 14% (n = 30) had a significantly lower mean serum albumin level, higher mean serum carbohydrate antigen 19-9 level, and a higher proportion of cases with pathological lymphatic invasion and showed a significantly worse overall survival than the patient group with an RDW ≤ 14% (n = 47). Similar findings were noted in both the overall study population and patients with pathological stage I disease. Multivariate analysis identified an RDW > 14% and pathological lymph node metastasis as independent risk factors for a poor postoperative survival.<h4>Conclusion</h4>The preoperatively measured RDW is a promising prognostic predictor in patients with DCC undergoing PD.

Bone marrow cytology plays a key role for the diagnosis and classification of hematological disease and is often the first step in the acute setting of unclear cytopenia. AI applications represent a powerful tool in digital image analysis and can improve the diagnostic workflow and accuracy. The aim of this study was to develop an algorithm for the automated detection and classification of hematopoietic cells in digitized bone marrow aspirate smears for potential implementation in the clinical laboratory. The AIFORIA create platform (Aiforia Technologies, Plc, Helsinki, Finland) was used to develop a convolutional neural network algorithm based on nine cell classes. Digitized bone marrow aspirate smears from normal hospital controls were used for AI training. External validation was performed on separate data sets. Automated cell classification was assessed in whole-slide images (WSI) and regions of interest (ROI). A total of 1950 single-cell annotations were applied for AI training with a final total class error of 0.15% with 99.9% precision and sensitivity (FI-score 99.2%). External validation showed an overall precision and sensitivity of 96% and 97% and a F1-score of 96%. Automated cell classification correlated highly across ROI with variable correlation to WSI. The average execution time for classifying 500 hematopoietic cells was < 1 s and ≤ 260 s for WSI. A cloud-based, deep-learning algorithm for automated detection and classification of hematopoietic cells in bone marrow aspirate smears is a very useful, reliable, and rapid screening tool in combination with cytomorphology.

Given that hereditary prostate cancer (PCa) accounts for only a small fraction of PCa phenotypes, there is still a substantial journey ahead in exploring the somatic genetic drivers contributing to sporadic PCa. The expression quantitative trait loci (eQTLs) data were sourced from the GTEx dataset for prostate-specific genes, and the summary statistic information was collected for 5854 genes. Genetic associations with PCa were extracted from three well-established consortiums: the UK Biobank (9131 cases and 173,493 controls), the PRACTICAL study (79,148 cases and 61,106 controls), and the FinnGen cohort (13,216 cases and 119,948 controls). To prioritize potential causal targets, additional analysis, including the protein-protein interaction (PPI), The Cancer Genome Atlas (TCGA) dataset, and the single-cell-type expression analysis, was performed. Generally, a total of 150 common significant genes with the same causal association with PCa were identified. Out of the 150 genes examined, 67.33% (101/150) were found to have protein-coding functions, while only 30.67% (46/150) of these genes had prior mentions in the scientific literature. Notably, the analysis of the TCGA dataset showed that only 44.67% (67/150) of the genes produced consistent results with the Mendelian randomization (MR) analysis. Furthermore, the evaluation of single-cell RNA-seq data and colocalization analysis singled out MSMB as a critical gene associated with the occurrence of PCa. We pinpointed a range of prostate-specific genes that display causal associations with the onset of PCa. Among these, the MSMB gene emerged as a pivotal factor linked to PCa, demonstrating robust consistency across all four assessments, including the MR, TCGA dataset, single-cell RNA-seq data, and colocalization analysis. These findings provided fresh perspectives on the pathogenesis of PCa and presented potential targets for drug development.

AXL, a receptor tyrosine kinase, has recently emerged as a potential therapeutic target against various types of cancer. Gilteritinib, a FDA-approved small-molecule inhibitor, is used for the treatment of patients with FLT3-mutated acute myeloid leukemia. However, the antitumor activity of gilteritinib in solid tumors remains poorly elucidated. In this study, we explored the antitumor activity of gilteritinib in AXL-expressing esophageal cancer (EC), ovarian cancer (OC), and gastric cancer (GC), along with the underlying molecular mechanisms. Our data demonstrated that gilteritinib significantly inhibited cell proliferation and spheroid formation by triggering apoptosis and cell cycle arrest in AXL-positive EC, OC, and GC cells. Moreover, we found that gilteritinib treatment repressed EC, OC, and GC cell migration and invasion. Mechanistically, RNA-seq analysis revealed that gilteritinib significantly downregulated multiple cancer-related pathways, including those related to apoptosis, the cell cycle, the mTOR pathway, the AMPK pathway, the p53 pathway, the FOXO pathway, the Hippo pathway, and the Wnt pathway. Gilteritinib inhibited a unique set of E2F- and MYC target-associated genes in EC, OC, and GC cells. Intriguingly, interrogation of the EC, OC, and GC cohort demonstrated that these genes were overexpressed and associated with poor prognosis. Gilteritinib also displayed strong antitumor effects on AXL-positive PDX-derived explants (PDXEs) and PDX-derived organoids (PDXOs) ex vivo and PDXs in vivo. Collectively, these findings reveal that gilteritinib represents a potent therapeutic agent for the treatment of AXL-positive solid tumors. Zhang et al. demonstrate superior therapeutic efficacy of Gilteritinib, a FDA-approved small-molecule inhibitor, in the AXL-expressing esophageal cancer, ovarian cancer and gastric cancer cell lines, PDXOs and PDXs models. This work highlights Gilteritinib as a novel and potent therapeutic approach for the treatment of AXL-positive solid tumors.

The frequent co-occurrence of chronic pain (CP) and depression is a well-known phenomenon, supported by both the high prevalence of major depression among CP patients and studies describing a substantial genetic correlation between the two phenotypes. Neuroticism, a trait characterised by maladaptive stress responses and a tendency to experience negative emotions, has been linked to both depression and the experience of pain. This study aimed to determine whether depression associated with CP represents a genetically distinct subtype and to explore the role of neuroticism in modulating genetic susceptibility to depression. To address these questions, we performed genome-wide association analyses for current depression utilising the UK Biobank dataset, followed by genome-wide by trait interaction analyses to assess the interaction effect of neuroticism, and polygenic risk score analyses to compare predictions. Our findings suggest that CP-related depression is a valid subtype of depression. In association with current depression, we identified a total of 49 novel genetic risk polymorphisms meeting the genome-wide significance threshold, including variants involved in synaptic plasticity and transcriptional regulation. Additionally, our results support that neuroticism has a prominent role in modulating the genetic risk of current depression independently of CP, which highlights the importance of considering personality traits and stress factors in understanding the genetic background of complex and heterogeneous phenotypes like depression.

The lack of target therapies is accountable for the higher mortality of various types of cancer. To address this issue, we selected a target mutated Kirsten rat sarcoma virus oncogene homologue, which plays a significant role in various cancers. Our study aims to identify selective biomarkers and develop diagnostic and therapeutic strategies for KRAS-associated genes using artificial intelligence. Initially, Genomic data, cancer epidemiology, proteomics network interactions, and omics enrichment were analyzed. Structured E-pharmacophore model aided in capturing the binding cavity using eraser algorithms and fabricating a new selective lead compound for the KRSA. The selective molecule was abridged inside the binding cavity and stability was validated through 100 ns molecular dynamics simulations. Epidemiological-neural network studies indicated KRAS mutations leads 40 types of cancer, exclusively pancreatic and colorectal cancers, with diploid and missense mutations as primary factors. Pathway analysis highlighted the involvement of the MAPK and RAS signaling pathways in cancer development and proteomics analysis identified RALGDS as a key protein. Protein-based pharmacophore analysis mapped the biologically active features such as donor, acceptor and aromatic ring with the designed ligands. The results of interaction interpretation illustrate that the amino acid Tyr566 formed an H-bond interaction with the amine group of the octyl ring system and 20 amino acids crafted to properly orient the molecule to fit inside the polar cavity of KRAS protein. The MMGBSA score of - 53.33 kcal/mol conformed to the well-configured binding with KRSA and realistic model simulation exposed the π-π, π-cationic and hydrophobic interactions stabilised the molecule inside the KRSA protein throughout 100 ns simulation. The study demonstrates the vitality of AI and network pharmacology to identify potential-target biomarkers for KRAS-associated genes, paving the way for improved cancer diagnostics and therapeutics.

The fallopian tube (FT) plays a crucial role in fertility, gynecological health, and high-grade serous ovarian cancer (HGSOC) development. Despite its importance, the spatial transcriptome of the FT's distinct anatomical regions (fimbria, infundibulum, ampulla, and isthmus) remains underexplored. Using the GeoMx Digital Spatial Profiler (DSP) and a targeted ~1800 gene panel, we analyze premenopausal FT epithelium, identifying region-specific gene expression patterns. Our analysis reveals upregulation of mature ciliated cell markers (FOXJ1, MLF1, SPA17, and CTSS) approaching the fimbria, elevated ROS and apoptosis-related transcripts (TXNIP, PRDX5, BAD, GAS1) in the distal FT, and a switch in cell-cell adhesion transcripts (CDH1, CDH3) along the distal-to-proximal axis. We also provide evidence that MHC-II transcripts in the FT are differentially regulated throughout the menstrual cycle, with lower expression in follicular phase. These results suggest spatially regulated expression of FT transcripts with implications for fertilization and early neoplastic changes contributing to HGSOC.

<h4>Background</h4>Heart failure (HF) is a prevalent and critical cardiac condition that leads to profound structural and functional changes in the heart. Although traditional treatments have shown partial efficacy, the long-term outcomes remain suboptimal. Emerging research has highlighted the pivotal role of oxidative stress and ferroptosis in HF progression. This study investigates a new therapeutic approach utilizing antioxidant polyphenol nanoparticles loaded with a STAT3 agonist (PN@Col) to target these pathways and improve age-related HF.<h4>Results</h4>Key cells and genes contributing to HF progression were identified via analysis of the GEO database, with single-cell RNA sequencing (scRNA-seq) and AUCell analysis used to evaluate differential gene expression. The STAT3 gene was highlighted as essential, and its functionality was further validated in vitro through cell experiments, confirming its impact on cardiomyocytes (CMs) in HF. Following the development of PN@Col, in vitro experiments showed that PN@Col effectively reduced oxidative stress and ferroptosis in CMs. In vivo studies in elderly HF mice demonstrated significant improvements in cardiac function following PN@Col treatment.<h4>Conclusions</h4>PN@Col offers a promising therapeutic approach to age-related HF by mitigating oxidative stress and ferroptosis in cardiomyocytes. These findings provide a solid scientific foundation for PN@Col as a potential novel treatment strategy for HF, supporting further exploration toward clinical application.

This review comprehensively examines the molecular basis of donkey meat characteristics and growth-associated genes, integrating findings from multiple omics approaches. This study examines the nutritional profile of donkey meat, which is rich in protein, essential amino acids, and unsaturated fatty acids. Through a systematic literature search across Web of Science, Google Scholar, PubMed, and Scopus databases (2000-2024), we collected and analyzed data from 400 research articles using predefined inclusion criteria focused on nutritional composition, omics approaches, and meat quality parameters in donkey populations. The study also evaluates various factors affecting meat quality, including breed differences, age, feeding management, and storage conditions. Advanced genomic and transcriptomic analyses have revealed numerous candidate genes, such as <i>ACTN3</i>, <i>BMP7</i>, <i>NR6A1</i>, <i>Wnt7a</i>, <i>HOXC8</i>, <i>LCORL</i>, <i>TPM2</i>, and <i>TPM3</i>, associated with growth traits and meat quality characteristics, providing valuable insights for genetic improvement programs. Furthermore, the review discusses various authentication methods for ensuring donkey meat quality and preventing adulteration, highlighting the integration of traditional and modern analytical approaches.

The fluorenyl methyl oxycarbonyl phenylalanyl-phenylalanine methyl ester (Fmoc-Phe-Phe-Ome) was synthetized using the liquid phase synthesis strategy. This derivative was separated by hydrophobic interaction chromatography, its purity was analyzed by RP-HPLC and it was characterized by mass spectrometry. This extremely hydrophobic peptide conjugate was incorporated into aqueous solutions of Pluronic^® F127 at low temperatures (below 10 °C). The temperature induced sol-gel transition was investigated by rheological measurements. A delay of the sol-gel transition, caused by the presence of low concentrations of Fmoc-Phe-Phe-Ome (up to 1%), enables better control of the gelation process. The viscoelastic properties of hybrid networks were investigated at 37 °C in different shear conditions. The Pluronic/peptide systems reported herein provide promising alternatives for developing innovative injectable gels as suitable platforms in cancer treatment.

Pulmonary hypertension (PH) is a vascular disease characterized by remodeling of the pulmonary arteries and right heart failure. Chronic obstructive pulmonary disease (COPD) patients often have PH, which can worsen symptoms and raise morbidity and mortality. There are several reasons for increased pulmonary vascular resistance, pulmonary vascular remodeling, and ultimately the development of PH in COPD. These factors include genetics, inflammation caused by chemicals breathed, and changes in the alveoli seen in COPD and its physiology. Genes involved in mRNA conversion, subcellular localization, splicing, and translation are all finely tuned by RBPs in their post-transcriptional regulation. Erythropoietin regulates cytokines, chemokines, proteins, growth factors, and other pro-inflammatory mediators that change the lung microenvironment. Over the past few years, we have learned more about how RBPs act in PH and COPD. Here, we discuss the existing understanding of RBPs' location in the same pathogenic pathways shared by PH and COPD in order to emphasize their potential relevance as disease determinant/biomarker and, consequently, for possible therapeutic targeting.

This study focused on examining how Portulaca oleracea L. extract (POLE) influences production performance, antioxidant capacity, immunity, anti-apoptotic ability, and intestinal health in chicks exposed to Escherichia coli O78(E. coli). A 2 × 2 factorial design was used to randomly divide male chicks into 4 groups: (1) basal diet (CON group), (2) basal diet supplemented with 0.5 g/kg POL (CPOL group), (3) basal diet with E. coli challenge (ECON group), and (4) basal diet supplemented with 0.5 g/kg POL as well as E. coli challenge (EPOL group).The experiment lasted for 19 days. The POL supplementation was found to decrease the feed conversion ratio and liver and spleen indexes and increase the average daily gain and bursa indexes (P<0.05). Moreover, in chicks infected with E. coli, POL reduced the levels of serum DAO and caspase 8 (P<0.05). POL notably elevated the serum levels of immunoglobulins and IL-10, an anti-inflammatory cytokine, which also decreased the levels of proinflammatory cytokines TNF-α and IFN-γ. At the same time, dietary POL enhanced the mRNA expression of genes related to antioxidation and reduced the expression of genes associated with proinflammatory cytokines and apoptosis in the liver, spleen, jejunum, and ileum. In addition, dietary POL repaired the intestinal barrier and injury. More importantly, by boosting the abundance of beneficial bacteria such as Butyricicoccus and Blautia, and reducing harmful bacteria like Enterococcus and Escherichia, POL induced changes in the gut microbiota composition. Spearman's correlation study revealed that Dorea and Butyricoccus had a strong positive link with intestinal barrier function and antioxidant capacity, while Escherichia had a substantial positive correlation with pro-inflammatory cytokines. In summary, this study suggests adding POL to the diet as a beneficial supplement to enhance chick performance.

Parvoviruses are small, single-stranded DNA viruses that have evolved sophisticated mechanisms to hijack host cell machinery for replication and persistence. One critical aspect of this interaction involves the manipulation of the host's DNA Damage Response (DDR) pathways. While the viral genome is comparatively simple, parvoviruses have developed strategies that cause significant DNA damage, activate DDR pathways, and disrupt the host cell cycle. This review will explore the impact of parvovirus infections on host genome stability, focusing on key viral species such as Adeno-Associated Virus (AAV), Minute Virus of Mice (MVM), and Human Bocavirus (HBoV), and their interactions with DDR proteins. Since parvoviruses are used as oncolytic agents and gene therapy vectors, a better understanding of cellular DDR pathways will aid in engineering potent anti-cancer agents and gene therapies for chronic diseases.

<h4>Background</h4>Hepatic tuberculosis in itself is a rare condition, and that causing portal hypertension is even rarer. We present a unique clinical scenario of portal hypertension in a 64-year-old woman, with tuberculosis causing both sinusoidal and prehepatic portal hypertension.<h4>Case presentation</h4>A 64-year-old woman presented with esophageal variceal bleeding. Evaluation revealed a rare combination of sinusoidal portal hypertension from hepatic tuberculosis and a prehepatic component of portal hypertension due to tubercular periportal lymphadenopathy compressing the portal vein at the hilum. Hepatic venous pressure gradient was 7 mm Hg, indicative of sinusoidal portal hypertension. Liver biopsy demonstrated bridging fibrosis and hepatic granulomas accounting for the sinusoidal component of portal hypertension. Since clinically significant portal hypertension is more than 10 mm Hg, variceal bleeding resulted from the additional element of prehepatic portal hypertension contributed by compression of extrahepatic portal vein by periportal lymph nodes. Positive tuberculosis polymerase chain reaction from lymph nodes confirmed the diagnosis and initiation of antitubercular therapy (ATT) led to significant clinical and biochemical improvement. This case represents a novel occurrence; hepatic tuberculosis causing both intrahepatic and prehepatic components of portal hypertension has not been reported in the literature.<h4>Conclusion</h4>This case sheds light on the rarity of hepatic tuberculosis causing portal hypertension and also the importance of considering this diagnosis in patients with atypical presentations of tuberculosis. Recognizing and treating this unique complication promptly with ATT can lead to favorable clinical outcomes.

<h4>Background & aims</h4>Effective control of chronic liver diseases (CLD) requires suppression of effector T cells by CD4⁺CD25⁺CD127^low regulatory T cells (Tregs). This study investigated the role of TIGIT, a co-inhibitory receptor, in CLD by examining the phenotype, recruitment, localisation, and function of TIGIT⁺Tregs and how TIGIT augments Treg function. We also elucidated the function of TIGIT⁺effector T cells on hepatocytes.<h4>Methods</h4>Liver infiltrating (CLD explants n = 7, donor liver n = 4) and peripheral (CLD blood n = 22, healthy control blood n = 10) TIGIT⁺Tregs and TIGIT⁺effector T cells were phenotyped by flow cytometry, and their localisation was examined by immunohistochemistry. Phenotypic and functional changes in TIGIT⁺Tregs in response to TIGIT agonism and IL-2 supplementation were also assessed. TIGIT⁺effector T cell-induced primary hepatocyte apoptosis was investigated using co-culture experiments and blocking assays.<h4>Results</h4>TIGIT⁺Tregs were more suppressive towards CD4⁺T cells than TIGIT^-Tregs (<i>p</i> = 0.04254), and their suppressive action was IL-10 dependent. TIGIT expression was highly enriched on intrahepatic Tregs compared to effector T cells (<i>p</i> <0.0001). TIGIT⁺Tregs and TIGIT⁺effector T cells expressed CXCR3 and VLA-4 and localised around hepatocytes which express TIGIT ligand, CD155. TIGIT⁺Tregs also exhibited significantly higher cytotoxic T lymphocyte-associated antigen-4 (CTLA-4; <i>p</i> = 0.0012), FoxP3 (<i>p</i> <0.0001), and CD39 (<i>p</i> <0.0001) expression than TIGIT^-Tregs. TIGIT agonism upregulated FoxP3 and CTLA-4 on Tregs, reduced proliferation, and increased TNF-α expression. Supplementing TIGIT⁺Tregs with IL-2 further enhanced FoxP3 and CTLA-4 expression. In contrast, TIGIT⁺effector T cells displayed reduced cytotoxicity towards hepatocytes, which reversed upon TIGIT blockade.<h4>Conclusions</h4>TIGIT⁺Tregs are highly suppressive and can be enhanced in response to TIGIT agonism and IL-2 stimulation, demonstrating their translational therapeutic potential. However, TIGIT blockade on CD8⁺T cells induces hepatitis, caution is required when using anti-TIGIT therapy.<h4>Impact and implications</h4>We identified a highly suppressive subset of regulatory T cells in the liver, defined as TIGIT⁺CD39⁺CTLA-4⁺Tregs. TIGIT agonists and IL-2 enhanced the suppressive function of this cell subset. The TIGIT ligand, CD155, is expressed on inflamed hepatocytes, and TIGIT blockade in oncology could instigate checkpoint inhibitor induced liver injury (CHILI). These findings have implications for future therapy in liver disease.

Rapid reduction of body size in populations responding to global warming suggests the involvement of temperature-dependent physiological adjustments during growth, such as mitochondrial alterations in the efficiency of producing metabolic energy, a process that is poorly explored, especially in endotherms. Here, we examined the mitochondrial metabolism and proteomic profile of red blood cells in relation to body size and cellular energetics in nestling shearwaters (Calonectris diomedea) developing at different natural temperatures. We found that nestlings of warmer nests had lighter bodies and smaller beaks at fledging. Despite the fact that there was no effect of environmental temperature on cellular metabolic rate, mitochondria had a higher inefficiency in coupling metabolism to allocable energy production, as evidenced by bioenergetic and proteomic analyses. Mitochondrial inefficiency was positively related to cellular stress represented by heat shock proteins, antioxidant enzymes and markers of mitochondrial stress. The observed temperature-related mitochondrial inefficiency was associated with reduced beak size and body mass, and was linked to a downregulation of cellular growth factors and growth promoters determining body size. By analyzing the links between environmental temperature, mitochondrial inefficiency and body size, we discuss the physiological alterations that free-living birds, and probably other endotherms, need to trigger to cope with a warming world.

Gamma-delta (γδ) T cells are a unique subset of T lymphocytes that play diverse roles in immune responses, bridging innate and adaptive immunity. With growing interest in their potential for cancer immunotherapy, a comprehensive and inclusive exploration of γδ T cell families, their development, activation mechanisms, functions, therapeutic implications, and current treatments is essential. This review aims to provide an inclusive and thorough discussion of these topics. Through our discussion, we seek to uncover insights that may harbinger innovative immunotherapeutic strategies. Beginning with an overview of γδ T cell families including Vδ1, Vδ2, and Vδ3, this review highlights their distinct functional properties and contributions to anti-tumor immunity. Despite γδ T cells exhibiting both anti-tumor and pro-tumor activities, our review elucidates strategies to harness the anti-tumor potential of γδ T cells for therapeutic benefit. Moreover, our paper discusses the structural intricacies of the γδ T cell receptor and its significance in tumor recognition. Additionally, this review examines conventional and emerging γδ T cell therapies, encompassing both non-engineered and engineered approaches, with a focus on their efficacy and safety profiles in clinical trials. From multifunctional capabilities to diverse tissue distribution, γδ T cells play a pivotal role in immune regulation and surveillance. By analyzing current research findings, this paper offers insights into the dynamic landscape of γδ T cell-based immunotherapies, underscoring their promise as a potent armamentarium against cancer. Furthermore, by dissecting the complex biology of γδ T cells, we learn valuable information about the anti-cancer contributions of γδ T cells, as well as potential targets for immunotherapeutic interventions.

The glymphatic system, a macroscopic waste clearance network in the brain, plays a vital role in maintaining neuronal health and brain homeostasis. Functionally analogous to the lymphatic system in other organs, the term "glymphatic" combines "glial" and "lymphatic." This system facilitates the exchange of cerebrospinal fluid (CSF) and interstitial fluid (ISF) in the parenchyma, aiding in the removal of soluble proteins and metabolites while distributing essential nutrients and signaling molecules. Its functionality is closely tied to aquaporin 4 (AQP4) water channels, located primarily on astrocytic endfeet, which mediate water movement between the CSF and ISF. Proper glymphatic function relies on the cellular distribution of AQP4 channels and its astroglial endfeet polarization. Emerging evidence links glymphatic dysfunction to several neurodegenerative disorders, including Huntington's disease (HD). Understanding the role of the glymphatic system in HD pathogenesis could provide novel insights into disease pathogenesis and new therapeutic approaches. This review examines the connection between glymphatic dysfunction and HD, highlighting future research directions and therapeutic advancement for HD. It explores pharmacological interventions and lifestyle modifications aimed at optimizing glymphatic function to improve HD management.

<h4>Purpose of review</h4>Chylomicron biosynthesis plays a vital role in supplying essential lipids and lipid soluble vitamins to peripheral tissues for various functions. Despite this, the intracellular synthesis, trafficking, and secretion of chylomicrons remains only partly understood. The purpose of this review is to summarize the role of established proteins in this process and bring attention to recently identified proteins to provide an up-to-date model of chylomicron biosynthesis.<h4>Recent findings</h4>Recently, several proteins have been shown to play a role in the initial formation and lipidation of chylomicrons at the endoplasmic reticulum (ER), which include: TM6SF2, PLA2G12B, PRAP1, and SURF4. In addition, mitochondria have been implicated in chylomicron metabolism, but mechanistic insight is missing. The trafficking of chylomicrons from the ER to the Golgi, and the subsequent trafficking from the Golgi to the basolateral side of enterocytes, however, remains a mystery.<h4>Summary</h4>Progress in the chylomicron biosynthesis field is largely associated with findings in VLDL biosynthesis. In addition, increased insight in events after prechylomicrons leave the ER is needed. Given the important role of chylomicron biosynthesis in whole-body lipid metabolism, further research into the molecular mechanisms is warranted.

<h4>Aim</h4>Our study mainly focused on exploring the expression and mechanism of PRDXs family members in OSCC, as well as the diagnostic and prognostic monitoring value of PRDXs family members in OSCC.<h4>Method</h4>We used bioinformatics tools to perform and visualize gene differential analysis on OSCC, analyse the expression of PRDXs family members in OSCC, and evaluate the diagnostic and prognostic monitoring value of PRDXs family members in OSCC patients. We utilized UALCAN, Cbioportal, and STRING websites to analyze the expression and gene mutations of the PRDXs family in pan-cancer, as well as the correlation of PRDXs family members. We used RT-qPCR technology to analyze the expression of PRDXs family members in OSCC cells. We used CCK8 technology to analyze the effect of PRDXs family members on the proliferation of OSCC cells.<h4>Result</h4>PRDX1, PRDX2, PRDX4 and PRDX5 are generally highly expressed in pan cancer, but PRDX6 is generally low expressed in pan-cancer. PRDX2 and PRDX6 have higher alteration frequency and the mutation of PRDXs family mainly focus on amplification in Pan-Cancer. PRDX1, PRDX4, and PRDX5 are highly expressed in OSCC tissue, while PRDX2 is low expressed in OSCC tissue. Similarly, PRDX1, PRDX4, and PRDX5 are also highly expressed in OSCC cells. Furthermore, PRDX1, PRDX4, and PRDX6 can promote the proliferation of OSCC cells. Except for PRDX6, all other members of the PRDXs family interact with TXN, and TXN plays a crucial role in the PRDXs family. PRDX4 has the highest diagnostic efficiency for OSCC, while PRDX2 and PRDX5 also have high diagnostic efficiency. The high expression of PRDX1 and PRDX6 suggests poor prognosis in OSCC patients, while the low expression of PRDX5 suggests poor prognosis in OSCC patients.<h4>Conclusion</h4>PRDXs family members are expressed to varying degrees in OSCC and have different diagnostic and prognostic monitoring values for OSCC, which may provide a new direction for the clinical diagnosis and treatment of OSCC patients.

Tuberculosis (TB) is an infectious disease that presents a serious risk to public health. Glycosyltransferase-related genes (GTRGs) are instrumental in assessing the risk of latent tuberculosis infection progressing to active TB. This study aims to develop novel, accurate, and effective diagnostic markers to enhance the early diagnosis and precision treatment of TB. We employed Weighted Gene Co-expression Network Analysis (WGCNA) to explore key genes that are notably linked toTB. In addition, we employed single-sample Gene Set Enrichment Analysis (ssGSEA) to examine the differences in immune cell infiltration between normal tissues and those affected by TB. The effectiveness of the potential biomarkers was evaluated through Receiver Operating Characteristic (ROC) curves and their expression patterns. We also conducted single-gene enrichment analysis to explore the biological functions and pathway activities linked to the characteristic genes. Finally, we constructed a competitive endogenous RNA (ceRNA) network to elucidate the potential regulatory mechanisms governing these genes. Through the screening of hub genes and differentially expressed genes from the GTRGs, we identified two potential biomarkers: B4GALT5 and KCNJ2. Evaluation results indicated that these characteristic genes displayed strong diagnostic performance in both the training and validation cohorts. Moreover, single-gene enrichment analysis revealed that these genes were primarily enriched in apoptosis pathways closely associated with TB treatment. Additionally, the construction of the mRNA-miRNA-lncRNA network identified 82 miRNAs and 65 lncRNAs. This study elucidates the roles of GTRGs in TB, identifies biomarkers associated with these groups, and establishes the lncRNA expression profile of characteristic genes. These findings provide a theoretical foundation for the early diagnosis of TB.

Senescent hepatocytes accumulate in metabolic dysfunction-associated steatotic liver disease (MASLD) and are linked to worse clinical outcomes. However, their heterogeneity and lack of specific markers have made them difficult to target therapeutically. Here, we define a senescent hepatocyte gene signature (SHGS) using in vitro and in vivo models and show that it tracks with MASLD progression/regression across mouse models and large human cohorts. Single-nucleus RNA-sequencing and functional studies reveal that SHGS+ hepatocytes originate from p21+ cells, lose key liver functions and release factors that drive disease progression. One such factor, GDF15, increases in circulation alongside SHGS+ burden and disease progression. Through chemical screening, we identify senolytics that selectively eliminate SHGS+ hepatocytes and improve MASLD in male mice. Notably, SHGS enrichment also correlates with dysfunction in other organs. These findings establish SHGS+ hepatocytes as key drivers of MASLD and highlight a potential therapeutic strategy for targeting senescent cells in liver disease and beyond.

Crohn's disease (CD) is a persistent inflammatory disorder primarily affecting the terminal ileum. The Tnf^ΔΑRE mice, which spontaneously develop CD-like ileitis due to TNF overexpression, represent a faithful model of the human disease. Here, via single-cell RNA sequencing in Tnf^ΔΑRE mice, we show that murine TNF-dependent ileitis is characterized by cell expansion in tertiary lymphoid organs (TLO), T cell effector reprogramming, and accumulation of activated macrophages in the submucosal granulomas. Within the stromal cell compartment, fibroblast subsets (telocytes, trophocytes, Pdgfra^loCd81^- cells) are less abundant while lymphatic endothelial cells (LEC) and fibroblastic reticular cells (FRC) show relative expansion compared to the wild type. All three fibroblast subsets show strong pro-inflammatory signature. TNFR1 loss or gain of function experiments in specific fibroblast subsets suggest that the Tnf^ΔΑRE-induced ileitis is initiated in the lamina propria via TNF pathway activation in villus-associated fibroblasts (telocytes and Pdgfra^loCd81^- cells), which are responsible for the organization of TLOs. Trophocytes drive disease progression in the submucosal layer, accompanied by the excessive formation of granulomas. These findings provide evidence for spatial regulation of inflammation by fibroblast subsets and underscore the pivotal role of fibroblasts in the inception and advancement of ileitis.

Circular RNAs (circRNAs) are an expanding class of largely unexplored RNAs which are prominently enriched in the mammalian brain. Here, we systematically interrogate their role in excitatory synaptogenesis of rat hippocampal neurons using RNA interference. Thereby, we identify seven circRNAs as negative regulators of excitatory synapse formation, many of which contain high-affinity microRNA binding sites. Knockdown of one of these candidates, circRERE, promotes the formation of electrophysiologically silent synapses. Mechanistically, circRERE knockdown results in a preferential upregulation of synaptic mRNAs containing binding sites for miR-128-3p. Overexpression of circRERE stabilizes miR-128-3p and rescues exaggerated synapse formation upon circRERE knockdown in a miR-128-3p binding site-specific manner. Overall, our results uncover circRERE-mediated stabilization of miR-128-3p as a means to restrict the formation of silent excitatory synaptic co-clusters and more generally implicate circRNA-dependent microRNA regulation in the control of synapse development and function.

<h4>Background</h4>Gastric cancer, characterized by rising global incidence and mortality, faces significant challenges due to the lack of effective early detection methods, delaying timely interventions and underscoring the need for novel biomarkers. Lipopolysaccharide-binding protein (LBP), implicated in cancers such as lung, colon, and cervical cancer, has emerged as a promising candidate. However, its specific roles and mechanisms in gastric cancer remain unclear, necessitating further investigation.<h4>Methods</h4>This study utilized data from The Cancer Genome Atlas (TCGA), the Gene Expression Omnibus (GEO), and the Human Protein Atlas (HPA) to assess LBP mRNA and protein expression levels in gastric cancer patients and explore their associations with clinical outcomes. Analytical techniques included volcano plots, protein-protein interaction networks, Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, gene set enrichment analysis (GSEA), and immune infiltration assessments. Furthermore, lentiviral vectors containing interference sequences targeting LBP were used to manipulate its expression in AGS and HGC-27 gastric cancer cell lines, enabling the analysis of gene knockdown effects on malignant behaviors. Western blotting (WB) was performed to validate the impact of LBP knockdown on the expression of key signaling pathway proteins.<h4>Results</h4>Our pan-cancer comparative analysis across 33 cancer types revealed significant upregulation of LBP in gastric cancer, with diagnostic ROC curve analysis yielding an AUC of 0.765. Univariate and multivariate Cox regression analyses revealed that high LBP expression was inversely related to patient survival. Additionally, immune infiltration and functional enrichment analyses revealed the involvement of LBP in pathways crucial to cancer development, such as immune response modulation and lipid metabolism. LBP knockdown in gastric cancer cell lines reduced proliferation, migration, and invasion. WB confirmed decreased expression of P65, P-P65, STAT3, and P-STAT3 upon LBP knockdown.<h4>Conclusion</h4>LBP is intricately linked to gastric cancer pathogenesis; it influences cell proliferation, migration, and invasion, thereby representing a valuable prognostic and diagnostic biomarker. This study not only highlights the potential of LBP as a therapeutic target but also provides the groundwork for future investigations into its mechanistic pathways in gastric cancer.<h4>Clinical trial number</h4>Not applicable. I would like to clarify that our research does not fall under clinical studies and therefore does not involve ethical concerns related to human or animal subjects. The cells used in this study are established cell lines purchased from a certified biotechnology company. All experimental procedures comply with standard research protocols and guidelines for cell line studies.

Neurodevelopmental disorders (NDDs) are a group of brain disorders with a neonatal or early childhood onset and are lifelong. Various factors including genetics, and environmental and immune-related risk factors have been associated with NDDs. Given the complex nature of these disorders, multiple animal models have been used to investigate their aetiology and underlying cellular and molecular mechanisms. Recently, zebrafish have attracted great attention as an emerging model for studying NDDs. In addition to their easy maintenance, short developmental cycle, ex utero embryonic evolution, and optical clarity, zebrafish have successfully recapitulated phenotypes seen in human genetic disorders. This review explores the growing role of zebrafish in NDD research, by summarizing recently developed zebrafish genetic models for autism spectrum disorder, schizophrenia, and cerebral palsy. We then explore the potential of zebrafish as a model for studying NDDs linked to immune system dysfunction.

The Golgi complex is the central sorting station of eukaryotic cells. Several unique trafficking pathways direct the transport of proteins between the Golgi and the endoplasmic reticulum, plasma membrane, and endolysosomal system. In this review we highlight several recent studies that use structural biology approaches to discover and characterize novel mechanisms cells use to control the flow of traffic through the Golgi. These studies provide important new insights into how activation of Arf and Rab GTPases is regulated, how cargo proteins are sorted during vesicle biogenesis, and how vesicle tethers identify their target compartments.

MicroRNAs (miRNAs) are critical regulators of the skeleton. In the growth plate, these small non-coding RNAs modulate gene networks that drive key stages of chondrogenesis, including proliferation, differentiation, extracellular matrix synthesis and hypertrophy. These processes are orchestrated through the interaction of pivotal pathways including parathyroid hormone-related protein (PTHrP), Indian hedgehog (IHH), and bone morphogenetic protein (BMP) signaling. This review highlights the miRNA-mRNA target networks essential for chondrocyte differentiation. Many miRNAs are differentially expressed in resting, proliferating and hypertrophic cartilage zones. Moreover, differential enrichment of specific miRNAs in matrix vesicles is also observed, providing means for chondrocytes to influence the function and differentiation of their neighbors by via matrix vesicle protein and RNA cargo. Notably, miR-1 and miR-140 emerge as critical modulators of chondrocyte proliferation and hypertrophy by regulating multiple signaling pathways, many of them downstream from their mutual target <i>Hdac4</i>. Demonstration that a human gain-of-function mutation in miR-140 causes skeletal dysplasia underscores the clinical relevance of understanding miRNA-mediated regulation. Further, miRNAs such as miR-26b have emerged as markers for skeletal disorders such as idiopathic short stature, showcasing the translational relevance of miRNAs in skeletal health. This review also highlights some miRNA-based therapeutic strategies, including innovative delivery systems that could target chondrocytes via cartilage affinity peptides, and potential applications related to treatment of physeal bony bridge formation in growing children. By synthesizing current research, this review offers a nuanced understanding of miRNA functions in growth plate biology and their broader implications for skeletal health. It underscores the translational potential of miRNA-based therapies in addressing skeletal disorders and aims to inspire further investigations in this rapidly evolving field.

The aristaless-related homeobox (Arx) transcription factor, located on the X chromosome, has been implicated in a wide range of neurological disorders, including intellectual disability and epilepsy, as well as diabetes and pancreatic developmental disorders. In the mouse brain, Arx is expressed not only in the olfactory bulb (OB) and cerebral cortex progenitor cells but also in these gamma-aminobutyric acid (GABA)-releasing interneurons. In the initial study, constitutive Arx knockout (KO) mice showed aberrant migration and a reduction in GABAergic interneurons in the neonatal OB. However, constitutive Arx KO mice with perinatal lethality preclude further analysis in adolescent or adult mice. To overcome this, Arx-floxed mice have been crossed with Cre driver mice to generate conditional KO mice with selective Arx deletion in distinct interneuron progenitors. These studies have identified Arx as a key transcriptional regulator involved in the generation, fate determination, and migration of cortical interneurons. This review focuses on the critical role of Arx in the development of progenitor cells and the migration of interneurons in the mouse OB and cerebral cortex, and discusses differences in Arx mutant-based abnormality between mouse mutants and human patients.

γδT cells represent a unique and versatile subset of T cells characterized by the expression of T-cell receptors (TCRs) composed of γ and δ chains. Unlike conventional αβT cells, γδT cells do not require major histocompatibility complex (MHC)-dependent antigen presentation for activation, enabling them to recognize and respond to a wide array of antigens, including phosphoantigens, stress-induced ligands, and tumor-associated antigens. While γδT cells are relatively rare in peripheral blood, they are enriched in peripheral tissues such as the skin, intestine, and lung. These cells play a crucial role in tumor immunotherapy by exerting direct cytotoxicity through the production of inflammatory cytokines (e.g., interferon-gamma (IFN-γ), tumor necrosis factor-alpha (TNF-α), and interleukin-17 (IL-17)) and cytotoxic molecules (e.g., perforin and granzyme). Recent advances in γδT cell research have elucidated their mechanisms of tumor recognition, including the detection of phosphoantigens and stress-induced ligands like MICA (MHC class I polypeptide-related sequence A), MICB (MHC class I polypeptide-related sequence B), and ULBP (UL16-binding protein). Furthermore, various strategies to enhance γδT cell-based tumor immunotherapy have been developed, such as <i>in vitro</i> expansion using phosphoantigen-based therapies, cytokine stimulation, and chimeric antigen receptor (CAR)-γδT cell engineering. These advancements have shown promising results in both preclinical and clinical settings, paving the way for γδT cells to become a powerful tool in cancer immunotherapy. This review highlights the key mechanisms, functions, and strategies to harness the potential of γδT cells for effective tumor immunotherapy.

Reproductive engineering encompasses a range of advanced tissue engineering techniques aimed at addressing infertility that is non-curable with current assisted reproductive technology (ART). The use of animal models has been crucial for these advancements, with a notable preference for non-human primates (NHPs) given their genetic, anatomical, and physiological similarities to humans. Therefore, NHPs are invaluable for studying reproductive engineering. Thus, in reproductive studies, NHPs bridge the anatomical and physiological gaps between rodent models and humans. Their shared features with humans, such as menstrual cycles, placentation, and hormonal regulation, allow for more accurate modeling of reproductive physiology and pathology. These traits make NHPs indispensable in the exploration of reproductive engineering, including infertility treatments, genetic engineering, and uterine transplantation. Reproductive engineering is a transformative field that addresses infertility and enhances reproductive health. By leveraging the unique traits of NHPs, researchers can deepen their understanding of reproductive processes and refine ART techniques for human use. Advances in genetic engineering have enabled the creation of transgenic NHP models, which have been used to modify genes to investigate roles for various purposes, and the process, as mentioned earlier, is closely related to the ART technique, including fertility, embryogenesis, and pregnancy. Therefore, the relation to reproductive studies and the necessity of the NHP model are prerequisites for reproductive engineering. The engineering of NHPs is critically related to integrating ethical practices and exploring complementary methodologies. This review overviews the types of NHP frequently used and studies using NHP for reproductive engineering. These studies may suggest a broader way to use NHP for reproductive engineering.

The study of the aqueous humor (AH) plays a key role in understanding the pathophysiology of glaucoma. The AH provides nutrition, maintains the appropriate intraocular pressure, and provides important information about the mechanisms of the disease. The development of modern technologies has allowed the use of more accurate analytical methods, which has proven to be a key factor in determining the changes occurring in the proteome of the aqueous humor of glaucoma patients. Recently, researchers have observed changes in the levels of proteins associated with inflammation, oxidative stress, the complement system, and extracellular matrix remodeling. They have also shown that these changes may be variable for different types of glaucoma. The objective of this review is to collect and summarize the current knowledge on the potential biomarkers and pathomechanisms involved in the pathogenesis of glaucoma. We hope that our review will contribute to the improvement of current diagnostic methods in this illness and, through a better understanding of the changes occurring during the progression of the disease, will enable the development of more effective preventive and therapeutic strategies in the future.

The mechanisms that influence human longevity are complex and operate on cellular, tissue, and organismal levels. To better understand the tissue-level mechanisms, we compared the organization of cell proliferation, differentiation, and cytoprotective protein expression in the squamous epithelium of the esophagus between mammals with varying lifespans. Humans are the only species with a quiescent basal stem cell layer that is distinctly physically separated from parabasal transit-amplifying cells. In addition to these stark differences in the organization of proliferation, human squamous epithelial stem cells express DNA repair-related markers, such as MECP2 and XPC, which are absent or low in mouse basal cells. Furthermore, we investigated whether the transition from basal to suprabasal is different between species. In humans, the parabasal cells seem to originate from cells detaching from the basement membrane, and these can already begin to proliferate while delaminating. In most other species, delaminating cells have been rare or their proliferation rate is different from that of their human counterparts, indicating an alternative mode of how stem cells maintain the tissue. In humans, the combination of an elevated cytoprotective signature and novel tissue organization may enhance resistance to aging and prevent cancer. Our results point to enhanced cellular cytoprotection and a tissue architecture which separates stemness and proliferation. These are both potential factors contributing to the increased fitness of human squamous epithelia to support longevity by suppressing tumorigenesis. However, the organization of canine oral mucosa shows some similarities to that of human tissue and may provide a useful model to understand the relationship between tissue architecture, gene expression regulation, tumor suppression, and longevity.

<h4>Introduction</h4>In a previous study, we identified an inverse relationship between adverse perinatal outcomes and iron status during late pregnancy of women recruited from a maternal hospital in Cartagena, Colombia. Some of these outcomes have also been linked to maternal inflammatory states. However, there is currently no clarity regarding the relationship between iron levels and proinflammatory markers during this period.<h4>Objective</h4>To estimate the relationship between inflammatory markers and serum ferritin in third-trimester pregnancies.<h4>Materials and methods</h4>Serum ferritin, hemoglobin, and proinflammatory cytokine levels were determined in women in Cartagena in their third trimester of pregnancy. We analyzed the relationship between ferritin levels and proinflammatory cytokines, as well as the relationship between serum ferritin, hemoglobin, and inflammatory cytokine levels with adverse perinatal outcomes.<h4>Results</h4>The levels of IL-6 were significantly associated with serum ferritin levels (β = 0.42, SE = 0.21, p = 0.04) but not with maternal age. Maternal serum ferritin had a positive weak correlation with the absolute number of lymphocytes and monocytes. Hemoglobin and maternal serum ferritin were weakly and inversely associated with birth weight. Serum ferritin but not IL-6 or IL-8 was associated with preterm birth.<h4>Conclusions</h4>We observed direct and mild associations of serum iron markers (serum ferritin, hemoglobin, and hematocrit) with lymphocyte counts. The inflammation marker, IL-6, was mildly associated with serum ferritin levels in late pregnancy. Women with elevated white blood cell counts and serum ferritin levels tended to have infants with lower birth weights. This fact suggests a potential involvement of iron in inflammatory processes during pregnancy, and conditions associated with inflammation in the final trimester may have adverse effects on perinatal outcomes.

<b>Background/Objectives</b>: Inborn errors of metabolism (IEMs) represent a diverse group of genetic disorders characterized by enzymatic defects that disrupt metabolic pathways, leading to toxic metabolite accumulation, deficits, or impaired macromolecule synthesis. While strict dietary interventions are critical for managing many of these conditions, hormonal and metabolic changes during puberty introduce new challenges. Advancements in early diagnosis and treatment have significantly extended the lifespan of individuals with IEMs. However, this increased longevity is associated with heightened risks of new medical problems, including obesity, insulin resistance, and type 2 diabetes mellitus (T2DM), as these complications share mechanistic features with those seen in obesity and T2DM. <b>Methods</b>: This mini-review examines current knowledge of the intricate interplay between pubertal hormones and metabolic pathways in IEM patients. <b>Results</b>: We address critical questions, such as if puberty intensifies the risk of metabolic derangements in these individuals and if there is a metabolic intersection where these disorders converge, leading to shared complications. We highlight the impact of puberty-induced hormonal fluctuations, such as growth hormone (GH) surges and sex steroid activity, on disorders like phenylketonuria, urea cycle defects, and fatty acid oxidation disorders. Moreover, we explore the role of dietary interventions in mitigating or exacerbating these effects, emphasizing the importance of balancing nutritional needs during growth spurts. <b>Conclusions</b>: A multidisciplinary approach integrating endocrinology, nutrition, and emerging therapies is advocated to optimize metabolic health during puberty. Addressing these challenges is critical for improving long-term outcomes for individuals with IEMs, particularly during this pivotal developmental phase.

Cancer is a global health challenge, and its development is closely linked to iron metabolism. Cancer cells have an increased demand for this element, which promotes their proliferation, invasion, and metastasis. Excess iron catalyzes the formation of reactive oxygen species (ROS), which can both induce ferroptosis and initiate oncogenic signaling pathways. The deregulation of iron metabolism in cancer patients leads to anemia or toxic iron overload and also affects the gut microbiota. Lactoferrin (LF), a glycoprotein with strong iron chelating properties, can regulate its availability to cancer cells, thereby limiting their growth and progression. By chelating free Fe ions, LF reduces oxidative stress and inhibits the mechanisms that promote carcinogenesis. Additionally, it exhibits immunomodulatory and anti-inflammatory effects and may enhance the body's anti-tumor response. This review analyses the mechanisms of action of lactoferrin in the context of cancer, with a particular focus on its chelating, antioxidant, and immunomodulatory properties. The multidirectional effects of LF make it a promising component of preventive and therapeutic strategies, requiring further clinical studies.

Ubiquitination is a dynamic and tightly regulated post-translational modification essential for modulating protein stability, trafficking, and function to preserve cellular homeostasis. This process is orchestrated through a hierarchical enzymatic cascade involving three key enzymes: the E1 ubiquitin-activating enzyme, the E2 ubiquitin-conjugating enzyme, and the E3 ubiquitin ligase. The final step of ubiquitination is catalyzed by the E3 ubiquitin ligase, which facilitates the transfer of ubiquitin from the E2 enzyme to the substrate, thereby dictating which proteins undergo ubiquitination. Emerging evidence underscores the critical roles of ubiquitin ligases in neurodevelopment, regulating fundamental processes such as neuronal polarization, axonal outgrowth, synaptogenesis, and synaptic function. Mutations in genes encoding ubiquitin ligases and the consequent dysregulation of these pathways have been increasingly implicated in a spectrum of neurodevelopmental disorders, including autism spectrum disorder, intellectual disability, and attention-deficit/hyperactivity disorder. This review synthesizes current knowledge on the molecular mechanisms underlying neurodevelopment regulated by Cullin-RING ubiquitin ligases-the largest subclass of ubiquitin ligases-and their involvement in the pathophysiology of neurodevelopmental disorders. A deeper understanding of these mechanisms holds significant promise for informing novel therapeutic strategies, ultimately advancing clinical outcomes for individuals affected by neurodevelopmental disorders.

To rapidly evaluate the effects of anticancer treatments in 3D models, an integrated approach is proposed, combining a droplet-based microfluidic platform for spheroid formation and single-spheroid chemotherapy application, label-free morphological analysis, and machine learning to assess treatment response. Morphological features of spheroids, such as size and color intensity, are extracted and selected using the Multivariate Information-based Inductive Causation (MIIC) algorithm, and used to train a neural network for spheroid classification into viability classes, derived from metabolic assays performed within the same platform as a benchmark. The model was tested on Ewing sarcoma cell line and patient-derived xenograft (PDX) cells, demonstrating robust performance across datasets. It accurately predicts spheroid viability, used to generate dose-response curves and to determine half-maximal inhibitory concentration (IC50) values comparable to traditional biochemical assays. Notably, a model trained on cell line spheroids successfully classifies PDX spheroids, highlighting its adaptability. Compared to convolutional neural network-based approaches, this method works with smaller training datasets and provides greater interpretability by identifying key morphological features. The droplet platform further reduces cell requirements, while single spheroid confinement enhances classification quality. Overall, this label-free experimental and analytical platform is confirmed as a scalable, efficient, and dynamic tool for drug screening.

<title>Abstract</title> <p>MicroRNA-34a (miR-34a) was closely associated with liver steatosis. However, the link between changes in miR-34a and the progression of liver steatosis remained unclear. In the work, sixty mice were randomly and equally selected into six groups: normal control group (NC), normal exercise group (NE), high-fat diet group (HFD), high-fat diet plus exercise group (HFE), miR-34a overexpression group (OE), and miR-34a overexpression plus exercise group (OEE). Live morphology showed that treadmill exercise intervention for 8 weeks reduced high-fat diet-induced liver steatosis in mice. 8-week treadmill exercise directly decreased mir-34a expression of mice in HFD group, confirmed in OE group. More, treadmill exercise enhanced the expression of PPARα and SIRT1, thereby affecting the downstream hepatic steatosis-associated target genes, including CPT1, CPT2, SLC27A4, SLC27A1, in addition to activating the expression of the central metabolic sensor AMPK. Following aerobic exercise intervention, miR-34a was upregulated, thereby affecting the expression of genes associated with hepatic steatosis, and this mechanism was confirmed in miR-34a overexpression mice. This study contributed to our understanding of the pathogenesis of hepatic steatosis and may provide new therapeutic approaches.</p>

The use of readily available prochiral or racemic quaternary carbons to access enantioenriched ones offers a promising alternative to conventional synthesis from tertiary or planar substrates. Unlike desymmetrization, which modifies an existing substituent with limited reactivity, a functional group swap can install a new motif, which is structurally distinct and nonderivable from the replaced group. However, achieving enantioconvergence in these quaternary-to-quaternary transformations is challenging, especially for acyclic stereocenters. Here, we report that acyl groups of β-ketonitriles can be stereoselectively replaced by allyl, propargyl, or benzyl moieties using easily accessible alcohols under palladium catalysis. The deacylative functionalization proceeds through a retro-Claisen-type elimination of ketonitrile with alkoxide and the absence of diastereoisomerism in the resulting ketenimine anion assists the subsequent asymmetric addition. Together with the pair of α-substituents, the retained nitrile and the incoming alkyl motif instill significant derivatization potential into the enantioenriched quaternary stereocenters.

<h4>Background</h4>Linker histones constitute a class of proteins that are responsible for the formation of higher-order chromatin structures. Core histones are integral components of nucleosome core particles (NCPs), whereas linker histones bind to linker DNA between NCPs. Heterochromatin protein 1 binding protein 3 (HP1BP3) displays sequence similarity to linker histones, with the exception of the presence of three globular domains in its central region. However, the function of HP1BP3 as a linker histone has not been analyzed previously. The present study aimed to elucidate the function of full-length HP1BP3 as a linker histone variant.<h4>Results</h4>The results of biochemical analyses demonstrate that HP1BP3 efficiently binds to NCPs with similar efficiency as linker histones, thereby forming a chromatosome. Notwithstanding the presence of three globular domains, the results suggest that a single HP1BP3 binds to a single NCP under our biochemical assay condition. Moreover, our findings revealed that the NCP binding activity of HP1BP3 is regulated by linker histone chaperones, nucleophosmin (NPM1) and template activating factor-I (TAF-I). The globular domains and the C-terminal disordered region of HP1BP3 are responsible for binding to histone chaperones. Chromatin immunoprecipitation-sequence analyses demonstrated that HP1BP3 exhibited weak preferences for the genomic loci where histone H3 active modification marks were enriched, whereas a linker histone variant, H1.2, showed weak preferences for the genomic loci where histone H3 inactive modification marks were enriched. It is noteworthy that the preferential binding tendencies of HP1BP3 and H1.2 to active and inactive genomic loci, respectively, are diminished upon the knockdown of either NPM1 or TAF-I.<h4>Conclusions</h4>Our findings indicate that HP1BP3 functions as a linker histone variant and that the chromatin binding preference of linker histones, including HP1BP3, is regulated by linker histone chaperones.

The transcription factor RORγt regulates the development of Th17 cells and their inflammatory cytokine IL-17─a pathway that can both clear bacterial pathogens and drive autoimmune diseases. An endogenous RORγt agonist with a noncanonical structure, a lysophosphatidylethanolamine (1-18:1-LPE or <b>1</b>), was recently identified, and its identity both increases our understanding of immune regulation and creates options for therapeutic intervention. Compound <b>1</b> could be formed directly through enzymatic cleavage of a suitable phosphatidylethanolamine (PE) by a phospholipase A2 (PLA2) or by "triggering" of a suitable plasmalogen with accompanying 1,2-acyl migration from the <i>sn</i>-2 to <i>sn</i>-1 positions of glycerol. This study illustrates the plausibility of a plasmalogen-based pathway through synthesis of the plasmalogen precursor (<b>2</b>) and triggering the plasmalogen's electron-rich vinyl ether with small electrophiles characteristic of inflammatory and tumor environments to create 1-18:1-LPE (<b>1</b>). The plasmalogen-based pathway is consistent with previous studies on the formation of <b>1</b>, and it also conforms to Lands rules for acyl chain distribution and provides a mechanism for immune signaling with both spatial and temporal control.

Enhancement of the metabolic conversion of cyclophosphamide (CPA) increases its therapeutic effects. Activation of the human constitutive androstane receptor (hCAR) induces CYP2B6, a key enzyme responsible for CPA bioactivation. Based on our previous hCAR activator DL5016, we designed and synthesized a series of new hCAR activators. Compared to DL5016, three new compounds <b>6i</b>, <b>6k</b> (DL5055), and <b>7e</b>, showed significantly improved activating potency for hCAR. Particularly, DL5055 activates hCAR with an EC₅₀ of 0.35 μM and <i>E</i>_MAX of 4.3, and does not activate hPXR and other related nuclear receptors. It induced the expression of CYP2B6 and caused the translocation of hCAR from the cytoplasm to the nucleus in human primary hepatocytes. DL5055 also induces the expression of Cyp2b10 (the mouse analog of human CYP2B6) in hCAR-transgenic mice. In addition, it significantly enhances the efficacy of CPA-based chemotherapy regimen, CHOP, in a coculture system and a mouse xenograft model <i>in vivo</i>.

Asthenoteratozoospermia, a prevalent cause of male infertility, lacks a well-defined etiology. DNAH12 is a special dynein featured by the absence of a microtubule-binding domain, however, its functions in spermatogenesis remain largely unknown. Through comprehensive genetic analyses involving whole-exome sequencing and subsequent Sanger sequencing on infertile patients and fertile controls from six distinct families, we unveiled six biallelic mutations in <i>DNAH12</i> that co-segregate recessively with male infertility in the studied families. Transmission electron microscopy (TEM) revealed pronounced axonemal abnormalities, including inner dynein arms (IDAs) impairment and central pair (CP) loss in sperm flagella of the patients. Mouse models (<i>Dnah12</i>^-/- and <i>Dnah12^mut/mut</i>) were generated and recapitulated the reproductive defects in the patients. Noteworthy, DNAH12 deficiency did not show effects on cilium organization and function. Mechanistically, DNAH12 was confirmed to interact with two other IDA components DNALI1 and DNAH1, while disruption of DNAH12 leads to failed recruitment of DNALI1 and DNAH1 to IDAs and compromised sperm development. Furthermore, DNAH12 also interacts with radial spoke head proteins RSPH1, RSPH9, and DNAJB13 to regulate CP stability. Moreover, the infertility of <i>Dnah12</i>^-/- mice could be overcome by intracytoplasmic sperm injection (ICSI) treatment. Collectively, DNAH12 plays a crucial role in the proper organization of axoneme in sperm flagella, but not cilia, by recruiting DNAH1 and DNALI1 in both humans and mice. These findings expand our comprehension of dynein component assembly in flagella and cilia and provide a valuable marker for genetic counseling and diagnosis of asthenoteratozoospermia in clinical practice.

Cardiac fibrosis, a hallmark of heart failure and various cardiomyopathies, represents a complex pathological process that has long challenged therapeutic intervention. High-throughput omics technologies have begun revolutionizing our understanding of the molecular mechanisms driving cardiac fibrosis and are providing unprecedented insights into its heterogeneity and progression. This review provides a comprehensive analysis of how techniques-encompassing genomics, epigenomics, transcriptomics, proteomics, and metabolomics-are providing insight into our understanding of cardiac fibrosis. Genomic studies have identified novel genetic variants and regulatory networks associated with fibrosis susceptibility and progression, and single-cell transcriptomics has unveiled distinct cardiac fibroblast subpopulations with unique molecular signatures. Epigenomic profiling has revealed dynamic chromatin modifications controlling fibroblast activation states, and proteomic analyses have identified novel biomarkers and potential therapeutic targets. Metabolomic studies have uncovered important alterations in cardiac energetics and substrate utilization during fibrotic remodeling. The integration of these multi-omic data sets has led to the identification of previously unrecognized pathogenic mechanisms and potential therapeutic targets, including cell-type-specific interventions and metabolic modulators. We discuss how these advances are driving the development of precision medicine approaches for cardiac fibrosis while highlighting current challenges and future directions in translating multi-omic insights into effective therapeutic strategies. This review provides a systems-level perspective on cardiac fibrosis that may inform the development of more effective, personalized therapeutic approaches for heart failure and related cardiovascular diseases.

The zinc finger antiviral protein (ZAP) depletes nonself RNAs through recognition of their elevated CpG dinucleotide content. CpG dinucleotides are sparse in most endogenous mammalian mRNAs, but a subset might potentially be modulated by ZAP. While CpG frequency alone is insufficient to predict ZAP-regulation, we developed an algorithm using experimentally determined compositional features to predict which endogenous mRNAs may be ZAP-regulated. Using ZAP-knockout mice, we demonstrate that levels of many host mRNAs that are algorithmically predicted ZAP targets are indeed increased when ZAP is absent. ZAP is interferon-inducible, and we also identify genes that are downregulated by ZAP during an innate immune response. Many ZAP-regulated gene products are extracellular matrix or of nucleosome components, whose ZAP-mediated control is conserved in human cells. Overall, we provide a tool for the prediction of ZAP target genes and reveal host mRNAs that are ZAP-regulated.

<h4>Objectives</h4>SARS-CoV-2 poses significant challenges to people living with diabetes (PLWD). This systematic review aimed to explore the impact of COVID-19 on mortality, complications associated with diabetes and haematological parameters among PLWD.<h4>Design</h4>Systematic review and meta-analysis using the Grading of Recommendations Assessment, Development and Evaluation (GRADE).<h4>Data sources</h4>EMBASE, MEDLINE, Cochrane Central Register of Controlled Trials and LILACS were searched between 1 December 2019 and 14 January 2025.<h4>Eligibility criteria for selecting studies</h4>Eligible studies included case-control and cohort studies involving PLWD categorised into two groups: those with confirmed SARS-CoV-2 infection and those without.<h4>Data extraction and synthesis</h4>Meta-analyses estimated the odds ratios (ORs) and mean differences (MDs) of outcomes including mortality, intensive care unit (ICU) admission, diabetic ketoacidosis (DKA), acute kidney injury, hospitalisation length and haematological parameters. We pooled results using random-effects models and assessed study quality with the Newcastle-Ottawa Scale. A funnel plot was used to detect potential publication bias. The overall certainty of evidence was assessed using GRADE.<h4>Results</h4>25 of 7266 unique studies were eligible, including 1 154674 PLWD (561 558 with COVID-19 and 593 116 without COVID-19). SARS-CoV-2 infection in PLWD was associated with significantly increased mortality (OR 2.52, 95% CI 1.45 to 4.36, I²=99%), acute kidney injury (3.69, 95% CI 2.75 to 4.94, I²=0%), random plasma glucose in subjects with type 1 diabetes (MD 20.38 mg/dL, 95% CI 7.39 to 33.36, I²=0%), haemoglobin A1C in subjects with type 2 diabetes (0.21%, 95% CI 0.05 to 0.38, I²=13%), creatinine (0.12 mg/dL, 95% CI 0.04 to 0.19, I²=0%), C reactive protein (38.30 mg/L, 95% CI 4.79 to 71.82, I²=82%) and D-dimer (1.52 µg/mL, 95% CI 0.73 to 2.31, I²=0%). No significant differences were observed in the incidence of ICU admission and DKA, hospitalisation length, haemoglobin, leucocyte, lymphocyte, neutrophil to lymphocyte ratio, platelet, blood urea nitrogen, estimated glomerular filtration rate, procalcitonin, albumin, ferritin and bilirubin among PLWD with and without SARS-CoV-2 infection.<h4>Conclusions</h4>SARS-CoV-2 infection is associated with elevated risks of mortality and acute kidney injury and poor glycaemic control in PLWD, alongside increased levels of inflammatory and coagulation biomarkers. These findings underscore the urgent need for tailored clinical management strategies for PLWD with COVID-19.<h4>Prospero registration number</h4>CRD42023418039.

DNA-protein interactions have traditionally been profiled via chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq). Cleavage Under Targets & Tagmentation (CUT&Tag) is a rapidly expanding technique that enables the profiling of such interactions in situ at high sensitivity. However, thorough evaluation and benchmarking against established ChIP-seq datasets are lacking. Here, we comprehensively benchmarked CUT&Tag for H3K27ac and H3K27me3 against published ChIP-seq profiles from ENCODE in K562 cells. Combining multiple new and published CUT&Tag datasets, there was an average recall of 54% known ENCODE peaks for both histone modifications. We tested peak callers MACS2 and SEACR and identified optimal peak calling parameters. Overall, peaks identified by CUT&Tag represent the strongest ENCODE peaks and show the same functional and biological enrichments as ChIP-seq peaks identified by ENCODE. Our workflow systematically evaluates the merits of methodological adjustments, providing a benchmarking framework for the experimental design and analysis of CUT&Tag studies.

<h4>Background</h4>Recent studies have identified a complex relationship between methylation patterns and the development of various cancers. Breast cancer (BC) is the second leading cause of cancer mortality among women. Approximately 5-20% of BC patients are at risk of BC brain metastases (BCBM). Although 5-methylcytosine (m5C) has been identified as an important regulatory modifier, its distribution in BCBM is not well understood. This study aimed to investigate the distribution of m5C in BCBM.<h4>Materials and methods</h4>Samples from BCBM (231-BR cells) and BC (MDA-MB-231 cells) groups were subjected to a comprehensive analysis of the m5C methylation in long non-coding RNA (lncRNA) using methylated RNA immunoprecipitation next-generation sequencing (MeRIP-seq). The expression levels of methylated genes in BC and adjacent tissues were verified through quantitative real-time polymerase chain reaction (RT-qPCR). Enrichment pathway analyses were through Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) to predict the potential functions of m5C in BCBM.<h4>Results</h4>The MeRIP-seq analysis identified 23,934 m5C peaks in BCBM and 21,236 m5C in BC. A total of 9,480 annotated genes (BCBM) and 8,481 annotated genes (BC) were mapped. Notably, 1,819 methylation sites in lncRNA were upregulated in BCBM, whereas 2,415 methylation sites were upregulated in BC. Significant m5C hypermethylated lncRNAs included ENST00000477316, ENST00000478098 and uc002gtt.1, whereas hypomethylated lncRNAs included ENST00000600912, ENST00000493668, ENST00000544651 and ENST00000464989. These results were verified by qPCR and MeRIP-qPCR in BC and BCBM. Considering the strong association between m5C RNA methylation regulators and lncRNA, we examined the expression levels of 13 m5C RNA methylation regulators and observed significant differences between BC tissues and adjacent normal tissues. In addition, the interaction between regulators of altered expression and the differentially expressed genes in vitro was analyzed. The GO and KEGG pathways analyses revealed that genes significantly associated with m5C sites in lncRNA were linked to the BCBM signaling pathways.<h4>Conclusion</h4>This uncovered significant variations in the levels and distribution of m5C in BCBM compared to BC. The findings provide a new theoretical understanding of the mechanisms of BCBM.

<h4>Background</h4>The aim of this study was to screen three major substance metabolism-related genes and establish a prognostic model for osteosarcoma.<h4>Methods</h4>RNA-seq expression data for osteosarcoma were downloaded from The Cancer Genome Atlas (TCGA) and GEO databases. Differentially expressed (DE) RNAs were selected, followed by the selection of metabolic-related DE mRNAs. Using Cox regression analysis, prognostic DE RNAs were identified to construct a prognostic model. Subsequently, independent prognostic clinical factors were screened, and the functions of the long non-coding RNAs (lncRNAs) were analyzed. Finally, the expression of signature genes was further tested in osteosarcoma cells using quantitative reverse transcription quantitative real-time polymerase chain reaction (qRT-PCR) and western blotting.<h4>Results</h4>A total of 432 DE RNAs, comprising 79 DE lncRNAs and 353 DE mRNAs were obtained, and then 107 metabolic-related DE mRNAs. Afterwards signature genes (LINC00545, LINC01537, FOXC2-AS1, CYP27B1, PFKFB4, PHKG1, PHYKPL, PXMP2, and XYLB) served as optimal combinations, and a prognostic score model was successfully proposed. Three verification datasets (GSE16091, GSE21257, and GSE39055) showed that the model had high specificity and sensitivity. In addition, two independent prognostic clinical factors (age and tumor metastasis) were identified. Finally, the concordance rate between the in silico analysis, qRT-PCR, and western blotting analysis was 88.89% (8/9), suggesting the robustness of our analysis.<h4>Conclusions</h4>The prognostic model based on the nine signature genes accurately predicted the prognosis of patients with osteosarcoma; CYP27B1, PFKFB4, PHKG1, PHYKPL, PXMP2, and XYLB may serve as metabolism-related biomarkers in osteosarcoma.

Microglia and astrocytes are the primary glial cells in the central nervous system (CNS) and their function is shaped by multiple factors. Regulation of CNS glia by the microbiota have been reported, although the role of specific bacteria has not been identified. We colonized germ-free mice with the type strain Akkermansia muciniphila (Am^T) and a novel A. muciniphila strain BWH-H3 (Am-H3) isolated from a subject with multiple sclerosis and compared to mice colonized with Bacteroides cellulosilyticus strain BWH-E5 (Bc) isolated from a healthy control subject. We then investigated the effect of these bacteria on microglia and astrocyte gene expression by RNA sequencing. We found altered gene expression profiles in brain microglia, with Akkermansia downregulating genes related to antigen presentation and cell migration. Furthermore, we observed strain specific effects, with Akkermansia H3 upregulating histone and protein binding associated genes and downregulating channel and ion transport genes. Astrocyte pathways that were altered by Akkermansia H3 mono-colonization included upregulation of proliferation pathways and downregulation in cytoskeletal associated genes. Furthermore, animals colonized with type strain Akkermansia and strain H3 had effects on the immune system including elevated splenic γδ-T cells and increased IFNγ production in CD4 + T cells. We also measured intestinal short chain fatty acids and found that both A. muciniphila strains produced proprionate while B. cellulosilyticus produced acetate, proprionate, and isovalerate. Taken together, our study shows that specific members of the intestinal microbiota influence both microglial and astroyctes which may be mediated by changes in short chain fatty acids and peripheral immune signaling.

The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor best known for mediating biological responses to a wide range of xenobiotics, such as dioxins and polycyclic aromatic hydrocarbons. Recently, AhR has emerged as an important player in cancer biology, with the potential for therapeutic applications through targeted modulation of its activity in specific cancer types. In this study, we report that 4,11-dichloro-BBQ (DiCl-BBQ), a benzimidazoisoquinoline, exhibits AhR-mediated antiproliferative activity in HepG2 hepatocellular carcinoma cells. DiCl-BBQ was found to decrease cell growth at nanomolar concentrations, and this antiproliferative effect persisted even after the compound's removal. Using inducible shRNA expression system, we demonstrated that the inhibitory effect of DiCl-BBQ was significantly reduced following AhR knockdown. Flow cytometric analysis revealed that DiCl-BBQ halted cell division and induced G1 cell cycle arrest in an AhR-dependent manner. Proteomic profiling identified the top four enriched pathways following DiCl-BBQ exposure: metabolism of RNA, translation, ribonucleoprotein complex biogenesis, and carboxylic acid metabolic processes. Notably, DiCl-BBQ caused a dramatic downregulation of translation-associated proteins, with this response diminished in AhR-depleted cells. Consistently, global protein synthesis was significantly repressed in DiCl-BBQ-treated cells. Together, these results indicate that DiCl-BBQ effectively inhibits HepG2 cells growth by inducing G1 cell cycle arrest and downregulating the protein translation machinery in an AhR-dependent manner.

Iron homeostatic is closely linked to the development of metabolic dysfunction-associated steatohepatitis (MASH). However, the underlying mechanisms remain poorly understood. HFE knockout (KO) mice were used to generate mild iron-overload models. MASH was induced by feeding mice a methionine- and choline-deficient (MCD) diet for 4 weeks. Iron overload significantly exacerbated the pathologies of MCD-induced MASH, including liver injury, hepatic lipid accumulation, inflammation, and fibrosis. Additionally, iron overload reshaped the composition of gut microbiota, and fecal microbiota transplantation assay proved that gut microbiota from iron-overload mice contributed to hepatic lipid accumulation in control mice. Furthermore, iron overload-induced dysbacteriosis altered the metabolite profiles, reducing short-chain fatty acid levels and increasing lipopolysaccharide (LPS) levels. Notably, elevated LPS levels upregulated the expression of aldo-keto reductase family 1 member B8 (Akr1b8), which accelerated lipid accumulation and inflammation in hepatocytes. Above results indicated that iron overload promoted MASH progression through the microbiota-gut-liver axis, mediated by LPS-induced activation of Akr1b8. These findings highlight the critical role of iron homeostasis and gut microbiota in MASH pathogenesis.

No abstract available.

This study aimed to use metabolomics to accurately reveal alterations in metabolites and potential regulatory mechanisms in patients with diabetic cortical cataracts (DCC). We first collected cortical samples from different pathological areas of the same lens in DCC patients for metabolomics. Then, we used transcriptomic analysis to study lactate's effect on gene expression in human lens epithelial cells (HLECs). An in vitro rat lens culture assay evaluated lactate's impact on lens transparency, and WB and immunofluorescence assessed lactate-induced apoptosis and oxidative damage in rat LECs. Furthermore, CHIP sequencing and LC-MS identified H3K18la separately modified genes and potential lactylation proteins in HLECs. Immunoprecipitation validated lactylation levels of proteins. Our findings identified 11 upregulated and 18 downregulated metabolites in the opacity zone of LFCs (OZ-LFCs) compared to the clear zone (CZ-LFCs) in DCC patients. We confirmed the differential lactate content between OZ-LFCs and CZ-LFCs and, through transcriptomic analysis, discovered that lactate affects gene expression, protein metabolism, and DNA repair in primary Human Lens epithelial cells (HLECs). Lactate-induced apoptosis and DNA repair hastened lens opacity in a high-sugar rat lens culture model. Lactylation-MS and H3K18la-ChIP sequencing revealed 591 H3K18la-modified genes and 953 lactylation proteins in HLECs. PKM2 and NPM1 lactylation was confirmed through immunoprecipitation. These findings improve our grasp of spatial dynamics in DCC patient metabolomics and suggest a new research path into lactylation modification to understand lactate's role in cataract formation.

Congenital heart disease (CHD) is the most prevalent human birth defect and remains a leading cause of mortality in childhood. Although advancements in surgical and medical interventions have significantly reduced mortality rates among infants with critical CHDs, many survivors experience substantial cardiac and extracardiac comorbidities that affect their quality of life. The etiology of CHD is multifactorial, involving both genetic and environmental factors, yet a definitive cause remains unidentified in many cases. Recent advancements in genetic testing technologies have improved our ability to identify the genetic causes of CHD. This review presents an updated summary of the established genetic contributions to CHD, including chromosomal aberrations and mutations in genes associated with transcription factors, cardiac structural proteins, chromatin modifiers, cilia-related proteins, and cell signaling pathways. Furthermore, we discuss recent findings that support the roles of non-coding mutations and complex inheritance in the etiology of CHD.

Pathogens have developed multiple strategies to modulate host immune defense mechanisms. Understanding how this is achieved has potential to inform novel therapeutics for diseases caused by immune dysfunction. Parasitic helminths are masters of immune evasion, via release of secreted products, resulting in chronic infection. Helminths secrete small regulatory microRNA (miRNAs), which can interact with host cells. Here we show that a single parasite miRNA (miR-5352), conserved across gastrointestinal (GI) nematodes, suppresses IL-13-induced GI epithelial cell differentiation and cytokine responses, and promotes stem cell maintenance. Mechanistically, this is achieved through targeted repression of critical host factors, including Klf-4 and the IL-22 receptor, together with modulation of Wnt and Notch signalling pathways. Nematode miR-5352 shows seed sequence conservation with mammalian miR-92a family members, indicating that through convergent evolution, GI nematodes exploit a host miRNA regulatory network to suppress host innate responses, promote tissue regeneration and establish a favourable environment for chronic infection.

<h4>Background</h4>Breast cancer (BRCA) remains by far the most life-threatening malignancy in women. Resistance to BRCA treatment may be counteracted by the induction of ferroptosis in combination with immunotherapy. The study aims develop iron death-related prognostic models to predict prognosis and immunotherapy effects in BRCA patients.<h4>Methods</h4>We collected and organized 22 ferroptosis-related pathways and quantified their pathway activities using single-sample gene set enrichment analysis (ssGSEA). Coenzyme Q10 (CoQ10) is a pathway associated with prognosis in patients with BRCA. We compared the differences between patients with different CoQ10 expressions in terms of prognosis, biological function, mutational profile, immune infiltration, immunotherapy, and chemotherapeutic drug sensitivity.<h4>Results</h4>Patients with high CoQ pathway activity had a worse prognosis. In addition, patients with high CoQ activity showed greater cell cycle activation and lower immune infiltration. Based on different CoQ10 expression patterns, we developed a CoQ10-related prognostic model. The accuracy and stability of CoQ10-related prognostic models were well validated in the training set and multiple validation sets. High-risk patients showed a propensity for immune depletion and tolerance to immunotherapy. There were also some differences in the sensitivity to different chemotherapeutic agents between high- and low-risk patients.<h4>Conclusions</h4>We have constructed and validated a CoQ10-related gene model that can predict the prognosis of BRCA. Critically, it may serve as a reference standard to guide outcome prognostication in patients with BRCA.

Deep tissue injuries (DTIs) pose significant reconstructive challenges, particularly when involving extensive soft tissue loss and exposure of vital structures. We report a case of a 69-year-old male with multiple comorbidities who developed a complex, full-thickness trochanteric wound following prolonged immobilization after a cardiac event. The injury, characterized by a 19 x 9 cm defect with compromised surrounding tissues - including the tensor fascia - precluded the use of conventional local flaps. Given the size and depth of the defect, a pedicled vertical rectus abdominis myocutaneous (VRAM) flap was selected for its robust vascularity, versatility, and ability to provide ample soft tissue bulk. Complete healing was observed at the six-month follow-up visit with no evidence of abdominal wall compromise or functional deficit. This case illustrates that the VRAM flap is a reliable and effective option for the reconstruction of large, complex DTIs in the proximal lower extremity, particularly when local flap options are compromised.

<h4>Objective</h4>To report a unique case of preimplantation genetic testing for a monogenic condition (PGT-M) for Huntington disease (HD) using both exclusion-based testing and direct nondisclosure testing across multiple generations and to highlight the strategies used to protect reproductive autonomy and privacy.<h4>Design</h4>Case report.<h4>Subjects</h4>A reproductive-aged nulliparous couple with the male partner's family history significant for HD who desired to conceive a child with PGT-M to build a family without the risk of HD inheritance while simultaneously maintaining the anonymity of carrier results to the partner and all living family members.<h4>Exposure</h4>Two in vitro fertilization (IVF) cycles with exclusion-based PGT-M in the first cycle and direct nondisclosure PGT-M in the second cycle, followed by 2 frozen embryo transfers (FETs).<h4>Main outcome measures</h4>Number of low-risk euploid blastocysts suitable for embryo transfer.<h4>Results</h4>The first IVF cycle using exclusion-based PGT-M resulted in 14 good-quality blastocysts with only 1 blastocyst deemed at low risk of inheriting the at-risk HD haplotype. The first FET was unsuccessful. The male partner's mother was tested and was found to be an HD carrier. The second IVF cycle used direct nondisclosure PGT-M, which resulted in 12 blastocysts suitable for transfer (both euploid and negative for HD). After the second failed FET, the male partner ultimately decided to undergo genetic testing for HD for himself and was negative for HD mutation. The couple then chose to attempt spontaneous conception and had a live birth of a healthy male infant without complications.<h4>Conclusion</h4>Multigenerational blinding of PGT-M for trinucleotide repeat disorders has great utility in preserving patient autonomy while limiting the risk of future progeny inheriting a life-limiting genetic condition. Careful, comprehensive counseling and multilevel strategies should be developed to enact these blinding measures to best serve patients and their families whose genetic information is being used for testing.

<b>Background and Clinical Significance</b>: Dental demineralization is a multifactorial process influenced by biofilm activity, diet, and systemic conditions. While gastroesophageal reflux disease (GERD) is known for its role in enamel erosion, its contribution to cariogenic processes remains underexplored. Additionally, Brugada syndrome, a genetic arrhythmia disorder, may indirectly affect oral health due to medical complexities and reduced motivation for dental care. This case highlights the management of extensive mineral loss in a patient with GERD and Brugada syndrome, emphasizing the importance of personalized remineralization strategies and interdisciplinary collaboration. <b>Case Presentation</b>: A 27-year-old male with Brugada syndrome, treated with a subcutaneous implantable cardioverter defibrillator (S-ICD), presented with widespread enamel demineralization, multiple active carious lesions, and gingival inflammation. Clinical evaluation revealed a high DMFT index (15), significant plaque accumulation, and an oral pH of 5.8, indicating an elevated risk of mineral loss. Poor hygiene habits, frequent sugar intake, and GERD-related acid exposure contributed to his condition. The therapeutic approach included patient education, fluoride-functionalized hydroxyapatite toothpaste and mousse, dietary modifications, and restorative procedures. After 120 days, improvements included enhanced enamel integrity, a reduction in plaque index (from 50% to 25%), and the resolution of gingival inflammation (BOP: 38% to 12%). <b>Conclusions</b>: This case underscores the importance of an integrated approach to managing dental demineralization in patients with systemic conditions. The combination of remineralization therapy, behavioral modifications, and structured follow-up yielded significant clinical benefits. Further research is needed to develop standardized protocols for individuals at high risk due to systemic factors affecting oral health.

<title>Abstract</title> <p>Mechanosensitive ion channels, such as Piezo1, have emerged as having fundamental roles in sensing the mechanical properties of the extracellular matrix (ECM). However, whether and how Piezo1 senses time-dependent ECM mechanical properties, that is viscoelasticity, remains unknown. To address this question, we combined an immortalised mesenchymal stem cell (MSC) line in which Piezo1 expression can be silenced with soft and stiff viscoelastic hydrogels that have independently tuneable elastic and viscous moduli. We demonstrate that Piezo1 is a mechanosensor of viscoelasticity in soft ECMs, both experimentally and throughout simulations using a modified viscoelastic molecular clutch model that incorporates Piezo1. Using RNA sequencing, we also identify the transcriptomic phenotype of MSC response to matrix viscoelasticity and Piezo1 activity, identifying gene signatures that modulate MSC’s mechanobiology in soft and stiff viscoelastic hydrogels.</p>

<title>Abstract</title> <p> Desmoplastic small round cell tumor (DSRCT) is an ultra-rare sarcoma with limited treatment options. We performed whole-genome/exome, transcriptome, and DNA methylome analysis in 30 refractory DSRCT patients, complemented by (phospho)proteomic profiling in nine, within a nationwide precision oncology program. In eight patients (27%), DSRCT was diagnosed based on molecular profiling. Although all patients had “quiet” genomes, 28 (93%) received 107 molecular-based management recommendations, including assessment of clinical trial eligibility in 17 (57%). Nearly half of recommendations (45%) were based on overexpression of tyrosine kinases, as well as SSTR3/5 and CLDN6, detected in 33% and 20% of cases, respectively. Thirteen patients (46%) received recommended therapies, yielding disease control in eight (62%; partial response, <italic>n</italic>  = 5; stable disease, <italic>n</italic>  = 3), including three long-lasting responses (≥ 12 months) to pazopanib and trastuzumab deruxtecan, triggered by ERBB2 overexpression in the absence of constitutive ERBB2 signaling. Thus, multi-omics profiling enables individualized DSRCT treatment. </p>

The amyloid hypothesis has been a leading narrative concerning the pathophysiological foundation of Alzheimer's and Parkinson's disease. At the two ends of the hypothesis lie the functional protein monomers and the pathology-defining amyloid fibrils, while the early stages of protein aggregation are populated by polymorphic, transient and neurotoxic oligomers. As the structure and activity of oligomers are intertwined, here we show oligomers arising from liquid-liquid phase separation and β-barrel formation, their routes to neurodegeneration, and their role in cerebrovascular perturbation. Together, this Perspective converges on the multifaceted oligomer-axis central to the pathological origin and, hence, the treatment of amyloid diseases.

Beckwith-Wiedemann Syndrome (BWS) is an epigenetic overgrowth syndrome caused by methylation changes in the human 11p15 chromosomal locus. Patients with BWS may exhibit hepatomegaly, as well as an increased risk of hepatoblastoma. To understand the impact of these 11p15 changes in the liver, we performed a multiomic study [single nucleus RNA-sequencing (snRNA-seq) + single nucleus assay for transposable-accessible chromatin-sequencing (snATAC-seq)] of both BWS-liver and nonBWS-liver tumor-adjacent tissue. Our approach uncovers hepatocyte-specific enrichment of processes related to peroxisome proliferator-activated receptor alpha (PPARA). To confirm our findings, we differentiated a BWS induced pluripotent stem cell model into hepatocytes. Our data demonstrate the dysregulation of lipid metabolism in BWS-liver, which coincides with observed upregulation of PPARA during hepatocyte differentiation. BWS hepatocytes also exhibit decreased neutral lipids and increased fatty acid β-oxidation. We also observe increased reactive oxygen species byproducts in BWS hepatocytes, coinciding with increased oxidative DNA damage. This study proposes a putative mechanism for overgrowth and cancer predisposition in BWS liver due to perturbed metabolism.

The prevalence of nonalcoholic steatohepatitis (NASH) is rising annually, posing health and economic challenges, with limited treatments available. Diosgenin, a natural steroidal compound found in various plants, holds potential as a therapeutic candidate. Recent studies have confirmed diosgenin's anti-inflammatory and metabolism-modulating properties. However, its therapeutic effects on NASH and the underlying mechanisms are still unclear. This study aims to explore diosgenin's protective effects and pharmacological mechanisms against NASH using network pharmacology, molecular docking, and experimental validation. We gathered potential targets of diosgenin and NASH from various databases to generate protein-protein interaction (PPI) networks. GO and KEGG pathway enrichment analyses identified key targets and mechanisms. Molecular docking confirmed the binding capacity between diosgenin and core target proteins. Additionally, a NASH cell model was developed to validate the pharmacological effects of diosgenin. Our investigation identified nine key targets (ALB, AKT1, TP53, VEGFA, MAPK3, EGFR, STAT3, CASP3, IGF1) that interact with diosgenin. Molecular docking indicated potential bindings interactions, while enrichment analyses revealed that diosgenin may enhance fatty acid metabolism via the PI3K-Akt pathway. Cellular experiments confirmed that diosgenin activates this pathway, reduces SCD1 expression, and decreases triglyceride and IL-6 levels. Our study elucidates that diosgenin may ameliorate triglyceride deposition and inflammation through the PI3K-Akt pathway.

Coccidioidomycosis or valley fever is a treatment-limited fungal infection endemic to the alkaline deserts of North and South America for which two classes of antifungals are typically used: the polyenes and the triazoles. In light of the limited usefulness of the echinocandins and a growing trend of azole resistance, it is essential that we identify novel antifungals. In this study, we have developed and optimized a screening methodology for identifying potential antifungals effective against <i>Coccidioides</i> spherule initials using a metabolic assay, used it to screen four diverse drug libraries with limited drug overlap, and established safety and efficacy data for a majority of the compounds, including the Broad Repurposing Hub, Prestwick Chemicals 1520, Selleck L8200 Anti-parasitic, and MedChemExpress CNS Penetrants libraries. Hits were defined as compounds with strong metabolic inhibition (≥70%), which were significantly different compared to the median plate readout (B-scores ≤ -3). We identified 30 promising hits and found 12 compounds exhibiting half-maximal inhibitory concentrations below 6 µM. Among these, oxethazaine, niclosamide ethanolamine, 10058-F4, niclosamide (NIC), and pentamidine isethionate showed synergy with amphotericin B, suggesting their potential use in combination therapy. Further assessment of lead compounds' effects on spherules was conducted by image flow cytometry. Additionally, we explored the potential to use an attenuated, Biosafety Level 2 containment mutant, <i>C. posadasii</i> ∆<i>cts2</i>/∆<i>ard1</i>/∆<i>cts3</i> (∆T), as a surrogate model for drug screening. Overall, our findings provide a foundation for future research focused on screening and developing novel coccidioidomycosis treatments.IMPORTANCEThe antifungal treatment arsenal is especially limited against <i>Coccidioides</i>. Due to toxicity concerns, amphotericin B is generally reserved for triazole-recalcitrant infections. Recent laboratory susceptibility tests show an increase in fluconazole resistance, highlighting a need for new treatments. We have developed a large-scale metabolic screening assay under Biosafety Level 3 containment to identify existing drugs with novel activity against <i>Coccidioides</i> spherules. This drug-repurposing approach represents a convenient and cost-effective strategy to increase the available antifungals effective against these infections.

<h4>Background</h4>Previously, we explored the role of Sox9 in the second heart field (SHF) in atrioventricular septation. For that study, we created a SHF-specific Sox9 knockout mouse. In addition to the presence of primary atrial septal defects in half of the offspring, we found that virtually all specimens also developed a ventricular septal defect. Histological analysis suggested that the ventricular septal defects resulted from developmental perturbation of the mesenchymal structures within the outflow tract. In the current study, we investigated the role of Sox9 in the SHF in the development of these tissues.<h4>Results</h4>Sox9 is expressed in all mesenchymal cell populations in the developing outflow tract, including a cohort of endocardial-derived cells that originate from the SHF-derived endocardium. SHF-specific deletion of Sox9 inhibits the formation of this cell population and ultimately leads to truncation of the mesenchymal outlet septum. This prevents complete fusion of this outlet septum with the atrioventricular mesenchymal complex, resulting in ventricular septal defects.<h4>Conclusions</h4>In combination with our first paper on the role of Sox9 in atrioventricular septation, data presented in this study demonstrate that Sox9 expression in the SHF is of critical importance for the proper formation of the septal structures in the developing heart.

Enterovirus 71 (EV71) is a major cause of hand, foot, and mouth disease, particularly affecting pediatric populations worldwide. The role of ZYG11B, a CUL2-complex-associated E3 ubiquitin ligase from the Zyg-11 family, in antiviral defense against EV71 remains unclear. To our knowledge, this study is the first to reveal that ZYG11B targets EV71 VP1 for proteasomal degradation via the ubiquitin-proteasome pathway, with CRL2^ZYG11B complex activity specifically driving K33-linked ubiquitination. Mass spectrometry and immunoprecipitation analyses confirmed the interaction between ZYG11B and VP1 and identified key domains required for binding both VP1 and CUL2. Comparative analyses showed that VP1 ubiquitination sites are highly conserved across related enteroviruses, including CA6, CA16, and EVD68. Functional assays further demonstrated that ZYG11B restricts these viruses, highlighting its potential as a broad-spectrum antiviral target. These findings establish ZYG11B as a critical effector in host antiviral responses and support its therapeutic potential for managing enterovirus infections.<h4>Importance</h4>E3 ubiquitin ligases and deubiquitinases have become important topics of competition between viruses and hosts. Here, we identified CRL2^ZYG11B as an E3 ubiquitin ligase complex capable of degrading structural protein VP1 of enteroviruses, making ZYG11B a broad-spectrum antiviral factor. We first proposed the inhibitory effect of ZYG11B on viruses and identified the structural domains of ZYG11B connecting substrates and CUL2, providing new targets for the design of antiviral drugs.

Neurodegenerative disorders, including Alzheimer's disease (AD), Parkinson's disease (PD), Amyotrophic Lateral Sclerosis (ALS), and Huntington's disease (HD), are significant global health challenges, owing to their profound impact on cognitive, motor, and behavioral functions. The etiology and progression of these disorders are influenced by a complex interplay of environmental factors and genetic predispositions with specific genetic markers, such as mutations in the APOE and HTT genes, which play pivotal roles. Current therapeutic interventions predominantly focus on symptom management; however, emerging strategies, including gene therapies, anti-amyloid agents, and neuroprotective approaches, are designed to directly target the underlying disease mechanisms. Advances in biomarker discovery and imaging methodologies have emerged as essential tools for early diagnosis and monitoring of therapeutic efficacy in these disorders. In the context of AD, cerebrospinal fluid (CSF) amyloid-beta (Aβ) and tau levels, along with positron emission tomography (PET) imaging, are well-established biomarkers. Similarly, CSF alpha-synuclein and dopamine transporter (DAT) imaging have been employed as diagnostic tools for PD. Moreover, emerging biomarkers, such as blood-based tau and the Aβ42/40 ratio for AD, as well as the neurofilament light chain (NfL) for ALS and PD, hold promise for enhancing early diagnostic accuracy and facilitating the longitudinal assessment of disease progression. This study comprehensively examined the molecular mechanisms underlying these neurodegenerative disorders, focusing on amyloid-beta plaque deposition and tau protein aggregation in AD, alpha-synuclein misfolding in PD, and aberrant protein aggregation in ALS and HD, thereby contributing to a deeper understanding of the pathophysiological basis of these disorders.

Unveiling the complexities of gene expression regulation, the study explores the intricate DNA-binding mechanisms of transcription factors (TFs). By employing the KaScape method previously developed to measure both bound and unbound populations at thermodynamic equilibrium, "anchoring elements" (AEs), 3-4 base pair sequences, are identified in Arabidopsis WRKY and human PU.1 TFs crucial for binding affinity. Building on the BEESEM method, the study introduces the AEEscape algorithm, which advances the AE concept by creating a precise model of the position-specific k-mer binding energy landscape. This method allows for the direct identification of the dominant role of AEs from experimental data. Moreover, when integrated with genomic data, it reveals an energetic funnel around transcription factor binding sites (TFBSs), which is directly correlated with the density of AEs (AED). The findings not only offer a fresh perspective on TF-TFBS interactions but also highlight the critical role of AED in gene regulation. These insights can pave the way for innovative strategies to manipulate gene expression.

Genomic defects caused by truncating mutations or deletions in the Retinoblastoma tumor suppressor gene (<i>RB1</i>) are frequently observed in many cancer types leading to dysregulation of the RB pathway. Here, we propose an integrative proteogenomic approach that predicts cancers with dysregulation in the RB pathway. A subset of these cancers, which we term as "RBness," lack <i>RB1</i> genomic defects and yet phenocopy the transcriptional profile of <i>RB1</i>-defective cancers. We report RBness as a pan-cancer phenomenon, associated with patient outcome and chemotherapy response in multiple cancer types, and predictive of CDK4/6 inhibitor response in estrogen-positive breast cancer. Using RNA interference and a CRISPR-Cas9 screen in isogenic models, we find that RBness cancers also phenocopy synthetic lethal vulnerabilities of cells with <i>RB1</i> genomic defects. In summary, our findings suggest that dysregulation of the RB pathway in cancers lacking <i>RB1</i> genomic defects provides a molecular rationale for how these cancers could be treated.

Prenatal exposure to cocaine causes abnormalities in foetal brain development, which are linked to later development of anxiety, depression and cognitive dysfunction. Previous studies in rodent models have indicated that prenatal cocaine exposure affects proliferation, differentiation and connectivity of neural cell types. Here, using cerebral organoids derived from the human iPSC cell line HPSI1213i-babk_2, we investigated cocaine-induced changes of the gene expression regulatory landscape at an early developmental time point, leveraging recent advances in single cell RNA-seq and single cell ATAC-seq. iPSC-cerebral organoids replicated well-established cocaine responses observed in vivo and provided additional information about the cell-type specific regulation of gene expression following cocaine exposure. Cocaine altered gene expression patterns, in part through epigenetic landscape remodelling, and revealed disordered neural plasticity mechanisms in the cerebral organoids. Perturbed neurodevelopmental cellular signalling and an inflammatory-like activation of astrocyte populations were also evident following cocaine exposure. The combination of altered neuroplasticity, neurodevelopment and neuroinflammatory signalling suggests cocaine exposure can mediate substantial disruption of normal development and maturation of the brain. These findings offer new insights into the cellular mechanism underlying the adverse effects of cocaine exposure on neurodevelopment and point to the possible pathomechanisms of later neuropsychiatric disturbances.

This study aims to predict and diagnose pediatric septic shock through the screening of immune infiltration-related biomarkers. Three gene expression datasets were accessible from the Gene Expression Omnibus repository. The differentially expressed genes were identified using the R 4.3.2 ( https://www.r-project.org/ ), followed by gene set enrichment analysis. Thereafter, the genes were identified utilizing machine-learning algorithms. The receiver operating characteristic curve was employed to assess the discrimination and effectiveness of the hub genes. The inflammatory and immune status of pediatric septic shock was evaluated through cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT). The correlation between diagnostic markers and infiltrating immune cells was further examined. Overall, we detected 12 differentially expressed genes. CD177, MCEMP1, MMP8, and OLAH were examined as diagnostic indicators for pediatric septic shock, revealing statistically significant differences (P < 0.01) and diagnostic efficacy in the validation cohort. The immune cell infiltration analysis suggests that various immune cells may contribute to the onset of pediatric septic shock. Furthermore, all diagnostic characteristics may exhibit varying degrees of correlation with immune cells. This study identifies four potential biomarkers-CD177, MCEMP1, MMP8, and OLAH-that provide diagnostic value and novel insights into immune dysregulation in pediatric septic shock. Through the integration of bioinformatics and machine learning methodologies, we offer a novel perspective on the immune mechanisms involved in pediatric septic shock, potentially facilitating more targeted and personalized therapies for individual patients.

<h4>Background</h4>C-terminal binding protein-2 (Ctbp2) is an evolutionarily conserved transcriptional repressor that regulates fundamental processes such as cell proliferation and apoptosis. However, the potential role of Ctbp2 in cardiomyocyte proliferation and heart regeneration remains unclear. In this study, we aim to explore the important role of Ctbp2 in cardiomyocyte proliferation and the regeneration of injured adult hearts.<h4>Methods and results</h4>In this study, we found that the expression of Ctbp2 in cardiomyocytes is downregulated after adulthood. Silencing Ctbp2 in cardiomyocytes on the post-natal day 1 (P1) reduced the proliferation ability of cardiomyocytes, whereas overexpressing Ctbp2 enhanced the proliferation ability of cardiomyocytes. Additionally, overexpressing Ctbp2 via adeno-associated virus-9 (AAV9) had no effect on the hearts of normal adult mice, but in the case of heart injury, overexpression of Ctbp2 in adult mice cardiomyocytes promoted cardiomyocyte proliferation. Mechanistically, the transcriptional repressor Ctbp2 acts as a metabolite sensor, and its regulation of cardiomyocyte proliferation is influenced by the metabolites NADH/NAD+ and fatty acyl-CoAs. Ctbp2 is activated by the intracellular accumulation of NADH during cardiomyocyte ischemia and hypoxia, inhibiting the transcriptional activity of the transcription factor FoxO1, thereby repressing the expression of the target genes and cell cycle negative regulators p21 and p27, allowing cardiomyocytes to re-enter the cell cycle. In contrast, normal adult cardiomyocytes mainly use fatty acid oxidation metabolism as their primary energy source, and the intracellular production of fatty acyl-CoAs inactivates Ctbp2, thus preventing it from inhibiting FoxO1 mediated cell cycle arrest.<h4>Conclusion</h4>In conclusion, this study demonstrates that the Ctbp2-FoxO1-p21/p27 axis can promote cardiomyocyte proliferation and heart regeneration. As a metabolite sensor, Ctbp2 is activated during cardiomyocyte ischemia and hypoxia, while it is inactivated under normal conditions. This controllable and transient regulation of cardiomyocyte proliferation can avoid the detrimental effects on cardiac function caused by long-term regulation of cardiomyocyte proliferation, such as hypertrophic cardiomyopathy or heart failure. This provides new targets and new ideas for addressing the issues of cardiomyocyte proliferation and heart regeneration.

<h4>Background</h4>Irinotecan is a widely used chemotherapy drug in colorectal cancer (CRC). The evolution and prognosis of CRC involve complex mechanisms and depend on the drug administered, especially for irinotecan. However, the specific mechanism and prognostic role of irinotecan-related regulators remain to be elucidated.<h4>Methods</h4>Data from public databases were used to explore the multiomic traits of irinotecan-related regulators through bioinformatics analysis. RT‒qPCR, western blotting, transmission electron microscopy and flow cytometry were used as experimental validations.<h4>Results</h4>Iriscore (irinotecan-related score) was constructed based on irinotecan-related regulators, and a high iriscore predicted a poor prognosis, poor therapeutic response and the MSS/MSI-L status. Single-cell analysis revealed that FSTL3 and TMEM98 were mainly expressed in CRC stem cells. Potential transcription factors (E2F1, STAT1, and TTF2) and therapeutic drugs (telatinib) that target irinotecan-related regulators were identified. FSTL3 was the core risk irinotecan-related regulator. Some ferroptosis regulators (GPX4, HSPB1 and RGS4) and related metabolic pathways (lipid oxidation and ROS metabolism) were correlated significantly with FSTL3. In vitro, irinotecan inhibited the expression of FSTL3 and ferroptotic defence proteins (GPX4 and SLC7A11), and induced lipid peroxidation and intracellular Fe (2+) ions concentration increased.<h4>Conclusions</h4>We confirmed that irinotecan-related regulators, especially FSTL3, have effective prognostic value in CRC and speculated that FSTL3 may promote CRC progression and affect ferroptosis, which is beneficial for identifying candidate targeted irinotecan-related regulators and accurate individualized treatment strategies for CRC.

Approximately 8% of the human genome consists of repetitive elements called tandem repeats (TRs): short tandem repeats (STRs) of 1-6 bp motifs and variable number tandem repeats (VNTRs) of 7 + bp motifs. TR variants contribute to several dozen monogenic diseases but remain understudied and enigmatic. It remains comparatively challenging to interpret the clinical significance of TR variants, particularly relative to single nucleotide variants. We present STRchive ( http://strchive.org/ ), a dynamic resource consolidating information on TR disease loci from the research literature, up-to-date clinical resources, and large-scale genomic databases, streamlining TR variant interpretation at disease-associated loci.

GenMineTOP, the first dual DNA-RNA comprehensive genomic profiling (CGP) test in Japan, was approved for reimbursement in 2023. To evaluate its clinical utility, we analyzed 1356 cases from the Center for Cancer Genomics and Advanced Therapeutics (C-CAT) database. Oncogenic genomic alterations were identified in 91.5% of cases. Somatic mutations were the most prevalent, followed by amplifications and fusion/exon skipping events. The DNA panel, covering 737 genes, detected not only alterations relevant to therapeutic decisions but also those providing insights into tumor biology. Among the latter, frequently observed examples included mutations in KMT2C (n = 28) and ARID1B (n = 24), and amplifications in GLI1 (n = 14) and YAP1 (n = 10), which are not included in other CGP tests approved in Japan. The RNA panel identified 105 fusion events, including 11 NTRK fusions (0.8%), of which five were NTRK3 fusions: two with the well-known ETV6-NTRK3 fusion and three with non-ETV6 partners. Forty-nine of these fusions were diagnostically significant, highlighting the utility of the RNA panel. Amplification-RNA expression analyses revealed strong correlations for MDM2, CDK4, EGFR, and ERBB2. In contrast, weaker correlations observed for MYC and FGFR1 highlighted the need for careful interpretation of amplification in these genes. Cancer type significantly influenced RNA expression, with KIT and TERT mutations linked to increased expression and significant overexpression observed in ALK, FGFR3, NTRK1, NTRK3, and RET fusions. In summary, this study demonstrated the real-world clinical utility of the dual DNA-RNA CGP test and provided a valuable resource for interpreting RNA expressions.

<h4>Background</h4>This research focused on exploring the association between coagulopathy scores and the survival outcomes, both short-term and long-term, in individuals diagnosed with liver cirrhosis complicated by sepsis.<h4>Methods</h4>This study retrospectively analyzed data from individuals with liver cirrhosis and sepsis who were admitted to the intensive care unit (ICU) at Beth Israel Deaconess Medical Center between 2008 and 2022. The main outcome of interest was all-cause mortality within 28 days post-admission, while the secondary outcome assessed mortality within 90 days. We used the Kaplan-Meier analysis to compare the mortality risk among the different groups. To evaluate the relationship between coagulopathy score and mortality risk in patients with liver cirrhosis and sepsis, a multivariate Cox proportional hazards regression analysis was performed. The predictive performance of the coagulopathy score for short- and long-term all-cause mortality was assessed using receiver operating characteristic (ROC) curve analysis, which included evaluation of its sensitivity, specificity, and area under the curve. Subgroup analyses were performed to evaluate the relationship between coagulopathy score and survival across different groups.<h4>Results</h4>The study included a total of 2,278 patients. Kaplan-Meier survival analysis demonstrated that individuals with elevated coagulopathy scores exhibited markedly higher rates of ICU mortality, in-hospital mortality, as well as 28-day and 90-day mortality, with all log-rank tests yielding P-values of less than 0.001. The results of the multivariate Cox regression analysis showed that an elevated coagulopathy score was independently linked to higher 28-day and 90-day all-cause mortality, both before and after controlling for potential confounders. ROC curve analysis showed that although the coagulopathy score was slightly less predictive of prognosis than the Model for End-stage Liver Disease score, it significantly outperformed the Sequential Organ Failure Assessment score and the Sepsis-induced Coagulopathy score. Subgroup analysis revealed no significant interaction between the coagulopathy score and survival across the different subgroups.<h4>Conclusions</h4>Higher coagulopathy scores in critically ill patients with liver cirrhosis and sepsis were independently associated with poor prognosis. Due to its simplicity and potential predictive value, the coagulopathy score can serve as an effective complement to existing clinical tools for managing critically ill patients with liver cirrhosis and sepsis.

<h4>Background</h4>This study aimed to evaluate the trends in antimicrobial prescription during the first 1.5 years of COVID-19 pandemic.<h4>Methods</h4>This was an observational, retrospective cohort study using patient-level data from Bangladesh, Brazil, India, Italy, Malawi, Nigeria, South Korea, Switzerland and Turkey from patients with pneumonia and/or acute respiratory distress syndrome and/or sepsis, regardless of COVID-19 positivity, who were admitted to critical care units or COVID-19 specialized wards. The changes of antimicrobial prescription between pre-pandemic and pandemic were estimated using logistic or linear regression. Pandemic effects on month-wise antimicrobial usage were evaluated using interrupted time series analyses (ITSAs).<h4>Results</h4>Antimicrobials for which prescriptions significantly increased during the pandemic were as follows: meropenem in Bangladesh (95% CI: 1.94-4.07) with increased prescribed daily dose (PDD) (95% CI: 1.17-1.58) and Turkey (95% CI: 1.09-1.58), moxifloxacin in Bangladesh (95% CI: 4.11-11.87) with increased days of therapy (DOT) (95% CI: 1.14-2.56), piperacillin/tazobactam in Italy (95% CI: 1.07-1.48) with increased DOT (95% CI: 1.01-1.25) and PDD (95% CI: 1.05-1.21) and azithromycin in Bangladesh (95% CI: 3.36-21.77) and Brazil (95% CI: 2.33-8.42). ITSA showed a significant drop in azithromycin usage in India (95% CI: -8.38 to -3.49 g/100 patients) and South Korea (95% CI: -2.83 to -1.89 g/100 patients) after WHO guidelines v1 release and increased meropenem usage (95% CI: 93.40-126.48 g/100 patients) and moxifloxacin (95% CI: 5.40-13.98 g/100 patients) in Bangladesh and sulfamethoxazole/trimethoprim in India (95% CI: 0.92-9.32 g/100 patients) following the Delta variant emergence.<h4>Conclusions</h4>This study reinforces the importance of developing antimicrobial stewardship in the clinical settings during inter-pandemic periods.

Acute cerebral infarction (CI) is characterized by acute onset, high disability rate, and high morbidity rate, which seriously threatens the health and safety of people and places a heavy burden on individuals and the country. This study aimed to explore the effects of butylphthalide on nerve cell ferroptosis in CI rats and its underlying mechanisms. Middle cerebral artery occlusion (MCAO) rat model was used to study the effect of butylphthalide on acute CI in vivo and oxygen glucose deprivation (OGD) model was used to study the effect of butylphthalide on acute CI in vitro. Our findings demonstrated that butylphthalide markedly reduced oxidative damage and ferroptosis in the brains of MCAO rats. Furthermore, we found that butylphthalide upregulated the netrin-1/deleted in colorectal cancer (DCC)/vascular endothelial growth factor (VEGF) signaling axis, which regulates NF-E2-related factor-2 (NRF2) expression and contributes to ferroptosis in the MCAO rat model and OGD-treated HT22 cells. Collectively, our findings indicate that butylphthalide inhibits oxidative stress-mediated ferroptosis in the MCAO rat model and OGD-treated HT22 cells by modulating the netrin-1/DCC/VEGF/NRF2 axis. In conclusion, our results reveal a novel mechanism for the protection of acute CIs by butylphthalide.

Rheumatoid arthritis (RA) is a chronic autoimmune disease that causes synovial joint inflammation as well as bone destruction and erosion, typically characterized by joint pain, swelling, and stiffness, with complications and persistent pain after remission posing a significant health burden for RA patients. The etiology of RA has not yet been fully elucidated, but a large number of studies have shown that the initiation of inflammation in RA is closely related to T-cell activation, the production of a variety of pro-inflammatory cytokines, macrophage M1/M2 imbalance, homeostatic imbalance of the intestinal flora, fibroblast-like synoviocytes (FLSs) and synovial tissue macrophages (STMs) in the synovial lumen of joints that exhibit an aggressive phenotype. While the resolution of RA is less discussed, therefore, we provided a systematic review of the relevant remission mechanisms including blocking T cell activation, regulating macrophage polarization status, modulating the signaling pathway of FLSs, modulating the subpopulation of STMs, and inhibiting the relevant inflammatory factors, as well as the probable causes of persistent arthritis pain after the remission of RA and its pain management methods. Achieving resolution in RA is crucial for improving the quality of life and long-term prognosis of patients. Thus, understanding these mechanisms provide novel potential for further drug development and treatment of RA.

Embryonic development is a complex process of concurrent events comprising cell proliferation, differentiation, morphogenesis, migration, and tissue remodeling. To cope with the demands arising from these developmental processes, cells increase their nutrient uptake, which subsequently increases their metabolic activity. Mitochondria play a key role in the maintenance of metabolism and production of reactive oxygen species (ROS) as a natural byproduct. Regulation of ROS by antioxidants is critical and tightly regulated during embryonic development, as dysregulation results in oxidative stress that damages essential cellular components such as DNA, proteins, and lipids, which are crucial for cellular maintenance and in extension development. However, during development, exposure to certain exogenous factors or damage to cellular components can result in an imbalance between ROS production and its neutralization by antioxidants, leading to detrimental effects on the developmental process. In this review article, we highlight the crucial role of redox homeostasis in normal development and how disruptions in redox balance may result in developmental defects.

<i>Caenorhabditis elegans</i> has been widely used as a model organism in neurodevelopment for several decades due to its simplicity, rapid growth, short life cycle, transparency, and rather simple genetics. It has been useful in modeling neurodegenerative diseases by the heterologous expression of the major proteins that form neurodegenerative-linked aggregates such as amyloid-<i>β</i> peptide, tau protein, and <i>α</i>-synuclein, among others. Furthermore, chemical treatments as well as the existence of several interference RNA libraries, transgenic worm lines, and the possibility of generating new transgenic strains create a magnificent range of possible tools to study the signaling pathways that could confer protection against protein aggregates or, on the contrary, are playing a detrimental role. In this review, we summarize the different <i>C. elegans</i> models of neurodegenerative diseases with a focus on Alzheimer's and Parkinson's diseases and how genetic tools could be used to dissect the signaling pathways involved in their pathogenesis mentioning several examples. Finally, we discuss the use of pharmacological agents in <i>C. elegans</i> models that could help to study these disease-associated signaling pathways and the powerful combinations of experimental designs with genetic tools. This review highlights the advantages of <i>C. elegans</i> as a valuable intermediary between <i>in vitro</i> and mammalian <i>in vivo</i> models in the development of potential new therapies.

Aims This study assessed sex-specific proteomic profiles by cardiovascular disease (CVD) phenotype (coronary artery disease [CAD] vs coronary microvascular dysfunction [CMD]) and describe their role in sex-specific pathways.<h4>Methods</h4>In a secondary biobank analysis of the Yale-CMD registry, adults with ischemic symptoms who underwent cardiac positron emission test/computed tomography were categorized as a) controls (normal coronary flow reserve (CFR) > 2 without perfusion defect or coronary calcification), b) having CMD (CFR < 2 without defect or calcification), or c) having CAD (known CAD or new perfusion defect). Using proximity extension assays (Olink® Explore 3072), we examined 2944 proteins. Differential protein expression was assessed using linear regression models, adjusting for age, race, body mass index, diabetes, dyslipidemia, hypertension, or smoking.<h4>Results</h4>Of 190 patients, 91 provided blood samples (mean age, 56 years; 66 %, females; 48 %, controls; 24 %, CAD; 27 %, CMD). Among controls, 15 proteins showed sex differences (5 proteins upregulated in females, 10 in males; false discovery rate [FDR < 0.05]). Upregulated in CAD patients were FSHB in females and INSL3 and EDDM3B in males (FDR < 0.05). Among CMD patients, SCGB3A1 and HGFAC were higher in females; INSL3, SPINT3, EDDM3B, and KLK3 were higher in males (FDR < 0.05). Per pathway analysis, females showed upregulation of immune pathways in CAD and lipid and glucose metabolism pathways in CMD. Males showed upregulated endothelial regulation of blood flow in CAD and increased angiogenesis in CMD.<h4>Conclusions</h4>Sex differences exist in the proteomic profiles of CAD and CMD patients, highlighting a need for precision medicine.

<h4>Background</h4>Congenital methemoglobinemia (metHb), a rare cause of neonatal cyanosis, results from the oxidation of ferrous to ferric iron in hemoglobin (Hb). The aim of this case report is to highlight the need to broaden the differential diagnosis of neonatal cyanosis and emphasizes the role of capillary blood gas analysis and genetic testing to exclude hereditary hematological causes. We report a previously unreported genetic mutation associated with congenital metHb.<h4>Case description</h4>We report the case of a term male neonate with cyanosis unresponsive to oxygen administration. Complementary studies were normal, including echocardiography, cerebral ultrasound, blood tests, blood culture, cytomegalovirus testing, glucose-6-phosphate dehydrogenase (G6PD) assessment, and Hb electrophoresis, with the exception of a mild left anterior pneumothorax. There was a discrepancy between arterial oxygen pressure (PaO₂) and oxygen saturation by pulse oximetry. Ultimately, co-oximetry revealed a metHb level of 20%, confirming the diagnosis of metHb. Next generation sequencing (NGS) identified a compound heterozygous missense mutation in the cytochrome B5 reductase (<i>CYB5R3</i>) gene: c673C>T (p.Arg225Cys) and c977A>G (p.His326Arg), both considered pathogenic/probably pathogenic. While the first mutation is documented, the second is not previously reported as a cause of congenital metHb. This compound heterozygous genotype in the <i>CYB5R3</i> gene may explain the phenotype observed in this patient with congenital metHb. Erythrocyte enzyme testing confirmed reduced CYB5R3 activity. Family genetic studies confirmed the patient's compound heterozygosity, with one mutation inherited from each parent and genetic counseling was offered. The patient has progressed favorably, achieving appropriate psychomotor development without neurological disorders. There has been a decrease in perioral cyanosis, with metHb levels dropping to 3%. Oxygen saturation reached normal levels (96%) by 2 years of age.<h4>Conclusions</h4>MetHb is a rare cause of cyanosis in children. The acquired form is the most common, due to exposure to oxidizing substances that increase metHb production. Congenital forms, however, are more frequent in neonates, and their evolution depends on specific mutations. Genetic testing is crucial for family counseling. Clinicians should suspect metHb in cases of cyanosis and hypoxia without respiratory distress, especially when there is no improvement with oxygen therapy and normal PaO₂, after excluding other more common causes such as respiratory, infectious and cardiological conditions.

<h4>Background</h4>Benign prostate hyperplasia (BPH) and prostate cancer (PCa) share several similarities, including androgen dependency and parallel increases in prevalence with age. Although PCa lags by 15-20 years, no causal association has been identified between BPH and PCa. To investigate the potential causal links between BPH and PCa, this study was performed in a two-sample Mendelian randomization (MR) design.<h4>Methods</h4>We retrieved single-nucleotide polymorphisms (SNPs) associated with BPH from genome-wide association studies (GWAS), which were obtained from the Integrative Epidemiology Unit database, and conducted a two-sample MR analysis to explore the causal relationship between BPH and PCa. The exposure dataset included 13,118 BPH cases and 72,799 controls, while the outcome dataset comprised 9,132 PCa cases and 173,493 controls, all of European ancestry. Four SNPs were selected as instrumental variables (IVs) after stringent filtering for linkage disequilibrium and potential confounding factors. The causal effect was estimated using the inverse-variance-weighted (IVW) method, supplemented by sensitivity analyses to assess heterogeneity and pleiotropy.<h4>Results</h4>The IVW analysis revealed that genetically predicted BPH was causally associated with a 1.02-fold increased risk of PCa [95% confidence interval (CI): 1.0076-1.0286, P<0.001]. Sensitivity analyses, including MR-Egger regression and leave-one-out analysis, confirmed the robustness of these findings, with no significant heterogeneity or pleiotropy detected.<h4>Conclusions</h4>This study provides genetic evidence supporting a causal relationship between BPH and an increased risk of PCa. These findings suggest that BPH may contribute to the development of PCa, potentially guiding future clinical practices in screening, diagnosis, and treatment strategies for BPH patients to mitigate PCa risk. Further validation in diverse populations and clinical studies is warranted to confirm these findings.

Neurodegenerative diseases (NDDs), including Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS), Huntington's disease (HD), and prion disease, represent a group of age-related disorders that pose a growing and formidable challenge to global health. Despite decades of extensive research that has uncovered key genetic factors and biochemical pathways, the precise molecular mechanisms underlying these diseases and effective therapeutic strategies remain elusive. <i>Caenorhabditis elegans</i> (<i>C. elegans</i>) has emerged as a powerful model organism for studying NDDs due to its unique biological features such as genetic tractability, conserved molecular pathways, and ease of high-throughput screening. This model provides an exceptional platform for identifying molecular targets associated with NDDs and developing novel therapeutic interventions. This review highlights the critical role of <i>C. elegans</i> in elucidating the complex molecular mechanisms of human NDDs, with a particular focus on recent advancements and its indispensable contributions to the discovery of molecular targets and therapeutic strategies for these NDDs.

<h4>Background</h4>Episodic angioedema with eosinophilia (Gleich syndrome) is a rare disease marked by periodic angioedema, fever, and severe eosinophilia, with limited understanding of its pathogenesis.<h4>Objective</h4>We sought to identify pathogenic factors contributing to severe Gleich syndrome through a comprehensive multiomics approach, using whole-genome sequencing (WGS) and RNA sequencing (RNA-seq).<h4>Methods</h4>A multiomics analysis was conducted on a 16- to 20-year-old female patient with severe Gleich syndrome, presenting with periodic high fever, extensive urticaria/eczema, and marked eosinophilia. The analysis included WGS and RNA-seq of blood samples.<h4>Results</h4>WGS revealed high-impact pathogenic mutations that have the potential to significantly alter gene function in 16 genes, including PR domain containing 16 (gene involved in transcriptional regulation). RNA-seq identified differentially expressed genes linked to immune response regulation and viral defense. Combined <i>z</i>-score analysis of WGS and RNA-seq highlighted angiotensin-converting enzyme as a key gene, with significant downregulation during disease progression that normalized with treatment. IFNG was also implicated.<h4>Conclusions</h4>The findings suggest that decreased angiotensin-converting enzyme expression, driven by PR domain containing 16 (gene involved in transcriptional regulation) mutations and altered IFNG expression, may contribute to increased bradykinin levels and activation of the arachidonic acid cascade, leading to the severe inflammation and angioedema characteristic of Gleich syndrome. This study underscores the utility of integrating WGS and RNA-seq data in elucidating the molecular basis of rare diseases and offers a foundation for developing therapeutic strategies for hypereosinophilic syndromes.

<h4>Background and aims</h4>Von Willebrand factor (vWF) plays a key role in hemostasis and is reported to be related to the outcome of advanced chronic liver disease. The present study aimed to investigate the relationship between vWF and other potential variables and portal vein thrombosis (PVT) in patients with decompensated cirrhosis.<h4>Methods</h4>Consecutive cirrhotic patients with gastroesophageal varices were admitted to our hospital between January 2020 and September 2022. Patients were prospectively recruited and divided into PVT and non-PVT groups. We collected clinical tests, biochemical tests, coagulation tests, and hemostatic protein profile data to explore the associated factors of PVT.<h4>Results</h4>A total of 128 patients were enrolled including 60 patients with PVT and 68 patients without PVT. Plasma levels of vWF [odds ratio (OR) = 1.015, 95% confidence interval (CI): 1.005-1.025, P  = 0.005], D-dimer (OR = 1.967, 95% CI: 1.141-3.389, P  = 0.015), and decreased portal vein velocity (PVV) (OR = 0.852, 95% CI: 0.769-0.944, P  = 0.002) were the variables independently associated with the existence of PVT. Area under the curve (AUC) analyses for vWF, D-dimer, and PVV were 0.779, 0.848, and 0.832, respectively. A nomogram model was established involving the three parameters, and the AUC was 0.919 (95% CI: 0.869-0.969). In the internal validation using bootstrap, the AUC was 0.919 (95% CI: 0.868-0.970).<h4>Conclusion</h4>Higher vWF levels were related to PVT in patients with decompensated cirrhosis, indicating that vWF might serve as a relevant factor for PVT, and a nomogram containing vWF, D-dimer, and PVV could be an important tool for PVT identification in cirrhotic patients.

The need for collaborative and transparent sharing of COVID-19 clinical trial and large-scale observational study data to accelerate scientific discovery and inform clinical practice is critical. Responsible data-sharing requires addressing challenges associated with data privacy and confidentiality, data linkage, data quality, variable harmonization, data formats, and comprehensive metadata documentation to produce a high-quality, contextually rich, findable, accessible, interoperable, and reusable (FAIR) dataset. This communication explores the experiences and lessons learned from sharing National Heart Lung and Blood Institute (NHLBI) COVID-19 clinical trial (including adaptive platform trials) and cohort study datasets through the NHLBI BioData Catalyst® (BDC) ecosystem, focusing on the challenges and successes of harmonizing these datasets for broader research use. Our findings highlight the importance of establishing standardized data formats, adopting common data elements and creating and maintaining robust data governance structures that address common challenges (i.e., data privacy and data-sharing limitations resulting from informed consent). These efforts resulted in a set of comprehensive and interoperable datasets from 5 clinical trials and 13 cohort studies that will enable downstream reuse in analyses and collaborations. The principles and strategies outlined, derived through experience with consortia data, can lay the groundwork for advancing collaborative and efficient data sharing.

<h4>Summary</h4> Pre-malignant transformation of pancreatic acinar cells by oncogenic Kras is dependent upon stochastic emergence of metaplastic cell states, through unknown mechanisms. We reveal that an early, transcriptionally-mediated effect of Kras is sporadic failure of proteostatic ER-phagy. Genetically-altered mice deficient in ER-phagy demonstrate that this event co-operates with Kras to drive acinar-ductal metaplasia (ADM) and subsequent cancer. Mechanistically, proteomics and high-resolution imaging uncover pathologic aggregation of a subset of ER proteins, including the injury marker REG3B, resulting from failure to physically interact with the ER-phagy receptor CCPG1. Spatial transcriptomics demonstrate that the appearance of sporadic intracellular aggregates upon Kras activation marks rare acinar cells existing in an injured, ADM-primed state. Importantly, engineered mutants of REG3B establish that aggregate formation is sufficient to directly engender this epithelial cell state. Pancreatic cancer can thus arise from stochastic pathologic protein aggregates that are influenced by and co-operate with an oncogene.

This article synthesizes the current knowledge on the epidemiology of metabolic dysfunction-associated steatotic liver disease (MASLD), its associated risks, and its genetic determinants. The findings presented in this article can be used to develop clinical strategies to reduce MASLD's growing global burden. MASLD has become a major global health concern due to increasing rates of obesity, sedentary lifestyles, and metabolic disorders. MASLD is a leading cause of end-stage liver diseases, including cirrhosis and hepatocellular carcinoma (HCC), and MASLD also significantly increases the risk of cardiovascular disease (CVD), thereby exerting dual effects on liver and cardiovascular health. MASLD was once referred to as nonalcoholic fatty liver disease, and this change in nomenclature reflects a growing focus on its metabolic underpinnings, facilitating the more precise diagnosis and clinical management of this disease. Epidemiological studies have demonstrated that the prevalence of MASLD is increasing worldwide, although the prevalence varies across regions and populations. Noninvasive diagnostic tools such as ultrasound and fatty liver indices along with biomarkers such as alanine aminotransferase (ALT) are crucial for early detection and risk stratification. Genetic research has identified key gene variants, including PNPLA3 (rs738409) and TM6SF2 (rs58542926), that influence MASLD susceptibility and progression, and these findings have created opportunities for improving precision medicine with respect to treating MASLD. Research has revealed an association between MASLD and major adverse cardiovascular events and increased mortality, which highlights the importance of integrating cardiovascular risk management into treatment strategies for MASLD. Future research should focus on advancing noninvasive diagnostics, leveraging genetic insights to provide tailored care, and implementing population-specific interventions to address regional variations.

RNA presents abundant opportunities as a drug target, offering significant potential for small molecule medicine development. The transcriptome, comprising both coding and noncoding RNAs, is a rich area for therapeutic innovation, yet challenges persist in targeting RNA with small molecules. RNA structure can be predicted with or without experimental data, but discrepancies with the actual biological structure can impede progress. Prioritizing RNA targets supported by genetic or evolutionary evidence enhances success. Further, small molecules must demonstrate binding to RNA in cells, not solely in vitro, to validate both the target and compound. Effective small molecule binders modulate functional sites that influence RNA biology, as binding to nonfunctional sites requires recruiting effector mechanisms, for example degradation, to achieve therapeutic outcomes. Addressing these challenges is critical to unlocking RNA's vast potential for small molecule medicines, and a strategic framework is proposed to navigate this promising field, with a focus on targeting human RNAs.

<h4>Background</h4>Systemic lupus erythematosus (SLE) is a complex autoimmune disease that has significant impacts on patients' quality of life and poses a substantial economic burden on society.<h4>Objective</h4>This study aimed to elucidate the molecular mechanisms underlying SLE by analyzing glucocorticoid-related genes (GRGs) expression profiles.<h4>Methods</h4>We examined the expression profiles of GRGs in SLE and performed consensus clustering analysis to identify stable patient clusters. We also identified differentially expressed genes (DEGs) within the clusters and between SLE patients and healthy controls. We conducted Gene Set Enrichment Analysis (GSEA) and Gene Set Variation Analysis (GSVA) to investigate biological functional differences, and we also conducted CIBERSORTx to estimate the number of immune cells. Furthermore, we utilized least absolute shrinkage and selection operator (LASSO) regression and Random Forest (RF) algorithms to screen for hub genes. We then validated the expression of these hub genes and constructed nomograms for further validation. Moreover, we employed single-sample Gene Set Enrichment Analysis (ssGSEA) to analyze immune infiltration. We also constructed an RNA-binding protein (RBP)-mRNA network and conducted drug sensitivity analysis along with molecular docking studies.<h4>Results</h4>Patients with SLE were divided into two subclusters, revealing a total of 2,681 DEGs. Among these, 1,458 genes were upregulated, while 1,223 were downregulated in cluster_1. GSVA showed significant changes in the pathways associated with cluster_1. Immune infiltration analysis revealed high levels of monocyte in all samples, with greater infiltration of various immune cells in cluster_1. A comparison of SLE patients to control subjects identified 269 DEGs, which were enriched in several pathways. Hub genes, including PTX3, DYSF and F2R, were selected through LASSO and RF methods, resulting in a well-performing diagnostic model. Drug sensitivity and docking studies suggested F2R as a potential new therapeutic target.<h4>Conclusion</h4>PTX3, DYSF and F2R are potentially linked to SLE and are proposed as new molecular markers for its onset and progression. Additionally, monocyte infiltration plays a crucial role in advancing SLE.

Huntington's disease (HD) is a devastating neurodegenerative disorder characterized by a variety of debilitating symptoms including abnormal motor control, cognitive impairment, and psychiatric disturbances. Despite significant efforts, efficacious treatments to alter the course of HD remain elusive, highlighting the need to explore new therapeutic strategies, including lifestyle changes that may delay the onset of symptoms and slow disease progression. Recent research indicates that time-restricted eating (TRE), a type of intermittent fasting where caloric intake is confined to a specific time window each day, may be beneficial in treating neurodegenerative diseases like HD. TRE has been found to enhance mitochondrial function, stimulate autophagy, lower oxidative stress, and improve cognitive performance. Although TRE has shown potential in HD animal models and non-HD populations, it has yet to be analyzed for safety, feasibility, and efficacy in persons with HD. Therefore, we propose a prospective interventional, open-label, single-arm, pilot study of 25 participants with late prodromal and early manifest HD to evaluate participant adherence to TRE diet - specifically, maintaining a 6-8-hour eating window every day for 12 weeks. Secondary measures will include pre- versus post-intervention assessment of body composition via bioelectrical impedance analysis, vital signs and safety labs, serum biomarkers of neurodegeneration, and standard HD behavioral, cognitive, and motor function clinical scales. Additional exploratory measures will evaluate sleep quality, physical activity, mood, dietary composition, and mitochondrial function. We expect that the diet will be safe, feasible, and may also improve biomarkers of disease progression in persons with HD. We anticipate this study will lay the foundation for future large-scale clinical trials to further evaluate the clinical efficacy of TRE in HD. This study has been registered on July 8, 2024 with ClinicalTrials.gov registration number NCT06490367 (https://clinicaltrials.gov/study/NCT06490367).

<p>Introduction: Atopic dermatitis (AD), allergic rhinitis (AR), and bronchial asthma (BA) are major allergic diseases in childhood. Pediatric allergic diseases are characterized by the "atopic march," where two or more allergic conditions can occur either simultaneously or sequentially. MicroRNAs (miRNAs) serve as fine regulators of gene expression, capable of modulating the clinical manifestations of allergic diseases posttranscriptionally. We investigated miRNAs commonly expressed in these three allergic diseases to enhance the understanding of their development and management.<h4>Methods</h4>We collected serum samples from subjects diagnosed with AD, AR, and BA as well as from healthy controls at Korea University Anam Hospital. Their miRNA expression patterns were analyzed using microarray technology. Additionally, we examined the allergic inflammatory response of miRNA through an allergic animal model.<h4>Results</h4>A total of 68 subjects were enrolled in the allergy group, consisting of 42 with AD, 13 with AR, and 13 with BA, while 10 children participated as controls. Microarray analysis revealed that miR-4497 expression levels were consistently downregulated in these three allergic disease groups. Following mast cell activation and miR-4497 transfection, reduced levels of macrophage-derived chemokines (MDCs) were observed. Furthermore, levels of IL-4, MDC, and methacholine Penh were significantly decreased in a miR-4497-treated mouse model.<h4>Conclusions</h4>MiR-4497 expressions were consistently downregulated in pediatric subjects with AD, AR, and BA. Allergic inflammation was significantly reduced in human mast cell-1 transfected with miR-4497 and in the treated mouse model. Further research is needed to elucidate the epigenetic mechanisms by which miR-4497 modulates allergic diseases and to explore its potential as a noninvasive biomarker for diagnosis and treatment. </p>.

Cone photoreceptors assemble to form a regular mosaic pattern in vertebrate retinas. In zebrafish, four distinct spectral cone types (red, green, blue, and ultraviolet), form a lattice-like pattern. However, the mechanism of cone mosaic formation has been unknown. Here we show that Down Syndrome Cell Adhesion Molecule b (Dscamb) regulates the cone mosaic pattern in zebrafish, especially via red-cone spacing. During photoreceptor differentiation, newly formed cones extend filopodium-like processes laterally to apical surfaces of neighboring cones. Interestingly, red cones extend filopodia, but promptly retract them when they meet their own cone type, suggesting filopodium-mediated, homotypic recognition and self-avoidance. This self-avoidance is compromised in zebrafish dscamb mutants, leading to abnormal clustering of red cones and subsequent disruption of regular cone spacing. Thus, apical filopodium-mediated spacing of the same cone type depends on Dscamb and is essential for cone mosaic formation in zebrafish.

Type 1 diabetes (T1D) is linked to an altered gut microbiota characterized by reduced short-chain fatty acid (SCFA) production. Oral delivery of a SCFA-yielding biotherapy in adults with T1D was followed by increased SCFAs, altered gut microbiota and immunoregulation, as well as delaying diabetes in preclinical models. Here, we show that SCFA-biotherapy in humans is accompanied by remodeling of the gut proteome and mucosal immune homeostasis. Metabolomics showed arginine, glutamate, nucleotide and tryptophan metabolism were enriched following the SCFA-biotherapy, and found metabolites that correlated with glycemic control. Fecal microbiota transfer demonstrated that the microbiota of SCFA-responders delayed diabetes progression in humanized gnotobiotic mice. The protected mice increased similar metabolite pathways to the humans including producing aryl-hydrocarbon receptor ligands and reducing inflammatory mucosal immunity and increasing IgA production in the gut. These data demonstrate that a potent SCFA immunomodulator promotes multiple beneficial pathways and supports targeting the microbiota as an approach against T1D. Trial registration: Australia New Zealand Clinical Trials Registry ACTRN12618001391268.

Upon encountering antigens, B cells may undergo multiple differentiation paths, including becoming plasma cells and memory B cells. Although it is well-known that transcription factors govern gene expression programs underpinning these fate decisions in transcriptional level, the role of post-transcriptional regulators, with a focus on RNA-binding proteins, in the fate determination are lesser known. Here we find by RNA interactome capture-coupled CRISPR/Cas9 functional screening that the Csde1-Strap complex plays an important role in plasma cell differentiation. Mechanistically, the Csde1-Strap complex establishes the expression kinetics of Bach2, a key regulator of plasma cell differentiation. Bach2 expression is rapidly induced to promote B cell expansion and then decreased to initiate plasma cell differentiation. The Csde1-Strap interaction is critical for their binding to Bach2 mRNA to couple its decay with translation to restrain the magnitude and duration of Bach2 protein expression. In the absence of Csde1 or Strap, Bach2 translation is de-coupled from mRNA decay, leading to elevated and prolonged expression of Bach2 protein and impaired plasma cell differentiation. This study thus establishes the functional RBP landscape in B cells and illustrates the fundamental importance of controlling protein expression kinetics in cell fate determination.

The pervasive occurrence of nasopharyngeal carcinoma (NPC) is intricately linked to Epstein-Barr virus (EBV) infection, making EBV and its associated pathways promising therapeutic targets for NPC and other EBV-related cancers. Lytic induction therapy, an emerging virus-targeted therapeutic strategy, capitalizes on the presence of EBV in tumor cells to specifically induce cytotoxicity against EBV-associated malignancies. Despite the expanding repertoire of compounds developed to induce EBV lytic reactivation, achieving universal induction across all infected cells remains elusive. The inherent heterogeneity of tumor cells likely contributes to this variability. In this study, we used the NPC43 cell line, an EBV-positive NPC in vitro model, and single-cell transcriptomics to characterize the diverse cellular responses to EBV lytic induction. Our longitudinal monitoring revealed a distinctive lytic induction non-responsive cellular state characterized by elevated expression of SOX2 and NTRK2. Cells in this state exhibit phenotypic similarities to cancer stem cells (CSCs), and we verified the roles of SOX2 and NTRK2 in manifesting these phenotypes. Our findings reveal a significant challenge for lytic induction therapy, as not all tumor cells are equally susceptible. These insights highlight the importance of combining lytic induction with therapies targeting CSC-like properties to enhance treatment efficacy for NPC and other EBV-associated cancers.

Metabolic dysfunction-associated steatotic liver disease (MASLD) is the most common chronic liver disease worldwide, with a prevalence as high as 32.4%. MASLD encompasses a spectrum of liver pathologies, ranging from steatosis to metabolic dysfunction-associated steatohepatitis (MASH), fibrosis, and, in some cases, progression to end-stage liver disease (cirrhosis and hepatocellular carcinoma). A comprehensive understanding of the pathogenesis of this highly prevalent liver disease may facilitate the identification of novel targets for the development of improved therapies. E3 ubiquitin ligases and deubiquitinases (DUBs) are key regulatory components of the ubiquitin‒proteasome system (UPS), which plays a pivotal role in maintaining intracellular protein homeostasis. Emerging evidence implicates that aberrant expression of E3 ligases and DUBs is involved in the progression of MASLD. Here, we review abnormalities in E3 ligases and DUBs by (1) discussing their targets, mechanisms, and functions in MASLD; (2) summarizing pharmacological interventions targeting these enzymes in preclinical and clinical studies; and (3) addressing challenges and future therapeutic strategies. This review synthesizes current evidence to highlight the development of novel therapeutic strategies based on the UPS for MASLD and progressive liver disease.

The hierarchical organization of the eukaryotic genome is crucial for nuclear activities and cellular development. Genetic aberrations can disrupt this 3D genomic architecture, potentially driving oncogenesis. However, current research often lacks a comprehensive perspective, focusing on specific mutation types and singular 3D structural levels. Here, pathological changes from chromosomes to nucleotides are systematically cataloged, including 10 789 interchromosomal translocations (ICTs), 18 863 structural variants (SVs), and 162 769 single nucleotide polymorphisms (SNPs). The multilayered analysis reveals that fewer than 10% of ICTs disrupt territories via potent 3D interactions, and only a minimal fraction of SVs disrupt compartments or intersect topologically associated domain structures, yet these events significantly influence gene expression. Pathogenic SNPs typically show reduced interactions within the 3D genomic space. To investigate the effects of variants in the context of 3D organization, a two-phase scoring algorithm, 3DFunc, is developed to evaluate the pathogenicity of variant-gene pairs in cancer. Using 3DFunc, IGHV3-23's critical role in chronic lymphocytic leukemia is identified and it is found that three pathological SNPs (rs6605578, rs7814783, rs2738144) interact with DEFA3. Additionally, 3DGAtlas is introduced, which provides a highly accessible 3D genome atlas and a valuable resource for exploring the pathological effects of genetic mutations in cancer.

For diverse neurodegenerative disorders, microglial cells are activated. Furthermore, dysfunctional and hyperactivated microglia initiate mitochondrial autophagy, oxidative stress, and pathological protein accumulation, ending with neuroinflammation that exacerbates damage to dopaminergic neurons and contributes significantly to the pathology of neurodegenerative disorder. Microglial over-activation is closely associated with the secretion of pro-inflammatory cytokines, the phagocytosis of injured neurons, and the modulation of neurotoxic environments. This review summarizes the role of microglia neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, multiple sclerosis, multiple system atrophy, amyotrophic lateral sclerosis, frontotemporal dementia, progressive supranuclear palsy, cortical degeneration, Lewy body dementia, and Huntington's disease. It also discusses novel forms of cell death such as ferroptosis, cuproptosis, disulfidptosis, and parthanatos (poly(adenosine diphosphate ribose) polymerase 1-dependent cell death), as well as the impact of regulatory factors related to microglial inflammation on microglial activation and neuroinflammation. The aim is to identify potential targets for microglial cell therapy in neurodegenerative diseases.

JOURNAL/nrgr/04.03/01300535-202602000-00043/figure1/v/2025-05-05T160104Z/r/image-tiff Global brain ischemia and neurological deficit are consequences of cardiac arrest that lead to high mortality. Despite advancements in resuscitation science, our limited understanding of the cellular and molecular mechanisms underlying post-cardiac arrest brain injury have hindered the development of effective neuroprotective strategies. Previous studies primarily focused on neuronal death, potentially overlooking the contributions of non-neuronal cells and intercellular communication to the pathophysiology of cardiac arrest-induced brain injury. To address these gaps, we hypothesized that single-cell transcriptomic analysis could uncover previously unidentified cellular subpopulations, altered cell communication networks, and novel molecular mechanisms involved in post-cardiac arrest brain injury. In this study, we performed a single-cell transcriptomic analysis of the hippocampus from pigs with ventricular fibrillation-induced cardiac arrest at 6 and 24 hours following the return of spontaneous circulation, and from sham control pigs. Sequencing results revealed changes in the proportions of different cell types, suggesting post-arrest disruption in the blood-brain barrier and infiltration of neutrophils. These results were validated through western blotting, quantitative reverse transcription-polymerase chain reaction, and immunofluorescence staining. We also identified and validated a unique subcluster of activated microglia with high expression of S100A8, which increased over time following cardiac arrest. This subcluster simultaneously exhibited significant M1/M2 polarization and expressed key functional genes related to chemokines and interleukins. Additionally, we revealed the post-cardiac arrest dysfunction of oligodendrocytes and the differentiation of oligodendrocyte precursor cells into oligodendrocytes. Cell communication analysis identified enhanced post-cardiac arrest communication between neutrophils and microglia that was mediated by neutrophil-derived resistin, driving pro-inflammatory microglial polarization. Our findings provide a comprehensive single-cell map of the post-cardiac arrest hippocampus, offering potential novel targets for neuroprotection and repair following cardiac arrest.

Due to the high prevalence of non-alcoholic fatty liver disease (NAFLD) and chronic hepatitis B virus (HBV) infection, a significant proportion of patients suffer from both conditions simultaneously. The management of NAFLD in patients with concurrent HBV infection presents unique challenges, primarily due to the complex interplay between these two diseases. Nanomaterials have gained widespread attention due to their ability to overcome the limitations of conventional therapies. This review provides an overview of the current advances in therapeutic nanomaterials for NAFLD and explores their potential applications for personalized and effective management in patients with concurrent HBV infection. Furthermore, we discuss the challenges and future directions in the development of nanomaterials for the treatment of coexisting liver diseases.

Ulcerative colitis (UC) is a chronic idiopathic inflammatory disease affecting the colon and rectum. Characterized by recurrent attacks, UC is often resistant to traditional anti-inflammatory therapies, imposing significant physiological, psychological, and economic burdens on patients. In light of these challenges, innovative targeted therapies have become a new expectation for patients with UC. A crucial pathological feature of UC is the impairment of the intestinal mucosal barrier, which underlies aberrant immune responses and inflammation. Intestinal stem cells (ISCs), which differentiate into intestinal epithelial cells, play a central role in maintaining this barrier. Growing studies have proved that regulating the regeneration and differentiation of ISC is a promising approach to treating UC. Despite this progress, there is a dearth of comprehensive articles describing the role of ISCs in UC. This review focuses on the importance of ISCs in maintaining the intestinal mucosal barrier in UC and discusses the latest findings on ISC functions, markers, and their regulatory mechanisms. Key pathways involved in ISC regulation, including the Wnt, Notch, Hedgehog (HH), Hippo/Yap, and autophagy pathways, are explored in detail. Additionally, this review examines recent advances in ISC-targeted therapies for UC, such as natural or synthetic compounds, microbial preparations, traditional Chinese medicine (TCM) extracts and compounds, and transplantation therapy. This review aims to offer novel therapeutic insights and strategies for patients who have long struggled with UC.

<h4>Background</h4>Chronic pancreatitis (CP) is a fibro-inflammatory syndrome with unclear pathogenesis and futile therapy. CP's microenvironment disrupts the fine-tuned balance of macrophage polarization toward a predominance of the M2-like phenotype associated with fibrosis. S100A9 is mainly expressed in monocytes as a potent regulator of macrophage phenotype and function. Here, we investigated the S100A9-related mechanisms underlying CP pathology induced by macrophages polarization.<h4>Methods</h4><i>S100a9</i> knockout (<i>S100a9</i> _-/-) mice and an <i>in vitro</i> coculture system of macrophages overexpressing <i>S100a9</i> and primary PSCs were constructed to investigate the effects and mechanisms of S100A9-mediated macrophage polarization on pancreatic inflammation and fibrosis underpinning CP pathology. Furthermore, a variety of S100A9-targeted small-molecule compounds were screened from U.S. Food and Drug Administration (FDA)-listed drug libraries through molecular docking and virtual screening techniques.<h4>Results</h4>In CP progression, S100A9 upregulation induces M2 macrophage polarization to accelerate fibrosis via thousand-and-one amino acid kinase 3 (TAOK3)-c-Jun N-terminal kinase (JNK) signaling pathway, and loss of S100A9 reduces CP injury <i>in vitro</i> and <i>in vivo</i>. Coimmunoprecipitation (co-IP) and molecular docking experiments proved that S100A9 may interact directly with TAOK3 through salt bridges and hydrogen bonding interactions of the residues in the S100A9 protein. Furthermore, cobamamide and daptomycin, as inactivators of the S100A9-TAOK3 interaction, can improve CP by inhibiting the polarization of M2 macrophages.<h4>Conclusions</h4>S100A9 is a significant promoter of M2-like macrophage-induced fibrosis in CP via the TAOK3-JNK signaling pathway. Cobamamide and daptomycin, targeted inhibitors of the S100A9-TAOK3 interaction, may become candidate drugs for CP immunotherapy.

Tinnitus is defined as the conscious awareness of a tonal or composite noise for which there is no identifiable corresponding external acoustic source, which becomes tinnitus disorder when the phantom sound is associated with suffering and/or disability. There is only limited knowledge about the time course of tinnitus disorder. Bereavement science has identified four different trajectories: resilience, recovery, chronic, and delayed. The question arises whether these four trajectories exist in tinnitus as well if one considers tinnitus as the loss of silence (at will). To verify whether these four trajectories exist, short-term tinnitus progression was analyzed retrospectively using an Ecological Momentary Assessment (EMA) approach, extracting the data from patients who started using the TrackYourTinnitus (TYT) app (version 1, Ulm University, 2013) from the start of their tinnitus perception. Four patients were identified retrospectively via the TYT app with acute tinnitus, and the bereavement trajectories were reconstructed based on EMA. In conclusion, this perspective suggests that the four known bereavement trajectories may exist in tinnitus, and prospective evaluations of larger samples are warranted to confirm or disprove this analogy between bereavement and tinnitus, in which tinnitus is conceived as the loss of (controllable) silence.

In this study, novel triblock copolymers, including poly(<i>N</i>-isopropylacrylamide)-<i>block</i>-poly(<i>ε</i>-caprolactone)-<i>block</i>-poly(<i>N</i>-isopropylacrylamide) (PNIPAM-<i>b</i>-PCL-<i>b</i>-PNIPAM), poly(<i>N</i>-vinyl-pyrrolidone)-block-poly(<i>ε</i>-caprolactone)-block-poly(<i>N</i>-vinyl-pyrrolidone) (PNVP-<i>b</i>-PCL-<i>b</i>-PNVP), poly(<i>N</i>-isopropylacrylamide-<i>co</i>-<i>N</i>,<i>N</i>-dimethylaminoethyl methacrylate)-<i>block</i>-poly(<i>ε</i>-caprolactone)-<i>block</i>-poly(<i>N</i>-isopropylacrylamide-<i>co</i>-<i>N</i>,<i>N</i>-dimethylaminoethyl methacrylate) (P(DMAEMA-<i>co</i>-NIPAM)-<i>b</i>-PCL-<i>b</i>-P(NIPAM-<i>co</i>-DMAEMA)), and poly(<i>N</i>,<i>N</i>-dimethylacrylamide)-<i>block</i>-poly(<i>ε</i>-caprolactone)-<i>block</i>-poly(<i>N</i>,<i>N</i>-dimethylacrylamide) (PDMA-<i>b</i>-PCL-<i>b</i>-PDMA), were synthesized via a combination of ring-opening polymerization (ROP) and reversible addition-fragmentation chain transfer (RAFT) polymerization. The synthesis was performed using novel bifunctional PCL-based RAFT macro chain transfer agents (macroCTAs; MXTPCL-X1 and MXTPCL-X2) with a <i>m</i>-xylene-bis(2-mercaptoethyloxy) core. Initially, <i>m</i>-xylene-bis(1-hydroxy-3-thia-propane) (MXTOH), which has not previously been used in lactone polymerization, was synthesized via the reaction of <i>α</i>,<i>α</i>'-dibromo-<i>m</i>-xylene with 2-mercaptoethanol in the presence of sodium in ethanol. Subsequently, Sn(Oct)₂-catalyzed ROP of <i>ε</i>-caprolactone (<i>ε</i>-CL) using MXTOH as an initiator yielded PCL-diol (MXTPCLOH). The resulting PCL-diol underwent further functionalization through esterification and substitution reactions, leading to the formation of PCL-based RAFT macroCTAs. Triblock copolymers were synthesized using these macroCTAs with AIBN as an initiator. The synthesized products, along with their intermediates, were characterized using FTIR and ¹H NMR spectroscopy. The number average molecular weight (M_n) and polydispersity index (<i>Ð</i>) of PCL-based macroCTAs were determined by using GPC analysis. The sensor capabilities of the synthesized novel triblock copolymers were investigated on the determination of syringic acid and it was determined that the most sensitive polymer was PNVP-<i>b</i>-PCL-<i>b</i>-PNVP (MXTP2). The working range was between 1.5 µg/mL and 15 µg/mL and the limit of detection (LOD) was found to be 0.44 µg/mL using DPV on MXTP2 polymer sensor.

We employed laser microdissection to selectively harvest histology-resolved tumors and stroma from formalin-fixed, paraffin-embedded head and neck squamous cell carcinoma (HNSCC) tissues. Peptide digests from the LMD-enriched HNSCC tissue were analyzed by quantitative mass-spectrometry-based proteomics using a data independent analysis approach. In paired samples, excellent proteome coverage was achieved, having quantified 6668 proteins with a median quantitative coefficient of variation under 10%. Significant differences in relevant functional pathways between the tumor and the stroma regions were observed. Extracellular matrix (ECM) was identified as a major component enriched in the stroma, including many cancer-associated fibroblast signature proteins in this compartment. We demonstrate the potential for comparative deep proteome analysis from a very low starting input in a scalable format. Correlating such results with clinical features or disease progression will likely enable the identification of novel targets for disease classification and interventions.

Cocaine use is a well-established risk factor for various cardiovascular complications, including acute myocardial infarction (MI). The pathophysiological mechanisms responsible for cocaine-induced MI are multifactorial, encompassing coronary vasoconstriction, increased myocardial oxygen demand, and thrombosis. While cocaine-related cardiovascular events are more commonly seen in individuals with pre-existing risk factors, cases involving young, otherwise healthy individuals remain rare, yet they present a significant concern. We present the case of a young male in his late teens who presented to the emergency department with acute-onset chest pain that began two hours following his first-time use of cocaine. On evaluation, it was an anterior wall MI. Urgent coronary angiography was performed, which showed an ostial cut-off in the left anterior descending artery, along with a Thrombolysis in Myocardial Infarction (TIMI) grade V thrombus. Percutaneous coronary intervention (PCI) was successfully performed, and TIMI III flow was achieved. He was discharged on day five post-procedure, and at a six-month follow-up, he was doing well. This case highlights the need for early recognition and prompt intervention, including coronary angiography and PCI, to improve outcomes. Furthermore, it emphasizes the potential for long-term success with proper follow-up care and adherence to prescribed therapies.

There is increasing evidence demonstrating that psychiatric conditions elevate the risk of developing accelerated atherosclerosis and early-onset cardiovascular disease (CVD), including myocardial infarction (MI). Several mechanisms contribute to this observation. The dysfunction of the autonomic nervous system and hyperactivity of the hypothalamic-pituitary-adrenal axis in these patients contribute to the development of MI. Additionally, patients with underlying psychiatric disorders often have abnormal levels of anti-inflammatory and pro-inflammatory cytokines, which can lead to early vascular damage and subsequent atherosclerosis. Elevated PAI-1 levels, reduced tPA activity, and the decreased brain-derived neurotrophic factor (BDNF), influenced by coagulation and inflammation, may contribute to depression and its link to MI. Oxidative stress, marked by increased reactive species and impaired antioxidant defenses, is associated with cellular damage and has been consistently implicated in schizophrenia and bipolar disorder, potentially contributing to myocardial infarction. Finally, molecular genetic studies have indicated that psychiatric disorders and myocardial infarction may share potential pleiotropic genes. The interplay between the psychiatric conditions and myocardial infarction underscores the importance of integrated care approaches to manage both mental and physical health.

Bioactive peptides derived from milk proteins offer promising potential that can be unlocked through hydrolysis. Enzymatic hydrolysis is particularly noteworthy because of its mild conditions and its efficacy in producing peptides with various biological activities. This study focused on creating whey protein hydrolysates using three enzymes: pepsin, trypsin, and papain. The degree of hydrolysis and the antioxidant properties of the resulting peptides were evaluated, and papain demonstrated the highest degree of hydrolysis, leading to its selection for further investigation. LC-MS was employed to identify peptide sequences from the papain-derived hydrolysate, resulting in the identification of 107 distinct peptide sequences These peptides were predicted to exhibit a range of potential biological activities, including antihypertensive, antidiabetic, antioxidant, antimicrobial, and immunomodulatory effects, as well as roles in regulating glucose homeostasis, maintaining cardiovascular health, and supporting overall metabolic function. In vitro tests revealed the significant antioxidant and antibacterial properties of the hydrolysate, confirming the potential of papain-derived peptides for use in functional food and pharmaceutical applications. The novelty of this study lies in the identification of novel peptides with promising biological activities. Additional in vitro and in vivo studies are required to fully elucidate the health benefits of these peptides.

<h4>Background: </h4> /Objectives: Instrumental Activities of Daily Living (IADL) are key indicators of autonomy and functional ability in older adults with neurocognitive disorders (NCDs). Their performance is influenced by cognitive, motor, and psychosocial factors. However, specific predictors of IADL performance across the NCD spectrum is less well-characterized. This study aimed to identify cognitive, motor, and caregiver-related determinants of IADL in individuals with minor and major NCDs. <h4>Methods:</h4> A cross-sectional study was conducted in 117 participants referred from a university dementia clinic. Standardized tools for IADL (Lawton IADL Scale), cognition [Addenbrooke’s Cognitive Examination III (ACE-III)], Functional Cognitive Assessment Scale (FUCAS)], motor functions, balance, and mobility [Tinetti Test, Timed Up and Go (TUG)], emotional status [Geriatric Depression Scale (GDS)], neuropsychiatric symptoms [Neuropsychiatric Inventory (NPI)], and caregiver burden [Zarit Burden Interview (ZBI)] were administered. Multiple regression analyses were performed to identify predictors of IADL score. <h4>Results:</h4> In the total sample (n=117), IADL performance was significantly predicted by ACE-III, FUCAS, and Tinetti-balance, explaining 75.1% of IADL variance. In minor NCD group (n=41), IADL performance was predicted by FUCAS, Tinetti-balance, and ZBI (adjusted R² =0.697). In major NCD group (n=76), ACE-III, FUCAS, Tinetti-balance, and disease duration were significant predictors (adjusted R²=0.673). For all models, worse profile on the previous variables predicted impaired IADL. <h4>Conclusions:</h4> Global cognitive decline, executive dysfunction in everyday problem-solving situations, balance impairment, and caregivers’ burden are critical determinants of IADL in NCDs. Comprehensive assessments and multidisciplinary interventions, including caregiver support, are essential for health promotion by preserving autonomy and functional independence in older adults.

<h4>Objective</h4>This study aimed to elucidate the expression profile and biological implications of peroxidase 5 (PRDX5) in bladder cancer (BC), specifically investigating its influence on BC progression through modulation of reactive oxygen species (ROS) levels and activation of ferroptosis pathways.<h4>Methods</h4>We employed urine proteomics data and transcriptomic information from the Cancer Genome Atlas (TCGA) to identify differentially expressed genes in BC tissues, focusing on PRDX5. Using single-cell RNA sequencing (scRNA-seq), we assessed PRDX5 distribution across various cell types in the tumor microenvironment. We conducted in vitro experiments to analyze the impact of PRDX5 on BC cell proliferation, migration, and invasion, while exploring its mechanisms of modulating ROS levels and ferroptosis. In vivo experiments were performed to observe PRDX5's influence on ferroptosis signaling in tissue contexts.<h4>Results</h4>We found significant upregulation of PRDX5 in BC tissues, with scRNA-seq revealing its enrichment in bladder epithelial cells, correlating with disease advancement and established BC markers. In vitro analyses showed that overexpressed PRDX5 enhanced proliferation, migration, and invasion of BC cells, while PRDX5 knockout produced opposing effects. Additionally, PRDX5 modulated ROS levels and impacted ferroptosis pathways. In vivo experiments confirmed that PRDX5 knockout inhibited tumor growth and activated ferroptosis signaling pathways in tissues.<h4>Conclusion</h4>Our study highlights the elevated expression of PRDX5 in BC and its role in promoting tumor progression through regulation of ROS levels and ferroptosis. PRDX5 may serve as a promising target for BC treatment, supporting further exploration of its potential in clinical applications.

Dysregulation of epigenetic mechanisms plays a crucial role in brain development and disease. Emerging largely evidence suggests that Receptor for Activated C-kinase 7 (RACK7), an epigenetic reader protein, may play a role in brain development and neural developmental disease, but in vivo explorations are still lacking. Here, a Rack7 conditional knock-out mouse model is established and shows that Rack7-deficient mice exhibit overt developmental defects associated with aberrant astrocyte development. Mechanistically, it is found that RACK7 interacts with the histone H3 lysine 27 (H3K27) methyltransferase, i.e., the Polycomb Repressive Complex 2 (PRC2) complex, to establish the genomic locations of Suppressor of Zeste 12 homolog (SUZ12) and H3K27 methylation. Deletion of Rack7 in astrocytes leads to a remarkable decrease of H3K27me3 chromatin localization genome-wide. Furthermore, RACK7 works together with H3K27me3 to prevent overactivation of the Wnt signaling pathway and other astrocyte differentiation genes are found. Collectively, this study provides new insights into the cellular and molecular mechanisms underlying brain development regulated by RACK7.

Peste des petits ruminants virus (PPRV) is an important pathogen that has long been a significant threat to small ruminant productivity worldwide. Iron metabolism is vital to the host and the pathogen. However, the mechanism underlying host-PPRV interactions from the perspective of iron metabolism and iron-mediated membrane lipid peroxidation has not been reported thus far. In this study, we identified a novel host long-noncoding RNA (lncRNA), APR, that impairs PPRV infectivity by sponging miR-3955-5p, a negative microRNA (miRNA) that directly targets the gene encoding the ferritin-heavy chain 1 (FTH1) protein. Importantly, we demonstrated that PPRV infection causes aberrant cellular iron accumulation by increasing transferrin receptor (TFRC) expression and that iron accumulation induces reticulophagy and ferroptosis, which benefits PPRV replication. Moreover, PPRV infection enhanced the localization of cellular iron on the endoplasmic reticulum (ER) and caused ER membrane damage by promoting excess lipid peroxidation to induce reticulophagy. Interestingly, APR decreased PPRV infection-induced accumulation of intracellular Fe²⁺ via miR-3955-5p/FTH1 axis and ultimately inhibited reticulophagy and ferroptosis. Additionally, our results indicate that interferon regulatory factor 1 promotes APR transcription by positively regulating APR promoter activity after PPRV infection. Taken together, our findings revealed a new pattern of PPRV-host interactions, involving noncoding RNA regulation, iron metabolism, and iron-related membrane lipid peroxidation, which is critical for understanding the host defense against PPRV infection and the pathogenesis of PPRV.IMPORTANCEMany viruses have been demonstrated to engage in iron metabolism to facilitate their replication and pathogenesis. However, the mechanism by which PPRV interacts with host cells from the perspective of iron metabolism, or iron-mediated membrane lipid peroxidation, has not yet been reported. Our data provide the first direct evidence that PPRV infection induces aberrant iron accumulation to promote viral replication and reveal a novel host lncRNA, APR, as a regulator of iron accumulation by promoting FTH1 protein expression. In this study, PPRV infection increased cellular iron accumulation by increasing TFRC expression, and more importantly, iron overload increased viral infectivity as well as promoted ER membrane lipid peroxidation by enhancing the localization of cellular iron on the ER and ultimately induced ferroptosis and reticulophagy. Furthermore, a host factor, the lncRNA APR, was found to decrease cellular iron accumulation by sponging miR-3955-5p, which directly targets the gene encoding the FTH1 protein, thereby attenuating PPRV infection-induced ferroptosis and reticulophagy and inhibiting PPRV infection. Taken together, the results of the present study provide new insight into our understanding of host-PPRV interaction and pathogenesis from the perspective of iron metabolism and reveal potential targets for therapeutics against PPRV infection.

Alzheimer's disease (AD) is the most common cause of dementia in the aged population. Histone acetylation is a major epigenetic mechanism linked to memory formation and cognitive function. Histone deacetylases (HDACs) are responsible for the deacetylation of lysine residues in histone proteins. Although pan-HDAC inhibitors are effective in ameliorating AD phenotypes in preclinical models, they are associated with potential unfavorable adverse effects and barely translated into clinical trials. Therefore, the development of novel HDAC inhibitors with a well isoform-selectivity has been desired in AD drug discovery. Among various HDAC isoforms, HDAC3 is highly expressed in neurons and exhibits detrimental effects on synaptic plasticity and cognitive function. Moreover, HDAC3 provokes neuroinflammation and neurotoxicity and contributes to AD pathogenesis. In this review, we highlight HDAC3 as an attractive therapeutic target for disease-modifying therapy in AD. In addition, we discuss the therapeutic potential of HDAC3 inhibitors in other neurological disorders.

Nanoparticles (NPs) are beneficial for delivery of drugs in a variety of settings, serving to protect their cargo and allow for sustained release. Polymeric NPs offer several advantages as therapeutics carriers due to their tunable characteristics like size and shape, ease of manufacturing, and biocompatibility. Despite this, there are no polymeric NPs that are approved for treatment of liver diseases. This is surprising since─when administered intravenously─the majority of NPs accumulate in cells in the liver. NP characteristics like size and surface charge can be altered to affect distribution to the liver, and even cellular distribution, but the conjugation of targeting ligands onto the NP surface for specific receptors on the cells is an important approach for enhancing cell specific delivery. Enhancing cell-specific targeting of conjugated NPs in the liver has two major hurdles: 1) avoiding accumulation of NPs in the liver resident macrophages known as Kupffer cells, which are optimized to phagocytose particulates, and 2) overcoming the transport barriers associated with architectural changes of the diseased liver. To identify the structures and mechanisms most important in NP design, NP administration during ex vivo perfusion (EVP)─achieved by anatomically isolating an organ by perfusing it outside the body─may be the most important and efficient approach. However, EVP is currently underutilized in the NP field, with limited research published on NPs delivered during liver EVP, and therefore representing an opportunity for future investigations.

Osteosarcoma (OS), the most prevalent primary malignant bone tumor, is characterized by a poor prognosis and high metastatic potential. Mitochondrial autophagy has been implicated in cancer suppression. This study aimed to identify prognostic genes associated with mitochondrial autophagy in OS. Public datasets, including TARGET-OS, GSE99671, and GSE21257, were retrieved for analysis. Differentially expressed genes (DEGs1) between OS and normal samples were identified from GSE99671. Single-sample Gene Set Enrichment Analysis (ssGSEA) was applied to quantify the enrichment scores of 29 mitochondrial autophagy-related genes (MARGs) in OS samples from TARGET-OS, categorizing them into high- and low-score groups to extract DEGs2. The intersection of DEGs1 and DEGs2 yielded mitochondrial autophagy-associated differentially expressed genes (MDGs). Prognostic genes were subsequently screened through a multi-step regression analysis, and a risk score was computed. TARGET-OS samples were stratified into high- and low-risk groups based on the optimal cutoff value of the risk score. GSEA was conducted between the two risk groups. Additionally, associations between prognostic genes and the immune microenvironment were explored. A total of 31 MDGs were identified from the overlap of 3,207 DEGs1 and 622 DEGs2. Five prognostic genes-KLK2, NRXN1, HES5, OR2W3, and HS3ST4-were further selected. Kaplan-Meier survival analysis indicated significantly reduced survival in the high-risk group. GSEA revealed enrichment in ABC transporter activity and glycolysis/gluconeogenesis pathways. Immunoanalysis demonstrated significant differences in 11 immune cell populations and three immune functions between risk groups, notably myeloid-derived suppressor cells (MDSCs) and Type 1 T helper cells. HS3ST4 exhibited the strongest positive correlation with macrophages, whereas NRXN1 showed the most pronounced negative correlation with memory B cells. Expressions of HAVCR2 and PDCD1LG2 were elevated in the low-risk group. Functional analysis indicated significant differences in dysfunction patterns between risk groups. This study identified five mitochondrial autophagy-related prognostic genes and constructed a risk model, offering novel insights into OS diagnosis and therapeutic strategies.

Effective treatment of pediatric acute leukemia is dependent on accurate genomic classification, typically derived from a combination of multiple time-consuming and costly techniques such as flow cytometry, fluorescence in situ hybridization (FISH), karyotype analysis, targeted PCR, and microarrays [1-3]. We investigated the feasibility of a comprehensive single-assay classification approach using long-read sequencing, with real-time genome target enrichment, to classify chromosomal abnormalities and structural variants characteristic of acute leukemia. We performed whole genome sequencing on DNA from diagnostic peripheral blood or bone marrow for 57 pediatric acute leukemia cases with diverse genomic subtypes. We demonstrated the characterization of known, clinically relevant karyotype abnormalities and structural variants concordant with standard-of-care clinical testing. Subtype-defining genomic alterations were identified in all cases following a maximum of 48 h of sequencing. In 18 cases, we performed real-time analysis- concurrent with sequencing-and identified the driving alteration in as little as 15 min (for karyotype) or up to 6 h (for complex structural variants). Whole genome nanopore sequencing with adaptive sampling has the potential to provide genomic classification of acute leukemia specimens with reduced cost and turnaround time compared to the current standard of care.

<h4>Background</h4>Genetic diversity in livestock and poultry is critical for adapting production systems to future challenges. However, inadequate management practices, particularly in developing countries, have led to the extinction or near extinction of several species. Understanding the genetic composition and historical background of local breeds is essential for their effective conservation and sustainable use. This study compared the genomes of 30 newly sequenced Ningqiang ponies with those of 56 other ponies and 104 horses to investigate genetic diversity, genetic differentiation, and the genetic basis of body height differences.<h4>Result</h4>Population structure and genetic diversity analyses revealed that Ningqiang ponies belong to southwestern Chinese ponies. They exhibit a moderate level of inbreeding compared to other pony and horse breeds. Mitochondrial DNA analysis indicated that Ningqiang and Debao ponies share the dominant haplogroups A and C, suggesting a likely common maternal origin. Our study identified low genetic differentiation and detectable gene flow between Ningqiang ponies and Datong horses. The study also indicated the effective population size of Ningqiang ponies showed a downward trend. These findings potentially reflect the historical formation of Ningqiang ponies and population size changes. A selection signal scan (CLR and θπ) within Ningqiang ponies detected several key genes associated with bone development (ANKRD11, OSGIN2, JUNB, and RPL13) and immune response (RIPK2). The combination of genome-wide association analysis and selective signature analysis (F_ST) revealed significant single nucleotide polymorphisms and selective genes associated with body height, with the most prominent finding being the TBX3 gene on equine chromosome (ECA) 8. Additionally, TBX5, ASAP1, CDK12, CA10, and CSMD1 were identified as important candidate genes for body height differences between ponies and horses.<h4>Conclusion</h4>The results of this study elucidate the genetic diversity, genetic differentiation, and effective population size of Ningqiang ponies compared to other ponies and horses, further deepen the understanding of their small stature, and provide valuable insights into the conservation and breeding of local horse breeds in China.

Retinopathy of prematurity (ROP) is a disorder that causes blindness in children at a high incidence. Retinal endothelial cells are damaged by variations in oxygen partial pressure, which leads to vascular obstruction and, eventually, ischemia and hypoxia, which cause the formation of new blood vessels. However, little is known about the molecular mechanism of hyperoxic vascular occlusion. High oxygen levels are thought to cause ferroptosis. In this study, experiments with both animal and in vitro models demonstrated that elevated expression of C-X-C motif chemokine ligand 10 (CXCL10)/C-X-C motif chemokine receptor 3 (CXCR3) in retinal vascular endothelial cells induced ferroptosis. Curcumin decreased ferroptosis by inhibiting the production of CXCL10/CXCR3. Curcumin also preserved distal sprouts and filopodia, increasing tip cell and astrocyte counts. As a result, we hypothesize that curcumin reduces ferroptosis and preserves retinal blood vessels under hyperoxic conditions by suppressing the CXCL10/CXCR3 axis. Coimmunoprecipitation (COIP) data were used to determine which proteins interact with CXCR3 during ferroptosis. For the first time, our study applied curcumin to treat eye diseases in oxygen-induced retinopathy (OIR) mice and explored the underlying mechanism in cell experiments, laying the foundation for clinical patients to use this drug. Exploring the interaction between CXCL10/CXCR3 and ferroptosis provides an experimental basis for using the CXCL10/CXCR3 axis as a therapeutic target for the treatment of ROP ophthalmopathy.

Histone H1s are basic nuclear proteins, which played key role in the binding of DNA and nucleosome, eventually the stability of eukaryotic chromatin. In most species, H1s possess an evolutionarily conserved nucleosome-DNA binding globular domain (GH1), which is conserved between species, especially in mammals. However, there is limited information on the phylogeny, structure and function of H1s in poplar. In the present research, 21 GH1-containing proteins found in Populus trichocarpa were classified into three subgroups (H1s, Myb (SANK) GH1 and AT-hook GH1) based on their domains. The Populus H1 proteins contained lysine-rich N-, C-terminal tails and a conserved GH1 domain, particularly the characteristic amino acids in the helix and strand structures of the five H1 subtypes. The phylogenetic and structure diversity analysis of GH1 proteins across different Populus species and model plants revealed three conserved subgroups with characteristic amino acids. The variation in the number of members across the five subtypes was consistent with the evolutionary relationships among Populus species. The conserved characteristic amino acids among same Populus subtype can be served as markers for subtype identification. Furthermore, the abundance analysis of H1s in Populus indicated their unique functions in young tissues and stages, which may be related to DNA methylation. The consistent expression pattern of H1 across Populus species was in accordance with collinearity pairs. Present analyses provided valuable information on the diversity and evolution of H1s in Populus, advocating further research of H1s in plants.

<h4>Objective</h4>Metabolic dysfunction-associated steatotic liver disease (MASLD) is highly prevalent in people living with HIV (PWH). Gut microbial translocation and gut damage may play a role in MASLD pathogenesis. We determined associations of circulating biomarkers of translocation and gut damage with hepatic steatosis and fibrosis in a large U.S. cohort of women with HIV (WWH) and without HIV.<h4>Design</h4>Vibration controlled transient elastography (VCTE) was conducted from 2013 to 2018 among 854 WWH and 349 women without HIV. Serum biomarkers were measured within 6 months of the VCTE: kynurenine to tryptophan (KT) ratio, intestinal fatty acid binding protein (I-FABP), and immune activation markers soluble CD14 (sCD14) and soluble CD163 (sCD163).<h4>Methods</h4>We used multivariable linear regression to evaluate independent associations of each biomarker, HIV serostatus, and demographic, metabolic, and HIV-specific covariates with hepatic steatosis [controlled attenuation parameter (CAP)] and fibrosis [liver stiffness (LS)].<h4>Results</h4>In multivariable analysis, increasing in KT ratio was associated with a 6 dB/m lower CAP and 6% higher LS, and sCD14 with a 5 dB/m lower CAP and 8% higher LS. sCD163 was not associated with CAP but was associated with a 12.5% higher LS value. I-FABP was not associated with either CAP or LS values.<h4>Conclusions</h4>Higher KT ratio, sCD14, and sCD163 were associated with increased hepatic fibrosis but not steatosis. In fact, higher KT ratio and sCD14 were associated with decreased steatosis. This suggests that microbial translocation and gut damage may contribute to the pathogenesis of fibrosis in WWH in a mechanism unrelated to increased steatosis.

How genomic DNA is folded during cell division to form the characteristic rod-shaped mitotic chromosomes essential for faithful genome inheritance is a long-standing open question in biology. Here, we use nanoscale DNA tracing in single dividing cells to directly visualize how the 3D fold of genomic DNA changes during mitosis at scales from single loops to entire chromosomes. Our structural analysis reveals a characteristic genome scaling minimum of 6-8 megabases in mitosis. Combined with data-driven modeling and molecular perturbations, we can show that very large and strongly overlapping loops formed by condensins are the fundamental structuring principle of mitotic chromosomes. These loops compact chromosomes locally and globally to the limit set by chromatin self-repulsion. The characteristic length, density, and increasingly overlapping structure of mitotic loops we observe in 3D fully explain how the rod-shaped mitotic chromosome structure emerges by self-organization during cell division.

Hypothalamic-Pituitary-Somatotropic (HPS) axis contains essential endocrine factors and plays diverse roles in the growth of teleost living in dynamic aquatic environments. In this study, 43 HPS axis genes were characterized in Chinese sea bass (Lateolabrax maculatus), the economically important marine fish highly adaptable to a wide range of temperatures and salinities. The phylogeny, conserved domain, molecular evolution and expression of L. maculatus HPS axis genes revealed their evolutionary conservation, with examples of functional divergence in duplication-originated genes (sst1a/1b, igf1ra/1rb). Weighted gene co-expression network analysis (WGCNA) among L. maculatus tissues revealed strong co-expression of HPS genes (ssts, igf1rs, igfbps) in brains than in livers and muscles, interacting with feeding (cartpt, negr1), metabolism (grik3, drd4), and growth (apba1) functional genes. Under temperature changes, L. maculatus HPS genes were more actively regulated in brains than in livers and muscles, with the hypothalamic and pituitary HPS genes mainly regulated in brains, whereas the peripheral HPS genes were regulated in livers and muscles. WGCNA revealed that HPS axis mainly interacted with stress and feeding activity in brains of L. maculatus under temperature stress, while it interacted with metabolism and growth activity in livers and muscles. Similar co-expression of HPS genes (sstrs, igf1rbs, igfbps) were with feeding (pik3r4), metabolism (mrps, ndufa12) and growth (sulf2, peli3, apod) functions in brains, indicating that HPS axis could regulate growth through coordinated mediation of the food-intake and energy metabolism in L. maculatus under environmental stress. Our results provided comprehensive understanding about the L. maculatus HPS axis responding to environmental stimuli, which are crucial for the growth regulation and will provide important insights into fast-growing L. maculatus cultivation.

Knee osteoarthritis (OA) is characterized by cartilage degeneration and significant reduction in lubrication. One strategy to recover the natural lubrication of the synovial fluid is the injection of hydrogel microspheres. Here, we have fabricated polyethylene glycol (PEG)-based hydrogel microspheres via a modified electrospraying setup. To improve throughout, crosslinking of PEG droplets was delayed until after droplet formation was complete. A custom-synthesized super-lubricious copolymer consisting of adhesive dopamine methacrylate (DMA), zwitterionic sulfobetaine methacrylate (SBMA), and fluorescent rhodamine B was used to dip-coat the PEG microspheres. Super-lubricious PEG microspheres coating reduced coefficient of friction by 57% compared to simulated synovial fluid, indicating beneficial lubrication properties. When injected into C57BL6 mice, PEG microspheres exhibited stability for up to 26 d and did not adversely affect mouse behavior. These super-lubricious PEG microspheres offer great promise to reduce the friction that is a hallmark of progressive OA, potentially mitigating the need for total knee arthroplasty.

<h4>Introduction</h4>Tumor-infiltrating B lymphocytes (TILBs) play a pivotal role in shaping the immune microenvironment of tumors (TIME) and in the progression of lung adenocarcinoma (LUAD). However, there remains a scarcity of research that has thoroughly and systematically delineated the characteristics of TILBs in LUAD.<h4>Method</h4>The research employed single-cell RNA sequencing from the GSE117570 dataset to identify markers linked to TILBs. A comprehensive machine learning approach, utilizing ten distinct algorithms, facilitated the creation of a TILB-related index (BRI) across the TCGA, GSE31210, and GSE72094 datasets. We used multiple algorithms to evaluate the relationships between BRI and TIME, as well as immune therapy-related biomarkers. Additionally, we assessed the role of BRI in predicting immune therapy response in two datasets, GSE91061 and GSE126044.<h4>Result</h4>BRI functioned as an independent risk determinant in LUAD, demonstrating a robust and reliable capacity to predict overall survival rates. We observed significant differences in the scores of B cells, M2 macrophages, NK cells, and regulatory T cells between the high and low BRI score groups. Notably, BRI was found to inversely correlate with cytotoxic CD8+ T-cell infiltration (r = -0.43, p < 0.001) and positively correlate with regulatory T cells (r = 0.31, p = 0.008). We also found that patients with lower BRI were more likely to respond to immunotherapy and were associated with reduced IC50 values for standard chemotherapy and targeted therapy drugs, in contrast to higher BRI. Additionally, the BRI-based survival prediction nomogram demonstrated significant promise for clinical application in predicting the 1-, 3-, and 5-year overall survival rates among LUAD patients.<h4>Discussion</h4>Our study developed a BRI model using ten different algorithms and 101 algorithm combinations. The BRI could be a valuable tool for risk stratification, prognosis, and selection of treatment approaches.

Flavonoids are a class of important polyphenolic compounds, renowned for their antioxidant properties. However, recent studies have uncovered an additional function of these natural flavonoids: their ability to inhibit ferroptosis. Ferroptosis is a key mechanism driving cell death in central nervous system (CNS) diseases, including both acute injuries and chronic neurodegenerative disorders, characterized by iron overload-induced lipid peroxidation and dysfunction of the antioxidant defense system. This review discusses the therapeutic potential of natural flavonoids from herbs and nutraceuticals as ferroptosis inhibitors in CNS diseases, focusing on their molecular mechanisms, summarizing findings from preclinical animal models, and providing insights for clinical translation. We specifically highlight natural flavonoids such as Baicalin, Baicalein, Chrysin, Vitexin, Galangin, Quercetin, Isoquercetin, Eriodictyol, Proanthocyanidin, (-)-epigallocatechin-3-gallate, Dihydromyricetin, Soybean Isoflavones, Calycosin, Icariside II, and Safflower Yellow, which have shown promising results in animal models of acute CNS injuries, including ischemic stroke, cerebral ischemia-reperfusion injury, intracerebral hemorrhage, subarachnoid hemorrhage, traumatic brain injury, and spinal cord injury. Among these, Baicalin and its precursor Baicalein stand out due to extensive research and favorable outcomes in acute injury models. Mechanistically, these flavonoids not only regulate the Nrf2/ARE pathway and activate GPX4/GSH-related antioxidant pathways but also modulate iron metabolism proteins, thereby alleviating iron overload and inhibiting ferroptosis. While flavonoids show promise as ferroptosis inhibitors for CNS diseases, especially in acute injury settings, further studies are needed to evaluate their efficacy, safety, pharmacokinetics, and blood-brain barrier penetration for clinical application.

<h4>Background</h4>Neuropathic pain (NP) is a kind of chronic pain that can lead to neurasthenia. The effectiveness of current drug treatment for NP is still unsatisfactory due to its side effects, addiction and withdrawal. In recent years, researchers have begun to develop nano-drug delivery systems for the diagnosis and treatment of NP diseases.<h4>Methods</h4>We developed a disulfide-bonded magnetic mesoporous silica dual-drug delivery system consisting of <i>curcumin</i> (<i>Cur</i>) and a calcitonin gene-related peptide (CGRP) antagonist (CGRPi), and characterized by electron microscopy, Dynamic Light Scattering (DLS), Zeta, specific surface area and pore size detection. At the cellular level, the biocompatibility of CGRPi@<i>Cur</i>@Fe₃O₄@mSiO₂-PEG (FMCC) nanoparticles were tested by CCK-8 and dead/alive staining kit in BV2 cells; Inflammation levels and oxidative stress were measured by enzyme linked immunosorbent assay (ELISA) in lipopolysaccharide (LPS)-induced BV2 neuroinflammation model. <i>In vivo</i>, chronic constriction injury (CCI) model was constructed, and the effect of FMCC on pain behavior of CCI mice was detected by von Frey filaments test and thermal hyperalgesia; The effects of FMCC on the anti-inflammatory and oxidative stress of CCI were determined by pathological tests (HE and ROS staining), RT-PCR and ELISA.<h4>Results</h4>FMCC had good biocompatibility and could be taken up by BV2 cells. At the cellular level, FMCC could effectively reverse oxidative stress, inflammation and CGRP expression in LPS-induced neuroinflammation model <i>in vitro</i>. At the animal level, the mice with CCI were administered with FMCC, which effectively reduced oxidative stress and inflammation and sustained relief of neuropathic pain.<h4>Conclusion</h4>This study provides a new approach for the treatment of neuropathic pain.

Dry cultivation of rice (DCR) is one of the important rice cultivation practices aimed at addressing freshwater resource shortages. However, the non-renewable nature of phosphate resources constrains agricultural development. In the context of the contradiction between rice, water, and phosphorus, there is little research on using the silicon phosphorus relationship to improve the phosphorus availability and uptake of DCR. This experiment used field soil and established five fertilization treatments: no phosphorus application, low phosphorus and normal phosphorus (0, 25, 75 kg·ha^-1 P₂O₅) (0P, 25P, 75P), along with two silicon levels (0, 45kg·ha^-1 SiO₂), resulting in the treatments 0P, 0PSi, 25P, 25PSi, and 75P. The soil phosphorus components and plant phosphorus uptake were analyzed. The results showed that adding silicon to 25P increased the Olsen-P content (14.37%) by increasing Ca₈-P (9.04%) and Al-P (19.31%). Additionally, root and leaf phosphorus content increased by 7.6% and 5.8%, respectively, comparable to the levels observed in the 75P treatment. On one hand, adding silicon increases malate (40.48%) and succinate (49.73%) content, enhances acid phosphatase activity, and increases the abundance of <i>Bradyrhizobium</i>, <i>Paenibacillus</i>, and <i>Bacillus</i>, as well as the proportion of <i>Fusarium</i>, forming an "organic acid microbial" activated phosphorus system. On the other hand, the addition of silicon alleviated phosphorus limitations by reducing ATP consumption in roots through a decrease in ATPase and P-ATPase content. This also minimized excessive NSC transport to roots, thereby promoting shoot growth by downregulating <i>SUT1</i>, <i>SWEET11</i>, <i>SUS2</i>, and <i>CIN2</i>. In addition to optimizing root-to-shoot ratio and providing sufficient energy, silicon addition also increases root volume and upregulates <i>OsPT2</i>, <i>OsPT4</i>, and <i>OsPT8</i>, thereby promoting phosphorus uptake. In summary, 25PSi optimizes the root-to-shoot ratio and promotes phosphorus conversion and uptake through organic acid, microbial, and energy pathways. Applying silicon is beneficial for the sustainable and efficient management of phosphorus in DCR.

We present two rare thyroid cancer cases, Hyalinizing trabecular tumor (HTT) and Warthin-like papillary thyroid carcinoma (WL-PTC) coexisting with an oncocytic PTC variant. A 64-year-old female patient presented with a 26 × 11.1 mm isoechoic thyroid nodule on ultrasound. Fine needle aspiration (FNA) cytology showed atypia of undetermined significance (TBS III). Three years later, new FNA cytology showed ''suspicious of malignancy (TBS V)''. The patient was thyroidectomized and pathology revealed HTT. The second patient, a 54-year-old woman presented with a 13 mm ultrasound thyroid nodule with irregular borders and microcalcifications. FNA cytology showed PTC, possibly a tall cell variant (TBS VI). The patient underwent thyroidectomy and pathology revealed WL-PTC coexisting with an oncocytic PTC variant. After radioiodine ablation the patient began levothyroxine therapy.

High-grade B-cell lymphoma (HGBL), not otherwise specified (NOS), is a rare entity within the spectrum of B-cell lymphomas. HGBL, NOS remains a diagnosis of exclusion with limited data available on the optimal clinical approach. We report a case of a 67-year-old man with HGBL, NOS with a germinal center B-cell (GCB) immunophenotype. The disease was characterized by an aggressive clinical course, refractory to multiple lines of cytotoxic chemotherapy, immunotargeted treatment, therapy with a PD-1 inhibitor, and haploidentical hematopoietic stem cell transplantation (haplo-<i>HSCT</i>). Ultimately, the disease progression led to the patient's death nine months post-diagnosis. A FISH assay identified a sole genetic rearrangement: BCL2/IGH. Whole-exome sequencing revealed a number of significant somatic mutations, such as TP53 p.C238G, B2M p.L12R, STAT6 p.D419G, STAT3 p.S614R, TREX1 p.T49fs, and CREBBP p.C367Ter, as well as a high focal amplification of the MUC3A gene and the deletion of the short arm of chromosome 17 (del(17p)). An inactivating somatic mutation in the TREX1 gene (p.T49fs) has not been previously described in patients with non-Hodgkin lymphomas. Additionally, our analysis uncovered a key cancer hallmark: tumor genomic instability, manifested as a high tumor mutational burden, which likely contributed to the aggressive disease course.

This study investigated the genetic causes of atypical cerebral palsy (CP) through chromosomal microarray (CMA) and exome sequencing (ES) in a cohort of 10 Korean patients to identify variants and expand the spectrum of mutations associated with atypical cerebral palsy. Whole ES and/or genome sequencing (GS) after routine karyotyping and CMA was performed to identify causative variants and expand the spectrum of mutations associated with atypical CP. In cases of atypical CP, scoliosis and/or kyphosis, ranging from mild to severe, were present in all patients. Epilepsy was a comorbidity in seven patients (70%), and intellectual disability (ID) was observed in varying degrees. This study identified three copy number variations (CNVs), including 15q11.2 microdeletion (<i>n</i> = 1), 17p11.2 duplication (<i>n</i> = 1), and 12p13.33p11.23 duplication/18p11.32 microdeletion (<i>n</i> = 1), and six likely pathogenic variants (LPVs) or pathogenic variants (PVs) detected in the <i>SLC2A1</i>, <i>PLAA</i>, <i>CDC42BPB</i>, <i>CACNA1D</i>, <i>ALG12</i>, and <i>SACS</i> genes (<i>n</i> = 6). These findings emphasize the significance of incorporating genetic testing into the diagnostic process for atypical CP to improve our understanding of its molecular basis and inform personalized treatment strategies. To further advance this research, future studies should focus on exploring genotype-phenotype correlations, assessing the functional impact of identified variants, and increasing the sample size to validate the observed patterns.

Cancer stem cells (CSCs) are a heterogeneous group of tumor cells that play a significant role in tumorigenesis, therapeutic resistance, and recurrence in liver hepatocellular carcinoma (LIHC). This study combines clinical data sets from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) with bulk RNA sequencing data. This study also features the GSE156625 single-cell RNA sequencing (scRNA) data set from the GEO to explore the prognostic significance of CSC biomarkers (BCSCs) in LIHC. In this research, we introduce a developed prognostic risk model that relies on nine specific BCSCs, including ADM, CCL5, CD274, DLGAP5, HOXD9, IGF1, S100A9, SOCS2, and TNFRSF11B. It was found that high-risk patients experience shorter overall survival rates when compared to low-risk patients. Additionally, the study characterized the composition of immune cells within the tumor microenvironment (TME) and revealed significant variations in gene-expression levels and mutation rates between different risk groups. The model suggests that liver cancer progression might be driven by immune evasion independent of PD-L1 and highlights the potential of the low-risk BCSC group being sensitive to various treatments. Our findings offer a promising foundation for personalized LIHC therapy and highlight the need for further experimental validation of the roles of these CSCs in disease progression.

Autoimmune hepatitis (AIH) is a chronic liver disease characterized by histological, clinical, and laboratory findings, including elevated liver enzymes, immunoglobulin G (IgG), and autoantibodies. Belimumab, a monoclonal antibody targeting B-lymphocyte stimulator (BLyS), is primarily approved for systemic lupus erythematosus (SLE) but shows promise in improving liver function tests (LFTs) in patients with concurrent AIH and SLE. We present the case of a 24-year-old female diagnosed with AIH and SLE, whose elevated LFTs initially resisted standard azathioprine therapy. Upon switching to mycophenolate and belimumab, a notable reduction in LFTs was observed. This case highlights belimumab's potential as an adjunct therapy in AIH, especially in patients with overlapping autoimmune conditions, supporting its role in reducing systemic inflammation and autoimmune activity.

<b>Background:</b> Hepatobiliary liver cancers (HBLCs) represent the sixth most common neoplasm in the world. Hepatocellular carcinoma (HCC) and cholangiocarcinoma (CC) constitute the main HBLC types, with alarming epidemiological projections. <b>Methods:</b> In recent decades, alterations in gut microbiota, with mutual implications on the gut-liver axis and gut-biliary axis permeability status, have been massively investigated and proposed as HBLC pathogenetic deus ex machina. <b>Results:</b> In the HCC setting, elevated intestinal levels of <i>Escherichia coli</i> and other Gram-negative bacteria have been demonstrated, resulting in a close association with increased lipopolysaccharide (LPS) serum levels and, consequently, chronic systemic inflammation. In contrast, the intestinal microbiota of HCC individuals feature reduced levels of <i>Lactobacillus</i> spp., <i>Bifidobacterium</i> spp., and <i>Enterococcus</i> spp. In the CC setting, evidence has revealed an increased expression of <i>Lactobacillus</i> spp., with enhanced levels of <i>Actynomices</i> spp. and <i>Alloscardovia</i> spp. Besides impaired strains/species representation, gut-derived metabolites, including bile acids (BAs), short-chain fatty acids (SCFAs), and oxidative-stress-derived products, configure a network severely impacting the progression of HBLC. <b>Conclusions:</b> In the era of Precision Medicine, the clarification of microbiota composition and functioning in HCC and CC settings can contribute to the identification of individual signatures, potentially providing novel diagnostic markers, therapeutic approaches, and prognostic/predictive tools.

<h4>Introduction</h4>Primary membranous nephropathy (pMN) is a frequent cause of nephrotic syndrome in adult patients without diabetes. Recognizing the major shift in the classification of pMN based on target antigen and the management of patients with pMN with more widespread use of rituximab (RTX), we sought to better characterize the clinical course and risk factors in adults and children with pMN.<h4>Methods</h4>We used the Cure Glomerulonephropathy (CureGN) prospective cohort of patients with pMN diagnosed using biopsy between 2010 and 2023. We report time to kidney outcomes using adjusted Cox proportional hazards models.<h4>Results</h4>In total, 591 patients (537 adults and 54 children) were evaluated with 9% reaching kidney failure. Anti-B cell therapy was used in 44% of patients. Age < 18 years, self-reported Black/African American race, proteinuria > 3 g/g, and lower estimated glomerular filtration rate (eGFR) at enrollment were associated with worse kidney survival. Black race (adjusted hazard ratio [HR]: 1.8; 95% confidence interval [CI]: 1.1-2.9) and age < 18 years (adjusted HR: 3.7; 95% CI: 2.0-7.1) were associated with an increased risk of kidney failure and/or > 40% eGFR decline after adjusting for exposure to immunosuppression. Latinx ethnicity was associated with a lower likelihood of reaching complete proteinuria remission (adjusted HR: 0.4; 95% CI: 0.2-0.7).<h4>Conclusion</h4>This study unveils self-reported Black race, young age (aged < 18 years) and Latinx ethnicity as potential risk factors associated with worse kidney outcomes.

Evaluating the impact of bacteriophages on bacterial communities is required to assess the future utility of phage therapy. Methods able to study bacterial polycultures in the presence of phages are useful to mimic evolutionary pressures found in natural environments and recapitulate complex ecological contexts. Bacteriophages can drive rapid genetic and phenotypic changes in host cells. However, the presence of other bacteria can also impact bacterial densities and community structure, and classical methods remain lengthy and resource intensive. Here, we introduce a microdroplet-based encapsulation method in which bacterial co-cultures are imaged using Z-stack brightfield microscopy. The method relies on automated droplet imaging using a novel AI-based autofocus function, coupled with morphology-based deep learning models for accurate identification of two morphologically distinct bacterial species. We show that we can monitor the relative growth dynamics of P. aeruginosa and S. aureus growing in 11 picolitre droplets for up to 24 hours. We demonstrate quantification of growth rates, bacterial densities and lysis dynamics of the two species without the need for plating. We show that a potent lytic phage of P. aeruginosa can either fully lyse the initial P. aeruginosa population or keep its density low long-term when in the presence of S. aureus .

Synucleinopathies such as Parkinson's disease (PD), dementia with Lewy bodies (DLB), and multiple system atrophy (MSA) are neurodegenerative diseases with shared clinical and pathological features. Aggregates of alpha-synuclein (αsyn) phosphorylated at serine 129 (PSER129) are hallmarks of synucleinopathies, which, for PD/DLB, are found predominantly in neurons, whereas in MSA, aggregates are primarily found in oligodendroglia. It remains unclear whether the distinct pathological presentations of PD/DLB and MSA are manifestations of unique or shared pathological processes. Using the in-situ proximity labeling technique of biotinylation by antibody recognition (BAR), we compared aggregated αsyn-interactomes (BAR-PSER129) and total αsyn-interactomes (BAR-MJFR1) between MSA (n = 5) and PD/DLB (n = 10) in forebrain and midbrain structures. Comparison between MSA and PD/DLB-enriched proteins revealed 79 PD/DLB-differentially abundant proteins and only three MSA-differentially abundant proteins (CBR1, CRYAB, and GFAP). Pathway enrichment analysis revealed that vesicle/SNARE-associated pathways dominated PD/DLB interactions, whereas MSA was strongly enriched for metabolic/catabolic, iron, and cellular oxidant detoxification pathways. A subnetwork of cytosolic antioxidant enzymes called peroxiredoxins drove cellular detoxification pathway enrichment in MSA. A network of 26 proteins, including neuronal-specific proteins (e.g., SYNGR3) with HSPA8 at the core, was shared between MSA and DLB/PD. Extracellular exosome pathways were universally enriched regardless of the disease or BAR target protein. In conclusion, synucleinopathies have divergent and convergent αsyn-aggregate interactions, indicating unique and shared pathogenic mechanisms. MSA uniquely involves oxidant detoxification processes in glial cells, while vesicular processes in neurons dominate PD/DLB. Shared interactions, specifically SYNGR3, between MSA and PD/DLB suggest that neuronal axons are the origin of both diseases. In conclusion, we provide αsyn protein interaction maps for two distinct synucleinopathies.

Interferon Regulatory Factors (IRFs) are critical modulators of immune and inflammatory responses, yet their roles in Alzheimer's disease (AD) and other neurodegenerative disorders remain incompletely understood. While IRFs are recognized for their regulatory functions in neuroinflammation, microglial activation, and neuronal survival, their dual roles as both drivers of pathological inflammation and mediators of neuroprotective pathways underscore a sophisticated regulatory paradox in neurodegenerative disorders. This review aims to synthesize current evidence on IRF-mediated neuroinflammation in AD and related diseases, focusing on the multifaceted functions of key IRF family members, including IRF1, IRF3, and IRF7. We critically evaluate their divergent roles: IRF1 and IRF3, for instance, exacerbate neuroinflammatory cascades and amyloid-beta (Aβ) pathology in AD, whereas IRF7 may paradoxically suppress inflammation under specific conditions. Additionally, we explore IRF dysregulation in Parkinson's disease, multiple sclerosis, amyotrophic lateral sclerosis, and Huntington's disease, emphasizing shared and distinct mechanisms across neurodegenerative disorders. Restoring IRF balance through genetic manipulation, small-molecule inhibitors, or microbiome-derived modulators could attenuate neuroinflammation, enhance Aβ clearance, and protect neuronal integrity. Ultimately, this work provides a framework for future research to harness IRF signaling pathways in the development of precision therapies for AD and other neurodegenerative diseases.

Crohn's disease (CD) is a chronic inflammatory disorder with potential progression to stricturing (B2) or penetrating (B3) phenotypes, leading to significant complications. Early identification of patients at risk for these complications is critical for personalized management. This study aimed to develop a predictive model using clinical data and a Korean-specific transcriptome-wide association study (TWAS) to forecast early progression in CD patients. A retrospective analysis of 430 Korean CD patients from 15 hospitals was conducted. Genotyping was performed using the Korea Biobank Array, and gene expression predictions were derived from a TWAS model based on terminal ileum data. Logistic regression models incorporating clinical and gene expression data predicted progression to B2 or B3 within 24 months of diagnosis. Among the cohort, 13.9% (60 patients) progressed to B2 and 16.9% (73 patients) to B3. The combined model achieved mean area under the curve (AUC) values of 0.788 for B2 and 0.785 for B3 progression. Key predictive genes for B2 included <i>CCDC154</i>, <i>FAM189A2</i>, and <i>TAS2R19</i>, while <i>PUS7</i>, <i>CCDC146</i>, and <i>MLXIP</i> were linked to B3 progression. This integrative model provides a robust approach for identifying high-risk CD patients, potentially enabling early, targeted interventions to reduce disease progression and associated complications.

Serotonin (5-HT), dopamine (DA), and norepinephrine (NE) are key monoamine neurotransmitters regulating behaviors, mood, and cognition. 5-HT affects early brain development, and its dysfunction induces brain vulnerability to stress, raising the risk of depression, anxiety, and autism in adulthood. These neurotransmitters are synthesized from tryptophan and tyrosine via hydroxylation and decarboxylation, and are metabolized by monoamine oxidase (MAO). This review aims to summarize the current findings on the role of dietary phytochemicals in modulating monoamine neurotransmitter biosynthesis, metabolism, and function, with an emphasis on their potential therapeutic applications in neuropsychiatric disorders. Phytochemicals exert antioxidant, neurotrophic, and neurohormonal activities, regulate gene expression, and induce epigenetic modifications. Phytoestrogens activate the estrogen receptors or estrogen-responsive elements of the promoter of target genes, enhance transcription of tryptophan hydroxylase and tyrosine hydroxylase, while inhibiting that of MAO. These compounds also influence the interaction between genetic and environmental factors, potentially reversing dysregulated neurotransmission and the brain architecture associated with neuropsychiatric conditions. Despite promising preclinical findings, clinical applications of phytochemicals remain challenging. Advances in nanotechnology and targeted delivery systems offer potential solutions to enhance clinical efficacy. This review discusses mechanisms, challenges, and strategies, underscoring the need for further research to advance phytochemical-based interventions for neuropsychiatric diseases.

<h4>Introduction</h4>Cytoplasmic inclusions are observed in motor neurons in amyotrophic lateral sclerosis (ALS) associated with the Cu/Zn superoxide dismutase mutation (mtSOD1). Although these inclusions are a hallmark of the disorder, degeneration is not necessarily initiated in the cytoplasm, nor are these structures the culprit of ALS. The nucleus stores genetic material and acts as the cell's control center, and a small fraction of mtSOD1 is reported to be distributed in the nucleus. We hypothesized that mtSOD1 in the nucleus contributes to motor neuron degeneration.<h4>Methods</h4>We explored the roles of mtSOD1 in relation to nuclear proteins, chromosomal DNA, and mRNA expression. An immortalized cell line derived from a transgenic ALS mouse model expressing mtSOD1-L126delTT with a FLAG was used for stable immunoprecipitation of mtSOD1-binding molecules using shotgun proteomics and chromatin immunoprecipitation-sequencing (ChIP-seq). We also examined mRNA expression by silencing whole SOD1 (innate mouse Sod1 and mtSOD1) or mtSOD1 alone and compared these patterns against those in non-silenced counterparts.<h4>Results</h4>We identified 392 mtSOD1-interacting proteins in the nucleus. Gene ontology (GO) revealed these proteins to be enriched for "mRNA processing." Notably, more than 11% of mtSOD1-interacting proteins were expressed concurrently with previously reported wild-type TAR DNA-binding protein 43 (TDP-43)-interacting proteins. ChIP-seq revealed that mtSOD1-interacting DNA portions showed a preference for zinc finger protein-binding motifs. GO analysis of the ChIP-seq data revealed that "mRNA processing" was again enriched among the genes harboring mtSOD1-binding domains. RNA expression analyses revealed that the presence of mouse Sod1 and mtSOD1 induced the overexpression of molecules related to "type 1 IFN responses."<h4>Conclusions</h4>We revealed that mtSOD1 interacted with nuclear proteins and specific DNA segments and that RNA expression was notably altered when mouse Sod1 and mtSOD1 were silenced. These interactions could play a pivotal role in motor neuron degeneration.

As a moonlighting protein with multiple enzymatic activities, peroxiredoxin 6 (PRDX6) maintains redox homeostasis, regulates phospholipid metabolism, and mediates intra- and inter-cellular signaling transduction. Its expression and activity can be regulated by diverse stressors. However, the roles and relevant mechanisms of these regulators in various conditions have yet to be comprehensively reviewed. In this study, these stressors were systematically reviewed both in vivo and in vitro and classified into chemical, physical, and biological categories. We found that the regulatory effects of these stressors on PRDX6 expression were primarily mediated via key transcriptional factors (e.g., NRF2, HIF-1α, SP1, and NF-κB), micro-RNAs, and receptor- or kinase-dependent signaling pathways. Additionally, certain stressors, including reactive oxygen species, pH fluctuations, and post-translational modifications, induced the structure-based functional switches in the PRDX6 enzyme. We further reviewed the altered expression of PRDX6 under various disease conditions, with a particular focus on neuropsychiatric disorders and cancers, and proposed the concept of PRDX6-related disorders (PRD), which refers to a spectrum of diseases mediated by or associated with dysregulated PRDX6 expression. Finally, we found that an exogenous supplementation of PRDX6 protein provided preventive and therapeutic potentials for oxidative stress-related injuries in both in vivo and in vitro models. Taken together, this review underscores the critical role of PRDX6 as a cellular orchestrator in response to various stressors, highlighting its clinical potential for disease monitoring and the development of therapeutic strategies.

Overproduction of reactive oxygen species and antioxidant superoxide dismutases (SOD1, SOD2) dysregulation contribute to chronic inflammation such as generated in inflammatory bowel diseases (IBD). A kinetic redox shotgun proteomic strategy (OcSILAC for Oxidized cysteine Stable Isotope Labelling by Amino acids in Cell culture) was used to explore the lipopolysaccharide (LPS) effects including LPS-induced oxidation and inflammation cascades on a dedicated intestinal epithelial cell line (HT29-MD2) together with the potential mitigating role of a Mn-based SOD-mimic Mn1. While LPS induced transient oxidative damages at early times (15 min), cells incubated with Mn1 showed, in this time frame, a significantly reduced cysteine oxidation, highlighting Mn1 antioxidant properties. Over time, cysteine oxidation of LPS-treated cells was counteracted by an overexpression of antioxidant proteins (SOD1, NQO1) and a late (6 h) preponderant increase in SOD2 level. Mn1, when co-incubated with LPS, attenuated the level of most LPS-modified proteins, that is, proteins involved in the inflammatory response. Our results highlight Mn1 as a potentially effective antioxidant and anti-inflammatory agent to consider in the treatment of IBD, as well as a useful tool for exploring the interconnection between oxidative stress and inflammation.

The widespread application of ionizing radiation (IR) in medicine, while beneficial, also poses potential risks that necessitate effective countermeasures. Both 2-(3-aminopropylamino) ethanethiol (WR-1065) and curcumin are recognized as radioprotective agents; however, their clinical utility is hindered by notable shortcomings that could be addressed through reactive oxygen species (ROS)-responsive amphiphilic nanomaterials. We introduced a newly synthesized poly (ethylene glycol) (PEG)-polycaprolactone (PCL) polymer integrated with diselenide bonds and curcumin (HOOC-SeSe-Cur-PEG-SeSe-Cur-PCL, PEG-Cur-SeSe-PCL). The resulting spherical nanoparticles (NPs), which self-assembled from this polymer, were uniform with an average diameter of 118 nm. As a carrier for WR-1065, these NPs demonstrated a loading capacity of 30.9% and an efficacy of 56.7%. Importantly, the degradation of WR-1065 within the NPs was minimal in gastric fluid, decreasing by only approximately 20% over a 6-hour period. The innovative aspect of these NPs is their design to destabilize in ROS-rich environments, facilitating the release of WR-1065 and curcumin. Indeed, the survival rate of mice increased to 50% when these NPs were orally administered prior to exposure to a lethal dose of whole-body irradiation (8 Gy). The radioprotective impact of WR-1065-loaded NPs was evident in the small intestine of irradiated mice, characterized by the amelioration of radiation-induced epithelial damage, reduction of DNA damage, and inhibition of the apoptotic pathway. Collectively, this oral nanocarrier system for WR-1065 and curcumin holds promise as a potential candidate for the prophylaxis and treatment of acute intestinal injuries induced by IR.

To investigate the differences in gene expression and functional enrichment associated with anaplasia and laterality in retinoblastoma patients. Two datasets were selected from the GEO database of the National Center for Biotechnology Information of the US, including chip data of gene expression in tumor tissue from 36 patients with retinoblastoma. After grouping by anaplasia or laterality, the data were reanalyzed with Student's t-test in R and Bioconductor software. The functional enrichment of genes significantly related to anaplasia and laterality was explored via GSEA. The functions of synapse assembly and synaptic signaling were enhanced in clinical patients with severe anaplasia, while the function of photoreceptors was reduced; abnormal conjugate eye movement and lipid metabolic processes were upregulated in unilateral patients. Gene expression may be different in retinoblastoma patients with different anaplasias and lateralities. The consequential difference in gene functional pathways could be associated with clinical symptoms.

Cohesin and condensin, two related protein complexes, play essential roles in ensuring the accurate segregation of the genome into daughter cells during cell division. However, the interaction between cohesin and condensin in embryonic stem cells remains unclear, as does the specific function of the meiosis-specific cohesin complex. Cohesin maintains the cohesion of replicated sister chromatids until their separation at anaphase, whereas condensin facilitates the reorganization of chromosomes into a highly compact structure characteristic of mitosis. First, we found via ChIP-seq analysis that cohesins (SMC3, RAD21, and REC8) and condensin (SMC4) share DNA binding sites in close proximity and directly interact with the insulator protein CTCF. Second, siRNA-regulated SMC3 depletion led to nuclear accumulation of SMC4. Third, embryonic stem (ES) cells uniquely harbor cohesin complexes containing the meiotic kleisin subunit REC8. RAD21 knockdown increased the proportion of SMC3-REC8 complexes. Our findings indicate that cohesin and condensin make important contributions to the functions of the chromosomal organization, and that meiotic cohesin may be specifically required for the mitotic program in ES cells.

Cyclic GMP-AMP synthase (cGAS) is an intracellular sensor of double-stranded DNA that triggers a pro-inflammatory response upon binding. The interest in cGAS as a drug discovery target has increased substantially over the past decade due to growing evidence linking its activation to numerous peripheral and neurological diseases. Here, we report the binding mode of previously described cGAS inhibitors while also uncovering the structural basis for the interspecies potency shifts within this chemotype. A single threonine to isoleucine substitution between human and mouse cGAS drives compound activity, as demonstrated by biochemical, cellular, and in vivo studies. Finally, we utilize a structurally enabled design approach to engineer a novel chemical inhibitor with excellent potency for both human and mouse enzymes by targeting key interactions within the enzyme active site. Overall, this work provides the framework for rational optimization of cGAS inhibitors and potential preclinical translational strategies.

<h4>Background</h4>Hepatocellular carcinoma (HCC) is high heterogeneity and remains an unmet medical challenge, but their metabolic heterogeneity has not been fully uncovered and required clinical applicable translational strategies.<h4>Methods</h4>By analyzing the RNA sequencing data in the in-house cohort and public HCC cohorts, we identified a metabolic subtype of HCC associated with multi-omics features and prognosis. Multi-omics alterations and clinicopathological information between different subtypes were analyzed. Gene signature, radiomics, contrast-enhanced ultrasound (CEUS), serum biomarkers were tested as potential surrogate methods for high throughput technology-based subtyping. Single-cell RNA sequencing analyses were employed to evaluate the immune characteristics changes between subtypes.<h4>Results</h4>By utilizing metabolic-related pathways, we identified two heterogeneous metabolic HCC subtypes, glycan-HCC and lipid-HCC, with distinct multi-omics features and prognosis. Kaplan-Meier and restricted mean survival time analyses revealed worse overall survival in glycan-HCCs. And glycan-HCCs were characterized with high genomic instability, proliferation-related pathways activation and exhausted immune microenvironment. Furthermore, we developed gene signatures, radiomics, CEUS and serum biomarkers for subtypes determination, which showed substantial agreement with high-throughput-based classification. Single-cell RNA-seq showed glycan-HCCs were associated with multifaceted immune distortion, including exhaustion of T cells and enriched SPP1 + macrophages.<h4>Conclusion</h4>Collectively, our analysis demonstrated the metabolic heterogeneity of HCCs and enabled the development of clinical translation strategies, thus promoting understanding and clinical applications about HCC metabolism heterogeneity.

<h4>Background</h4>& Objective: Hyalinizing trabecular tumor of the thyroid (HTT) is a rare, low-risk neoplasm that poses diagnostic challenges. Very recently, PAX8::GLIS3 rearrangements were found to characterize HTT. We aimed to explore HTT's genetic profile, focusing on PAX8::GLIS3 rearrangements and GLIS3 immunohistochemical staining.<h4>Methods</h4>We conducted a retrospective study involving 8 cases histologically diagnosed as HTT. RNA sequencing and immunohistochemical staining for GLIS3 were performed on all cases.<h4>Results</h4>The study included five females and three males, with a tumor size ranging from 3 to 45 mm. RNA sequencing analysis showed PAX8::GLIS3 rearrangement in 6 cases (86 %). No other molecular alterations were found. However, one case failed due to the tissue quality, and one case did not show any gene fusion. Immunohistochemical staining for GLIS3 revealed nuclear positive expression in tumor cells for all cases where gene fusion was detected (100 %). A control group of 20 HTT mimickers showed no immunostaining for GLIS 3.<h4>Conclusion</h4>Our study confirms the consistent presence of PAX8::GLIS3 rearrangement in hyalinizing trabecular tumor (HTT) of the thyroid. Additionally, our novel finding of GLIS3 expression via immunohistochemistry enhances diagnostic precision for these tumors. Notably, our series demonstrates the correlation between positive GLIS3 expression and detection of PAX8::GLIS3 fusion by RNA sequencing, potentially expediting HTT diagnosis.

<h4>Purpose</h4>Initiated in 2010, the Genetics of Glucose regulation in Gestation and Growth (Gen3G) prospective cohort investigates the pathophysiology of impaired glycaemic regulation in pregnancy and evaluates its impact on both the mothers and her offspring health trajectory. Follow-up visits 3 and 5 years after delivery aimed to investigate pregnancy-related risk factors such as maternal obesity and gestational hyperglycaemia in relation to the mother's metabolic health after pregnancy, and with offspring health outcomes such as risk of obesity and neurodevelopmental problems in early childhood. We also investigated molecular mechanisms involved in the fetal programming of these later health outcomes.<h4>Participants</h4>Of the 1024 women originally recruited in the first trimester of pregnancy, we have targeted the 854 who had complete glucose tolerance test data and the 724 newborns who provided placenta and/or cord blood samples for follow-up recruitment. Of these, 695 mother-child dyads agreed to be contacted for the prospective follow-up visits. 448 and 521 mother-child dyads completed the research visits at 3 and 5 years after delivery respectively.<h4>Findings to date</h4>At both visits, we collected the mother's and child's medical history, lifestyle (using validated questionnaires), sociodemographic status, anthropometric measurements, mother's blood samples, child's saliva samples and growth charts. At the 5-year-old visit, we additionally collected the mother's and child's urine and stool samples and the child's blood samples; we performed a 75 g oral glucose tolerance test in the mothers and assessed the body composition in children using dual-energy X-ray absorptiometry. Using the Gen3G rich longitudinal data set, we have enhanced the understanding of the pathophysiology and characterisation of the heterogeneity of gestational diabetes mellitus, and we have shown that gestational hyperglycaemia and insulin resistance are associated with offspring epigenetics (DNA methylation) variations in the placenta, cord blood and blood at 5 years of age, as well as with offspring anthropometric, metabolic and neurodevelopmental outcomes in early childhood.<h4>Future plans</h4>We are currently conducting a prospective follow-up of mothers and their children 12 years after delivery to study how prenatal and early-life metabolic factors may programme childhood adiposity and obesogenic dietary behaviours. This follow-up should be completed by the end of 2026.

Anoikis resistance in hepatocellular carcinoma (HCC) cells boosts survival and metastasis. This study aimed to establish an anoikis-related genes (ARGs)-based model for predicting HCC patients' outcomes and investigate the clinicopathological significance and function of crucial ARGs. The transcriptional expression patterns for HCC cohorts were compiled from TCGA, GEO and ICGC. Univariate and LASSO multivariate analyses were performed to screen for prognostic ARGs. Gain- and loss-of-function studies, RNA sequencing, and mass spectrometry were employed to elucidate the underlying mechanisms of ARGs in HCC. We established a five-gene ARGs risk model for HCC prognosis, with an AUC value of 0.812 for 1-year survival. Among the five genes, Rac family small GTPase 3 (RAC3) was upregulated in HCC relative to adjacent normal tissues and negatively correlated to overall survival and disease-free survival of patients with HCC. Silence of RAC3 in HCC cells resulted in an increased cell apoptosis and diminished cell proliferation and invasion. Mechanistically, we uncovered that RAC3 binding with SOX6 propelled the advancement of HCC cells through NNMT-mediated stimulation of the cAMP/MAPK/Rap1 signaling. In particular, EHop-016, a small molecule inhibitor targeting RAC3, significantly suppressed HCC progression.

Colospheroids contain colon cancer stem cells (CSCs) that cause colorectal cancer metastasis (mCRC). Colorectal cancer (CRC) is the second leading cause of cancer-related deaths in the U.S. Little is known about the role of mitochondria in the survival and metastatic ability of CSCs. In this study, we investigate the effect of andrographolide (AGP) and melatonin (MLT) on mitochondrial dynamics (including fusion and fission) and the expression of mitochondrial ribosomal proteins (MRPs). Our results show that AGP and MLT synergistically reduce the total active mitochondrial mass, downregulate fusion and fission proteins, reduce OXPHOS proteins, and lead to CSC growth inhibition via Nrf2 and KEAP1 signaling. Microarray revealed 4389 differentially expressed mRNAs in the AGP and MLT combination compared to the control. Results exhibiting a three-fold induction/reduction were validated by qRT-PCR and immunoblot. MRPS6, a mitochondrial ribosomal (Mitoribosome) small subunit protein, was dramatically downregulated by AGP + MLT treatment compared to control. MRPS6 inhibition by siRNA reduced mCRC cell viability. Molecular docking-based protein-ligand interactions showed that AGP has direct physical interaction with MRPS6 and increases the binding affinity of MLT to MRPS6. This drug combination downregulated genes in the NRF2 (NFE2L2) pathway in CSCs. MRPS6 may be directly linked to CSC proliferation and could be a therapeutic target for this population. Functionally, MRPS6 knockdown significantly reduced colony formation, with enhanced suppression in AGP + MLT-treated cells. In xenograft models, the AGP-MLT combination synergistically decreased MRPS6 expression and increased apoptosis, as evidenced by TUNEL assays, demonstrating the therapeutic potential of targeting MRPS6 in CRC.

Peripheral neuropathy (PN) is a prevalent condition characterized by damage to peripheral nerves, often linked to risk factors such as diabetes. This condition results from various forms of neural damage, including injury to the cell body, axons, or demyelination, frequently beginning with small and thinly or unmyelinated fibers. Such nerve damage disrupts normal signaling, leading to symptoms like numbness, tingling, and pain. Effective nerve repair and regeneration, particularly through remyelination, are essential therapeutic objectives. While vitamin B12's role in repair processes has been well established, emerging evidence suggests that other neurotropic vitamins, specifically B1 and B6, also contribute significantly to nerve health and symptom relief in PN. In this study, we demonstrate that a combination treatment of vitamins B1, B6, and B12 enhances repair and oxidative stress responses in co-cultures of neural and Schwann cells, leading to improved cell maturation and connectivity compared to vitamin B12 alone. Furthermore, proteomic analysis supports these observations at the molecular level, with enhanced cellular recycling processes like proteasome enhancement, as well as protein synthesis upregulation, needed to rebuild nerve connections and combatting oxidative stress. Our combined morphological and molecular results highlight the potential therapeutic advantage of the B1, B6, and B12 combination over vitamin B12 alone.

Primary cardiac lymphoma (PCL) is a rare malignant disease and its presentation varies depending on the degree of infiltration and location in the myocardium; hence its diagnosis can be challenging. We present a case of a 67-year-old otherwise healthy male who initially presented with recurrent syncope found to have a pericardial effusion and complete heart block. Paratracheal biopsy of a fluorodeoxyglucose (FDG)-avid lymph node was consistent with diffuse large B-cell lymphoma. Diagnosis is usually identified histologically, but imaging is key in guiding biopsy and monitoring disease regression. Chemotherapy is the mainstay of treatment. In this case report, we present a unique presentation of primary cardiac lymphoma presenting as complete heart block with extra-cardiac lymph node involvement and review its management.

The molecular approach to understanding the mechanisms of emerging diseases, like COVID-19, has largely accelerated the search for successful therapeutical strategies. In this work, we present an extensive molecular dynamics (MD) analysis of two forms of the SARS-CoV-2 main protease M^Pro. We analyzed the free form (apo) and compared the results with those coming from the (holo) form bound to the inhibitor Boceprevir, an FDA-approved drug repurposed for COVID-19 therapy. We applied Dynamic Cross Correlation (DCC) analysis to the MD simulations to trace the concerted motion patterns within the protein structure. Although symmetric, the homodimer in the bound form showed clearly asymmetric dynamical behavior. In particular, the presence of concerted motions was detected in the protomer where the expulsion of the substrate from the active site happened. Such behavior was not observed in the same time lapses in the apo form. These results highlight a sort of 'symmetry breaking', making a symmetric structure to display functional induced asymmetric behavior in response to a perturbation. This highly coordinated dynamics in response to an external cue confirms the character of 'complex molecular machines' of biopolymers.

The B cell lymphoma 2 (BCL2) protein family critically controls apoptosis by regulating the release of cytochrome c from mitochondria. In this cutting-edge review, we summarize the basic biology regulating the BCL2 family including canonical and non-canonical functions, and highlight milestones from basic research to clinical applications in cancer and other pathophysiological conditions. We review laboratory and clinical development of BH3-mimetics as well as more recent approaches including proteolysis targeting chimeras (PROTACs), antibody-drug conjugates (ADCs) and tools targeting the BH4 domain of BCL2. The first BCL2-selective BH3-mimetic, venetoclax, showed remarkable efficacy with manageable toxicities and has transformed the treatment of several hematologic malignancies. Following its success, several chemically similar BCL2 inhibitors such as sonrotoclax and lisaftoclax are currently under clinical evaluation, alone and in combination. Genetic analysis highlights the importance of BCL-X_L and MCL1 across different cancer types and the possible utility of BH3-mimetics targeting these proteins. However, the development of BH3-mimetics targeting BCL-X_L or MCL1 has been more challenging, with on-target toxicities including thrombocytopenia for BCL-X_L and cardiac toxicities for MCL1 inhibitors precluding clinical development. Tumor-specific BCL-X_L or MCL1 inhibition may be achieved by novel targeting approaches using PROTACs or selective drug delivery strategies and would be transformational in many subtypes of malignancy. Taken together, we envision that the targeting of BCL2 proteins, while already a success story of translational research, may in the foreseeable future have broader clinical applicability and improve the treatment of multiple diseases.

No abstract available.

<h4>Introduction</h4>Longitudinal comparative characterisation of dementia syndromes may aid differential diagnosis, prognostication and intervention implementation.<h4>Methods</h4>We compared the behavioural and cognitive characteristics of 84 behavioural variant frontotemporal dementia (bvFTD), 29 left and 14 right-dominant semantic dementia (SDL and SDR) and 49 Alzheimer's disease (AD) patients over a follow-up period of 2.4 ± 1.6 years using the Cambridge Behavioural Inventory Revised (CBI-R) and Addenbrooke's Cognitive Examination third edition (ACE-III).<h4>Results</h4>Linear mixed modelling of time effects found progression of all CBI-R domains, aside from sleep, beliefs and mood domains, and all ACE-III domains. Modelling of group effects found that bvFTD had greater symptoms than AD in most CBI-R domains. Notably, SDL and SDR compared differently with AD and bvFTD; whilst SDR did not differ significantly from bvFTD in any CBI-R domain, SDL had less severe symptoms than bvFTD in everyday skills, motivation, sleep and eating habits; whilst SDL had greater disturbances in abnormal behaviour and stereotypic behaviour than AD, SDR had greater disturbances in addition in motivation and eating habits. Motivation, eating habits, abnormal behaviour and stereotypic behaviour were the most frequently different behavioural domains between groups.<h4>Conclusion</h4>We have shown that the combined, longitudinal use of existing behavioural and cognitive assessments could capture distinct clinical profiles of common and rare dementia syndromes. Our findings also highlight the importance of select behavioural domains such as motivation and the usefulness of separate clinical characterisations of SDL and SDR.

Bovine respiratory disease (BRD) poses a significant risk of morbidity and mortality in preweaned dairy calves. Research indicates that this multifactorial disorder can be attributed to the involvement of various pathogens. Currently, there is little information from genome-wide association studies (GWAS) for BRD resistance in young calves based on objective measures and classification of the disease. In this study, we moved forward in phenotyping BRD by coupling two diagnostic tests, the thoracic ultrasonography (TUS) and Wisconsin respiratory score (WISC), in order to assess susceptible and resistant animals to BRD. A total of 240 individuals were scored for BRD using TUS and WISC. A GWAS was performed using a selective genotyping approach to identify Quantitative Trait Loci (QTL) for BRD resistance. A total of 47 calves classified as BRD resistant (TUS ≤  1/ WISC ≤  4) and 47 as BRD susceptible (TUS =  5/ any WISC) were genotyped with the NEOGEN's GGP Bovine 100K SNP chip. QTL were then identified comparing the SNPs allelic frequencies between the two groups. A total of 28 QTL regions (QTLRs) were defined according to significative SNPs, 141 genes were annotated in the defined QTLRs. The genes were functionally classified into 4 main categories, i.e., i) regulation of systemic arterial blood pressure, ii) fertility, iii) immune function, and iv) filament cytoskeleton. Furthermore, 61 out of 141 genes identified here can be considered promising candidate genes since they were already associated with BRD resistance in published GWAS studies in dairy cattle. The ASB9, BMX, EPSTI1, and OLFM4 genes were identified in 4 of the 6 considered studies. This study paves the way for further research to mine the genome for resistance to respiratory diseases, utilizing an accurate classification process.

No abstract available.

Endochondral ossification generates most of the load-bearing bones, recapitulating it in human cells remains a challenge. Here, we report generation of SOX9⁺ sclerotomal progenitors (scl-progenitors), a mesenchymal precursor at the pre-condensation stage, from human pluripotent stem cells and development of osteochondral induction methods for these cells. Upon lineage-specific induction, SOX9⁺ scl-progenitors have not only generated articular cartilage but have also undergone spontaneous condensation, cartilaginous anlagen formation, chondrocyte hypertrophy, vascular invasion, and finally bone formation with stroma, thereby recapitulating key stages during endochondral ossification. Moreover, self-organized growth plate-like structures have also been induced using SOX9⁺ scl-progenitor-derived fusion constructs with chondro- and osteo-spheroids, exhibiting molecular and cellular similarities to the primary growth plates. Furthermore, we have identified ITGA9 as a specific surface marker for reporter-independent isolation of SOX9⁺ scl-progenitors and established a culture system to support their expansion. Our work highlights SOX9⁺ scl-progenitors as a promising tool for modeling human skeletal development and bone/cartilage bioengineering.

There are some drawbacks such as the propagation and spread of bacteria and viruses during the use of normal paper. Therefore, this work designed a starch styrene-acrylic antibacterial emulsion for improving the paper properties. The modified antimicrobial monomer was prepared by the subject-object recognition of β-cyclodextrin with hydrophobic modified titanium dioxide. The antibacterial performance of prepared emulsion was tested by Escherichia coli, Staphylococcus aureus. And the mechanical properties of the modified paper were measured according to the national standards. The results showed that the antibacterial emulsion has excellent comprehensive performance with the viscosity of 1750 mPa·s, the inhibition ring diameter of 11.82 mm, the good chemical stability and storage stability. Therefore, the proposed cationic starch styrene-acrylic antibacterial emulsion has promising applications in paper surface modification.

Thyroid hormones are produced by the thyroid gland and are essential for regulating metabolism, growth and development. Maintenance of circulating thyroid hormone levels within an appropriate range is thus a prerequisite for health. In vivo, this objective is, at least in part, facilitated through an extracellular storage depot of thyroglobulin, the glycoprotein precursor for thyroid hormones, in the thyroid follicular lumen. The molecular basis for how soluble thyroglobulin molecules form such dense depot assemblies remains elusive. Here, we describe in vitro biophysical analysis of thyroglobulin phase behaviour, suggesting that thyroglobulin is prone to undergoing ionic strength-dependent phase separation, leading to the formation of liquid-like condensates. Fluorescence photobleaching measurements further show that these condensates age as a function of time to form reversible gel-like high density storage depots of thyroglobulin. IF experiments on mouse and human thyroid follicles ex vivo reveal that spherical globules of Tg protein dense phase are present in the follicular lumen, consistent with the idea that Tg undergoes phase separation. These findings reveal a molecular mechanism for the last-come-first-served process of thyroglobulin storage and release, suggesting a role for extracellular phase separation in thyroid hormone homeostasis by providing organizational and architectural specificity without requiring membrane-mediated confinement.

<h4>Background</h4>Porcine reproductive and respiratory syndrome virus (PRRSV) can be transmitted across the maternal-fetal-interface from an infected gilt to her fetuses. Although fetal infection status and disease outcomes vary, the mechanisms are not completely understood. The objective was to assess targeted placental structural and transporter-related gene expression patterns. At day 85 of gestation pregnant pigs were challenged with PRRSV, and at 12 days post maternal infection sows and fetuses were sacrificed, and the placental tissue was collected. Grouping of fetuses was by preservation status and PRRS viral load (VL): control (CTRL, n = 14), viable and low VL fetus (VIA_LVF, n = 15), viable and high VL fetus (VIA_HVF, n = 21), meconium mild and low VL fetus (MECm_LVF, n = 14), meconium mild and high VL fetus (MECm_HVF, n = 14), and meconium severe and high VL fetus (MECs_HVF, n = 13). NanoString was used to evaluate the expression of 86 genes: actin cytoskeleton signaling, arachidonic acid pathway, integrin signaling, intercellular junctions, transporters, and VEGF signaling. Statistical analyses were performed using Limma with P ≤ 0.05 considered significant.<h4>Results</h4>We identified 1, 7, 0, 29, and 39 differentially expressed genes in VIA_LVF, VIA_HVF, MECm_LVF, MECm_HVF, and MECs_HVF, respectively, contrasted to CTRL. Placental transporter genes were significantly impacted (i.e., downregulation of SLC1A3, SLC1A5, SLC2A1, SLC2A3, SLC2A5, SLC2A10, SLC2A12, SLC7A4, SLC16A5, SLC16A10, and SLC27A6; and upregulation of SLC2A2, SLC16A3, and SLC27A4), compared to CTRL. Actin cytoskeleton signaling (ARHGEF6 and ARHGEF7), arachidonic acid (PTGES3 and PTGIS), integrin signaling (FN1 and ITGB6), intercellular junctions (CDH3 and CDH11), and VEGF signaling (MAPK3 and HPSE) gene groupings were significantly impacted, compared to CTRL.<h4>Conclusion</h4>Data reported here indicate that fetal PRRSV infection levels rather than fetal demise is necessary for transcriptional dysregulation of the fetal placenta, with a tendency towards more downregulation in the target gene sets among susceptible fetuses. These results generally support that in susceptible fetuses there is altered solute transportation, placental structural integrity, and reduced angiogenesis. The data described here is associated with fetal PRRS resistance/resilience and susceptibility.

<h4>Background</h4>The states of Schwann cells undergo significant shifts during nerve regeneration. Previous studies have shown the expression of Runx2 is locally upregulated within the affected areas. However, the regulatory mechanisms underlying its epigenetic control remain unclear.<h4>Methods</h4>To investigate the epigenetic mechanisms through which Runx2 influences the phenotypic transition of repair Schwann cells. Runx2 siRNA fragments and Runx2 overexpression plasmids were constructed. Healthy adult Sprague-Dawley (SD) rats weighted 100-150 g, regardless of sex, were randomly selected. Following the establishment of a sciatic nerve crush injury model, samples were collected for qPCR analysis at 4 and 7 days post-injury. In vitro, the alterations in cell morphology, proliferation, apoptosis, and the ability to promote neural regeneration following the downregulation or upregulation of Runx2 in Schwann cells were assessed. A comprehensive analysis of transcriptome data, ATAC sequencing, and CUT&Tag sequencing of histones and transcription factors in SCs after Runx2 overexpression, along with single-cell RNA sequencing data from GSE216665 and Sox2 overexpression data from RSC96 in GSE94590, was conducted to elucidate the mechanism of action of Runx2, which was subsequently validated using dual luciferase assays.<h4>Results</h4>Runx2 expression increased locally during the early stages of injury, primarily localized within Zhu Schwann cells (Zhu SCs). Runx2-overexpressing Schwann cells, when cultured in vitro, underwent a transformation from long, spindle-shaped He Schwann cells (He SCs) to flat, rounded Zhu SCs. Multi-omics analysis indicated that Runx2-OE may positively feedback-regulate its expression by opening transcriptional regulatory regions and binding to its own gene regulatory domains. Furthermore, it could also activate transcription factors such as Sox2, transitioning them from a transcriptionally silent to an active state, thereby enhancing Sox2 expression and synergistically regulating the phenotypic transition of Schwann cells.<h4>Conclusions</h4>Runx2 can activate and recruit downstream stemness factors, such as Sox2, by modulating chromatin accessibility and histone modification status within Schwann cells, thereby promoting and maintaining the timely phenotypic transformation of Schwann cells following injury.

Immunotherapy, particularly immune checkpoint inhibitor therapy, has demonstrated clinical benefits in solid tumours. Despite its satisfactory clinical efficacy, it still faces several issues, such as limited eligibility, low response rates and cytotoxicity. Cancer epigenetics implies that tumour cells exhibit unique phenotypes because of their unique characteristics, thus reprogramming of the epigenome holds promise for cancer therapy. Epigenetic regulation plays an important role in regulating gene expression during tumour development and maintenance. Epigenetic regulators induce cancer cell cycle arrest, apoptosis and differentiation of cancer cells, thereby exerting anti-tumour effects. Recent studies have revealed a significant correlation between epigenetic regulatory factors and immune checkpoint therapy. Epigenetics can modulate various aspects of the tumour immune microenvironment and immune response to enhance the sensitivity of immunotherapy, such as lowering the concentration required and mitigating cytotoxicity. This review primarily discusses DNA methyltransferase inhibitors, histone deacetylase inhibitors, enhancer of zeste homolog 2 inhibitors and lysine-specific demethylase 1 inhibitors, which are associated with transcriptional repression. This repression alters the expression of genes involved in the immune checkpoint, thereby enhancing the effectiveness of immunotherapy. We also discuss the potential and challenges of tumour immunotherapy and highlight its advantages, application challenges and clinical research on integrating epigenetic regulatory factors with tumour immunotherapy.

Non-energetic roles for glucose are largely unclear, as is the interplay between transcription factors (TFs) and ubiquitous biomolecules. Metabolomic analyses uncovered elevation of intracellular glucose during differentiation of diverse cell types. Human and mouse tissue engineered with glucose sensors detected a glucose gradient that peaked in the outermost differentiated layers of the epidermis. Free glucose accumulation was essential for epidermal differentiation and required the SGLT1 glucose transporter. Glucose affinity chromatography uncovered glucose binding to diverse regulatory proteins, including the IRF6 TF. Direct glucose binding enabled IRF6 dimerization, DNA binding, genomic localization, and induction of IRF6 target genes, including essential pro-differentiation TFs GRHL1, GRHL3, HOPX, and PRDM1. These data identify a role for glucose as a gradient morphogen that modulates protein multimerization in cellular differentiation.

Glioblastomas are the most prevalent primary brain tumors and are associated with a dramatically poor prognosis. Despite an intensive treatment approach, including maximal surgical tumor removal followed by radio- and chemotherapy, the median survival for glioblastoma patients has remained around 18 months for decades. Glioblastoma is distinguished by its highly complex mechanisms of immune evasion and pronounced heterogeneity. This variability is apparent both within the tumor itself, which can exhibit multiple phenotypes simultaneously, and in its surrounding microenvironment. Another key feature of glioblastoma is its "cold" microenvironment, characterized by robust immunosuppression. Recent advances in single-cell RNA sequencing have uncovered new promising insights, revealing previously unrecognized aspects of this tumor. In this review, we consolidate current knowledge on glioblastoma cells and its microenvironment, with an emphasis on their biological properties and unique patterns of molecular communication through signaling pathways. The evidence underscores the critical need for personalized poly-immunotherapy and other approaches to overcome the plasticity of glioblastoma stem cells. Analyzing the tumor microenvironment of individual patients using single-cell transcriptomics and implementing a customized immunotherapeutic strategy could potentially improve survival outcomes for those facing this formidable disease.

Ferroptosis, a non-apoptotic, iron-dependent form of regulated cell death, is closely related to the pathogenesis of neurodegenerative diseases. Stem cells and their derivatives exhibit remarkable potential in modulating ferroptosis, offering promising therapeutic intervention for neurodegenerative diseases. In this review, we systematically explore neurological aging and its association with cognitive impairment and neurodegenerative diseases, with focus on the molecular mechanisms of ferroptosis in neurodegenerative diseases and the potential therapeutic strategies of stem cell derivatives for neurological diseases.

Prechamber jet ignition, as an efficient ignition technology, can enhance ignition stability and enable rapid combustion. The mixture formation and flow dynamics inside the prechamber are very important for the jet ignition process and engine performance. Active prechamber is an effective method to achieve turbulent jet ignition, but at present there is currently limited understanding of the impact of auxiliary fuel injection (AFI) in an active prechamber. In this study, it is suggested to use auxiliary hydrogen injection to improve the mixture in the prechamber, thereby improving the ignition performance of the prechamber jet. The influences of AFI on the combustion process and engine performance are studied by numerical simulation. Under different AFI strategies, the in-cylinder flow, ignition, and combustion processes are simulated. The effect of different AFI schemes on prechamber combustion, jet characteristics, combustion process in the main chamber, active radicals, and engine performance are compared. The results show that operating the natural gas engine under lean burn conditions increases the indicated thermal efficiency and lowers NO _<i>x</i> emissions. The introduction of an auxiliary hydrogen injection shortens the time interval between the spark ignition timing and the injection timing of the hot jet, thereby advancing the ignition timing for lean combustion in the main chamber. As the amount of hydrogen injected rises, the injection velocity and temperature of the prechamber jet increase, so the jet ignition performance is strengthened. Moreover, the auxiliary hydrogen that flows into the main chamber increases the chemical activity of the lean mixture present there. The combination of the prechamber jet ignition with auxiliary hydrogen injection significantly improves the ignition performance and accelerates the lean burn rate in the main chamber, showing the potential to expand the lean burn limit of natural gas engines.

Drug-induced liver injury (DILI) results from the liver toxicity caused by drugs or their metabolites. Gallic acid (GA) is a naturally occurring secondary metabolite found in many fruits, plants, and nuts. Recently, GA has drawn increasing attention due to its potent pharmacological properties, particularly its anti-inflammatory and antioxidant capabilities. To the best of our knowledge, this is the first review to focus on the pharmacological properties of GA and related molecular activation mechanisms regarding protection against hepatotoxicity. We also provide a thorough explanation of the physicochemical properties, fruit sources, toxicity, and pharmacokinetics of GA after reviewing a substantial number of studies. Pharmacokinetic studies have shown that GA is quickly absorbed and eliminated when taken orally, which restricts its use in development. However, the bioavailability of GA can be increased by optimizing its structure or changing its form of administration. Notably, according to toxicology studies conducted on a range of animals and clinical trials, GA rarely exhibits toxicity or side effects. The antioxidation mechanisms mainly involved Nrf2, while anti-inflammatory mechanisms involved MAPKs and NF-κB signaling pathways. Owing to its marked pharmacological properties, GA is a prospective candidate for the management of diverse xenobiotic-induced hepatotoxicity. We also discuss the applications of cutting-edge technologies (nano-delivery systems, network pharmacology, and liver organoids) in DILI. In addition to guiding future research and development of GA as a medicine, this study offers a theoretical foundation for its clinical application.

Autoimmune-induced alopecia, such as alopecia areata, involves immune-mediated damage to hair follicles, leading to significant hair loss. Emerging therapies that stabilize hypoxia-inducible factor 1-alpha (HIF-1α) show promise in counteracting follicular degradation and supporting hair regrowth. This communication highlights the potential of iron chelators, specifically deferoxamine (DFO) and deferiprone (DFP), to stabilize HIF-1α by reducing iron availability, thereby promoting vascularization, cellular proliferation, and a regenerative environment in the hair follicle niche. Clinical trials with iron chelators demonstrated improvements in hair density, thickness, and elasticity, as well as a reduction in hair loss by up to 66.8% over six months. These findings underscore the therapeutic potential of iron chelators in autoimmune alopecia management. Future research should explore the synergistic use of iron chelators with immune-modulating therapies, positioning them as viable options in the evolving field of alopecia treatment.

<b>Rationale:</b> X-ray computed tomography (CT) is crucial in precision medicine for diagnostic and therapeutic guidance. However, current small molecule CT contrast agents pose risks such as nephrotoxicity, short blood circulation time, limited scan durations, potential thyroid impact, and immune responses. These challenges necessitate the development of kidney-safe nanoparticle (NP)-based contrast agents (CAs). <b>Methods:</b> We developed safe intravenous blood pool NP-based CT CAs at a clinical-equivalent dose of 300 mgI/kg, suitable for vascular and hepatic imaging. Our iodinated lipid nanoemulsions (ILNEs) were optimized for shelf-life stability, osmolarity, and viscosity for excellent injectability. The ILNEs were designed to offer high contrast and were tested for minimal protein interaction, prolonged blood circulation, and hepatic clearance. <i>In vitro</i> studies, along with tests in mice and porcine models, were conducted to confirm safety, cytocompatibility, and absence of tissue damage. <b>Results:</b> The ILNEs demonstrated high x-ray attenuation, improved contrast enhancement, extended stability, and batch-to-batch consistency. They exhibited minimal protein interaction, prolonged blood residency of about 4 h, and hepatic clearance within three days, avoiding nephrotoxicity. Blood and thyroid-stimulating hormone (TSH) analyses, along with kidney and liver function tests, confirmed the safety of ILNEs. <b>Conclusion:</b> Our ILNEs offer a promising alternative to current CT contrast agents, with improved safety and efficacy profiles. The results support further toxicity evaluations for clinical translation, highlighting the potential of ILNEs in vascular and hepatic imaging without the associated risks of nephrotoxicity.

The combination of oncolytic viruses (OVs) with other immunotherapies, such as immunostimulatory therapies, is a current research hotspot; however, optimizing their therapeutic potential remains to be fully explored. Here, we designed a novel oncolytic herpes simplex virus 2 expressing Fms-like tyrosine kinase 3 ligand (OH2-FLT3L), which induces an antitumor cytotoxic T cell immune response by activating dendritic cells (DCs). We found that OH2-FLT3L specifically infects tumor cells, induces immunogenic cell death (ICD), and releases a large number of tumor-specific antigens, which bound to danger signals and facilitated antigenic cross-presentation by DCs, significantly enhancing T cell activation and function. Experimental results showed that OH2-FLT3L significantly increased the proportion of activated DCs, enhanced the antitumor immune response, and effectively converted "cold" tumors into "hot" tumors. In addition, when combined with anti-PD-1 antibody, OH2-FLT3L further enhanced therapeutic efficacy. In conclusion, OH2-FLT3L, as a novel oncolytic virus, demonstrates the potential to enhance antitumor immune responses through DC activation.

The protease-antiprotease balance is involved in many biological processes, including blood coagulation, tissue remodeling, inflammation and immune responses. The aim of this study is to determine the balance between SERPINs and some related proteases in the lungs of stable COPD patients. In this cross-sectional study, the expression and localization of human SERPINs (anti-proteases) and some related proteases were measured in the lung parenchyma of mild-moderate COPD (MCOPD, n = 13) patients, control smokers (CS, n = 14) and control nonsmokers (CNS, n = 12) using transcriptome analysis, immunohistochemistry, and ELISA tests. Peripheral lung transcriptomic data showed increased mRNA levels of tissue plasminogen activator (tPA), cathepsin-L and caspase-1 as well as increased SERPINs A6, B3, B5, B11, B13 in the COPD group compared to the CNS group. At the protein level, IHC analysis showed that tPA and cathepsin-L increased in the bronchiolar epithelium and alveolar septa of the CS and COPD groups compared to the CNS group, as well as SERPINB5 and B13 in the alveolar macrophages and alveolar septa of the CS and COPD groups compared to the CNS group. SERPINA6 was shown to be decreased in the bronchiolar epithelium, bronchiolar lamina propria, and alveolar septa of the CS and COPD groups compared to the CNS group and was positively correlated with lung function. SERPINB3 was decreased in the alveolar septa of the CS group compared to the CNS group. The ELISA tests showed that in the total lung extracts, decreased levels of SERPINA6 and increased caspase-1 were shown in the COPD group compared to the CNS or both control groups, respectively. These data show an imbalance, at the protein level, of SERPINs and some related proteases in the lungs of the CS and stable COPD groups. These alterations may play a role in damaging the lung parenchyma of susceptible COPD patients.

<h4>Background and aims</h4>Inherited metabolic liver diseases (IMLDs) have complex etiologies and vary widely in clinical presentation, with a significant overall incidence. With the advancements in diagnostic and treatment technologies, an increasing number of children with inherited metabolic diseases are surviving into adolescence and adulthood. These advancements have improved our understanding of the IMLD disease spectrum and clinical outcomes. This study aimed to analyze changes in the disease spectrum and epidemiological characteristics of inherited metabolic liver diseases (IMLD) over the past 20 years in two specialized liver disease hospitals in northern China.<h4>Methods</h4>A retrospective analysis was conducted on IMLD cases diagnosed between January 1, 2002, and December 31, 2023, at two liver disease specialty hospitals in Beijing. Data were obtained from inpatient and outpatient hospital information systems, with diagnoses based on national and international IMLD diagnosis and treatment guidelines.<h4>Results</h4>A total of 2,103 IMLD patients were analyzed, including 1,213 adults and 890 children. IMLD accounted for 4.58‰ of hospitalized liver disease patients during this period. The most common IMLD was Wilson's disease, comprising 68% of all IMLD cases. The number of diagnosed IMLD types increased from 15 to 32 across two 11-year periods (2002-2012 and 2013-2023). Among pediatric patients, glycogen storage disease and Alagille syndrome were more prevalent in those under one year of age, while Wilson's disease was prevalent across all age groups. In adult IMLD patients, Wilson's disease, polycystic liver disease, and hereditary hyperbilirubinemia were more frequently observed.<h4>Conclusions</h4>Over the past 20 years, both the number of diagnosed IMLD cases and disease diversity have significantly increased, with Wilson's disease remaining the most prevalent IMLD. These findings provide valuable insights for the long-term management of IMLD patients and the allocation of healthcare resources.

Myocardial ischemia/reperfusion (I/R) usually triggers a series of molecular and cellular changes, which yield excessive oxidative stress and massive cardiomyocyte death, leading to sterile inflammation, cardiac fibrosis, and, eventually, heart failure. Over the past two decades, numerous studies have demonstrated that noncoding RNAs (ncRNAs), including microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs), involve almost every aspect of adverse cardiac remodeling induced by I/R. They have emerged as key regulators in the process of cardiac cell death (i.e. apoptosis, necroptosis, ferroptosis, pyroptosis, and PANoptosis), fibrosis, angiogenesis, and immune responses during myocardial I/R. Herein, this review summarizes recent advancements on ncRNA-mediated regulation of cardiac cell death, cardiac angiogenesis, fibrosis, and macrophage function as well as intercellular communication following myocardial I/R. Finally, the therapeutic potential of ncRNAs for treating myocardial I/R injury and future research directions are also discussed.

<h4>Background</h4>Chronic prostatitis (CP)/chronic pelvic pain syndrome is the most common urological disorder in young and middle-aged men. A previous study showed that melatonin attenuates prostate inflammation through Sirt1-dependent suppression of the nonobese diabetic-like receptor thermal protein domain-associated protein 3 inflammasome in mouse models of experimental autoimmune prostatitis (EAP). However, the main differentially expressed proteins (DEPs) in melatonin-treated mice with EAP have not yet been fully identified.<h4>Materials and methods</h4>Mouse models of EAP were established. The pathological morphology of the prostate tissues was observed using hematoxylin-eosin staining. Chronic pelvic pain sensitivity was assessed using suprapubic allodynia. Inflammation-related cytokines were detected using an enzyme-linked immunosorbent assay. These methods were used to validate the successful establishment of the EAP mouse model. Tandem mass tag proteomics was used to identify the proteomic markers in melatonin-treated EAP mice. Next, we visualized the DEPs using bioinformatic analyses. Finally, we measured the expression of mitochondrial creatine kinase 1 and gap junction β-1, which were identified by the tandem mass tag in all groups, using Western blotting to explore the key proteins involved in the anti-inflammatory effects of melatonin on EAP.<h4>Results</h4>We identified 5910 proteins, with quantitative information available for over 85% of the total. We found 53 DEPs in mice between the EAP and control groups and 22 DEPs between the EAP-Melatonin and EAP groups. Bioinformatic analysis suggested significant alterations in immunosuppression, inflammatory chemotaxis, and energy metabolism signaling in EAP mice treated with melatonin. These alterations were confirmed using Western blotting.<h4>Conclusions</h4>Melatonin effectively relieves CP/chronic pelvic pain syndrome-related symptoms in mice with EAP. Mitochondrial kinases are potential key proteins in the treatment of EAP with melatonin, and these biomarkers may provide direction for studying the molecular mechanisms of melatonin in the treatment of CP.

Sepsis-induced acute lung injury (ALI) involves severe lung dysfunction and leads to high morbidity and mortality rates due to the lack of effective treatments. The somatic nuclear autoantigenic sperm protein (sNASP)/tumor necrosis factor receptor-associated factor 6 (TRAF6) axis plays a crucial role in regulating inflammatory responses during sepsis through Toll-like receptor 4 (TLR4) signaling. However, it is unclear whether deubiquitinating enzymes affect the TRAF6/sNASP axis. In this study, we showed that cylindromatosis (CYLD) directly binds to the sNASP and prevents TRAF6 activation. When TLR4 is activated, phosphorylation of sNASP releases CYLD from the TRAF6/sNASP complex, leading to TRAF6 autoubiquitination and the production of proinflammatory cytokines. To stop TRAF6 activation, a complex of sNASP, TRAF6, and CYLD is reformed once dephosphorylation of sNASP occurs by protein phosphatase 4 (PP4). Silencing sNASP negated the inhibitory effects of CYLD on interleukin (IL)-6 and TNF-α production after lipopolysaccharide (LPS) treatment. Similarly, the absence of CYLD also reduced PP4's negatively regulated production of proinflammatory cytokines, indicating that phosphorylation is crucial for the interaction between sNASP and CYLD as well as TRAF6 activation. Finally, mice infected with a recombinant adenovirus carrying the CYLD gene (Ad-CYLD WT), but not a mutation, showed significant reductions in cecal ligation and puncture (CLP)-mediated lung injury and proinflammatory cytokine production. In conclusion, CYLD alleviated sepsis-induced inflammation by interacting with the TRAF6/sNASP axis. These findings suggest that CYLD could be a potential therapeutic target for treating sepsis-induced ALI.

Deep vein thrombosis (DVT) and pulmonary embolism are vascular occlusive disorders categorized under the term venous thromboembolism. Venous thromboembolism affects ≈900 000 people per year in the United States alone. Understanding of the multifaceted process of DVT has improved in recent years, and current DVT treatments reduce thrombus propagation, but they also increase bleeding risk and fail to accelerate natural venous thrombus resolution. Multiple inflammatory cytokines regulate the development and subsequent resolution of DVT. One family of cytokines involved in DVT and venous thrombus resolution is the TGF-β (transforming growth factor-β) family. A comprehensive understanding of the control of venous thrombus formation and resolution by the TGF-β family could lead to the development of novel treatments for DVT that target ≥1 of the TGF-β isoforms. The aim of this review is to describe studies of the roles of the TGF-β isoforms in venous thrombus formation and resolution and to highlight opportunities for future research. TGF-β isoforms include TGF-β1, TGF-β2, and TGF-β3. TGF-β1 has a well-characterized role in the positive regulation of venous thrombus formation and the negative regulation of venous thrombus resolution. Further research is necessary, however, to understand the potential roles of TGF-β2 and TGF-β3 in venous thrombus formation and resolution. Given that TGF-β1 expression increases during venous thrombosis and that inhibition or knockdown of TGF-β1 reduces thrombus burden, TGF-β1 represents a potential diagnostic marker for DVT and a putative target for therapies that aim to prevent or treat DVT.

In holothurians, the regenerative process following evisceration involves the development of a 'rudiment' or 'anlage' at the injured end of the mesentery. This regenerating anlage plays a pivotal role in the formation of a new intestine. Despite its significance, our understanding of the molecular characteristics inherent to the constituent cells of this structure has remained limited. To address this gap, we employed state-of-the-art scRNA-seq and hybridization chain reaction fluorescent in situ hybridization analyses to discern the distinct cellular populations associated with the regeneration anlage. Through this approach, we successfully identified 13 distinct cell clusters. Among these, two clusters exhibit characteristics consistent with putative mesenchymal cells, while another four show features akin to coelomocyte cell populations. The remaining seven cell clusters collectively form a large group encompassing the coelomic epithelium of the regenerating anlage and mesentery. Within this large group of clusters, we recognized previously documented cell populations such as muscle precursors, neuroepithelial cells, and actively proliferating cells. Strikingly, our analysis provides data for identifying at least four other cellular populations that we define as the precursor cells of the growing anlage. Consequently, our findings strengthen the hypothesis that the coelomic epithelium of the anlage is a pluripotent tissue that gives rise to diverse cell types of the regenerating intestinal organ. Moreover, our results provide the initial view into the transcriptomic analysis of cell populations responsible for the amazing regenerative capabilities of echinoderms.

Sleep is crucial for cognitive functions and life span across species. While sleep homeostasis and cognitive processes are linked through cellular and synaptic plasticity, the signaling pathways connecting them remain unclear. Here, we show that Drosophila insomniac (inc) short sleep mutants, which lack an adaptor protein for the autism-associated Cullin-3 ubiquitin ligase, exhibited enhanced Pavlovian aversive olfactory learning and memory, unlike other sleep mutants with normal or reduced memory. Through a genetic modifier screen, we found that a mild reduction of Protein Kinase A (PKA) signaling specifically rescued the sleep and longevity phenotypes of inc mutants. However, this reduction further increased their excessive memory and mushroom body overgrowth. Since inc mutants displayed higher PKA signaling, we propose that inc loss-of-function suppresses sleep via increased PKA activity, which also constrains the excessive memory of inc mutants. Our data identify a signaling cascade for balancing sleep and memory functions, and provide a plausible explanation for the sleep phenotypes of inc mutants, suggesting that memory hyperfunction can provoke sleep deficits.

Mental disorders are a representative type of brain disorder, including anxiety, major depressive depression (MDD), and autism spectrum disorder (ASD), that are caused by multiple etiologies, including genetic heterogeneity, epigenetic dysregulation, and aberrant morphological and biochemical conditions. Psychedelic drugs such as psilocybin and lysergic acid diethylamide (LSD) have been renewed as fascinating treatment options and have gradually demonstrated potential therapeutic effects in mental disorders. However, the multifaceted conditions of psychiatric disorders resulting from individuality, complex genetic interplay, and intricate neural circuits impact the systemic pharmacology of psychedelics, which disturbs the integration of mechanisms that may result in dissimilar medicinal efficiency. The precise prescription of psychedelic drugs remains unclear, and advanced approaches are needed to optimize drug development. Here, recent studies demonstrating the diverse pharmacological effects of psychedelics in mental disorders are reviewed, and emerging perspectives on structural function, the microbiota-gut-brain axis, and the transcriptome are discussed. Moreover, the applicability of deep learning is highlighted for the development of drugs on the basis of big data. These approaches may provide insight into pharmacological mechanisms and interindividual factors to enhance drug discovery and development for advanced precision medicine.

The γ-aminobutyric acid type A receptors (GABA_ARs) are ligand-gated anion channels that mediate fast inhibitory neurotransmission in the mammalian central nervous system. GABA_ARs form heteropentameric assemblies comprising two α1, two β2, and one γ2 subunits as the most common subtype in mammalian brains. Proteostasis regulation of GABA_ARs involves subunit folding within the endoplasmic reticulum, assembling into heteropentamers, receptor trafficking to the cell surface, and degradation of terminally misfolded subunits. As GABA_ARs are surface proteins, their trafficking to the plasma membrane is critical for proper receptor function. Thus, variants in the genes encoding GABA_ARs that disrupt proteostasis result in various neurodevelopmental disorders, ranging from intellectual disability to idiopathic generalized epilepsy. This review summarizes recent progress about how the proteostasis network regulates protein folding, assembly, degradation, trafficking, and synaptic clustering of GABA_ARs. Additionally, emerging pharmacological approaches that restore proteostasis of pathogenic GABA_AR variants are presented, providing a promising strategy to treat related neurological diseases.

The influence of coagulation on glioma biology has not been comprehensively elucidated. This study explores the role of coagulation-related genes (CRGs) in glioblastoma (GBM) from the perspectives of the tumor microenvironment (TME), differences in coagulation function among GBM patients, treatment, and prognosis. Somatic mutation analysis was performed on single nucleotide polymorphism (SNP) and copy number variation data from GBM patients in the TCGA cohort. Publicly available single-cell RNA sequencing data were used to analyze the role of coagulation in the GBM TME and its underlying biological mechanisms. Unsupervised clustering of GBM patients from the CGGA693 cohort was conducted, and coagulation function for each patient was assessed using ssGSEA scoring. Prognosis was assessed with Kaplan-Meier survival analysis, and immune infiltration was analyzed through ESTIMATE. A risk signature based on five CRGs (CFI, GNG12, MMP2, LEFTY2, and SERPINC1) was constructed and validated using LASSO regression and random survival forest analyses to predict responses to immunotherapy and identify potential sensitive drugs. Finally, the roles of LEFTY2 and SERPINC1 in GBM progression was verified by immunohistochemistry, cell counting kit-8 (CCK8) assay and wound healing assay, and the anti-GBM effect of the drug PLX4720 was verified by CCK8 assay, wound healing assay, and colony formation assay. Somatic mutation analysis revealed SNP events of CRG mutations in 117 out of 461 GBM cases (25.38%). Single-cell analysis of the GBM TME revealed significant activation of the coagulation pathway in endothelial cells, with intercellular communication mediated via the SPP1-integrin pathway (p < 0.01). Clustering analysis and ssGSEA identified two coagulation-related subtypes in GBM: coagulation-activated and coagulation-inhibited subtypes. Patients in the coagulation-activated subtype exhibited shorter overall survival and poorer prognosis compared to those in the coagulation-inhibited subtype (p = 0.0085). Immune infiltration analysis showed lower tumor purity and higher levels of immune-suppressive cells in the coagulation-activated subtype (p < 0.001). The CRG-based risk signature accurately predicted prognosis (p < 0.0001) and responses to immunotherapy in the IMvigor210 cohort (p = 0.0062). Based on the risk model, PLX4720 was identified as a potential sensitive drug (p < 0.001), and drug validation experiments demonstrated that PLX4720 inhibited the proliferation and migration of glioma cells (p < 0.0001). In vitro experiments demonstrated that LEFTY2 and SERPINC1 were significantly overexpressed in GBM compared to normal brain tissue, and knockdown of LEFTY2 and SERPINC1 inhibited glioma cell proliferation and migration (p < 0.05). The CRG-based risk signature model effectively predicts the prognosis of GBM patients and aids in assessing the efficacy of ICI therapy and chemotherapy. Furthermore, the genes LEFTY2, SERPINC1 and the drug PLX4720 offer potential directions for the development of novel therapeutic strategies for GBM.

Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cellular variability by capturing gene expression profiles of individual cells. The importance of cell-to-cell variability in determining and shaping cell function has been widely appreciated. Nevertheless, differential expression (DE) analysis remains a cornerstone method in analytical practice. Current computational analyses overlook the rich information encoded by variability within the single-cell gene expression data by focusing exclusively on mean expression. To offer a deeper understanding of cellular systems, there is a need for approaches to assess data variability rather than just the mean. Here we present spline-DV, a statistical framework for differential variability (DV) analysis using scRNA-seq data. The spline-DV method identifies genes exhibiting significantly increased or decreased expression variability among cells derived from two experimental conditions. Case studies show that DV genes identified using spline-DV are representative and functionally relevant to tested cellular conditions, including obesity, fibrosis, and cancer.

HIV-1 initiates replication by its transactivator Tat, hijacking the positive transcription elongation factor b (P-TEFb) in the host cell. Most P-TEFb is maintained in an inactive state by 7SK snRNP until it is brought to the transcription initiation complex by cellular or viral transactivators that accelerate transcription and facilitate the production of full-length viral transcripts. Here, we report that HIV-1 infection triggers liquid-liquid phase separation of LARP7, a central component of 7SK snRNP. Tat is incorporated into HIV-1-induced LARP7 condensates after infection. Conserved lysine residues in the intrinsically disordered region of LARP7 are essential for both its phase separation and the inhibition of Tat-mediated transcription. These findings identify a mechanism wherein P-TEFb and Tat are sequestered within LARP7 condensates, restraining HIV-1 transcription.

<h4>Background</h4>Taraxacum mongolicum is rich in phenolic acids and is widely utilized in food and medicine globally. Our previous research demonstrated that the abscisic acid (ABA) hormone significantly enhances chicoric acid accumulation in T. mongolicum. SNF1-related protein kinase 2s (SnRK2s) are extensively involved in ABA signaling and have the potential to regulate the biosynthesis of phenolic acids.<h4>Results</h4>In this study, liquid chromatography-mass spectrometry (LC-MS) and transcriptomic analyses revealed that the TmbZIP1-Tm4CL1 pathway plays a crucial role in the transcriptional regulation of chicoric acid biosynthesis. Seven TmSnRK2s were identified in T. mongolicum and classified into three groups. Analysis of the TmSnRK2s promoters (2000 bp in length) indicated that the three most prevalent stress-related elements were ABA, methyl jasmonate (MeJA), and light. ABA treatments (0 h, 2 h, 4 h, 8 h, and 24 h) showed that all seven TmSnRK2s were significantly modulated by ABA, with the exception of SnRK2.7. TmSnRK2.2, TmSnRK2.3, TmSnRK2.6, and TmSnRK2.7 were localized in both the cytoplasm and nucleus, whereas TmSnRK2.1 and TmSnRK2.5 were exclusively observed in the cytoplasm. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays indicated that TmSnRK2.1, TmSnRK2.3, TmSnRK2.6, and TmSnRK2.7 interact with TmbZIP1. The motifs 'Q(S/G)(V/D)(D/E)(I/L)××I(I/V)×EA' and 'D×(D/ED××D)' are identified as the core sites that facilitate the binding of TmSnRK2s to TmbZIP1. Dual-luciferase reporter assays demonstrated that TmSnRK2.3 and TmSnRK2.6 enhance the stability of TmbZIP1 binding to proTm4CL1.<h4>Conclusion</h4>These findings enhance our understanding of the specific roles of certain members of the TmSnRK2 family in the biosynthesis pathway of chicoric acid.

<h4>Background</h4>The human T-cell lymphotropic virus type 1 (HTLV-1) is a retrovirus that causes HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). HAM/TSP is a chronic inflammatory neurodegenerative disease characterized by leukocyte infiltration in the spinal cord. T-lymphocytes are the most important targets of HTLV-1 infection, but monocytes are also infected. Monocytes from HTLV-1-infected individuals exhibit important functional differences compared to cells from uninfected donors. Here, we investigated the effects of cell-cell physical contact and/or secreted factors of HTLV-1-infected cells in monocyte activation and differentiation.<h4>Methods</h4>The THP-1 human monocytic cell line was co-cultured with a human cell line transformed by HTLV-1 (MT-2) for 6 days. To determine the effects of co-culturing HTLV-1-infected cells in THP-1 monocytes cells were characterized by flow cytometry, immunofluorescence microscopy, and real-time PCR. Computational analysis of published transcriptomic datasets was realized to compare molecular profiles of macrophages and mononuclear cells from HTLV-1 carriers.<h4>Results</h4>Co-culture of monocytes with HTLV-1-infected cells induced macrophage differentiation and upregulation of typical macrophages-associated molecules (HLA-DR, CD80, and CD86), increased cytokine (TNFα, IL-6, and IL-1β) levels and their coding genes expression. Consistently, published transcriptomic datasets showed changes in important genes associated with inflammation during HAM/TSP in patients. The presence of HTLV-1-infected cells in the culture also induced significant upregulation of Interferon Stimulated Genes (ISG), indicating viral infection. Monocyte activation and differentiation into pro-inflammatory macrophages occurred in a cell-to-cell contact-independent manner, suggesting the role of factors secreted by infected cells.<h4>Conclusions</h4>Together, our results indicated that HTLV-1-infected cells induced monocyte differentiation into macrophages inflammatory, predominantly.