Biology subjects

KUMAR, A.

Publications and source records attributed to KUMAR, A..

10 recordsLinked to original sources

bioRxiv2026

Hepatocyte TEAD1 drives epithelial-stromal remodeling during cholestatic liver injury

Background & AimsPrimary sclerosing cholangitis (PSC) is a progressive cholangiopathy characterized by ductular remodeling, inflammation, and periportal fibrosis, for which effective medical therapies remain limited. The Hippo pathway effector TEAD1 has been implicated in liver regeneration and fibrogenesis; however, its role in cholestatic injury remains poorly defined. We investigated whether hepatocyte TEAD1 regulates injury-associated remodeling in a PSC-mimicking model and whether this mechanism is conserved in human PSC liver. MethodsHepatocyte-specific TEAD1 knockout mice (Alb-TEAD1-/-) and littermate controls were subjected to DDC-induced cholestatic injury. Ductular reaction, fibrosis, inflammation, and bile acid-related gene programs were assessed by histology, immunostaining, and gene expression analyses. Translational relevance was evaluated using bulk and single-cell transcriptomic datasets from human PSC liver. ResultsHepatocyte TEAD1 deletion attenuated DDC-induced fibrosis, ductular expansion, and inflammatory cell accumulation, while preserving hepatocyte proliferative responses. TEAD1-deficient livers exhibited reduced expression of profibrotic mediators, including Spp1, Ctgf, and Cyr61, with decreased extracellular matrix deposition. In contrast, canonical transcriptional adaptations to cholestatic stress, including suppression of bile acid uptake, induction of efflux pathways, and repression of bile acid synthesis genes, were preserved in the absence of TEAD1. Analysis of human PSC datasets demonstrated coordinated upregulation of TEAD1 and TEAD-associated target genes. Single-cell transcriptomic analysis further revealed hepatocyte-enriched TEAD1 expression and activation of a TEAD1 target gene program across all hepatic zones in PSC, with effect sizes exceeding those observed in non-parenchymal populations. TEAD1 activation was accompanied by co-expression of profibrotic mediators and downregulation of hepatocyte differentiation markers, consistent with a maladaptive hepatocyte state. ConclusionsHepatocyte TEAD1 drives ductular, inflammatory, and fibrogenic remodeling during cholestatic injury without disrupting bile acid metabolic adaptation. These findings identify TEAD1 as a hepatocyte-intrinsic regulator of epithelial-stromal crosstalk and establish conserved activation of this pathway in human PSC, supporting TEAD-directed signaling as a therapeutic target.

pathology↗

bioRxiv2025

p21-activated kinase regulates Rab3a vesicles to repair plasma membrane damage caused by Amyloid-β oligomers

The interaction of amyloid-{beta} (A{beta}) peptides with the plasma membrane (PM) is a potential trigger that initiates the formation of higher-order aggregates, membrane alterations/damage, and progressive neurotoxicity in Alzheimers disease (AD). In a previous study, we showed that oligomers of A{beta}1-42 (oA{beta}1-42) induced PM damage, resulting in PM repair cascade via lysosomal exocytosis coupled with endocytosis, and facilitation of tunneling nanotubes (TNTs)-like membrane protrusions to promote direct cell-to-cell transfer of aggregates. In this study, we demonstrated that PM damage induced by oligomers of the aggregation-prone peptide A{beta}1-42 significantly facilitates PM repair by enhancing phosphorylated p21-activated kinase 1 (pPAK1)-dependent endocytosis and Rab3a-dependent exocytosis in SH-SY5Y and SK-N-SH neuronal cells compared to control and oA{beta}1-40 treated cells. We studied the kinetics of pPAK1-dependent endocytosis and the fusion of EGFP-Rab3a vesicles near the PM using total internal reflection fluorescence (TIRF) microscopy. IPA-3, a selective non-ATP competitive inhibitor of PAK1, inhibits endocytosis of oA{beta} peptides and Rab3a-dependent PM repair. Further, shRNA-mediated knockdown of the Rab3a gene inhibits pPAK1 and disrupts PM repair. Repair of damaged PM is a vital protective mechanism for non-proliferative cells like neurons, as disruption in PM repair leads to gradual neuronal cell death. However, there was no explicit understanding of PM repair in response to A{beta} oligomers. This study revealed the interconnected action of Rab3a and pPAK1 in PM repair in response to oA{beta}-mediated damage, and its potential correlation in AD pathogenesis.

cell biology↗

bioRxiv2024

Anti-Tumor Potential of AEV01 in Glioma and Hepatocellular Carcinoma: In Vitro and Xenograft Model Studies.

Gliomas and hepatocellular carcinoma (HCC) are aggressive cancers with poor prognoses, often leading to less than a year of survival. Therapeutic resistance underscores the need for novel therapeutic strategies. AEV01, derived from Picrorhiza kurroa, has shown promise as a potential anticancer agent. In this context, the current study aimed to evaluate the anti-tumor efficacy and safety profile of AEV01 both in vitro and in vivo in glioblastoma and HCC models. Briefly, cytotoxicity and apoptosis were assessed using MTT assays and AO/EtBr staining, while ELISA and immunofluorescence measured inflammatory markers, TP53 and CD36 expression. In vivo, ELISA was performed against the inflammatory and tumor suppressor markers while, histopathological analysis assessed tumor morphology and organ toxicity. AEV01 exhibited dose-dependent cytotoxicity against U-87 MG glioblastoma and HepG2 liver cancer cells, with optimal concentrations at 400 {micro}g and 300 {micro}g respectively. Treatment downregulated inflammatory markers, CD36 expression and concomitantly increased TP53 expression. Xenograft models depicted similar results, with reduced tumor markers expression, reduced tissue architecture, and no significant organ toxicity. Thus, AEV01 demonstrated potent anti-tumor activity with a favorable safety profile, suggesting its potential as a novel therapeutic agent for gliomas and HCC, warranting further clinical investigation.

cancer biology↗

bioRxiv2024

Inhibition of Proteasome Activity Facilitates Definitive Endodermal Specification of pluripotent Stem Cells by influencing YAP signaling

Understanding the molecular players that control the specification of definitive endoderm is imperative to obtain the homogenous population of pancreatic {beta}-cells from stem cells. Though the Ubiquitin proteasome system (UPS) has been envisaged as a crucial intracellular protein degradation system, its role in germ layer specification remains elusive. In this study, using a mouse embryonic stem cells model system (mESCs) we observed decreased proteasomal activity specifically during endoderm, but not in meso- or ecto-derm differentiation. Extraneous inhibition of proteasomal activity during differentiation enhanced the expression of endodermal genes specifically. Enhancing proteasomal activity by including the activator IU1 in the induction culture, inhibited definitive endodermal differentiation. Further, inhibiting proteasomal activity at the definitive endodermal stage resulted in enhanced generation of insulin-positive cells. A similar increase in endodermal gene expression by inhibiting proteasomal activity was observed in miPSC and hiPSC differentiated towards endodermal lineage. Mechanistic insight showed no contribution of endoplasmic reticulum unfolded protein response but revealed the involvement of the YAP signaling pathway in proteasome-inhibited enhanced endodermal differentiation. Unravelling the specific involvement of UPS in endodermal cell fate specification in pluripotent stem cells paves the way for obtaining better qualitative and quantitative definitive endodermal cells for plausible cellular therapy in the future.

cell biology↗

bioRxiv2023

Kappa opioid receptor induces epigenetic silencing of brain derived neurotropic factor via HDAC5 in treatment-resistant depression

Treatment-resistant depression (TRD) occurs in almost 50% of depressed patients. Central kappa opioid receptor (KOR) agonism has been demonstrated to induce depression and anxiety, while KOR antagonism alleviate depression like symptoms in rodent models and TRD in clinical studies. Previously, we have shown that sustained KOR activation leads to TRD-like phenotype in mice, and modulation of brain-derived neurotrophic factor (BDNF) expression in the prefrontal cortex (PFC) appears to be one of the molecular determinants of the antidepressant response. In the present study, we observed that sustained KOR activation by a selective agonist, U50488, selectively reduced the Bdnf transcripts II, IV, and Bdnf CDS (protein-coding Exon IX) in the PFC and cultured primary cortical neurons, which was blocked by selective KOR antagonist, norbinaltorphimine. Considering the crucial role of epigenetic pathways in BDNF expression, we further investigated the role of various epigenetic markers in KOR induced BDNF downregulation in mice. We observed that treatment with U50488 resulted in selective and specific downregulation of acetylation at the 9th lysine residue of the histone H3 protein (H3K9ac) and upregulation of HDAC5 expression in the PFC. Further, using anti-H3K9ac and anti-HDAC5 antibodies in chromatin immune precipitation assay, we detected decreased enrichment of H3K9ac and increased HDAC5 binding at Bdnf II and IV transcripts after U50488 treatment, which were blocked by a selective KOR antagonist, norbinaltorphimine. Further mechanistic studies using HDAC5 selective inhibitor, LMK235, in primary cortical neurons, and adeno-associated viral shRNA mediated HDAC5-knockdown in the PFC of mice, we demonstrated an essential role of HDAC5 in KOR-mediated reduction of Bdnf expression in the PFC and depression-like symptoms in mice. These results suggest that KOR engages multiple pathways to induce depression-like symptoms in mice, and provide novel insights into the mechanisms by which activation of KOR regulates major depressive disorders.

neuroscience↗

bioRxiv2022

Zic3 enables bimodal regulation of tyrosine hydroxylase expression in dopaminergic neurons of olfactory bulb and midbrain

Dopaminergic (DA) neurons in the Olfactory bulb (OB) are involved in odor detection and discrimination. Transcription factor (TF) regulatory network responsible for their fate specification remains poorly understood and the spatial regulation of DA neurons remains elusive. In this study, mice exposed to odor stimulant exhibited specific upregulation of Zinc finger transcription factor of Cerebellum (ZIC) 3 along with Tyrosine Hydroxylase (TH). Stringent co-expression analysis showed ZIC3 and TH dual positive neurons in OB. Genetic manipulation showed ZIC3 to be both essential and sufficient to drive TH expression and essential for odor perception. ZIC3 interacts with ER81 and binds to region encompassing ER81 binding site in DA neurons and is indispensable for TH expression. In midbrain (MB), in the absence of ER81, ZIC3 switches its molecular partner and binds to Pitx3 promoter-a DA fate determinant. Under ectopic expression of ER81 in MB DA neurons, propensity of ZIC3 binding to Pitx3 promoter is compromised and its occupancy on Th promoter encompassing ER81 binding site is established, finally culminating in desired TH expression. Together, these findings reveal a unique ZIC3 mediated bimodal regulation of TH in OB and MB to ultimately facilitate DAergic fate.

neuroscience↗

bioRxiv2020

Signature of selection in composite Vrindavani cattle of India

Vrindavani is an Indian composite cattle breed developed by crossbreeding taurine dairy breeds with native indicine cattle in the 1960s. About 190,000 semen doses of Vrindavani bulls have been distributed to the farmers till date. The animals are under artificial and natural selection for higher milk production and adaptation to the tropical climate, respectively. However, the selection response for production and adaptation traits in the Vrindavani genome is not explored. In this study, we provide the first overview of the selection signatures in the Vrindavani genome. 96 Vrindavani cattle were genotyped using the BovineSNP50 BeadChip and the SNP genotype data of its constituent breeds were collected from a public database. Within-breed selection signatures in Vrindavani were investigated using the integrated haplotype score (iHS). Vrindavani was also compared to each of its parental breeds to discover between-population signatures of selection using two approaches, cross-population extended haplotype homozygosity (XP-EHH) and fixation index (FST). Selection of signature identifies 11 common region identified by more than one harbouring genes such as LRP1B, TNNI3K, APOB, CACNA2D1, FAM110B and SPATA17 associated with production and adaptation. Overall, our results suggested stronger selective pressure on regions responsible for adaptation compared to milk yield.

genetics↗

bioRxiv2020

Development and Use of miRNA-derived SSR Markers to Study Genetic Diversity, Population Structure and Characterization of Genotypes for Heat Tolerance Breeding in Bread Wheat (Triticum aestivum L.)

Wheat is one of the most important cereal crop in the world. Heat stress is an important abiotic stress limiting wheat production and productivity in the world including south-east Asia. The importance of miRNAs in gene expression under various biotic and abiotic stresses is well documented. Molecular markers, especially SSR markers, plays an important role for the success in molecular plant breeding programs. The discovery of SSRs from non-coding regions has been a challenging task. Therefore, development of novel miRNA-based SSRs from the conserved portions of the genome will prove useful for the study of genetic diversity of heat-responsive miRNA-genes in wheat. In the present study, efforts are made to mine SSR markers from 96 members of heat-responsive miRNA-genes of wheat followed by their validation using 37 contrasting (heat tolerance/susceptible) wheat genotypes. Among a set of 13 miRNA-SSRs used,7 SSRs were found polymorphic. Among these polymorphic SSR markers, three found to be very informative SSRs (HT-169j, HT-160a and HT-160b) and could largely discriminate heat tolerant genotypes from the heat susceptible ones. Further analysis based on Polymorphism Information Content (PIC) revealed that miRNA genes were more diverse in susceptible genotypes compared to tolerant genotypes. Ours is the first report that the genic/miRNA markers could be successfully used to study wheat diversity, population structure and characterization of trait specific germplasm. The important and useful miRNA-based SSRs, therefore, would serve as best markers in the marker-assisted breeding programs aimed at enhancing heat tolerance of Indian wheat.

genomics↗

bioRxiv2020

Cloning and characterization of Osmotin (OsmSt) alleles from potato cultivar Kufri Chipsona 1

The present study was focussed to clone and sequence characterise alleles of osmotin from cDNA of Solanum tuberosum L. cultivar Kufri Chipsona 1. The genes vary in sizes as well as were found to have eleven point mutations throughout the coding sequence. One deletion of 7 bp was also found in smaller form of the gene having molecular weight of 19.91 KDa. Osmotin gene is known to impart resistance/tolerance to various fungal diseases in addition to its role as an osmoprotectant, thus, cloned osmotin alleles from important processing grade potato cultivar could become potential candidates for molecular breeding of potato.

plant biology↗

bioRxiv2020

The Effect of Gelling agent, medium pH and silver nitrate on adventitious shoot regeneration in Solanum tuberosum

Vegetative propagation of potato makes the crop vulnerable to many seed borne diseases. The importance of the crop in attainment of food security makes it an important candidate for in vitro propagation and genetic manipulations. To undertake crop improvement programmes, development of an efficient regeneration protocol is a pre-requisite. Therefore, the present report was focussed to study various factors affecting shoot organogenesis in potato cultivar Kufri Chipsona 1. The incorporation of silver nitrate (10 {micro}M) to the regeneration medium (MS medium supplemented with BA and GA3) was found to induce shoot organogenesis in 32.11% of leaf and 59.99% of internodal explants. An increase in mean number of shoots regenerated per leaf (5.31) and internodal (8.67) explant was also observed upon addition of silver nitrate to the medium. Similarly, solidification of medium with clarigel and its adjustment to pH 5.8 was found optimum for increasing shoot organogenesis frequency in potato. Among the two types of explants tested, a better response was observed from internodes in comparison with leaf explants. The regenerated shoots were tested for clonal fidelity using PCR based molecular markers [Random Amplified Polymorphic DNA (RAPD) and Inter-Simple Sequence Repeats (ISSR)] and were found true to type.

plant biology↗