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Perturb-seq against putative NAFLD target genes in differentiated HepaRG cells

ABSTRACT: We used Perturb-seq to characterize the role of putative NAFLD genes prioritized from molecular human genetic studies in differentiated HepaRG cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE238219 | GEO | 2024/08/30

REPOSITORIES: GEO

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Project description:Inorganic arsenic, a ubiquitous environmental contaminant of food and drinking water, is a human carcinogen associated with lung, liver, prostate, renal, and bladder cancers. It has been postulated that inorganic arsenic targets stem cells or partially differentiated progenitor cells, causing their oncogenic transformation. This is proposed to be one of the key mechanisms in arsenic-associated carcinogenesis; however, the underlying mechanisms for this process remain largely unknown. To address this question, human liver HepaRG cells, at progenitor and differentiated states, were continuously treated with a non-cytotoxic concentration of 1 μM sodium arsenite (NaAsO2). Briefly, in Experiment 1, three days after the initial seeding, 1 μM NaAsO2 was added to the media and the cells were maintained in the NaAsO2-containing media for an additional 25 days. In Experiment 2, fourteen days after the initial seeding, 1 μM NaAsO2 was added to the media and the cells were maintained in the NaAsO2-containing media for an additional 14 days. In Experiment 1 and Experiment 2, control and NaAsO2-treated cells were harvested on the 28th day after the initial seeding. In Experiment 3, twenty-eight days after the initial seeding, the terminally-differentiated cells were treated continuously with 1 μM NaAsO2 for an additional 14 days and then harvested. Transcriptomic analysis of NaAsO2-treated progenitor-like HepaRG cells (Experiment 1 and Experiment 2) identified 743 and 639 differentially expressed genes, respectively, among which 343 genes were expressed in common. Pathway analysis of common differentially expressed genes demonstrated a substantial inhibition of cellular metabolic pathways, mainly lipid and xenobiotic metabolism, and cell death pathways. In contrast, cell proliferation, cell survival, and inflammation, were substantially activated. Treatment of differentiated HepaRG cells with NaAsO2 (Experiment 3) resulted in prominent gene expression changes, with a total of 1058 transcripts being significantly different from the control HepaRG cells. Pathway analysis of differentially expressed genes in NaAsO2-treated cells differentiated HepaRG cells showed activation of cellular death-associated pathways and inhibition of cell survival and cell proliferation.

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Perturb-seq against putative NAFLD target genes in differentiated HepaRG cells

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