Epigenetic regulation of ID4 in the determination of the BRCAness phenotype in breast cancer

Abstract

BRCAness breast tumors represent a group of sporadic tumors characterized by a reduction in BRCA1 gene expression. As BRCA1 is involved in double-strand breaks (DSBs) repair, dysfunctional BRCA pathway could make a tumor sensitive to DNA damaging drugs (e.g., platinum agents). Thus, accurately identifying BRCAness could contribute to therapeutic decision making in patients harboring these tumors. The purpose of this study was to identify if BRCAness tumors present a characteristic methylation profile and/or were related to specific clinicopathological features. BRCAness was measured by MLPA in 63 breast tumors; methylation status of 98 CpG sites within 84 cancer-related genes was analyzed by MS-MLPA. Protein and mRNA expressions of the selected genes were measured by quantitative real-time PCR and Western Blot. BRCAness was associated with younger age, higher nuclear pleomorfism, and triple-negative (TN) status. Epigenetically, we found that the strongest predictors for BRCAness tumors were the methylations of MLH1 and PAX5 plus the unmethylations of CCND2 and ID4. We determined that ID4 unmethylation correlated with the expression levels of both its mRNA and protein. We observed an inverse relation between the expressions of ID4 and BRCA1. To the best of our knowledge, this is the first report suggesting an epigenetic regulation of ID4 in BRCAness tumors. Our findings give new information of BRCAness etiology and encourage future studies on potential drug targets for BRCAness breast tumors.

Proteogenomic analysis of Inhibitor of Differentiation 4 (ID4) in basal-like breast cancer

“…In the first, ID4 acts to suppress DNA repair proficiency and so cooperates with BRCA1 haploinsufficiency to promote genomic instability and tumourigenesis. This is consistent with the positive correlation between ID4 expression and 'BRCAness' (15), a defect in BRCA1 function in the absence of germline BRCA1 mutations (78). However perhaps more likely is the opposing scenario, that ID4 amplification and overexpression promote DNA damage repair, consistent with our observations of ID4 association with MDC1 at fragile sites and the ongoing requirement for ID4 in BLBC proliferation that we previously reported (11).…”

A novel role for the HLH protein Inhibitor of Differentiation 4 (ID4) in the DNA damage response in basal-like breast cancer

“…A defect in BRCA1 function in the absence of germline BRCA1 mutations, termed BRCAness (Konstantinopoulos et al, 2010, Lips et al, 2013, Liu et al, 2014, Turner et al, 2004) correlates with sensitivity to platinum-based chemotherapies and PARP inhibitors, both traditionally used to treat BRCA1 -mutant cancer, especially HGSOC.Consistent with this proposal, ID4 expression correlates with BRCAness in breast cancer (Branham et al, 2016) and we now show that women with /D4-amplified HGSOC, treated primarily with platinum-based agents, have improved survival. Together, these observations lead us to postulate that overexpression of ID4 may function to suppress HR function, contributing to a BRCA-ness phenotype in BRCA1-wild type cells.…”

“…ID4 and BRCA1 have been shown to inversely correlate in expression (de Candia et al, 2006, Roldán et al, 2006, Wen et al, 2012, Crippa et al, 2014, Junankar et al, 2015, Branham et al, 2016): however, this is the first demonstration of a biochemical interaction of ID4 with DNA damage foci and the DNA damage repair apparatus.…”

“…By elucidating the genetic drivers and dependencies of BLBC, we aim to improve our understanding of this complex, heterogeneous disease, potentially leading to the identification of novel targets and therapeutics. ID4 is required for normal mammary gland development (Junankar et al, 2015, Best et al, 2014, Dong et al, 2011) and acts as a proto-oncogene in BLBC (Beger et al, 2001, Branham et al, 2016, Crippa et al, 2014, de Candia et al, 2006, Junankar et al, 2015, Roldan et al, 2006, Shan et al, 2003, Thike et al, 2015, Wen et al, 2012). Depletion of ID4 reduces BLBC cell line growth in vitro and in vivo (Junankar et al, 2015), suggesting that ID4 controls critical, yet unknown pathways in BLBC.…”

“…We and others have previously shown ID4 to be a master regulator of mammary stem cell self-renewal in the normal mammary gland (Junankar et al, 2015, Best et al, 2014, Dong et al, 2011), as well as important for the aetiology of BLBC. ID4 is overexpressed in a subset of BLBC patients, marking patients with poor survival outcome, and is necessary for the growth of BLBC cell lines (Beger et al, 2001, Branham et al, 2016, Crippa et al, 2014, de Candia et al, 2006, Junankar et al, 2015, Rold á n et al, 2006, Shan et al, 2003, Thike et al, 2015, Wen et al, 2012). Precisely how ID4 mediates this function in BLBC is unclear.…”