Biology subjects

Singh, R. P.

Publications and source records attributed to Singh, R. P..

14 recordsLinked to original sources

bioRxiv2026

BCL11B targeting in tumor CD8+ T cells amplifies anti-tumor response by blocking exhaustion while promoting stemness and cytotoxicity

Tumor infiltrating CD8+ T cells (TILs) progress to a state of terminal exhaustion (Ttex) which have impaired functionality and are nonrenewable. However their precursors (Tpex) are renewable and can generate efficient effector cells. We started from the observation that melanoma patients undergoing therapy with checkpoint inhibitors show increased survival when their T cells have low BCL11B mRNA. In line with this, ablation of Bcl11b in CD8+ TILs conferred a superior anti-tumor response in murine melanoma and ovarian cancer models. Bcl11b KO TILs failed to progress to the Ttex state and retained elevated stemness. Bcl11b exerted its role by repressing expression of essential transcription factors (TF) controlling stemness, and conversely by promoting expression of exhaustion-associated TFs and inhibitory receptor genes, through complex epigenetic control. In addition, Bcl11b KO CD8+ T cells showed increased Ag-specific cytolytic activity and elevated Gzmb and Prf1 proteins, but no increase in their mRNAs, however presented higher expression of genes with role in translation. Furthermore, CRISPR-CAS9-mediated deletion of BCL11B in human TILs from a patient with poor response to adoptive cell therapy with autologous TILs, improved their cytolytic activity and promoted expression of the stemness-associated TF TCF1, underlying its potential therapeutic use. HIGHLIGHTS- Adoptive transfer of Bcl11b KO CD8+ TILs surpasses WT in tumor burden reduction - Bcl11b ablation reprograms TILs and impairs the progression to Ttex state - Bcl11b KO CD8+ T cells have elevated cytotoxicity and kill only Ag-MHCI targets - BCL11B deletion in nonresponder ACT-TIL improves cytolytic activity and elevates TCF1 GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=64 SRC="FIGDIR/small/742578v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@c3b965org.highwire.dtl.DTLVardef@1c09d75org.highwire.dtl.DTLVardef@a19748org.highwire.dtl.DTLVardef@d2fd6b_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2026

GeneAutomate: A Browser-Based, Integer-Indexed Platform for Dual-Gene-List Functional Annotation and Interactive Network Visualization

Comparative interpretation of two gene lists, for example, two treatment arms, two tissues, or a discovery and a validation cohort, is a routine task in functional genomics. While several tools offer dual-list comparison (e.g., EnrichmentMap, RRHO packages), they typically require local software installation, R/Bioconductor, or manual reconciliation of separate single-list outputs. Most widely used web-based enrichment tools (DAVID, g:Profiler, Enrichr, ShinyGO, WebGestalt) are built around the analysis of a single gene list at a time, and those that support comparison often lack interactive, publication-ready visualization or depend on server-side query latency. Here we present GeneAutomate, a browser-based tool purpose-built for side-by-side comparison of two gene lists. GeneAutomate performs Over-Representation Analysis (ORA) against Gene Ontology (GO) and Reactome using an exact hypergeometric test with Benjamini-Hochberg false discovery rate correction, and Gene Set Enrichment Analysis (GSEA) when ranked (log2 fold-change) input is supplied, alongside Protein-Protein Interaction (PPI) subgraph extraction from BioGRID physical interactions. All reference data (Gene Ontology, Reactome, BioGRID, and NCBI/Ensembl identifier cross-references) are pre-compiled offline into a single integer-indexed database of approximately 32 MB for Homo sapiens, in which every gene identifier Ensembl ID, Entrez ID, official symbol, or alias is resolved to one canonical integer prior to any user query. This design removes live database round-trips from the runtime path, enabling fast, at-your-desk enrichment without installation or a server-side per-query bottleneck. The tool renders thirteen interactive, D3.js- and Cytoscape.js-based comparative visualizations, including a Rank-Rank Hypergeometric Overlap (RRHO) heatmap, a GO-slim "Radar/Spider" functional fingerprint, and chord/edge-bundled cross-talk diagrams that are, to our knowledge, not offered as an integrated set by any existing academic or commercial ORA/GSEA platform. GeneAutomate is an unfunded, individual student project developed with feedback from a professor, and is in its final stage of development. It requires no installation or login. We describe the tools architecture, statistical methods, and comparative feature set relative to established academic tools (DAVID, ShinyGO, g:Profiler, Enrichr, WebGestalt, STRING, PANTHER, GeneMANIA, Cytoscape, clusterProfiler, GSEA, Metascape) and commercial platforms (IPA, MetaCore, Pathway Studio, iPathwayGuide, Partek Pathway), and we state candidly the current versions limitations, which are planned to be the added in next version: single-species (human-only) coverage, no upstream regulator analysis, and comparison currently limited to two (occasionally three) concurrent lists. GeneAutomate is available at https://geneautomate.tech/.

bioinformatics↗

bioRxiv2026

Genetic analysis and mapping of adult plant stripe rust resistance loci in CIMMYT wheat 'Kijil under Mexican and Chinese field environments

Stripe rust, caused by Puccinia striiformis f. sp. tritici, can cause severe yield losses in wheat (Triticum aestivum L.) during epidemics. Breeding resistant wheat varieties remains the most cost-effective approach to manage this disease; and the identification of new resistance loci is essential for maintaining genetic diversity. The CIMMYT-derived wheat line Kijil was highly resistant to stripe rust in both Mexican and Chinese environments. A population of 153 F recombinant inbred lines (RILs) was derived from a cross between Kijil and the susceptible parent Apav#1. The population was phenotyped for stripe rust resistance across seven environments in two countries and genotyped using a genotyping-by-sequencing (GBS) platform. Inclusive composite interval mapping (ICIM) was uesd to construct a genetic map and identify significant resistance quantitative trait loci (QTLs) using 5,468 polymorphic markers. Mapping revealed the known resistance loci Yr29, Yr30 and QYr.hzau-3AS, along with two novel loci, QYr.hzau-2BS and QYr.hzau-5DL, across both Chinese and Mexican rust environments. Among these, QYr.hzau-2BS accounted for 11.75% to 19.19% of the phenotypic variance. A corresponding KASP marker, KASP_2BS, was developed to facilitate maker-assisted selection. Based on the mapping interval, four candidate genes underlying this locus were predicted. Further analysis revealed that Yr29 showed significant additive effects with other stripe rust resistance genes/loci, and the combination of Yr29, Yr30, and QYr.hzau-2BS reduced disease severity by up to 67.8%. Our findings suggest that Kijil and RILs carrying Yr29, Yr30, and QYr.hzau-2BS can serve as valuable donors for breeding wheat varieties with improved stripe rust resistance. Author summaryStripe rust is an important disease that seriously threatens the yield and quality of wheat. It is crucial to explore new resistant resources and cultivate durable resistant varieties in the current breeding programme. In this study, we analysed the genetic basis of resistance to stripe rust in the wheat line "Kijil", which has broad-spectrum resistance to stripe rust. Through genetic mapping, we identified five quantitative trait loci for stripe rust, including two new resistance loci. A closely linked KASP marker, KASP_2BS, was developed for the QYr.hzau-2BS, which can be used for rapid and accurate screening of resistant plants in early breeding populations. Meanwhile, within this QTL region, we screened four candidate genes based on expression analysis. In addition, it was found that polymerization of QYr.hzau-2BS with known resistance genes, Yr29 and Yr30, significantly enhanced resistance and reduced disease severity to low levels and near immunity. In conclusion, this study provides new genetic resources, practical molecular markers and effective gene polymerization strategies for breeding wheat for stripe rust resistance. Kijil and the lines containing resistance loci have important breeding utilization value.

plant biology↗

bioRxiv2024

AyurPhenoClusters define common molecular roots for rare diseases and uncover ciliary dysfunctions in syndromic conditions

The heterogeneity of underlying causes and the variability of symptoms across Multiple organs in rare diseases present significant challenges when approached from an organ-centric perspective. Ayurveda, however, takes a multisystem perspective, assessing diseases through kinetic (Vata:V ), metabolic (Pitta:P ), and structural (Kapha:K ) dimensions, each with distinct phenotypic and molecular correlates. This study explores rare diseases from a systems perspective by integrating Ayurveda and unifying terminologies from both disciplines using Human Phenotype Ontology (HPO). Experts categorized 10,610 HPO terms into Ayurvedic phenotypic groups (V/P/K ) and applied the Expectation Maximization (EM) algorithm to cluster 12,678 diseases. This yielded six distinct clusters, termed AyurPhenoClusters, with 2,814 diseases uniquely classified and enriched for V/P/K phenotypes. Functional annotation of these, highlighted key biological processes: (i) embryogenesis and skeletal morphogenesis, (ii) endocrine and ciliary functions, (iii) DNA damage response and cell cycle regulation, (iv) inflammation and immune response, (v) immune function, hemopoiesis, and telomere aging, and (vi) small molecule metabolism and transport. Notably, the K predominant cluster had the highest ciliary gene enrichment (43%), followed by the V predominant cluster (16%), suggesting potential ciliopathies in V cluster. This systems-based approach enhances the understanding of rare diseases by bridging Ayurveda with modern medicine, for improved diagnostics and therapeutics

genetics↗

bioRxiv2024

Clonal spheroids capture functional and genetic heterogeneity of head and neck cancer

Head and neck cancer squamous cell carcinoma (HNSCC) cells exhibit both structural and functional diversity, making them valuable models for understanding tumor heterogeneity at clinical levels. In this study, we generated single-cell-derived spheroids (SCDS) from HNSCC cell lines and patient tumor cells using scaffold- and non-scaffold-based methods to assess this variability. A distinct structural variability among these SCDS, categorized as hypo- and hyperproliferative spheroids based on size, was observed. Hyperproliferative spheroids demonstrated heightened proliferative and tumorigenic potential and increased sensitivity to cisplatin and radiation, while hypoproliferative spheroids exhibited enhanced migratory capabilities. Single-cell RNA sequencing (scRNA-seq) of hypo- and hyperproliferative spheroids provided insights into the transcriptional landscape of HNSCC cells, validating the observed structural and functional heterogeneities within primary tumors. These functionally and genetically characterized spheroids offer valuable tools for the development of next-generation therapeutics. Statement of SignificanceEstablishment and characterization of single-cell-derived spheroids from head and neck cancer cells, employing scaffold and non-scaffold materials, demonstrate functional and genetic heterogeneity. Single-cell analysis reveals correlations between genetic diversity and spheroid functionality. These characterized spheroids offer potential for advancing therapeutics development.

cancer biology↗

bioRxiv2023

New genome reveals molecular signatures of adaptation to nocturnality in moth-like butterflies (Hedylidae)

Nearly all animals have a preferred period of daily activity (diel-niche), which is strongly influenced by the light environment. Sensory systems, particularly vision, are adapted to light, and evolutionary transitions to novel light environments, especially light limited ones, can impose strong constraints on eye evolution, color, and motion vision. The adaptive changes in sensory abilities of animals during these transitions, both at the genetic and neural levels, are largely unexplored. Butterflies and moths, with their diverse diel-niche shifts, are an ideal group for investigating the gene evolution linked to these transitions. While most butterflies are day-flying, hedylid butterflies are unique in being primarily nocturnal, and they represent an important evolutionary shift from diurnality to nocturnality in this clade. Here, we sequence the first high-quality Hedylidae genome and functionally annotate genes to understand genomic changes associated with shifts in diel niche. Comparing Hedylidae visual genes against day- and night-flying Lepidoptera species revealed that visual genes are highly conserved, with no major losses. However, hedylid butterfly opsins were more similar to nocturnal moths than their diurnal congeners. Tests on the evolutionary rates (dN/dS) confirmed that color vision opsins were under strong selection, similar to nocturnal moths. We propose that a convergent event of sequence evolution took place when these butterflies became nocturnal, approximately 98 million years ago.

evolutionary biology↗

bioRxiv2022

Whole-genome and mitogenome based in silico analysis of select Plasmodium and identification of a novel drug molecule against the malaria parasite

Malaria, caused by a parasite known as Plasmodium, is one of the leading causes of death, worldwide, especially in the third world countries of Africa and Asia. Plasmodium does not only infect humans but also reptiles, birds and other mammals. However, they are the secondary hosts for this parasite. The primary host of Plasmodium is female Anopheles mosquitoes. Long term researchers have formulated drugs against this deadly pathogen but the current emergence of multi-drug resistance strains of Plasmodium has created a recurring concern. Identification of new drug molecules and understanding their mechanism of action is an urgent need to combat this battle. However, for that, we need to first understand the genomic strategies taken up by Plasmodium to survive the host immune system. With the advancement of high-throughput sequencing techniques, the whole genomes of Plasmodium have been sequenced which can help us in advancing our strategies against Plasmodium. In this study, we performed a thorough analysis of the genomic features of Plasmodium along with its evolution. This revealed a codon biased co-evolution among the parasite and respective hosts. Reverse ecology and protein-protein interactions were studied among Plasmodium and Homo sapiens revealing a complex biological interaction among them governing the host-parasite interaction as well as drug resistance capability among Plasmodium. The molecular docking and simulation studies have found a new drug-target site within mitogenome coding proteins. Those sites were targeted with Cymbopogonol, a phyto-compound derived from Cymbopogon (Lemongrass). Along with Cymbopogonol few other Cymbopogon derived compounds were also found to be effective as new anti-malarial drug molecules. This is the first report on the effect of Cymbopogon derived compounds on Plasmodium and is open for a clinical trial.

bioinformatics↗

bioRxiv2021

Effect of Human Mesenchymal Stem Cells on Freund's adjuvant-induced Rheumatoid Arthritis in Sprague Dawley Rats

IntroductionMesenchymal stem cells (MSC) therapy is a new approach to treat RA. Studies evaluating anti-inflammatory effects of MSCs per RA severity are scarce. Our primary objective was to evaluate anti-inflammatory effects, change in cytokine levels and cartilage regeneration of two different MSC preparations delivered through two different routes of administration in three RA stages: mild, moderate and severe. MethodsHuman-derived umbilical cord tissue MSCs (hUCT-MSCs) and human bone marrow-derived MSCs (hBM-MSCs) delivered via intra-plantar and intravenous routes were tested in Freunds adjuvant-induced arthritis in rats. Arthritis severity was based on the arthritis score (<3=mild, 3=moderate and 4=severe). Assessments included changes in arthritis scoring, paw swelling, haematology parameters, biomarkers (TNF and IL-10) and histopathology analysis. ResultsMSC treatment significantly reduced arthritis scores in all treatment groups. IL-10 levels increased 30 days after treatment with (IP)hUCT-MSCs (P=0.0241), (IV)hUCT-MSCs (P=0.0095) and (IP)hBM-MSCs (P=0.0002). TNF- levels reduced compared to positive control at 30 days: (IP)hUCT-MSCs (P=0.0060), (IV)hUCT-MSCs (P=0.0003), (IP)hBM-MSCs (P=0.0005), (IV)hBM-MSCs (P<0.0001) and continued through 30-60 days. Microscopic examination showed regenerative changes in animal joints treated with both intra-plantar or intravenous MSCs. Arthritis scores reduced in all RA severity groups while benefits (changes in IL-10 and TNF-alpha) were more pronounced in moderate and severe RA. Haematology parameters remained similar among all animal groups at baseline, 30 days and 60 days indicating safety of MSCs. ConclusionTreatment with hUCT MSCs and hBM MSCs were safe, well-tolerated and effectively reduced joint inflammation, synovial cellularity and pro-inflammatory cytokine levels in CFA-induced RA rat model.

cell biology↗

bioRxiv2021

Colon Innervating TRPA1 Positive Nociceptors Influence Mucosal Health In Mice

IntroductionTransient receptor potential ankyrin-1 positive (TRPA1+ve) nociceptors, primarily present as peptidergic neuronal afferents in the colon are sensors of disturbance in lower gastrointestinal tract including pain induced by different pathologies. Their therapeutic role in the alleviation of chronic pain (receptor antagonism and receptor desensitization) associated with inflammatory bowel diseases (IBD) is reported. However, there is limited literature available about their role in formation and sustenance of the mucosal layer, and its interaction with host physiology as well as luminal microbial community. The aim of this study focuses on the effects of nociceptive TRPA1 channel desensitization on colonic mucus production and gut health. MethodsTRPA1+ve nociceptors were desensitized by rectal administration of capsazepine. Ileum, colon was harvested and cecum content was collected. We performed morphological/histological analysis, gut permeability alteration, gene expression changes, colon metabolite profiling, and gut microbial abundance in these animals. ResultsWe found that presence of TRPA1-positive nociceptors is required for mucus layer integrity, using an intra-rectal capsazepine-induced TRPA1 desensitization model. Desensitization of TRPA1 positive nociceptors resulted in damaged mucosal lining, resultant increase in gut permeability and altered transcriptional profile of genes for goblet cell markers, mucus regulation, immune response and tight junction proteins. The damage to mucosal lining prevented its role in enterosyne (short chain fatty acids) actions. ConclusionThese results suggest that caution may need to be exercised before employing TRPA1 desensitization as a therapeutic option to alleviate pain caused due to IBD.

pharmacology and toxicology↗

bioRxiv2021

Mucin-mimetic action of capsaicin improves high fat diet-induced gut barrier dysfunction in mice colon

The gut barrier - including tight junction proteins and mucus layers, is the first line of defense against physical, chemical, or pathogenic incursions. This barrier is compromised in various health disorders. Capsaicin, a dietary agonist of Transient receptor potential vanilloid 1 (TRPV1) channel, is reported to alleviate the complications of obesity. While its mode of action is well established to enhance energy expenditure, metabolism and prevent dysbiosis, the more local effects on the host gut - particularly the gut barrier and mucus system remain elusive. We employed a diet-induced obesity model to investigate the effect of capsaicin on the gut barrier and mucus production and to understand the involvement of mucus, bacteria, and TRPV1 in these phenomena. Mucin feeding reflected most of the effects produced by capsaicin, indicating that mucus modulation by capsaicin plays a crucial role in its anti-obesity effects. Capsaicin, bacteria and the host mucus system seem to act in a cyclic cascade involving TRPV1, which can be activated by capsaicin and various bacteria. These findings provide new insight into the role of TRPV1 in maintaining a healthy gut environment. HIGHLIGHTSO_LIExogenous mucin feeding produced anti-obesity effects similar to capsaicin in mice. C_LIO_LIMucin and capsaicin improved TJP expression, intestinal permeability and gut microbial diversity. C_LIO_LICapsaicin modulated bacterial diversity in vitro, independently of the host. C_LIO_LIProbiotic bacteria and butyrate activated TRPV1 in transfected HEK cells. C_LIO_LIAnti-obesity action of capsaicin is not exclusive to TRPV1 agonism. C_LIO_LICapsaicins action as colonic mucus secretagogue - plays a crucial part in its anti-obesity benefits. C_LI

pharmacology and toxicology↗

bioRxiv2021

Functional characterisation of the Nep1-like protein effectors of the necrotrophic pathogen - Alternaria brassicae

Alternaria brassicae is an important necrotrophic pathogen that infects the Brassicaceae family. Alternaria brassicae, like other necrotrophs, also secretes various proteinaceous effectors and metabolites that cause cell death to establish itself in the host. However, there has been no systematic study of A. brassicae effectors and their roles in pathogenesis. The availability of the genome sequence of A. brassicae in public domain has enabled the search for effectors and their functional characterisation. Nep1-like proteins are a superfamily of proteins that induce necrosis and ethylene biosynthesis. They have been reported from a variety of microbes including bacteria, fungi, and oomycetes. In this study, we identified two NLPs from A. brassicae viz. AbrNLP1 and AbrNLP2 and functionally characterised them. Although both AbrNLPs were found to be secretory in nature, they localised differentially inside the plant. AbrNLP2 was found to induce necrosis in both host and nonhost species, while AbrNLP1 could not induce necrosis in both species. Additionally, AbrNLP2 was shown to induce pathogen-associated molecular pattern (PAMP)-triggered immunity in both host and nonhost species. Overall, our study indicates that AbrNLPs are functionally and spatially (subcellular location) distinct and may play different but important roles during the pathogenesis of A. brassicae.

plant biology↗

bioRxiv2021

Human gut Bacteroides uniformis utilizes mixed linked β- glucans via an alternativestrategy

Human gut microbial communities have a tremendous impact on well-being of the human health by producing myriad of metabolites. Polysaccharide utilizing capability of these microbial communities is a key driving force in shaping the composition of gut microbiota. Previous studies suggest that genes responsible for {beta}- glucans utilizing in Bacteroides are present in a polysaccharide utilization locus (PUL). However, recent observations show that Bacteroides uniformis lacks such PUL archetypal organisation for efficient utilization of pustulan ({beta}1-6) and mixed linkage ({beta}1-4/ {beta}1-3) glucans, and its mechanism is yet to be studied. Here, we first used BuGH16 for production of important two mixed linked {beta}- glucan-oligosaccharides, and then demonstrate kinetics of the BuGH3MLG. The B. uniformis JCM13288T coordinates between PUL associated glycoside hydrolase (GH)-16 and distantly localised bespoke GH 3 (BuGH3MLG) for efficient utilization of mixed linkage ({beta}1-4/ {beta}1-3) glucans. BuGH3MLG found to be cleaved {beta}1-4, {beta}1-3 and {beta}1-6 glucan-oligosaccharides. Such understanding of glycan utilization mechanism of human gut bacterial communities is crucial for development of nutraceutical therapy and improving health of human being.

biochemistry↗

bioRxiv2021

Picozoa are archaeplastids without plastid

The endosymbiotic origin of plastids from cyanobacteria gave eukaryotes photosynthetic capabilities and launched the diversification of countless forms of algae. These primary plastids are found in members of the eukaryotic supergroup Archaeplastida. All known archaeplastids still retain some form of primary plastids, which are widely assumed to have a single origin. Here, we used single-cell genomics from natural samples combined with phylogenomics to infer the evolutionary origin of the phylum Picozoa, a globally distributed but seemingly rare group of marine microbial heterotrophic eukaryotes. Strikingly, the analysis of 43 single-cell genomes shows that Picozoa belong to Archaeplastida, specifically related to red algae and the phagotrophic rhodelphids. These picozoan genomes support the hypothesis that Picozoa lack a plastid, and further reveal no evidence of an early cryptic endosymbiosis with cyanobacteria. These findings change our understanding of plastid evolution as they either represent the first complete plastid loss in a free-living taxon, or indicate that red algae and rhodelphids obtained their plastids independently of other archaeplastids.

evolutionary biology↗

bioRxiv2020

Comprehensive bioinformatic analysis of newly sequenced Turdoides affinis mitogenome reveals the persistence of translational efficiency and dominance of NADH dehydrogenase complex-I in electron transport system over Leiothrichidae family

Mitochondrial genome provides useful information about species with respect to its evolution and phylogenetics. We have taken the advantage of high throughput next-generation sequencing technique to sequence the complete mitogenome of Yellow-billed babbler (Turdoides affinis), a species endemic to Peninsular India and Sri Lanka. Both, reference-based and de-novo assemblies of mitogenome were performed and observed that de-novo assembled mitogenome was most appropriate. The complete mitogenome of yellow-billed babbler (assembled de-novo) was 17,671 bp in length with 53.2% AT composition. Thirteen protein-coding genes along with 2 rRNAs and 22 tRNAs were detected along with duplicated control regions. The arrangement pattern of these genes was found conserved among Leiothrichidae family mitogenomes. Downstream bioinformatics analysis revealed the effect of translational efficiency and purifying selection pressure over all the thirteen protein-coding genes in yellow-billed babbler mitogenome. Moreover, genetic distance and variation analysis indicated the dominance of NADH dehydrogenase complex-I in the electron transport system of T. affinis. Evolutionary analysis revealed the conserved nature of all the protein-coding genes across Leiothrichidae family mitogenomes. Our limited phylogenetics results suggest that T. affinis is closer to Garrulax.

genomics↗