Assessing the basal gene expression of cancer cell lines for in vitro transcriptomic toxicology screening

ABSTRACT In vitro toxicology has used immortalized cancer cell lines as model human systems for decades. However, these cell lines pose problems in designing toxicity testing programs as they inherently do not represent normal human biology. There is also a huge number of such cell lines to choose from, derived from human cancer cells from nearly every tissue. We explored the idea of using available basal gene expression data (NCI-60 cell line panel and Human GTEx tissue data) to determine if there was sufficient variability in cell line gene expression to group cell lines by relevance to specific human tissues. The transcriptomic analysis suggests that the variability in gene expression in cancer cell lines and in normal human tissue is minimal. The overall basal gene expression of cancer cells lines even overlapped normal human tissue gene expression. While some human tissues (e.g., lung) have basal expression profiles that do not appear to be like any cancer cell line, including cancers that may be derived from the same tissue, most human tissues show basal expression profiles comparable to several cancer cell lines. These results are important to address the genomic baseline and variability of cancer cell lines used for new approach methods of toxicity testing.