Biology subjects

Agarwala, S.

Publications and source records attributed to Agarwala, S..

4 recordsLinked to original sources

bioRxiv2025

Vcam1 in endothelial and stromal cells regulates hematopoietic stem cell contact with the niche

Hematopoietic stem and progenitor cells (HSPCs) are essential for differentiation into all blood cell types. In mammals, the interaction between HSPCs and the fetal liver niche during development is critical for stem cell maturation. Integrin alpha 4 (Itga4) on HSPCs and vascular cell adhesion molecule (Vcam1) on niche cells are critical for HSPC colonization of the fetal liver (FL). Itga4 and Vcam1 also function in the zebrafish equivalent of the FL, the caudal hematopoietic tissue (CHT), however, the specific niche cells that express Vcam1 remain unclear. Using multiple approaches, including fluorescent in situ hybridization, we found Vcam1 is expressed in endothelial cells (ECs) and mesenchymal stromal cells (MSCs), but not macrophages. Time-lapse live imaging of itga4 mutants showed the Itga4-Vcam1 axis is required for HSPC retention in the CHT niche, but not homing or lodgment. Our results show that Itga4 on HSPCs and Vcam1 on ECs and MSCs are involved in retention in the CHT niche. SummaryBlood stem cell interaction with the niche microenvironment during development is critical for establishing a robust stem cell pool into adulthood. This study determines the niche cell types that present Vcam1 in the embryo and allow interaction with blood stem cells.

developmental biology↗

bioRxiv2024

Quantitative analyses of structure-function heterogeneity of individual mitochondrial components reveal an early role of small-mitochondrial-networks in priming neoplastic transformation

Lack of quantitative understanding of the marked heterogeneity of multifaceted mitochondria poses challenges in unraveling their translatable role. Here, we hierarchically untangled multilevel heterogeneity of mitochondrial networks and non-networks by simultaneously analysing their structure-function within single components and their units, in cells and tissues. Such mito-SinComp quantitative analyses revealed that redox levels of mitochondrial networks and their dramatic intra-network heterogeneity can be predicted by structural features through a translatable machine-learning approach. Mito-SinComp identified and quantitatively characterized a redox-tuned subpopulation of Small-Mitochondrial-Networks(SMNs) that specifies stemness. These SMNs are generated by severing of nodes of oxidized Hyperfused-Mitochondrial-Networks(HMNs), are ten-folds smaller with specific network complexity and elevated mt-DNA nucleoid abundance. Thus, HMN to SMN conversion supports elevated expression of mtDNA genes in establishing MT-ND1(redox)-KRT15(stemness) transcriptomic interaction, as revealed by coupled scRNA-seq. This stemness priming of non-transformed cells is sustained after neoplastic transformation and is detected in patient transcriptome, demonstrating translational relevance of SMNs.

cell biology↗

bioRxiv2021

RFX6-mediated dysregulation defines human β cell dysfunction in early type 2 diabetes

A hallmark of type 2 diabetes (T2D), a major cause of world-wide morbidity and mortality, is dysfunction of insulin-producing pancreatic islet {beta} cells1-3. T2D genome-wide association studies (GWAS) have identified hundreds of signals, mostly in the non-coding genome and overlapping {beta} cell regulatory elements, but translating these into biological mechanisms has been challenging4-6. To identify early disease-driving events, we performed single cell spatial proteomics, sorted cell transcriptomics, and assessed islet physiology on pancreatic tissue from short-duration T2D and control donors. Here, through integrative analyses of these diverse modalities, we show that multiple gene regulatory modules are associated with early-stage T2D {beta} cell-intrinsic defects. One notable example is the transcription factor RFX6, which we show is a highly connected {beta} cell hub gene that is reduced in T2D and governs a gene regulatory network associated with insulin secretion defects and T2D GWAS variants. We validated the critical role of RFX6 in {beta} cells through direct perturbation in primary human islets followed by physiological and single nucleus multiome profiling, which showed reduced dynamic insulin secretion and large-scale changes in the {beta} cell transcriptome and chromatin accessibility landscape. Understanding the molecular mechanisms of complex, systemic diseases necessitates integration of signals from multiple molecules, cells, organs, and individuals and thus we anticipate this approach will be a useful template to identify and validate key regulatory networks and master hub genes for other diseases or traits with GWAS data.

cell biology↗

bioRxiv2020

Defining the ultrastructure of the hematopoietic stem cell niche by correlative light and electron microscopy

The blood system is supported by hematopoietic stem and progenitor cells (HSPCs) found in a specialized microenvironment called the niche. Many different niche cell types support HSPCs, however how they interact and their ultrastructure has been difficult to define. Here we show that single endogenous HSPCs can be tracked by light microscopy, then identified by serial block-face scanning electron microscopy (SBEM) at multiscale levels. Using the zebrafish larval kidney marrow (KM) niche as a model, we followed single fluorescently-labeled HSPCs by light sheet microscopy, then confirmed their exact location in a 3D SBEM dataset. Our approach allowed us to identify dopamine beta-hydroxylase (dbh) positive ganglia cells as a previously uncharacterized functional cell type in the HSPC niche. By integrating multiple imaging modalities, we could resolve the ultrastructure of single rare cells deep in live tissue and define all contacts between an HSPC and its surrounding niche cell types.

developmental biology↗