Biology subjects

Mukhopadhyay, P.

Publications and source records attributed to Mukhopadhyay, P..

6 recordsLinked to original sources

bioRxiv2023

Integrative proteomics and transcriptomics of human T-cells reveals temporal metabolic reprogramming following TCR-induced activation

T-cells are critical components of the adaptive immune system. Upon activation, they acquire effector functions through a complex interplay between mRNA transcripts and proteins, the landscape of which remains to be fully elucidated. In this resource article, we present an integrative temporal proteomic and transcriptomic analysis of primary human CD4+ and CD8+ T-cells following ex vivo activation with anti-CD3/CD28 Dynabeads. Our data reveal a time-dependent dissociation between the T-cell transcriptome and proteome during activation. A transient downregulation of GLUT1, the central glucose transporter in T-cells, marked the onset of reprogramming in both CD4+ and CD8+ T-cells. At late activation, CD4+ T-cells upregulated enzymes associated with degradation of fatty acids while CD8+ T-cells preferentially upregulated enzymes in the metabolism of cofactors and vitamins. Surprisingly, we found that activated CD4+ and CD8+ T-cells became transcriptionally more divergent at the same time their proteome became more similar. In addition to the metabolic reprogramming highlighted in our analysis, this dataset provides a public resource for understanding temporal molecular changes governing the acquisition of effector functions by T-cells.

systems biology↗

bioRxiv2021

The miR-424/503 cluster modulates Wnt/β-catenin signaling in the mammary epithelium by regulating the expression of the LRP6 co-receptor

During the female lifetime, the enlargement of the epithelial compartment dictated by the ovarian cycles is supported by a transient increase in the MaSC population. Notably, activation of Wnt/{beta}-catenin signaling is an important trigger for MaSC expansion. Here, we report that the miR-424/503 cluster is a novel modulator of canonical Wnt-signaling in the mammary epithelium that exerts its function by targeting the LRP6 co-receptor. Additionally, we show that the loss of this microRNA cluster is associated with breast cancers possessing high levels of Wnt/{beta}-catenin signaling.

cancer biology↗

bioRxiv2020

Single-cell analysis identifies TCF4 and ID3 as a molecular switch of mammary epithelial stem cell differentiation.

It is well known that the expansion of the mammary epithelium during the ovarian cycles in female mammals is supported by the transient increase in mammary epithelial stem cells (MaSCs). However, dissecting the molecular mechanisms that govern MaSC function and differentiation is poorly understood due to the lack of standardized methods for their identification and isolation. The development of robust single-cell mRNA sequencing () technologies and the computational methods to analyze them provides us with novel tools to approach the challenge of studying MaSCs in a completely unbiased way without. Here, we have performed the largest scRNA-seq analysis of individual mammary epithelial cells (~70,000 cells). Our study identified a distinct cell population presenting molecular features of MaSCs. Importantly, further purification and additional in-depth single-cell analysis of these cells revealed that they are not a fully homogenous entity. Instead, we identified three subpopulations representing early stages of lineage commitment. By tracking their molecular evolution through single-cell network analysis we found that one of these subpopulations represents bipotent MaSCs from which luminal and basal lineages diverge. Importantly, we also confirmed the presence of these cells in human mammary glands. Finally, through expression and network analysis studies, we have uncovered transcription factors that are activated early during lineage commitment. These data identified E2-2 (Tcf4) and ID3 as a potential molecular switch of mammary epithelial stem cell differentiation.

developmental biology↗

bioRxiv2020

Th2-like T-follicular helper cells promote functional antibody production during Plasmodium falciparum infection

The most advanced malaria vaccine only has approximately 30% efficacy in target populations, and avenues to improve next generation vaccines need to be identified. Functional antibodies are key effectors of both vaccine induced and naturally acquired immunity, with induction driven by T-follicular helper cells (TfH) CD4+ T cells. We assessed circulating TfH (cTfH) responses and functional antibody production in human volunteers experimentally infected with Plasmodium falciparum. Longitudinal single-cell RNA-sequencing of cTfH revealed peak transcriptional activation and clonal expansion of major cTfH subsets occurred at day 8 following infection and a population structure of cTfH capturing phenotypical subsets of Th1- and Th2-like cells. Among 40 volunteers, infection resulted in the emergence of activated ICOS+ cTfH cells. During peak infection, activation was restricted to Th2-like cTfH cells, while Th1-like cTfH cell activation occurred one week after treatment. To link cTfH activation to antibody induction, we assessed the magnitude and function of anti-malarial IgM and IgG after infection. The functional breadth and magnitude of parasite-specific antibodies was positively associated with Th2-cTfH activation. In contrast, Th1-cTfH activation was associated with the induction of plasma cells, which we have previously shown have a detrimental role in germinal cell formation and antibody development. Thus, we identified that during P. falciparum malaria infection in humans, the activation of Th2-cTfH but not other subsets correlates with the development of functional antibodies required for protective immunity. Data for the first time identify a specific cellular response that can be targeted by future malaria vaccines to improve antibody induction.

immunology↗

bioRxiv2019

Chromatin interactome mapping at 139 independent breast cancer risk signals

Genome-wide association studies have identified 196 high confidence independent signals associated with breast cancer susceptibility. Variants within these signals frequently fall in distal regulatory DNA elements that control gene expression. We designed a Capture Hi-C array to enrich for chromatin interactions between the credible causal variants and target genes in six human mammary epithelial and breast cancer cell lines. We show that interacting regions are enriched for open chromatin, histone marks for active enhancers and transcription factors relevant to breast biology. We exploit this comprehensive resource to identify candidate target genes at 139 independent breast cancer risk signals, and explore the functional mechanism underlying altered risk at the 12q24 risk region. Our results demonstrate the power of combining genetics, computational genomics and molecular studies to rationalize the identification of key variants and candidate target genes at breast cancer GWAS signals.

molecular biology↗

bioRxiv2018

Different genetic mechanisms mediate spontaneous versus UVR-induced malignant melanoma

Genetic variation conferring resistance and susceptibility to carcinogen-induced tumorigenesis is frequently studied in mice. We have now turned this to melanoma using the collaborative cross (CC), a resource of mouse strains designed to discover genes for complex diseases. We studied melanoma-prone transgenic progeny across seventy CC genetic backgrounds. We mapped a strong quantitative trait locus for rapid onset spontaneous melanoma onset to Prkdc, a gene involved in detection and repair of DNA damage. In contrast, rapid onset UVR-induced melanoma was linked to the ribosomal subunit gene Rrp15. Ribosome biogenesis was upregulated in skin shortly after UVR exposure, Mechanistically, variation in the \"usual suspects\" by which UVR may exacerbate melanoma, defective DNA repair, melanocyte proliferation, or inflammatory cell infiltration, did not explain melanoma susceptibility or resistance across the CC. Instead, events occurring soon after exposure, such as dysregulation of ribosome function, which alters many aspects of cellular metabolism, may be important.

cancer biology↗