Abstract P1-05-09: Association of co-amplicons with immune infiltration in subtypes of HER2-Positive breast cancer
Authors: Singh S , Gilmore H , Somlo G , Abu-Khalaf M , Sikov W , Harris L , Varadan V 
Published: March 2017

Abstract
Background: HER2+ breast cancers are heterogeneous at both clinical and molecular levels. We and others have determined that the HER2-Enriched subtype exhibits the highest rate of pathologic complete response (pCR) to neoadjuvant chemotherapy and trastuzumab (T), while the HER2-Basal subtype is resistant to anti-HER2 therapy (Carey et al, JCO 2015;Varadan et al, CCR 2016). Additionally, we reported that signatures of immune cell infiltration and immune cell subsets evaluated after one dose of T can predict pCR to preoperative T and chemotherapy (Varadan et al, CCR 2016). Given recent evidence for improved immune response with increasing mutational load, we chose to characterize the association of somatic mutations and copy-number alterations with subtypes of HER2+ breast cancer and immune modulation after one dose of T.
Methods: Fresh tumor core biopsies were taken at baseline and 2 weeks after one dose of either T or nab-paclitaxel (N) from 60 patients with stage II-III HER2+ cancers enrolled on a multicenter trial (BrUOG 211B). All patients then received 18 weeks of T+N+carboplatin. 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. Whole-exome sequencing (WES) was performed on a total of 86 samples (49 baseline, 37 brief-exposure), sequenced at an average depth of 90X. Somatic mutations were detected by applying multiple mutation-detection algorithms on the WES data, followed by stringent quality control using public and in-house variant databases, and mutation data curated from 11,000 tumors sequenced by the TCGA. Somatic copy-number alterations were estimated using a published algorithm, ENVE (Varadan et al, Genome Med 2015) that robustly detects somatic copy-number alterations in WES tumor profiles. We employed previously defined gene-expression signatures (Varadan et al, CCR 2016) of total immune infiltration and immune cell subsets, to assess for association with genomic aberrations.
Results: HER2-Basal tumors exhibited lower average copy number for HER2 and were less likely to have high-level amplifications of co-amplicons (e.g. 11q13, 20q13) with the exception of the MYC amplicon (8q24). They also exhibited a non-significant (P=0.33) trend towards higher mutational burden (Avg=85) compared to HER2-Luminals (Avg=79). A majority of somatic mutations (62%, 2282/3666) persisted after a single-dose of either T or N, while 17% (624/3666) were not detectable after brief-exposure. There was no association between immune infiltration and mutational burden in any HER2 subtype. Tumors harboring FGFR1 (8p11) amplifications exhibited higher gene-signature levels for macrophages (P=0.0073) and T-cells (P=0.0493) but not B-cells (P=0.213).
Conclusions: The HER2-Basal subtype is less likely to respond to trastuzumab-based neoadjuvant therapy and exhibits lower numbers of common amplicons. The disappearance of mutations after brief-exposure to therapy may be due to either tumor heterogeneity/sampling or clonal selection. The association of 8p11 amplifications with increased T-cell infiltration suggests that this amplicon may play an immunogenic role in HER2+ breast cancer. These results warrant further investigation in larger cohorts.
Citation Format: Singh S, Gilmore H, Somlo G, Abu-Khalaf M, Sikov W, Harris L, Varadan V. Association of co-amplicons with immune infiltration in subtypes of HER2-Positive breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-05-09.