Study Finds Immortalized Liver Cell Lines Differ Significantly from Primary Tissue in Gene Regulation
Researchers used ATAC-seq to compare cis-regulatory elements (CREs) in four immortalized liver cell lines against primary liver tissue, finding substantial differences in chromatin accessibility, transcription factor binding, and gene regulation. Immortalized cell lines are a cornerstone of biomedical research due to their convenience and reproducibility, but prior work in blood and skin had already flagged discrepancies with primary cells. The findings raise concerns about the validity of conclusions drawn from liver cell line experiments, particularly those involving gene regulatory mechanisms.
A study posted to bioRxiv examined whether four commonly used immortalized liver cell lines accurately model the cis-regulatory element (CRE) landscape of primary human liver tissue. Using ATAC-seq, a technique that maps open chromatin regions where gene regulation occurs, the researchers identified widespread differences between each cell line and primary liver in terms of accessible CREs, the transcription factors predicted to bind them, and the downstream genes they likely regulate. Attempts to improve cell line fidelity by modifying culture conditions according to published recommendations did not meaningfully close the gap with primary tissue. These results extend earlier findings from blood and skin cell lines, suggesting the problem of regulatory network divergence is not tissue-specific but may be a general feature of immortalization. The authors caution that researchers should carefully consider these limitations when designing experiments or interpreting results obtained from liver cell lines. The work does not argue that cell lines are without value, but underscores the need for awareness of their regulatory differences from the tissues they are meant to model.
What's missing
As a preprint, the work has not yet undergone peer review, and the generalizability of the ATAC-seq findings to functional gene expression outcomes remains to be directly validated. The study also does not address whether newer 3D organoid or primary cell culture systems might better recapitulate the primary liver regulatory landscape.
What different sources said
- bioRxivCenter
Deciphering the limitations of immortalized hepatocyte cell lines for the study of liver cis-regulatory elements
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