Abstract 2960: TRIM29 is a novel biomarker for basal-like breast cancer

Abstract

Abstract Basal-like breast cancer is a subtype of tumors associated with aggressive clinical behavior and poor prognosis. The genes responsible for their aggressive phenotype have not been well characterized and may provide an opportunity for targeted therapies. Tripartite motif-containing 29 (TRIM29) is a member of the TRIM protein family. Microarray and RT-qPCR analyses shows TRIM29 overexpressed in Basal-like breast tumors and it is highly correlated to other basal tumor markers such as CK5/6, CK17, EGFR, and FOXC1. We recently observed using immunohistochemistry that TRIM29 predominantly localizes to the nucleus in basal tumor epithelial cells, in contrast to a cytoplasmic localization seen in ER-positive tumors. Thus, TRIM29 may act as a transcriptional regulatory factor involved in carcinogenesis. In order to investigate the role of TRIM29 in the initiation and progression of Basal-like breast cancer, we employed chromatin immunoprecipitation and massively parallel sequencing (ChIP-seq) to create a genome-wide profile of in vivo TRIM29-binding sites in MDA-MB-468 cells, a human breast cancer cell line. ChIP-seq analysis revealed 94 putative TRIM29 binding regions in the cancer genome of MDA-MB-468 cells with an estimated false discovery rate of less than 5%. One TRIM29 binding motif was found in the TRIM29 binding regions with a core consensus sequence of CTGTCTCC. We also identified some known cancer genes in close proximity to TRIM29 binding sites, including JUND, FBXO31, CCND3, EGFR, and FOXC1. In addition to mapping TRIM29-DNA binding sites, we used co-immunoprecipitation (co-IP) coupled with tandem mass spectrometry to identify proteins that interact with TRIM29 in MDA-MB-468 cells. Proteins that co-precipitated with TRIM29 included splicing factor proline/glutamine-rich (SFPQ, a transcriptional co-repressor), poly(A) binding protein (PABPC4); FUS and TAF15 RNA polymerase II (both are proto-oncoproteins and transcriptional activators), and A kinase anchor protein 13 (AKAP13, an adaptor protein involved in protein kinase A signaling pathway). Confirmation of the initial co-IP results was achieved through several independent techniques, including detection of binding partners in TRIM29 precipitates by Western blot and reciprocal co-IP using antibodies to partner proteins and detection of TRIM29 in the precipitates. Overall, results from our studies indicated that besides functioning as a transcription factor, TRIM29 may also participate in signal transduction pathways by forming protein complexes. Our studies have identified new biomarkers for basal-like breast cancers and revealed kinases that could potentially be targeted by biologic therapies. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2960.