ArticleInternational journal of molecular sciences2023
Comparative Transcriptomic Analysis of Three Common Liver Cell Lines.
Article in International journal of molecular sciences, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Cell line identity rather than medium composition determines transcriptomic profiles of HepaRG and HuH7 cells cultured in chemically defined or serum-based media: comparison with primary human hepatocytes.Archives of toxicology · 2026Article
- Longstanding Transcriptional Activation of APOA1 and PON1 in Human Hepatocytes by CRISPR/dCas9 Technology: Transcriptomic Profile and Crosstalk with Endothelial Cells.International journal of molecular sciences · 2026Article
- EvoRMD: integrating biological context and evolutionary RNA language models for interpretable prediction of RNA modifications.Genome biology · 2026Article
- Curcumin ameliorates hepatic insulin resistance by activating PINK1/Parkin-mediated mitophagy.Scientific reports · 2026Article
- Dual-specificity phosphatase 6 interferes with the repressive activity of forkhead box O1 towards CYP4A11 that mediates lipid accumulation in the liver.Scientific reports · 2026Article
- Three Noble Metal Nanoparticles Demonstrated Distinct Biological Interactions and Cell Death Pathways in Human Hepatocarcinoma Cell Lines.Nanotechnology, science and applications · 2026Article
- Evaluation of the Immortalized Primary Human Hepatocyte Cell Line Fa2N-4 as a Model for Metabolic Dysfunction-Associated Steatotic Liver Disease.Gastro hep advances · 2026Article
- Drug-Metabolizing Gene Expression Identity: Comparison Across Liver Tissues and Model Cell Lines.Biomedicines · 2025Article
- Optimizing Cell Density and Unveiling Cytotoxic Profiles of DMSO and Ethanol in Six Cancer Cell Lines: Experimental and In Silico Insights.Methods and protocols · 2025Article
- Establishment, identification, and transcriptome analysis of a Sertoli cell line from ovoviviparous black rockfish Sebastes schlegelii.Fish physiology and biochemistry · 2025Article
- Contrasting Effect of Curcumin on Hepatitis B Virus Replication According to the Hepatoma Cell Line.Pathogens (Basel, Switzerland) · 2025Article
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Authors and funding
3 authors.
Funding
Abstract
backgroundComparative transcriptomic analysis is a powerful approach for investigating the molecular mechanisms underlying various physiological and pathological processes, including liver disease. The liver is a vital organ with diverse functions, including metabolism and detoxification. In vitro models of liver cells, such as HepG2, Huh7, and Hep3B, have been widely used to study liver biology and pathology. However, there is limited information on the heterogeneity of these cell lines at the transcriptomic level.
objectiveThis study aimed to conduct a comparative transcriptomic analysis of three common liver cell lines (HepG2, Huh7, and Hep3B) using publicly available RNA-sequencing data. In addition, we compared these cell lines to primary hepatocytes, cells isolated directly from liver tissue and considered the gold standard for studying liver function and disease.
methodsOur study included sequencing data with the following criteria: total number of reads over 20,000,000, average read length of over 60 base pairs, Illumina sequencing, and non-treated cells. The data for the three cell lines were compiled: HepG2 (97 samples), Huh7 (39 samples), and Hep3B (16 samples). We performed differential gene expression analysis using the DESeq2 package, principal component analysis, hierarchical clustering on principal components, and correlation analysis to explore the heterogeneity within each cell line.
resultsWe identified numerous genes and pathways differentially expressed between HepG2, Huh7, and Hep3B, such as oxidative phosphorylation, cholesterol metabolism, and DNA damage. We report that the expression levels of important genes differ significantly between primary hepatocytes and liver cell lines.
conclusionOur study provides new insights into the transcriptional heterogeneity of commonly used liver cell lines and highlights the importance of considering specific cell line. Consequently, transferring results without considering the heterogeneity of cell lines is impractical and may lead to inaccurate or distorted conclusions.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.