RNA fusions: An untapped source of neoantigens for immune based breast cancer prevention and treatment across all subtypes of breast cancers

Background: Breast tumors are considered immunologically cold with an overall low to moderate mutation burden resulting in limited neoantigen repertoire that can be used for discovering a breast cancer vaccine. RNA fusions lead to the generation of neoantigens that are more immunogenic than insertion or deletion mutations. Identification of such targets in high risk mammary tissue and tumors represent novel opportunities for breast cancer prevention and treatment. The objective of this study was to characterize the prevalence of chimeric RNAs in precancerous breast tissue and breast tumors from sporadic breast cancer patients. Methodology: Fusions were identified by RNA sequencing 225 breast tissues from breast tumors and paired adjacent- and distant- tissues of 25 Her2 positive, 25 hormone receptor positive (HR) and 25 triple negative (TN) patients. The RNA sequencing reads were processed through modified ARRIBA fusion discovery pipeline for fusion calling. Breast samples obtained from cancer-free women undergoing breast reduction surgery were obtained from Komen Tissue Bank and used as controls to exclude normal mammary tissue associated chimeric RNAs from analysis. Results: All major subtypes of breast tumors (TNBC, Her2+ and HR+) express RNA fusions. TNBC and Her2+ tumors expressed substantially larger number of unique RNA fusions than HR+ breast tumors. Every tumor sample possessed at least 2 novel RNA fusions. In line with high genomic instability of TNBC subtype of breast cancer, about 1/3 of the TN breast tumors expressed greater than 15 RNA fusions. We found non-coding RNAs to be also implicated in the biogenesis of RNA fusions in addition to coding genes. Approximately 1/5 th of RNA fusions identified in sporadic breast tumors were driven from at least one oncogene partner. Interestingly, we found a substantial number of RNA fusions to possess multiple break points suggesting multiple areas within a gene that are prone to break and fuse with another gene partner. In line with patient tumor heterogeneity, RNA fusions in breast tumors were overwhelming private. In order to identify RNA fusions that are relevant for breast cancer prevention, we investigated the presence of RNA fusions in the paired adjacent samples as compared to the index tumor. Although, we found preneoplastic breast tissue to possess a rich repertoire of RNA fusions, majority of these were different from those identified in paired breast tumors. Conclusions: RNA fusions are frequently present in breast tumors as well as at risk breast tissue and may provide novel opportunities for developing vaccines for breast cancer prevention and treatment.