Biology subjects

Raghav, S. K.

Publications and source records attributed to Raghav, S. K..

6 recordsLinked to original sources

bioRxiv2026

A Glycolysis-Fatty Acid Metabolic Axis Shapes Human Tfh Cell Function

Follicular helper T (Tfh) cells orchestrate germinal centre-derived humoral immunity by providing essential help to B cells. Despite their key role in humoral immunity, the metabolic processes that guide Tfh differentiation and functions in human remain poorly understood. In this study, we used a human ex vivo Tfh differentiation model to investigate how key metabolic pathways influence Tfh cell differentiation and helper function. Human naive CD4 T cells were differentiated into Tfh cells, and glycolysis was selectively inhibited during early differentiation to assess its effects on cell fate, function, and transcriptomic landscape. Unexpectedly, early glycolytic inhibition enhanced Tfh cell differentiation but significantly impaired their function, including reduced IL-21 secretion and diminished B cell help. Transcriptomic analyses further revealed downregulation of fatty acid metabolic pathways when glycolysis was inhibited. To better understand this link, we disrupted fatty acid synthesis and oxidation and observed a marked decline in helper functions, including IL-21 and IFN-{gamma} production. Interestingly, acetate supplementation partially restored IFN-{gamma} secretion in glycolysis inhibited conditions, but not IL-21, suggesting that some functional requirements cannot be compensated by alternative metabolic sources. These findings identify glycolysis during early differentiation as a key regulator of human Tfh cells fate and reveal a glycolysis-dependent fatty acid metabolic axis that selectively controls Tfh function. This metabolic checkpoint provides mechanistic insight into tuning Tfh cells and Tfh-driven humoral immunity in vaccination and autoimmunity.

immunology↗

bioRxiv2022

Genotypic and phenotypic diversity of the multidrug-resistant Mycobacterium tuberculosis strains from eastern India

Mycobacterium tuberculosis (Mtb) poses a great challenge to human health and wellbeing and hinders economic growth of a region. India along with other south east Asian countries are known as high Tuberculosis burden countries. Adoption of whole genome sequencing in studying genetic diversity, evolution, transmission pattern and drug resistance development provided a great opportunity for developing and improving diagnostic and therapeutic approaches. In our study we have sequenced 118 Mtb whole genome from North East(NE) and Odisha as a representative of the diversity in eastern region of India for the first time. We observed high prevalence of multi-drug resistant(MDR) lineage-2(n=52) strains in NE whereas presence of mostly lineage-1(n=30) & 3 (n=11) strains in Odisha. The MDR strains from Sikkim demonstrated similar resistance profile of fluroquinolones and pair-wise SNP distances showed presence of local transmission clusters. We also detected significant enrichment of short INDELs in MDR samples in contrast to drug susceptible samples. This study provides molecular level insight into Mtb strains of eastern region in comparison with Indian and global perspective.

microbiology↗

bioRxiv2022

CMTM6 mediates cisplatin resistance in OSCC by regulating AKT/c-MYC driven ribosome biogenesis

CMTM6, a type 3 transmembrane protein, is known to stabilize the expression of programmed cell death ligand 1 (PD-L1) and hence facilitates the immune evasion of tumor cells. Recently, we demonstrated that CMTM6 is a major driver of cisplatin resistance in oral squamous cell carcinomas (OSCC). However, the detailed mechanism how CMTM6 rewires cisplatin resistance in OSCC is yet to be explored. RNA sequencing analysis of cisplatin resistant OSCC lines stably expressing NtShRNA and CMTM6 ShRNA revealed that CMTM6 might be a potential regulator of ribosome biogenesis network. Knocking down CMTM6 significantly inhibited transcription of 47S precursor rRNA and hindered the nucleolar structure, indicating reduced ribosome biogenesis. When CMTM6 was ectopically over expressed in CMTM6KD cells, almost all ribosomal machinery components were rescued. Mechanistically, CMTM6 induced the expression of C-Myc, which promotes RNA polymerase I mediated rDNA transcription. In addition to this, CMTM6 also found to regulate the AKT-mTORC1-dependent ribosome biogenesis and protein synthesis in cisplatin resistant lines. The nude mice and zebrafish xenograft experiments indicate that blocking ribosome synthesis either by genetic inhibitor (CMTM6KD) or by pharmacological inhibitor (CX-5461), significantly restores cisplatin medicated cell death in chemoresistant OSCC. Overall, our study suggests that CMTM6 is a major regulator of ribosome biogenesis network and targeting ribosome biogenesis network is a viable target to overcome chemoresistance in OSCC. The novel combination of CX-5461 and cisplatin deserves further clinical investigation in advanced OSCC.

cancer biology↗

bioRxiv2021

NCoR1 and SMRT fine-tune inflammatory versus tolerogenic balance in dendritic cells by differentially regulating STAT3 signaling

Dendritic cell (DC) fine-tunes inflammatory versus tolerogenic responses to protect from immune-pathology. However, the role of co-regulators in maintaining this balance is unexplored. NCoR1-mediated repression of DC immune-tolerance has been recently reported. Here we found that depletion of NCoR1 paralog SMRT (NCoR2) enhanced cDC1 activation and expression of IL-6, IL-12 and IL-23 while concomitantly decreasing IL-10 expression/secretion. Consequently, co-cultured CD4+ and CD8+ T-cells depicted enhanced Th1/Th17 frequency and cytotoxicity, respectively. Comparative genomic and transcriptomic analysis demonstrated differential regulation of IL-10 by SMRT and NCoR1. SMRT depletion represses mTOR-STAT3-IL10 signaling in cDC1 by downregulating NR4A1. Besides, Nfkbia and Socs3 were down-regulated in Ncor2 (Smrt) knockdown cDC1, supporting increased production of inflammatory cytokines. Moreover, studies in mice showed, adoptive transfer of SMRT knockdown cDC1 in OVA-DTH induced footpad inflammation led to increased Th1/Th17 and reduced tumor burden after B16 melanoma injection by enhancing oncolytic CD8+ T-cell frequency, respectively. We also depicted decreased Ncor2 expression in Rheumatoid Arthritis, a Th1/Th17 disease.

immunology↗

bioRxiv2020

Intra-host variability in global SARS-CoV-2 genomes as signatures of RNA editing: implications in viral and host response outcomes

During the course of the COVID-19 pandemic, large-scale genome sequencing of SARS-CoV-2 has been useful in tracking its spread and in identifying Variants Of Concern (VOC). Besides, viral and host factors could contribute to variability within a host that can be captured in next-generation sequencing reads as intra-host Single Nucleotide Variations (iSNVs). Analysing 1, 347 samples collected till June 2020, we recorded 18, 146 iSNV sites throughout the SARS-CoV-2 genome. Both, mutations in RdRp as well as APOBEC and ADAR mediated RNA editing seem to contribute to the differential prevalence of iSNVs in hosts. Noteworthy, 41% of all unique iSNVs were reported as SNVs by 30th September 2020 in samples submitted to GISAID, which increased to [~]80% by 30th June 2021. Following this, analysis of another set of 1, 798 samples sequenced in India between November 2020 and May 2021 revealed that majority of the Delta (B.1.617.2) and Kappa (B.1.617.1) variations appeared as iSNVs before getting fixed in the population. We also observe hyper-editing events at functionally critical residues in Spike protein that could alter the antigenicity and may contribute to immune escape. Thus, tracking and functional annotation of iSNVs in ongoing genome surveillance programs could be important for early identification of potential variants of concern and actionable interventions. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=177 SRC="FIGDIR/small/417519v3_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@12b6ac2org.highwire.dtl.DTLVardef@16df897org.highwire.dtl.DTLVardef@dbbec2org.highwire.dtl.DTLVardef@c8de14_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2018

Bedsect: An integrated web server application to perform intersection, visualization and functional annotation of genomic regions from multiple datasets

A large number of genomic regions captured during next generation sequencing (NGS) data analyses are generally overlapped to answer a variety of biological questions. Though several command-line tools are available to perform such analysis, there is lack of a comprehensive web server application to perform the genomic region intersections from multiple datasets, to generate a plot for the subsets of the overlapped regions and to perform integrated functional annotation. To address this gap, we have developed a user-friendly integrated web server application i.e. Bedsect, where users can upload genomic regions from multiple datasets without any file number limitation and perform intersection analysis along with visualization of the intersection regions as UpSet and Correlation plot using integrated Shiny application. Bedsect also integrates GREAT for functional annotation, gene ontology, and biological pathways enrichment analysis from identified unique as well as intersected genomic regions. These genomic regions can be further uploaded in the UCSC genome browser for visualization of the results as custom tracks directly from the tool. Bedsect is available at http://imgsb.org/bedsect/.

bioinformatics↗