Abstract 5175: Mutational and copy number profiling of cancer-related genes in 26 human tumor xenografts and their correlations with antitumor drug sensitivities
Authors: Kobunai Takashi , Tsunekuni Kenta , Matsuoka Kazuaki , Tsukihara Hiroshi , Takechi Teiji 
Published: July 2016

Abstract
Background: Tumor responses to antitumor drugs are variable, but predicting these responses is important when selecting effective chemotherapy treatments. Our aim was to identify variations or alterations in gene copy number that influence cancer cells’ susceptibilities to standard chemotherapeutic agents. Methods: Twenty-six human cancer cell lines representing the five main tumor types were subcutaneously implanted into nude mice and tested for sensitivity to fluorinated pyrimidines (UFT, TS-1, 5’-DFUR, and capecitabine), CDDP, CPT-11, and paclitaxel. The cell lines included lung (AOI, LC-11, Lu-99, LX-1, LC-6, Lu-134, Lu-130), colon (KM12C, KM12C/FU, HCT-15, COL-1, CO-3), pancreas (PAN-3, PAN-4, PAN-12, H-48, MIAPaCa-2, BxPC-3), gastric (SC-2, ST-40, 4-1ST, SC-4) and breast (MC-2, MX-1, MDA-MB-435SHM, MDA-MD-231). Genomic DNA was prepared from frozen tumor tissues. Mutations in 48 genes from the TruSeq Amplicon Cancer Panel were screened using the MiSeq system (Illumina, San Diego, CA). Somatic copy number alterations were analyzed by high-density SNP arrays (Affymetrix, Santa Clara, CA). Results: Of the 225 amplicons (187 non-overlapping regions) in the cancer panel, 86% achieved a minimum average sequencing depth of 1000X and the average coverage across all target regions was 5374X. In 26 tumors, sequencing detected 55 somatic mutations in 18 out of 48 cancer related genes of high prognostic or therapeutic significance, such as TP53, APC, PTEN, and SMAD4. Mutation frequencies across 26 xenografts were 73.1% (TP53), 38.5% (KRAS), 15.4% (APC), 11.5% (SMAD4 and RET), 7.7% (BRAF, GNAS, and PTEN), and 3.8% (CTNNB1, GNAQ, HNF1A, HRAS, IDH1, KIT, NOTCH1, PIK3CA, SMO, and STK11). Tumor xenografts with TP53 mutations were significantly less sensitive to CDDP and CPT-11 than wild-type cell lines (P&lt;0.05). The APC mutation conferred resistance to paclitaxel. Copy number gain was observed at 23.1% (KRAS), 15.1% (EGFR), and 11.5% (JAK2 and CDK2NA). Copy number loss was observed at 30.8% (CDK2NA), 19.2% (SMAD4), and 15.4% (PTEN). Cell lines with more copies of CDK2NA and JAK2 were more sensitive to CDDP, while cell lines with fewer copies of PTEN were more sensitive to CDDP. Similarly, copy number gain of CDH1 conferred resistance to UFT, while copy number gain of KRAS sensitized tumors to 5’-DFUR. The copy number of 48 genes determined by the GeneChip array moderately agreed with those estimated by local GC-content adjusted coverage profiles in the sequencing analysis (average Pearson's correlation coefficient = 0.66, 95%CI = 0.54-0.69). Conclusions: Integrated analysis of mutational profiling and gene copy number may be useful to elucidate candidate genes influencing susceptibility of cancer cells to antitumor drugs.
Citation Format: Takashi Kobunai, Kenta Tsunekuni, Kazuaki Matsuoka, Hiroshi Tsukihara, Teiji Takechi. Mutational and copy number profiling of cancer-related genes in 26 human tumor xenografts and their correlations with antitumor drug sensitivities. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5175.