Molecular Medicine

The ultimate cause of blindness in glaucoma is the death of retinal ganglion cells, and understanding the mechanism behind retinal ganglion cell loss during glaucoma could lead to the development of novel treatments for glaucoma. Endothelin-1 has been shown to mediate retinal ganglion cell death during glaucoma through impairment of mitochondrial function. Retinal ganglion cells are highly metabolically active, and susceptible to oxidative damage and decreased respiratory capacity. Mitophagy is the process whereby damaged mitochondria are degraded to prevent further propagation of oxidative damage. The current study evaluates the effect of endothelin-1 on mitophagy in retinal ganglion cells. Electron microscopy revealed endothelin-1 administration lead to a decrease in healthy mitochondria in the optic nerve. The MitoQC mouse was used to evalute mitophagy in response to endothelin-1, along with immunohistochemical analysis of mitophagy proteins. Mitophagy follows different trends in the optic nerve and retinal ganglion cell bodies following endothelin-1 administration, mitophagy was increased in the optic nerve but decreased in the retina following endothelin administration. With elevation of intraocular pressure, mitophagy was increased in the retina but decreased in the optic nerve. In retinal ganglion cells, parkin expression and activation was unchanged 24 hours after endothelin-1 administration, but was decreased 72 hours following endothelin-1 administration. Taken together, these results suggest that endothelin-1 impacts mitophagy through parkin-independent mechanisms in retinal ganglion cell bodies, and the ganglion cell bodies and optic nerve appear to have different responses to endothelin-1.

BackgroundCancer-associated cachexia is characterized by progressive loss of skeletal muscle and adipose tissue driven by systemic inflammation and metabolic dysregulation. AMP-activated protein kinase (AMPK) is a central regulator of energy homeostasis, but its role in cachexia and its therapeutic potential remains incompletely defined. We investigated AMPK signaling during cachexia and whether pharmacological AMPK activation alone or combined with ghrelin could ameliorate disease manifestations. MethodsCachexia was induced in male C57BL/6 mice by Lewis lung carcinoma (LLC) implantation. Additional models included fibrosarcoma (CHX and MN/MCA1) and chronic lymphocytic choriomeningitis virus (LCMV) infection. AMPK was activated using AICAR and BC1618 (AB), alone or combined with ghrelin (AB+G). Metabolic, inflammatory, and functional outcomes were assessed in hypothalamus, skeletal muscle, adipose tissue, and serum. ResultsLLC-bearing mice developed cachexia characterized by reduced body weight, lean and fat mass, hypophagia, and elevated circulating IL-6 and corticosterone. Cachectic LLC mice displayed increased Il6 and Il1{beta} expression in hypothalamus, skeletal muscle, and white adipose tissue (WAT). Furthermore, AMPK activation failed to increase in hypothalamus or peripheral tissues despite profound energy deficit. A similar defect in AMPK responsiveness was observed in CHX and LCMV models, indicating a conserved feature of cachexia. AB treatment in LLC mice reduced circulating IL-6 and corticosterone levels and decreased skeletal muscle atrogene expression and IL-6/STAT3 signaling, partially preserving muscle mass, fiber size, and grip strength. However, food intake remained low, and WAT was largely unresponsive, maintaining elevated Il6 expression and tissue loss. Ghrelin alone increased food intake in LLC mice but did not ameliorate the cachectic phenotype. In contrast, AB+G restored food intake and prevented loss of lean and fat mass. LLC AB+G mice exhibited reduced hypothalamic Il6 and serotonin transporter (Slc6a4) expression, normalized adipocyte morphology and serum leptin levels, decreased adipose Il6 and Atgl expression and reduced WAT sympathetic innervation. AB+G further lowered circulating corticosterone levels, and provided greater protection against muscle wasting, with increased Pgc1 expression and improved muscle function. Neither intervention affected tumor growth or tumor inflammatory gene expression. ConclusionsCancer cachexia is associated with a central and peripheral failure to appropriately activate AMPK signaling in response to the energetic stress imposed by cachexia. Combined AMPK activation and ghrelin administration exerted complementary effects on energy homeostasis, inflammation, and tissue wasting, resulting in greater protection against cachexia than either intervention alone. These findings support combined AMPK-ghrelin targeting as a promising therapeutic strategy for cancer cachexia.

Hepatocellular carcinoma (HCC) remains a leading cause of cancer-related mortality worldwide despite recent therapeutic advances, driven in part by its marked etiological and molecular heterogeneity and the lack of broadly effective therapeutic targets. Identifying conserved tumor dependencies shared across distinct etiological backgrounds may provide new opportunities for targeted therapy. Here, we developed an integrative computational framework to systematically integrate transcriptomic, functional genomics, and clinical datasets for the identification and prioritization of candidate tumor dependency genes in liver cancer. We reanalyzed transcriptomic data from murine models of liver cancer driven by genotoxic (DEN), oncogenic (c-Myc), and inflammatory (lymphotoxin) stimuli, identifying more than 380 genes consistently upregulated across all tumor models. Functional enrichment analysis revealed a strong overrepresentation of cell cycle-related pathways and liver cancer signatures. Integration with DepMap dependency datasets identified 26 genes with strong dependency scores. Candidate genes were further prioritized by comparing their expression across models of liver regeneration, chronic liver injury, and liver cancer. Analysis of the TCGA-LIHC cohort confirmed significant overexpression of all 26 genes in human HCC, with high expression associated with poor patient survival. Together, these findings establish an integrative framework for identifying conserved tumor dependencies, providing a prioritized set of proliferation-associated genes for functional evaluation as therapeutic targets in HCC.

Photoreceptors are among the most metabolically active cells in the retina and are therefore highly sensitive to fluctuations in oxygen availability. Age-related tissue changes in the eye affect oxygen delivery to the outer retina, which may result in hypoxic stress within photoreceptors and can contribute to disease development and retinal degeneration. To investigate how chronic hypoxic signalling affects photoreceptor metabolism, we examined a rod-pecific Vhl knockout mouse (RodVhl), in which constitutive HIF activation mimics the molecular response to hypoxia. Combining a cell-type-enriched multi-omics approach with metabolic flux analysis, we identified an early metabolic response in the retina of Rod{Delta}Vhl mice prior to degeneration. This response was characterized by a shift towards an oxidative redox environment indicated by a decrease in nucleotide precursors and an increased antioxidant response. While steady-state glycolytic flux remained unchanged, the dynamic 13C-glucose tracing revealed accelerated carbon flow through the three-carbon glycolytic intermediates, indicating a carbon rerouting. Outer segment lipidomics revealed selective remodelling of phosphatidylcholine and phosphatidylethanolamine species toward more oxidation-resistant and elongated acyl chains, supported by early gene upregulation of essential enzymes involved in fatty acid elongation, desaturation and oxidation. Together, these findings indicate a coordinated shift in metabolic and lipid pathways in photoreceptors under chronic hypoxic stress, consistent with an adaptive response that may help preserve outer segment integrity and improve stress resilience.

BackgroundTumor-associated neutrophils (TANs) are emerging as functionally heterogeneous and plastic cells in the tumor microenvironment. In immunologically cold tumors, elevated neutrophil abundance correlates with poor prognosis and resistance to immune checkpoint inhibition (ICI). Whether distinct anti-tumoral neutrophil states can be induced by different immunotherapies and how they relate to treatment efficacy remains unclear. MethodsUsing the syngeneic MOC2-huEGFR (M2h) mouse model of head and neck squamous cell cancer (HNSCC), we treated tumor-bearing mice with agonistic anti-CD40 monoclonal antibody (mAb) (aCD40), TNF, Cetuximab, or a combination of all three, designated Neutrophil Activating Therapy (NAT). In addition to evaluating anti-tumor efficacy, we performed single-cell multiomics RNA and protein sequencing, followed by bioinformatics analyses and flow cytometry validation. NAT-induced anti-tumor efficacy and related neutrophil states were also assessed in another cold tumor model, 9464D-GD2 neuroblastoma. Murine treatment-induced neutrophil gene signatures were then evaluated using clinical, proteomic, and transcriptomic data from HNSCC patients. ResultsFive transcriptionally distinct neutrophil states (N0-N4), including precursor state CD49d+ N4, were identified using the M2h model. N0 neutrophils (immunosuppressive/quiescent) dominated untreated tumors, but not in successful treatments. ISG+ N1 neutrophils and CCR3+ N3 neutrophils expanded by aCD40, TNF, and NAT treatment with anti-tumoral gene signatures and found more interacting with CD8+ T cells from bioinformatics analysis. N2 neutrophils reflected a recently established hypoxia-adapted state found in all treatments. ICAM1 (CD54) emerged as a marker of treatment-induced neutrophil activation, discriminating N1, N2, and N3 neutrophils from N0 neutrophils, validated by flow cytometry. In the 9464D-GD2 neuroblastoma model, NAT treatment also reduced the N0 dominance seen in untreated tumors in the HNSCC model but failed to induce anti-tumoral neutrophil states. In 23 HNSCC patients who received ICI therapy, ICAM1 protein expression in neutrophils trended toward association with responder status (TMA-level p=0.029), and ICAM1 neutrophil gene expression also trended toward association with improved overall survival in TCGA data (HR=0.75, p=0.059). ConclusionsDistinct immunotherapy-induced neutrophil states are defined by transcriptional profiles enriched in different functional pathways, associated with both anti-tumor and pro-tumor signatures. ICAM1 identifies activated neutrophils and potentially serves as a biomarker of ICI response in HNSCC, warranting further clinical validation. WHAT IS ALREADY KNOWN ON THIS TOPICNeutrophil heterogeneity has received increasing attention, with studies identifying antitumoral neutrophil populations, either at baseline or induced by treatment. Several effective treatment regimens involve an anti-CD40 agonist (aCD40) antibody, among them Neutrophil Activating Therapy (NAT), which combines aCD40, TNF, and a tumor antigen binding antibody designed to reprogram neutrophils. NAT could thus be particularly effective in cold, myeloid-rich tumors that are largely unresponsive to conventional immunotherapies such as checkpoint blockade, enacting these anti-tumoral effects through similar and different mechanisms; however, this has not been tested. WHAT THIS STUDY ADDSThis study adds a single-cell multi-omics framework for defining treatment-induced neutrophil heterogeneity in MOC2-huEGFR and 9464D-GD2 tumors, two immunologically cold models. It highlights ICAM1/CD54 and interferon-stimulated genes as markers of a dominant antitumor neutrophil state, while showing that neutrophil state composition variy across tumor models. HOW THIS STUDY MIGHT AFFECT RESEARCH, PRACTICE, OR POLICYThese results support the efficacy of a myeloid-modulating therapy built around aCD40 and TNF in a cold murine head and neck cancer model, and to a lesser extent in a cold murine neuroblastoma model. ICAM1/CD54 expression in neutrophils was also identified as a promising marker of antitumor activity and treatment response. More broadly, this work suggests that incorporating aCD40 and/or TNF into existing treatment regimens could improve outcomes, while ICAM1/CD54-high neutrophils may serve as a useful therapeutic readout.

The histone variant H2A.J is implicated in radiation-induced senescence by promoting the transcription of inflammatory genes. While H2A.J expression increases in renal tubular epithelial cells (TECs) following ionizing radiation (IR), its functional role remains poorly understood. To investigate this, constitutive H2A.J knock-out (KO) mice and wild-type (WT) controls were subjected to CT-guided IR (fractionated whole-body or localized kidney IR). Kidneys were analyzed at acute, intermediate, and chronic stages using immunofluorescence, histochemistry, automated image analysis, and electron microscopy. In WT TECs, IR induced rapid chromatin incorporation and C-terminal serine phosphorylation of H2A.J. Conversely, KO kidneys exhibited significantly more severe histopathological damage, including tubular dilation, flattened epithelium, associated with increased apoptosis, and premature senescence, characterized by persistent DNA damage with lamin B1 loss. Notably, KO TECs displayed disrupted mitochondrial networks and reduced brush borders even at baseline, which were further exacerbated by IR. Unlike WT controls, KO kidneys developed progressive tubular atrophy and incipient fibrosis, indicating a failure in regenerative capacity. Our findings suggest that H2A.J loss impairs tubular regeneration due to defective mitochondrial activation, resulting in insufficient energy supply for coordinated repair. Collectively, these results identify H2A.J as a critical stress-adaptive histone variant essential for the epigenetic regulation of tissue repair following radiation-induced damage. One Sentence SummaryIn irradiated kidney, the loss of histone variant H2A.J impairs the chromatin-mediated adaptation of mitochondrial function in tubular epithelial cells, thereby exacerbating cellular stress - characterized by increased induction of apoptosis and senescence - and ultimately leading to tubular atrophy. Translational RelevanceAcute and chronic kidney injury are frequent complications of genotoxic cancer therapies. Chemo- and radiotherapy induce DNA lesions that trigger cell death and senescence, often leading to irreversible renal damage. However, renal regeneration can occur through the dedifferentiation, proliferation, and redifferentiation of surviving tubular epithelial cells (TECs). This repair process is governed by epigenetic mechanisms that regulate the DNA damage response (DDR) and adapt gene expression programs. Following ionizing radiation (IR), epigenetic remodeling involves the incorporation of histone variants that modulate chromatin accessibility for stress-responsive transcription factors. We identify the histone variant H2A.J as a constitutive component of renal TECs, significantly upregulated after exposure to ionizing radiation (IR). Using H2A.J knock-out (KO) mice, we demonstrate that its absence disrupts acute damage responses and prevents coordinated repair, severely impairing regeneration. Mechanistically, H2A.J deficiency compromises mitochondrial function under postirradiation metabolic stress, driving the transition from acute injury to chronic kidney disease via persistent inflammation and maladaptive tubulointerstitial repair. Targeting these epigenetic drivers offers a promising strategy for regenerating damaged kidney tissue in oncology.

Purpose: To identify transcript-level variants in crystallin genes in paediatric patients with unilateral cataracts. Methods: Anterior capsulorhexis (n=12) from patients underwent surgical management of congenital unilateral cataracts was collected. Total RNA was isolated from lens epithelial cells, and complementary DNA (cDNA) was synthesized. Full-length RNA transcripts of 10 lens-specific crystallin genes were PCR-amplified and analysed via Sanger sequencing. Identified transcript variants were further validated using genomic DNA (gDNA) through Sanger sequencing. In addition, the full-length (~7,535 bp) CRYBA1 genomic region was sequenced using Oxford Nanopore Technology. Results: Aberrant low molecular weight (LMW) amplicons (~370 bp) of the CRYBA1 transcript were identified in three patients presented with unilateral cataract. Of 3 patients, 2 had persistent fetal vasculature (PFV) and 1 had pre-existing posterior capsular defect (PPCD). Sanger sequencing revealed a precise loss of exons 2 to 4 in the CRYBA1 RNA transcript. No coding, splice-site, or large deletion variants were detected in the genomic DNA of the patients or their parents. In silico analysis predicted two possible truncated proteins arising from these alternatively spliced transcripts: one comprising the first 11 amino acids of the N-terminal region with a loss of all Greek key motifs, and another comprising 90 amino acids encoded by exons 5 and 6, initiated from an alternative start codon in exon 5, and loss of Greek key motifs 1 & 2. Conclusion: The precise skipping of exons 2 to 4, consistent with canonical splicing signals (5-prime-GU...AG-3-prime), in the absence of genomic alterations, suggests the presence of alternatively spliced (AS) CRYBA1 transcripts in human lenses. This is the first report documenting AS-CRYBA1 transcripts in association with childhood cataracts with PFV and PPCD.

Abstract Background: The lack of effective biomarkers and therapeutic targets to overcome radioresistance in cervical cancer remains a major clinical challenge. Tumor necrosis factor receptor-associated factor 6 (TRAF6), an E3 ubiquitin ligase pivotal in immune and inflammatory signaling, has been implicated in various malignancies. However, its role in radioresistance in cervical cancer remains unclear. Methods: TRAF6 expression was evaluated in cervical cancer tissues from 162 patients who underwent postoperative radiotherapy at our institution and in 304 cases from the TCGA-CESC cohort. The prognostic significance of TRAF6 was assessed using Kaplan-Meier and Cox regression analyses. A nomogram integrating TRAF6 expression with clinicopathological factors was constructed to predict overall survival (OS) and progression-free survival (PFS). The functional role of TRAF6 in malignant phenotypes and radiosensitivity was investigated using shRNA-mediated knockdown in HeLa and C33A cervical cancer cells. Immune cell infiltration patterns associated with TRAF6 expression were analyzed using ssGSEA and xCELL algorithms based on TCGA data. Results: TRAF6 expression was significantly elevated in cervical cancer tissues compared with adjacent normal tissues (70.99% vs. control, P < 0.001) and was higher in radioresistant than in radiosensitive patients (P < 0.001). High TRAF6 expression was associated with shorter OS (HR = 18.73, P = 0.004) and PFS (HR = 8.44, P < 0.001) and was identified as an independent risk factor for radiotherapy resistance (OR = 8.44, P < 0.001). The TRAF6-integrated nomogram demonstrated good predictive accuracy for OS (C-index = 0.7351) and PFS (C-index = 0.7444). TRAF6 knockdown in cervical cancer cells significantly suppressed proliferation, migration, and invasion, while substantially enhancing radiosensitivity of tumor cells. Functional enrichment analysis revealed that TRAF6-related genes were enriched in autophagy, mitophagy, and HPV infection pathways. Immune cell infiltration analysis showed that TRAF6 expression correlated with distinct immune cell profiles, characterized by enrichment of activated dendritic cells, M1 macrophages, and regulatory T cells, alongside depletion of cytotoxic effectors such as CD8+ T cells and {gamma}{delta} T cells. Conclusions: TRAF6 could be a prognostic biomarker associated with poor outcomes and indicator of radiotherapy resistance in cervical cancer, TRAF6 represents a potential therapeutic target for overcoming radioresistance in cervical cancer.

The IgG Fc chain carries a single N-linked glycan which may undergo changes. Increased agalactosylated N-glycans are associated with rheumatoid arthritis (RA) and regarded as pro-inflammatory. Dysregulated neutrophils can make important contributions to host tissue damage. In RA, immune complexes (ICs) that have precipitated onto synovial joint surfaces activate neutrophils via Fc receptors, promoting localised inflammation. We engineered recombinant human monoclonal IgG with agalactosylated or galactosylated N-glycans, generated immobilised ICs and stimulated healthy donor and RA patient blood-derived neutrophils, comparing reactive oxygen species (ROS) production as read-out of neutrophilic inflammation. Both healthy donor and RA patient neutrophils generated less ROS when stimulated with ICs made from agalactosylated IgG. Mechanistically this was due to poorer binding of agalactosylated ICs to neutrophil FcgammaRs, causing lower activation of Akt and p38 MAPK. Both are required for immobilised IC-mediated stimulation of the neutrophil NADPH oxidase. Taken together, this suggests that disease-associated, agalactosylated IgG does not in fact promote inflammation and host tissue injury, at least not by acting on neutrophils. We propose that rather than promoting inflammation, agalactosylated IgG N-glycans that accompany inflammatory disease may arise as part of a compensatory mechanism that is aimed at reducing excessive inflammation and host tissue injury.

The intermittent energy restriction (iER) represents an effective dietary strategy for improving metabolic diseases including metabolic dysfunction-associated steatotic liver disease (MASLD) and type 2 diabetes mellitus (T2DM), yet the underlying mechanisms remain elusive. In this study, we integrated human clinical data, mouse models, and in vitro experiments to investigate the role of iER in modulating the gut-liver axis in comorbid MASLD and T2DM. We demonstrate that an iER diet improves hyperglycemia, hepatic steatosis and decreases the abundance of gut pathogen Klebsiella pneumoniae, which is strongly associated with reductions in blood endotoxin, lipopolysaccharide (LPS) levels, suggesting a potential role of K. pneumoniae-derived LPS in mediating effects of the iER on hepatometabolic improvements. We confirm that K. pneumoniae-derived LPS exacerbates lipid accumulation and inflammation using an in vitro model. Mechanistically, we reveal a core target of protein lysine acetylation (Kac), hydroxyacyl-CoA dehydrogenase -subunit (HADHA) Lys353 in the liver of db/db mice through a multi-omics analysis. The iER decreases HADHA-K353 acetylation and enhances its enzyme activity. A Kac-mimicking mutation (K353R) increases its enzyme activity and stability, blocks its binding to the inflammasome adaptor ASC, and alleviates lipid accumulation and inflammation in K. pneumoniae-derived LPS induced in vitro model. This study provides novel insights into the potential benefits of the iER in comorbid MASLD and T2DM.

Phenylketonuria (PKU) is a genetic metabolic disorder caused by the lack of functional phenylalanine hydroxylase (PAH). Elevated levels of phenylalanine (Phe) are known to be neurotoxic; however, the molecular mechanisms underlying Phe's effects remain elusive. This study investigates the impact of PKU on proteostasis, redox balance, and metabolism in BTBR PAHenu2 mice, a severe disease animal model. Combined proteomics and metabolomics revealed impaired redox homeostasis in the brain and disrupted mitochondrial energy metabolism (ATP and TCA intermediates). The dysregulation was further supported by decreased levels of ATP, reduced glutathione (GSH), cysteine, and reduced catalase activity. Western blot analyses revealed substantial remodeling of protein degradation systems: the 19S regulatory (Rpt1) subunit and 26S proteasome content and activity were significantly increased, and ubiquitinated protein levels were elevated, indicating protein turnover and activation of the ubiquitin-proteasome system. Autophagy was also activated, as evidenced by a reduced LC3-II/LC3-I ratio, decreased p62 levels, unchanged ATG5 levels, and increased HSPA8 protein expression. By contrast, UPR markers remained stable despite an increase in the oxidized-to-reduced PDI ratio, suggesting a localized shift without activation of a full ER stress response. In parallel, systemic alterations were assessed in whole blood. Indeed, GSH, cysteine, ATP and ADP were decreased in PKU, whereas NADPH increased. These changes were accompanied by reduced activities of GSH reductase and GSH peroxidase, thereby confirming metabolic and redox disruption. Collectively, these findings indicate that PKU is associated with activation of protein degradation pathways as an adaptive response to cellular stress combined with redox imbalance and energy dysregulation.

BACKGROUNDMetabolic dysfunction-associated steatotic liver disease (MASLD) is a systemic immunometabolic disorder rapidly increasing worldwide, affecting nearly 38% of adults. Gut dysbiosis and host genetic factors, such as PNPLA3 I148M variant, modulate disease development and progression. Through the gut-liver axis, increased intestinal permeability enables microbial translocation to the liver, promoting inflammation and metabolic disruption. However, the composition and functional potential of the hepatic microbiome remain poorly characterized. Understanding its relationship with histological injury and genetic susceptibility may provide novel mechanistic insights. We hypothesized that the hepatic microbiome composition and function are associated with histological severity and PNPLA3 genotype in this disease. AIMTo characterize the hepatic microbiome and assess its association with histological severity and PNPLA3 genotype. METHODSThis cross-sectional observational study included 30 patients with MASLD from a tertiary care hospital. Liver tissue underwent shotgun metagenomic sequencing. Histological severity was assessed using the NAFLD Activity Score (NAS). PNPLA3 genotype was determined by PCR. Differential abundance and functional enrichment analyses were performed using MaAsLin2. Somatic variants were identified using Mutect2. Correlation networks were constructed using Spearmans correlation coefficients. RESULTSPatients with advanced histological injury (NAS [&ge;]5) and PNPLA3 I148M carriers showed a trend toward higher somatic mutational load and a markedly reduced microbial abundance. Analyses revealed broad compositional shifts across bacterial, fungal, viral, and eukaryotic taxa, affecting both commensal and context-dependent pathobiont lineages. Pseudomonas species were enriched, whereas Siphoviridae phages were depleted in advanced disease and PNPLA3 I148M carriers. Functional analysis revealed enrichment of pathways related to nutrient transport and metabolic stress adaptation, while TonB-associated functions were enriched in advanced liver injury but depleted in PNPLA3 I148M carriers. Network analysis identified Sphingomonas leidyi as a keystone node associated with hexosamine metabolism. Salmonella enterica abundance positively correlated with somatic variant burden, suggesting a link between microbial signatures and genomic instability. Histological progression and the risk PNPLA3 genotype were accompanied by marked topological simplification, reflecting less resilient community structures. CONCLUSIONSThe hepatic microbiome in MASLD is a low-biomass, polymicrobial ecosystem shaped by the host genetic background. Its functional activity, taxonomic composition and system architecture bidirectionally relate to liver DNA instability and the severity of histological damage. Core tipThis study characterizes the multi-kingdom hepatic microbiome in MASLD using FFPE-derived metagenomics. We demonstrate that microbial abundance-including bacteria, fungi, protozoa, and viruses- significantly decreases with increased histological severity and the PNPLA3 risk genotype. Rather than global diversity shifts, results showed that disease progression could be linked to specific functional adaptations and simplified microbial network connectivity. In addition, we described associations between specific taxa and somatic mutational burden, suggesting a link between microbial signals and genomic instability. These findings indicate that changes in the liver microbiome as a whole, rather than specific taxonomic modifications, influence MASLD pathophysiology.

Objective: Clonal hyperexpansion of CD4 T cells is a characteristic feature of rheumatoid arthritis (RA). Equally large T cell clones also arise in physiological ageing or latent viral infection and adopt a replicative senescence programme - a tolerance mechanism that limits immune activation by innate-like reprogramming and proliferative arrest. We aimed to characterise the senescence programme of hyperexpanded CD4 T cell clones in RA and to define their clinical associations. Methods: Hyperexpanded T cell clones were characterised by single-cell RNA and T cell receptor profiling of peripheral T cells from RA patients and healthy donors. Flow cytometric validation was performed in two cross-sectional cohorts (n=15, n=45), paired blood and synovial fluid (n=20) or synovial tissue (n=18) sampling, and a non-interventional study of co-stimulatory blockade with abatacept (n=6). Results: Hyperexpanded CD4 T cell clones exhibited a CCR7-CD27- phenotype and accumulated in RA joints. Their frequency correlated with disease activity and their surface profile was modulated by abatacept, suggesting susceptibility to therapeutic intervention. At the molecular level, hyperexpanded clones converged on a phenotype consistent with replicative senescence, characterised by natural killer (NK) cell-reminiscent cytotoxic reprogramming, loss of co-stimulatory molecules, and reduced translational activity. However, compared with healthy donor counterparts, hyperexpanded RA CD4 T cell clones showed reduced senescence-associated cytotoxic and NK cell markers, and increased IL-7 receptor signalling, indicating attenuated senescence and preserved capacity for homeostatic proliferation. Conclusion: We propose that replicative senescence insufficiently constrains hyperexpanded clones in RA, resulting in sustained antigen reactivity in autoreactive clones and perpetuation of chronic inflammation.

Background & Aims: Hepatocellular carcinoma (HCC) remains a leading cause of cancer mortality, with most patients presenting at advanced stages requiring systemic therapy. Despite promising outcomes with immune checkpoint inhibitors (ICI), responses remain variable due to an immunosuppressive tumor microenvironment. Y90 radioembolization offers potential immune priming, but only a subset of patients benefit. Here, we apply spatial multi-omics to delineate baseline and treatment-induced immune features and identify predictive signatures of progressive disease (PD) for early detection of patients unlikely to benefit from therapy. Approach & Results: Paired baseline (Day 0) and on-treatment (Day 35) biopsies were obtained from 33 patients, following Y90 radioembolization (Day 14) and nivolumab. Multiplex immunohistochemistry (mIHC) was used for cell-cell interaction analysis. A subset was further profiled using Visium (n=13) for tissue category-specific analysis and NanoString GeoMx DSP (n=12) for cell type-resolved transcriptomic and pathway analyses. Global spatial transcriptomics analysis revealed minimal baseline immune activity in PD, indicating an intrinsically immune-deficient TME. Despite treatment-induced activation, PD exhibited reduced CD8+ T cell abundance and limited reinvigoration of exhausted subsets, and persistent LAG-3-associated exhaustion. DSP showed downregulation of antigen presentation and T cell activation pathways. Macrophage profiling revealed enrichment of CD38+ phenotypes, contrasting CXCL9-CXCR3-associated responses in responders. Furthermore, a 72-gene PD signature was identified and validated in TCGA, associating with poorer survival. Conclusions: Integrated spatial multi-omics reveals that PD in HCC is associated with an immune-deficient TME, characterized by LAG-3-associated CD8+ exhaustion and immunosuppressive macrophages. A 72-gene signature enables early identification and supports alternative therapeutic strategies.

Pancreatic cancer (PC) exhibits a striking association with depression, with neuropsychiatric symptoms frequently preceding diagnosis. However, the biological mechanisms linking pancreatic tumor development to central nervous system dysfunction remain poorly understood. Here, we investigated the impact of PC progression on adult hippocampal neurogenesis using complementary orthotopic xenograft and genetically engineered mouse models. Tumor-bearing mice developed depressive-like behavioral abnormalities accompanied by reduced adult hippocampal neurogenesis, including depletion of neural stem cell populations and immature neurons in both dorsal and ventral dentate gyrus regions. In the genetic model, neurogenic impairment progressed in parallel with disease severity. Exposure of primary hippocampal neural stem cells to serum derived from tumor-bearing mice selectively impaired cell survival, indicating that circulating factors are sufficient to compromise neurogenic capacity. Consistent with this, cytokine profiling revealed profound systemic inflammatory alterations, with IL-6 emerging as the only cytokine consistently elevated across both models. Together, our findings identify disruption of the adult hippocampal neurogenic niche as a previously unrecognized consequence of pancreatic cancer progression and provide a biological framework for pancreatic cancer-associated depression.

Dietary methionine restriction has been shown to improve metabolic health and treat multiple diseases. Methionine metabolism regulates transmethylation reactions, including N6-methyladenosine (m6A) RNA methylation, by modulating the availability of S-adenosyl methionine (SAM). Both m6A RNA methylation and methionine metabolism are involved in the regulation of the circadian clock. However, it remains unclear whether dietary methionine influences circadian rhythms through the regulation of m6A RNA modification. In this study, we investigated the effects of short-term methionine deprivation on the diurnal oscillations of m6A RNA methylation in the mouse liver. We found that a methionine-deficient (MD) diet reprogrammed the cyclic expression patterns of m6A writers, erasers, and readers. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) revealed that the MD diet induced de novo diurnal m6A oscillations in genes associated with RNA processing, protein translation, protein ubiquitination, and mTORC1 signaling pathways. RNA-seq and quantitative proteomics analyses demonstrated that MD-induced changes in m6A RNA levels were linked to alterations in mRNA and protein abundance. We observed that dynamic m6A RNA methylation of the transcripts encoding two key enzymes, MAT2A and CBS, helps maintain methionine homeostasis in response to methionine starvation. These findings identify m6A RNA methylation as a key mechanism linking methionine metabolism to circadian regulation.

Early-life adversity durably alters neural development through complex mother-offspring interactions whose underlying mechanisms remain poorly understood. We investigated how neonatal maternal separation (NMS) affects the large repertoire of maternal behaviors and subsequently influences spinal nociceptive circuit development and pain responses in rat offspring. Rat dams underwent NMS from postnatal day 2 (P2) to P12, 3h/day, and maternal behaviors were assessed before and after the separation period. These behaviors were compared to those of control (non-separated) dams. Offspring spinal cord and dorsal root ganglia were analyzed at P14 and P24 for several neurotrophic, glutamatergic, and GABAergic gene expression patterns. Offspring nociceptive sensitivity was also assessed at P24. NMS induced increased maternal behaviors (including longer arched-back nursing, higher nest occupancy, and better pup retrieval efficiency), alongside reduced self-care behaviors. These behavioral adaptations were correlated with spinal gene reprogramming in offspring, characterized by a biphasic developmental pattern. At P14, we observed elevated neurotrophic signaling alongside increased GABAergic and glutamatergic markers. By P24, neurotrophic factors decreased while compensatory changes emerged, yet persistent excitatory-inhibitory imbalances remained evident. Parallel to these results, NMS rats also showed mechanical and thermal hot hypersensitivity at P24. These findings reveal that despite apparent maternal behavioral compensation following NMS, offspring exhibit neurotrophic-driven developmental dysregulation resulting in persistent spinal circuit alterations. The disconnect between maternal behavioral normalization and sustained molecular changes suggests that early separation stress triggers enduring neurobiological cascades independent of ongoing maternal care quantity, with long-term consequences for sensory processing and pain sensitivity.

Objective We developed a patient- and joint-specific explant co-culture system to model active psoriatic arthritis (PsA) and capture donor-specific tissue responses to therapeutic interventions. Methods Based on convergent joint pathology between end-stage osteoarthritis (OA) and PsA, OA cartilage-bone and synovium tissues from arthroplasty patients were exposed to synovial fluid (SF) obtained from PsA and OA patients. Histological outcomes (synovitis, proteoglycan distribution), curated gene expression, soluble mediators, and proteinase activity were assessed over 7-21-days. Model responses to dexamethasone (DEX) and the anti-tumor necrosis factor antibody adalimumab (ADA) were evaluated. Results PsA SF induced distinct inflammatory and tissue remodeling responses compared to OA SF and control conditions, including altered cartilage proteoglycan distribution, increased synovitis, and tissue-specific transcriptional changes. Multivariate analyses identified distinct osteochondral and synovial transcriptional responses to PsA SF, characterized by reduced osteochondral COL2A1 expression and increased synovial expression of inflammatory and matrix-remodeling genes, including MMP1 and CXCL8. DEX and ADA elicited donor-specific responses across histological, transcriptional, and protein readouts. Among multivariable model outputs, histologic synovitis scores emerged as the most clinically aligned parameter, demonstrating associations with baseline PsA donor disease activity, active joint counts, pain, high-sensitivity C-reactive protein (hsCRP), and radiographic scores. Synovitis score changes to DEX and ADA treatments also aligned with corresponding PsA SF donor clinical improvements to corticosteroid and TNF-modifying therapies. Conclusion This osteochondral-synovial explant co-culture model captured donor-specific inflammatory and treatment-responsive features of PsA SF-induced pathology, thereby providing a clinically relevant ex vivo platform for studying patient-specific therapeutic responses in PsA.

Despite the significant technical advancement in spatial transcriptomics, its clinical usage is largely untapped. Here, we develop an integrated system, ENDO-Genome, for minimally invasive in-body transcript sampling to facilitate live spatial transcriptomic analysis of human internal organs. This is achieved by integrating a nanoarrayed biochip with existing endoscope to perform pressure-sensor-calibrated "Touch & Go" RNA extraction directly from human internal organs, including the highly vascularized liver or kidney, without the need for tissue biopsy, voiding any bleeding risks. By a demonstration using gastrointestinal endoscopy, multiplexed landscape of 55 mRNA transcripts was obtained from multiple locations of human intestinal tract via a 5-minute operation in routine examinations. Benefiting from a sequencing-free approach, each assay costs less than 10 US dollars. For the clinical study involving 15 Crohn' s disease (CD) patients, no complication case was reported out of 47 ENDO-Genome operations, showcasing the gentle deposition and excellent safety of the technique. The live spatial transcriptomics provides direct in vivo pictures of the heterogenous spatial transcriptional programs underlying CD pathological response at different intestinal locations, revealing distinct ileal phenotypes. This is manifested by unique microscale scattering of inflammation gene clusters, along with the discovery of a tissue-specific cooperative mechanisms between inflammation and RNA methylation regulations at single- or multi-cell scales.

Introduction: Progressive multiple sclerosis (MS), including primary progressive MS (PPMS) and non-active secondary progressive MS (nSPMS), remains an unmet need, as few treatments target innate immune pathways. Masitinib (AB1010) is a selective tyrosine kinase inhibitor that targets c-Kit and colony-stimulating factor 1 receptor pathways. This mechanism disrupts mast cell-microglia interactions, key innate immune effectors in progressive MS pathogenesis, reducing neuroinflammation and neuronal damage. In the phase 3 AB07002 trial, masitinib (4.5 mg/kg/d) over 96 weeks met its primary endpoint. Comparable signals in PPMS and nSPMS indicated masitinib benefited both phenotypes. Secondary analyses showed that masitinib lowered the progression to wheelchair dependence (EDSS [&ge;]7, 12 weeks) and reduced the 12-week confirmed EDSS progression risk by 37% versus placebo, although the results were underpowered for these endpoints. Methods: This study aimed to confirm that oral masitinib achieves central nervous system (CNS) concentrations sufficient to modulate CSF1R and wild-type c-Kit, thereby underpinning its neuroprotective potential. Male Sprague Dawley rats (n=12, ~200 g) were administered a single oral dose (30 mg/kg). Plasma and brain samples were collected at 2, 4, 8, and 24 hours post-dose (n=3 per time point). Masitinib (AB1010) and its metabolite (AB3280) were quantified in plasma and brain homogenates using LC-MS/MS. Results: Masitinib reached a brain Cmax of 223.5 ng/mL (~450 nM), exceeding IC50 values for CSF1R and wild-type c-KIT by ~5-fold and 2-fold, respectively, indicating effective CNS target engagement. The active metabolite AB3280 also achieved brain Cmax levels with full inhibitory activity. Masitinib demonstrated consistent CNS penetration supported by a proportional plasma-to-brain exposure relationship. Conclusion: The favorable CNS penetration and safety profile of masitinib, alongside its unique mast cell inhibition, position it as a compelling candidate for progressive MS treatment, either as monotherapy or in combination with other agents. This multifaceted immunomodulatory approach addresses critical unmet needs in progressive MS and supports further clinical development.