Biology subjects

Camat, D.

Publications and source records attributed to Camat, D..

4 recordsLinked to original sources

bioRxiv2025

A Single-Cell Atlas Of Human Pediatric Liver Reveals Age-Related Hepatic Gene Signatures

Background & AimsThe liver plays a critical role in metabolism and immune function, yet the contributions of its heterogeneous cell types to these processes remain unclear. While most liver studies focus on adults, pediatric liver diseases often present differently, underscoring the need for age-specific research. Approach & ResultsTo better understand cellular drivers of childhood liver diseases, we generated single-cell RNA-seq (scRNA-seq) maps of the normal pediatric liver and used this map to examine disease-related populations in biopsies from pediatric patients with Intestinal Failure-Associated Liver Disease (IFALD). The normal pediatric liver map consists of 42,660 cells from 9 donors aged 2-17 years. Compared to normal adult liver (26,372 cells; 7 donors, age 26-69) pediatric livers exhibited differences in myeloid populations. Specifically, pediatric Kupffer-like cells (MARCO+C1QA+VSIG4+) exhibited higher expression of immune activation genes, including CCL4, CCL3 and IL1B. In vitro stimulation confirmed more IL1-{beta} secreting myeloid cells in pediatric versus adult livers, supporting these findings. Using the pediatric atlas as a reference, we analyzed three IFALD biopsies (11,969 cells; 3 donors, ages 4 months-9 years) and identified increased expression of fibrosis-associated genes (e.g., LY96) in Kupffer-like cells. Additionally, mesenchymal cells in IFALD showed fibrotic gene modules resembling adult liver cells more than healthy pediatric cells. These signatures, undetectable when comparing IFALD to adult liver alone, highlighting the value of a pediatric map. ConclusionsTaken together, our healthy pediatric liver atlas reveals distinct age-related signatures and provides background against which to interpret pediatric liver disease data. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=194 SRC="FIGDIR/small/649149v2_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@8d4131org.highwire.dtl.DTLVardef@1b336d2org.highwire.dtl.DTLVardef@d43ddeorg.highwire.dtl.DTLVardef@29fadf_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2025

A Single-Cell Woodchuck Liver Atlas Identifies Healthy and Disease-Related Cellular Programs Conserved in Human

BackgroundModel organisms allowing for longitudinal examinations of liver disease pathogenesis are pivotal for the development of new therapeutic modalities. The eastern North American woodchuck develops chronic hepatitis and liver cancer after woodchuck hepatitis virus (WHV) infection, mirroring aspects of the natural history of the human hepatitis B virus (HBV). However, the cellular landscape of the woodchuck liver and the cell-level relevance of WHV infection to HBV infection is currently uncharacterized. MethodsWe employed single-cell RNA sequencing (RNA-seq) to generate an atlas of healthy woodchuck liver (63,389 cells, n=8) and peripheral blood mononuclear cells (PBMCs) (26,972 cells, n=7). Cell-specific and hepatic zonation gene signatures were validated using spatial transcriptomics (n=1). We employed our atlas to examine immune activation in stimulated precision cut-liver slices (PCLS) and disease-related pathway activation in chronic WHV infection (11,797 cells, n=3). We further employed our atlas to examine shared disease pathways between WHV infection and human HBV infection. ResultsOur atlas revealed woodchuck hepatic cellular diversity comparable to human and murine livers. Applying single-nucleus RNA-seq to PMA/ionomycin-stimulated precision cut liver slices revealed inflammation-associated activation signatures in T cell, myeloid and endothelial cell compartment. Finally, we describe intrahepatic T cells in chronic WHV hepatitis with both exhaustion and activation-associated signatures that resemble intrahepatic T cell genes signatures described in human chronic HBV. ConclusionsWe present a multi-omic atlas of healthy, diseased and ex vivo stimulated woodchuck liver. By identifying shared pathological processes between WHV and HBV infections, our findings reinforce the value of this preclinical model in translational research. This resource aims to advance studies on HBV pathogenesis and oncogenesis to speed the development of novel therapeutic strategies. Impact and Implications/Lay summaryThe liver plays important roles in metabolism, detoxification, and immune processes; liver transplantation is often the only treatment option for severe chronic liver diseases. Therefore, developing animal models that reflect human liver disease and can be studied throughout the disease course is crucial for the discovery of new treatment options. The woodchuck is an animal that develops chronic hepatitis and liver cancer after infection with woodchuck hepatitis virus, which models the human hepatitis type B virus infection (HBV) and associated hepatic carcinoma. However, our understanding of the cells that compose the woodchuck liver is limited, making it challenging to design and test cell-based therapeutics. In this study, we atlased the healthy and chronically infected woodchuck liver, found that liver cell types in woodchuck resemble those in humans, and employed the atlas to show similarities between WHV and HBV at the cell level, reinforcing the potential of WHV-infected woodchuck as a model for human HBV disease. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=196 SRC="FIGDIR/small/641192v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@18fdd40org.highwire.dtl.DTLVardef@6ccf2org.highwire.dtl.DTLVardef@7923e1org.highwire.dtl.DTLVardef@122a8d2_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2023

Single-cell and spatial transcriptomics reveals the human liver immunological landscape and myeloid dysfunction in PSC.

BackgroundPrimary sclerosing cholangitis (PSC) is an immune-mediated cholestatic liver disease characterized by bile retention, biliary tree destruction, and progressive fibrosis leading to end stage liver disease and transplantation. There is an unmet need to understand the cellular composition of the PSC liver and how it underlies disease pathogenesis. As such, we generated a comprehensive atlas of the PSC liver and a reference healthy liver dataset using multiple multi-omic modalities and functional validation. MethodsIn this work, we employed single-cell (12,000 cells), single-nuclei (23,000 nuclei), and spatial transcriptomics (1 sample by 10x Visium and 3 samples with multi-region profiling by Nanostring GeoMx DSP) to profile the cellular ecosystem in 5 patients with PSC. Transcriptomic profiles were compared to 100k single cell transcriptomes and spatial transcriptomics controls from 24 healthy neurologically deceased donor (NDD) livers. Flow cytometry and intracellular cytokine staining was performed to validate PSC-specific differences in immune phenotype and function. ResultsPSC explants with cirrhosis of the liver parenchyma and prominent periductal fibrosis were associated with a unique population of hepatocytes which transformed to a cholangiocyte-like phenotype. These hepatocytes were surrounded by diverse immune cell populations, including monocyte-like macrophages, liver-resident and circulating natural killer (NK) cells. Inflamed cholangiocytes, fibrosis-resident hepatic stellate cells, and endothelial cells released cytokines that recruited CD4+T-cells, dendritic cells, and neutrophils to the PSC liver. Tissue-resident macrophages, by contrast, were reduced in number and exhibited a dysfunctional inflammatory response to LPS and IFN-{gamma} stimulation. ConclusionsWe present the first comprehensive atlas of the PSC liver and demonstrate hyper-activation and exhaustion-like phenotypes of myeloid cells and markers of chronic cytokine expression in late-stage PSC lesions. Lay SummaryPrimary sclerosing cholangitis (PSC) is a rare liver disease characterized by chronic inflammation and irreparable damage to the bile ducts. Due to a limited understanding of the underlying pathogenesis of disease, there remains a paucity of treatment options. As such, we sequenced healthy and diseased livers to compare the activity, interactions, and localization of immune and non-immune cells. This revealed that outside PSC scar regions, hepatocytes are transitioning to bile duct cells, whereas within the scars, there is an accumulation of immune cells. Of these cells, macrophages that typically contribute to tissue repair were enriched in immunoregulatory genes and were less responsive to stimulation. These cells are likely involved in maintaining hepatic inflammation and could be targeted in novel therapeutic development.

cell biology↗

bioRxiv2022

Single cell profiling reveals strain-specific differences in myeloid inflammatory potential in the rat liver

Liver transplantation is currently the only treatment for end-stage liver disease and acute liver failure. Liver transplant rejection is among the most lethal complications of transplantation, and therapeutic development is limited by our lack of a comprehensive understanding of the cellular landscape of the liver. The laboratory rat (Rattus norvegicus), ideal in size as a model for surgical procedures, is a strong platform to study liver biology in the context of liver transplantation. Liver allograft rejection is known to be strain-specific in the rat model, although the transplantation is accepted without rejection in some strains, it leads to acute rejection in others. To shed light on the cellular landscape of the rat liver and build a foundation for strain comparison, we present a comprehensive single-cell transcriptomics map of the healthy rat liver of Lewis and Dark Agouti strains. Using a novel computational pipeline we developed to guide the detailed annotation of our rat liver atlas, we discovered that hepatic myeloid cells have strong Lewis and Dark Agouti strain-specific differences focused on inflammatory signaling pathways. We experimentally validated these strain-specific differences in myeloid inflammatory potential in vitro using intracellular cytokine staining. Our work provides the first examination of the multi-strain healthy rat liver by single cell transcriptomics and uncovers key insights into strain-specific differences in this valuable model animal. SummaryThe laboratory rat (Rattus norvegicus) is a standard model animal for orthotopic liver transplantation. Transplanting a liver from a Dark agouti (DA) to a Lewis (LEW) strain rat leads to transplant rejection and the reverse procedure leads to tolerance. Understanding this strain difference may help explain the cellular drivers of liver allograft rejection post-transplant. This study uses single-cell transcriptomics to better understand the complex cellular composition of the rat liver and unravels cellular and molecular sources of inter-strain hepatic variation. We generated single-cell transcriptomic maps of the livers of healthy DA and LEW rat strains and developed a novel, factor analysis-based bioinformatics pipeline to study data covariates, such as strain and batch. Using this approach, we discovered variations within hepatocyte and myeloid populations that explain how the states of these cells differ between strains in the healthy rat, which may explain why these strains respond differently to liver transplants.

genomics↗