Biology subjects

Patel, M.

Publications and source records attributed to Patel, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Prenatal Inflammation as a Determinant of Long-Term Cardiovascular Risk: Evidence from a Murine Model

Background Intrauterine inflammation is associated with increased lifetime cardiovascular disease (CVD) risk in offspring, yet long-term molecular mechanisms remain underexplored. We investigated the lasting cardiometabolic, hemodynamic, and vascular effects of prenatal inflammatory exposure in adult offspring using a mouse model. Methods On day 15 of gestation, pregnant CD-1 mice were randomized to receive intraperitoneal (IP) injections of either lipopolysaccharide (LPS group) or saline (SAL group). Blood samples were collected before and after injection to measure IL-6 concentrations. Blood pressure (BP) in offspring was measured at 6-8 months of age using the tail-cuff method, and tissues were collected. Protein was extracted from the brain cortex to measure cytokines utilizing the xMAP Luminex assay. The C-reactive protein (CRP) was measured in serum. Gene expression of IL-6, NOS3, NFkB, AT-1, and Trp53 was determined by real time RT-qPCR in the aorta. The experimental unit was a mother. Results were analyzed using the appropriate statistical methods. Results Maternal LPS administration induced significant acute systemic inflammation (P<0.05 for IL-6). At 6-8 months after delivery, maternal circulating CRP was significantly higher in LPS mice as compared to SAL (P=0.02). In offspring at 6-8 months of age, systolic BP was significantly elevated in LPS groups compared with SAL animals (P=0.04). LPS-exposed offspring exhibited higher total body and visceral adipose tissue weights. Aortic expression of the angiotensin II type 1 receptor (AT1) and NFkB were significantly upregulated (P=0.04 and P=0.03, respectively). Cortices of LPS offspring displayed a pro-inflammatory profile with increased total Inflammatory score, elevated pro-inflammatory IL-1{beta}, and reduced anti-inflammatory IL-4 and IL-10. Furthermore, protective Trp53 gene expression was significantly downregulated in both the aorta (P=0.01) and heart (P=0.04). Conclusion A single mid-gestation inflammatory insult programs long-term cardio-inflammatory perturbations in offspring and results in long-term systemic inflammation in mothers. Prenatal LPS exposure induces persistent visceral obesity, hypertension, vascular RAS upregulation, central neuroinflammation, and cardiac/vascular Trp53 suppression in adult offspring, offering a mechanistic link between prenatal inflammation and offspring CVD risk.

developmental biology↗

bioRxiv2026

Antennal Lobe Dynamics And The Generation Of Diverse Response Patterns To Mechanosensory Stimulation

Sensory integration within antennal lobe (AL) is thought to play a role in the guidance of odor tracking, though while responses to olfactory input within the AL have been well-studied, responses to mechanosensory stimuli, in the form of wind speed, have received less scrutiny. Recent experimental work has systematically characterized mechanosensory responses of individual neurons within the AL, showing four distinct response patterns, labeled as sustained, transient, biphasic, and offset types; furthermore, these experiments have demonstrated that the distribution of response patterns, as well as the response type of a fixed neuron, can vary with stimulus intensity (wind speed). In this work, we develop a realistic biophysical model of the AL and, using this model, we show that internal AL dynamics are capable of generating the response patterns observed experimentally - namely, we find that response type is determined by the interplay of slow synaptic inhibition, an intrinsic calcium dependent potassium (SK) current, and stimulus strength, and hence that a heterogeneous distribution of slow inhibition and SK current strength across the AL can lead to the emergence of all four types at a fixed wind speed. Moreover, similar to experiment, we find that the distribution of response patterns across the AL changes with wind speed. Finally, we examine the distribution of response types in the presence of a simulated odor stimulus as well as odor separation by the AL in the presence versus absence of a strong mechanosensory signal.

neuroscience↗

bioRxiv2026

Function-driven geometry directs human pilosebaceous unit development

Single-cell technologies have generated cell censuses of tissues, however, how tissue geometry reflects functional needs remains poorly characterized. The human pilosebaceous unit offers a tractable model, a prenatally-formed complex mini-organ combining hair and sebum production with a stem cell reservoir. Using histomorphology, spatial transcriptomics, and single-cell multiomics on the same human prenatal scalp skin samples (8-19 post-conception weeks), integrated and analyzed using machine learning approaches, we built a spatiotemporal map of pilosebaceous unit development. We demonstrate that epithelial-mesenchymal interactions coordinate cellular fate and organogenesis, using an in vitro hair-bearing skin organoid model to validate this tissue-patterning. In addition, we show sebaceous gland developmental programmes are overcome during tumor formation. Our large-scale multi-modal analysis provides a unique framework for understanding form and function of tissues with applications in tissue engineering and pathology.

developmental biology↗

bioRxiv2026

Zebrafish prph2a/b and rom1a/b serve distinct functions during cone and rod outer-segment assembly.

Inherited retinal disorders are significant contributors of blindness worldwide. Mutations in Peripherin-2 (PRPH2), a highly conserved vertebrate tetraspanin membrane protein responsible for formation and maintenance of OS morphology, have been shown to cause diverse types of inherited photoreceptor cell (PRC) disorders including but not limited to Leber congenital amaurosis, cone-rod dystrophy, and retinitis pigmentosa. In this study we used a cone-rich diurnal zebrafish model to characterize the loss of PRPH2 function. Of the four PRPH2 zebrafish orthologs only prph2a and prph2b were found to be expressed in PRCs. CRISPR-mediated single mutants of prph2a and prph2b did not yield striking rod or cone phenotypes. Double prph2a/2b mutants exhibited early loss of all cone cells, preceded by cone outer segment disorganization in the form of whorls akin to the phenotypes observed in PRPH2+/- mice. Surprisingly rod photoreceptor cells were not affected and in fact exhibited a striking lengthening of rod OSs with normal disc formation. Overgrowth of rod OSs proceeded up to 1 year, but no degeneration was observed. To determine how rod OS can persist without prhp2a/b we targeted rom1a and rom1b using CRISPR. Injection of rom1a/b crRNA resulted in complete loss of both rod and cone OSs in the prph2a/b double mutants. Surprisingly, inhibition of rom1a/b alone resulted in the loss of rod but not cone OSs. These findings suggest that unlike in mammals, zebrafish rom1a/b is essential for rod OS formation while prph2a/b is essential for cone OSs.

developmental biology↗

bioRxiv2026

Multi-scale modeling of human tissues from spatial transcriptomics with TERRA

Spatial transcriptomics maps gene expression at cellular resolution, revealing how cells organize into multicellular niches. Yet computational analyses remain dataset-specific, without a transferable representation of tissue organization that generalizes across datasets, tasks and tissues or predicts how tissues behave under perturbation. We present TERRA, a foundation model pretrained on 112 million human cells profiled by spatial transcriptomics. From a single pretrained backbone, TERRA yields embeddings at the scale of cells, the genes they express and the neighborhoods in which they reside, and supports spatial in silico perturbation, all applied zero-shot to unseen tissues. At the cell level, in newly generated spatial data for developing pancreas, TERRA identified an islet-associated capillary state which we posit represents a developmental precursor of the mature islet microvasculature. At the gene level, in untreated kidney sections, in silico knockout of immune-checkpoint targets predicted a gene program of immune-checkpoint-blockade-associated nephrotoxicity, which we validated in treatment-exposed tissue and recovered in blood. At the neighborhood level, TERRA mapped macrophages across tissues to identify recurring cross-organ niches, which we term archetypes, including a tumor-boundary niche associated with poor prognosis in kidney cancer. Together, TERRA captures the spatial and multicellular logic of human tissue and predicts, in silico, its response to perturbation, providing a multi-scale framework for tissue biology, therapeutic development and clinical application.

genomics↗

bioRxiv2026

Cellular Morphology and Motility Defects are Conserved Phenotypes of Trisomy 21 Despite Heterogeneous Adhesion Mechanisms

Down syndrome is a neurodevelopmental disorder caused by the trisomy of human chromosome 21 (T21). Down syndrome is associated with a wide range of variable clinical features, including congenital heart defects and slow wound healing; however, intellectual disability is ubiquitous and results, in part, from altered neuronal connectivity. Here, we used three sets of control and T21 human fibroblasts, and one set of human induced pluripotent stem cell (hiPSC)-derived cortical neurons, to examine whether changes in cellular morphology and motility are consistent across cell types in Down syndrome and to elucidate the underlying mechanisms. We found that fibroblast morphology is dysregulated in all T21 fibroblast lines. Using a transwell migration assay, cellular migration is decreased in two of the three T21 fibroblast lines. T21 hiPSC-derived cortical neurons also exhibit morphological defects, including a decrease in the length of the longest neurite and growth cone area. Because of these significant changes in morphology and motility in T21 cells, we examined proteins in the focal adhesion complex, which links the intracellular cytoskeleton to the extracellular matrix and directly controls these processes. Multiple proteins in the adhesion complex, including paxillin, vinculin, talin, and RACK1, are dysregulated in T21 fibroblasts and hiPSC-derived neurons, but these changes have high inter-individual variability. Taken together, these findings suggest that altered cellular morphology and motility are conserved features of Down syndrome that arise through heterogeneous alterations in adhesion networks. Thus, this work significantly contributes to the recent literature highlighting the need for personalized medicine in Down syndrome.

cell biology↗

bioRxiv2026

Multilayered specificity of transcription factor binding at cytokine promoters

Transcription factors (TFs) regulate gene expression through sequence-specific DNA binding, and their genomic occupancy is further influenced by TF expression, activation state, and protein-protein interactions. How these mechanisms determine context-specific gene regulation remains incompletely understood, particularly for tightly controlled immune genes such as cytokines. Here, we use paired yeast one-hybrid (pY1H) assays to systematically examine DNA binding of 236 TFs and 392 TF-pairs across 106 cytokine gene promoters. Of the 1,619 TF-promoter interactions identified, 555 required TF cooperativity and 410 were antagonized by at least one TF partner, suggesting that TF-DNA binding is highly dependent on TF partners. Usage of different partners can drastically alter a TFs target repertoire and may result in the recruitment of different transcriptional cofactors. Integration with existing data on TF expression and activation further showed that cooperativity and antagonism provide additional, underappreciated layers of DNA-binding specificity.

systems biology↗

bioRxiv2026

Spatial lung niches shape Pseudomonas aeruginosa persistence

Chronic Pseudomonas aeruginosa lung infection is a major cause of morbidity and mortality in people with pre-existing lung disease. Once established, infection is rarely eradicated and often persists despite prolonged antimicrobial therapy, but the underlying mechanisms remain poorly understood. To define how P. aeruginosa occupies and adapts to diseased lung tissue, we applied host-pathogen spatial transcriptomics to profile over 23 million lung cells from explanted and resected lungs from people with Cystic Fibrosis (CF) and chronic obstructive pulmonary disease (COPD), mapping bacterial niches and transcriptional states in situ. We found that P. aeruginosa adopted distinct niche-linked states across chronically infected human lung tissue. Bacterial burden was highest in airway lumens, but bacteria also occupied submucosal glands, parenchyma and, unexpectedly, blood vessel lumens in CF tissue. Within airway lumens, two coupled host-pathogen states emerged: an alginate-rich biofilm-like state linked to PI3-positive neutrophil inflammation and host chemical-sensing programmes; and a motile, quorum-sensing state with activated type 6 secretion linked to human ciliary stress, epithelial remodelling and proteolytic injury. Intravascular bacteria co-localised with neutrophils, fibrin and vascular-remodelling signatures, suggesting local breach of barrier integrity and subsequent immune containment. P. aeruginosa also displayed disease-specific cellular associations, with neutrophil-dominated interactions in CF and greater association with macrophages and dendritic cells in COPD. Together, these data reveal chronic P. aeruginosa infection as a spatially partitioned ecosystem in which anatomical microenvironments impose distinct bacterial lifestyles and host inflammatory states. This niche-resolved framework helps explain how persistent infection can diversify within a single lung and suggests that eradication therapies may need to target multiple anatomical and cellular niches to be effective.

immunology↗

bioRxiv2026

RAEM: random-access electron microscopy for revisitable 3D imaging

Volume electron microscopy is essential for understanding cells, tissues, and neural circuits in their native 3D context, but many biological specimens are too large to image exhaustively at nanometer resolution. Researchers therefore must choose between broad anatomical context and ultrastructural detail. We introduce random-access electron microscopy (RAEM), a framework for studying fixed tissue repeatedly across scales rather than imaging it once at a single resolution. RAEM first builds a lower resolution 3D survey of the specimen, then uses accumulated human or AI-derived knowledge of that volume to guide the microscope back to selected physical sites for high resolution imaging. By linking reconstructed 3D coordinates to precise electron-beam positions on the original sections, RAEM enables targeted imaging of membranes, vesicles, and other nanoscale structures within specimens that would be impractical to image exhaustively. We demonstrate RAEM with vesicle-resolved imaging of synaptic boutons in human cortex, targeted imaging of more than one million human cortical mitochondria, hierarchical imaging of a nematode nervous system, and retrospective targeting of a previously published petabyte-scale human cortical volume. RAEM turns serial-section EM into a query-driven, multi-resolution approach for scalable biomedical discovery.

neuroscience↗

bioRxiv2026

FALCON: Closed-Loop Multi-Objective Optimization of Lipid Nanoparticles for Cell-Selective mRNA Delivery

Efficient, cell type-selective delivery of genetic payloads remains a central challenge in the development of gene and cell therapies. Lipid nanoparticles (LNPs) offer a versatile delivery platform, but their optimization is hindered by reliance on brute-force screening methods that are laborious, resource-intensive, and focus on single targets. Here, we present FALCON (Framework for Active Learning-driven Compositional Optimization of Nanoparticles), a closed-loop pipeline that leverages iterative screening, surrogate modeling, and multi-objective optimization to accelerate LNP compositional design. In B cell-targeted validation experiments, FALCON-optimized LNPs achieved a 1.8-fold increase in splenic B cell transfection in vivo compared with reference compositions. When optimized for selectivity, FALCON LNPs displayed an 84-fold improvement in selective transfection of splenic B cells over off-target liver populations and enabled spleen-tropic behavior across factorial panels of varying ionizable and helper lipid chemistries. In vaccine studies, these LNPs induced higher IgG2c antibody titers and a more Th1-biased immune profile. FALCON was also deployed to optimize LNPs for myeloid cell-selective delivery, achieving enhanced in vivo selectivity following systemic administration both across and within spleen and liver compartments. Our results establish FALCON as a useful tool for data-driven design of LNP compositions for precision gene delivery.

bioengineering↗

bioRxiv2026

Matched pancreatic cancer liver metastatic model system reveals cancer cell-dependent organotropism and site-specific tumor microenvironment reflective of human disease

Background: Pancreatic ductal adenocarcinoma (PDAC) mortality is driven largely by liver metastatic disease; however, the malignant cell states and tumor microenvironmental features of PDAC liver metastases remain obscure. Methods: We developed a transplant model system of matched pancreatic and liver tumors to study PDAC metastatic progression. Using this model, we identified murine PDAC cell lines with distinct liver metastatic capacities and performed multiomic profiling of matched primary pancreatic and metastatic liver tumors. Transcriptional programs associated with high and low liver tropism were defined and evaluated across tumor models and independent human PDAC datasets. Spatial and tumor-immune interaction analyses were used to characterize microenvironmental niches, immune composition, and cellular relationships within primary and metastatic tumors. Results: A high-liver-tropic transcriptional program was enriched in high liver-tropic cell lines and malignant cells within liver metastases, conserved across human PDAC datasets, and associated with inferior patient survival. High- and low-liver-tropic tumor states occupied distinct liver microenvironmental niches and exhibited different tumor-immune communication networks, accompanied by local and systemic changes in immune composition. Liver metastases also displayed features of enhanced immunosuppression, including increased proximity of CD4+ and CD8+ T cells to tumor cells and greater spatial association between regulatory T cells and exhausted CD8+ T cells. Conclusions: These findings identify conserved PDAC cell states associated with differential liver metastatic capacity and demonstrate that liver metastasis is accompanied by spatial and immunologic remodeling of the tumor microenvironment. Together, the study provides a framework for understanding how tumor-intrinsic metastatic programs interact with site-specific immune ecosystems in PDAC.

cancer biology↗

bioRxiv2026

Effects of Bimodal Olfactory and Mechanosensory Inputs in the Antennal Lobe of the Honeybee Apis mellifera

Animals often aggregate information from multiple different sensory modalities to accurately assess and react to a stimulus. It is often assumed that cross-modality integration mostly occurs at high-level processing centers, such as the mammalian cortex or insect mushroom bodies. However, we hypothesized that integration could occur relatively early in the sensory pathways. The insect antennal lobe is one such location, receiving direct inputs from the antennae via the antennal nerve. These inputs are highly multimodal, including olfactory, mechanosesnory, and gustatory information, all of which are relevant to foraging honeybees (Apis mellifera). Here we assess integration by recording electrophysiological spike data within the honeybee antennal lobe while exposing the bee to various combinations of wind speed and odor concentration. This paper accompanies another publication by Joseph Reed and Mainak Patel approaching the same question from a modelling perspective, where their model corroborates our data and vice versa. Together, we show that integration occurs within this early layer of processing, while also demonstrating the complex relationship of these two closely-linked stimuli. SIGNIFICANCEAccurate perception depends on the brains ability to combine information from multiple senses, commonly thought belonging to high level of information processing. Using the European honeybee, Apis mellifera, we show strong evidence that olfactory and mechanosensory signals interact at an early stage of neural processing, within the antennal lobe, producing stimulus representations closely-linked to the animals navigation and decision-making. By identifying a tractable model for early multisensory processing, this work offers broader insight into how animals construct reliable representations of their environment.

neuroscience↗

bioRxiv2026

SARM1 is required for macrophage immunophenotype switching that is essential for nerve repair

SARM1 is a key executor of Wallerian degeneration in axons. Global knockout of sarm1 in mice delays degeneration for several weeks. Recently, we reported that Schwann cell reprogramming, inflammation, and axon regeneration are also delayed in these animals. Several studies have also indicated that SARM1 has essential regulatory functions in macrophages (M{phi}). However, the role of SARM1 in M{phi} in the context of peripheral nerve injury remains unknown. Here, we report that loss of sarm1 impairs splenic M{phi} from adopting immunological stimuli driven immunophenotypes in culture. Through a combination of cell culture, Western blotting, gene expression analysis, in vivo injection of M{phi} into sciatic nerves, and generation of cell specific sarm1 conditional knockout mouse lines, we found that SARM1 is required for proper immunophenotypes in M{phi}. Loss of sarm1 in macrophages increases neurite length of sensory neurons in culture but delays regeneration in a model of peripheral nerve injury. We identified dysregulation of several inflammatory and anti-inflammatory immunological stimuli pathways and altered regulation of both iNOS and Arginase-1 in Sarm1-/- M{phi}. In culture, Sarm1-/- M{phi} display difficulty phagocytosing and clearing myelin debris and this was recapitulated in vivo with a M{phi} specific sarm1 knockout line. Generation of M{phi} and neuronal sarm1 conditional knockout mice further indicated that SARM1 is required in both cell types for an efficient response to peripheral nerve injury. This study provides the first evidence that SARM1 signaling in M{phi} is required for injury induced inflammation, degeneration, and axon regeneration.

neuroscience↗

bioRxiv2026

Myeloid Gi signaling acts as a weight-independent immunometabolic switch controlling systemic insulin sensitivity

Metabolic dysfunction does not necessarily correlate with adiposity. Metabolically healthy obese individuals and insulin-resistant lean individuals represent a fundamental paradox that implicates immune cell intrinsic mechanisms in the pathogenesis of type 2 diabetes. Here, we identify myeloid Gi signaling as a previously unrecognized determinant of whole-body glucose homeostasis. Single-cell transcriptomic analysis of adipose tissue macrophages from obese mice and humans reveals marked alteration in Gnai isoform, suggesting that myeloid Gi signaling is functionally engaged during metabolic disease. Using complementary myeloid-specific rodent models of Gi inhibition (pertussis toxin) and chemogenetic Gi activation (DREADD), we demonstrate that inhibition of Gi signaling improves glucose tolerance and enhances insulin sensitivity under both regular chow and high-fat diet conditions, independent of body weight and energy expenditure. Whereas acute Gi activation in lean mice modestly enhances glucose disposal, the same intervention during diet-induced obesity markedly impairs systemic glucose homeostasis, revealing context-dependent pathway function. Mechanistically, Gi inhibition amplifies macrophage cAMP-CREB signaling to drive IL-6 production, engaging STAT3- and AMPK-dependent pathways in adipose tissue and skeletal muscle to support insulin action. Conversely, Gi activation engages a previously uncharacterized G{beta}{gamma}-mTOR/AKT-JNK cascade, driving IL-1{beta} secretion that directly impairs insulin signaling in adipocytes and myotubes. Pharmacological IL-6 receptor blockade abolishes the metabolic benefits of Gi inhibition, whereas IL-1 receptor antagonism fully rescues Gi activation-induced metabolic dysfunction, establishing these cytokines as obligate downstream effectors. This signaling architecture is conserved in human macrophages, and ATAC-seq profiling reveals chromatin remodeling at cAMP-CREB and IL-6 regulatory pathway loci, consistent with the observed transcriptional reprogramming. Together, these findings establish myeloid Gi signaling as a weight-independent immunometabolic switch that couples opposing cytokine programs to systemic insulin sensitivity and identify this pathway as a therapeutic target in obesity-associated metabolic disease. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/713834v1_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@15e4576org.highwire.dtl.DTLVardef@224cd5org.highwire.dtl.DTLVardef@1e24888org.highwire.dtl.DTLVardef@1080bf3_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

physiology↗

bioRxiv2026

Transporter-Mediated Uptake of Microcystin-LR in Human Trophoblasts: Regulation By Oxygen Concentration and Cell Fusion

BackgroundRising global temperatures and eutrophication are increasing the intensity and frequency of cyanobacterial harmful algal blooms that release toxins including microcystin-LR (MC-LR). MC-LR inhibits protein phosphatases in the human liver and brain, but its accumulation in the placenta is unclear. Placental transporter expression varies across pregnancy and is influenced by physiological cues, such as low oxygen concentrations which activate HIF1A, and trophoblast cell fusion forming syncytiotrophoblasts that engage CREB-driven transcription. This study examined whether MC-LR accumulates in placental cells, which transporters mediate uptake, and how these transporters are regulated by HIF1A and CREB. MethodsIntracellular accumulation of MC-LR (0.1-10 {micro}M, 3 hour) was measured in human cytotrophoblasts (JAR, BeWo) and extravillous trophoblasts (HTR-8/SVneo) by western blotting for MC-LR-adducted proteins. Organic anion transporting polypeptide (OATP) involvement was tested using cyclosporin A (10 {micro}M), an OATP inhibitor, before exposure to the OATP substrate or MC-LR. Cells were also cultured under 3%, 8%, or 20% O2 to induce hypoxic responses or treated with forskolin (a potent intracellular cAMP inducer) to stimulate cell fusion before MC-LR exposure. ResultsMC-LR accumulated in all three placenta cell lines in a concentration-dependent manner. Cyclosporin A reduced MC-LR uptake by 57% in JAR cells, confirming OATP-mediated transport. Low O2 increased OATP4A1 expression and function but reduced protein phosphatase expression, decreasing MC-LR-bound proteins by 52-72%. Forskolin increased OATP4A1 expression and enhanced MC-LR uptake >2.5-fold. ConclusionMC-LR enters placental trophoblasts via active OATP transport, likely OATP4A1, and uptake increases under hypoxia and trophoblast fusion.

pharmacology and toxicology↗

bioRxiv2026

BRD4 represses developmental and neuronal genes through interactions with polycomb complexes

BRD4 is best known as a transcriptional co-activator, yet heterozygous loss-of-function variants cause craniofacial and neurodevelopmental abnormalities through unclear mechanisms. Using human embryonic stem cells and neural organoids as an in vitro model of human embryonic brain development, we show that BRD4 represses polycomb-regulated developmental and neuronal genes. BRD4 co-occupies bivalent promoters with PRC1.6 and directly interacts with PCGF6 and RING1B through its C-terminal domain. H3K23ac contributes to BRD4 recruitment through BD2, linking acetylated chromatin recognition to polycomb-associated repression. Acute BRD4 depletion alters PRC1.6 occupancy, reduces ubiquitination of H2AK119 and rapidly increases developmental gene transcription. In neural organoids, BRD4 BD2 mutations alter neuronal cell composition and increase expression and chromatin accessibility associated with neuronal transcription-factor programmes. These findings establish BRD4 as a context-dependent chromatin regulator that prevents premature activation of developmental genes and provide mechanistic insight into BRD4-associated neurodevelopmental disorders.

molecular biology↗

bioRxiv2026

Reference-free microsatellite instability detection from tumor sequencing using intrasample variability modeling

Microsatellite instability (MSI) is a key predictive biomarker across multiple tumor types, but current next-generation sequencing (NGS)-based callers oftendependon matched normals, large reference panels, or pretrained machine-learning models, which limits portability across assays and sequencing centers. We developed PROMIS (PROfiling of Microsatellite InStability), a tumor-only, reference-free pipeline that detects MSI by leveraging intrasample variability at predefined microsatellite loci. PROMIS models repeat-length distributions with a discrete mixture framework to distinguish stable germline configurations from unstable loci with additional allele populations. Locus-level classifications are aggregated into a continuous MSI score, defined as the fraction of unstable loci, which can then be used to classify samples as MSI-high or microsatellite-stable. We benchmarked PROMIS in colorectal (CRC), endometrial (UCEC), and gastric (STAD) cancers from The Cancer Genome Atlas (TCGA). PROMIS achieved an overall AUC of 0.995 and cohort-specific AUCs of 1.00 in CRC and STAD and 0.999 in UCEC, comparable to establi shed tools despite not using matched normals or pretrained models. Subsampling and in silico dilutions showed robust performance with substantially fewer loci and down to 3% tumor fraction. Finally, in prostate and CRC cell-free DNA (cfDNA) cohorts, including Illumina TSO500 data and an 18-gene panel, PROMIS yielded assay-agnostic MSI scores concordant with orthogonal tissue- and panel-based classifications.

bioinformatics↗

bioRxiv2026

Tumor-infiltrating natural killer cell profiling for therapeutic stratification in patients with resectable non-small cell lung cancer

ObjectiveNeoadjuvant chemoimmunotherapy has improved outcomes in resectable non-small cell lung cancer (NSCLC), yet its real-world implementation is often challenged by surgical delays, immune-mediated fibrosis, and postoperative complications. Smokers with NSCLC, despite a high risk for surgical morbidity, show enhanced responses to neoadjuvant chemoimmunotherapy. This study aimed to identify smoking-associated immune cell determinants that could guide treatment strategies. MethodsSingle-cell RNA sequencing (scRNAseq) was performed on 61 lung tissues from non-smokers and smokers to identify smoking-related immune compositions. The scRNAseq data from 19 invasive lung adenocarcinomas were used to validate their presence in the tumor-immune microenvironment. Bulk RNA sequencing data from 102 resected NSCLC and 24 NSCLC patients treated with neoadjuvant chemoimmunotherapy followed by surgery were used for in silico cellular deconvolution and outcome analyses. ResultsAmong 135 lung cellular phenotypes, two natural killer (NK) cell subsets were strongly associated with smoking and chronic obstructive pulmonary disease (COPD) severity. "Stress-responsive" NK (NKSR) cells exhibited immature features and cytokine-responsive features, and "Adaptive and immunoregulatory NK" (NKAIR) cells showed mature features and elevated multiple immune checkpoint expression. High intratumoral NKSR cells correlated with improved survival after surgery, particularly in current smokers. Conversely, tumors with low NKSR and high NKAIR cells responded more favorably to neoadjuvant chemoimmunotherapy. ConclusionsIntratumoral NK cell phenotyping may aid in therapeutic stratification in patients with NSCLC. NKSR cell preservation predicts benefit from upfront surgery, while NKAIR cell enrichment indicates improved response to neoadjuvant chemoimmunotherapy. These NK cell profiles may help optimize treatment by balancing therapeutic benefit and risk. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/696292v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@168bc03org.highwire.dtl.DTLVardef@10fa947org.highwire.dtl.DTLVardef@132a92dorg.highwire.dtl.DTLVardef@100e4a4_HPS_FORMAT_FIGEXP M_FIG C_FIG Central Picture O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/696292v1_ufig2.gif" ALT="Figure 2"> View larger version (21K): org.highwire.dtl.DTLVardef@1a2d3b4org.highwire.dtl.DTLVardef@f8f84borg.highwire.dtl.DTLVardef@17510bcorg.highwire.dtl.DTLVardef@9da763_HPS_FORMAT_FIGEXP M_FIG C_FIG NK cell profiling for treatment stratification in resectable NSCLC Central MessageTumor-infiltrating NK cell profiling identifies distinct immune phenotypes that can inform personalized treatment strategies in resectable NSCLC. Perspective statementAbundance of intratumoral stress-responsive NK cells predicts favorable outcomes after upfront surgery, whereas enrichment of adaptive and immunoregulatory NK cells suggests greater benefit from neoadjuvant chemoimmunotherapy. These findings support incorporating NK-cell profiling into preoperative decision-making to optimize therapy selection and balance risks in the high-risk surgical population.

immunology↗