Abstract 5560: A high-throughput cellular genetics approach to identifying genes associated with sorafenib response and toxicity
Authors: Daniel J. Crona, Oscar Suzuki, O. Joseph Trask, Amber Frick, Bethany Parks, Tim Wiltshire, Federico Innocenti
Journal: Cancer Research (2014)

Abstract Background: Sorafenib is an oral multikinase inhibitor, approved for hepatocellular, renal and thyroid carcinomas, which decreases tumor angiogenesis and proliferation. The antitumor efficacy and toxicity profiles of sorafenib vary among patients. No predictive biomarkers of sorafenib activity exist to help guide clinicians. Novel pathways and targets of sorafenib activity remain to be identified. We aimed to identify novel genes associated with sorafenib activity by using an in vitro methodology based upon mouse genomics. Methods: We profiled primary mouse embryonic fibroblasts (MEFs) from 32 inbred strains for sorafenib cytotoxicity utilizing high content imaging and simultaneous evaluation of cell health parameters. The 32 strains have been genomically characterized previously (PMID: 21623374). MEF cells were treated with varying concentrations (0-300 µM) of sorafenib, incubated for 24 h or 72 h, and then fixed and stained. Nuclear staining was used to assess sorafenib cytotoxicity and establish our cell viability phenotype. Dose response curves were generated from data, and EC50 values for each strain were identified using a Brain-Cousens model. Genome-wide association mapping, using the SNPster algorithm, was performed on cell viability EC50 values to identify quantitative trait loci (QTLs) associated with sorafenib cytotoxicity. Approximately 277,000 single nucleotide polymorphisms were tested, and genomic loci with p-values &amp;lt; 3.5x10-5 were selected for additional analyses. Results: Interstrain EC50 variability among the 32 MEF strains was observed after 24 h (21-121 µM) and 72 h (17-32 µM) sorafenib incubations. We identified three total peaks associated with cell viability: two on chromosome 13 (23 Mb apart; p = 3.4x10-5 and = 1.6x10-5, respectively), and one on chromosome 4 (p = 2.2x10-5). From these three peaks, we have identified candidate genes that may underlie variability in sorafenib cytotoxicity. A total of 16 genes expressed in MEF cells at mRNA level are present in these QTLs. Of particular interest, we identified one locus that contains Nfyc, a gene that encodes the C subunit of the NF-Y transcription factor. This transcription factor complex is conserved between humans and mice. In humans, NF-Y regulates MYC signaling and DNA-dependent transcription of PDGFR-β (a primary target of sorafenib) (PMID: 12167641). Conclusions: Our innovative high-throughput cellular genetics approach has identified three regions with genetic loci potentially associated with sorafenib cytotoxicity. This approach is capable of identifying robust interstrain cellular differences in sorafenib activity. Functional validation of Nyfc and other promising candidates should be conducted. Citation Format: Daniel J. Crona, Oscar Suzuki, O. Joseph Trask, Amber Frick, Bethany Parks, Tim Wiltshire, Federico Innocenti. A high-throughput cellular genetics approach to identifying genes associated with sorafenib response and toxicity. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5560. doi:10.1158/1538-7445.AM2014-5560