Abstract 2981: The epithelial to mesenchymal transition (EMT) produces colorectal cancer subpopulations with strikingly different mutation profiles

Abstract

Abstract The epithelial-mesenchymal transition (EMT) has been well-recognized as an important mechanism promoting cancer cell invasion and “stemness”, metastasis and therapeutic resistance. While the EMT-related differential gene expression has been extensively elucidated, genetic understanding of this process in cancer is largely lacking. Using unsupervised analysis, we previously identified an “intrinsic” differential gene expression signature in colorectal cancer (CRC) that was prognostic and highly correlated (p = 10−134) to EMT. Thus, we hypothesized that whole exome sequencing (WES), guided by gene expression phenotype, might identify mutations underpinning the EMT program. We first sorted 2144 CRC tumors based on their assigned degree (scores) of EMT. Ten tumors from the bottom 15% of tumors and nine tumors from the top 15% of tumors were selected, with paired normal control tissues. The WES data were then processed to identify non-synonymous SNVs, indels and LOH. We observed a striking difference in the mean number of variation per tumor (p<10−4) for those with low (epithelial-like) vs. high (mesenchymal-like) EMT scores (low = 282 vs. high = 3). Further analysis suggests that there may be two subpopulations in the low EMT tumors − those with >400 mutations (4/10, avg. 608) that were subsequently confirmed for microsatellite instability (MSI) status through BAT testing where indels in TGFBR2 were seen often with BRAF mutations (3/4); those with 12-144 mutations (6/10, avg. 65), which still demonstrated significant increases in mutation accounts compared to the high EMT tumors (0-5 mutations, avg. 2.8). Surprisingly, unlike their low EMT counterparts, the high EMT tumors displayed almost no known driver gene mutations (except a TP53 mutation observed in one high EMT sample with p<0.01). This potentially important finding was confirmed by analysis of another 468 CRC tumors that underwent targeted exome sequencing of 1321 cancer-related genes; that is, tumors in the subgroup lacking mutations of common driver genes such as APC (truncated mutations), KRAS, TP53 and BRAF (V600E) had significantly higher EMT scores compared to other subgroups. Moreover, WES identified a limited number of mutated genes in high EMT tumors, among which FAM186A was the most frequently mutated gene with p<10−4. Alternately, RNAseq was also performed on five high and three low EMT samples for whole transcriptome analysis, which identified a list of the most deregulated genes, isoforms and coding sequences (e.g. SPP1, THBS2, THBS4 and SNAIL1 upregulated in high EMT tumors) as well as novel mutations (e.g. CDCP1 that was reported as a cell surface marker of migrating colon cancer stem cells). Therefore, our next-generation sequencing analysis has discovered the most mesenchymal-like CRCs as a novel, genetically distinct subpopulation lacking common driver mutations. Citation Format: Mingli Yang, Michael J. Schell, Norman H. Lee, Timothy J. Yeatman. The epithelial to mesenchymal transition (EMT) produces colorectal cancer subpopulations with strikingly different mutation profiles. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2981. doi:10.1158/1538-7445.AM2015-2981