Biology subjects

Giri, s.

Publications and source records attributed to Giri, s..

6 recordsLinked to original sources

bioRxiv2026

Longitudinal and stability-aware analysis reveals treatment-specific microRNA response signatures following immune-reconstitution and B-cell-targeted therapies in multiple sclerosis

Disease-modifying therapies (DMT)s) for relapsing-remitting multiple sclerosis (RRMS) act through distinct immunological mechanisms, yet the within-patient molecular response programs associated with these therapies remain incompletely defined. Here, we reanalysed publicly available PBMC miRNA microarray data (GSE230064) using a longitudinal, robustness-focused framework to compare therapy-associated miRNA response patterns following cladribine versus ocrelizumab treatment. Baseline (t0) and 6-month post-treatment (t1) samples were paired within individuals and technical replicates consolidated prior to analysis, yielding a final paired cohort of 4 cladribine-treated and 6 ocrelizumab-treated patients. Within each treatment arm, we quantified per-patient {Delta}-miRNA (t1-t0) values and prioritized therapy-associated response features using a multi-evidence framework integrating effect direction, magnitude, directional consistency across individuals, and leave-one-out sensitivity. Cladribine treatment was associated with a highly coordinated, directionally concordant upregulation of five miRNAs including hsa-miR-27a-3p, hsa-miR-27b-3p, hsa-miR-503-5p, hsa-miR-148a-3p, and hsa-miR-26a-5p, all exhibiting 100% directional stability across patients and mean {Delta}-expression values ranging from +0.77 to +1.38. These miRNAs target pathways relevant to MS pathophysiology, including Th17/Treg balance, Wnt-{beta}-catenin signaling, macrophage polarization, and epigenetic immune regulation. In contrast, ocrelizumab elicited a more selective response pattern, with five miRNAs including hsa-miR-100-5p, hsa-miR-410-3p, hsa-miR-432-5p, hsa-miR-296-5p, and hsa-miR-485-3p showing moderate directional stability (83%) and greater inter-individual heterogeneity, consistent with the more targeted mechanism of CD20+ B-cell depletion. Notably, the two treatment-associated signatures were non-overlapping, with hsa-miR-27b-3p representing the only miRNA shared with prior cross-sectional analyses of this dataset. The identified ocrelizumab-associated miRNAs implicate pathways including mTOR/IGF1R signaling, NF-{kappa}B regulation, RNA editing, and mitochondrial biogenesis, several of which are dysregulated in progressive MS. Together, these findings demonstrate that cladribine and ocrelizumab induce distinct, treatment-specific miRNA response architectures that reflect their divergent immunological mechanisms. This work establishes a stability-aware analytic template for extracting reproducible longitudinal miRNA signals from small paired RRMS cohorts and provides a ranked set of biologically plausible candidate miRNAs for prospective validation and mechanistic investigation.

immunology↗

bioRxiv2024

Targeting mitochondrial metabolism with CPI-613 in chemoresistant ovarian tumors

BackgroundThere is evidence indicating that chemoresistance in tumor cells is mediated by the reconfiguration of the tricarboxylic acid cycle, leading to heightened mitochondrial activity and oxidative phosphorylation (OXPHOS). Previously, we have shown that ovarian cancer cells that are resistant to chemotherapy display increased OXPHOS, mitochondrial function, and metabolic flexibility. To exploit this weakness in chemoresistant ovarian cancer cells, we examined the effectiveness of the mitochondrial inhibitor CPI-613 in treating preclinical ovarian cancer. MethodsChemosensitive OVCAR3, and chemoresistant CAOV3 and F2 ovarian cancer cells lines and their xenografts in nude mice were used. Functional metabolic studies were performed using Seahorse instrument. Metabolite quantification was performed using LC/MS/MS. ResultsMice treated with CPI-613 exhibited a notable increase in overall survival and a reduction in tumor development and burden in OVCAR3, F2, and CAOV3 xenografts. CPI-613 suppressed the activity of pyruvate dehydrogenase and alpha-ketoglutarate dehydrogenase complex, which are two of its targets. This led to a reduction in OXPHOS and tricarboxylic acid cycle activity in all 3 xenografts. The addition of CPI-613 enhanced the responsiveness of chemotherapy in the chemoresistant F2 and CAOV3 tumors, resulting in a notable improvement in survival rates and a reduction in tumor size as compared to using chemotherapy alone. CPI-613 reduced the chemotherapy-induced OXPHOS in chemoresistant tumors. The study revealed that the mechanism by which CPI-613 inhibits tumor growth is through mitochondrial collapse. This is evidenced by an increase in superoxide production within the mitochondria, a decrease in ATP generation, and the release of cytochrome C, which triggers mitochondria-induced apoptosis. Our study demonstrates the translational potential of CPI-613 against chemoresistant ovarian tumors.

cancer biology↗

bioRxiv2024

Nrf2 regulates the activation-driven expansion of CD4+ T-cells by differentially modulating glucose and glutamine metabolism

SUMMARYUpon antigenic stimulation, CD4+T-cells undergo clonal expansion, elevating their bioenergetic demands and utilization of nutrients like glucose and glutamine. The nuclear factor erythroid 2-related factor 2 (Nrf2) is a well-known regulator of oxidative stress, but its involvement in modulating the metabolism of CD4+T-cells remains unexplored. Here, we elucidate the role of Nrf2 beyond the traditional antioxidation, in modulating activation-driven expansion of CD4+T-cells by influencing their nutrient metabolism. T-cell-specific activation of Nrf2 enhances early activation and IL-2 secretion, upregulates TCR-signaling, and increases activation-driven proliferation of CD4+T-cells. Mechanistically, high Nrf2 inhibits glucose metabolism through glycolysis but promotes glutamine metabolism via glutaminolysis to support increased T-cell proliferation. Further, Nrf2 expression is temporally regulated in activated CD4+T-cells with elevated expression during the early activation, but decreased expression thereafter. Overall, our findings uncover a novel role of Nrf2 as a metabolic modulator of CD4+T-cells, thus providing a framework for improving Nrf2-targeting therapies and T-cell immunotherapies.

immunology↗

bioRxiv2023

Immuno-Responsive Gene-1: A mitochondrial gene regulates pathogenic Th17 in CNS autoimmunity mouse model

Pathogenic Th17 cells play crucial roles in CNS autoimmune diseases such as multiple sclerosis (MS), but their regulation by endogenous mechanisms remains unknown. Through RNA-seq analysis of primary brain glial cells, we identified immuno-responsive gene 1 (Irg1) as one of the highly upregulated gene under inflammatory conditions. Validation in the spinal cord of animals with experimental autoimmune encephalomyelitis (EAE), an MS model, confirmed elevated Irg1 levels in myeloid, CD4, and B cells in the EAE group raising the concern if Irg1 is detrimental or protective. Irg1 knockout (KO) mice exhibited severe EAE disease, increased mononuclear cell infiltration, and increased levels of triple-positive CD4+ T cells expressing IL17a, GM-CSF, and IFN{gamma}. A lack of Irg1 in macrophages elevates Class II expression, promoting the polarization of myelin-primed CD4+ T cells into pathogenic Th17 cells via the NLRP3/IL-1{beta} axis. Adoptive transfer in Rag-1 KO and single-cell RNA sequencing highlighted the crucial role of Irg1 in shaping pathogenic Th17 cells. Moreover, bone marrow chimeras revealed that immune cells lacking Irg1 maintained pathogenic and inflammatory phenotypes, suggesting its protective role in autoimmune diseases, including MS. SignificanceImmunoresponsive gene 1 (Irg1) was identified as a significantly elevated gene under inflammatory conditions through in vitro and in vivo models. Using global knockout mice, we identified Irg1 as a protective endogenous gene that negatively regulates pathogenic Th17 cells. Single-cell RNA sequencing of infiltrating cells during EAE revealed that Irg1 knockout enhanced the expression of pathogenic Th signatures in CD4+ T cells, indicating a robust proinflammatory environment. Irg1 negatively regulates IL-1{beta} in macrophages, which is essential for the differentiation of pTh17 CD4+ T cells, potentially clarifying the exacerbation of EAE in knockout animals. Our study identified Irg1 as a negative regulator of both innate and adaptive immune responses in a CNS autoimmunity model.

immunology↗

bioRxiv2023

Pyruvate dehydrogenase dependent metabolic program affects oligodendrocyte maturation and remyelination

The metabolic need of the premature oligodendrocytes (Pre-OLs) and mature oligodendrocytes (OLs) are distinct. The metabolic control of oligodendrocyte maturation is not fully understood. Here we show that the terminal maturation and higher mitochondrial respiration in the oligodendrocyte is an integrated process controlled through pyruvate dehydrogenase (Pdh). Combined bioenergetics and metabolic studies show that mature oligodendrocytes show elevated TCA cycle activity than the premature oligodendrocytes. Our signaling studies show that the increased TCA cycle activity is mediated by the activation of Pdh due to inhibition of pyruvate dehydrogenases isoform-1 (Pdhk1) that phosphorylates and inhibits Pdh. Accordingly, when Pdhk1 is directly expressed in the premature oligodendrocytes, they fail to mature. While Pdh converts pyruvate into the acetyl-CoA by its oxidative decarboxylation, our study shows that Pdh also activates a unique molecular switch required for oligodendrocyte maturation by acetylating the bHLH family transcription factor Olig1. Pdh inhibition via Pdhk1 blocks the Olig1-acetylation and hence, oligodendrocyte maturation. Using the cuprizone model of demyelination, we show that Pdh is deactivated during the demyelination phase, which is reversed in the remyelination phase upon cuprizone withdrawal. In addition, Pdh activity status correlates with the Olig1-acetylation status. Hence, the Pdh metabolic node activation allows a robust mitochondrial respiration and activation of a molecular program necessary for the terminal maturation of oligodendrocytes. Our findings open a new dialogue in the developmental biology that links cellular development and metabolism. These findings have far-reaching implications for the development of therapies for a variety of demyelinating disorders including multiple sclerosis.

neuroscience↗

bioRxiv2021

Blood-based untargeted metabolomics in Relapsing-Remitting Multiple Sclerosis revealed the testable therapeutic target

Metabolic aberrations impact the pathogenesis of multiple sclerosis (MS) and possibly can provide clues for new treatment strategies. Using untargeted metabolomics, we measured serum metabolites from 35 relapsing-remitting patients and 14 healthy age-matched controls. Out of 632 known metabolites detected, 60 were significantly altered in relapsing-remitting MS (RRMS). Bioinformatics analysis identified an altered "metabotype" in RRMS patients, represented by 4 changed metabolic pathways of glycerophospholipid, citrate cycle, sphingolipid, and pyruvate metabolism. Interestingly, the common upstream metabolic pathway feeding these 4 pathways is the glycolysis pathway. Real-time bioenergetic analysis of the patient derived peripheral blood mononuclear cells, showed enhanced glycolysis, supporting the altered metabolic state of immune cells. Experimental autoimmune encephalomyelitis mice treated with the glycolytic inhibitor, 2-deoxy-D-glucose ameliorated the disease progression and inhibited the disease pathology significantly by promoting the anti-inflammatory phenotype of monocytes/macrophage in the central nervous system. Our study suggests that targeting glycolysis offers a potential target for MS.

neuroscience↗