Biology subjects

Sinha, S.

Publications and source records attributed to Sinha, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Intracranial characterization of gamma in humans in response to auditory gratings

Activity in the gamma frequency range (>30Hz) serves as a neural hallmark of stimulus encoding across multiple sensory modalities. Based on its distinct properties, this activity could be classified as broadband or narrowband oscillations. Visual stimuli, such as a grating, induce narrowband oscillations, which have shown promise as diagnostic markers for neurological disorders. However, such tasks are discomforting for the subjects. These can be made subject-friendly by swapping the stimulus for an auditory one; however, most auditory stimuli elicit a broadband activity. In search of an ideal candidate to induce auditory narrowband oscillations, we previously recorded responses to auditory gratings in electroencephalography (EEG) recordings (Gulati & Ray, 2024) using a passive listening paradigm. We observed a focal sustained broadband increase in high gamma activity (70-150Hz), which was not selective towards any stimulus attributes. Nevertheless, since EEG represents activity of a large population, it remained unclear whether observed activity represented a broadband increase or comprised multiple narrowband rhythms, and whether it was indeed untuned. To elucidate this, we recorded invasively from the regions on and around the superior temporal gyrus, closer to Heschl's gyrus of seven patients undergoing epilepsy resection surgery. Patients were either under anesthesia or fully awake while we presented auditory gratings through loudspeakers. We found a transient increase in broadband gamma activity (30-100Hz) followed by a sustained suppression of beta rhythm (14-28Hz). This broadband gamma was selective for slower spectro-temporal modulations. Our result compares the responses obtained across different recording scales and corroborates that auditory gratings produce broadband but not narrowband gamma activity.

neuroscience↗

bioRxiv2026

Evaluation of Densified Collagen Tubes as an Interposition Graft in Abdominal Aorta

A major challenge in vascular tissue engineering is the development of scalable fabrication methods capable of producing vascular grafts with suitable mechanical properties and hemocompatibility for both preclinical evaluation and future clinical translation. Using a recently developed method to generate acellular vascular grafts from densified collagen hydrogel, we present a proof-of-concept in vivo evaluation of the scalable collagen graft technology. Thick-walled, genipin-crosslinked grafts, representative of a fabrication approach applicable to clinically relevant vessel sizes, were implanted as interposition grafts in the rat abdominal aorta. These grafts supported rapid neointima formation and re-endothelialisation of the luminal surface but developed late thrombosis, highlighting the challenges of evaluating clinically scalable grafts in small-animal models. To enable assessment of the platform in millimetre-scale vessels, we developed a thin-walled (~100 {micro}m), non-crosslinked graft using a constrained densification approach and hyaluronic acid-mediated modulation of collagen fibril assembly to improve compliance matching and hemocompatibility, with the latter providing a matrix-level approach that may complement surface-bound antithrombotic coatings. These grafts remained patent for up to 17 weeks and exhibited neointima formation, re-endothelialisation, and early cellular infiltration into the graft wall. Together, these findings demonstrate in vivo functionality of densified collagen vascular grafts and establish a foundation for future evaluation in larger animal models.

bioengineering↗

bioRxiv2026

Somatic DDX41 mutations confer neomorphic splicing activity in the pathogenesis of myelodysplastic neoplasms

Germline mutations in the RNA helicase DDX41 are the most common genetic predisposition to myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML), representing 5-7% of AML. Over 70% of patients acquire a somatic mutation at specific hotspots (R525H/G530D) in the helicase domain of DDX41 in trans, which is linked to disease progression. DDX41 has diverse cellular functions, including RNA splicing, ribosome biogenesis, R-loop resolution and inflammation. However, the mechanisms by which somatic DDX41 mutations drive MDS/AML pathogenesis are yet to be determined. Here, we systematically evaluated the function of pathogenic, missense germline and somatic DDX41 mutations. We report that DDX41 somatic mutations are gain of function alleles and fail to rescue AML cell growth, distinct from germline DDX41 mutations. DDX41 somatic mutations R525H and G530D drive widespread splicing changes in isogenic AML cell lines, consistent in genetically engineered murine bone marrow HSPCs and CD34+ cells from DDX41-mutant MDS/AML patients. Mechanistically, DDX41-R525H exhibits increased RNA binding affinity compared to wildtype, with aberrantly spliced RNA targets overlapping with enriched binding. Strikingly, aberrant splicing of SEPTIN7 is enriched exclusively in CD34+ HSPCs of patients harboring both germline and somatic DDX41 mutations but absent in samples with germline mutation alone or lacking DDX41 mutations altogether. SEPTIN7 mis-splicing introduces a premature stop codon resulting in its downregulation at the protein level. SEPTIN7 is a known regulator of cytokinesis, HSC polarity and repopulation capacity. Our results identify a novel mis-spliced candidate, SEPTIN7, whose deregulation implicates a mechanism by which the DDX41 somatic mutations promote dysplastic hematopoiesis.

cancer biology↗

bioRxiv2026

Scalable Computational Phenomics of Nuclear Morphology

Interpretable computational pathology is constrained by a trade-off between scalable learned representations and biologically explicit phenotypes. Here we present NucXplore, a nuclear phenomics framework that converts each hematoxylin-and-eosin (H&E)-stained nucleus into 129 explicitly defined features spanning morphology, chromatin, intensity, texture, color, and spatial context. A Rust-based implementation accelerates extraction 17.6-fold over the Python reference implementation. Across three histopathology cohorts, NucXplore outperformed classical descriptors and larger deep-learning embeddings while retaining feature attribution. Applied to human skin, hierarchical multiple-instance models resolved eight cellular compartments and decoded age and sun-exposure states, revealing a largely shared aging program with age and cell-specific exposure-dependent recalibration. Conditional flow matching and neural ODE integration transformed cross-sectional phenotypes into model-implied trajectories, uncovering a midlife velocity minimum, late-life re-acceleration, and cell-specific changes in trajectory magnitude and direction. Source-free domain adaptation enabled preliminary transfer of age-associated predictions to an independent hospital cohort. NucXplore thus unifies interpretable representation, high-performance computing, and dynamical modeling for cellular phenotyping from routine histology.

pathology↗

bioRxiv2026

Single-cell immune repertoire atlas maps coordinated circulating adaptive immune states in inflammatory bowel disease

Single-cell studies have defined immune states in inflammatory bowel disease (IBD), but how adaptive receptor histories organize circulating immunity remains unclear. We generated a single-cell transcriptomic atlas of peripheral blood from 249 participants with Crohn's disease, ulcerative colitis, or non-IBD control status, including 182 with productive TCR and BCR recovery. Expanded TCR clonotypes marked inflammatory-memory and cytotoxic states, while distinct but similar paired TCRs shared inflammatory programs across participants. BCR lineage maturation linked IgA-associated mucosal and plasma B cell programs to somatic mutation and class switching, distinguishing maturation-associated biology from clonal expansion. Helper, regulatory, and cytotoxic T-cell programs covaried with B-cell states, and inferred interactions nominated reciprocal antigen-presentation and helper pathways. Repertoire-based machine learning distinguished diagnosis, inflammation, and contemporaneous six-month treatment-response status. Together, this atlas connects receptor architecture to coordinated systemic immune remodeling, establishes a foundation for repertoire-informed patient stratification, and prioritizes candidate mechanisms of IBD pathogenesis.

immunology↗

bioRxiv2026

Single-cell profiling reveals stromal niche and α5β1 regulation of neutrophil phenotypes in ulcerative colitis

Background and Aims: Fibroblast-neutrophil interactions are implicated in ulcerative colitis (UC) treatment resistance, but whether fibroblasts modify neutrophil inflammatory activity remains unclear. We investigated responses to fibroblast exposure, stromal depletion, and 5{beta}1-directed treatment. Methods: We integrated human and mouse colonic single-cell RNA sequencing (scRNA-seq), spatial protein profiling (CODEX), fibroblast-neutrophil coculture, and dextran sulfate sodium (DSS) mouse colitis with fibroblast activation protein (FAP) ablation or 5{beta}1-directed treatment. Readouts included cellular representation and protein fluorescence via flow cytometry, neutrophil extracellular trap (NET)-associated elastase activity, RNA programs and epithelial responses using scRNA-seq. Results: Inflamed UC tissue contained higher fractions of inflammatory fibroblasts and oncostatin M (OSM)- and CXCR4-associated neutrophils. Inflammatory fibroblasts had higher FAP-5{beta}1 module scores, and proximity to FAP-high fibroblasts was associated with higher neutrophil OSM and CXCR4 fluorescence. UC fibroblasts increased neutrophil OSM, CXCR4 and myeloperoxidase (MPO) fluorescence and NET-associated elastase activity relative to control fibroblasts, while 5{beta}1-directed treatment attenuated these responses. Both mouse FAP ablation and 5{beta}1 blockade in DSS colitis reduced histologic inflammation and overall neutrophil frequency. Ablation broadly reduced recovered neutrophil representation, whereas blockade increased OSM-positive and PADI4-positive percentages within neutrophils despite lower MPO fluorescence within these subsets. Both interventions were associated with lower epithelial chemokine scores but distinct absorptive and mucus/secretory responses. Conclusions: Fibroblast exposure modifies neutrophil inflammatory phenotype and effector-associated activity, identifying candidate therapeutic pathways in UC. Evaluating these responses alongside neutrophil representation and tissue inflammation could inform pharmacodynamic assessment of stromal-directed therapies.

immunology↗

bioRxiv2026

Nitrotoxin metabolism in bacteria may have emerged from a diverse oxidoreductase reservoir

Bacterial transformation of 3 nitropropionic acid (3NPA) is typically viewed through canonical nitronate monooxygenases (NMOs), yet sequence annotation poorly resolves function across this flavoprotein family. Here we show that the environmental YrpB/NMO associated oxidoreductase space is dominated by YrpB related proteins: across 13 metagenomes, 83.1% of 390 conserved domain supported candidates were YrpB-associated. Cultivation along an Eisenia fetida feed gut cast continuum recovered 31 phylogenetically diverse 3NPA responsive bacteria, revealing that this phenotype is distributed across multiple lineages. Using the previously genome-sequenced Serratia sp. EWG9 as a tractable exemplar, we demonstrate sustained 3NPA supported growth, 44% parent compound depletion and a broad early transcriptional reorganization. Its focal oxidoreductase OXR01 occupies overlapping YrpB/NMO sequence space and shows stable predicted 3NPA accommodation without strong transcriptional induction. These findings reposition canonical NMOs as one component of a broader, ecologically distributed oxidoreductase reservoir for bacterial nitrotoxin responsiveness.

microbiology↗

bioRxiv2026

Peripheral nerve-derived extracellular vesicles are dynamically regulated in chemotherapy-induced painful peripheral neuropathy

Communication between Schwann cells (SCs) and other cells in the peripheral nerve remains incompletely understood. Extracellular vesicles (EVs) are important mediators of cell-cell communication, however, understanding the function of EVs in vivo is challenging in part because of difficulty in determining the cell type from which EVs originate. To identify SC EVs in vivo, we created a novel P0-Cre-turbo-GFP/human-CD9-EV reporter mouse. EVs were isolated from sciatic nerves without disrupting cell integrity. SC-derived EVs were identified by high-resolution microscopy and fluorescence nanoparticle tracking analyses. To test whether sciatic nerve EV (snEV) populations are regulated under neuropathological conditions, we treated mice with the chemotherapy agent, paclitaxel, which induces neuropathic pain. Proteomes of healthy and neuropathic snEVs differed as determined by LC-MS/MS. Proteins essential for maintenance of axonal integrity and SC myelination were identified selectively in healthy snEVs, whereas neuropathic snEVs contained increased levels of metabolic enzymes and receptors associated with neuronal excitability. Neuropathic snEVs contained diminished levels of EVs derived from SCs. These EVs differed in size from normal snEVs and triggered altered cell-signaling responses in sensory neurons. The appearance of neuropathic EVs correlated with the development of pain-related behaviors. Our findings demonstrate that peripheral nerve EV physiology is dynamically regulated in peripheral neuropathy.

neuroscience↗

bioRxiv2026

The diverse functions of viral microproteins

A large fraction of the uncharacterized proteome consists of microproteins. Viruses, rich in microproteins with potent activities, provide a unique system for exploring their functions and evolution. Here, we systematically annotate viral microproteins through a phenotype-first approach: construction of a >50,000-element small ORF library spanning the microprotein-coding potential of human-infecting viruses, followed by broad screens that enrich candidates for high-resolution profiling by Perturb-seq, mass spectrometry, AI-guided structure prediction, and mechanistic studies. This atlas identified >2,000 active microproteins that modulate host pathways through diverse mechanisms, including molecular mimicry, hijacking of key regulators, and altering subcellular localization. We further show the oncogenic potential of BNLF2b, an uncharacterized Epstein-Barr virus microprotein linked to nasopharyngeal carcinoma. Three principles emerge: viral microproteins are diverse and often multifunctional, show widespread convergence toward shared functions, and serve as reservoirs of evolutionary innovation. These findings elucidate how viral microproteins occupy a large functional landscape, establish them as versatile tools for host manipulation, and provide a framework for functional annotation of uncharacterized proteins, contributing toward predictive systems virology.

systems biology↗

bioRxiv2026

Tumor-specific Kinase Motif Enrichment Analysis Identifies Personalized Therapeutic Cancer Targets

Gastroenteropancreatic neuroendocrine tumors (GEP-NETs) are an uncommon and poorly understood malignancy with low mutational burden, lacking well-defined oncogenic drivers. GEP-NET mortality frequently results from extensive hepatic metastases. Accordingly, we interrogated phosphoproteomic data from GEP-NET liver metastases and patient-matched uninvolved liver to identify tumor-specific signaling and targetable tumor vulnerabilities using Kinase Motif Enrichment Analysis (KMEA), a new tool leveraging the recent Kinase Library compendium of the substrate motif specificity for nearly the entire human kinome. KMEA identified patient tumor-specific upregulation of mTOR or casein kinase 2 (CK2) activity that would be undiscoverable by standard personalized genomic and transcriptomic approaches. Striking concordance was observed between KMEA predictions for specific tumors, and their sensitivity to inhibitors of mTOR or CK2 using patient tumor-derived organoids. These findings reveal potential clinically-actionable protein kinases hyperactivated in GEP-NETs, and more broadly indicate a general method for personalized cancer treatment using phosphoproteomics and KMEA-derived kinase activity signatures.

cancer biology↗

bioRxiv2026

Convergent genomic variation and wild-type composite RNA-seq profiling identify candidate modules associated with 3-nitropropionic acid utilization in Leclercia barmai

3-Nitropropionic acid (3-NPA) is a toxic nitroaliphatic compound, but the genomic basis of bacterial adaptation to 3-NPA remains incompletely resolved, especially in organisms lacking a canonical nitronate monooxygenase. Here, we used phenotype screening, whole-genome resequencing, targeted UHPLC-MS/MRM, and composite RNA-seq profiling to investigate 3-NPA utilization in Leclercia barmai EMC7. Following attempted Tn5-Mob mutagenesis and kanamycin-based recovery, two independently derived mutants, LTM01 and LTM14, showed impaired growth under 3-NPA-dependent minimal conditions. No stable transposon insertion was detected in either mutant. Comparative genome analysis instead revealed convergent loss-of-function (LOF) mutations affecting amino acid metabolism, nitrogen allocation, central carbon metabolism, cofactor-linked functions, transport, and metal-redox homeostasis, while the predicted flavin-dependent nitro-redox candidate and canonical nitrate/nitrite reduction loci were not disrupted. Targeted UHPLC-MS/MRM analysis showed that wild-type EMC7 depleted approximately 50% of 3-NPA within 36 h, whereas the mutants displayed poor 3- NPA-utilization phenotypes under the same growth framework. Wild-type RNA-seq under glucose-3NPA relative to glucose-KNO3 identified a broad expression profile involving flavin-redox functions, nitrogen assimilation, oxidative-stress response, envelope stress, efflux, cofactor metabolism, and iron homeostasis. Integration of mutant LOF profiles with wild-type gene expression data showed that several disrupted genes or functional counterparts belonged to modules showing expression changes during the wild-type glucose-3NPA response. These findings identify candidate adaptive modules associated with 3-NPA utilization in EMC7, including nitrogen redistribution, carbon entry, sulfur-redox support, cofactor supply, transport, envelope remodeling, and metal-redox control. These results extend the landscape of metabolic adaptation beyond canonical pathways in environmental bacteria.

microbiology↗

bioRxiv2026

Cytoplasmic DNA Sensing Links LINE-1 Expression to Neuronal Senescence in Alzheimer's Disease

Cellular senescence contributes to neurodegeneration in Alzheimers disease (AD), yet brain-penetrant senotherapeutic strategies remain limited. Here, we identify long interspersed nuclear element 1 (LINE-1) retrotransposons as key regulators of neuronal senescence and the senescence-associated-secretory-phenotype (SASP) in AD. Using transdifferentiated induced neurons (iNs) that preserve donor-specific aging-associated molecular signatures, we show that pharmacological inhibition of LINE-1 with nucleoside reverse transcriptase inhibitors (nRTIs) or antisense oligonucleotides reduces p16 expression, suppresses SASP and interferon-stimulated gene programs, and attenuates paracrine induction of reactive astrogliosis. Spatial transcriptomic analysis of human AD brain tissue further supports that senescent neurons with high LINE-1 expression are localized to inflammatory niches in the brain. Although bulk analysis finds no significant differences in LINE-1 expression between AD and control neurons, long-read single-cell RNA sequencing of iNs identifies a subset of neurons with elevated LINE-1 activity which display transcriptional signatures of neurodegeneration, immune activation, and senescence are enriched in AD relative to controls. RNA velocity analysis indicates that LINE-1 activation precedes the induction of canonical senescence markers, supporting a causal rather than consequential role. Mechanistically, LINE-1-derived cytoplasmic DNA activates the cGAS-STING innate immune pathway in post-mitotic neurons, and inhibition of cGAS phenocopies the effects of LINE-1 suppression. Together, these findings establish a LINE-1/cGAS-STING axis as a driver of neuronal senescence in AD and highlight LINE-1 inhibition as a tractable senomorphic strategy for neurodegenerative disease.

neuroscience↗

bioRxiv2026

A Two-Arm Metabolic-Efflux Adaptation Framework in Klebsiella pneumoniae under Mixed Pharmaceutical Exposure: rutA-Linked Oxidative Entry and rutR-Associated Regulation

Chemically complex pharmaceutical mixtures in wastewater and sludge can affect microbial adaptation; however, the responses to different co-occurring compounds have not been elucidated well. In this study, the adaptation of a strain derived from hospital sludge, Klebsiella pneumoniae SS02, to 17-ethinylestradiol (EE2), warfarin sodium, and their combination has been studied. The organism grows under all three conditions, and pre-exposure experiments show induction and cross-induction to substrates. UHPLC MS/MS analyses demonstrated that there is conditional depletion of the parent compound EE2 by [~]15% at 36 h post-treatment compared to initial concentrations, but not for the abiotic and non-adapted controls. The rate of warfarin sodium depletion was approximately [~]30% within 36 h and was in accordance with first order kinetics (k = 0.0102 /h; t{square}/{square}= 67.9 h). Under the combined treatment regime, there was a delay in warfarin sodium depletion, suggesting staged substrate consumption. Growth inhibition with efflux inhibitors confirmed transport-driven tolerance. A genome-based study revealed the coordinated response strategy that involved a proposed flavin-dependent monooxygenase (RutA), an oxidative entry into the pathway; redox processing linked to Hpa; aromatic metabolism through {beta}-ketoadipate pathway; and RND efflux system. The structural study additionally supported ligand-mediated decrease in DNA binding affinity of RutR, which is in agreement with de-repression of the substrate-activated regulatory mechanism. All these findings lead to the development of a dual-strategy for adaptation model in which oxidative modification and efflux-mediated protection work together under the influence of a mixture of pharmaceuticals.

microbiology↗

bioRxiv2026

Mutation E300 recommended by protein language models gives ChrimsonR amplified photocurrent response

A central challenge in opsin engineering is identifying mutations that reliably improve desired functional properties, a task made difficult by the enormous mutation space and limited throughput of electrophysiological screening. Improving opsin properties such as photocurrent amplitude and light sensitivity have the potential to broaden the use of opsins to low-light and deep-tissue applications. With this goal, we applied zero-shot protein language models (ESM-1b/1v) to recommend ChrimsonR mutations and experimentally validated all 17 of these variants using whole-cell patch clamp electrophysiology (n=6 cells per mutation). Despite many mutations reducing function, protein language models identified both known functional residues and unconventional substitutions that produced large functional gains and synergized with K176R to improve kinetics. Two mutations, E300G and E300P, increased sustained photocurrents from 66 pA (control) to 305 pA and 255 pA at 635 nm, reduced EC50 at 575 nm from 0.19 mW to 0.07 mW, and altered kinetics ({tau}off increased from 0.06 s up to 0.40 s). Our results suggest that protein language models, even without task-specific training, can be used alongside electrophysiological measurements as a strategy for screening opsins for enhanced photocurrent.

neuroscience↗

bioRxiv2026

HTRA1 deficiency in COL4A1 mutant hiPSC-derived astrocytes, a convergent mechanism of cerebral small vessel disease

Cerebral small vessel disease (cSVD) is a major contributor to stroke and cognitive decline, ultimately leading to vascular dementia (VaD). Genetic factors play a key role in disease susceptibility and progression, and variants in COL4A1 cause one of the most common forms of genetic cSVD. COL4A1 encodes the 1 chain of collagen type IV which is the major structural component of the basement membrane, a specialised extracellular matrix (ECM) structure, in the vasculature. In addition to this vascular basement membrane (vBM), in the central nervous system (CNS), the neurovascular unit (NVU) also has a unique parenchymal basement membrane (pBM) that is largely produced by astrocytes and forms a critical interface anchoring astrocyte end-feet to vascular cells. Together, these BMs play essential roles in regulating blood-brain barrier (BBB) function. However, the role of the pBM in cSVD has been relatively less investigated compared to the vBM. The lack of relevant human disease models that faithfully recapitulate the pBM, makes it difficult to dissect pBM-related cell-cell and cell-matrix interactions specific to cSVD, hindering the identification of effective therapeutic targets. In this study, we hypothesised that astrocyte-mediated ECM remodelling contributes to BBB dysfunction in COL4A1-associated cSVD. To investigate this, human induced pluripotent stem cells (iPSCs) derived from a patient carrying the COL4A1G755Rvariant and its isogenic control line were differentiated into astrocytes and brain microvascular endothelial cells (BMECs). Comparing to isogenic controls, the COL4A1G755Rastrocytes significantly reduced the expression of ECM-related genes and increased glutamate uptake. ECM preparations from COL4A1G755R astrocytes significantly damaged the tight junction (TJ) structure formed by control iPSC-BMECs and failed to rescue the TJ integrity in COL4A1G755R BMECs. The secretome from COL4A1G755Rastrocytes exacerbated the ECM defects in COL4A1G755R BMECs. Most importantly, COL4A1G755R astrocytes exhibited reduced expression of HTRA1, a serine protease that regulates both ECM turnover and homeostasis, and increased TGF-{beta} signalling. Functional rescue by recombinant human HTRA1 protein rescues TJ defects in COL4A1G755R BMECs, and normalized TGF-{beta} signalling and glutamate uptake in COL4A1G755R astrocytes. Together, these findings define a previously unrecognised astrocyte-driven pBM mechanism in COL4A1-associated cSVD and highlight HTRA1 in ECM remodelling as a therapeutic target for cSVD.

neuroscience↗

bioRxiv2026

Antibody Blockade of Ly49/MHC-I interactions enhances Innate and Adaptive Immunity Against Cancer Metastasis

BackgroundAntibody-mediated blockade of innate receptor-MHC-I interactions represents a promising strategy to enhance anti-tumor immunity, particularly against metastatic cancers resistant to conventional checkpoint inhibitors. In this study, we investigated the effects of the pan anti-MHC-I monoclonal antibody M1/42, which targets MHC-I interactions with Ly49, selectively expressed on murine NK cell subsets. MethodsWe administered M1/42 to mice and assayed the proliferation and activation immune cells. Anti-tumor activity of growth and metastasis of checkpoint inhibitor-resistant pancreatic ductal adenocarcoma (PDAC) and B16F10 melanoma were assessed, complemented by extensive cellular phenotypic and RNA expression analysis. Binding and cryo-electron microscopic (cryo-EM) and X-ray crystallographic structural studies of M1/42 complexed with the mouse MHC-I molecule, H2-Dd, examined the Ab interaction site in comparison with those of Ly49 inhibitory receptors. ResultsM1/42 administration in mice robustly unleashed the proliferation and activation of natural killer (NK) cells, memory CD4+ and CD8+ T cells, dendritic cells, and macrophages in both lymphoid and non-lymphoid tissues, independent of Fc{gamma} receptors. M1/42 significantly restricted the growth and metastasis of checkpoint inhibitor-resistant pancreatic ductal adenocarcinoma (PDAC) and B16F10 melanoma in the liver and lungs, accompanied by increased tumor infiltration of effector CD8+ T cells, reduction of T regulatory cells, and a pro-inflammatory cytokine milieu. The anti-tumor effects of M1/42 depend on NK cells and are associated with upregulation of genes involved in antigen processing, interferon gamma responsiveness, and Th1 cytokine production, while downregulating inhibitory PD1/11 signaling. Structural analysis indicated that the effect of M1/42 on Ly49/MHC-I interactions was not due to direct steric competition. ConclusionsCollectively, these findings demonstrate that M1/42 unleashes coordinated innate and adaptive immune responses, overcoming tumor-induced immunosuppression and resistance to checkpoint blockade. This approach represents a paradigm shift in cancer immunotherapy, offering potential for more effective treatment of metastatic cancers that evade immune surveillance through MHC-I modulation. KEY MESSAGESO_ST_ABSWhat is already known on this topicC_ST_ABSA pan anti-mouse MHC-I mAb (M1/42) blocks interaction with several NK inhibitory receptors (Ly49A or Ly49C) resulting in NK cell activation and anti-viral and anti-tumor responses in vitro and in vivo. Other pan anti-human MHC-I mAbs (DX17 and W6/32) function similarly, blocking LILRB inhibitory receptor interaction of myeloid cells and NK cells. These stimulate human immune cells in humanized mouse models. What this study addsThis study analyzes the effects of the pan anti-mouse MHC-I mAb on NK and myeloid cell activation in detail, in the absence of T or B cells, and independent of FcR interaction. Additionally we analyze several mouse models of metastatic tumor progression, indicative of the progressive activation not only of the innate immune response, but also adaptive responses. The molecular mechanism of the mAb blocking of inhibitory receptors is revealed by cryo-EM and X-ray structures of M1/42 Fab/MHC-I (H2-Dd) complexes. How this study might affect research, practice, or policyElucidation of the details of the inhibitory effects of the mouse pan anti-mouse MHC-I mAb provides not only a more advanced understanding of the murine model system, but suggests additional functional avenues to be explored using the parallel an anti-human MHC-I mAbs.

cancer biology↗

bioRxiv2026

Stromal state plasticity defines risk and therapeutic opportunity in recalcitrant inflammatory bowel disease

Inflammatory bowel diseases (IBD) remain a relapsing, treatment-refractory disorder marked by progressive tissue injury and inflammation despite expanding immune-targeted therapies. We established a prospective cohort integrating stromal biobanking, functional phenotyping, cross-cohort benchmarking, and outcome modeling to define disease-anchored cellular states. Colonic myofibroblasts from 34 individuals spanning health, ulcerative colitis, and Crohns disease resolved into two dominant states: inflammatory (IMFs) and quiescent (QMFs) myofibroblasts. QMF predominance forecasted remission, whereas IMF predominance increased the odds of worsening endoscopic severity despite therapy escalation during follow-up by [~]4.6-fold, linking early stromal biology to clinical outcomes. Unlike QMFs, IMFs exhibited a senescence-associated secretory phenotype that impaired epithelial stemness, barrier integrity, and innate immune fitness. State-guided prioritization identified EDNRB-antagonism as a high-confidence stromal intervention, reversing pathogenic phenotypes across orthogonal assays and species. Outcome simulation positioned stromal-state reversibility by EDNRB-antagonism as a precision axis, reducing odds of recalcitrance by [~]96.4% and reframing treatment resistance as a reversible stromal state. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=185 HEIGHT=200 SRC="FIGDIR/small/720931v2_ufig1.gif" ALT="Figure 1"> View larger version (88K): org.highwire.dtl.DTLVardef@3b2c50org.highwire.dtl.DTLVardef@da5400org.highwire.dtl.DTLVardef@1c100c1org.highwire.dtl.DTLVardef@1882e1_HPS_FORMAT_FIGEXP M_FIG C_FIG In this work, Tindle et al. identify reversible stromal states that govern remission vs. recalcitrant outcomes in IBD and nominate precision reprogramming of pathogenic myofibroblasts as a new therapeutic strategy.

physiology↗

bioRxiv2026

Genetic Programming of Bacterial Microcompartments: Operon Order as a Tool for Nanoscale Morphogenesis

Gene order is a powerful design principle for protein nanomachines. In nature, gene organisation ensures the precise assembly of functional protein nanostructures. We demonstrate how genetic repositioning of the key structural gene pduN, within the operon encoding a self-assembling protein nanocompartment, sculpts the morphology and function of bacterial microcompartments (BMCs). Relocating pduN to new operonic positions dramatically altered the size, shape, and catalytic output of BMCs, despite identical protein sequences. These shifts reveal how gene order may control nanoscale assembly and compartmentalised function. Our findings establish operon architecture as a programmable genetic framework for nanostructure morphogenesis and provide a synthetic biology strategy to engineer self-assembling nanodevices with customised geometries and activities.

synthetic biology↗