Molecular Medicine

Background Genome-wide association studies have identified >200 loci associated with IBD, yet the causal gene for most remains unknown. As multiple epithelial functions have been linked with susceptibility to IBD, there is a need to prioritize candidate causal genes for functional studies in this cellular context. Methods Using a standardized definition of regions implicated by index SNPs from three GWAS studies, we categorized regions as containing: (1) a known casual gene, (2) a single gene or (3) multiple genes. We then developed an IBD Priority Score to rank genes based on genetic, genomic and functional data. We next developed and applied an Epithelial Priority Score, based on expression patterns and quantitative traits, to prioritize genes for functional validation in epithelial models. Two candidate genes identified through this approach were tested for their impact on viral response pathways in HT-29 cells. Results The IBD Priority Score prioritized a single gene in 71 of the 104 regions containing multiple genes. The Epithelial Priority Score identified 31 epithelial candidates. Functional studies demonstrated that IRF6 enhanced, whereas IRF8 suppressed, antiviral responses in intestinal epithelial cells stimulated with Poly(I:C). Conclusions Combining multiple genetic, genomic, and functional data is a useful approach for prioritizing the most likely causal gene within IBD GWAS loci, and for prioritizing functional validation studies in epithelial cells and tissues. Moreover, we provide functional evidence for two IBD genes playing a role in the regulation of anti-viral responses in intestinal epithelial cells.

BackgroundKnee osteoarthritis (KOA) is a prevalent degenerative joint disease in which synovial inflammation and fibrosis are closely linked to pain, stiffness, and functional limitation. Growing evidence suggests that metabolic dysregulation, particularly in lipid metabolism, is involved in KOA pathogenesis, but the underlying mechanisms remain incompletely defined. MethodsSprague Dawley rats underwent bilateral anterior cruciate ligament transection to establish a KOA model; sham-operated rats served as controls. RNA sequencing of synovial tissues was performed to identify differentially expressed genes (DEGs) and enriched pathways, followed by GO/KEGG and GSEA analyses. In vivo, adeno-associated virus vectors were used to overexpress or knock down PPAR-{gamma} and phosphoenolpyruvate carboxykinase 1 (PCK1) via intra-articular injection. Ex vivo, primary rat fibroblast-like synoviocytes (FLSs) were stimulated with IL-1{beta} and transfected with PPAR-{gamma} or PCK1 siRNA/overexpression plasmids. synovitis and fibrosis were evaluated by HE, Masson, and Sirius Red staining, immunofluorescence, ELISA, RT-qPCR, and Western blotting. ResultsRNA-seq revealed 621 up-regulated and 228 down-regulated genes in KOA synovium versus sham, with DEGs significantly enriched in PPAR signaling, adipocytokine, and AMPK pathways. Metabolism-related genes including Fabp5, Plin1, Adipoq, Lep, and Pck1 were up-regulated. GSEA indicated downregulation of PPAR-{gamma} signaling in KOA synovium. In vivo and ex vivo, PPAR-{gamma} expression was reduced in KOA, whereas PCK1, FABP5, and ADIPOQ were increased. PPAR-{gamma} overexpression alleviated synovial inflammation, collagen I deposition, and fibrosis, and suppressed FABP5, ADIPOQ, and PCK1 expression; PPAR-{gamma} knockdown produced the opposite effects. Functional studies showed that PCK1 overexpression aggravated synovial inflammatory cell infiltration and fibrosis, elevated IL-1{beta}, IL-18, and TGF-{beta}, and decreased TIMP1 levels in serum, synovial tissue, and FLSs supernatants, whereas PCK1 silencing reversed these changes. ConclusionsThe PPAR-{gamma}/PCK1 metabolic axis modulates synovitis and fibrosis in KOA. Downregulation of PPAR-{gamma} and consequent upregulation of PCK1 promote synovitis and fibrotic remodeling. These findings identify the PPAR-{gamma}/PCK1 pathway as a potential therapeutic target for KOA.

Inflammatory bowel disease (IBD) often involves disrupted intestinal epithelial barrier, but therapies specifically targeting this barrier are limited. We found that downregulated AUF1 (HNRNPD) contributes to defective barrier integrity in ulcerative colitis (UC). Compared to controls, its expression level was decreased and inversely correlated with clinical severity. Knocking down AUF1 in human and mouse colonic organoids led to impaired barrier function, with reduced Occludin and upregulated Claudin-2, mimicking characteristic IBD-associated mucosal alterations. Distinct RNA-binding activity of AUF1 protein isoforms contributed to these changes: p37 stabilized Occludin mRNA and blocked microRNA-122/Ago2-mediated repression, whereas p40 promoted Claudin-2 mRNA degradation via ubiquitin-proteasome pathway. Restoring AUF1 expression in organoids enhanced epithelial properties and, when transplanted into mice with established colitis, accelerated mucosal healing and epithelial regeneration in recipient mice and decreased fibrosis. Our study unravelled a post-transcriptional mechanism important for intestinal homeostasis and demonstrated a concept of using engineered organoids for treating IBD.

Introduction: Genome-wide association studies have identified a common variant at chr19q13.33 within the FUT2 locus as a determinant of colorectal cancer (CRC) susceptibility, with each risk allele conferring an approximately 7% increase in risk (OR 1.07, P = 6.11E--10). This locus regulates expression of FUT2, a fucosyltransferase involved in 1,2- glycosylation, and has also been associated with circulating vitamin B12 (B12) concentrations in genome-widestudies. Objective: To determine whether FUT2 influences CRC-risk through effects on circulating B12 and to test causal relationships across genetic, experimental, and clinical data. Methods: We performed summary-data-based Mendelian randomisation using FUT2 eQTLs from GTEx colon tissue and genome-wide association data for plasma B12 (Generation Scotland), with mediation analysis estimating the proportion of effect mediated by B12. Causal inference was then tested in vivo using Fut2 knockout and wild-type mice exposed to azoxymethane/dextran sodium sulphate (AOM/DSS), with or without B12 supplementation. Results: Genetically predicted higher FUT2 expression was associated with lower B12 levels ( {beta} = -0.735, SE = 0.110, P = 2.63E-11) and reduced CRC-risk ({beta} = -0.256, SE = 0.058, P = 5.85 E -5). Mediation analysis suggested ~80% of the effect of FUT2 on CRC risk is mediated via B12. In mice, neither Fut2 deficiency nor B12 supplementation alone induced tumours, but both significantly increased tumour burden under chemical carcinogenic challenge, with comparable effect sizes.

Osteosarcoma (OS) is one of the top ranking and deadliest primary malignant bone tumor of youngsters and adolescents. OS has poor prognostic features due to its immunosuppressive "cold" tumor microenvironment, obstructing the anti-tumor effector functions of immune cells (including cytotoxic CD8 T lymphocytes). Recent developments have focused on the role of Gut Microbiota in modulating effector immune responses in various cancers. However, the immunomodulatory role of gut microbiota and its derived gut-associated metabolites (GAMs) in OS still remains unclear. Here we report that peripheral CD8 T lymphocytes in osteosarcoma patients are less frequent in circulation, hypo-producers of effector cytokines (IFN-{gamma} and TNF-), and have compromised metabolic fitness. We characterized and investigated the effect of a panel of microbiota-derived GAMs on CD8 T lymphocytes, confirming their immunomodulatory role with respect to CD8 T lymphocytes activation, cellular metabolism and effector functions. Indole-3-lactic acid (ILA; product of tryptophan metabolism), was observed to be the strongest immunostimulant among all the GAMs studied. ILA enhanced the anti-tumor effector functions of CD8 T lymphocytes through increased glucose uptake, a higher mitochondrial bio-mass and increased production of IFN-{gamma} and TNF-. Moreover, ILA-primed cytotoxic T lymphocytes exhibited considerably higher cytotoxicity and increased apoptosis of osteosarcoma cells (U2OS). Altogether, our data demonstrates that ILA acts as a microbial-derived immune modulator to metabolically reprogram and restore dysfunctional CD8 T lymphocytes against osteosarcoma. This study for the first time demonstrates the therapeutic potential of exploiting the nexus between "Gut-Immune-Bone Tumor" ternary as a safe and cost-effective combinatorial immunotherapy against osteosarcoma. Graphical AbstractIndole-3-Lactic Acid (ILA) Reinvigorates CD8+ T-Cell Immunity in Osteosarcoma Circulating CD8+ T cells from osteosarcoma patients exhibit impaired metabolic fitness, reduced effector cytokine production, and diminished tumoricidal activity. Screening of gut-associated metabolites identified the microbial tryptophan metabolite indole-3-lactic acid (ILA) as the most potent immunomodulator. ILA restores glucose uptake and mitochondrial biomass, enhances IFN-{gamma} and TNF- production, promotes polyfunctional CD8+ T-cell responses, and significantly improves CTL-mediated killing of osteosarcoma cells, highlighting its potential as a microbiota-derived immunometabolic therapeutic for osteosarcoma. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/741694v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@10416a4org.highwire.dtl.DTLVardef@16a99b8org.highwire.dtl.DTLVardef@19201cforg.highwire.dtl.DTLVardef@b4ca26_HPS_FORMAT_FIGEXP M_FIG C_FIG

Obesity is a global epidemic characterized by metabolic dysfunction, with white adipose tissue playing a pivotal role in these processes. Noncoding RNAs, such as long non-coding RNAs (lncRNAs) and short non-coding RNAs (e.g., microRNAs), have been identified as an emerging class of regulatory molecules that can influence metabolic function. Here, the Dleu2/miR-15a/16-1 cluster (known as 13q14-Minimal Deleted Region, i.e., MDR), which encodes the lncRNA Dleu2 and miR-15a/16-1, a previously unrecognized player in metabolic function, is shown to contribute to obesity and insulin resistance. Using a combination of phenotypic and molecular approaches, this study establishes that MDR governs metabolic regulation for the first time. In a nutshell, this study identifies a new role of a lncRNA-miRNA cluster, previously implicated exclusively in cancer, in the regulation of obesity, thereby extending its biological significance beyond oncology. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=184 SRC="FIGDIR/small/745519v1_ufig1.gif" ALT="Figure 1"> View larger version (68K): org.highwire.dtl.DTLVardef@424a1borg.highwire.dtl.DTLVardef@f6e3eorg.highwire.dtl.DTLVardef@10ebf0borg.highwire.dtl.DTLVardef@120803c_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIDeletion of MDR contributes to obesity, insulin resistance, and impaired energy metabolism C_LIO_LILoss of MDR reduces circulating adiponectin levels, indicating metabolic dysfunction C_LIO_LIMDR regulates satiety signaling in visceral adipose tissue and increases serum leptin levels C_LIO_LIMDR modulates several unrecognized new transcriptional regulators in obesity C_LIO_LIFirst evidence to establish the metabolic role of MDR beyond cancer biology C_LI

It is clear that the human retina and its underlying retinal pigment epithelium and choroid (RPE/choroid) form an interdependent metabolic ecosystem, but how metabolism differs between the cone-rich macula and rod-rich periphery remains unclear. Using targeted metabolomics, we quantified 133 metabolites in paired macular and peripheral neural retina and RPE/choroid explants from human donor eyes following short-term culture to restore metabolic activity. Distinct metabolic differences were identified between retinal regions and between tissues. Compared with the peripheral retina, the macula showed metabolic features consistent with greater glycolytic activity, increased NADH availability and higher levels of the neurotransmitter-associated metabolites N-acetyl-aspartate (NAA) and N-acetyl-aspartyl-glutamate (NAAG), consistent with increased energetic and neuronal activity. Compared with peripheral RPE/choroid, the macular RPE/choroid had higher levels of the flavin cofactor FAD together with NAD-related metabolites, including NAD, NADP and NAAD. Comparisons between the neural retina and RPE/choroid further showed that the neural retina was primarily associated with energy production and neurotransmission, whereas the RPE/choroid was associated with cofactor metabolism, nucleotide salvage and lipid metabolism. These findings are consistent with metabolic coupling between the neural retina and RPE/choroid. The macula has metabolic features consistent with high energetic demand, providing a potential metabolic basis for its selective vulnerability in macular disease.

Background Idiopathic Pulmonary Fibrosis (IPF) is a fatal chronic lung disease with limited therapeutic options. While alveolar epithelial injury and fibroblast activation are well-studied, endothelial-mesenchymal transition (EndoMT) is emerging as a critical pathogenic mechanism. The regulatory role of exosomal miRNAs in pulmonary fibrosis remains unclear. This study investigates serum exosomal miRNAs, particularly let-7a-5p, in modulating EndoMT during the onset of pulmonary fibrosis. Methods Clinical cohorts of IPF patients and healthy controls were enrolled. Serum exosomal miRNAs were profiled, followed by differential expression and functional enrichment analyses. In vitro experiments involved human pulmonary artery endothelial cells (HPAECs) transfected with let-7a-5p mimic or inhibitor. Dual-luciferase reporter assays confirmed the binding between let-7a-5p and TGFBR1. HPAECs were co-cultured with lung epithelial cells to examine paracrine signaling. In vivo studies used a bleomycin-induced mouse model with let-7a-5p agomir administration. Assessments included histopathological staining, hydroxyproline content, Western blot, qPCR, micro-CT, and pulmonary function tests. Results Let-7a-5p was significantly downregulated in serum exosomes from IPF patients, correlating with clinical indicators. Mechanistically, let-7a-5p directly bound the TGFBR1 3'UTR to inhibit its expression. Inhibition of let-7a-5p upregulated -SMA, FN1, smad2/3 phosphorylation, and collagen I, while downregulating CD31 and VE-cadherin. Therapeutically, let-7a-5p mimic reversed bleomycin-induced EndoMT and suppressed epithelial-mesenchymal transition (EMT) via paracrine signaling. Mice administered agomir showed reduced fibrosis, improved lung function, and suppressed TGF-{beta}/Smad signaling. Conclusion Serum exosomal let-7a-5p suppresses pulmonary fibrosis by targeting TGFBR1 to inhibit EndoMT. Its downregulation in IPF patients correlates with disease progression, highlighting its biomarker potential.

PurposeTo investigate whether rapamycin can regulate microglial activation and polarization via mTOR and its downstream signals via autophagy both in vivo and in vitro. MethodsThe in vivo study used wild type C57BL/6 mice that were intraperitoneally injected with rapamycin (2 mg/kg) plus ONC. The BV2 cell line was used in the in vitro study and the cells were incubated with rapamycin (50 nM) or transfected with a specific mTOR-targeting small interfering RNA (si-mTOR). Immunohistochemical staining was used to observe the changes in the morphology and cell surface area of microglia and Weste blotting analysis was used for detection of the changes in the proteins related autophagy, microglia polarization and mTOR pathway after the retinal tissue or the cell samples were collected. ResultsThese results indicate that rapamycin increases autophagy and M2 polarization by inhibiting p-mTOR in wild-type C57BL/6 mice in vivo. In the BV2 cell line, rapamycin and si-mTOR can enhance autophagy and promote M2 polarization by inhibiting the p-mTOR/p-Unc-51-like kinase 1 (p-ULK1) pathway. ConclusionsIn conclusion, this work contributes to the understanding of the complex interplay among rapamycin, autophagy and microglial activation/polarization, highlights the downstream signaling pathway of mTOR, and highlights the potential therapeutic effects of autophagy-modulating drugs in retinal neuroinflammation and neurodegeneration after TON.

Adult zebrafish efficiently regenerate skeletal muscle following different types of injury; however, the molecular programs involved in repair after extensive cryoinjury remain to be comprehensively characterized. Here, we explored the transcriptomic response of adult zebrafish skeletal muscle at 7 days post cryoinjury (dpci), a stage marked by ongoing tissue clearance, progenitor expansion, myogenic differentiation, and nascent myofiber formation, and compared it with phase-matched stab wound injury. Cryoinjury induced a broad transcriptional response, with 5,330 differentially expressed genes. Integrated enrichment and protein-protein interaction analyses revealed that, at 7 dpci, zebrafish skeletal muscle functions as an integrated regenerative system in which immune remodeling, progenitor expansion, myogenic differentiation, extracellular matrix reconstruction, mechanotransduction, biosynthetic adaptation, proteostasis, and intracellular trafficking operate simultaneously. In parallel, mature sarcomeric and oxidative metabolic programs were suppressed, consistent with ongoing tissue reconstruction and structural immaturity. Comparison with stab-wounded skeletal muscle revealed substantial transcriptional conservation, as 612 of 717 stab-wound-responsive genes (85%) were also differentially expressed after cryoinjury. Shared upregulated genes formed coherent functional modules related to proliferation, extracellular matrix organization and signaling, immune regulation, muscle differentiation, and protein processing. Thus, distinct injury modalities converge on a common regenerative program, while cryoinjury elicits a quantitatively broader transcriptional response. These findings support a conserved regenerative architecture of adult zebrafish skeletal muscle repair, in which interconnected biological modules act coordinately, with the breadth of transcriptional engagement reflecting regenerative demand.

Neural stem cell (NSC) transplantation is a promising strategy for repairing the injured spinal cord, but transplanted cells typically require immunosuppressive therapy to prevent rejection, even for induced pluripotent stem cell (iPSC)-derived autologous grafts. However, the effects of immunosuppressive drugs on neurite outgrowth and axonal regeneration, processes critical for neural circuit reconstruction, have not been fully characterized. In this study, we tested nine clinically relevant immunosuppressants on human iPSC-derived neurons and primary human spinal cord NSCs in vitro at concentrations approximating clinical exposure levels. The drug panel included FK-506 (tacrolimus), cyclosporine A (CsA), rapamycin, belatacept (Nulojix), etanercept (Enbrel), mycophenolate mofetil (CellCept), cyclophosphamide (Cytoxan), prednisone, and azathioprine (Imuran). Neurite outgrowth was quantified via automated high-content imaging. Multiple agents, including CsA, Imuran, Nulojix, and CellCept, induced significant reductions in neurite outgrowth in a cell type- and dose-dependent manner, with CsA producing the most robust and consistent inhibition across both cell lines. In contrast, FK-506 showed no significant effect on neurite extension at clinically relevant concentrations. Consistent with the in vitro results, human neural progenitor cell grafts in a rodent spinal cord injury model exhibited significantly reduced graft-derived axon extension in the host spinal cord when hosts were treated with CsA rather than FK-506. These findings demonstrate that immunosuppressant choice can profoundly influence neural graft integration and axonal regeneration. Our study underscores the importance of preclinical evaluation of immunosuppressive regimens and suggests that selecting agents such as FK-506 over CsA may improve outcomes in future stem cell-based therapeutic trials for spinal cord injury and related disorders of the central nervous system.

Hyperglycaemia is a hallmark of diabetes and a major risk factor for diabetic kidney disease (DKD). However, the molecular consequences of long-term cumulative hyperglycaemia (CH) remain unclear. As a stable epigenetic modification, DNA methylation may capture past glycaemic exposure. Here, we assessed CH-associated DNA methylation in 1,245 participants with type 1 diabetes (T1D) from Finland and the United Kingdom-Republic of Ireland cohorts. We identified 17 CH-associated CpGs, with the strongest association at cg19693031 (TXNIP). Longitudinal analyses demonstrate that these CH-associated DNA methylation levels remain stable despite short-term glycaemic fluctuations, suggesting lasting epigenetic imprints of earlier metabolic control. Integrative analyses combining genomic, epigenetic, and proteomic data characterized these CpGs and potential target proteins. Mendelian randomization suggested a causal association between cg20853880 (KLF11) and DKD, supported by chromatin accessibility and kidney KLF11 expression. Our findings suggest that epigenetic changes contribute to metabolic memory and may mediate the effects of hyperglycaemia on DKD.

Background: Uveal melanoma (UM) and cutaneous melanoma (CM) both originate from the same cell line. This proposes the possibility of a shared mechanism between entities, requiring explicit investigation. Methods: Data from GWAS Catalog and DisGeNET were used to identify shared variation-disease associations (VDAs) between UM and CM. The results were validated using the Ensembl database. In the next step, the STRING database was used to identify the protein-protein interaction. Results: Subsequently, 109 unique VDAs were identified for UM and 880 for CM. However, only 2 VDAs were found to be shared among UM and CM in different ethnic groups. These shared VDAs were rs12203592 of the IRF4 gene, rs12913832 of the HECT and RLD domain-containing E3 ubiquitin protein ligase 2 (HERC2) gene. Notably, PPI network assessment through STRING showcased that OCA2 and IRF4 directly interacted with HERC2. Conclusion: While HERC2 acts as a poor prognostic factor in uveal melanoma, IRF4 status is a key prognostic indicator in both UM and CM. Identifying IRF4 allele contributions enables a better understanding of melanoma pathogenesis and fosters the development of disease-specific approaches.

Preeclampsia is a pregnancy complication characterized by hypertension, proteinuria, and end-organ dysfunction. Abnormal placentation leading to reduced placental perfusion may contribute to its development. Previous studies demonstrated that the activation of the apelin receptor (APJ) system has hypotensive, renoprotective, and antioxidant effects in preeclamptic rat models. Apelin and elabela (ELA) can stimulate the proliferation of trophoblast cells, suggesting a role in embryonic development. However, the mechanisms underlying the actions of apelin or ELA in trophoblast cells are not well understood, particularly in hypoxic settings. The immortalized HTR-8/SVneo trophoblastic cells were treated with cobalt chloride (CoCl2) at 0.2 mM for 24 hours to mimic hypoxic conditions. RT-qPCR, ELISA or Western blotting was used to measure mRNA or protein levels of apelin, elabela, and the components of IL-6 signaling in cell lysates or conditioned media. The exposure to CoCl2 increased total apelin and elabela content approximately 2-fold in the conditioned media but did not affect APJ levels. CoCl2 upregulated proinflammatory cytokine concentrations: soluble fms-like tyrosine kinase 1 (sFlt-1), soluble gp130 (sgp130), interleukin-6 (IL-6), and sIL-6 receptor (IL-s6R). Both apelin and elabela downregulated IL-6 mRNA but had no effect on sFlt-1 mRNA. Apelin attenuated sgp130, while ELA decreased the membrane form of IL-s6R. Apelin also decreased the pSTAT3/STAT3 ratio. CoCl2-induced hypoxia upregulated the pro-inflammatory milieu in HTR-8/SVneo cells. Local activation of this peptidergic system may be a compensatory response of the trophoblast cells to hypoxia as exogenous apelin and elabela treatment ameliorated the hypoxia-induced pro-inflammatory milieu.

Abstract Objective: To identify clinical and genetic factors associated with variation in glycemic response to glucagon-like peptide-1 receptor agonist (GLP-1RA) therapy among adults with type 2 diabetes, with a focus on common GLP1R variations, polygenic risk load, and pancreas-specific regulation annotation. Research Design and Methods: We conducted a retrospective cohort study using electronic health record (EHR)-linked biobank data from the All of Us research workbench platform that included 5784 adults with type 2 diabetes who initiated GLP-1RA therapy. Baseline HbA1c was measured within 3 months before medication initiation, and follow-up HbA1c was measured after 3 months. The patients with type 2 diabetes were classified as good responders (HbA1c reduction [&ge;] 2.5 percentage point) or poor responders (HbA1c reduction <0.5 percentage point). Models adjusted for demographic characteristics, anthropometric and metabolic measures, blood pressure, body mass index (BMI), lipid profile, liver function tests, polygenic risk score, and GLP1R variant carrier status were compared between the two groups. Common GLP1R variations were further investigated for carrier frequency and associated HbA1c levels before and after medication use. Results: The cohort included 3194 good responders and 2590 poor responders. Good responders were younger than poor responders (55.2 vs. 58.6 years) and had significantly higher glycemic improvement. HbA1c levels fell from 9.2% to 6.3% in good responders and 8.4% to 8.1% in poor responders, resulting in an absolute HbA1c reduction of 2.9% and 0.3%, respectively. Good responders also showed larger decreases in fasting glucose, BMI, systolic and diastolic blood pressure, triglycerides, total cholesterol, LDL cholesterol, and liver enzymes, as well as minor improvements in HDL-C. After multivariable adjustment, Poor responders had a greater T2D polygenic risk score (0.38 vs. 0.21), more GLP1R coding variant carrier status (10.1% vs. 8.0%), and a higher overall GLP1R variant burden (22.8% vs. 19.2%). Variant-level studies revealed rs2268650 and rs2003132 enrichment among poor responders, with negative post-treatment HbA1c patterns in carriers, whereas good-response carriers showed significant HbA1c improvement. Conclusions: Response to GLP-1RA in T2D is associated with baseline clinical and metabolic status, as well as inherited genetic susceptibility, which includes common GLP1R variation and a larger polygenic risk burden. Integrating clinical and pharmacogenomic profiling may improve patient classification and provide insight into treatment failure in poor responders.

Despite advances in treatment, HIV-1 infection continues to remain a major global health challenge, prompting ongoing efforts to understand the mechanisms that enable natural viral suppression and immune control. Elite controllers (ECs), a rare subset of PLWH individuals, naturally suppress HIV-1 replication without antiretroviral therapy, highlighting the importance of host-related factors in viral control. Understanding the mechanisms underlying this unique phenotype is crucial for developing novel therapeutic strategies. Previous studies from our group identified certain EC-specific metabolites, called dipeptides (DPs), and investigated their antiviral properties. We hypothesize that these dipeptides may potentially affect epithelial barrier integrity by modulating the expression of tight junction proteins, which in turn influences the mucosal barrier function, a key factor in HIV-1 pathogenesis. Therefore, in this study we investigated the impact of ten EC-specific DPs on tight junction (TJ) gene and protein expression in epithelial models derived from the female reproductive and gastrointestinal tracts, where we observed enhanced expression of different TJ genes (CLDN1, CLDN3, CLDN4, CLDN7, CLDN14, TJP1, TJP2, OCLN) and proteins (CLDN1, CLDN7, and CLDN14), suggesting the potential influence of these dipeptides on epithelial barrier function. Furthermore, we also examined different proteomic profiles between dipeptide (WG)-treated HeLa CD4+ CCR5+ cells compared with the untreated ones, and observed significantly reduced abundance of pro-inflammatory proteins, such as RELB Proto-Oncogene (RELB), TNF--induced protein 1 (TNFAIP1), TNF receptor superfamily member 1A (TNFRSF1A), and IL-32, in dipeptide-treated cells; and increased expression of proteins associated with tissue homeostasis (SMAD family member 5 [SMAD5]), cellular proliferation (transforming growth factor {beta} receptor 3 [TGFBR3]), and epithelial integrity, like CD81. Interestingly, KEGG analysis revealed possible attenuation of NF-{kappa}B, MAPK, TNF, and JAK-STAT signaling pathways, along with the enrichment of mTOR and PI3K-AKT pathways in treated HeLa CD4+ CCR5+ cells. Overall, this study investigated the potential interplay between tight junction proteins and key signaling pathways involved in maintaining epithelial barrier integrity and modulating immune activation, potentially contributing to both HIV-1 control and to the chronic inflammation associated with infection.

Knee osteoarthritis (KOA) affects an estimated 374 million people worldwide and has no approved disease-modifying treatment. Intra-articular micro-fragmented adipose tissue (MFAT) outperformed hyaluronic acid (HA) on patient-reported outcomes in our recent double-blind randomized trial (ISRCTN88966184), yet the molecular basis of this differential efficacy is unknown, and the two interventions have not previously been compared at the level of their in vivo molecular response in human KOA. Here we apply an interpretable artificial-intelligence data-fusion framework, based on non-negative matrix tri-factorization, to longitudinally collected plasma from this cohort, integrating proteomics, N-glycomics, miRNA transcriptomics and patient genetics with prior protein-protein and miRNA-gene regulatory networks at baseline, one and six months. The framework jointly decomposes all data modalities at each timepoint into shared, interpretable factors, from which we derive data-driven pathways of genes and of miRNAs and recover new patient-gene and patient-miRNA associations. These pathways were biologically coherent, showing significant enrichment in Gene Ontology Biological Process and Reactome Pathway annotations. By six months, the two treatments left clearly distinct molecular signatures: HA remained dominated by canonical OA pathogenic processes, including cartilage-degrading effectors such as MMP13 and LIMK2 and markers of synovial inflammation, whereas MFAT shifted the systemic landscape toward chondroprotection, anti-inflammatory signalling and bone-cartilage homeostasis, with prioritized effectors including SIRT7 and NDUFC1. To our knowledge, these are the first systems-level molecular data directly comparing the in vivo response to the two treatments in human KOA, providing initial evidence that MFAT acts as a disease-modifying intervention and demonstrating the value of interpretable data fusion for uncovering treatment mechanisms in small translational cohorts.

Spinal muscular atrophy (SMA) is increasingly recognized as a multisystem disorder involving non-neuronal cells, yet the role of Schwann cells (SCs) in late-onset SMA (loSMA) remains unclear. We investigated age-dependent peripheral nerve pathology in a four-copy SMN2 mouse model of loSMA. Sciatic nerves from wild-type and loSMA mice were analyzed at postnatal (P) days 20, 35, 70, and >100 using semi-thin morphometry, immunofluorescence for MBP, Sox10, Sox2, and F4/80, and nerve conduction studies. loSMA nerves showed reduced myelin thickness at all time points and smaller axon diameters at P20 and P35. G- ratios were reduced at P20 but increased from P35 onward, indicating progressively altered axon-myelin relationships. MBP immunofluorescence intensity, compound muscle action potential amplitude, and nerve conduction velocity were reduced in loSMA mice at P>100. The proportion of Sox2+ SCs increased from P35 onward, while Sox10+ cell abundance increased at later stages. F4/80+ macrophages were transiently elevated at P35 and correlated with Sox2+ cell numbers at this stage. These findings demonstrate age-dependent myelin abnormalities, altered SC states, and transient accumulation of macrophages in loSMA peripheral nerves. Whether these changes are SC-autonomous or secondary to chronic axonal dysfunction remains to be determined.

Global incidence and outcomes of glioma have been found to vary significantly by region, however research into the disease continues to lack diversity. Here we investigated epigenetic patterns in glioma subtypes from cohorts collected from China and the USA. We retrospectively analysed the Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas (TCGA) datasets following reclassification of glioma subtypes based on the WHO 2021 central nervous system (CNS) tumour classification. We used DNA methylation and transcriptomics data to identify methylation-driven cancer genes in the CGGA cohort, assessed their prognostic value and compared against the non-Hispanic White cohort in the TCGA database to consider ethnic influence. Furthermore, we used machine learning classification and clustering techniques to identify methylation patterns in glioma subgroups. Here, we showed that DNA methylation profiles of CGGA glioblastomas have a methylation signature more similar to TCGA high-grade astrocytomas: 58.1% of CGGA glioblastomas were identified as high-grade astrocytomas using classification modelling. Assessment of survival revealed that CGGA glioblastoma patients had a significantly better survival rate than non-Hispanic White glioblastoma patients (p = 0.037). Four key methylation-driven genes were identified in the CGGA glioblastoma samples: GLDN, PRKDC, S100A1 and NCAPH. Hypermethylation of GLDN significantly suppressed gene expression in all glioma subtypes in only the East Asian cohort; a gene that has not been previously described as a driver in gliomas. Together these data suggest alternative epigenetic mechanisms occurring in glioma subtypes of different ethnic populations, which is important for our understanding of glioma and strategies for personalized treatment.

Obesity is a significant public health concern. Early-onset obesity in the context of rare disease can reflect genetically-mediated pathology or elevated susceptibility through indirect mechanisms. Mapping the diverse characteristics and needs of young people with obesity in the rare disease population is a first step toward mechanistic and translational research. We carried out a retrospective comparative analysis of demographic, genotypic, phenotypic and health service utilisation data for young people with obesity (cases: n=500) and without obesity (controls: n=11,444) from the UK 100,000 Genomes Project rare disease cohort. Cases and controls were recruited prior to genomic diagnosis, across clinical disorder categories. We observed significant association between socioeconomic deprivation and obesity risk. Young people with obesity had significantly higher utilisations of acute care and mental health services, indicating an overall higher health burden. A curated panel of 519 candidate obesity-associated genes demonstrated aggregate association with obesity, although no single gene reached significance. Phenotypic comparison between cases and controls highlighted increased multi-organ and neurological system involvement, highlighting the overlap between neurodevelopmental and obesity risks. Within the case group, we conducted cluster analysis to identify early-onset obesity groups with different phenotypic profiles, potentially arising from different causal pathways - this identified six obesity subgroups of interest, with differing involvement of neurodevelopmental and other systems. Our study confirms that obesity co-occurs with a wide range of factors within the rare disease population, and is associated with significant physical and mental health needs, requiring holistic lifelong care.