Biology subjects

Sharma, A.

Publications and source records attributed to Sharma, A..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Candidozyma auris utilizes transferrin, but not heme-bound iron for in vivo virulence

Candidozyma auris (C. auris) is an emerging multidrug-resistant fungal pathogen, and its dissemination to the bloodstream and deep-seated organs is associated with high mortality. The limited antifungal armory and pipelines against C. auris pose a major challenge in disease management. Addressing this threat requires a deeper understanding of fungal virulence mechanisms that promote persistence and of host factors that drive susceptibility. Previous in vitro studies showed that iron enhances C. auris resistance to azoles and echinocandins, whereas iron chelation mitigates this effect. Here, we demonstrate that C. auris does not utilize cell-free heme or induce hemolysis but instead extracts and uses iron from transferrin to support growth and virulence. Deletion of the SIT1 siderophore transporter in C. auris attenuated fungal growth and reduced renal injury, while increased transferrin-iron saturation worsened disease outcomes in immunocompetent mice, highlighting the importance of transferrin-bound iron uptake. Mechanistically, C. auris exploits transferrin-bound iron to enhance ergosterol biosynthesis and activate antioxidant defenses, promoting resistance to neutrophil- and caspofungin-mediated killing. These findings identify elevated transferrin saturation as a novel host susceptibility risk factor for disseminated C. auris infection and reveal how iron availability reshapes fungal physiology to drive infection persistence.

microbiology↗

bioRxiv2026

Chronic Mild Stress Impairs Hippocampal Myelination through SOX6-Dependent Dysfunction of Oligodendrocyte Lineage Cells

Chronic stress induces structural and functional changes in the brain, increasing susceptibility to major depressive disorder and other mental illnesses. Myelination deficits are a key pathological feature of stress-related disorders, yet the molecular mechanisms linking chronic stress to oligodendrocyte dysfunction remain poorly understood. Here, we used single-nucleus multiome sequencing to map gene expression and chromatin-accessibility remodeling in the hippocampus of mice exposed to chronic unpredictable mild stress (CUMS), a model that simulates key features of human daily stressors. CUMS induced broad molecular reprogramming across hippocampal cell populations, with stress-responsive gene networks significantly enriched for depression-associated genes. The oligodendrocyte lineage showed heightened vulnerability, with CUMS preferentially disrupting immature OPC/intermediate states and impairing OPC migration, OPC-to-ODC lineage progression, intercellular communication, and myelination. Integrated multiomic analysis identified stage-specific cis-regulatory elements and stress-sensitive gene regulatory networks, converging on SOXD transcription factors, particularly SOX5 and SOX6, as key regulators of OPC dysfunction. SOX6 ChIP-seq confirmed direct SOX6 binding at regulatory elements associated with genes controlling OPC morphogenesis, migration, and glutamatergic signaling. CUMS reduced SOX6 protein levels and SOX6-associated regulatory network activity in OPCs, whereas OPC-specific enhancer-driven restoration of SOX6 rescued stress-induced defects in OPC migration and myelination. Together, these findings define a stress-sensitive SOXD/SOX6 regulatory mechanism linking chronic stress to oligodendrocyte lineage dysfunction and myelination deficits, identifying SOX6 as a functional regulatory node with therapeutic potential for stress-related brain pathology.

neuroscience↗

bioRxiv2026

Expanded Proteome Coverage Powered by Advanced Ion Processing Enables Deep Single-Cell Drug Response Subtyping in Human Stem Cell Derived Cardiomyocytes

Single-cell proteomics (SCP) enables the study of cellular heterogeneity at the functional level but remains limited by incomplete proteome coverage and high data missingness. Here, we present an enhanced label-free SCP workflow that leverages the timsUltra AIP mass spectrometry platform equipped with the Athena Ion Processor (AIP). Across a controlled dilution series of human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs), AIP-enabled acquisition consistently increased proteome depth and detection consistency across cells at all input levels. In single iPSC-CMs, the timsUltra AIP quantified up to 3,858 protein groups, averaging [~]1,300 proteins per cell, enabling robust proteome-level classification of cardiomyocyte subtypes. Using a reference-based protein classifier, cells were stratified into mature cardiomyocytes and less differentiated cell states, revealing substantial baseline heterogeneity. Importantly, increased single-cell sensitivity translated directly into biological insight, as approximately 30% of differentially expressed proteins associated with subtype-specific drug responses were detected exclusively by timsUltra AIP. Application of this workflow to PR-364 (a mitophagy boosting drug) dose-response experiment uncovered distinct, subtype-dependent pathway adaptations. Mature cardiomyocytes exhibited dose-dependent increases in mitochondrial and metabolic pathway activity, while immature cells showed enrichment of cytoskeletal and developmental programs. These effects were partially obscured in simulated bulk analyses, highlighting the value of single-cell resolution. Together, these results demonstrate that improved fragment ion transmission and utilization translate directly into enhanced biological insight, enabling more comprehensive and functionally relevant single-cell proteomics.

molecular biology↗

bioRxiv2026

Oncofetal RNA-binding proteins of IGF2BP family suppress IRF-3 and NF-kB dependent transcription downstream of cytosolic RNA sensors

Activation of innate inflammatory signaling and tumor-specific antigen presentation in cancer cells provides a foundation for anti-cancer immunotherapies. Here, we show that the insulin-like growth factor 2 mRNA-binding proteins (IGF2BP1, IGF2BP2, and IGF2BP3), which are upregulated across diverse human malignancies, including acute myeloid leukemia (AML), suppress RNA-sensing pattern recognition receptor signaling and downstream ISRE-and NF-{kappa}B-dependent transcription. Among these pathways, RIG-I signaling is particularly sensitive to IGF2BP-mediated inhibition. This suppressive effect is strongest when all three IGF2BP paralogs are co-expressed, especially in embryonic-like hematoendothelial cells and leukemia stem cells. Mechanistically, IGF2BPs suppress innate immune signaling by directly binding to TNFAIP3 mRNA and promoting its expression. Consequently, inhibition of IGF2BPs activates innate immune signaling and induces MHC class I gene expression in AML cells, highlighting IGF2BPs as promising therapeutic targets to enhance RIG-I- and TLR-based cancer immunotherapies. HighlightsO_LIIGF2BP family of proteins regulate PRR responses C_LIO_LIIGF2BP levels affect chromatin accessibility and pan-transcriptome C_LIO_LISV40 large T antigen induces de novo expression of IGF2BPs C_LIO_LITNFAIP3 mRNA levels and stability are regulated by IGF2BPs C_LI

cancer biology↗

bioRxiv2026

Detoxification of host-relevant H2O2 shapes Pseudomonas aeruginosa population gradients in flow

During infection, bacterial populations need to overcome low levels of host-generated H2O2. However, experiments almost always use high H2O2 levels that are rarely found in hosts. Here, we use microfluidics to investigate how host-relevant H2O2 impacts populations of the human pathogen Pseudomonas aeruginosa in flow. Using long-channel microfluidic devices, we establish that cells at the front of a population remove H2O2 and protect their downstream neighbors. Population-level protection is mediated by three OxyR-regulated scavenging systems (KatA, KatB, AhpCF), which are each sufficient to detoxify host-relevant H2O2. Mutants lacking all three systems are sensitive to H2O2 but can be cross-protected by resistant cells when co-cultured. Cross-protection is abolished in higher flow regimes, where H2O2 is delivered faster than cells can remove it. Our results demonstrate how local detoxification provides global protection, which results in spatial gradients across bacterial populations in flow. Together, our findings highlight how biological, chemical, and physical factors collectively determine the fate of bacterial populations in host-relevant environments.

microbiology↗

bioRxiv2026

The Chromosome-Scale Genome of Phyllanthus niruri Reveals Candidate Genes and a Putative Biosynthetic Framework for Phyllanthin Formation.

Phyllanthus niruri (Phyllanthaceae) is a medicinally important herb known for producing phyllanthin, a bioactive dibenzylbutane lignan with reported hepatoprotective and antioxidant properties. However, the biosynthetic basis of phyllanthin production remains unresolved, largely due to the absence of a reference genome for the species. We report a Chromosome-Scale Assembly of P. niruri generated by integrating PacBio HiFi long reads and Illumina short reads, followed by reference-guided scaffolding against Phyllanthus cochinchinensis. The assembly has an L50 of 7 and 97.6% BUSCO completeness. Annotation predicted 19,254 protein-coding genes (91.1% functionally annotated), with phenylpropanoid biosynthesis emerging as the most enriched specialized-metabolism pathway in the genome. Using pathway-guided genome mining, structural similarity analysis, and comparative metabolic reconstruction, we propose a putative biosynthetic pathway for phyllanthin originating from the phenylpropanoid-lignan branch through secoisolariciresinol-like intermediates, followed by terminal O-methylation reactions. A total of 305 unique candidate genes associated with the proposed pathway were identified, including expanded families of dirigent proteins, peroxidases, secoisolariciresinol dehydrogenases, and O-methyltransferases. Comparative transcriptomic analyses across related Phyllanthus species further supported the proposed pathway through coordinated expression of lignan-associated genes and tissue-specific enrichment of O-methyltransferases. This work provides the first reference genome for P. niruri and a prioritized candidate gene set for functional characterization of phyllanthin biosynthesis.

genomics↗

bioRxiv2026

Dual-compartment engagement of STAR-family proteins SAM68 and QKI by LINC00941 sustains oncogenic fitness in RAS-driven lung cancer

Long non-coding RNAs (lncRNAs) are increasingly recognised as effectors of oncogenic signalling, yet the transcriptional programmes through which driver mutations regulate lncRNA expression remain poorly defined. Here we identify LINC00941 as a direct transcriptional target of FOSL1, an AP-1 transcription factor downstream of the KRAS-MAPK pathway, establishing the first FOSL1-regulated lncRNA in lung adenocarcinoma (LUAD). LINC00941 is significantly upregulated in LUAD across multiple independent cohorts, and its depletion via siRNAs, shRNAs, and antisense oligonucleotides (ASOs) induces proliferative arrest and stress-induced premature senescence, accompanied by transcriptomic suppression of cell cycle and DNA damage response (DDR) genes. Mechanistically, LINC00941 operates through a dual-compartment mechanism engaging two STAR-family RNA-binding proteins in distinct subcellular contexts. In the nucleus, LINC00941 binds SAM68 through its 700-1300 nucleotide region and shields it from proteasomemediated degradation, thereby sustaining SAM68-dependent PARP1 activation and DDR competency; RNF123 is identified as a candidate E3 ligase mediating SAM68 turnover in the absence of LINC00941. In the cytoplasm, LINC00941 sequesters QKI, preventing its nuclear translocation; LINC00941 depletion releases QKI to the nucleus, driving alternative splicing dysregulation including validated NUMB exon 12 exclusion, and QKI co-depletion rescues the anti-proliferative phenotype both in vitro and in xenograft models. Multi-cohort survival analysis across three independent LUAD datasets (n=649) identifies LINC00941 as an independent prognostic factor for poor overall survival. Gymnotic ASO-mediated targeting of LINC00941 significantly suppresses xenograft tumour growth without systemic toxicity, providing preclinical proof-of-concept for therapeutic tractability. Together, these findings establish LINC00941 as a compartment-specific oncogenic scaffold within the KRAS-FOSL1 transcriptional axis and a tractable therapeutic target in LUAD.

cancer biology↗

bioRxiv2026

Extreme Hydrophobicity of Cytotoxic Drugs Enables Design of Next Generation Antibody-Drug Conjugates Nanotherapeutics

Antibody and protein-drug conjugates (XDCs) have emerged as promising cancer therapeutics, yet their clinical utility remains constrained by dose-limiting toxicities and narrow therapeutic windows. These safety challenges stem primarily from two factors: premature payload release during systemic circulation, and poor physicochemical properties inherent to the hydrophobic cytotoxic drugs they carry. Prior strategies attempted to address these limitations by appending water-soluble tags to reduce overall conjugate hydrophobicity, but achieved only modest improvements. As a result, the hydrophobic nature of cytotoxic payloads has remained a persistent obstacle in XDC development. Here, we report a fundamentally different chemical strategy that reframes this liability as a design opportunity. Rather than masking drug hydrophobicity, we exploit it as the driving force for self-assembly of facially amphiphilic protein-drug conjugates with programmable drug moieties (PDCs). In this architecture, the hydrophobic cytotoxic drug and the hydrophilic protein serve as the core and shell, respectively, spontaneously assembling into monodisperse, well-defined spherical protein nanotherapeutics of controlled size. This design principle transforms a longstanding physicochemical challenge into a functional engineering tool, enabling precise nanostructure formation without sacrificing potency. In vitro studies confirm that the resulting nanotherapeutics effectively kill cancer cells, establishing a strong foundation for further therapeutic development.

pharmacology and toxicology↗

bioRxiv2026

South Asian Maternal Lineage haplogroup R30 Provides Phylogenetic Evidence of human dispersal across South Asia

South Asia is central to debates on early human dispersals, particularly the Out of Africa model and Eurasian colonization. Studies of M haplogroups have been used to support both Northern and Southern route hypotheses, but current archaeological and genetic evidence in the region remains contradictory. In the present work, we find that in addition to haplogroup M lineages, a few R lineages exhibit ancient, locally rooted variation, with R30 being one of the widespread haplogroup of R lineages across South Asia. To better understand South Asian demographic history, we investigated the phylogeographic distribution of haplogroup R30, an indigenous lineage. We used 190 complete modern and ancient sequences from diverse mainland and island populations including incorporation of 44 newly generated sequences which enabled the refinement of the R30 phylogeny and the identification of a novel basal lineage, R30c. Bayesian and {rho}-based age estimates suggest that R30 originated in the Indian subcontinent ~50 kya. Early diversification likely occurred in Northern India, giving rise to R30b (~44 kya), while R30a and R30c differentiated primarily in Southern India. Several subclades of haplogroup R30 exhibit strong signatures of founder effects, particularly among the language isolate Vedda of Sri Lanka, Uru Kurumban of Southern India, and the populations of the Lakshadweep archipelago. Bayesian skyline analyses indicate long-term demographic stability followed by rapid lineage expansion ~20 kya and more recent declines consistent with localised drift and relatively recent founder events. The presence of early-diverging R30 lineages in Thailand and Indonesia further supports long-term connections between South and Southeast Asia. Overall, archaeological and genetic evidence point towards the multiple migrations for South Asia colonizations.

evolutionary biology↗

bioRxiv2026

Dynamic s-acylation of schizophrenia-linked antioxidants explicate the redox flexibility of human microglia during inflammation.

Cysteine proteome essentially regulates cellular adaptability during stress. Proteomic cysteines are reversibly modified to avoid loss through oxidation. Reversible cysteine-modifications beneficially preserve cellular stress-response mechanisms by regulating the transient activation of substrate proteins. Cysteine acylation (or s-acylation) is one such extensively documented reversible protein modification. Inflammation-responsive changes in s-acylation facilitate the plasticity of immune-partitioned brains by dynamically determining the utilization of stress-buffering (substrate) cysteine-proteins in microglia, the primary immune-reactive brain cells. However, the inflammation-responsiveness of cysteine-acylation in microglia is not elaborately measured at a large-scale. Therefore, we observed the differential (quantitative) s-acylation of proteins in cultured human (HMC3) microglia by implementing comparative MLCC-based chemoproteomic workflows. Parallelly, we characterized the molecular consequences of HMC3 cell treatment with 2-bromopalmitate, a general s-acylation inhibitor, by performing immunocytochemistry and proteomic experiments. We also identified the s-acylation-dependent microglial inflammatory responses through live spatiotemporal tracking and confocal microscopy, following treatment of microglia with PAMPs (LPS or IFNy). Finally, from our proteomic studies of postmortem human brain tissues, we confirmed major protein-causals of schizophrenia, a redox-related brain disorder, to undergo inflammation-responsive s-acylation. This report provides a first comprehensive library of cysteine-proteins differentially processed through inflammation-responsive acylation in microglia. It also outlines the inflammation-responsive s-acylation of key NRF2-antioxidants, including peroxiredoxins (especially PRDX2) and glutathione synthetase (GSS), as a biochemical signature of early-stage inflammation and oxidative-stress in microglia. More importantly, the innovative proteo-informatic workflows designed for this research work can be reliably repurposed to identify bifunctional theragnostic protein markers of many complex disorders and diseases.

biochemistry↗

bioRxiv2026

Cannabidiol rescues age-associated cognitive decline in mouse model

This study addresses key gaps in our understanding of the cognitive changes associated with normal brain aging and their underlying structural and functional correlates. Declining levels of brain endocannabinoids (eCB), particularly 2-arachidonoylglycerol (2-AG), are thought to contribute to age-related cognitive impairment, but the mechanisms involved remain poorly understood. Here, we show that levels of 2-AG and its synthesizing enzyme, diacylglycerol lipase- (DAGL-), are significantly reduced in the medial prefrontal cortex (mPFC) of aged mice. This decline is associated with impairments in mood and memory, as demonstrated by behavioral analyses. Immunofluorescence studies further revealed reduced expression of cannabinoid receptors CB1 and CB2 on microglia in aged brains, suggesting that diminished eCB signaling may contribute to enhanced neuroinflammation. Consistent with this idea, microglia from aged mice exhibited increased HMGB1-TLR4-NF-{kappa}B signaling, indicative of a pro-inflammatory state. LC-HR-MS analysis also showed elevated glutamate levels and reduced glutamine and GABA levels in the mPFC, linking impaired eCB signaling to excitotoxic imbalance during aging. Importantly, intraperitoneal administration of cannabidiol (CBD) to aged mice reversed mood and memory deficits, restored CB1 and CB2 receptor expression, attenuated HMGB1-TLR4-NF-{kappa}B signaling, and normalized the glutamate-glutamine/GABA balance in the mPFC. Collectively, these findings identify eCB signaling as a critical regulator of age-associated cognitive decline and support CBD as a potential therapeutic strategy to promote healthy brain aging. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=188 SRC="FIGDIR/small/711942v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@e9c9ddorg.highwire.dtl.DTLVardef@c3fbd2org.highwire.dtl.DTLVardef@c9d5eforg.highwire.dtl.DTLVardef@fc4371_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIReduction of 2-AG in the brains medial prefrontal cortex (mPFC) over time is a hallmark of cognitive decline. C_LIO_LIPro-inflammatory signalling such as HMGB1 (High Mobility Group Box 1)-TLR4 (Toll-like receptor 4)-NF-kB (Nuclear Factor kappa B) signalling are elevated in aged brain. C_LIO_LIAltered glutamine-glutamate/GABA cycle associated with reduced 2-AG levels. C_LIO_LICBD administration mitigates cognitive decline associated with aging and diminishes neuroinflammation. C_LI

neuroscience↗

bioRxiv2026

PRMT5 as an Epigenetic Target for Group 3 (MYC-driven) Medulloblastoma

BackgroundGroup 3 (MYC-driven) medulloblastoma (MB) is a highly aggressive brain tumor with poor-prognosis and limited treatment options. We previously identified protein-arginine methyltransferase-5 (PRMT5) as a promising target in Group 3 MB with its control on MYC protein stability. In this follow up study, we further mechanistically investigated PRMT5 control on MYC transcription and targeted it pharmacologically for therapeutic proof-of-concept. MethodsUsing pharmacogenetic inhibition approaches against PRMT5 in MYC-amplified (Group 3) MB cell line and neurosphere models in vitro and in vivo, we investigated molecular mechanism(s) and anti-cancer efficacy of PRMT5 inhibition. ResultsOur experiments demonstrated that PRMT5 epigenetically regulates MYC transcription in MYC-amplified MB cells by binding to the proximal-promoter region of the MYC gene and contributing to the enriched symmetric-dimethylation of histone H4R3 in the same region. We further showed that PRMT5 is recruited to the MYC promoter by its interaction with BRD4, the major BET-protein responsible for MYC transcription. PRMT5 inhibition caused the suppression of MYC-induced transcriptional programs and target genes, with widespread disruption of splicing across the transcriptome, particularly affecting metabolism-related gene products. Pharmacologic inhibition of PRMT5 using a panel of selective small-molecule inhibitors demonstrates suppression of cell growth/survival in a MYC-dependent manner in MB cells. Moreover, our in vivo analyses of PRMT5 inhibition, in mice treated with one of the potent pharmacologic inhibitors, particularly a lipid-decorated form of it, demonstrated reduced cerebellar tumor growth with suppressed MYC expression and prolonged survival of mice with MYC-amplified MB xenografts. ConclusionsOur findings establish a functional link between PRMT5 and MYC-mediated transcriptional regulation, suggesting a promising therapeutic approach targeting the PRMT5-MYC axis for MYC-driven MB. Key PointsO_LIPRMT5 acts as an epigenetic regulator of MYC transcription, RNA splicing and associated energy metabolism in MYC-driven MB. C_LIO_LIPRMT5 inhibition selectively suppresses cell growth/survival in MYC-driven MB. C_LIO_LIPRMT5 inhibition reduces tumor burden and prolongs survival in a MYC-driven MB mouse model. C_LI Importance of the StudyGroup 3 medulloblastoma is a highly aggressive pediatric brain tumor marked by MYC amplification, malignant clinical behavior, and poor survival outcomes despite intensive multimodal therapy. Because MYC remains largely undruggable, there is an urgent need for effective and less toxic treatment options for affected children. This study identifies protein arginine methyltransferase 5 (PRMT5) as a key epigenetic regulator of MYC transcription and MYC-dependent oncogenic programs in Group 3 MB. We show that PRMT5 is recruited to the MYC promoter via BRD4, sustains MYC-driven transcription and RNA splicing networks associated with metabolism, and supports MB tumor growth. Importantly, pharmacologic inhibition of PRMT5 using a selective brain-penetrant inhibitor suppresses MYC expression, reduces cerebellar tumor burden, and prolongs survival in MYC-amplified MB models. These findings provide a strong translational rationale for PRMT5 inhibition as a targeted therapeutic strategy for high-risk MB, with the potential to improve outcomes while reducing treatment-related toxicity.

cancer biology↗

bioRxiv2026

Pipette: Encoding scientific literature into an executable Skill Graph for multi-agent bioinformatics

The cost of genomic sequencing has fallen by several orders of magnitude, yet data analysis remains a bottleneck concentrated among researchers with specialized computational expertise. While Large Language Models can generate bioinformatics code, they frequently produce incoherent multi-step workflows due to the absence of domain-specific analytical constraints. Here, we present Pipette, a multi-agent AI framework that orchestrates end-to-end bioinformatics workflows through natural language interaction, guided by a literature-derived Skill Graph. This directed, edge-weighted knowledge graph, extracted from over 20,000 peer-reviewed publications, constrains workflow generation to biologically valid analytical transitions, preventing incomplete or incoherent workflows. We benchmarked Pipette across four biological domains using published datasets: single-cell RNA-seq analysis of peripheral blood mononuclear cells and a human pancreas atlas, bulk RNA-seq differential expression in rice under environmental stress, and two structure-based computational drug design workflows. In ablation against two LLMs operating without Skill Graph constraints, Pipette matched or exceeded both baselines across all quantitative metrics while uniquely completing multi-step cross-domain transitions. We further evaluated Pipette on a clinical genomics task, where it executed an ACMG/AMP-compliant variant classification on a reference human genome. In all cases, Pipette recapitulated established biological and clinical findings while generating a fully reproducible, machine-readable provenance record. By reducing the computational expertise required to execute standard genomic analyses, Pipette lowers the barrier between sequencing data and biological insight for bench scientists. Pipette is available at https://pipette.bio.

bioinformatics↗

bioRxiv2026

Microprotein Regulates G-quadruplex Driven RNA Aggregation

Repeat expansions of the hexanucleotide GGGGCC in C9orf72 form aberrant phase transitions that have been linked to Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. RNA structures such as G-quadruplexes and hairpins play important roles in these processes. Here, we show that the human microprotein ZNF706 acts as a modulator of G-quadruplex formation and RNA phase behavior. ZNF706 antagonizes pathological gel-solid transitions by melting hexanucleotide repeat G-quadruplex structures converting gel-like aggregates into more dynamic condensates. Loss of ZNF706 enhances the cellular production clearance of hexanucleotide repeat-mediated dipeptide repeat proteins, while overexpression suppresses their production and promotes clearance. Mechanistically, ZNF706 influences hexanucleotide repeat condensate fluidity and viscoelasticity. We find ZNF706 acts as an RNA chaperone that remodels repeat RNA structures and solubilizes RNA aggregates. This activity represents one mechanism whereby cells can regulate G-quadruplex driven phase transitions linked to neurodegenerative diseases.

cell biology↗

bioRxiv2026

Title: Multimodal profiling reveals Mycobacterium tuberculosis restricts lung mitochondrial immunometabolism to promote pathogenesis

Early events in the lung that shape protective immune responses to M. tuberculosis (Mtb) infection are not well understood but are critical for developing better vaccines and immunomodulatory therapies for tuberculosis. Here, we used high-dimensional flow cytometry, single-cell transcriptomics, and untargeted metabolomics to define the early lung immune environment that precedes the development of protective versus pathogenic outcomes following aerosolized Mtb infection of mice. We show that Mtb induced sustained glycolysis in the lung while restricting oxidative phosphorylation (OXPHOS) and impairing mitochondria, in part through the Mtb serine protease Hip1, leading to low energy output and suboptimal macrophage-T cell interactions that promoted pathogenic immunity. However, robust induction of mitochondrial OXPHOS, amino acid metabolism, and fatty acid oxidation in the early lung resulted in high ATP output and enhanced innate-T cell signaling networks that stimulated protective immune responses. Moreover, we identified a novel mitochondrial immunometabolic lung signature associated with protective outcomes to Mtb infection in animal models and humans. Our studies identify induction of mitochondrial dysfunction as a mechanism employed by Mtb to manipulate lung immunometabolism to its benefit and reveal that maintenance of intact mitochondrial metabolism in the early lung is pivotal for generating protective outcomes to Mtb infection.

immunology↗

bioRxiv2026

Gut microbiome-dependent IL-1 signaling is a mediator of ACVR1R206H-driven heterotopic ossification

Inflammatory diseases cause significant morbidity and mortality, but their pathobiology is often difficult to dissect due to complex genetic-environmental interactions. Genetic forms of heterotopic ossification, such as fibrodysplasia ossificans progressiva (FOP), reduce genetic variability, allowing careful dissection of non-genetic drivers of inflammation. While >95% of FOP patients harbor the ACVR1R206H mutation, patients exhibit significant variability in disease progression, suggesting a role of environmental drivers. Here, we identify the gut microbiome as a regulator of inflammation-driven HO in FOP. Metagenomic profiling of cohabitating FOP/unaffected sibling pairs revealed a pathogenic gut microbiome profile in FOP patients (Bray-Curtis, p < 0.05). In Pdgfr-Cre/Acvr1R206H (FOP) mice, gut microbiome ablation by antibiotics reduced spontaneous HO formation (47.4% reduction, p < 0.05) and reduced plasma IL-1 pathway activity. IL-1{beta} blockade in FOP mice suppressed trauma-induced HO formation. These findings identify a gut microbiome-IL-1-HO axis with modifiable targets for developing treatments for HO and related inflammatory conditions. One Sentence SummaryAntibiotic disruption of the gut microbiome reduces HO in FOP mice via an IL-1 mediated pathway.

immunology↗

bioRxiv2026

Bridging the microstructural gap in human connectomics using hierarchical phase-contrast tomography as a reference for diffusion MRI in the human brain

Diffusion MRI (dMRI) allows us to image the human connectome non-invasively, yet it provides indirect estimates of axonal orientations based on the diffusion of water molecules in millimeter-scale voxels, hence struggling to resolve complex micrometer-scale fiber geometries. Invasive methods for imaging axonal orientations ex vivo, e.g. histology, are destructive and limited to small volumes, creating a critical need for a non-destructive modality for imaging microscopic fiber orientations in 3D. Here, we use Hierarchical Phase-Contrast Tomography (HiP-CT) to characterize white matter architecture at the microscale. Applying structure-tensor analysis to HiP-CT data, we compute fiber Orientation Distribution Functions and perform tractography analogous to dMRI. Across multiple brain regions, HiP-CT derived fiber architecture shows strong correspondence with that derived from dMRI while revealing substantially greater microstructural complexity. Despite its label-free nature, we demonstrate that vascular structures minimally confound HiP-CT orientation estimates. These results establish HiP-CT as a reference microscopic modality that can complement dMRI in multi-scale studies of white-matter organization.

neuroscience↗

bioRxiv2026

The Colonic Mucus Layer is Thinner and is Associated with Goblet Cell Hyperplasia in the db/db Mouse Model of Type 2 Diabetes

Background & AimsDiabetes mellitus has been associated with both intestinal barrier dysfunction and peripheral neuropathy leading to increased risk of infection. The mucus layer forms a physical barrier against pathogens and is a critical component of the intestinal barrier that may be impaired in diabetes. This study aimed to assess how diabetes impacts goblet cells (GCs), mucus layer integrity, and innervation in the colon. MethodsFluorescence microscopy was used to investigate GCs, the mucus layer, and innervation in the colon of db/db mice. Custom open-access image analysis pipelines were developed to quantify GC numbers, location and content, mucus thickness, bacterial colonization, and innervation density in intestinal tissue sections. We also treated mice with the clinically used glucagon-like peptide 1 receptor (GLP-1R) agonist liraglutide to assess its capacity to reverse pathological changes to GCs and the mucus layer in a model of established type 2 diabetes (T2DM). ResultsThe mucus layer was significantly thinner in the colon of db/db mice with established diabetes and bacteria more readily colonized the epithelium and crypts. Intercrypt GC numbers were significantly reduced in db/db mice. However, there were significantly more GCs per crypt, and crypts were elongated in the db/db colon. Innervation was reduced in the mucosa and external muscle of the colon, consistent with diabetic neuropathic changes. Liraglutide treatment increased the size of GCs but had no effect on GC numbers, mucus thickness, or innervation in this model of established T2DM. ConclusionsMucus barrier dysfunction and GC hyperplasia is evident in the db/db colon. Increased microbial penetrability through the mucus layer suggests potential implications for the increased risk of gastrointestinal infection in diabetes.

physiology↗