High-throughput Transcriptomics Screen of 137 Per- and Polyfluoroalkyl Substances (PFAS) in U-2 OS Cells

High-throughput transcriptomics (HTTr) was undertaken to quantify and characterize the biological effects of chemicals observed in human-derived in vitro test systems. A set of 137 structurally diverse PFAS was tested using the HTTr assay in the human-derived cell type U-2 OS (osteosarcoma). The PFAS studies were carried out as a part of a larger screening study of a total of 1323 chemicals. Chemicals were randomized to treatment plates (cells plus media) in triplicate. Plates also contained reference treatments for quality control purposes. The TempO-Seq human whole transcriptome assay (Yeakley et al., 2017) was used to identify biological pathway altering concentrations (BPACs) and characterize the biological activity of test chemicals. For this analysis, a catalog of 11,037 gene expression signatures collated from multiple public sources were analyzed using concentration-response modeling of signature enrichment scores determined using single-sample gene set enrichment analysis (ssGSEA) (Barbie et al. 2009) with DESeq2-moderated fold change values as input (Love et al. 2014). A sample was considered active if 25 or more signatures were concentration-responsive and the BPAC was calculated as the 5th percentile of benchmark concentrations (BMCs) of active signatures.