Biology subjects

Subhadarshini, S.

Publications and source records attributed to Subhadarshini, S..

6 recordsLinked to original sources

bioRxiv2025

SIRT2 attenuates stress-induced skeletal muscle atrophy by inhibiting glucocorticoid receptor signaling

Skeletal muscle atrophy occurs in several diseases and is associated with chronic stress. Studies indicate that glucocorticoid receptor signalling is the major signalling pathway that mediates stress-induced muscle degeneration. Although the glucocorticoid signalling pathway is relatively well characterized, there is a need to identify modulators of this pathway that may be useful for drug targeting to ameliorate muscle atrophy. SIRT2 is a mammalian Sirtuin isoform known to mediate the longevity benefits of calorie restriction and exercise. Currently, the role of SIRT2 in regulating stress-induced skeletal muscle atrophy is unclear. Our study found that SIRT2 is a critical regulator of muscle homeostasis and is required to protect against stress-induced muscle atrophy. Interestingly, SIRT2 levels are reduced during glucocorticoid-induced muscle atrophy in mice. SIRT2 depletion exacerbates glucocorticoid-induced reduction in myotube diameter and atrophy gene expression. In contrast, SIRT2 overexpression ameliorates myotube atrophy in primary myotubes. Our findings indicate that SIRT2 knockout mice are susceptible to glucocorticoid-induced muscle atrophy, while muscle-specific SIRT2-transgenic mice exhibit improved muscle function and are protected from glucocorticoid-induced atrophy. Mechanistically, SIRT2 binds to the glucocorticoid receptor to negatively regulate its activity, possibly via deacetylation of critical residues in its DNA-binding domain. Our findings suggest that SIRT2 activation may protect against glucocorticoid-induced skeletal muscle atrophy and serve as a potential therapeutic target for treating muscle atrophy.

pathology↗

bioRxiv2025

Gain of Function p53 mutant R273H confers distinct methylation profiles and consequent partial or full EMT states to colon tumour

p53 is the second most frequently mutated gene in colorectal cancer. While different p53 mutations have been correlated with metastasis, the distinct phenotypes exhibited by site-specific mutations of p53 are not well elucidated. Here, we analyse transcriptomic and methylation data from TCGA-COAD cohort to understand the epigenetic impact of three most prevalent hotspot mutations of p53 (R175H, R273H and R282W). We observed that p53 R273H mutation associates with a partial epithelial-mesenchymal transition (pEMT) state and metastatic progression. In vitro ChIP-seq experiments conducted on p53R27H harbouring HT29 cells revealed an enrichment of mutant p53 R273H at pEMT or mesenchymal gene sets. Further, simulations from a gene regulatory network incorporating the interactions of p53R273H with EMT regulators explain how this mutation shapes the phenotypic landscape accessible to cancer cells. Finally, single-cell transcriptomic analysis of colorectal tumours reveals R273H-linked enrichment of partial and mesenchymal EMT phenotypes across tumour subpopulations in CRC. Overall, we identified distinct epigenetic regulation regulating partial EMT and consequent aggressive behaviour triggered by p53R273H. These findings can help devise effective therapeutic strategies for p53 mutant specific colon tumours. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=177 SRC="FIGDIR/small/662954v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@7d424dorg.highwire.dtl.DTLVardef@18bfcaborg.highwire.dtl.DTLVardef@17950c8org.highwire.dtl.DTLVardef@1a698f9_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract CaptionC_FLOATNO Mutation in Tp53 at R273H associates with DNA hypermethylation and elevated pEMT and metastatic signatures as compared to R175 and R282W mutations in colon tumours suggesting of devising novel therapeutic intervention strategies based on p53 mutation profiles. C_FIG

bioinformatics↗

bioRxiv2025

Repurposing statins in combination therapy for effective ablation of metastatic breast cancer

Metastatic breast cancer (mBC) remains an incurable disease with limited treatment options, highlighting the need for novel therapeutic approaches. Combination therapy with chemotherapeutic agents along with targeted therapy are the most common methods of treatment used in the terminal stages of the disease. Eventual development of resistance to these approaches, leading to fatal outcomes suggests the presence or emergence of a heterogenous population of cells intrinsically resistant to commonly used regimens. Previous work identified a heterogeneous population of metastatic tumor cells with distinct molecular characteristics driven by Macc1 (Metastasis Associated in Colon Cancer 1) overexpression, which could be targeted by lovastatin (transcriptional inhibitor of Macc1). Building on this foundation, the efficacy of lovastatin in targeting metastatic cells with high Macc1 expression was evaluated in lung metastasis, and the regulatory pathways governing Macc1 expression and lovastatin treatment in mBC were investigated. The expression of Macc1, in breast cancer biopsies provides insights into the intra and inter tumor heterogeneity of the Macc1 gene and its correlation with disease outcomes. While some studies suggest synergistic effects between statins and chemotherapeutic agents, comprehensive evaluations of various combinations and their therapeutic outcomes are still needed. The therapeutic efficacy of lovastatin combined with chemotherapy to determine the most effective treatment regimen that maximizes tumor cell ablation demonstrated that lovastatin can effectively ablate the chemoresistant tumor cells in mBC. The translational implications of this research will identify patient subgroups that may benefit most from statin-chemotherapy combinations that could support the repurposing of statins as cost-effective adjuvant therapies for mBC.

cancer biology↗

bioRxiv2025

An integrative molecular systems approach unravels mechanisms underlying biphasic nitrate uptake by plant nitrate transporter NRT1.1

Elucidating the mechanisms of transport kinetics in plants is crucial to develop crops that can use nutrients efficiently. The plant nitrate transporter NRT1.1 rapidly switches between high- and low-affinity transport modes to maintain an optimal uptake amidst fluctuations in nitrate levels. This functional switch is regulated by NRT1.1 phosphorylation, but the precise mechanisms remain poorly understood. Here, using an integrated molecular and systems-level modeling, we identify mechanisms underlying biphasic behaviour of NRT1.1. Phosphorylation of NRT1.1 and its binding to nitrate impacts its overall flexibility and synergistically modulates its global conformation, impacting the nitrate transport rate. Integrating these observations with a regulatory network involving kinases CIPK8/CIPK23 and calcium binding proteins CBL1/9, reveals that in high nitrate conditions, CIPK8-mediated sequestration of CBL1 disrupts the CIPK23-CBL complex required for NRT1.1 phosphorylation, switching NRT1.1 to a low-affinity mode. Together, our findings untangle the molecular complexity enabling NRT1.1 phosphorylation switch with broader implications in nitrate sensing and molecular-level adaption to fluctuating external nutrient levels.

systems biology↗

bioRxiv2023

Single-Site Phosphorylation Elicits Structural, Dynamic, and Accessibility Changes in Proteins at both Proximal and Distal Regions to the Phosphosite.

Phosphorylation, a fundamental cellular mechanism, intricately regulates protein function and signaling pathways. Our study employs extensive computational analyses on a curated dataset of phosphorylated and unphosphorylated protein structures to explore the multifaceted impact of phosphorylation on protein conformation. Our findings reveal that phosphorylation induces not only local changes at the phosphorylation site but also extensive alterations in distant regions, showcasing its far-reaching influence on protein structure-dynamics. Using Normal Mode Analysis (NMA), we investigate changes in protein flexibility post-phosphorylation, highlighting an enhanced level of structural dynamism. Through in-depth case studies on Polyubiquitin-B and Glycogen Synthase Kinase-3 Beta, we elucidate how phosphorylation at distinct sites leads to variable structural and dynamic modifications, potentially dictating functional outcomes. While phosphorylation largely preserves residue motion correlation, it significantly disrupts low-frequency global modes, presenting a dualistic impact on protein dynamics. We also explore alterations in the total accessible surface area (ASA), emphasizing region-specific changes around phosphorylation sites. This study sheds light on phosphorylation-induced conformational changes, dynamic modulation, and surface accessibility alterations, contributing to a comprehensive understanding of cellular regulation and suggesting promising avenues for therapeutic interventions.

biophysics↗

bioRxiv2023

Dynamical modelling of proliferative-invasive plasticity and IFN-gamma signaling in melanoma reveals mechanisms of PD-L1 expression heterogeneity

Phenotypic heterogeneity of melanoma cells contributes to drug tolerance, increased metastasis, and immune evasion in patients with progressive disease. Diverse mechanisms have been individually reported to shape extensive intra- and inter-tumoral phenotypic heterogeneity, such as IFN{gamma} signaling and proliferative to invasive transition, but how their crosstalk impacts tumor progression remains largely elusive. Here, we integrate dynamical systems modeling with transcriptomic data analysis at bulk and single-cell levels to investigate underlying mechanisms behind phenotypic heterogeneity in melanoma and its impact on adaptation to targeted therapy and immune checkpoint inhibitors. We construct a minimal core regulatory network involving transcription factors implicated in this process and identify the multiple "attractors" in the phenotypic landscape enabled by this network. Our model predictions about synergistic control of PD-L1 by IFN{gamma} signaling and proliferative to invasive transition were validated experimentally in three melanoma cell lines - MALME3, SK-MEL-5 and A375. We demonstrate that the emergent dynamics of our regulatory network comprising MITF, SOX10, SOX9, JUN and ZEB1 can recapitulate experimental observations about the co-existence of diverse phenotypes (proliferative, neural crest-like, invasive) and reversible cell-state transitions among them, including in response to targeted therapy and immune checkpoint inhibitors. These phenotypes have varied levels of PD-L1, driving heterogeneity in immune-suppression. This heterogeneity in PD-L1 can be aggravated by combinatorial dynamics of these regulators with IFN{gamma} signaling. Our model predictions about changes in proliferative to invasive transition and PD-L1 levels as melanoma cells evade targeted therapy and immune checkpoint inhibitors were validated in multiple data sets from in vitro and in vivo experiments. Our calibrated dynamical model offers a platform to test combinatorial therapies and provide rational avenues for the treatment of metastatic melanoma. This improved understanding of crosstalk among PD-L1 expression, proliferative to invasive transition and IFN{gamma} signaling can be leveraged to improve the clinical management of therapy-resistant and metastatic melanoma.

cancer biology↗