Abstract 2488: Characterization of gene fusions in paired primary and metastatic samples of breast cancer in the AURORA molecular screening program
Authors: Benelli Matteo , Biagioni Chiara , Fimereli Danai , Hilbers Florentine S. , De Angelis Claudia , Vivancos Ana , Venet David , Vingiani Andrea , Irrthum Alexandre , Van Dooren Veerle , Vuylsteke Peter Willem , Servitja Sonia , Reis-Filho Jorge , Curigliano Giuseppe , Oliveira Mafalda , Piccart Martine , Aftimos Philippe 
Published: September 2020

Abstract
Introduction
Gene fusions (GFs) are genomic alterations with oncogenic potential. This class of alterations is highly actionable with targeted therapies showing high rates of durable responses in agnostic settings such as tumors with NTRK fusions. Recurrent GFs are rare in metastatic breast cancer (mBC) and ESR1 fusions drive endocrine resistance. AURORA is a molecular screening program for patients with mBC early in the course of their disease, collecting primary tumors, metastatic samples, liquid samples and longitudinal clinical follow-up data.
Experimental procedures
Patients are enrolled at the diagnosis of metastatic disease or after 1 line of therapy. Targeted gene sequencing of 411 BC genes is performed on the primary tumor, a metastatic sample, whole blood for germline variants and, for a subset of these genes, on tumor DNA from a baseline plasma sample. RNA-seq is performed on primary and metastatic tumor tissue samples. GFs were identified by rnafusion, a pipeline implementing 5 widely-used tools. Only GFs detected by at least 3 tools or 2 tools and 1 GF database match were considered for downstream analysis. Selected GFs were validated in-silico by FusionInspector. GFs detected in independent human normal tissue datasets were filtered out. Findings were correlated to available genomics, transcriptomics and clinical data.
Results
GFs data were generated from 316 paired primary/metastatic samples from 158 patients with curated clinical and genomic data: 97 ER+/HER2- (61.4%), 37 triple-negative (23.4%) and 24 HER2+ (15.2%). A total of 538 fusions were called in the primary samples (mean = 3.4 per sample) and 707 in the metastatic samples (mean = 4.5) with a validation rate of 72%. The gene fusion burden in metastatic samples was higher than in the primary (p&lt;1e-4), especially for ER+ patients. In metastatic samples, gene fusion burden by PAM50 subtype was higher for basal, HER2-E and LumB when compared to LumA (max p=2e-3). A total of 400 acquired GFs were identified (mean=2.5 per sample), involving relevant BC genes, such as ESR1, ERBB2, NF1 and FGFR1.The presence of fusions involving actionable genes was associated with a shorter progression-free survival (PFS) on therapies in the metastatic setting (median PFS=8 vs 17 months, p=0.001).
Conclusions
We report on the characterization of GFs in a large cohort of patients with mBC. Through the analysis of matched primary and metastatic tumor samples from 158 patients, we delineated the landscape of acquired gene fusions in BC. We observed a significant increase of gene fusion burden in metastatic compared to corresponding primary samples, involving key BC genes. Fusions involving actionable genes were associated with shorter PFS. Additional integrative analyses combining detected GFs and available genomics, gene expression and/or patients' treatments and outcomes are ongoing and will be presented during the meeting.
Citation Format: Matteo Benelli, Chiara Biagioni, Danai Fimereli, Florentine S. Hilbers, Claudia De Angelis, Ana Vivancos, David Venet, Andrea Vingiani, Alexandre Irrthum, Veerle Van Dooren, Peter Willem Vuylsteke, Sonia Servitja, Jorge Reis-Filho, Giuseppe Curigliano, Mafalda Oliveira, Martine Piccart, Philippe Aftimos. Characterization of gene fusions in paired primary and metastatic samples of breast cancer in the AURORA molecular screening program [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 2488.