Abstract 304: HER2 basal tumors have frequent mutation of HER3 and are more resistant to HER2-targeted therapy
Authors: Varadan Vinay , Singh Salendra , Gilmore Hannah , Parsai Shikha , Somlo George , Abu-Khalaf Maysa , Sikov William , Harris Lyndsay N. 
Published: July 2016

Abstract
Background: HER2 tumors are heterogeneous at both the clinical and molecular levels (Harris et al 2007, Varadan, AACR 2015). We and others have identified a distinct molecular subtype termed ‘HER2 basal’ that demonstrates lower response to preoperative trastuzumab and is characterized by overexpression of the ‘basal-like’ signature genes (Harris, CCR 2007; Carey, JCO 2015). We sought to better understand the molecular underpinnings of the HER2 basal phenotype by performing whole exome sequencing (WES) in a cohort of HER2 tumors treated with trastuzumab-containing preoperative therapy.
Methods: A multicenter trial (BrUOG 211B) was conducted to determine predictors of pathologic complete response (pCR) to trastuzumab (T)-containing preoperative therapy. Sixty HER2+ Stage II-III patients were enrolled and assigned to either a single dose of T or nab-paclitaxel (N) followed by T+N+carboplatin (TNC). Fresh tumor core biopsies were taken at baseline and 2 weeks after the initial dose of T or N. PAM50 subtyping was performed using gene expression data from patient tumor biopsies and tumors were classified into HER2-Enriched, HER2-Luminal and HER2-Basal subtypes based on ER/PR IHC values and relative expression of the proliferation-associated genes within the PAM50 gene list. WES was performed on a total of 86 samples (49 baseline and 37 from the post brief-exposure timepoint), with each sample sequenced at an average depth of 90X. Somatic mutations (single nucleotide variants and short indels) were assessed using Genome Analysis Toolkit (GATK) UnifiedGenotyper followed by a robust pipeline comparing multiple databases to eliminate germline variants. Copy-number estimation was performed on the WES data using a novel algorithm, ‘ENVE’ (Varadan, Genome Med, 2015) that robustly identifies somatic copy-number alterations.
Results: WES profiles of HER2 basal tumors (n = 6) revealed lower average copy number for HER2 (2.5 vs 5.8) and were less likely to have high-level amplification (&gt;4 copies per cell) of other amplicons (e.g. 11q13, 20q13) with the exception of 8q24. The so-called ‘Myc’ amplicon was co-amplified in all subtypes relatively equally (3/6 in HER2-B, 11/19 in HER2-E, 10/23 in HER2-L). HER2-B tumors were also characterized by higher frequency of mutations in Rb (2/6 versus 1/42; P = 0.0376) and HER3 (4/6 vs 2/42; P = 0.0011) compared with other subtypes and frequent alteration of p53 (4/6 versus 17/42; P = 0.22). pCR to preop TNC was HER2-B 3/8, HER2-E 10/20, HER2-L 6/21, not significant in this small cohort. The presence of HER3 mutations suggests a potential mechanism for the previously reported poor clinical response to preoperative anti-HER2 therapy in HER2 basal tumors.
Conclusions: The HER2 basal subtype is more likely to exhibit mutations in HER3 and is less likely to respond to trastuzumab-based therapy. Larger cohorts are required to confirm these findings and trials of other HER2 targeted agents in this subtype should be considered.
Citation Format: Vinay Varadan, Salendra Singh, Hannah Gilmore, Shikha Parsai, George Somlo, Maysa Abu-Khalaf, William Sikov, Lyndsay N. Harris. HER2 basal tumors have frequent mutation of HER3 and are more resistant to HER2-targeted therapy. [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 304.