Biology subjects

Singh, V.

Publications and source records attributed to Singh, V..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Environmental impacts of Broiler chicken production in the North Eastern Himalayan region of India: Evaluation using the Life Cycle Assessment approach

The study presents the first comprehensive environmental assessment of broiler chicken production in India, from a cradle-to-farm-gate perspective, using the Life Cycle Assessment (LCA) approach. The objective of the study was to identify environmental hotspots in the broiler production system. All inflows and outflows of the broiler production system were mapped to construct the life-cycle inventory. This study uses a system boundary that extends from the cradle to the farm gate. Inventory data for the broiler chicken farms were collected from six different farms, which is typical of the Indian broiler production system, and background data were sourced from the Ecoinvent 3.0 database. For the LCA study, SimaPro (v 9.3.0.3) was used with the ReCiPe 2016 Midpoint impact assessment methodology. For this study, the functional unit of the "1-kg live weight chicken produced was taken into consideration". The environmental impact categories assessed were mainly Global Warming Potential in hundred years (GWP), stratospheric ozone depletion, freshwater eutrophication, terrestrial ecotoxicity, land use, etc. Results showed that broiler chicken feed was primarily responsible for environmental impacts, followed by transportation and electricity. Broiler chicken production had a total GWP of 3.77 kg CO2-eq per kilogram of live weight. Specifically, the energy component of feed, viz., maize production, was the main source of environmental impact. The process of transporting feed and chicks to the broiler farm also had a significant environmental impact. The broiler production system was found to have moderate environmental impacts compared to other published LCA studies of chicken production. Based on the findings of the present study, we proposed actionable items to further improve the environmental efficiency of broiler chicken production in India.

ecology↗

bioRxiv2026

Histone neutralization protects the ischemic brain against stroke-associated pneumonia

Bacterial pneumonia aggravates ischemic stroke via mechanisms that still remain to be determined. In ischemic stroke patients and mice exposed to middle cerebral artery occlusion, we show that stroke-associated pneumonia markedly worsens clinical stroke outcome. In mice, pneumonia induced 3 days after stroke impaired neurological recovery and increased brain neutrophil infiltrates, blood-brain barrier breakdown, cerebral microvascular thrombosis, and progressive brain atrophy. The antibiotic amoxicillin only partially ameliorated pneumonia-associated neurological deficits and neutrophil infiltrates. Neutrophils were critical mediators of pneumonia-induced blood-brain barrier breakdown and microvascular thrombosis. Notably, administration of a neutralizing anti-histone antibody during pneumonia--unlike degradation or blockade of neutrophil extracellular trap formation or myeloperoxidase inhibition--restored long-term neurological recovery and prevented brain atrophy in stroke-associated pneumonia mice. This study identifies extracellular histones as key drivers of secondary inflammatory brain injury and establishes histone neutralization as a therapeutic strategy with an extended treatment window in the post-acute stroke phase. One Sentence SummaryNeutralizing extracellular histones reverses pneumonia-driven secondary brain injury and restores long-term recovery after ischemic stroke.

neuroscience↗

bioRxiv2025

scDNA: Single Cell DNA analysis software toolkit for subclonality discovery and assessment.

Advances in single cell multi-omics technologies have allowed for investigation into genotype-immunophenotype relationships and dynamic clonal changes in cancer patient samples. These technologies provide rich insights into genetic profiling, drivers of disease progression, and subclonal dynamics. Increased adoption and throughput of these technologies, necessitate accessible computational tools for processing and analysis. Toward developing easy to use computational tools, we introduce the Single Cell DNA (scDNA) package that allows for rapid analysis of single-cell molecular profiling. Our platform aims to provide a diagnostic summary tool for sample quality control, representative subclonal architecture within a sample, demultiplexing functionality for multi-sample processing, copy number variation, and mutation trajectory analysis to identify order of subclonal mutation acquisition. We showcase a series of vignettes on hematopoiesis datasets for each aim that reflects recently deployed uses of scDNA. Additionally, we show scDNA provides a modular, user-friendly framework that readily feeds into other standard software pipelines.

genomics↗

bioRxiv2025

Caenorhabditis briggsae ancestral genomic hyper-diversity contrasts with globally distributed genome-wide haplotypes

Comparative genomics provides a powerful framework to uncover the molecular and evolutionary mechanisms that shape genetic diversity within and across species, revealing how shared and lineage-specific processes influence their evolutionary trajectories through time. The nematode Caenorhabditis briggsae is distributed world-wide and is a comparative model to Caenorhabditis elegans in the biology of development, cellular mechanisms, neurobiology, genetic mappings of complex traits, and genome evolution. Following massive collection efforts by the nematode research community, we present the isolation of over 2,000 wild strains and analyses of genome sequences that catalog over six million single-nucleotide and insertion-deletion variants. This genome and strain resource provide a powerful means to interrogate the causal genetic bases of phenotypic variation for diverse traits. Additionally, we describe its global population structure and discover new and genetically distinct groups within this primarily self-fertilizing species, including groups of highly related strains that were sampled across different continents. We leverage expansive genetic variation to decipher the effects of linkage and selection on the distribution of genetic diversity across the genome and across geographic regions. Within the species, we find genomic regions with extremely high levels of genetic variation similar to hyper-divergent regions found in C. elegans and other species. These regions harbor new genes and variation enriched for environmental sensing and pathogen responses. In comparison to the outbreeding sister species Caenorhabditis nigoni, we conclude that long-term balancing selection has maintained substantial functional variation since the divergence from their outbreeding ancestor, likely in response to differences in the ecological niche. Overall, this massive strain resource enables future comparative genetics and genomics studies, including genome-wide association studies between Caenorhabditis species.

genomics↗

bioRxiv2025

Tissue-Adhesive Endoscopic Tattoo Inks for Precise Marking and Surveillance of Gastrointestinal Lesions

Accurate marking of lesions and polyps is essential for effective management of gastrointestinal (GI) diseases, including colorectal cancer. Existing FDA-approved endoscopic carbon suspensions diffuse extensively within tissue and can extravasate intraperitoneally, compromising lesion localization, increasing fibrosis risk, and triggering inflammatory responses. These limitations reduce surgical precision and adversely affect patient outcomes. Here, we developed Tissue Adhesive Tattoos, generation 2 (TAT2) inks, composed of iron oxide nanoparticles encapsulated in bioadhesive polymers to improve spatial accuracy while maintaining high endoscopic contrast. TAT2 inks exhibit easy injectability, long-term stability, low macrophage inflammation, and strong spatial localization in ex vivo porcine intestinal tissue. Compared to clinical carbon ink, which spreads widely, TAT2 inks remained sharply localized with excellent contrast after submucosal injection in live mice and pigs. TAT2 also enabled visualization from both luminal and serosal surfaces and supported precise quadrant marking. Additionally, TAT2 inks were MR-compatible, expanding multimodality. Overall, TAT2 inks are biocompatible, non-inflammatory, precisely localized, and improve endoscopic marking for GI disease. TeaserEngineered bioadhesive tattoo inks deliver precise, durable GI marking with minimal spread and compatibility across imaging modalities.

bioengineering↗

bioRxiv2025

Oxidative-stress related increase in keratoconus tear MDA and GPX3 while NRF2-antioxidant functions decrease in stromal cells

Keratoconus (KC) is a common eye disease where the cornea undergoes degenerative thinning and steepening. The absence of biomarkers for early diagnosis prior to the onset of overt corneal phenotypes and the lack of curative treatments rooted in a fundamental understanding of KC biology remain significant challenges. To address these issues, we investigated the role of unresolved oxidative stress in KC pathogenesis. Malondialdehyde (MDA) a lipid peroxidation byproduct that accumulates during oxidative stress was significantly elevated in the tears of KC patients compared to unaffected controls and positively correlated with maximal keratometry (Kmax), a measure of KC severity. Similarly, the secreted antioxidant glutathione peroxidase 3 (GPX3), was significantly increased in patient tears, and strongly correlated with Kmax. In a cell culture model of oxidative stress, KC corneal stromal cells displayed increased apoptosis and suboptimal activation of NRF2, a transcription factor master regulator of antioxidant genes. Conversely, inhibition of NRF2 in donor stromal cells elicited KC-like cellular phenotype, whereas sulforaphane, an NRF2 booster restored antioxidant gene expression and the deposition of cornea-typical collagens. Our study identified cellular antioxidant signaling dysregulations in keratoconus where sulforaphane treatment may be restorative. Consistent increases in patient tear MDA and GPX3 present these as promising biomarkers for KC diagnosis and severity predictions.

cell biology↗

bioRxiv2025

Decoding the Circulating Proteome: Matrix and Immune Context Markers Shape Early Multi-Cancer Detection

BackgroundBlood-based proteomics offers a complementary path to multi-cancer early detection (MCED) by capturing the tumor secretome and host response. We analyze recent (2020-2025) evidence and add pathway/hallmark context, cross-platform validation, and proteome-scale protein-protein interaction (PPI) inference to guide translational panel design. MethodsWe reviewed extensive prospective and multi-cancer studies using Olink, SomaScan, and mass spectrometry, contrasting case-control versus prospective performance. Candidates were organized into Known and Novel sets and mapped with GeneCodis (GO/KEGG/Reactome) and Cancer Hallmarks. Clinical relevance was assessed using GEPIA 3.0 Cox Forest plots and TCGA-survival Kaplan-Meier curves (median split; log-rank). Protein-level corroboration used TPCPA/RPPA Z-score distributions across tumor types. To contextualize molecular crosstalk, we incorporated in silico PPI prediction to evaluate whether candidates cluster into interaction sub-modules relevant to secretory/TGF-{beta}, matrix remodeling, and immune-follicular biology. ResultsBeyond classic antigens/inflammatory markers (e.g., CEACAM5, WFDC2/HE4, GDF15), the Novel set converged on a matrix-immune-secretory axis comprising ECM proteases (MMP12, ADAM8), antigen presentation/B-cell programs (CD74, CXCL13), secretory/TGF-{beta} signaling (TGFB1), and epithelial invasion (CDCP1). Forest plots show adverse hazards for secretory/matrix genes across multiple epithelial cancers, while immune-follicular genes exhibited context-dependent effects; TCGA-survival curves reproduced these directions. TPCPA demonstrated tumor-type-specific protein elevation, supporting detectability. PPI inference organized candidates into coherent interaction modules (e.g., TGFB1, CDCP1 protease, and CXCL13; CD74 hubs), reinforcing multiplex, not single-marker, readouts. ConclusionsCross-platform agreement, augmented by PPI-defined interaction modules, supports a two-bucket MCED strategy that pairs high-risk secretory/matrix markers with immune-context sensors to enhance sensitivity, tissue-of-origin interpretability, and clinical triage. Prospective validation and down-selection to a cost-scalable targeted assay are warranted for population screening.

cancer biology↗

bioRxiv2025

An improved Solanum verrucosum genome provides insight into potato centromeres and epigenetic regulation

Solanum verrucosum is a wild diploid potato species notable for carrying the uncharacterised Rpi-ver1 gene conferring resistance to Phytophthora infestans, possessing unusually structured centromeres, and exhibiting the rare trait of self-compatibility, the genetic basis of which remains unknown. Here, we present a high-quality genome assembly and annotation of S. verrucosum accession CPC54. A comprehensive inventory of resistance genes is provided, and candidate genes for Rpi-ver1 are identified through remapping approaches. The sequence and epigenetic landscape of centromeres are resolved, revealing a mosaic of repeatless and repetitive domains. These centromeres consist of tandem arrays of kilobase-sized repeats, some of which show signatures of transposable element origin. Specific subfamilies of CRM and Tekay elements appear to have adapted to centromeric regions. The basis of self-compatibility in S. verrucosum is investigated with respect to the S-RNase gene, which is found to be present and intact, but expressed at very low levels. Notably, upstream insertions of transposable elements are present that may interfere with its expression.

plant biology↗

bioRxiv2025

An unbiased survey of distal element-gene regulatory interactions with direct-capture targeted Perturb-seq

Identifying the impact of distal regulatory elements on gene expression is a core challenge in human genetics. Large-scale CRISPR screens have not captured lower effect size element-gene interactions due to selection bias and limited statistical power. We developed a framework for highly powered CRISPR screens, consisting of Direct-Capture Targeted Perturb-seq (DC-TAP-seq), unbiased target selection, and a pipeline accounting for statistical power. Surveying 10,000 random distal element-gene pairs revealed most element-gene interactions have effect sizes <10%, which were virtually undetectable in prior studies. Most interactions occur within 100kb, many elements bind CTCF without classical enhancer chromatin, and housekeeping genes have similar frequencies of distal regulatory elements but with weaker effects. We also highlight limitations of predictive models and suggest that new models consider elements with smaller effect sizes. Our study provides an expanded view of distal regulatory elements and a framework for building more comprehensive maps of distal regulation.

genomics↗

bioRxiv2025

Differential Regulation of NHE3 Expression in Type 1 and Type 2 Diabetic Intestine: Impaired Endosomal Regulation of NHE3 Expression in Type 1 Diabetes

Chronic diarrhea is a frequent gastrointestinal complication in both type 1 (T1D) and type 2 diabetes (T2D), though the underlying mechanisms differ: T1D is linked to autonomic neuropathy and disrupted transporter regulation, while T2D is often linked to medications and intestinal inflammation. Using streptozotocin-induced mouse models of T1D and T2D, we observed increased luminal fluid in the small intestine of both. Given the role of Na+/H+ exchanger 3 (NHE3) in fluid absorption and its loss in most diarrheal diseases, we examined NHE3 expression across intestinal segments. In T1D, NHE3 protein was significantly reduced in the duodenum and jejunum without changes in mRNA, suggesting post-transcriptional regulation. In contrast, T2D mice exhibited reduced NHE3 protein and mRNA, restricted to the proximal colon. To investigate mechanisms underlying NHE3 loss in T1D, we evaluated endosomal scaffolding proteins involved in NHE3 trafficking. While our previous work showed that the Sorting Nexin-27 (SNX27)-retromer complex does not regulate NHE3 protein stability, we found that SNX17 was significantly decreased in the small intestine of T1D mice but unchanged in T2D. SNX17 knockdown in SK-CO15 cells reduced NHE3 activity and stability. A GST pull-down assay showed that SNX17 interacts with the C-terminus of NHE3. Mutation of the NHE3 distal NPxY motif disrupted this interaction, leading to reduced NHE3 expression and increased degradation. These findings reveal segment-specific and mechanistically distinct causes of diabetic diarrhea in T1D versus T2D, and identify SNX17 loss as a contributor to reduced NHE3 stability and activity in T1D, likely promoting diabetic diarrhea. New and NoteworthyThis study identifies distinct mechanisms of impaired sodium absorption contributing to diabetic diarrhea in type-1 and type-2 diabetes. We identify SNX17 as a novel regulator of NHE3 in the small intestine, showing that SNX17 loss in T1D contributes to post-translational NHE3 destabilization. In contrast, T2D-associated NHE3 downregulation is transcriptional and confined to the colon. These findings reveal disease- and region-specific regulatory pathways that drive impaired fluid absorption in diabetes, with direct implications for the development of targeted therapies. Graphical abstract Schematic overview of differential NHE3 regulation in diabetic diarrhea.In Type 1 Diabetes (T1D), reduced SNX17 expression in the small intestine causes increased degradation of NHE3 and impaired sodium absorption. In Type 2 Diabetes (T2D), SNX17 levels remain unchanged in the small intestine, but NHE3 expression is transcriptionally downregulated in the proximal colon. These distinct mechanisms contribute to segment-specific differential regulation of NHE3 in T1 and T2D diabetes. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/675364v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@eabf0aorg.highwire.dtl.DTLVardef@1a46891org.highwire.dtl.DTLVardef@cd2d5corg.highwire.dtl.DTLVardef@5d185b_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2025

Arg80 Orchestrates a Metabolic-Translational Proteostasis Network in S. cerevisiae

Proteostasis or protein homeostasis is essential for cellular function and organismal health. While many models of cytosolic proteostasis emphasize heat shock response as critical for regulating cellular protein folding, a comprehensive understanding of transcriptional modules that may regulate cytosolic protein folding is lacking. Through a focused screening for transcription factors, we provide evidence that a number of transcriptional programs unlinked to canonical proteotoxic response are involved in maintaining cellular homeostasis of protein folding. Among these, Arg80, a regulator of arginine metabolism, was activated during proteotoxic stress and found essential for mitigating it. We show that proteostasis imbalance in arg80{Delta} cells is caused by excess arginine accumulation, which is sufficient to impair protein folding. We reveal a complex interplay between arginine repression (Arg80), trehalose biosynthesis (Tps2), and the integrated stress response (Gcn2) in combating proteotoxic insults. We posit that multiple metabolic pathways integrate with classical protein quality control networks to regulate the protein folding environment. Harnessing these metabolic circuits may offer new avenues to modulate proteostasis when needed.

systems biology↗

bioRxiv2025

A quantitative framework for predicting odor intensity across molecule and mixtures

In vision and hearing, standardized units such as lumens (for brightness) and decibels (for loudness) allow consistent quantification of stimulus intensity, enabling precise control of sensory experiences. Olfaction, by contrast, currently lacks a robust quantitative framework linking physical stimulus properties directly to perceived odor intensity, complicating efforts to accurately characterize and manipulate aromas. To bridge this gap, we used a precisely controlled odor delivery system combined with deep learning models to predict the intensity of both single molecules and mixtures from physical properties. These models allowed us to develop an automated, quantitative method that accurately identifies which volatile components meaningfully contribute to aroma perception, overcoming the limitations of traditional heuristic approaches such as odor activity values and demonstrating practical utility in complex naturalistic odors.

neuroscience↗

bioRxiv2025

A Shared Amyloid Architecture in Cardiac Fibrils from Three Neuropathy-Associated ATTR Variants

ATTR amyloidosis results from the systemic accumulation of wild-type (ATTRwt) or mutant (ATTRv) transthyretin amyloids, leading to multi-organ dysfunction and death. The disease exhibits variable pathology and penetrance, and its relationship with the amyloid structure remains unclear. Patients carrying the neuropathy-associated variants ATTRvI84S and ATTRv-V122{Delta} present polymorphic ATTR fibrils, in contrast to the consistent morphology reported for most ATTR fibrils to date. Here, we aim to elucidate a potential link between neuropathic symptomatology, distinct mutations, and amyloid structural diversity, using cryo-EM. We determined the ex-vivo fibril structures from the variants ATTRv-P24S, ATTRv-A25S, and ATTRv-D38A, whose patients presented variable clinical manifestations, including neuropathy. Our findings revealed that, despite differences in mutations and diverse clinical phenotypes, these variants share a common amyloid core previously identified in ATTRwt and several other cardiac ATTRv. This structural consistency is significant for the development of structure-guided diagnostic tools capable of addressing the diverse spectrum of ATTR amyloidosis. HighlightsO_LIDetermines transthyretin amyloid structures of three human ATTRv by cryo-EM C_LIO_LIDetermines the structure of three ex-vivo ATTRv fibrils linked to polyneuropathy. C_LIO_LIReveals structural similarities of ATTRv amyloid cores. C_LIO_LIReveals a common fold despite the different mutations and symptomatology. C_LIO_LIContributes to the understanding of transthyretin aggregation in patients with diverse phenotypes C_LI

biophysics↗

bioRxiv2025

Phased Potato Genome Assembly and Association Genetics Enable Characterisation of the Elusive H1 Resistance Locus Against Potato Cyst Nematodes

The complexity of potato genetics, characterised by tetrasomic inheritance, has contributed to slower genetic gain in potato compared to other major crops. Disease resistance genes, often found in large clusters of highly similar paralogs and alleles, further complicate genetic studies. The H1 resistance locus, introgressed into potato cultivars from Solanum tuberosum spp. andigena, has been successfully used for over 60 years to control Globodera rostochiensis in Europe. Although previous genetic studies mapped this resistance to chromosome 5, the complete structure of the locus remained elusive. To reduce genomic complexity, we generated a dihaploid of the cultivar Athlete, DH4_Athlete, carrying the H1 resistance locus, and produced a phased haplotype representation of the H1 interval using Oxford Nanopore sequencing. Combined with RenSeq-based association genetics, this approach allowed us to reconstruct the entire H1 locus, including recombination points at both the 5' and 3' ends of the interval.

plant biology↗

bioRxiv2025

Comparative Assessment of Chlorella vulgaris Cultivation in Synthetic, Oligotrophic and Industrial Wastewater for Sustainable Biomass Production

This study evaluates the physiological and biochemical responses of Chlorella vulgaris cultivated in synthetic BG11 medium, oligotrophic water, and industrial wastewater under controlled laboratory conditions with optimized pH and nitrogen-to-phosphorus (N:P) ratios. The highest cell density, growth rate, and pigment accumulation were observed in BG11 at neutral pH and higher N:P ratios. Moderately adjusted N:P ratios in industrial wastewater produced comparable biomass yields and improved photosynthetic efficiency, demonstrating its potential as a cost-effective medium for integrated wastewater treatment and algal biomass production. In contrast, oligotrophic water severely limited growth due to nutrient deficiency. FTIR analyses indicated that C. vulgaris maintains essential biochemical components under nutrient stress through adaptive metabolism. This comparative study provides new insights for designing scalable, sustainable microalgal cultivation systems that link biomass production with wastewater management within a circular bioeconomy framework.

systems biology↗

bioRxiv2025

Structural polymorphism of ex-vivo ALECT2 amyloid fibrils revealed by cryo-EM

ALECT2 amyloidosis is a rare systemic disease characterized by the pathological deposition of leukocyte cell-derived chemotaxin-2 (LECT2) as amyloid fibrils, primarily affecting the kidneys and liver. The molecular mechanisms underlying LECT2 aggregation remain poorly defined, hindering diagnostic and therapeutic development. Here, we present cryo-electron microscopy structures of ex-vivo ALECT2 fibrils extracted from a patients kidney. We identified three fibril polymorphs: a predominant single-protofilament morphology and two minor double-protofilament morphologies. The dominant single-protofilament morphology comprises the full-length 133-residue LECT2 protein and retains all three native disulfide bonds. Low-resolution reconstructions of double-protofilament morphologies suggest they adopt a similar fold to the single protofilament morphology, but form paired assemblies with different inter-filament interfaces. Mass spectrometry also reveals acetylation within the fibrils. These findings offer critical insights into the structural basis of ALECT2 amyloid formation and identify molecular features that could inform future diagnostic and therapeutic approaches.

biophysics↗

bioRxiv2025

Structural variability of apolipoprotein A-I amyloid fibrils across organs, mutations, and clinical presentations, revealed by cryo-EM

Hereditary apolipoprotein A-I (AapoA-I) amyloidosis is a rare systemic disease caused by the deposition of amyloid fibrils formed by apolipoprotein A-I in multiple organs, leading to severe clinical outcomes. With no available therapies or diagnostic tools, defining the structure of AApoA-I fibrils is crucial to understanding disease mechanisms and guiding intervention. Using cryo-electron microscopy, we analyzed AApoA-I fibrils from the heart, kidney, liver, and spleen of patients carrying G26R, L90P, and R173P mutations. G26R fibrils, regardless of organ, exhibited untwisted morphologies and could not be resolved structurally. Conversely, L90P and R173P fibrils displayed a compact diabolo-shaped conformation in all organs analyzed. Their high-resolution maps enabled visualization of cis-Proline 66, which may represent a potential conformational switch during fibril formation. Our findings suggest that mutation-driven polymorphism may influence organ tropism and clinical presentation. This work advances our understanding of AapoA-I fibril assembly and provides insights toward developing targeted clinical tools.

biophysics↗

bioRxiv2025

Transcriptomic Profiles from Normal and Tumor Tissue Samples Reveal Distinct Venule Populations and Novel Tumor Endothelial Cell Markers in Breast Cancer

BackgroundThe breast tumor microenvironment (TME) is a complex milieu composed of many factors contributing to breast cancer (BC) heterogeneity and therapeutic resistance. Aberrant tumor vasculature in the TME limits nutrient and drug delivery, inhibits anti-tumor immunity, and contributes to a lack of cancer therapy efficacy. Utilizing publicly available scRNA-seq datasets, this study characterizes differences between normal breast and breast tumor endothelial cells (EC), provides insights into tumor endothelial cell subtypes, endothelial anergy, and identifies novel, tumor-specific vascular therapeutic targets. MethodsGene expression data from normal and breast tumor tissue samples were integrated, and the EC subset was extracted via canonical gene marker expression. The EC subset was clustered and evaluated for cell subtypes and differentially expressed genes (DEG). Normal EC (NEC) and tumor EC (TEC) markers were further assessed for correlation to bulk gene expression and patient survival outcomes in cBioPortal and Kaplan-Meier Plotter. Cell type gene expression specificity was evaluated in the 3CA single-cell RNA-seq datasets across multiple cancers. ResultsThis analysis revealed differences in NEC and TEC subtype populations. Breast NEC contained similar proportions of venule and capillary populations, while breast TEC demonstrated a majority of the venule subtype. Further, TEC venules were phenotypically distinct from the NEC venules. Consistent with endothelial anergy, suppression of the key adhesion protein SELE was noted, as well as several pro-inflammatory cytokines including IL6, CCL2, and CXCL8, likely downstream of aberrant NF-kB signaling. Differential gene expression analysis identified several TEC specific up-regulated genes compared to NEC, including CLEC14a, IGFBP4, EMCN, and ADM5. CLEC14a, EMCN, and ADM5 were further validated in the single-cell Curated Cancer Cell Atlas (3CA) to be highly specific to the endothelial cell clusters across multiple tumor types, while IGFBP4 was diversely expressed in endothelial, fibroblast, and some malignant cell types. ADM5, a novel tumor vascular marker, was enhanced in TEC venules and less so in arteriole or capillaries. High expression of ADM5 was associated with poor breast cancer patient survival in the basal PAM50 cancer subtype compared to normal and luminal subtypes. Further, across multiple cancer types, high ADM5 expression was associated with reduced patient survival in anti-PD1- and anti-CTLA4-treated patients but not in anti-PDL-treated patients. ConclusionsIntegration of single-cell RNA-seq data identified an anergic-like response in breast TEC and multiple, highly specific markers to TEC not found in normal breast tissue. CLEC14a and EMCN were validated as TEC markers, extending their annotation in breast TEC, and ADM5 identified as a novel TEC marker in breast and other cancers. Moreover, as ADM5 is associated with reduced patient overall survival, this data suggests that a better understanding of ADM5 and other TEC-specific response pathways may provide novel approaches to reactivate anergic TECs and lead to effective therapeutic interventions for cancer patients. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=96 SRC="FIGDIR/small/661087v2_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@a81bf2org.highwire.dtl.DTLVardef@c2b983org.highwire.dtl.DTLVardef@216ab9org.highwire.dtl.DTLVardef@1e5bebb_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

cancer biology↗