Abstract 2117: Immune contexture of breast cancer subtypes in real-world molecular data
Authors: Wang Xuya , Li Bin , Szabo Peter M. , Chang Han , Roberts Mustimbo , Walsh Alice M. 
Published: September 2020

Background: Breast cancer has been extensively characterized molecularly with cohorts such as The Cancer Genome Atlas (TCGA). However, as the standard of care evolves, there is a need for contemporaneous datasets with more detailed treatment and outcomes data. The ORIEN Avatar database (M2Gen, Tampa, FL) consists of clinical and tumor sequencing data from treatment-naive or on-treatment biopsies. This study evaluates the quality of ORIEN Avatar's RNA-sequencing (RNASeq) data, interrogates the impact of prior treatment on PAM50 subtyping, and reports associations between breast cancer subtypes and estimated immune cell populations.

Methods: In the ORIEN Avatar dataset, RNASeq data were prepared using a multistep normalization process. We assessed the quality of normalized RNASeq data using 3 modalities. Using a principal-component (PC) analysis, we interrogated the association of gene expression with potential technical and biological factors, including processing batch effects, preservation methods, and treatment status. We evaluated concordance between immunohistochemistry (IHC)-based subtyping and intrinsic subtyping using the PAM50 gene expression signature. Prevalence of in silico-derived tumor-infiltrating immune cell compositions in ORIEN Avatar compared with TCGA breast cancer samples was investigated.

Results: The ORIEN Avatar breast cancer cohort comprised 560 patients with RNASeq data. The first 3 PCs (accounting for 11%, 9%, and 7% of total explained variance, respectively) were associated with biological factors, including PAM50 subtyping and HER2 receptor and hormone receptor (HR) status. PAM50 subtype was largely concordant with IHC subtype, per clinical record of biomarker testing, and prior treatment status did not impact PAM50 subtyping. We observed that 68% of basal samples were triple negative by IHC, 92% of luminal samples were HER2-negative and HR-positive by IHC, and 62% of HER2-enriched samples per RNASeq were HER2 receptor positive by IHC. Several in silico-derived tumor-infiltrating immune cell compositions, including activated CD4 memory T cells, M0 macrophages, and activated dendritic cells, were enriched in triple-negative breast cancer samples, consistent with TCGA. Correlative analysis of RNASeq data with other biomarker data and clinical outcome is planned.

Conclusions: Our results using real-world (RW) ORIEN Avatar RNASeq data were consistent with molecular profiling of breast cancer assessed using IHC and TCGA. This proof-of-concept study found no association between prior treatment status and PAM50 intrinsic subtyping. Our analysis provides a framework to assess the quality of RW molecular profiling and highlights the feasibility of leveraging harmonized molecular data to replicate and discover novel biological evidence.

Citation Format: Xuya Wang, Bin Li, Peter M. Szabo, Han Chang, Mustimbo Roberts, Alice M. Walsh. Immune contexture of breast cancer subtypes in real-world molecular data [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2117.