Abstract B185: Epithelial cancer cell-expressed genes contribute to clinically relevant immune-based classifications of breast cancer
Authors: Shepherd Jonathan , Perou Charles 
Published: February 2019

Abstract
Introduction: With the development of immunotherapies for breast cancer therapy, reliable methods to evaluate the extent and type of immune involvement present in tumors and investigation of its effect on patient prognosis and treatment are needed. Identifying tumor-specific features that affect immune involvement will be a key to understand tumor-immune involvement. Therefore, we evaluated expression of immune-related mRNA signatures in TCGA breast cancer data to identify distinct immune-related tumor subsets and asociated prognostic values. We also evaluated immune cell features, including B cell and T-cell receptor richness and diversity, as well as epithelial tumor cell-specific features, including somatic mutations, copy number alterations and differential RNA expression between identified groups. Methods: More than 130 published immune related gene signatures were evaluated in 1095 breast tumors and 97 normal mammary samples. Groups were identified by consensus based hierarchical clustering of the immune signatures, using the proportion of ambiguous clustering to select the optimal number of groups. An ElasticNet model trained on TCGA data was applied to two other breast tumor datasets to predict immune group classification. RNA-sequencing (RNAseq) data from 70 breast cancer cell lines and from human tumor xenografts passaged in immune-compromised mice and processed through a human specific sequencing pipeline provided in vitro and in vivo sources of epithelial cancer cell expression with limited stromal content that was used to filter TCGA bulk RNAseq data for epithelial expressed genes. Results: We identified three distinct immune groups present in breast cancer: immune-low, immune-normal, and immune-high. The immune-high group is characterized by high T-cell scores, including both cytotoxic and regulatory T-cell signatures, and increased B cell and macrophage signatures. The immune-normal set shows signs of normal epithelia and low proliferation. The immune-low group has very low immune cell signatures. Intrinsic breast cancer subtypes (Basal, luminal A, Luminal B, Her2 and Normal-like) are present in each of the immune groups; however, enrichment of basal tumors in immune-high, luminal tumors in the immune-low, and normal mammary, normal-like tumors and luminal A tumors in the immune-normal group demonstrate an interaction between intrinsic tumor type and immune involvement. Immune groups are prognostic in TCGA, with the immune-high group having improved recurrence-free survival. Two more breast tumor datasets confirmed improved survival for basal tumors in the immune-high group relative to the immune-low tumors. Total mutation burden, unique somatic mutations, and copy number alterations did not show significant changes between immune-low and –high groups, whereas RNA expression differs between groups. Selecting for genes with evidence of expression by epithelial breast cancer cells identified over 8,000 genes differentially expressed between the immune-low and –high groups, with CCL5, ACAP1, PVRIG, SLA2, LCK and CD8A being among the most significant. Conclusion: Breast cancer can be divided into three clinically relevant immune-related groups. Immune-high has high immune involvement, showing of markers for cytotoxicity and immune suppression and exhaustion. These patients have improved survival, but may still benefit from immune checkpoint inhibition. Immune-normal is reflective of a normal mammary immune state, suggesting a microenvironment that has not been strongly altered by the tumor. Immune-low appears to demonstrate exclusion of immune cells from the tumor, even though tumors contain predicted neoantigens. These patients have poor survival and novel therapeutic strategies to activate immune involvement need to be developed. Epithelial cancer cell expressed many immune-related genes, including CCL5, LCK and CD8A, which may be critical determinants of immune cell attraction.
Citation Format: Jonathan Shepherd, Charles Perou. Epithelial cancer cell-expressed genes contribute to clinically relevant immune-based classifications of breast cancer [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr B185.