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Culturing of primary mouse hepatocytes is associated with major changes to the proteome and transcriptome

ABSTRACT: Primary hepatocytes are a commonly used in vitro model for studying liver metabolism, but prolonged culturing results in dedifferentiation. Here we characterized the transcriptome and proteome of whole liver and primary hepatocytes as either freshly isolated cells or after 24 hours of 2D-culturing. We found that after 24 hours of 2D-culturing, hepatocytes showed differential expression of over 10,000 genes and 3,000 proteins compared to freshly isolated cells. This was accompanied by a reduced transcriptional heterogeneity and a loss of zonal markers. Cultures contained ~10% non-hepatocytes, including stellate- and dedifferentiated endothelial cells. Culturing also increased abundance of proteins associated with oxidative stress and inflammation, and changed mitochondrial, extracellular, and ribosomal protein abundance. The data generated are available in the shiny-app “Hepamorphosis”. Our finding show that primary mouse hepatocytes undergo significant changes in culture, limiting theirutility for studying physiological and molecular mechanisms related to the liver.

INSTRUMENT(S):

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Hepatocyte, Liver

SUBMITTER: Ben Stocks

LAB HEAD: Jonas T. Treebak

PROVIDER: PXD068742 | Pride | 2025-09-25

REPOSITORIES: Pride

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			Action	DRS
	20210930_PRI_TIMS4_PRIEvo1_P094_R0275_44min_S10_S2-D10_1_2795.d.rar	Other
	20210930_PRI_TIMS4_PRIEvo1_P094_R0275_44min_S11_S2-D11_1_2796.d.rar	Other
	20210930_PRI_TIMS4_PRIEvo1_P094_R0275_44min_S12_S2-D12_1_2797.d.rar	Other
	20210930_PRI_TIMS4_PRIEvo1_P094_R0275_44min_S13_S2-E1_1_2798.d.rar	Other
	20210930_PRI_TIMS4_PRIEvo1_P094_R0275_44min_S14_S2-E2_1_2799.d.rar	Other

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