Biology subjects

Sharma, I.

Publications and source records attributed to Sharma, I..

9 recordsLinked to original sources

bioRxiv2026

Elevated endocytic trafficking mediated by GPRASP2 maintains HSC fidelity.

Endolysosomal trafficking supports cellular homeostasis through coordinated regulation of extrinsic signaling inputs. Hematopoietic stem cell (HSC) function requires a tightly regulated balance between quiescence for long-term preservation and rapid activation for blood production. Although lysosomal regulation of metabolism and quiescence has been linked to stem cell maintenance, the contribution of endocytic routing to lysosomal function remains incompletely understood. Here, we show that quiescent HSCs rely on elevated endocytosis to maintain self-renewal. This activity is mediated in part by GPRASP2, a post-endosomal sorting protein. HSCs enriched in GPRASP2 are functionally dormant yet molecularly primed for activation however, in response to proliferative cues, dormant HSCs exhibit reduced signaling and proliferation. Disruption of GPRASP2-mediated endocytosis induces rapid proliferation and increased expression of signaling constituents, consistent with a model in which elevated endocytosis attenuates signaling through receptor internalization. Thus, we identify endocytosis as a mechanism by which HSCs limit functional exhaustion arising from chronic activation.

cell biology↗

bioRxiv2025

SKiM-GPT: Combining Biomedical Literature-Based Discovery with Large Language Model Hypothesis Evaluation

BackgroundGenerating and testing hypotheses is a critical aspect of biomedical science. Typically, researchers generate hypotheses by carefully analyzing available information and making logical connections, which are then tested. The accelerating growth of biomedical literature makes it increasingly difficult to keep pace with connections between biological entities emerging across biomedical research. Recently developed automated means of generating hypotheses can generate many more hypotheses than can be easily tested. One such approach involves literature based discovery (LBD) systems such as Serial KinderMiner (SKiM), which surfaces putative A B C links derived from term co occurrence. However, LBD systems leave three critical gaps: (i) they find statistical associations, not biological relationships; (ii) they can produce false positive leads; and (iii) they do not assess agreement with a hypothesis in question. As a result, LBD search results often require costly manual curation to be of practical utility to the researcher. Large language models (LLMs) have the potential to automate much of this curation step, but standalone LLMs are hampered by hallucinations, lack of transparency in information sources, and the inability to reference data not included in the training corpus. ResultsWe introduce SKiM-GPT, a retrieval-augmented generation (RAG) system that combines SKiMs co-occurrence search and retrieval with frontier LLMs to evaluate user- defined hypotheses. For every chosen A-B-C SKiM hit, SKiM-GPT retrieves appropriate PubMed abstract texts, filters out irrelevant abstracts with a fine-tuned relevance model, and prompts an LLM to evaluate the users hypothesis, given the relevant abstracts. Importantly, the SKiM-GPT system is transparent and human-verifiable: it displays the retrieved abstracts, the hypothesis score, and a justification for the score grounded in the texts and written in natural language. On a benchmark consisting of 14 disease-gene-drug hypotheses, SKiM-GPT achieves strong ordinal agreement with four expert biologists (Cohens {kappa} = 0.84), demonstrating its ability to replicate expert judgment. ConclusionsSKiM-GPT is open-source (https://github.com/stewart-lab/skimgpt) and available through a web interface (https://skim.morgridge.org), enabling both wet-lab and computational researchers to systematically and efficiently evaluate biomedical hypotheses at scale.

bioinformatics↗

bioRxiv2025

Neutrophil TLR2 signaling promotes lipid accumulation and vascular plaque growth

Neutrophils are short-lived cells that are produced by the billions every day to circulate throughout the body and surveil all tissues. They are a key component of the innate immune system that play essential roles in antimicrobial immunity, but can also instigate sterile inflammatory diseases like gout and cancer. Immunometabolic paradigms that were developed by studying T cells and macrophages establish that cellular metabolic programming dictates immune function. Neutrophils have long been known as glucose-reliant and highly glycolytic. But surprising neutrophil heterogeneity has recently been described, and roles for lipids have been reported in both granulopoiesis and mature neutrophil effector function. Therefore, we set out to uncover how neutrophils acquire lipids from their environment and how this influences their functionality in the context of lipotoxicity. We found that neutrophils take up both free fatty acids and complex lipoproteins, but that their uptake is regulated through different signaling pathways. Neutrophil lipoprotein uptake is inducible by certain TLR2 signals, and this causes neutrophils to depolymerize their actin fibers and stop moving. Using a mouse model of atherosclerosis, we show that neutrophils in the plaque are lipid-laden and that neutrophil-deficient mice are protected from atherosclerotic plaque growth. Lipoprotein uptake causes neutrophils to recruit macrophages, conditional ablation of TLR2 on neutrophils prevents their lipid uptake and storage, and these mice are also protected against atherosclerosis. Our work highlights an important understudied role for lipids in neutrophil biology, and the importance of studying different lipid classes and different signaling pathways in neutrophils as compared to other myeloid populations.

immunology↗

bioRxiv2025

Dyr726, a brain-penetrant inhibitor of PI3Kα, Type III receptor tyrosine kinases, and WNT signalling

The vast majority of clinical small molecule multi-kinase inhibitors (mKI) report abject failures in targeting cancers with high stem cell contents like high-grade glioma and colorectal cancers. The FDA-approved mKIs to date ablate receptor tyrosine kinase signaling but do not target the paradoxical WNT signaling which is a key survival driver for the self-renewing cancer stem cells. The WNT pathway enhances cancer plasticity and triggers relapse of highly heterogenous tumours. Using de novo synthesis and structure-activity-relationship (SAR) studies with blood-brain-barrier (BBB) penetrant mKI scaffolds, we designed a highly potent and selective small molecule inhibitor of PI3K, PDGFR/KIT, and the WNT pathway denoted Dyr726. Dyr726 is superior to clinical mKIs and inhibits PI3K-AKT-mTOR and WNT-pathway signaling at multiple nodes thereby impeding proliferation, invasion, and tumour growth. Phospho-proteomic, structural, and target engagement analyses, combined with in vitro, in vivo efficacy, and pharmacokinetic studies reveal that Dyr726 is a brain-penetrant small molecule which effectively reduces tumour volume and extends survival of murine orthotopic models. Our current work establishes a first-in-class brain penetrant small molecule mKI which simultaneously antagonize the PI3K-AKT-mTOR and WNT pathways in preclinical cancer stem cell cultures, adult and pediatric primary organoids, and orthotopic murine models with positive efficacy in combination with clinical standard of care.

cancer biology↗

bioRxiv2025

Site-1 Protease is a negative regulator of sarcolipin promoter activity

The timed contraction and relaxation of myofibers in tissues such as the heart and skeletal muscle occurs via the tightly regulated movement of calcium ions into and out of the sarcoplasmic reticulum (SR). In skeletal muscle, this phenomenon enables humans to exercise, perform day-to-day tasks, and to breathe. Sarcolipin, a small regulatory protein, prevents calcium ions from entering the SR by binding to and inhibiting SERCA, contributing to myofiber contraction. Disruptions in sarcolipin expression are implicated in the pathophysiology of obesity and musculoskeletal disease. However, the mechanisms regulating sarcolipin expression are not clearly understood. We recently showed that Site-1 Protease (S1P) is a regulator of skeletal muscle function and mass. Here, we report that deleting S1P in mouse skeletal muscle increases sarcolipin expression, without impacting calcium SR flux. In cultured cells, S1P negatively regulates sarcolipin by activating the transcription factor ATF6, which inhibits basal- and calcineurin-stimulated sarcolipin promoter activity. We identified a cAMP response element binding protein (CREB) binding site on the sarcolipin promoter that is necessary for promoter activation, and show that in muscle, CREB binds to the sarcolipin promoter and that this binding is enhanced when S1P is deleted. These discoveries expand our knowledge of S1P biology and the mechanisms controlling calcium regulatory genes.

molecular biology↗

bioRxiv2025

Class I histone deacetylases catalyze lysine lactylation

Metabolism and post-translational modifications (PTMs) are intrinsically linked and the number of identified metabolites that can covalently modify proteins continues to increase. This metabolism/PTM crosstalk is especially true for lactate, the product of anaerobic metabolism following glycolysis. Lactate forms an amide bond with the {varepsilon}-amino group of lysine, a modification known as lysine lactylation, or Kla. Multiple independent mechanisms have been proposed in the formation of Kla, including p300/CBP-dependent transfer from lactyl-CoA, via a high-energy intermediate lactoylglutathione species that non-enzymatically lactylates proteins, and several enzymes are reported to have lactyl transferase capability. We recently discovered that class I histone deacetylases (HDACs) 1, 2, and 3 can all reverse their canonical chemical reaction to catalyze lysine {beta}-hydroxybutyrylation. Here we tested the hypothesis that HDACs can also catalyze Kla formation. Using biochemical, pharmacological, and genetic approaches, we found that HDAC-catalyzed lysine lactylation accounts for the majority of Kla formation in cells. Dialysis experiments confirm this is a reversible reaction that depends on lactate concentration. We also directly quantified intracellular lactyl-CoA and found that Kla abundance can be uncoupled from lactyl-CoA levels. Therefore, we propose a model in which the majority of Kla is formed through enzymatic addition of lactate by HDACs 1, 2, and 3.

biochemistry↗

bioRxiv2024

Wastelands or Preferred-lands? Indicators for redefining Desert conservation

Desert ecosystems though crucial in shaping global climate, are often perceived to have limited function and are frequently designated as wastelands due to low biotic diversity and abundance. We explore the functional properties of desert through assessment of spatio-temporal variations of avian species richness and insect abundance of the relatively understudied Thar in Rajasthan. The study was conducted across four contrasting ecoregions (Western Thar (WT), Eastern Thar (ET), Transitional Zone (TZ), and Cultivated Zone (CZ) spanning 33 counties of Rajasthan. Monthly avian diversity were obtained from crowdsourced eBird data. Insect diversity and abundance accross the ecoregions were curated from the annual surveys of ZSI, India. The leads were corroborated with five years feeding behaviour observational data recorded from a representative site spanning 852 acres. There was a significant seasonal differences in bird species richness between the ecoregions with the most pronounced variations between summer and winter and CZ exhibiting the highest spatial variability followed by WT. WT also recorded the highest insect diversity and abundance, especially the orders Orthoptera, Hymenoptera, Coleoptera, Lepidotera and Diptera. The correlation matrix between bird and insect abundance and Kernel Density Estimation (KDE) plot indicated the relation between diverse dietary preferences and migratory patterns. These observations challenge the conventional notion that resource-limited environments harbour lesser biodiversity especially in arid environments. The dominance of insectivory among winter migrants aligns with the higher density of resident arthropods and emphasizes the pivotal role of insects as a food source during the migratory period. The adaptability of resident species to varied food sources, particularly arthropods, provides a means to strategically navigate during resource constraints. This study thus provides a unique framework to (a) redefine the functional importance of desert using migratory birds as prominent ecological indicators. (b) include an ecological criteria during policy formulation for biodiversity conservation. It also emphasizes reevaluation of deserts during designation of wastelands especially in the unique WT eco-regions when evolving developmental as well as ecological restoration strategies.

ecology↗

bioRxiv2023

Impaired embryo sac cellularization by PMEI gene mutation affects gamete specification and twin plants in Arabidopsis

Arabidopsis lines with loss-of-function mutations in the gene encoding Embryo sac Pectin MethylEsterase Inhibitor (Atepmei) were found to have short silique and high seed sterility. Examination of tissue-cleared mature ovules (FG7-stage) revealed irregularly positioned nuclei within the embryo sacs. Instead of horse-shoe-shaped ovules, defective globular ovules without proper micropylar and chalazal ends were found. Embryo sac cell-type-specific GFP marker expression studies confirmed gamete and accessory cell identity alterations. Egg cell-specific marker (DD45) expression analysis confirmed the presence of multiple egg cells in the mutant embryo sacs, possibly due to defect in embryo sac cellularization. These supernumerary egg cells were functional as evident from the production of twin embryos when supernumerary sperm cells were provided. The results of Ruthenium red and tannic acid-ferric chloride staining of Atepmei mutant developing ovules, conferred its interaction with the specific PME in proper cell wall formation and maintenance around embryo sac nuclei which also coincide with its fate as a specific gamete. This is the first report implicating role of cell wall in gamete cell fate determination by altering cell-cell communication. Our analysis of the twin-embryo phenotype of epmei mutants also sheds light on the boundary conditions for double fertilization in plant reproduction.

plant biology↗

bioRxiv2019

LRRK2 is recruited to phagosomes and co-recruits Rab8 and Rab10 in human pluripotent stem cell-derived macrophages

The Parkinsons disease-associated gene, LRRK2, is also associated with immune disorders and infectious disease, and is expressed in immune subsets. Here, we characterise a platform for interrogating the expression and function of endogenous LRRK2 in authentic human phagocytes, using human induced Pluripotent Stem Cell-derived macrophages and microglia. Endogenous LRRK2 is expressed and upregulated by interferon-{gamma} in these cells, including a 187kD cleavage product. Using LRRK2 knockout and G2019S isogenic repair lines, we find that LRRK2 is not involved in initial phagocytic uptake of bioparticles, but is recruited to LAMP1(+)/Rab9(+) maturing phagosomes, and LRRK2 kinase inhibition enhances its residency at the phagosome. Importantly, LRRK2 is required for Rab8a and Rab10 recruitment to phagosomes, implying that LRRK2 operates at the intersection between phagosome maturation and recycling pathways in these professional phagocytes.

immunology↗