Multiplatform Analysis of Primary and Metastatic Breast Tumors from the AURORA US Network identifies microenvironment and epigenetics drivers of metastasis
Authors: Perou Charles , Garcia-Recio Susana ,   Toshinori Hinoue4, Wheeler Gregory , Kelly Benjamin , Garrido-Castro Ana , Pascual Tomás , De Cubas Aguirre , Xia Youli , McClure Marni , Rajkovic Andrei , Karaesmen Ezgi , Smith Markia , Fan Cheng , Creighton Chad , Bowen Jay , Leraas Kristen , Burns Robyn , Coppens Sara , Wheless Amy , Rezk Salma , Garrett Amy , Parker Joel , Foy Kelly , Shen Hui , Park Ben , Krop Ian , Anders Carey , Gastier-Foster Julie , Rimawi Mothaffar , Nanda Rita , Lin Nancy , Isaacs Claudine , Marcom P. , Storniolo Anna , Couch Fergus , Chandran Uma , Davis Michael , Silverstein Jonathan , Ropelewski Alexander , Liu Minetta , Hilsenbeck Susan , Norton Larry , Richardson Andrea , Symmans William , Wolff Antonio , Davidson Nancy , Carey Lisa , Lee Adrian , Balko Justin , Hoadley Katherine , Laird Peter W. , Mardis Elaine , King Tari 
Published: January 2022

Abstract

Patients with metastatic breast cancer (MBC) typically have short survival times and their successful treatment represents one of most challenging aspects of patient care. This poor prognostic behavior is in part due to molecular features including increased tumor cell clonal heterogeneity, multiple drug resistance mechanisms, and alterations of the tumor microenvironment. The AURORA US Metastasis Project was established with the goal to identify molecular features specifically associated with metastasis. We therefore collected and molecularly characterized specimens from 55 metastatic breast cancer (BC) patients representing 51 primary cancers and 102 metastases. The 153 unique tumors were assayed using RNAseq, tumor/germline DNA exomes and low pass whole genome sequencing, and global DNA methylation microarrays. We found intrinsic molecular subtype differences between primary tumors and their matched metastases to be rare in triple negative breast cancer (TNBC)/Basal-like subtype tumors. Conversely, tumor subtype changes were relatively frequent in estrogen receptor positive (ER+) cancers where ~30% of Luminal A cases switched to Luminal B or HER2-enriched (HER2E) subtypes. Clonal evolution studies identified changes in expression subtype coincident with DNA clonality shifts, especially involving HER2 amplification and/or the HER2E expression subtype. We further found evidence for ER-mediated downregulation of genes involved in cell-cell adhesion in metastases. Microenvironment differences varied according to tumor subtype where ER+/Luminal metastases had lower fibroblast and endothelial cell content, while TNBC/Basal-like metastases showed a dramatic decrease in B cells and T cells. In 17% of metastatic tumors, we identified DNA hypermethylation and/or focal DNA deletions near HLA-A that were associated with its’ significantly reduced expression, and with lower immune cell infiltrates. We also identified low immune cell features in brain and liver metastases when compared to other metastatic sites, even within the same patient. These findings have direct implications for the treatment of metastatic breast cancer patients with immune- and HER2-targeting therapies and suggest potential novel therapeutic avenues for the improvement of outcomes for some patients with MBC.