Concentration- and duration-associated transcriptional changes in HepG2 cells following long-term nominal nanomolar...

Perfluorooctanoic acid (PFOA) is a persistent environmental contaminant whose transcriptional effects under prolonged low-dose exposure remain insufficiently characterized. We investigated transcriptomic responses in HepG2 cells exposed to nominal PFOA concentrations of 1, 10, or 100nM for 6- or 12-weeks using RNA-seq, differential expression analysis, Gene Ontology enrichment, gene set enrichment analysis (GSEA), and weighted gene co-expression network analysis (WGCNA). No differentially expressed genes (DEGs) were detected at 1nM PFOA at either time point. At 10nM and 100nM PFOA, respectively, 149 and 183 DEGs were identified after 6 weeks, predominantly downregulated, compared with 10 and 56 DEGs after 12 weeks. The 6-week response included induction of immediate-early genes (FOS, EGR1) and repression of transcriptional and developmental regulators. At 12 weeks, six downregulated genes, including FOS, FOSB, and PLA2G2A, were shared between concentrations, with no shared upregulated genes. GSEA showed negative enrichment of transcriptional and developmental gene sets at both time points, whereas protein folding and stress response gene sets were enriched only at 6 weeks. WGCNA identified one dominant concentration-associated module at 6 weeks and several smaller modules at 12 weeks, most showing preservation across exposure durations. Together, these findings demonstrate concentration- and duration-associated transcriptional differences following prolonged nanomolar PFOA exposure, while the underlying biological mechanisms and potential contributions of culture-associated changes require further investigation.