Biology subjects

Ganguly, N. K.

Publications and source records attributed to Ganguly, N. K..

4 recordsLinked to original sources

bioRxiv2025

Circulating Biomarkers for Therapeutic Response to Immune Checkpoint Inhibitor Therapy in Patients with Advanced Lung Cancer

Immune checkpoint inhibitors (ICIs) have demonstrated remarkable efficacy in the treatment of advanced lung cancer (ALC), but not all patients benefit. To identify responders, patient selection, categorization, and the identification of specific predictive biomarkers are crucial. Our research aims to identify circulating metabolites that could be used to stratify patients into potential responders prior to the initiation of ICIs and to monitor clinical response in real-time during treatment. In the discovery phase, plasma samples (n = 25) from ALC patients receiving ICIs were analyzed using unbiased metabolomics and validated in a distinct patient cohort (n = 39). Five potential biomarkers were identified (FC > 1.5, p 0.05, AUC 0.81-1), including Thiourea and a combined metabolite panel (CMP) consisting of sphingosine-1-phosphate, gentisic acid, glutathione, and 4-hydroxybutanone. Early on-treatment high plasma levels of Thiourea were significantly associated with 5-year progression-free survival [Hazard ratio (HR) = 0.038, 95% confidence interval (CI) = 0.013-0.107, p<0.001] and overall survival [HR = 0.048, 95% CI = 0.019-0.120, p<0.001]. Low levels of CMP early on treatment were significantly associated with progression-free survival [HR = 8.119, 95% CI: 3.767-17.501, p<0.001] and overall survival [HR = 7.367, 95% CI: 3.517-15.433, 3.517-15.433, p<0.001]. This predictive plasma metabolite panel could serve as promising circulating biomarkers for predicting the therapeutic response of ICIs in ALC patients.

cancer biology↗

bioRxiv2025

Cytokine profiling identifies circulating IL-2, IL23 and sPD-L1 as prognostic biomarkers for treatment outcomes in Non-Small cell Lung Cancer patients undergoing anti-PD1 therapy

BackgroundThis study investigates the predictive potential of circulating cytokines for response and survival outcomes in patients with advanced non-small cell lung cancer (NSCLC) undergoing immune checkpoint inhibitor (ICI) therapy. Materials and MethodsA cohort of 64 patients with advanced NSCLC receiving ICI therapy were included. Baseline serum samples were collected prior to ICI initiation and profiled using a multiplex cytokine panel. Logistic regression, Cox regression, and Kaplan-Meier survival analysis were employed to assess associations between cytokine levels, therapeutic response, progression-free survival (PFS), and overall survival (OS). Gene expression levels of key cytokines were validated in peripheral blood mononuclear cells (PBMCs) using quantitative real-time PCR. ResultsElevated baseline levels of IL-2, IL-23, and sPD-L1 were significantly associated with clinical response to ICI therapy. Among these, sPD-L1 emerged as an independent predictor of response (AUC = 0.87). Multivariate Cox regression showed IL-2 (HR = 0.67), sPD-L1 (HR = 0.15), and IL-23 (HR = 1.18) were significantly associated with PFS and also predictive of OS. Notably, combined profiling of IL-2 and sPD-L1 enhanced predictive power (AUC = 0.95 for both PFS and OS). RT-PCR analysis of PBMCs corroborated these findings, confirming upregulation of IL-2 in responders and elevated IL-23 expression in non-responders. ConclusionBaseline cytokine profiling particularly of IL-2, sPD-L1, and IL-23 provides important prognostic and predictive information in advanced NSCLC patients undergoing ICI therapy. These biomarkers may facilitate more personalized approaches to immunotherapy and guide clinical decision-making.

cancer biology↗

bioRxiv2023

Chandipura Virus forms cytoplasmic inclusion bodies through phase separation and proviral association of cellular protein Kinase R and stress granules protein TIA-1

Negative-strand RNA viruses form cytoplasmic inclusion bodies (IBs) representing virus replication foci through phase separation or bio-molecular condensation of viral and cellular proteins, as a hallmark of their infection. Alternatively, mammalian cells form stalled-mRNA containing antiviral stress granules (SGs), as a consequence of phosphorylation of eukaryotic initiation factor 2 (eIF2) through condensation of several RNA-binding proteins including TIA-1. Whether and how Chandipura virus (CHPV), an emerging human pathogen causing influenza-like illness, coma and death; forms IBs and evades antiviral SGs, remains unknown. By confocal imaging on CHPV-infected Vero-E6 cells, we found that CHPV infection doesnt induce formation of distinct canonical SGs. Instead, CHPV proteins condense and co-localize together with SG-proteins to form heterogeneous IBs, which ensued independent of the activation of eIF2 and eIF2 Kinase, Protein Kinase R (PKR). Interestingly, siRNA-mediated depletion of PKR or TIA-1 significantly decreased viral transcription and virion production. Moreover, CHPV infection also caused condensation and recruitment of PKR to IBs. Compared to SGs, IBs exhibited significant rapidity in disassembly dynamics. Altogether, our study demonstrates that CHPV-replication co-optimizing with SG-proteins and revealing unprecedented proviral role of TIA-1/PKR, may have implication in understanding the mechanisms regulating CHPV-IB formation, and designing antiviral therapeutic. ImportanceCHPV is an emerging tropical pathogen reported to cause acute influenza-like-illness and encephalitis in children with very high mortality rate of [~]70%. Lack of a vaccines and an effective therapy against CHPV makes it a potent pathogen for causing an epidemic in tropical parts of globe. Given these forewarnings, it is of paramount importance that CHPV biology must be understood comprehensively. Targeting of host factors offers several advantages over targeting the viral components due to in general higher mutation rate in viral genome. In this study, we aimed at understanding the role of those cellular RNA binding proteins in CHPV replication, which form SGs. Our study helps understand participation of cellular factors in CHPV replication and could help develop effective therapeutics against the virus.

microbiology↗

bioRxiv2023

Huntingtin Interacting Protein-1 expression is regulated via HIF2 axis in Lung Adenocarcinoma

Non-Small Cell Lung Cancer (NSCLC) patients are diagnosed late when the disease has metastasized. Kras is a prevalent mutation in NSCLC besides EGFR and TP53 and targeted therapies against this have been challenging. We have explored deregulation of an endocytic adapter protein, Huntingtin Interacting Protein-1(HIP1) and its relevance in a Kras mutant lung adenocarcinoma cell line as a model system. HIP1 RNA expression is observed to be significantly reduced in high-grade and metastatic lung cancer patients as compared to low-grade tumours and this correlates with poor survival. HIP1 depletion followed by global proteome profiling in A549 cells identified metabolic pathways to be majorly upregulated, followed by RNA transport and surveillance, amongst others. HIP1 depletion also significantly increased anchorage independent growth and invasion of these cells. However, the EMT markers did not follow the canonical regulation. We observed E-Cadherin and Vimentin induction, which is suggestive of collective migration. Additionally, we observed a hypoxic microenvironment to induce HIP1 expression, mediated by Hypoxia Inducible Factor 2 (HIF2), suggesting that a HIF2-HIP1 axis can cause tumour suppression and needs further exploration.

cancer biology↗