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Comparative Transcriptomic Analysis of Three Common Liver Cell Lines

Background: Comparative 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...

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Autores principales: Arzumanian, Viktoriia, Pyatnitskiy, Mikhail, Poverennaya, Ekaterina
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10218629/
https://www.ncbi.nlm.nih.gov/pubmed/37240140
http://dx.doi.org/10.3390/ijms24108791
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author Arzumanian, Viktoriia
Pyatnitskiy, Mikhail
Poverennaya, Ekaterina
author_facet Arzumanian, Viktoriia
Pyatnitskiy, Mikhail
Poverennaya, Ekaterina
author_sort Arzumanian, Viktoriia
collection PubMed
description Background: Comparative 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. Objective: This 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. Methods: Our 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. Results: We 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. Conclusion: Our 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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spelling pubmed-102186292023-05-27 Comparative Transcriptomic Analysis of Three Common Liver Cell Lines Arzumanian, Viktoriia Pyatnitskiy, Mikhail Poverennaya, Ekaterina Int J Mol Sci Article Background: Comparative 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. Objective: This 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. Methods: Our 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. Results: We 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. Conclusion: Our 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. MDPI 2023-05-15 /pmc/articles/PMC10218629/ /pubmed/37240140 http://dx.doi.org/10.3390/ijms24108791 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Arzumanian, Viktoriia
Pyatnitskiy, Mikhail
Poverennaya, Ekaterina
Comparative Transcriptomic Analysis of Three Common Liver Cell Lines
title Comparative Transcriptomic Analysis of Three Common Liver Cell Lines
title_full Comparative Transcriptomic Analysis of Three Common Liver Cell Lines
title_fullStr Comparative Transcriptomic Analysis of Three Common Liver Cell Lines
title_full_unstemmed Comparative Transcriptomic Analysis of Three Common Liver Cell Lines
title_short Comparative Transcriptomic Analysis of Three Common Liver Cell Lines
title_sort comparative transcriptomic analysis of three common liver cell lines
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10218629/
https://www.ncbi.nlm.nih.gov/pubmed/37240140
http://dx.doi.org/10.3390/ijms24108791
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