Network-guided multi-omics characterizes stress-associated transcriptional and metabolic alterations in PFOA-exposed HK-2 proximal tubular cells.

Abstract

Perfluorooctanoic acid (PFOA) is a persistent per- and polyfluoroalkyl substance that undergoes active renal handling, yet the molecular response of proximal tubular cells remains poorly resolved. We integrated network toxicology with matched RNA sequencing and untargeted LC-MS metabolomics in PFOA-exposed HK-2 cells, then compared the resulting model with an external rat kidney transcriptome, public perturbation signatures and cellular assays. The network analysis yielded 657 kidney-relevant candidates. RNA sequencing identified 407 upregulated and 443 downregulated genes, with induction of ATF4-DDIT3-TRIB3 and redox-related genes and repression of E2F, G2-M, mitotic-spindle and DNA-replication programs. Annotation-audited metabolomics retained 61 exploratory responsive features (7 increased and 54 decreased), showing nominal shifts involving nucleotide, amino-acid and carbon-energy intermediates. Cross-platform prioritization highlighted TRIB3, CDKN1A, SLC7A11, ATF3, DDIT3, HMOX1 and SQSTM1. External WGCNA and perturbation-signature analyses showed partial transcriptomic concordance with the main stress, metabolic and cell-cycle patterns. In concentration-group validation experiments, PFOA increased apoptosis, G0/G1 accumulation and lipid peroxidation, lowered EdU incorporation and the GSH/GSSG ratio, and induced the prioritized genes. These data define a PFOA-responsive proximal-tubule stress program accompanied by redox imbalance, exploratory metabolic shifts and proliferative restraint.