Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: To investigate the spatial dynamics of immune cells in the liver, particularly myeloid cells, we utilized the Xenium spatial transcriptomics platform to examine gene zonation patterns in pediatric and adult livers. We explored the expression of 477 genes in two pediatric and three adult livers (one adult sampled 3 times, for a total of 7 Xenium samples). Our analysis revealed significant zonation of gene expression within Kupffer cells (KC-like). The zonation of KC-like marker genes suggests that the differential gene expression observed in the dissociated pediatric liver map may be due to shifts in the spatial organization of KC-like cells in the pediatric liver. These findings underscore the importance of spatial transcriptomics in understanding age-related differences in immune cell behavior within the liver and provide new insights into the complex spatial dynamics of myeloid cells in pediatric versus adult livers.

ORGANISM(S): Homo sapiens

PROVIDER: GSE286254 | GEO | 2025/04/21

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	GSE286254_RAW.tar	Raw
	GSE286254_Xenium_panel_Human_Multi_Tissue_plus_Liver.csv.gz	Csv
	filelist.txt	Txt

Items per page:

1 - 4 of 4

Similar Datasets

Perturbed liver gene zonation in a mouse model of non-alcoholic steatohepatitis

Project description:Liver zonation characterizes the separation of metabolic pathways along the lobules and is required for optimal hepatic function. Wnt signaling is a master regulator of spatial liver zonation. A perivenous-periportal Wnt activity gradient orchestrates metabolic zonation by activating genes in perivenous hepatocytes, while suppressing genes in their periportal counterparts. The understanding of liver gene zonation and zonation regulators in disease was limited. Non-alcoholic steatohepatitis (NASH) is a chronic liver disease characterized by fat accumulation, inflammation, and fibrosis. Here, we investigated the perturbation of liver gene zonation in a mouse NASH model by combination of spatial transcriptomics, bulk RNAseq and in situ hybridization. Wnt target genes represented a major subset of genes showing altered spatial expression in the NASH liver. The altered Wnt target gene expression level and zonation spatial pattern were in line with the upregulation of Wnt regulators and the augmentation of Wnt signaling. Particularly, we found that the Wnt activator Rspo3 expression was restricted to the perivenous zone in control livers, whereas expanded to the periportal zone in NASH livers. AAV8-mediated RSPO3 overexpression in controls resulted in a zonation change, and further amplified the disturbed zonation of Wnt target genes in NASH, but had no impacts on steatosis, inflammation and fibrosis. In summary, our study demonstrated the alteration of Wnt signaling in a mouse NASH model, leading to perturbed liver zonation.

2024-08-01 | GSE248077 | GEO

miRNA expression in spatially-sorted hepatocytes

Project description:The mammalian liver is composed of repeating hexagonal units termed lobules. Spatially-resolved single-cell transcriptomics revealed that about half of hepatocyte genes are differentially expressed across the lobule. Technical limitations impede reconstructing similar global spatial maps of other hepatocyte features. Here, we used zonated surface markers to sort hepatocytes from defined lobule zones with high spatial resolution. We applied transcriptomics, miRNA array measurements and Mass spectrometry proteomics to reconstruct spatial atlases of multiple zonated hepatocyte features. We found that protein zonation largely overlapped mRNA zonation, with the periportal HNF4α as an exception. We identified zonation of miRNAs such as miR-122, and inverse zonation of miRNAs and their hepatocyte target genes, implying potential regulation through zonated mRNA degradation. These targets included the pericentral Wnt receptors Fzd7 and Fzd8 and the periportal Wnt inhibitors Tcf7l1 and Ctnnbip1. Our approach facilitates reconstructing spatial atlases of multiple cellular features in the liver and other structured tissues.

2019-07-26 | GSE134827 | GEO

Enhanced Spatial Transcriptomics Analysis of Mouse Lung Tissues Revealed Cell-Specific Gene Expression Changes Associated with Pulmonary Hypertension

Project description:We developed a method that utilizes floating mounting of thin sections of fixed frozen mouse lung tissue onto Xenium slides for the fluorescent in situ hybridization (FISH) and imaging–based spatial transcriptomics analysis of gene expression using the Xenium platform provided by 10X Genomics. Spatial transcriptomics techniques provide a comprehensive view by merging gene expression data with spatial context within their native tissue architecture. However, the Xenium pipeline has been validated only for formalin-fixed paraffin-embedded (FFPE) and fresh frozen sections by 10X Genomics. Notably, many researchers prefer paraformaldehyde-fixed cryosections for immunohistochemistry and in situ hybridization. In our study, we assessed the compatibility of standard fixed frozen mouse lung sections with the Xenium protocol. Our findings reveal that these sections not only align well with the Xenium platform but also offer superb imaging and gene expression quantification, even with limited number of genes in the Xenium panel. This protocol can serve as a valuable resource for preparing various tissues where FFPE and fresh frozen samples present challenges.

2024-09-30 | GSE277936 | GEO

Single-cell transcriptomics uncovers zonation of function in the mesenchyme during liver fibrosis

Project description:We profile the transcriptomes of ~30,000 mouse single cells to deconvolve the hepatic mesenchyme in healthy and fibrotic liver at high resolution. We reveal spatial zonation of hepatic stellate cells across the liver lobule, designated portal vein-associated HSC and central vein-associated HSC, and uncover an equivalent functional zonation in a mouse model of centrilobular fibrosis. Our work illustrates the power of single-cell transcriptomics to resolve key collagen-producing cells driving liver fibrosis with high precision.

2019-11-01 | GSE137720 | GEO

Kolbe2019 - Spatio-temporal liver zonation

Project description:Metabolism of the adult liver in mice and human is spatially zonated with hepatocytes along the axis from each portal vein to the nearest central vein expressing enzymes in a zonated manner. Upstream of that functional zonation, interactions of Wnt and Hh signaling are orchestrating and self-organizing the spatial expression patterns. This spatio-temporal model is derived from experimental data and explores the interacting signaling pathways. To run this model, use the free, open-source software Morpheus (download for Windows, macOS, Linux from https://morpheus.gitlab.io).

2021-09-30 | MODEL2009110001 | BioModels

A single-cell atlas of the woodchuck liver maps an immune landscape and hepatocyte zonation patterns reflective of the human liver [spatial transcriptomics]

Project description:The mammalian liver plays important roles in metabolism, detoxification, immune responses, and in severe liver disease in which transplantation is often the only therapeutic option. Model organisms that allow for the longitudinal examination of liver disease progressions are pivotal for the development of new therapeutic modalities. The eastern North American woodchuck is such a model organism that develops chronic hepatitis and liver cancer after infection with woodchuck hepatitis virus, which closely models the human disease. However, the cellular landscape of the woodchuck liver remains unmapped. In this study, we applied single-cell RNA sequencing to profile matched liver and blood from eight healthy woodchucks, performed spatial transcriptomics to examine zonation and annotated these data via a high-quality woodchuck genome reference that we generated. Here, we report woodchuck transcriptomic cell atlases of 63,389 cells from eight healthy woodchuck livers, 26,972 cells from seven healthy woodchuck PBMC samples, and spatial transcriptomics results for two liver slices from one woodchuck, where we observed expected hepatic cellular diversity comparable to human and murine livers. Furthermore, we assessed the inflammatory potential of woodchuck liver resident immune cells through single-nucleus RNA sequencing of PMA/ionomycin-stimulated precision cut liver slices (9,208 nuclei). Our study provides a map of the woodchuck liver, analogous to the human liver map, as a resource for the field to support future studies in this model organism.

2025-04-08 | GSE264107 | GEO

A single-cell atlas of the woodchuck liver maps an immune landscape and hepatocyte zonation patterns reflective of the human liver [scRNA-seq]

2025-04-08 | GSE264104 | GEO

A single-cell atlas of the woodchuck liver maps an immune landscape and hepatocyte zonation patterns reflective of the human liver [snRNA-seq]

2025-04-08 | GSE264112 | GEO

Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches (spatial)

Project description:Analysis of CITE-seq data , Nuclei RNA-seq data and single cell RNA-seq data on CD45+ and CD45- cells isolated from the livers of mice fed a standard diet (SD) or western diet (WD; fat, cholesterol and sugar), from healthy and steatotic human livers, from hamster liver, pig liver, chicken liver, monkey liver and zebrafish liver. We also performed Spatial Transcriptomics analysis on heatlhy mouse livers, NAFLD mouse livers, healthy human livers and steatotic human livers.

2022-01-11 | GSE192741 | GEO

Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches (single cells)

2022-01-11 | GSE192740 | GEO