Abstract 3412: Genomic signature of trastuzumab neoadjuvant therapy predictive of patient survival in HER2-positive breast cancer
Authors: Briones Natalia , Facista Salvatore , Halperin Rebecca , Heaton Paul , Mahadevan Daruka , Hendricks Wiiliam , Kim Suwon 
Published: August 2019

Abstract
Although the adjuvant use of trastuzumab has significantly improved survival, therapy resistance still plagues HER2-positive breast cancer patients. A recent clinical trial study showed that tumors exposed to single dose trastuzumab have increased Immune index and PD-1 expression1, suggesting that trastuzumab not only blocks HER2 signaling but also alters the tumor immune microenvironment. In order to identify genomic signature(s) of tumors that correlate with trastuzumab-induced tumor immune response, we analyzed eight HER2-positive breast tumors samples from patients treated with 2 or more cycles of neoadjuvant trastuzumab. First, we assessed the tumor immune environment using immunohistochemistry (IHC) with a specific interest in PD-1, a T cell immune checkpoint marker. Second, we conducted DNA/RNA sequencing and identified gene mutations and expression signatures. Lastly, we used the gene signature to evaluate survival outcomes of breast cancer patients using the TCGA dataset. DNA sequencing detected that two tumors contained deleterious TP53 mutations, two tumors activating PIK3CA mutations, and one tumor a GATA1 inactivating mutation, closely reflecting the prevalent gene mutation frequencies previously reported in breast cancer. Unsupervised clustering of the RNA sequencing data revealed two distinct clades in this patient cohort. The pathway analysis showed the gene list that distinguished the two clades included inflammatory genes such as TNFα and CXCL10 as well as immune checkpoint genes, CTLA-4 and iCOS. IHC staining for immune cell markers was consistent with the RNA sequencing results showing the presence of a large number of T cells positive for CD4, CD8, or PD-1 in tumors expressing pro-inflammatory genes. Supervised clustering of the two clades identified a gene signature composed of 59 upregulated and 24 downregulated genes in the “pro-inflammatory” clade. The gene signature effectively stratified HER2 breast cancer patients in the TCGA dataset with a striking Hazard Ratio of 7.3 (n=182, p = 0.0026, 95% C.I. 2.01-27.23) and patients with the “pro-inflammatory” tumors had significantly favorable survival outcomes. This patient stratification by the gene signature was uniquely specific to HER2-positive breast cancer, indicating a functional relevance of the gene signature related to HER2 cancer biology and/or therapy. These results support the idea that trastuzumab elicits local immune response, which contributes to therapeutic efficacy. Furthermore, patients with tumors containing the “pro-inflammatory” gene signature may benefit from immune checkpoint inhibitor therapy in combination with trastuzumab.
1Varadan et al (2016) Clin Cancer Res 22(13):3249-99
Citation Format: Natalia Briones, Salvatore Facista, Rebecca Halperin, Paul Heaton, Daruka Mahadevan, Wiiliam Hendricks, Suwon Kim. Genomic signature of trastuzumab neoadjuvant therapy predictive of patient survival in HER2-positive breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3412.