Baseline Gene Expression in Human Derived Cell Lines

Many research organizations are exploring the use of high-throughput profiling (HTP) assays such as transcriptomics and image-based phenotypic profiling for in vitro bioactivity screening and hazard evaluation of chemicals. HTP assays can be used to characterize the response of many human-derived cell types to chemicals. However, no cell-based in vitro model will express all the potential molecular targets and pathways that are present in the human body that could be perturbed, resulting in toxicity. Therefore, an envisioned approach for the use of HTP assays in chemical bioactivity screening involves panels of cell lines that express complementary (partially non-overlapping) sets of molecular targets. In this study, baseline gene expression in 53 different human-derived cell lines was characterized using the TempO-Seq human whole transcriptome assay. The cell line set included 36 human cancer-derived cell lines and 17 engineered or spontanously immortalized human cell lines. The baseline gene expression data can inform what set(s) of molecular targets are expressed across the cell line collection and inform researchers regarding the choice of cell lines for chemical screening studies.