Abstract 3436: Early mutated genes and subsequent mutational trajectory in breast cancer subtypes
Authors: Cheung Yee Him , Wu Jie , Varadan Vinay , Dimitrova Nevenka 
Published: August 2018

Abstract
Current analyses on somatic mutations mainly involve counting samples as either carriers or non-carriers. Such a binary approach can identify the frequently mutated genes, but may miss the early mutated genes that are critically involved in tumorigenesis, but only in a small specific group of patients. This work is an attempt to identify such early mutated genes that drive the etiology of each breast cancer subtype by analyzing the variant allele frequency (VAF) of somatic mutations, which is a good proxy for mutational timeline. We further studied their pathway associations and subsequent trajectory of mutational progression. In this study, we analyzed the 72,084 non-synonymous somatic mutations in 16,164 genes of 817 TCGA breast cancer samples (HER2+: 65, Luminal A: 415, Luminal B: 176, Basal: 136 and Normal-like: 25) using VAF adjusted by sample purity derived from multiple methods. Gene allele frequency (GAF) is obtained by choosing the maximum VAF per gene per sample. For each subtype, we shortlisted 100 genes with highest number of mutation carriers and ranked them by decreasing average GAF across the carriers. We assume genes with higher average GAF are more likely to harbor clonal mutations that occur during early tumor progression. We then performed Inflo Network Analysis on RNA-Seq expression data to identify the dysregulated pathway interactions associated with the early mutated genes. The top two genes with the highest presence of mutations within each subtype are as follows: (a) HER2+: ERBB2 (VAF = 0.39 ± 0.21, n = 4), KAT6A (0.31 ± 0.09, 4), (b) Luminal A: CTCF (0.41 ± 0.19, 13), MAP2K4 (0.37 ± 0.14, 24), (c) Luminal B: MAP2K4 (0.46 ± 0.11, 5), TP53 (0.46 ± 0.17, 64), and (d) Basal: SCN10A (0.46 ± 0.29, 5), MYH9 (0.43 ± 0.16, 5). Among them, the genes with the strongest support are MAP2K4 (n = 24) for Luminal A and TP53 (n = 64) for Luminal B. Network analysis with Inflo on the same samples reveals that MAP2K4 mutation carriers are most strongly associated with the down regulations of “Regulation of Androgen receptor activity (target: JUN)” and “regulation of p38-alpha and p38-beta (target: DUSP8)” in Luminal A, with a difference in average Inflo score of -2.24 and -2.22 respectively; whereas TP53 mutation carriers are most strongly associated with the down regulations of “direct p53 effectors (target: RPS27L)” and “RB tumor suppressor/ checkpoint signaling in response to dna damage (target: CDK2)” in Luminal B, with a difference of -2.98 and -2.67 respectively. We found further that both PIK3CA and TTN were frequently co-mutated with TP53 in all subtypes. However, TTN mutations in general have lower VAF, indicating their late emergence in tumor progression. Our work shows the potential of VAF analysis for identifying driver genes, understanding tumor progression and evaluating the impact of a mutation on a patient. As future work, we may improve the VAF estimates by adjusting for CNVs and weight each variant by pathogenicity.
Citation Format: Yee Him Cheung, Jie Wu, Vinay Varadan, Nevenka Dimitrova. Early mutated genes and subsequent mutational trajectory in breast cancer subtypes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3436.