Gene Expression Data Explorer
Info Gene counts are sourced from ARCHS4, which provides uniform alignment of GEO samples. You can learn more about ARCHS4 and its pipeline here.
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GROUP CONDITION SAMPLES
epcam+ cells
GSM6725659 GSM6725660 GSM6725661 GSM6725662 GSM6725663 GSM6725664 GSM6725665
GSM6725654 GSM6725655 GSM6725656 GSM6725657 GSM6725658
Description

Submission Date: Nov 10, 2022

Summary: Background and Aims: During severe or chronic hepatic injury, biliary epithelial cells (BECs), also known as cholangiocytes, undergo rapid reprogramming and proliferation, a process known as ductular reaction (DR), and allow liver regeneration by differentiating into both functional cholangiocytes and hepatocytes. While DR is a hallmark of chronic liver diseases, including advanced stages of non-alcoholic fatty liver disease (NAFLD), the early events underlying BEC activation are largely unknown. Since NAFLD initiates with increased lipid accumulation, a stage called steatosis; we hypothesized that BECs isolated directly from steatotic livers might address current knowledge gaps in early BEC activation.

Approach and Results: Here, we used methods allowing isolation and extensive transcriptional characterization of BECs from chow diet (CD)- and high-fat diet (HFD)-fed mice livers. We demonstrate that BECs readily accumulate lipids during HFD feeding and that lipid overload induces the conversion of adult cholangiocytes into active BECs through upregulation of the cell cycle and DNA replication signature. This event is accompanied by significant downregulation of extracellular matrix organization in BECs derived from HFD-fed mice livers but not CD-fed mice livers. Mechanistically, we found that lipid overload unleashes the activation of the E2F transcription factors in BECs, which drives cell cycle progression.

GEO Accession ID: GSE217739

PMID: 36876915

Description

Submission Date: Nov 10, 2022

Summary: Background and Aims: During severe or chronic hepatic injury, biliary epithelial cells (BECs), also known as cholangiocytes, undergo rapid reprogramming and proliferation, a process known as ductular reaction (DR), and allow liver regeneration by differentiating into both functional cholangiocytes and hepatocytes. While DR is a hallmark of chronic liver diseases, including advanced stages of non-alcoholic fatty liver disease (NAFLD), the early events underlying BEC activation are largely unknown. Since NAFLD initiates with increased lipid accumulation, a stage called steatosis; we hypothesized that BECs isolated directly from steatotic livers might address current knowledge gaps in early BEC activation.

Approach and Results: Here, we used methods allowing isolation and extensive transcriptional characterization of BECs from chow diet (CD)- and high-fat diet (HFD)-fed mice livers. We demonstrate that BECs readily accumulate lipids during HFD feeding and that lipid overload induces the conversion of adult cholangiocytes into active BECs through upregulation of the cell cycle and DNA replication signature. This event is accompanied by significant downregulation of extracellular matrix organization in BECs derived from HFD-fed mice livers but not CD-fed mice livers. Mechanistically, we found that lipid overload unleashes the activation of the E2F transcription factors in BECs, which drives cell cycle progression.

GEO Accession ID: GSE217739

PMID: 36876915

Visualize Samples

Info Visualizations are precomputed using the Python package scanpy on the top 5000 most variable genes.

Precomputed Differential Gene Expression

Info Differential expression signatures are automatically computed using the limma R package. More options for differential expression are available to compute below.

Signatures:

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Control Condition

Perturbation Condition

Only conditions with at least 1 replicate are available to select

Differential Gene Expression Analysis
Info Differential expression signatures can be computed using DESeq2 or characteristic direction.
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Bulk RNA-seq Appyter

This pipeline enables you to analyze and visualize your bulk RNA sequencing datasets with an array of downstream analysis and visualization tools. The pipeline includes: PCA analysis, Clustergrammer interactive heatmap, library size analysis, differential gene expression analysis, enrichment analysis, and L1000 small molecule search.