Biology subjects

Bhatt, D.

Publications and source records attributed to Bhatt, D..

14 recordsLinked to original sources

bioRxiv2026

High-resolution analysis of T cell subsets, clonality, and trajectories in psoriasis

Psoriasis is sustained by type 17 immunity, yet how transcriptionally defined T-cell states are clonally organized across lesions, clinically uninvolved skin, and the circulation remains incompletely understood. We performed paired single-cell RNA and T-cell receptor (TCR) sequencing of T cells isolated from two spatially separated lesions, non-lesional skin, and peripheral blood from 23 participants with psoriasis, together with healthy skin and blood comparators. We resolved 19 cutaneous T-cell populations and found that lesions were enriched for IL-17-associated CD4+ and CD8+ states and activated regulatory T-cell states. CD8+ Tc17 cells showed prominent clonal expansion, and expanded clonotypes contributed more prominently to skin than to blood. Clonotype sharing was greatest between paired lesions, while clonotypes detected in cutaneous IL-17-associated cells mapped to multiple circulating phenotypes, indicating that blood and skin capture complementary features of the disease-associated repertoire. At the sample level, T-cell composition separated 57 lesional samples into two recurrent compositional states that were largely concordant across paired body sites. HLA-C*06:02 status was associated with differences in pretreatment lesional CD8+ T-cell composition, clonotype overlap, and clonal-size distributions. Exploratory longitudinal analyses in eight treated participants showed heterogeneous remodeling of T-cell composition and clonotype detection after therapy. Together, these findings define tissue-restricted and tissue-shared features of the psoriatic T-cell repertoire and identify clonal architecture across skin sites and blood as an organizing feature of lesion heterogeneity.

immunology↗

bioRxiv2026

Biochar suppression of antibiotic resistance genes in the soil microbiome

Antimicrobial resistance (AMR) in soils frequently arises from low-level antibiotic presence in agriculture systems where livestock receive antibiotics for disease prevention. Here we assess the influence of oak (Quercus robur) wood biochar (pyrolysis at 7600C) on the microbiome of a parkland soil, after 300 days of incubation, in the presence and absence of the antibiotic sulphamethazine (SMZ). Stable isotope probing coupled to metagenomics was carried out to identify metabolically active microorganisms and quantify antimicrobial resistance gene (ARG) prevalence. Across all treatments, Pseudomonadota and Actinobacteriota dominated (63-78%), with Pseudomonadota enriched in the biologically active heavy water fraction. Gemmatimonadota increased, and Bacillota decreased in heavy fractions, while minor phyla displayed variable shifts. Biochar significantly reduced ARG prevalence in the active heavy water metagenome from 23,485 ARGs in control soils to 10,002 ARGs in biochar-amended soils, while SMZ alone increased to 26,193 ARGs found in their metagenome. Combined biochar and SMZ treatment resulted in lower ARGs (16,890 ARGs) than both control and SMZ-only soils, likely due to a combination of ARG adsorption, antibiotic immobilisation, and microbial community restructuring. These results highlight the potential of biochar as a soil amendment for mitigating the proliferation of AMR in agriculture environments.

microbiology↗

bioRxiv2026

A Poly(rC)-Binding Protein Mediates Iron Delivery to Ferritin in Anopheles stephensi

Iron homeostasis is essential for both the Plasmodium parasite and its hosts, the mosquito and human; however, the molecular mechanisms governing intracellular iron trafficking remain poorly understood. In mammals, poly(rC)-binding proteins (PCBPs) function as major iron chaperones by delivering Fe2+ to ferritin and other iron-dependent proteins, yet their role in insects has not been investigated. Here, we provide the first structural and functional characterization of the PCBP from a major malaria vector, Anopheles stephensi. Comparative structural and evolutionary analyses showed that insect PCBPs are most closely related to human PCBP3. Coordinated expression and co-localization of AsPCBP with ferritin following blood feeding suggested a conserved role in mosquito iron homeostasis. Functional analyses demonstrated that KH2-KH3 linker and KH3 domain of PCBP, plays an important role in the AsPCBP-ferritin interaction and that deletion of these regions, unexpectedly increased ferritin binding affinity but impaired iron delivery, indicating that these regions are dispensable for complex formation but essential for efficient iron transfer. Collectively, our results identify PCBP as a key component of mosquito iron homeostasis that could be exploited for the development of novel antimalarial strategies.

biochemistry↗

bioRxiv2025

Variable Schwann cell merlin inactivation is targetable with TEAD1 inhibition in schwannomas.

Schwann cell tumors occur frequently in association with the vestibular nerves, leading to sensorineural hearing loss, and brainstem compression. In humans, unilateral vestibular schwannomas (VS) occur sporadically (VSspo)1, or bilaterally with neurofibromatosis type 2 syndrome (NF2) - VSnf2.2 VS formation is driven by sub-haploid NF2 gene dosage3, typically by biallelic loss.4,5 Loss of merlin promotes hippo/TEAD dependent transcriptional reprogramming, proliferation, and paracrine signaling that varies across time, and tumor volume.4,6 These variations lead to a clinically unpredictable course, and incomplete response to treatment. We hypothesized that Schwann cell merlin inactivation state determines cell-wise hippo/TEAD dependency and drives schwannoma pathogenesis. We analyzed clinical samples from VSspo and VSnf2 with a multi-omics approach and detected variation in merlin activity within tumor Schwann cell population. We found that tumor-driving merlin-depleted Schwann cells (Schwannmer-) exhibited elevated hippo activity that was predominantly driven by TEAD1. In-silico TEAD1 perturbation led to a reversal to merlin intact Schwann phenotype. These findings, and tumor cell growth suppression were confirmed in NF2fl/fl;Peri-Cre mouse model7, and in human derived schwannoma cells treated with a pan-TEAD auto palmitoylation inhibitor VT3989.8 Our computational and experimental results confirm that TEAD1 inhibition could be a potent, targeted strategy for schwannomas.

cancer biology↗

bioRxiv2025

Phosphoproteomic dysregulation drives tumor proliferation in Cushing's disease

Pituitary adenomas constitute up to 20% of primary brain tumors, yet somatic mutations are only found in 15% of pituitary adenomas. Epigenomic dysregulation has been proposed as a tumorigenic mechanism in pituitary adenomas causing Cushings disease (CD). We created paired datasets of human CD adenomas and en-route margin adult human pituitary glands and assayed their chromatin accessibility, DNA methylation, transcriptomic, proteomic and phospho-proteomic landscapes. In CD adenomas, we found epigenetic reactivation of a neurodevelopmental phosphoprotein program typically lost in the post-natal pituitary gland. CD cells overexpressed PPP1R17, a potent endogenous inhibitor of the ubiquitous protein phosphatase PP2A. Mechanistically, PPP1R17 overexpression in normal murine pituitary cells recapitulated the adenoma phenotype, and PPP1R17-mediated tumorigenesis was reversible using an FDA-approved small molecule PP2A agonist both in-vitro and in-vivo. Our findings highlight aberrant peptide phosphorylation as a targetable mechanism in CD. Significance statementCushings disease (CD) causes significant morbidity and mortality despite best medical and surgical treatment. Surgery is the mainstay of treatment, but carries perioperative risks and is frequently followed by remission. There is a paucity of effective medical treatments, due in part to a limited understanding of tumor mechanisms. The majority of CD adenomas are wild-type, with no known causal mutations. Our study identifies phosphoproteomic dysregulation as a mechanism of CD tumorigenesis common to wild-type and mutant CD adenomas. We target this pathway in-vivo and in-vitro using an FDA-approved small molecule. Our study proposes a novel therapeutic strategy for patients with CD.

cancer biology↗

bioRxiv2025

NAPRT expression and epigenetic regulation in pediatric rhabdomyosarcoma as a potential biomarker for NAMPT inhibition

PurposeNew treatments are needed to improve survival in children with rhabdomyosarcoma (RMS). NAD biosynthesis, regulated by the enzymes NAPRT and NAMPT, represents a metabolic vulnerability due to high NAD turnover in cancers. Although NAMPT inhibitors (NAMPTi) show preclinical promise, clinical translation has been limited by toxicity and the lack of predictive biomarkers. Here, we evaluated NAPRT expression in RMS and its potential as an actionable biomarker to guide NAMPTi therapy. Experimental DesignNAPRT promoter methylation, transcript levels, and protein expression were assessed in RMS cells, PDXs, and primary tumors (n=109) from the Childrens Oncology Group. In vitro sensitivity to NAMPTi was tested in molecularly diverse and isogenic RMS cell lines, examining the role of NAPRT expression in mediating cytotoxicity and the ability of nicotinic acid (NA) to rescue viability. In vivo efficacy was assessed using NAPRT-isogenic orthotopic xenograft models. ResultsNAPRT promoter hypermethylation was found in a subset of RMS models and patient samples. Immunohistochemistry showed loss of NAPRT protein in 30-40% of tumors, defined as <1% tumor cell staining. Methylation modestly correlated with protein expression. NAPRT-silenced cells were highly sensitive to NAMPTi, driven by NAD depletion and not reversible with NA. In vivo, NAMPTi induced significant tumor regression, which was not abrogated with NA administration in NAPRT-silenced models. ConclusionsNAPRT loss occurs in a subset of RMS, offering a potential strategy to expand the therapeutic window of NAMPTi. Further research is needed to understand NAPRT regulation and optimize biomarker assay strategies for use in future clinical trials.

cancer biology↗

bioRxiv2025

Learning evoked centrality dynamics in the schizophrenia brain: Entropy, heterogeneity and inflexibility of brain networks

BackgroundBrain network dynamics are responsive to task induced fluctuations, but such responsivity may not hold in schizophrenia (SCZ). We introduce and implement Centrality Dynamics (CD), a method developed specifically to capture task-driven dynamic changes in graph theoretic measures of centrality. We applied CD to fMRI data in SCZ and Healthy Controls (HC) acquired during a learning paradigm. MethodsfMRI (3T Siemens Verio) was acquired in 88 participants (49 SCZ). Time series were extracted from 246 functionally defined cerebral nodes. We applied a dynamic widowing technique to estimate 280 partially overlapping connectomes (30,135 region-pairs in each connectome). In each connectome we calculated every nodes Betweenness Centrality (BC) before building 246 unique time series (representing a nodes CD) from a nodes BC in successive connectomes. Next, in each group nodes were clustered based on similarities in CD. ResultsClustering gave rise to fewer sub-networks in SCZ, and these were formed by nodes with greater functional heterogeneity. These sub-networks also showed greater ApEn (indicating greater stochasticity) but lower amplitude variability (suggesting less adaptability to task-induced dynamics). Higher ApEn was associated with worse clinical symptoms. LimitationsCentrality Dynamics is a new method for network discovery in health and schizophrenia but will need further extension to other tasks and psychiatric conditions, before we achieve a fuller understanding of its promise. ConclusionThe brains functional connectome is not static under task-driven conditions, and characterizing the dynamics of the connectome will provide new insight on the dysconnection syndrome that is schizophrenia. Centrality Dynamics provides novel characterization of task-induced changes in the brains connectome and shows that in the schizophrenia brain, learning-evoked sub-network dynamics were less responsive to learning evoked changes and showed greater stochasticity.

neuroscience↗

bioRxiv2025

Chemical Inhibition of Splicing-Related Protein Kinases Reveals Phosphorylation-Driven Regulation of RNA Alternative Splicing in Arabidopsis Seedlings

Serine / arginine (SR) protein kinases (SRPKs) are capable of transmitting external signals to the spliceosome by phosphorylating SR proteins. In plants, few studies have looked at the regulation of RNA splicing by post-translational modification (PTMs), despite the spliceosome and splicing factor proteins exhibiting extensive phosphorylation. Many of these PTM events have the potential to dramatically change the expression of various genes, such as those involved in abiotic stress. Here, we sought to explore the regulatory function of Arabidopsis thaliana SRPKs in the context of RNA alternative splicing. To do so, we utilized four well-known and well-characterized chemical inhibitors specifically designed to target and inhibit SRPK enzymatic activity. Our data found that SRPK chemical inhibitors SPHINX31 and SRPIN340 induced shorter root development phenotypes and an abolishment of root hair formation. Using a multi-omics approach combining transcriptomics and phosphoproteomics, we find extensive changes in the splicing of genes involved in root development, RNA splicing, cytoskeletal organization, and cell differentiation. We also reveal splicing factors exhibiting differential alternative splicing as well as a down-regulated in their phosphorylation status. Overall, our data indicate that AtSRPKs phosphorylate diverse splicing factors and influence the alternative splicing of genes involved in root development and a wide-range of related pathways.

plant biology↗

bioRxiv2024

Time spent in conversation over meals predicts default network function: Evidence from a passive mobile-sensing and fMRI study.

Sharing meals with others, often referred to as commensality, fosters social connection and may have been essential to human brain evolution. Here, we investigate whether shared meals impact social brain processes through the conversations they afford. If so, then time spent in conversation over meals should affect the default network- a set of interconnected cortical regions reliably associated with the social exchange of ideas. To test this possibility, we combined passive-mobile sensing with neuroimaging. Undergraduate participants had an application on their smartphone for two months that unobtrusively captured their time spent in conversation, as well as their location on and around campus. In between these two months, participants completed a resting state scan. Time spent in conversations around meals (e.g., at cafeterias and restaurants) during the prior month predicted greater functional connectivity in the dorsomedial default network subsystem, specifically between the left inferior frontal gyrus (LIFG) portion and the rest of the subsystem regions. This relationship was preferential to: (1) time spent in conversation over the past (vs. future) month, (2) connectivity with the LIFG (vs. other dorsomedial subsystem nodes), (3) the dorsomedial subsystem (vs. other default network subsystems), (4) eateries (vs. other locations), and (5) time spent around conversation at eateries, rather than time at eateries more generally. Follow-up analyses further revealed results were driven by a ventral portion of the LIFG, with peaks in voxel-connectivity associated with language, social, memory, and affective processes, as determined by the meta-analytic platform, NeuroSynth. Time spent in conversation over meals may exercise social cognitive processes supported by the dorsomedial subsystem, a network key to social communication, understanding, and connection.

neuroscience↗

bioRxiv2022

A pathogen-induced putative NAC transcription factor mediates leaf rust resistance in barley

Leaf rust, caused by Puccinia hordei, is one of the most widespread and damaging foliar diseases affecting barley (Hordeum spp.). The barley leaf rust resistance locus Rph7, located on the short arm of chromosome 3H, confers defence at all growth stages and was previously shown to have unusually high sequence and haplotype divergence. Earlier, four candidate genes for Rph7 were reported and, despite an in-depth comparative sequence analysis and haplotypic characterisation, the causal gene could not be resolved. Here, we successfully cloned Rph7 utilising a fine mapping approach in combination with an RNA-Seq based expression analysis. We identified three up-regulated and pathogen-induced genes with presence/absence variation (PAV) at this locus. Sequence analysis of chemically induced Rph7 knockout mutant lines identified multiple independent non-synonymous variants, including a premature stop codon in a single non-canonical resistance gene that encodes a 302-amino acid protein. Progeny from four independent transgenic lines segregated for the expected avirulent Rph7 infection type in response to several avirulent P. hordei pathotypes, however, all plants were susceptible to a single virulent pathotype confirming the specificity. Structural analysis using an AlphaFold2 protein model suggests that Rph7 encodes a putative NAC transcription factor, as it shares structural similarity to ANAC019 from Arabidopsis, with a C-terminal BED domain. A global gene expression analysis suggests Rph7 is involved in the activation of basal defence.

genetics↗

bioRxiv2022

An autoactive NB-LRR gene causes Rht13 dwarfism in wheat

Semidwarfing genes have greatly increased wheat yields globally, yet the widely used gibberellin (GA) insensitive genes Rht-B1b and Rht-D1b have disadvantages for seedling emergence. Use of the GA sensitive semidwarfing gene Rht13 avoids this pleiotropic effect. Here we show that Rht13 encodes a nucleotide-binding site/leucine-rich repeat (NB-LRR) gene. A point mutation in the semidwarf Rht-B13b allele autoactivates the NB-LRR gene and causes a height reduction comparable to Rht-B1b and Rht-D1b in diverse genetic backgrounds. The autoactive Rht-B13b allele leads to transcriptional upregulation of pathogenesis-related genes including class III peroxidases associated with cell wall remodelling. Rht13 represents a new class of reduced height (Rht) gene, unlike other Rht genes which encode components of the GA signalling or metabolic pathways. This discovery opens new avenues to use autoactive NB-LRR genes as semidwarfing genes in a range of crop species, and to apply Rht13 in wheat breeding programmes using a perfect genetic marker.

plant biology↗

bioRxiv2022

Targeted Sequencing of Alzheimers Disease Genes in Gujarat Cohort

Alzheimers Disease (AD) is the most common type of dementia affecting cognitive and behavioural functions. Its a complex disease that results from the modest effect of gene interaction and environmental factors, as a result of which its exact pathogenesis is still unknown. In the present study, we have performed an association study of exonic regions of 94 genes with AD using the Haloplex target enrichment method and genotyping of 4 genes NOTCH4(rs367398), NEP(rs61760379), APOE (rs121918398), and ATP7B(rs1801243) using PCR RFLP technique. In this study, we screened 32 AD cases and 11 control samples. We have identified 19 variants assigned to 16 genes that were significantly associated with AD with a p-value < 0.05. However, no variants have passed multiple test corrections except NOTCH4/rs367398 genotyped using the PCR-RFLP approach. The functional enrichment analysis of the significant genes for the disease indicates that the genes are significantly involved in AD. Also, functional enrichment analysis for biological processes using ClueGo and network analysis using the STRING database indicated that the genes are directly and indirectly playing a role in AD pathogenesis. The eQTL analysis of the variants with GTEx dataset indicate that out of 19 variants ACHE/rs1799806 and NOTCH4/rs367398 variants is showing significant eQTL for the neighbouring genes for different brain regions and whole blood. Regardless, additional studies with a large cohort are required to establish the role and prevalence of these variants in the local population of Gujarat.

genomics↗

bioRxiv2020

Systematic comparison of high-throughput single-cell RNA-seq methods for immune cell profiling

BackgroundElucidation of immune populations with single-cell RNA-seq has greatly benefited the field of immunology by deepening the characterization of immune heterogeneity and leading to the discovery of new subtypes. However, single-cell methods inherently suffer from limitations in the recovery of complete transcriptomes due to the prevalence of cellular and transcriptional dropout events. This issue is often compounded by limited sample availability and limited prior knowledge of heterogeneity, which can confound data interpretation. ResultsHere, we systematically benchmarked seven high-throughput single-cell RNA-seq methods. We prepared 21 libraries under identical conditions of a defined mixture of two human and two murine lymphocyte cell lines, simulating heterogeneity across immune-cell types and cell sizes. We evaluate methods by their cell recovery rate, library efficiency, sensitivity, and ability to recover expression signatures for each cell type. We observed higher mRNA detection sensitivity with the 10x Genomics 5 v1 and 3 v3 methods. We demonstrate that these methods have fewer drop-out events which facilitates the identification of differentially-expressed genes and improves the concordance of single-cell profiles to immune bulk RNA-seq signatures. ConclusionOverall, our characterization of immune cell mixtures provides useful metrics, which can guide selection of a high-throughput single-cell RNA-seq method for profiling more complex immune-cell heterogeneity usually found in vivo.

immunology↗

bioRxiv2018

The wheat Sr22, Sr33, Sr35 and Sr45 genes confer resistance against stem rust in barley

In the last 20 years, stem rust caused by the fungus Puccinia graminis f. sp. tritici (Pgt), has re-emerged as a major threat to wheat and barley cultivation in Africa and Europe. In contrast to wheat with 82 designated stem rust (Sr) resistance genes, barleys genetic variation for stem rust resistance is very narrow with only seven resistance genes genetically identified. Of these, only one locus consisting of two genes is effective against Ug99, a strain of Pgt which emerged in Uganda in 1999 and has since spread to much of East Africa and parts of the Middle East. The objective of this study was to assess the functionality, in barley, of cloned wheat Sr genes effective against Ug99. Sr22, Sr33, Sr35 and Sr45 were transformed into barley cv. Golden Promise using Agrobacterium-mediated transformation. All four genes were found to confer effective stem rust resistance. The barley transgenics remained susceptible to the barley leaf rust pathogen Puccinia hordei, indicating that the resistance conferred by these wheat Sr genes was specific for Pgt. Cloned Sr genes from wheat are therefore a potential source of resistance against wheat stem rust in barley.

plant biology↗