Biology subjects

Sharma, R.

Publications and source records attributed to Sharma, R..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

CASM regulates p62/KEAP1/NRF2 antioxidant responses to lysosome damage

Effective lysosome function is essential for health, and declines with ageing and disease. Upon lysosome damage, cells mount a complex stress response to restore homeostasis. Membrane ATG8ylation plays a central role, orchestrating lysosome repair, replacement and removal, either directly at the damaged membrane, via CASM (conjugation of ATG8s to single membranes), or at nascent autophagosomes, during lysophagy. Here, we identify a novel role for CASM in driving an antioxidant response to lysosome stress. Following damage, CASM regulates both lysosome ubiquitination and p62 recruitment. Membrane-associated p62 undergoes S349-phosphorylation, which permits KEAP1 sequestration, thereby releasing master transcription factor, NRF2. Liberated NRF2 translocates to the nucleus and promotes transcription of antioxidant and detoxifying genes, co-ordinating a cytoprotective response, in a CASM-dependent manner. These findings position CASM as a major upstream response to lysosome stress and uncover the p62/KEAP1/NRF2 axis as a novel effector pathway, termed SOLAR (SQSTM1/p62 Oligomer-mediated lysosome antioxidant response). HighlightsO_LICASM recruits p62/SQSTM1 as an effector protein during lysosome damage C_LIO_LICASM acts upstream to enhance ubiquitination of damaged lysosomes C_LIO_LICASM-recruited p62 engages KEAP1/NRF2 to drive antioxidant gene transcription (SOLAR) C_LI

cell biology↗

bioRxiv2026

Proteomic and Transcriptomic Differences in Ischemic Stroke Patients with Atrial Fibrillation Versus Carotid Atherosclerosis

BackgroundIschemic stroke occurring in the setting of atrial fibrillation (AF) or carotid atherosclerosis (CA) may reflect distinct underlying biological processes. We integrated proteomic, transcriptomic, and genetic data from different sources to identify circulating proteins and molecular pathways associated with ischemic stroke in patients with AF versus CA. MethodsWe conducted a nested proteomic study within the UK Biobank comparing plasma protein levels among ischemic stroke patients with AF (n=539) and CA (n=127). Linear regression models were used to evaluate 2,923 proteins measured using the Olink Explore platform (false discovery rate [FDR] <0.05). In a separate Yale cohort, we evaluated expression of genes encoding identified proteins in thrombectomy clot single-cell RNA sequencing data from ischemic stroke patients with AF (n=7) or CA (n=7), including cell type-specific expression patterns. We then used summary statistics to perform 2-sample Mendelian randomization analyses using cis-protein quantitative trait loci to evaluate associations between genetically predicted levels of proteins identified in prior analyses and ischemic stroke subtypes. Exploratory pathway enrichment analyses were also performed. ResultsTwelve circulating proteins differed significantly between ischemic stroke patients with AF versus CA. AF was associated with higher levels of NTproBNP, NPPB, and ACP5, and lower levels of APCS, ANGPT2, PAMR1, PRCP, PROS1, LARP1, F7, F10, and LEO1 (all FDR<0.05). Clot transcriptomic analyses showed corresponding differential expression of ACP5, PRCP, LARP1, ANGPT2, and LEO1 across AF versus CA patients. Pathway analyses suggested enrichment of coagulation-related pathways among proteins associated with CA and natriuretic peptide signaling pathways among proteins associated with AF. Mendelian randomization analyses demonstrated associations between genetically predicted protein levels and ischemic stroke subtypes (AF or CA), including cardioembolic stroke for NTproBNPand ischemic stroke for ANGPT2, ACP5, APCS, and PAMR1. ConclusionComplementary proteomic, transcriptomic, and genetic analyses identified differing molecular profiles among ischemic stroke patients with AF versus CA. These findings support established biomarkers, including NTproBNP and coagulation-related proteins, while identifying additional candidate pathways that may contribute to biological differences between these stroke-associated conditions. Further validation in clinically adjudicated and longitudinal cohorts is needed.

neuroscience↗

bioRxiv2026

SIRT5-dependent regulation of ASL controls arginine metabolism and T cell function

NAD supplementation blunts Th1 and Th17 inflammation, in part, through arginine metabolism-dependent regulation of mitochondrial energetics, redox balance and signal transduction. Whether the NAD+-dependent sirtuin deacylases contribute to this regulation is unknown. Here, we show that both SIRT1 and SIRT5 transcript levels are induced in CD4+ T cells in human participants following oral supplementation of the NAD+ precursor nicotinamide riboside (NR). Among the sirtuin family members, SIRT5 rather than SIRT1 emerged as the predominant regulator of arginine and fumarate metabolism. Genetic depletion or pharmacologic inhibition of SIRT5 attenuated NR-mediated increases in arginine and fumarate and abolished the anti-inflammatory -effects of NR on Th1 and Th17 cytokine production. In contrast, the responses to exogenous arginine or citrulline supplementation were preserved, indicating that SIRT5 functions upstream of arginine biosynthesis. Metabolomic profiling further demonstrated that SIRT5 is required for NR-induced remodeling of the arginine biosynthetic pathway. Mechanistically, SIRT5 physically interacted with arginosuccinate lyase (ASL), promoted ASL-dependent arginine accumulation, and regulated ASL post-translational acylation, including glutarylation and malonylation. Loss of SIRT5 disrupted NR-mediated redox homeostasis, antioxidant gene expression, and cytokine suppression. Collectively, these findings identify SIRT5 as a critical mediator of NAD precursor-induced metabolic remodeling that links ASL-dependent arginine metabolism to redox balance and effector function in human CD4 T cells.

immunology↗

bioRxiv2026

Mycobacteriophage D29-Derived LysB Enhances Anti-Tubercular Therapy in Experimental Pulmonary Tuberculosis

Adjunctive therapies that enhance the efficacy of existing antitubercular drugs are needed for drug-resistant tuberculosis. We evaluated the efficacy of intranasally administered recombinant D29 LysB, a mycobacteriophage-derived mycolylarabinogalactan esterase, in murine and guinea pig models of pulmonary tuberculosis. BALB/c mice and guinea pigs were aerosol-infected with Mycobacterium tuberculosis H37Rv and treated for 4 weeks with LysB alone or with standard antitubercular therapy (ATT: rifampicin, isoniazid, pyrazinamide). Outcomes included pulmonary and extrapulmonary bacterial burden (CFU), lung and spleen histopathology, cytokine profiling, and humoral immune responses. LysB monotherapy produced modest pulmonary CFU reductions. When given adjunctively with ATT, LysB produced an additional 0.6-0.7 log10 reduction in lung CFU compared with ATT alone and decreased splenic dissemination in both species. Combination therapy improved tissue pathology, reducing granulomatous involvement and preserving pulmonary architecture. LysB treatment increased TNF- with a moderate rise in IL-10, a profile consistent with enhanced antibacterial immunity without excessive inflammatory damage. Repeated intranasal administration was well tolerated; no IgE-mediated hypersensitivity was detected. LysB-specific IgG developed but did not diminish therapeutic efficacy. These results show that intranasal D29 LysB augments the bactericidal and histopathological effects of standard ATT in vivo and support further development of inhaled phage-derived lysins as adjunctive therapies for drug-resistant tuberculosis. ImportanceTuberculosis remains a major cause of infectious mortality worldwide, and the increasing burden of multidrug-resistant and extensively drug-resistant disease continues to challenge effective treatment. New therapeutic approaches that complement conventional antibiotics are urgently needed. In this study, intranasally delivered recombinant mycobacteriophage-derived LysB was well tolerated and enhanced treatment efficacy in experimental pulmonary tuberculosis. Adjunctive LysB improved bacterial clearance, reduced tissue pathology, and modulated host immune responses in both murine and guinea pig models. These findings highlight phage-derived endolysins as promising inhalable adjunctive therapeutics for drug-resistant tuberculosis.

microbiology↗

bioRxiv2026

Precision survival estimation in acute myeloid leukemia using evolutionary learning-derived microRNA signature

BackgroundAcute myeloid leukemia (AML) remains the most lethal acute leukemia in adults, with 5-year overall survival below 32% despite recent advances including venetoclax-, FLT3-, IDH1/2-, and Menin-targeted therapies. Clinical outcomes remain highly heterogeneous across patients, highlighting the need for robust molecular biomarkers capable of improving prognostic precision. MicroRNAs (miRNAs) are critical regulators of hematopoietic differentiation, apoptosis, and therapeutic resistance and are differentially expressed across AML subtypes. However, their clinical translation has been limited by high dimensionality, feature redundancy, and relatively small cohort sizes. MethodsWe developed and evaluated the AML Survival Estimator (AMLS), an inheritable bi-objective combinatorial genetic algorithm integrated with support vector regression (SVR), using TCGA-LAML miRNA expression profiles (n = 156). AMLS was benchmarked against ten widely used machine-learning approaches, including penalized regression, tree-based ensembles, support-vector regression, k-nearest neighbors, and multilayer perceptron models. Performance was assessed using stratified cross-validation with Pearson correlation (R), Harrells concordance index (C-index), and mean absolute error (MAE). Functional characterization of the derived miRNA signature was performed through consensus target integration followed by pathway enrichment, gene ontology analysis, network reconstruction, and Kaplan-Meier risk stratification. ResultsAMLS achieved superior prognostic performance with pooled out-of-fold metrics of Pearson R = 0.86, C-index = 0.788, and MAE = 7.49 months, substantially outperforming all comparator models. Restricting analyses to the AMLS-derived 28-miRNA signature improved all baseline learners by approximately 2-4-fold, with the multilayer perceptron achieving R = 0.674; however, none matched the native AMLS framework, indicating that the evolutionary optimization strategy contributes predictive information beyond feature selection alone. The prognostic signature included biologically established AML-associated miRNAs, including hsa-miR-191, hsa-miR-29c, hsa-miR-125b, hsa-miR-148a, hsa-miR-15b, hsa-miR-10b, and hsa-miR-30c, linked to DNA methylation, apoptosis, cell-cycle regulation, and oncogenic Wnt/MAPK signaling pathways. Functional analyses demonstrated significant enrichment of canonical AML-associated pathways, including p53, PI3K-AKT, TGF-{beta}, JAK-STAT, FoxO, and hematopoietic lineage signaling. ConclusionsOur findings demonstrate that evolutionary learning integrated with SVR can recover a compact and biologically interpretable miRNA prognostic signature that substantially outperforms conventional machine-learning approaches for AML survival prediction. The identified miRNA network converged on key leukemogenic pathways involved in apoptosis, cell-cycle regulation, and oncogenic signaling, supporting both the biological relevance and prognostic utility of the framework. Given the minimally invasive and quantitatively scalable nature of miRNA profiling, this approach may provide a practical molecular adjunct for improving prognostic assessment and precision medicine strategies in AML. Abstract FigureSchematic overview of the AMLS framework. Left: acute myeloid leukemia, a clonal hematological malignancy with persistent prognostic heterogeneity. Middle: AMLS couples an evolutionary learning-based feature selection algorithms to support vector regression for miRNA-based survival modeling. Right: AMLS recovers a 28-miRNA prognostic signature that predicts overall survival with Pearson R = 0.86 and MAE = 7.5 months. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=86 SRC="FIGDIR/small/727196v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@11ead1org.highwire.dtl.DTLVardef@4f5c19org.highwire.dtl.DTLVardef@277de1org.highwire.dtl.DTLVardef@b95c9a_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2026

Genome-resolved house microbiome exhibits location-specific metabolic partitioning, and harbors hosts with clinically relevant antibiotic resistance genes

Residential indoor surfaces are recognized as diverse microbial ecosystems, while their genome-based organization and functional repertoires remain understudied. We recovered 2304 metagenome-assembled genomes (MAGs) from shotgun metagenomic sequencing of 10 houses in New Delhi, India. Genome-resolved analysis revealed a highly structured microbial community and substantial unexplored diversity, with 60% Species-level Genome Bins (SGBs) (629/1014) unclassified at the species level. Metabolism reveals a conserved metabolic core, along with spatial functional enrichment: the living area was significantly different from the bathroom and kitchen areas. The prevalent MAG species of the house microbiome, Paracoccus marcusii, Ottowia sp. 018060485, and Kocuria palustris, showed strain-level diversity with no stratification by house, but a subtle location-wise grouping. Potential pathogens, along with a wide range of antimicrobial resistance genes (ARGs), were identified across the MAGs, with 64 ARGs associated with mobile elements. Phylogenomic analysis of Escherichia coli MAGs indicated a split between commensal-like fecal lineages and pathotype-associated clusters, like Intestinal Pathogenic E. coli (InPEC). These results suggest that residential house microbiomes harbor microbial communities with both diverse metabolic capacity and clinical relevance. Together, these findings establish a reference for future indoor microbiome research and provide a foundation for antimicrobial resistance surveillance and the development of bio-informed building-infrastructures.

microbiology↗

bioRxiv2026

BLOC1S1 regulates autolysosomal and exosomal dynamics during CD4⁺ T cell differentiation

Although the endolysosome system is central to intracellular recycling, signal transduction, and intercellular communication via exocytosis, its role in immunoregulation remains incompletely defined. We recently identified that CD4+ T cell-specific depletion of BLOC1S1, a component of multiprotein complexes regulating endolysosomal biology, predisposes toward type 2 (Th2) immunity. We therefore hypothesized that the study of BLOC1S1-deficient CD4+ T cells would expand our understanding of endolysosomal dynamics in Th2 function. Here, we demonstrate that CD4+ T cell BLOC1S1 deficiency resulted in aberrant lysosomal distribution, accumulation of endosomal vesicles, and increased exocytosis, which collectively correlated with enhanced Th2 immune responses. The phenotype was associated with upregulation of key components of the exocytosis machinery, including RAB11 and VAMP7. Functional inhibition of these vesicle trafficking proteins following siRNA knockdown of RAB11 and VAMP7 significantly attenuated Th2 cytokine secretion in BLOC1S1-deficient CD4+ T cells, highlighting their essential role in exosome-mediated cytokine export. Furthermore, exosomes derived from BLOC1S1-deficient CD4+ T cells promoted Th2 polarization in recipient cells, indicating a mechanism of intracellular amplification. Together, these findings identify BLOC1S1 as a critical regulator of lysosomal dynamics and exocytic vesicle fusion, thereby linking intracellular trafficking mechanisms to Th2 immune regulation.

immunology↗

bioRxiv2026

Identification of septoria nodorum blotch susceptibility genes in hard winter wheat

Key message Characterized and unknown septoria nodorum blotch susceptibility/resistance genes were identified in contemporary U.S. hard winter wheat. The necrotrophic fungus Parastagonospora nodorum is the causal agent of septoria nodorum blotch (SNB) of wheat. To determine the prevalence of SNB sensitivity genes in a contemporary U.S. hard winter wheat (HWW), we evaluated a panel of 619 breeding lines and cultivars against five P. nodorum isolates and five necrotrophic effectors (NEs), SnToxA, SnTox1, SnTox3, SnTox267 and SnTox5, and genotyped the panel using genotyping-by-sequencing (GBS) markers and diagnostic Kompetetive-allele specific PCR (KASP) markers for the sensitivity genes Tsn1-B1, Snn1-B1, and Snn3-B1/B2. GBS analysis identified 34,357 GBS-single nucleotide polymorphism (SNP) markers. Evaluations against P. nodorum isolates showed that 40-67% of the genotypes were susceptible in the panel. Toxin infiltration assays showed that 54%, 2%, 37%, 13%, and 15% of the genotypes were sensitive to SnToxA, SnTox1, SnTox3, SnTox267, and SnTox5, respectively. Diagnostic KASP markers for Tsn1-B1, Snn1-B1, and Snn3-B1/B2 showed prediction accuracies of 98%, 75%, and 92% for the corresponding effectors SnToxA, SnTox1, and SnTox3, respectively. Genome-wide association studies (GWAS) not only confirmed the presence of the previously characterized sensitivity genes Tsn1-B1, Snn1-B1, Snn2, Snn3-B1/B2, and Snn5-B1, but also identified new loci to be associated with responses to P. nodorum isolates and NEs. Of which, Qsnb.osu-2AS on chromosome 2AS was associated with responses to all five isolates. We developed KASP markers KASP_S4B_643615365, KASP_ S2D_16184991, and KASP_S2A_9833162 linked to Snn5-B1, Snn2, and Qsnb.osu-2AS, respectively. These findings should guide breeding for SNB resistance in hard winter wheat.

genetics↗

bioRxiv2026

Mapping of Stripe Rust and Leaf Rust Resistance Genes in the Hard Red Winter Wheat Population Green Hammer/Lonerider

Stripe rust and leaf rust, caused by Puccinia striiformis f. sp. tritici and P. triticina, respectively, are the most destructive wheat diseases in the southern Great Plains. Green Hammer is a hard red winter wheat (HRWW) cultivar released by Oklahoma State University in 2018 and has demonstrated a stable adult plant resistance to stripe rust and race-specific seedling resistance to leaf rust. To identify and map rust resistance loci, 109 doubled haploid (DH) lines derived from the cross between Green Hammer and another HRWW cultivar, Lonerider, were developed. Lonerider showed adult plant resistance to stripe rust but was susceptible to multiple P. triticina races. The DH lines were evaluated for stripe rust at the adult plant stage in greenhouse and field environments across Oklahoma, Kansas, and Washington, and for leaf rust at the seedling stage against seven U.S. P. triticina races and at the adult plant stage in Oklahoma and Texas. Genotyping-by-sequencing generated 6,078 polymorphic single-nucleotide polymorphisms used for genetic mapping. Quantitative trait loci (QTL) analysis identified 14 stripe rust and 8 leaf rust resistance QTL. For stripe rust, a major QTL in Green Hammer, QYr.osughln-2AS, was identified in the proximity of the 2NvS translocation. Three other major stripe rust resistance QTL were identified in Lonerider on chromosomes 2AL (two QTL) and 2BS (one QTL). For leaf rust, QLr.osughln-1DS and QLr.osughln-2DS.1 were the two major QTL identified in Green Hammer and most likely correspond to the all-stage resistance genes Lr21 and Lr39, respectively. In this study, we identified previously characterized genes as well as unknown genes that can be utilized in wheat breeding programs to enhance resistance to leaf rust and stripe rust.

genetics↗

bioRxiv2026

Spatial transcriptomics implicates the thalamus and cortex in autism and schizophrenia

The past decade has seen tremendous progress in the identification of genes associated with complex neuropsychiatric disorders, including autism spectrum disorder (ASD) and schizophrenia. Expression patterns of these genes in single cell data strongly implicate excitatory and inhibitory neurons; however, there are limited data on the brain regions involved - a critical question for neurobiology. Spatial transcriptomics provide an opportunity to perform systematic multiregional analyses to provide insights into this question. Here, we have generated a spatial transcriptomics dataset encompassing the diverse anatomical territories of the adult mouse brain sagittal midsection. We compare neuropsychiatric gene enrichment by applying Gene Fraction Enrichment Score (GFES), a novel statistic method that controls for differing neuronal proportions across regions. ASD-associated genes identified by exome sequencing were most enriched in the thalamus followed by the cortex. Schizophrenia genes from genome-wide association studies were also enriched in the thalamus, along with the hippocampus and cortex. These findings add to the evidence that the thalamus plays a major role in neuropsychiatric disorders whilst supporting roles for the cortex and hippocampus. The results highlight shared and distinct patterns for pleiotropic brain disorders that could elucidate common underlying mechanisms and circuitry.

neuroscience↗

bioRxiv2026

A neuropsychiatric disease-associated mutation in LRRC8B disrupts cellular calcium signaling, mitochondrial function, and bioenergetics

Leucine-rich repeat-containing 8 (LRRC8) proteins form the volume-regulated anion channel (VRAC) and participate in diverse physiological processes, including cell volume regulation, gliotransmitter release, and insulin secretion. In mammals, five paralogs (LRRC8A-E) exist; LRRC8A is the obligatory subunit that assembles into functional hexameric channels with LRRC8C, D, or E. LRRC8B is distinct: we previously demonstrated its role in regulating endoplasmic reticulum (ER) Ca{superscript 2} homeostasis and ER Ca{superscript 2} leak. A LRRC8B variant (Y380S) identified in an Indian family with severe mental illness has been associated with disease pathology, but its molecular and cellular consequences remain unknown. Here, we show that this disease-associated mutant perturbs Ca{superscript 2} signalling, mitochondrial bioenergetics, and redox homeostasis. Both wild-type and mutant LRRC8B localize to the ER and mitochondria. LRRC8B knockdown significantly reduced mitochondrial Ca{superscript 2} uptake and maximal respiratory the Y380S mutant phenocopied LRRC8B knockdown, altering ER Ca{superscript 2} release, elevating basal cytosolic Ca{superscript 2}, and impairing mitochondrial Ca{superscript 2} uptake, consistent with a dominant-negative mechanism. The mutant further induced mitochondrial dysfunction, including loss of membrane potential, oxidative stress, and defective antioxidant responses, ultimately compromising cellular bioenergetics and viability. Mechanistically, the Y380S mutation disrupted LRRC8B interaction with the mitochondrial outer membrane channel VDAC. These findings identify LRRC8B-VDAC coupling as a key determinant of mitochondrial Ca{superscript 2} handling and provide a mechanistic link between LRRC8B dysfunction and neuropsychiatric disease. HighlightsO_LIA psychiatric disease-associated LRRC8B variant (Y380S) acts as a dominant-negative regulator of ER Ca{superscript 2} homeostasis. It enlarges the releasable ER Ca{superscript 2} pool and reduces cell viability. C_LIO_LILRRC8B promotes mitochondrial Ca{superscript 2} uptake through interaction with VDAC. The Y380S mutation disrupts this interaction, reducing mitochondrial Ca{superscript 2} uptake. C_LIO_LIThe Y380S mutant increases mitochondrial superoxide production without activating compensatory antioxidant responses. C_LIO_LIThe mutant also causes mitochondrial membrane depolarization and bioenergetic failure, as evidenced by reduced oxygen consumption rate and ATP production. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/718892v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@1f314d3org.highwire.dtl.DTLVardef@1dc3908org.highwire.dtl.DTLVardef@124445aorg.highwire.dtl.DTLVardef@39326_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2026

PROTAC internalization and target degradation require clathrin-mediatedendocytosis

Proteolysis-targeting chimeras (PROTACs) are emerging as potent tools for targeted protein degradation that overcome many of the limitations of traditional small molecule inhibitors. Yet how these hetero-bifunctional therapeutics enter cells remains a mystery. While passive diffusion is conventionally assumed, the bulky structure of PROTACs suggests that active transport may be required. Recently, the fatty acid transporter CD36 was identified as a key receptor for PROTACs. However, because the uptake mechanism of CD36 is itself unknown, how PROTACs enter cells remains a mystery. Here we show that PROTAC uptake and function require clathrin-mediated endocytosis. We uncover previously unrecognized clathrin adaptor-binding motifs in the CD36 C-terminus and use live-cell imaging to visualize the recruitment of both CD36 and PROTACs to sites of clathrin-mediated endocytosis on the cellular plasma membrane. Strikingly, disruption of clathrin assembly through either genetic or pharmacological means abolishes all detectable PROTAC-induced protein degradation, demonstrating that the clathrin pathway is required for the function of PROTACs that utilize diverse E3 enzymes against multiple targets. These results elucidate the molecular mechanism of PROTAC entry into cells, providing critical information for optimizing cellular uptake and response to targeted degraders.

pharmacology and toxicology↗

bioRxiv2026

ELMO1 dependent efferocytosis protects from nephrotoxin induced acute kidney injury

Acute kidney injury (AKI) is a sudden episode of kidney failure linked to a wide range of health conditions. High mortality in AKI highlights the need to identify new therapeutic approaches. Homeostasis in multicellular organisms is exquisitely regulated by phagocytosis of apoptotic cells, also known as efferocytosis. Apoptotic cells are frequently observed at sites of inflammation, including in AKI. Engulfment and cell motility protein-1 (ELMO1) is a regulator of the actin cytoskeleton that promotes apoptotic cell removal by phagocytes during efferocytosis. Mutations in the human ELMO1 gene are linked with diabetic nephropathy and, in animal models of this disease, high ELMO1 levels promote renal dysfunction. However, the role of ELMO1 in AKI was not known. Here, we describe the links between ELMO1 and kidney pathology and test global and tissue-specific ELMO1-deficient mice in models of AKI. While global loss of Elmo1 expression did not impact the immediate loss of renal function after ischemia-reperfusion elicited AKI, ELMO1 deficiency resulted in increased tissue injury in AKI caused by cisplatin injection. Cisplatin induced robust renal cell apoptosis that was significantly elevated in mice with the global loss of ELMO1, but not in mice with the macrophage-specific Elmo1 deletion. Using primary cell culture and immunofluorescence approaches, we highlight the role of ELMO1 in efferocytosis by several renal cell types, suggesting possible additive effects during nephrotoxic injury.

pathology↗

bioRxiv2026

POLQ-driven repair scars shape the immunogenic landscape of homologous recombination-deficient pancreatic cancer

Pancreatic cancer (PC) is broadly resistant to immune checkpoint blockade, although a subset of homologous recombination-deficient (HRD) tumors exhibits durable immune engagement. The genomic features that distinguish these immune-responsive tumors from immune-inert HRD tumors remain poorly understood. Here we identify a microhomology-mediated end joining (MMEJ) repair scar, the MMEJ Deletion Footprint (MDF), as a genomic readout of POLQ-associated error-prone repair that enriches for frameshift indels. Across the multi-omic discovery cohort integrating tumor genomics, single-nucleus transcriptomics and spatial immune profiling, MDF-high HRD PC exhibited increased frameshift-indel-derived neoantigens and interferon programs. MDF was further associated with remodeling of the myeloid compartment toward MHC II-high dendritic cell-like antigen-presenting macrophage states and the immune synapse architecture marked by increased spatial interaction between APC-like macrophages and cytotoxic CD8+ T cells. These tissue-level features aligned with a functional trajectory shift of CD8+ T cells, consistent with effective anti-tumor immunity and was associated with favorable clinical outcomes of patients. Together, our findings position MMEJ-linked repair scarring as actionable biology that connects an HRD genotype to immune organization and suggests rational immunotherapy combinations that may enhance antigen presentation and myeloid activation to extend durable benefit in HRD-lineage cancers.

cancer biology↗

bioRxiv2026

MEF2A is a negative regulator of β-Cell maturation and function

Pancreatic beta cells produce and secrete insulin to maintain glucose homeostasis. Due to their high secretory activity, beta cells rely heavily on endoplasmic reticulum (ER) function and are particularly susceptible to ER stress, which contributes to beta cell dysfunction in diabetes. However, the transcriptional mechanisms linking ER stress to beta cell failure remain poorly understood. In this study, we investigated the role of the transcription factor Mef2a in ER stress-mediated beta cell dysfunction using primary mouse islet cells. ER stress induced by thapsigargin increased Mef2a expression and activated canonical unfolded protein response (UPR) pathways. Overexpression of Mef2a reduced beta cell proliferation, suppressed expression of key beta cell transcription factors including Pdx1, MafA, NeuroD1, and Nkx6.1, and impaired glucose-stimulated insulin secretion. Mef2a overexpression also altered mitochondrial respiration, characterized by reduced glucose-coupled respiration and increased maximal respiratory capacity. In contrast, Mef2a knockdown attenuated ER stress induced activation of ATF6 and IRE1/XBP1 dependent UPR genes. Importantly, reducing Mef2a expression preserved beta cell identity gene expression and improved insulin secretion during ER stress induced by thapsigargin or tunicamycin. Together, these findings identify Mef2a as a stress-responsive regulator that contributes to ER stress-mediated beta cell dysfunction and suggest that modulating Mef2a activity may help preserve beta cell function during metabolic stress.

molecular biology↗

bioRxiv2026

Suppression of early pro-inflammatory senescent signature post-radiotherapy mitigates chronic bone damage

Cellular senescence has been implicated in the pathophysiology of radiotherapy-related bone loss. Based on our previous work, clearance of senescent cells using genetic and pharmacological tools alleviates the anomalies associated with radiation-associated bone deterioration. The pro-inflammatory senescence associated secretome referred to as senescence associated secretory phenotype (SASP), is a hallmark of cellular senescence. The modulation of SASP by senomorphic drugs, potentially can suppress the pro-inflammatory secretome of senescent cells, irrespective of the underlying senescence mechanism. In this study we tested a senomorphic drug, ruxolitinib, a Janus kinase inhibitor (JAKi), during acute and chronic radiotherapy related effects on the bone. Our clinical data indicate an early increase in several pro-inflammatory SASP proteins following radiotherapy of spinal metastasis in prostate cancer patients. Longitudinal assessment of SASP-related genes confirmed this acute elevation in several SASP markers in systemic circulation following irradiation of mouse femurs. In a proof-of-concept study, following two preclinical radiotherapy regimens of cumulative doses of 30Gy (5 x 6Gy) and 60Gy (5 x 12Gy), a senomorphic approach of JAKi treatment was more effective in alleviating radiation-related bone loss compared to the senolytic cocktail of D+Q. Early and intermittent suppression of SASP using JAK inhibitors alleviated chronic bone deterioration, diminished telomere dysfunction, lowered senescence and SASP marker expression, reduced bone-marrow adiposity, and mitigated radiation related lymphatic impairment. Overall, our study shows that early targeting of SASP proteins could be a potential therapeutic to prevent radiotherapy-related chronic bone loss and risk of fractures. Lay SummaryRadiotherapy as part of cancer treatment is correlated with an acute increase in senescent cells. Here we show that the pro-inflammatory senescence associated secretory phenotype (SASP) becomes much more prominent soon after radiotherapy in both patients and mice. Suppression of the SASP using a Janus kinase inhibitor, ruxolitinib, reduced the overall senescent cell burden, improved bone architecture by promoting bone formation, reduced bone marrow adiposity, and mitigated radiation-induced lymphatic impairment. Overall, these findings suggest that early inhibition of the SASP may help mitigate several bone anomalies and prevent long-term bone loss and fractures after radiotherapy. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=132 SRC="FIGDIR/small/708630v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@1487404org.highwire.dtl.DTLVardef@1b8e481org.highwire.dtl.DTLVardef@1a20032org.highwire.dtl.DTLVardef@baf75b_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2026

4,5-dihydroxyhexanoic acid is a robust circulating and urine marker of mitochondrial disease and its severity

Management of patients with mitochondrial respiratory chain diseases is challenging, in part because of our incomplete understanding of pathogenesis and a lack of biomarkers. Unknown metabolites account for >90% of detected features in modern metabolomics experiments and hold immense untapped promise for new basic and biomedical research. We recently used mass spectrometry-based metabolomics to identify and validate 19 circulating blood-based biomarkers for patients with the mitochondrial DNA (mtDNA) m.3243A>G pathogenic variant, which is the most frequent cause of the mitochondrial disorder MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes). However, the most significantly changing biomarker corresponded to an "unknown" metabolite. Here, we combine cheminformatics with analytical chemistry and identify that feature as 4,5-dihydroxyhexanoic acid (4,5-DHHA), a metabolite previously associated with inherited defects of gamma-aminobutyric acid (GABA) catabolism, but with no prior links to mitochondrial respiratory chain disorders. We validate this finding in an independent MELAS cohort and further show that 4,5-DHHA levels correlate with disease severity and are elevated in patients with other forms of mitochondrial disease and sepsis. Furthermore, brain 4,5-DHHA levels were elevated in two genetic mouse models of mitochondrial disease. In vitro and tissue culture experiments indicate that 4,5-DHHA is generated when the GABA catabolite succinic semialdehyde reacts with an intermediate of the pyruvate dehydrogenase reaction and is sensitive to mitochondrial complex I function. Our work identifies 4,5-DHHA as a robust plasma and urine marker of mitochondrial dysfunction in humans and reveals new connections between the respiratory chain and GABA metabolism. Significance StatementInborn errors of the mitochondrial respiratory chain cause severe, progressive diseases, yet effective treatments and biomarkers remain limited. Modern metabolomics detects thousands of molecules in biofluids, but the vast majority are unidentified. In this study, we investigate the most significantly altered blood metabolite in patients with the most common mitochondrial disease - MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes) - and identify it as an 4,5-dihydroxyhexanoic acid (4,5-DHHA). We show that 4,5-DHHA is reproducibly elevated and correlates with severity. Levels are increased across multiple mitochondrial disorders as well as in sepsis and rise when respiratory chain function is impaired. These findings establish 4,5-DHHA as a promising biomarker of mitochondrial dysfunction and reveal a link to dysregulated GABA metabolism.

biochemistry↗

bioRxiv2026

Telomere length of both parents contribute to heritable POT1 cancer-predisposition syndrome

Germline mutations in POT1 are linked to familial cancer predisposition, and somatic POT1 mutations occur recurrently in tumors. These mutations promote oncogenesis by enabling aberrant telomere elongation. For inherited POT1 mutations, a critical question is the extent to which elongated telomeres are transmitted to the next generation from the POT1 carrier parent and whether the inherited excessively long telomeres elevate cancer risk. Using a nanopore sequencing approach that provides haplotype-specific telomere length measurements, we examined telomere inheritance in families harboring POT1 mutations. We found that individuals preferentially inherit their longest telomeres from the carrier parent, consistent with extensive telomere elongation in the carrier germline, whereas comparatively short telomeres are predominantly inherited from the non-carrier parent. Analysis of carrier and non-carrier siblings further showed that telomeres inherited from both parents are elongated in POT1 carriers, with the shortest telomeres undergoing preferential elongation. These findings support a potential mechanism of genetic anticipation in which POT1 mutations progressively reduce the likelihood that short telomeres capable of enforcing telomere-based tumor suppression are inherited from the carrier parent. Together, our results demonstrate that telomeres inherited from both parents jointly shape telomere-based tumor suppressive barriers. Summary sentenceAllele specific nanopore sequencing reveals that POT1 mutations reshape germline and somatic telomere dynamics, uncovering a novel mechanism of generational anticipation driven by preferential elongation of short inherited telomeres.

genetics↗