Abstract P3-06-09: Incidence of ROS1 genomic alterations in breast cancer
Authors: Force Jeremy , Sokol Ethan S , Taylor Mary Love , Huang Dale , Marcom Paul K , Davare Monika , Marks Jeffrey 
Published: March 2020

Abstract
Background: ROS1 is an important proto-oncogene involved in the development of various cancers and increased expression is a poor prognostic feature in breast cancer. Activation of the ROS1 tyrosine kinase receptor has been reported and is being targeted with several FDA approved small molecule inhibitors, primarily in lung cancer. However, the frequency and type of ROS1 alterations in breast cancer have not been fully explored. The purpose of this study was to identify the incidence and type of ROS1 genomic alterations occurring in breast cancer as a prelude to potentially targeting this protein in the setting of metastatic breast cancers that harbor these changes.
Methods: We queried 21,125 breast cancer samples (~50% from distant metastatic sites) from the Foundation Medicine breast cancer database, 5,964 breast cancer samples from five publicly available breast cancer databases (MBC Project, INSERM, METABRIC, TCGA, MSK-IMPACT), and 217 breast cancer samples from Project GENIE v6.5 to identify the incidence of ROS1 alterations in breast cancer. We identified fusion partner genes and classified each alteration type into the following categories: fusion, rearrangement, short variant (missense or indel), or copy number variation. A computational approach was used to distinguish somatic from germline single nucleotide polymorphisms in the Foundation Medicine database (Sun et. al., 2018). PolyPhen2 and in vitro analyses were used to investigate the effect of ROS1 nonsynonymous mutations on the ROS1 protein. Using Foundation Medicine, we made associations with ROS1 alterations and receptor status, histologic subtype, metastatic site, tumor mutational burden, and co-occurring mutated genes. Estrogen receptor (ER) status was available for 2,371 samples. HER2 status and all other analyses were identified from the entire cohort.
Results: The incidence of any ROS1 alteration across the Foundation Medicine breast cancer database, including variants of unknown significance, was 4.6% and ranged from 1.67% to 6.9% from the five publicly available breast cancer databases and Project GENIE. Foundation Medicine samples revealed 5 (0.024%) breast cancers with ROS1 fusions, 86 (0.41%) with rearrangements, 733 (3.47%) with short nucleotide variants, and 182 (0.86%) with copy number variations. ROS1 alterations occurred similarly in HER2, TNBC, and ER+ breast cancers, 5.24%, 4.5%, and 4.37%, respectively (ns, all p&gt;0.2). Invasive ductal carcinoma, invasive lobular carcinoma, and metaplastic carcinoma harbored ROS1 alterations at 4.35%, 3.65%, and 4.36%, respectively (ns, all p&gt;0.3). ROS1 alterations were significantly associated with metastatic breast cancer spread to the brain (p=0.0005) and lymph nodes (p=0.017). There were 18 gene mutations significantly co-occurring with ROS1 alterations when controlling for multiple comparisons. The top 5 were TP53 (OR 1.55, p=3.12 × 10−8), RB1 (OR 1.66, p=0.0001), NOTCH3 (2.27, p=0.0001), TAF1 (OR 4.82, p=0.0002), and ARID1A (OR 1.71, p=0.0003).
Conclusions: A modest incidence of genomic alterations in ROS1 occurs across all breast cancer subtypes and histologies and may be more actionable than currently recognized. New somatic alterations in the ROS1 gene were identified from Foundation Medicine that were not detected in publicly available databases or Project GENIE. Investigations using PolyPhen2 and in vitro analyses of ROS1 gene activation from these newly discovered somatic alterations and other short variant mutations are currently being investigated in our lab with results to be reported. Co-occurring mutations reveal a unique genotype associated with ROS1 alterations that may play a biologic role in ROS1-mediated pathogenesis and should be explored further. ROS1 alterations occurring in breast cancers might be leveraged in an innovative personalized medicine treatment approach for breast cancer patients.
Citation Format: Jeremy Force, Ethan S Sokol, Mary Love Taylor, Dale Huang, Paul K Marcom, Monika Davare, Jeffrey Marks. Incidence of ROS1 genomic alterations in breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P3-06-09.