Biology subjects

Kumari, D.

Publications and source records attributed to Kumari, D..

8 recordsLinked to original sources

bioRxiv2026

Hepatic Differentiation of Human Pluripotent Stem Cells into Functional In Vitro Models Recapitulating Native Liver Complexity for MASLD Modelling

Human in vitro hepatic models that accurately recapitulate liver function are essential for fundamental and translational research; however, currently utilised models for disease modelling and drug discovery lack physiological fidelity and require prolonged culture time. Here, we present a streamlined 10-day protocol for efficient and reproducible differentiation of human pluripotent stem cells into hepatocyte like cells (HLCs) and hepatic liver organoids (HLOs). Both models exhibited mature hepatocyte differentiation, as evidenced by albumin secretion and CYP3A4 metabolic activity. Interestingly, HLOs display enhanced multicellular complexity incorporating endothelial, stellate, and macrophage populations along with hepatocytes, thereby more closely recapitulating the native liver microenvironment than HLCs. Here, steatosis was induced in both platforms, which resulted in triglyceride accumulation and upregulated lipogenic markers (DGAT1, DGAT2). However, only HLOs recapitulated advanced disease characteristics, including inflammatory (IL-10) and fibrotic (alpha SMA, COL1A1) responses. Resmetirom, a thyroid hormone receptor-{beta} agonist, significantly reduced steatosis and restored molecular signatures in both models. Additionally, transplanted HLOs demonstrated prolonged survival and displayed host-derived vascularization, thereby validating in vivo maturation. Collectively, HLCs provides a rapid and physiologically relevant liver model, with HLOs offering superior utility for disease modelling, therapeutic evaluation, and regenerative applications due to their enhanced functional and physiological relevance.

cell biology↗

bioRxiv2025

14-3-3ε, a universal adaptor protein, could bind to the tail domain of Kinesin-2 motor subunit KIF3B

KIF3A/KIF3B/KAP complex is a subfamily of kinesin-2 proteins and is known to transport cargoes like N-cadherin, Rab4 vesicles, Par3-Par6-aPKC complex and intraflagellar proteins. The adaptor proteins to recruit the heterotrimeric kinesin-2 to its specific cargoes are not identified, and hence, not much is known about the mechanism for its cargo recognition and binding. The 14-3-3 family proteins form homo and heterodimers and bind to several types of receptors and protein kinases/phosphates to bring together a multiprotein complex regulating cell signalling. In this study, we show that one of the 14-3-3 isoforms,14-3-3{varepsilon}, can bind to KIF3B in vitro. We mapped the 14-3-3{varepsilon} binding site on the C-terminal tail domain of KIF3B with the help of acceptor photobleaching-Foster Resonance Energy Transfer and split-APEX2 assays. With this evidence, we propose for the first time that 14-3-3{varepsilon} can be a potential adaptor for kinesin-2.

cell biology↗

bioRxiv2025

Microenvironmental arginine restriction sensitizes pancreatic cancers to polyunsaturated fatty acids by suppression of lipid synthesis

Nutrient limitation is a characteristic feature of poorly perfused tumors. In contrast to well-perfused tissues, nutrient deficits in tumors impose metabolic constraints on cancer cells. The metabolic constraints created by the tumor microenvironment can lead to vulnerabilities in cancers. Identifying the metabolic constraints of the tumor microenvironment and the vulnerabilities that arise in cancers can provide new insight into tumor biology and identify promising antineoplastic targets. To identify how the microenvironment constrains the metabolism of pancreatic tumors, we challenged pancreatic cancer cells with microenvironmental nutrient levels and analyzed changes in cellular metabolism. We found that arginine limitation in pancreatic tumors perturbs saturated and monounsaturated fatty acid synthesis by suppressing the lipogenic transcription factor SREBP1, in part via activation of the amino acid sensor GCN2. Synthesis of these fatty acids is critical for maintaining a balance of saturated, monounsaturated, and polyunsaturated fatty acids in cellular membranes. Because of microenvironmental constraints on fatty acid synthesis, pancreatic cancer cells and tumors are unable to maintain lipid homeostasis when exposed to polyunsaturated fatty acids, leading to cell death by ferroptosis. In sum, arginine restriction in the tumor microenvironment constrains lipid metabolism in pancreatic cancers, which renders these tumors vulnerable to polyunsaturated-enriched fats.

cancer biology↗

bioRxiv2024

MSH2 is not required for either maintenance of DNA methylation or repeat contraction at the FMR1 locus in fragile X syndrome

BackgroundRepeat-induced epigenetic changes are observed in many repeat expansion disorders (REDs). These changes result in transcriptional deficits and/or silencing of the associated gene. MSH2, a mismatch repair protein that is required for repeat expansion in the REDs, has been implicated in the maintenance of DNA methylation seen in the region surrounding expanded CTG repeats at the DMPK locus in myotonic dystrophy type 1 (DM1). Here, we investigated the role of MSH2 in aberrant DNA methylation in two additional REDs, fragile X syndrome (FXS) that is caused by a CGG repeat expansion in the 5 untranslated region (UTR) of the fragile X messenger ribonucleoprotein 1 (FMR1) gene, and Friedreichs ataxia (FRDA) that is caused by GAA repeat expansion in intron 1 of the frataxin (FXN) gene. ResultsIn contrast to what is seen at the DMPK locus in DM1, loss of MSH2 did not decrease DNA methylation at the FMR1 promoter in FXS embryonic stem cells (ESCs) or increase FMR1 transcription. This difference was not due to the differences in the CpG density of the two loci as a decrease in DNA methylation was also not observed in a less CpG dense region upstream of the expanded GAA repeats in the FXN gene in MSH2 null induced pluripotent stem cells (iPSCs) derived from FRDA patient fibroblasts. Surprisingly given previous reports, we found that FMR1 reactivation was associated with a high frequency of MSH2- independent repeat contractions that resulted a permanent loss of DNA methylation. ConclusionsOur results suggest that there are mechanistic differences in the way that DNA methylation is maintained in the vicinity of expanded repeats among different REDs even though they share a similar mechanism of repeat expansion. The high frequency of transcription- induced MSH2-independent contractions we have observed may contribute to the mosaicism that is frequently seen in carriers of FMR1 alleles with expanded CGG-repeat tracts. Given the recent interest in the therapeutic use of transcription-driven repeat contractions, our data may have interesting mechanistic, prognostic, and therapeutic implications. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC="FIGDIR/small/629815v1_ufig1.gif" ALT="Figure 1000"> View larger version (20K): org.highwire.dtl.DTLVardef@1a6a59aorg.highwire.dtl.DTLVardef@1c25fdborg.highwire.dtl.DTLVardef@23394eorg.highwire.dtl.DTLVardef@876445_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2023

All three MutL complexes are required for repeat expansion in a human stem cell model of CAG-repeat expansion mediated glutaminase deficiency.

The Repeat Expansion Diseases (REDs) arise from the expansion of a disease-specific short tandem repeat (STR). Different REDs differ with respect to the repeat involved, the cells that are most expansion prone and the extent of expansion. Furthermore, whether these diseases share a common expansion mechanism is unclear. To date, expansion has only been studied in a limited number of REDs. Here we report the first studies of the expansion mechanism in induced pluripotent stem cells derived from a patient with a form of the glutaminase deficiency disorder known as Global Developmental Delay, Progressive Ataxia, And Elevated Glutamine (GDPAG; OMIM# 618412) caused by the expansion of a CAG-STR in the 5 UTR of the glutaminase (GLS) gene. We show that alleles with as few as [~]120 repeats show detectable expansions in culture despite relatively low levels of R-loops formed at this locus. Additionally, using a CRISPR-Cas9 knockout approach we show that PMS2 and MLH3, the constituents of MutL and MutL{gamma}, the 2 mammalian MutL complexes known to be involved in mismatch repair (MMR), are essential for expansion. Furthermore, PMS1, a component of a less well understood MutL complex, MutL{beta}, is also important, if not essential, for repeat expansion in these cells. Our results provide insights into the factors important for expansion and lend weight to the idea that, despite some differences, the same mechanism is responsible for expansion in many, if not all, REDs.

genetics↗

bioRxiv2022

Human-Sloth Bear (Melursus ursinus) Conflicts in Nawada Forest Division, Nawada, Bihar, India

Sloth bears (Melursus ursinus) are endemic to the Indian subcontinent and frequently come into conflict with human. Both in Rajauli Wildlife Sanctuary (RWLS) and Kauwkol Forest Range (KFR), sand mining operations create heavy noise during the summer for stone crushing which could be the cause of disturbance in the sloth bear territory and sloth bear attacks during the summer and winter. During the study period of 2016 to 2018, a total of 16 sloth bear attacks were incidently reported in various ranges of NFD. There was a marked seasonal variation in human casualties by sloth bear in the study area. Out of 16 cases, highest number of casualties were observed in monsoon (n=8, 50%) as compared to casualties in Summer (n=5, 31.25%) and winter (n=3, 18.75%) season. Most of the attacks were reported during 4.01-8.00 hours (n=6, 37.5%), followed by incidences occurred during evening time, 16.01-20.00 hours (n=4, 25%), 8.01-12.00 hrs (n=3, 18.75%) and 12.01-16.00 (n=2, 12.5%). Moreover, males (n=10) were shown to have a 62 percent attack rate compared to females (n=6; 38 percent). The data also shows that the frequency of attacks on victims engaged in various activities were related to their intensity of usage of specific habitats. It is reported that highest incidences of HSBC occurred when the victims were engaged in NTFP collection (37.5%), followed by victims engaged in walking (25%), farming (18.75%), defection (12.5%) and cattle grazing (6.25%) activities. We recommend education programs among the people to reduce human injury through mitigation techniques.

ecology↗

bioRxiv2022

Restoration of beta-GC trafficking improves the lysosome function in Gaucher disease

Lysosomes function as a primary site for catabolism and cellular signaling. These organelles digest a variety of substrates received through endocytosis, secretion and autophagy with the help of resident acid hydrolases. Lysosomal enzymes are folded in the endoplasmic reticulum (ER) and trafficked to lysosomes via Golgi and endocytic route. The inability of hydrolase trafficking due to mutations or mutations in its receptor or cofactor leads to cargo accumulation (storage) in lysosomes, resulting in lysosome storage disorder (LSD). In Gauchers disease (GD), the lysosomes accumulate glucosylceramide due to a lack of {beta}-glucocerebrosidase ({beta}-GC) activity that causes lysosome enlargement/dysfunction. We hypothesize that improving the trafficking of mutant {beta}-GC to lysosomes may delay the progression of GD. RNAi screen using high throughput based lysosomal enzyme activity assay followed by reporter trafficking assay utilizing {beta}-GC-mCherry lead to the identification of nine potential phosphatases. Depletion of these phosphatases in HeLa cells enhanced the {beta}-GC activity by increasing the folding and trafficking of Gauchers mutants to the lysosomes. Consistently, the lysosomes in primary fibroblasts from GD patients restored their function upon the knockdown of these phosphatases. Thus, these studies provide evidence that altering phosphatome activity possibly delays the GD and forms an alternative therapeutic strategy for this genetic disease. Key pointsO_LIPhosphatome RNAi screen identified both activators and inhibitors of cellular glucocerebrosidase activity C_LIO_LIDepletion of selective phosphatases in HeLa cells improved the folding and trafficking of mutant {beta}-glucocerebrosidase to lysosomes C_LIO_LIKnockdown of selective phosphatases restored the low basal {beta}-glucocerebrosidase activity to that of wild-type in primary cells derived from Gauchers disease patients C_LIO_LIDepletion of selective phosphatases displayed variable {beta}-GC activity in neuropathic and non-neuropathic Gauchers disease patient cells C_LI

cell biology↗

bioRxiv2021

Identification and Characterization of novel mutants of Nsp13 Protein among Indian SARS-CoV-2 isolates.

SARS-CoV-2, the causative agent of COVID-19 has mutated rapidly which enabled them to adapt and evade the immune system of the host. Emerging SARS-CoV-2 variants with crucial mutations pose a global challenge in context of therapeutic drugs and vaccines being developed globally. There are currently no specific therapeutics or vaccines available to combat SARS-CoV-2 devastation. In view of this, the current study aimed to identify and characterize the mutations found in the Nsp13 of SARS-CoV-2 in Indian isolates. Non-structural protein, Nsp13 protein sequences from Indian isolates were analyzed by comparing with the first reported Severe acute respiratory syndrome Corona Virus-2 (SARS-CoV-2) protein sequence from Wuhan, China. Out of 825 Nsp13 protein sequences, a total of 38 mutations were observed among Indian isolates. Our data show that mutations in Nsp13 at various positions (H164Y, A237T, T214I, C309Y, S236I, P419S, V305E, G54S, H290Y, P53S, A308Y, and A308Y) have a significant impact on the proteins stability and flexibility. Also, the impact of Nsp13 mutations on the protein function were predicted based on PROVEAN score that includes 15 mutants as neutral and 23 mutants as deleterious effect. Furthermore, B-cell epitopes contributed by Nsp13 were identified using various predictive immunoinformatic tools. Immunological Parameters of Nsp13 such as antigenicity, allergenicity and toxicity were evaluated to predict the potential B-cell epitopes. The predicted peptide sequences were correlated with the observed mutants. Our predicted data showed that there are seven high rank linear epitopes as well as 18 discontinuous B-cell epitopes based on immunoinformatic tools. Moreover, it was observed that out of total 38 identified mutations among Indian SARS-CoV-2 Nsp13 protein, four mutant residues at position 142 (E142), 245 (H245), 247 (V247) and 419 (P419) are localised in the predicted B cell epitopic region. Altogether, the results of the present in-silico study might help to understand the impact of the identified mutations in Nsp13 protein on its stability, flexibility and function.

bioinformatics↗