Abstract P6-08-01: Inverse relationships between high somatic copy number load and immune phenotypes in breast cancer
Authors: Bense RD , van der Vegt B , de Vries EGE , van Vugt MATM , Schröder CP , Fehrmann RSN 
Published: May 2016

Abstract
Introduction
Currently, there is no clear biomarker to predict which breast cancer patient may benefit from immunotherapy. High somatic point mutational load is thought to lead to immune activation and CD8+ T cell activation and infiltration. In addition, pre-existing CD8+ T cells distinctly located at the invasive tumor margin are associated with expression of the PD-1/PD-L1 immune inhibitory axis and may predict response to PD-1 targeted therapy. However, breast tumors are considered copy number-driven rather than mutational-driven cancers. Therefore, in order to identify which breast cancer patients may potentially benefit from immunotherapy, we investigated relations between copy number load and CD8+ T cell abundance, immune pathways and immune activation scores in a large set of publically available breast cancer expression profiles.
Methods
Functional genomic mRNA-profiling (Fehrmann et al., Nat Genet, 2015) was used to capture the downstream effect of somatic copy number alterations on gene expression levels. This method allowed using gene expression profiles to quantify somatic copy number load occurring in tumor samples in a univariate measurement called the copy number load index (CNL-index). Immune activation scores were calculated according to two known gene immune signatures (Teschendorff et al., Genome Biol, 2007 and Desmedt et al., Clin Cancer Res, 2008). Cibersort (Newman et al., Nat Methods, 2015) was applied to estimate CD8+ T cell abundance. Publicly available gene expression profiles of 7,270 primary breast cancer samples were used. The relation between CNL-index, immune activation scores and disease-free survival (DFS), defined as time from diagnosis until distant metastasis development, was assessed by multivariate cox-regression analysis including age, ER and HER2 status, tumor size, lymph node involvement, tumor grade and treatment regimen. Gene set enrichment analysis (GSEA) was applied to assess relations between immune pathways and CNL-index.
Results
In primary breast cancer, low CNL-index was found in 1,796 samples (24.7%) versus 5,474 samples with a high CNL-index (75.3%). Higher CNL-index was correlated with shorter DFS (HR 2.51, P = 1.6x10-4), whereas higher immune activation scores were associated with prolonged DFS (HR 0.199, P = 0.003 and HR 0.347, P = 0.017). CD8+ T cell abundance was negatively correlated with the CNL-index (Spearman R = -0.14, P = 8.11x10-34). GSEA showed enrichment of immune pathways amongst genes that negatively correlated with CNL-index. Subset analysis in 1,555 TNBC samples showed low CNL-index in 287 samples (18.5%) versus high CNL-index in 1,268 samples (81.5%). Similar to the entire breast cancer set, CD8+ T cell abundance and CNL-index were negatively correlated in TNBC (Spearman R = -0.11, P = 4.11x10-05). Immune pathway enrichment in genes in TNBC also negatively correlated to CNL-index.
Conclusion
High CNL-index (i.e. high copy number load) is inversely related to immunoactivation, immune pathways and CD8+ T cell abundance. This implies that in breast cancer, tumors with low CNL-index may be intrinsically sensitive to immune modulation, which warrants further confirmation in prospective trials.
This research was supported by Dutch Cancer Society Grants RUG 2010-4739 and RUG 2013-5960.
Citation Format: Bense RD, van der Vegt B, de Vries EGE, van Vugt MATM, Schröder CP, Fehrmann RSN. Inverse relationships between high somatic copy number load and immune phenotypes in breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-08-01.