Abstract P2-06-09: Identification of oncogenic gene fusions in triple-negative breast cancer metastatic to the brain
Authors: Gonzalez-Ericsson P , Lehmann B , Mobley B , Chen Y-Y , Pietenpol J , Sanders ME 
Published: May 2019

Abstract
BACKGROUND: As many as 24% of breast cancer (BC) patients develop metastasis to the brain and 27% of these occur in patients with triple negative (TN) BC. The brain (#2) and lung (#1) are the most common sites of TNBC metastasis. Half of women with metastatic (m) TNBC will die within one year. Novel therapies for women with mTNBC, especially to the brain, are desperately needed. TNBCs often exhibit genomic instability, resulting in gene fusions and other chromosomal rearrangements. Such alterations are long recognized as oncogenic drivers and effective drug targets in hematologic and other solid malignancies. We aimed to identify these alterations in mTNBC with Segmental Transcript Analysis (STA), a novel population-based algorithm ranking genes based on likelihood of harboring a gene rearrangement by identifying abrupt changes in transcript expression.
RESULTS: We performed RNAseq on 25 mTNBC, 4 matched primary BC, 2 normal cerebellum and 2 normal cerebral cortex samples. TNBC subtype analysis showed an enrichment of basal-like (BL) 2 and mesenchymal (M) subtypes among mTNBC to the brain compared to primary (p) BC in the TCGA. A principal component analysis demonstrated mTNBC and their matched primaries clustered together, indicating the pairs were more closely related to each other genetically than to other mTNBCs. When the gene expression patterns of pBC were compared with their brain metastases following adjustment for contamination with normal brain tissue, an upregulation of mesenchymal genes (p63/p73 axis) and primitive/embryonic genes (NOTCH and PAX family) were noted in the brain mTNBC. We confirmed a modest to marked upregulation of p63 expression by immunohistochemistry across all TNBC subtypes, most notably in BL1 and BL2. STA found three gene rearrangements: EHF-WT1, NF1-VWDE and JAG1-Chr20. Two of these are potential driver gene rearrangements. The first, in a tumor of M subtype, results from fusion of the 5'UTR of EHF to WT1. The resulting fusion transcript is predicted to encode a truncated WT1 protein; loss of the N-terminal regulatory region of WT1 would likely cause constitutive activation. We also identified a truncating rearrangement in the Notch ligand JAG1 in a tumor of LAR subtype. JAG1 is a membrane bound ligand for the Notch receptor and the breakpoint occurs just distal to the DSL domain essential for Notch interaction. This rearrangement occurs within an intergenic chromosomal region, introduces an abrupt stop codon and generates a truncated protein lacking a transmembrane domain. An intact signal peptide should localize the protein to the endoplasmic reticulum; however, loss of the transmembrane domain would likely lead to secretion rather than membrane insertion. This alteration is predicted to constitutively stimulate Notch activity in a paracrine fashion. If the rearrangement functions in this manner, neutralizing antibodies to the N-terminal portion of JAG1 should have therapeutic efficacy.
DISCUSION: EHF-WT1 and JAG1-Chr20 are potential driver rearrangements novel to brain mTNBC. The JAG1 rearrangement predicts constitutive production of Notch transcription factors and is potentially targetable. Continued interrogation of mTNBC for discovery of additional oncogenic fusions driving BC biology is warranted.
Citation Format: Gonzalez-Ericsson P, Lehmann B, Mobley B, Chen Y-Y, Pietenpol J, Sanders ME. Identification of oncogenic gene fusions in triple-negative breast cancer metastatic to the brain [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-06-09.