Spatial Recovery of the Hepatic Lobule Using Single Cell RNA Sequencing
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE116140 | GEO | 2018/07/17
REPOSITORIES: GEO
Similar Datasets
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
Project description:Liver zonation characterizes the separation of metabolic pathways along the lobules and is required for optimal function. Wnt/beta-catenin signaling controls metabolic zonation by activating genes in the perivenous hepatocytes, while suppressing genes in the periportal counterparts. We now demonstrate that glucagon opposes the actions of Wnt/beta-catenin signaling on gene expression and metabolic zonation pattern. The effects were more pronounced in the periportal hepatocytes where 28% of all genes were activated by glucagon and inhibited by Wnt/beta-catenin. The glucagon and Wnt/beta-catenin receptors and their signaling pathways are uniformly distributed in periportal and perivenous hepatocytes and the expression is not regulated by the opposing signal. Collectively, our results show that glucagon controls gene expression and metabolic zonation in the liver through a counter play with the Wnt/beta-catenin signaling pathway.
2018-03-01 | GSE110673 | GEO
Project description:Liver zonation characterizes the separation of metabolic pathways along the lobules and is required for optimal function. Wnt/beta-catenin signaling controls metabolic zonation by activating genes in the perivenous hepatocytes, while suppressing genes in the periportal counterparts. We now demonstrate that glucagon opposes the actions of Wnt/beta-catenin signaling on gene expression and metabolic zonation pattern. The effects were more pronounced in the periportal hepatocytes where 28% of all genes were activated by glucagon and inhibited by Wnt/beta-catenin. The glucagon and Wnt/beta-catenin receptors and their signaling pathways are uniformly distributed in periportal and perivenous hepatocytes and the expression is not regulated by the opposing signal. Collectively, our results show that glucagon controls gene expression and metabolic zonation in the liver through a counter play with the Wnt/beta-catenin signaling pathway.
2018-03-01 | GSE110672 | GEO
Project description:The structural-functional organization of ammonia and glutamine metabolism in the liver acinus involves highly specialized hepatocyte subpopulations such as glutamine producing perivenous scavenger cells. However, it is still unclear whether this cell population is homogeneous and involves further subpopulations. This was investigated in the present study by proteome profiling of periportal glutamine synthetase-negative hepatocytes and perivenous glutamine synthetase (GS) expressing scavenger cells isolated from mouse and rat liver. Apart from established markers of GS+ hepatocytes such as glutamate transporter 1 (GLT1), ornithine aminotransferase (OAT) or ammonium transporter Rh type B (RHBG), we identified novel scavenger cell-specific proteins such as the basal transcription factor 3 (BTF3) and the heat-shock protein 25 (HSP25). Interestingly, BTF3 and HSP25 were heterogeneously distributed among GS+ hepatocytes as shown by immunofluorescence analyses in mouse, rat and human liver slices. Feeding experiments showed that RHBG but not GS protein levels were increased in the liver of mice fed with a high protein diet compared to standard chow. While the spatial distribution of GS and carbamoylphosphate synthetase-1 (CPS1) was not affected, periportal areas constituted by GLS2 positive hepatocytes were enlarged or reduced in response to high or low protein diet, respectively. The data suggest that the population of perivenous GS+ scavenger cells is heterogeneous and not uniform as previously suggested which may reflect a functional heterogeneity, possibly relevant for liver regeneration.
2021-08-05 | PXD023561 | Pride
Project description:Verma2016 - Ca(2+) Signal Propagation Along Hepatocyte Cords
This model is described in the article:
Computational Modeling of
Spatiotemporal Ca(2+) Signal Propagation Along Hepatocyte
Cords.
Verma A, Makadia H, Hoek JB,
Ogunnaike BA, Vadigepalli R.
IEEE Trans Biomed Eng 2016 Oct; 63(10):
2047-2055
Abstract:
The purpose of this study is to model the dynamics of
lobular Ca(2+) wave propagation induced by an extracellular
stimulus, and to analyze the effect of spatially systematic
variations in cell-intrinsic signaling parameters on sinusoidal
Ca(2+) response.We developed a computational model of lobular
scale Ca(2+) signaling that accounts for receptor- mediated
initiation of cell-intrinsic Ca(2+) signal in hepatocytes and
its propagation to neighboring hepatocytes through gap
junction-mediated molecular exchange.Analysis of the
simulations showed that a pericentral-to-periportal spatial
gradient in hormone sensitivity and/or rates of IP3 synthesis
underlies the Ca(2+) wave propagation. We simulated specific
cases corresponding to localized disruptions in the graded
pattern of these parameters along a hepatic sinusoid.
Simulations incorporating locally altered parameters exhibited
Ca(2+) waves that do not propagate throughout the hepatic
plate. Increased gap junction coupling restored normal Ca(2+)
wave propagation when hepatocytes with low Ca(2+) signaling
ability were localized in the midlobular or the pericentral
region.Multiple spatial patterns in intracellular signaling
parameters can lead to Ca(2+) wave propagation that is
consistent with the experimentally observed spatial patterns of
Ca(2+) dynamics. Based on simulations and analysis, we predict
that increased gap junction-mediated intercellular coupling can
induce robust Ca(2+) signals in otherwise poorly responsive
hepatocytes, at least partly restoring the sinusoidally
oriented Ca (2+) waves.Our bottom-up model of agonist-evoked
spatial Ca(2+) patterns can be integrated with detailed
descriptions of liver histology to study Ca(2+) regulation at
the tissue level.
This model is hosted on
BioModels Database
and identified by:
MODEL1603110003.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2024-09-02 | BIOMD0000000834 | BioModels
Project description:Hepatocytes of the mammalian liver are organized in liver lobules and operate in a spatially-dependent manner. Cells in different positions along the lobule’s porto-cenrtal axis, defined by the directionality of blood flow, express different genes and perform different liver tasks. Gradients of the transcriptome along liver lobule axis has been recently established, yet not for the hepatocyte proteome. We used two surface markers whose levels are inversely zonated – CD73 with a decreasing gradient from pericentral to periportal hepatocytes and E-cadherin with increasing gradient from portal to central hepatocytes. By staining for both surface markers, we efficiently isolated bulk populations of hepatocytes from distinct lobule layers by Fluorescence Activated Cell Sorting (FACS). Over all, we sorted 100,000 hepatocytes from each of eight spatially distinct populations, from five different mice. Cells were washed, digested by trypsin and subjected to LC-MS/MS. More cells from same populations from the same mice were also collected for mRNA sequencing and microRNA microarray profiling, to achieve a multi-omic view on spatially sorted hepatocytes, for better understanding of the transcriptomic and post-transcriptomic levels of regulation of liver zonation.
2019-08-06 | PXD014512 | Pride
Project description:Hepatocellular carcinomas (HCCs) exhibit a diversity of molecular phenotypes, raising major challenges in clinical management. HCCs detected by surveillance programs at an early stage are candidates for potentially curative therapies (local ablation, resection, or transplantation). In the long term, transplantation provides the lowest recurrence rates. Treatment allocation is based on tumor number, size, vascular invasion, performance status, functional liver reserve, and the prediction of early (<2 years) recurrence, which reflects the intrinsic aggressiveness of the tumor. Well-differentiated, potentially low-aggressiveness tumors form the heterogeneous molecular class of nonproliferative HCCs, characterized by an approximate 50% beta-catenin mutation rate. To define the clinical, pathological, and molecular features and the outcome of nonproliferative HCCs, we constructed a 1,133-HCC transcriptomic metadata set and validated findings in a publically available 210-HCC RNA sequencing set. We show that nonproliferative HCCs preserve the zonation program that distributes metabolic functions along the portocentral axis in normal liver. More precisely, we identified two well-differentiated, nonproliferation subclasses, namely periportal-type (wild-type beta-catenin) and perivenous-type (mutant beta-catenin), which expressed negatively correlated gene networks. The new periportal-type subclass represented 29% of all HCCs; expressed a hepatocyte nuclear factor 4A-driven gene network, which was down-regulated in mouse hepatocyte nuclear factor 4A knockout mice; were early-stage tumors by Barcelona Clinic Liver Cancer, Cancer of the Liver Italian Program, and tumor-node-metastasis staging systems; had no macrovascular invasion; and showed the lowest metastasis-specific gene expression levels and TP53 mutation rates. Also, we identified an eight-gene periportal-type HCC signature, which was independently associated with the highest 2-year recurrence-free survival by multivariate analyses in two independent cohorts of 247 and 210 patients. CONCLUSION: Well-differentiated HCCs display mutually exclusive periportal or perivenous zonation programs. Among all HCCs, periportal-type tumors have the lowest intrinsic potential for early recurrence after curative resection. (Hepatology 2017;66:1502-1518).
2023-07-25 | GSE237977 | GEO
Project description:Human pluripotent stem cells (hPSCs) offer a unique cellular model to study lineage specifications of the primary germ layers during human development. We profiled single-cell RNA-seq (scRNA-seq) on four lineage-specific progenitor cells derived from hESCs. Our scRNA-seq analyses revealed each type of progenitors display various extend of heterogeneity. Specifically, definitive endoderm cells (DECs) not only show a greater degree of heterogeneity, but are also enriched in metabolic signatures. Followed by detailed temporal scRNA-seq profiling along DEC differentiation, we reconstructed a differentiation trajectory using a novel statistical pipeline named Wave-Crest. Wave-Crest further identifies candidate regulators during the transitioning phase from Brachyury (T)+ mesendoderm towards CXCR4+ DEC state. To functionally test identified novel regulators; we generated a live cell monitoring system, a T-2A-EGFP knock-in reporter cell line via CRISPR/CAS9. We demonstrated that, among the top candidate genes, KLF8 plays a pivotal role modulating mesendoderm to DEC differentiation. In this submission, 1810 raw fastq files are provided; 212 are re-analysis from GSE64016. Four expected count matrices are provided - 1) 1018 single cells from snapshot progenitors; 2) 758 single cells from time couse profiling; 3) 19 bulk RNA-seq sample from snapshot progenitors; 4) 15 bulk RNA-seq sample from time course profiling. Total 1018 single cells from snapshot progenitors and 758 single cells from time couse profiling. Matchd population bulk RNA-seq samples for both the progenitors snapshot (19 samples) and time course profiling (15 samples) also included in this submission. These data set are used to detect the transitioning phase from mesendoderm to definitive endoderm.
2016-07-21 | E-GEOD-75748 | biostudies-arrayexpress
Project description:The primitive streak emerges during the 14th day of human development and establishes dorsoventral and antero-posterior (craniocaudal) body axes. Segmentation along the craniocaudal axis is governed by Hox genes; four clusters of transcription factors whose 3’ to 5’ expression correlates with position along the axis. The precise utilisation of Hox genes in different cell types remains incompletely characterised in humans. In this study, we applied single-cell and spatial transcriptomics to contiguous regions of the human fetal spine between the 5th and 13th post-conception weeks. We built a detailed developmental atlas to examine the segmental expression of Hox genes across different cell types, observing that the Hox code was displayed by all anatomically fixed cell types along the craniocaudal axis. By contrast, mature derivatives of neural crest cells retained the anatomical Hox code of their origin within the crest, a pattern reproduced across neural crest derivatives in other human fetal organs. These findings indicate that scars of Hox gene expression persist in crest cells which may serve as barcodes of neural crest migration.
| EGAD00001009801 | EGA
Project description:Abstract from Vermillion et al: During vertebrate development, progenitor cells give rise to tissues and organs through a complex choreography that commences at gastrulation. A hallmark event of gastrulation is the formation of the primitive streak, a linear assembly of cells along the anterior-posterior (AP) axis of the developing organism. To examine the primitive streak at a single-cell resolution, we measured the transcriptomes of individual chick cells from the streak or the surrounding tissue (the rest of the area pellucida) in Hamburger-Hamilton stage 4 embryos. The single-cell transcriptomes were then ordered by the statistical method Wave-Crest to deduce both the relative position along the AP axis and the prospective lineage of single cells. The ordered transcriptomes reveal intricate patterns of gene expression along the primitive streak.
2018-04-18 | GSE89910 | GEO