Spatial transcriptomics analysis of mouse liver tissue during Alcohol-associated liver disease development and resolution
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE304111 | GEO | 2025/08/20
REPOSITORIES: GEO
Similar Datasets
Project description:Abstinence is beneficial for patients with alcohol-associated liver disease (ALD), but disease resolution after alcohol cessation occurs slowly and only in a subset of patients. Mechanisms of fibrosis resolution in ALD are not yet fully understood. Previous work highlights the importance of liver niche remodeling around areas of fibrosis that involves protein and metabolite mediated cell-cell crosstalk between hepatocytes and non-parenchymal cells. We aimed to study the mechanisms of ALD resolution using spatial transcriptomics. We found that retinoic acid metabolism strongly associated with improved fibrosis resolution in a mouse model of ALD. In agreement with this finding, mice treated with RAR agonist AM580 after alcohol cessation showed improved fibrosis resolution. Spatial transcriptomics analysis of agonist treated mice and controls suggested that RAR activation dramatically altered liver niches thus promoting pro-resolving changes in liver cells.
2026-03-23 | GSE320403 | GEO
Project description:Alcohol-associated liver disease (ALD) affects millions of people worldwide, while pharmacological therapies are limited. CCAAT/enhancer binding protein α (CEBPA) in hepatocytes is known to regulate the progression of liver fibrosis; however, the role of hepatocyte-specific CEBPA in modulating the ALD progression is still unknown. Here, hepatic CEBPA expression was found to be decreased during ALD progression in humans. CebpaΔHep mice had enhanced ALD induced both in short-term and long-term alcohol feeding. Temporal and spatial hepatocyte-specific CEBPA loss at the later stage of ALD in CebpaΔHep,ERT2 mice functionally promoted ALD. Mechanistically, hepatocyte CEBPA loss directly deactivated Orm1 expression in hepatocytes that resulted in reduced secretion of ORM1 and enhancement of ALD progression. Both hepatocyte ORM1 expression and serum ORM1 levels were found to be negatively correlated with the ALD progression in humans, while loss of hepatocyte ORM1 in mice sharply enhanced ALD. Both forced hepatocyte-specific CEBPA overexpression and hepatocyte-specific ORM1 overexpression by adeno-associated viruses rescued the progression of ALD in CebpaΔHep mice. Notably, treatment of recombinant ORM1 protein improved the progression of ALD in CebpaΔHep mice. These results reveal a key role for hepatocyte-specific CEBPA-ORM1 axis in ALD progression, which supports hepatocyte CEBPA to be a novel therapeutic target for the treatment of ALD.
2026-03-03 | GSE291057 | GEO
Project description:Abstinence is an important therapeutic intervention for patients with alcohol-associated liver disease (ALD). However, fibrosis improvement after cessation is not uniform and some patients do not improve. We aimed to use scATAC-seq analysis in a mouse model of ALD to define the mechanism of poor ALD resolution. We analyzed differentially accessible regions in livers from control, ALD, or 4 weeks post alcohol cessation mice and identified transcription factors activated in ALD that remained activated after alcohol withdrawal. The top hit was C/EBPβ. We found that hepatocyte specific Cebpb knockout prevented ALD development, while knockout at the time of alcohol cessation promoted fibrosis resolution.
2024-09-12 | GSE276692 | GEO
Project description:A comprehensive understanding of the fetal liver niche during development offers a lens into a unique natural multifunctional multicellular environment. Here we use a spatial transcriptomic and histologic analysis approach to identify and histologically confirm RNA-based markers in human fetal liver tissue within a key developmental window in which the liver is a major site of hematopoiesis, just prior to the increased growth phase of the final trimester. Within this window, the fetal liver niche encompasses the unique coexistence of cells of both endodermal and mesenchymal origin with the unique environment fostering hematopoietic cell development as well as hepatocyte function. Single-cell resolution spatial imaging reveals epithelial, hematopoietic, endothelial, and stromal cell populations in shared cellular microenvironments. Here, our single-cell spatial transcriptomic and imaging approach enables, captures, and confirms the complex phenomena of ductal plate expression and CXCL12 homing to the hematopoietic stem cell niche (HSC) in the liver. An RNA-based understanding of the functional diversity and in situ spatial organization of the fetal liver niche is critical for adequate validation and authentication in recapitulating and re-engineering these regenerative environments in vitro.
2026-02-27 | GSE306606 | GEO
Project description:Background: Alcohol-associated hepatitis (AH) is the clinical manifestation of alcohol-associated liver disease (ALD). AH is a complex disease encompassing the dysregulation of many cells and cell subpopulations. This study used a hepatic spatial transcriptomic and proteomic approach (10X Genomics Visium) to identify hepatic cell populations and their associated transcriptomic and proteomic alterations in human AH. Methods: Formalin fixed parraffin embedded liver tissue from AH patients (n=2) and non-ALD controls (donors) (n=2) were used for Visium spatial transcriptomic and proteomic analysis. Results: AH cell clusters and cell markers were drastically different in regard to tissue pattern and number of cell type as compared to non-ALD controls. Cholangiocytes, endothelial cells, macrophages, and stellate cells were more profuse in AH relative to non-ALD controls. Transcriptionally, proliferating cell nuclear antigen positive (PCNA+) hepatocytes in AH more closely resembled cholangiocytes suggesting they were non-functional hepatocytes derived from cholangiocytes. Further, mitochondria protein coding genes were reduced in AH vs non-ALD control hepatocytes, suggesting reduced functionality and loss of regenerative mechanisms. Macrophages in AH exhibited elevated gene expression involved in exosomes as compared to non-ALD controls. The most upregulated macrophage genes observed in AH were those involved in exosome trafficking and cellular migration. Gene and protein signatures of disease associated hepatocytes (ANXA2+/CXCL1+/CEACAM8+) were elevated in AH and could visually identify a pre-malignant lesion. Conclusions: This study identified global cell type alterations in AH and distinct transcriptomic changes between AH and non-ALD controls. These findings characterizes cellular plasticity and profuse transcriptomic and proteomic changes that are apparent in AH and contributes to the identification of novel therapeutics.
2024-12-02 | GSE278662 | GEO
Project description:Liver fibrosis is a major cause of death worldwide. As a progressive step in chronic liver disease, fibrosis is almost always diagnosed too late with limited treatment options. Here, we uncover the spatial transcriptional landscape driving human liver fibrosis using single nuclei RNA and Assay for Transposase-Accessible Chromatin (ATAC) sequencing to deconvolute multi-cell spatial transcriptomic profiling in human liver cirrhosis.Through multi-modal data integration,we define molecular signatures driving cell state transitions in liver disease and define an impaired cellular response and directional trajectory from hepatocytes to cholangiocytes associated with disease remodelling.We identifypro-fibrogenic signatures in non-parenchymal cell subpopulations co-localised within the fibrotic niche and localise transitional cell states at the scar interface. This combined approach providesa spatial atlas of gene regulation and defines molecular signatures associated liver diseasefor targeted therapeutics or as early diagnostic markers of progressive liver disease. This is the 10X Visium data for the work.
2025-03-14 | E-MTAB-13132 | biostudies-arrayexpress
Project description:Liver fibrosis is a major cause of death worldwide. As a progressive step in chronic liver disease, fibrosis is almost always diagnosed too late with limited treatment options. Here, we uncover the spatial transcriptional landscape driving human liver fibrosis using single nuclei RNA and Assay for Transposase-Accessible Chromatin (ATAC) sequencing to deconvolute multi-cell spatial transcriptomic profiling in human liver cirrhosis.Through multi-modal data integration,we define molecular signatures driving cell state transitions in liver disease and define an impaired cellular response and directional trajectory from hepatocytes to cholangiocytes associated with disease remodelling.We identifypro-fibrogenic signatures in non-parenchymal cell subpopulations co-localised within the fibrotic niche and localise transitional cell states at the scar interface. This combined approach providesa spatial atlas of gene regulation and defines molecular signatures associated liver diseasefor targeted therapeutics or as early diagnostic markers of progressive liver disease. This is the 10X Visium data for the work.
2025-04-04 | E-MTAB-14960 | biostudies-arrayexpress
Project description:Alcohol-associated liver disease (ALD) is a major cause of alcohol related mortality. Recently we identified hepatic demethylases KDM5B and KDM5C as important sex-specific epigenetic regulators of alcohol response in the liver. In this study we aimed to study the molecular mechanisms of KDM5-dependent ALD development and resolution. We found that alcohol induces pathological changes in cell-cell communication in the liver that are in part mediated by epigenetic changes in hepatocytes mediated by histone demethylase KDM5B. Using cell type specific knockout mice, we found that KDM5B histone demethylase was a key regulator of alcohol-induced epigenetic changes in hepatocytes. Moreover, it regulated hepatocytes-non-parenchymal cell crosstalk that promoted inflammation and fibrosis development in ALD. This mechanism was specific to females. In males KDM5B deficiency was not sufficient to prevent fibrosis development. In contrast KDM5B demethylase loss promoted fibrosis resolution in both males and females. This mechanism involved changes in hepatocyte-macrophage crosstalk and LXRα activation, which we identified to be critical for the fibrosis resolution process. CONCLUSION: In summary, KDM5B demethylase is a regulator of cell-cell crosstalk involved in disease progression in females and in disease resolution in both sexes.
2023-10-07 | GSE244240 | GEO
Project description:Nicotinamide mononucleotide adenylyltransferase 1 (NMNAT1), an NAD+ synthetase in Preiss-Handler and salvage pathways, governs nuclear NAD+ homeostasis. This study investigated the role of NMNAT1 on alcohol-associated liver disease (ALD). Decreased NMNAT1 expression and activity were observed in the liver of alcohol-associated hepatitis patients and either liver or primary hepatocytes from ALD mice. F-box and WD repeat domain containing 7 (FBXW7)-regulated interferon regulatory factor 1 (IRF1) ubiquitination degradation contributed to alcohol-inhibited NMNAT1 transcriptional level. Hepatic NMNAT1 knockout aggravated alcohol-induced hepatic NAD+ decline and further hepatic steatosis and liver injury. Metabolomics and transcriptomics interaction revealed that cysteine sulfinic acid decarboxylase (CSAD)-regulated taurine pathway was involved in NMNAT1-disrupted hepatic lipid metabolism in ALD. Hepatic CSAD overexpression or taurine supply attenuated hepatic NMNAT1 knockout-aggravated ALD, respectively. Hepatic NMNAT1 loss inhibited NMN-protected ALD. Replenishing hepatic NMNAT1 reversed liver lipid accumulation in ALD mice. These findings identified NMNAT1 as a promising therapeutic target for ALD.
2025-05-25 | GSE297696 | GEO
Project description:Spatial transcriptomics analysis of mouse liver tissue during Alcohol-associated liver disease development and resolution
| PRJNA1298930 | ENA