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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| Format: | Article |
| Language: | English |
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MDPI AG
2023-05-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/10/8791 |
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| author | Viktoriia Arzumanian Mikhail Pyatnitskiy Ekaterina Poverennaya |
| author_facet | Viktoriia Arzumanian Mikhail Pyatnitskiy Ekaterina Poverennaya |
| author_sort | Viktoriia Arzumanian |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-11T03:40:05Z |
| format | Article |
| id | doaj.art-e35f38d6232f4aeebcbdc917bbe870b5 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-11T03:40:05Z |
| publishDate | 2023-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-e35f38d6232f4aeebcbdc917bbe870b52023-11-18T01:42:07ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-05-012410879110.3390/ijms24108791Comparative Transcriptomic Analysis of Three Common Liver Cell LinesViktoriia Arzumanian0Mikhail Pyatnitskiy1Ekaterina Poverennaya2Institute of Biomedical Chemistry, 119121 Moscow, RussiaInstitute of Biomedical Chemistry, 119121 Moscow, RussiaInstitute of Biomedical Chemistry, 119121 Moscow, RussiaBackground: 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.https://www.mdpi.com/1422-0067/24/10/8791liver cell linesHepG2Huh7Hep3BRNAseq |
| spellingShingle | Viktoriia Arzumanian Mikhail Pyatnitskiy Ekaterina Poverennaya Comparative Transcriptomic Analysis of Three Common Liver Cell Lines International Journal of Molecular Sciences liver cell lines HepG2 Huh7 Hep3B RNAseq |
| 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 | liver cell lines HepG2 Huh7 Hep3B RNAseq |
| url | https://www.mdpi.com/1422-0067/24/10/8791 |
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