FOXA1 hypermethylation: link between parity and ER-negative breast cancer in African American women?

Abstract

Background Reproductive factors, particularly parity, have differential effects on breast cancer risk according to estrogen receptor (ER) status, especially among African American (AA) women. One mechanism could be through DNA methylation, leading to altered expression levels of genes important in cell fate decisions. Methods Using the Illumina 450K BeadChip, we compared DNA methylation levels in paraffin-archived tumor samples from 383 AA and 350 European American (EA) women in the Women’s Circle of Health Study (WCHS). We combined 450K profiles with RNA-seq data and prioritized genes based on differential methylation by race, correlation between methylation and gene expression, and biological function. We measured tumor protein expression and assessed its relationship to DNA methylation. We evaluated associations between reproductive characteristics and DNA methylation using linear regression. Results 410 loci were differentially methylated by race, with the majority unique to ER− tumors. FOXA1 was hypermethylated in tumors from AA versus EA women with ER− cancer, and increased DNA methylation correlated with reduced RNA and protein expression. Importantly, parity was positively associated with FOXA1 methylation among AA women with ER− tumors (P = 0.022), as was number of births (P = 0.026), particularly among those who did not breastfeed (P = 0.008). These same relationships were not observed among EA women, although statistical power was more limited. Conclusions Methylation and expression of FOXA1 is likely impacted by parity and breastfeeding. Because FOXA1 regulates a luminal gene expression signature in progenitor cells and represses the basal phenotype, this could be a mechanism that links these reproductive exposures with ER− breast cancer.

Genetic Ancestry–dependent Differences in Breast Cancer–induced Field Defects in the Tumor-adjacent Normal Breast

“…In addition, FOXA1 regulatory regions are highly susceptible for DNA methylation and transcriptional repression, particularly in the context of BRCA1 deficiency (49). Furthermore, ER À tumors in AA women show elevated FOXA1 DNA methylation compared with ER À tumors of EA women (30). Recent studies have also demonstrated racial differences in plasma levels of cytokines with CCL2, CCL11, IL4, and IL10 being higher in EA women, and IL1RA and IFNa2 being higher in AA women (50).…”

“…While higher expression of FOXA1 in the primary tumor is associated with better outcome, its overexpression in metastatic and/or anti-estrogen-resistant tumors is associated with rewiring of ERa signaling and poor outcome (26)(27)(28)(29). In addition, it is suggested that FOXA1 gene is preferentially methylated in tumors of AA women (30). Because of its relative importance in breast cancer, we assessed our TMA for FOXA1 expression.…”

Differences in microRNA expression in breast cancer between women of African and European ancestry

“…Among the 58 breast tumors included in the miRNA-seq, RNA-seq was performed on 50 tumors, as described previously (22). Briefly, a 1 μg's aliquot of RNA quantified by Quant-iT RiboGreen RNA assay Kit (Invitrogen #R11490) was used for library preparation using TruSeq(r) Stranded Total RNA LT with Ribo-Zero TM Gold (Illumina #RS1222301).…”

Genome-wide DNA methylation and expression patterns of microRNAs in relation to breast cancer subtypes among American women of African and European ancestry

“…Speci c methylation patterns have been associated with high tumor grade and ER negativity of breast cancer (4,(7)(8)(9). In our own studies and others, analyses restricted to CpG dinucleotides (CpGs) within and nearby PCGs, show differences in DNA methylation patterns in tumors by ER status and between AA and EA women (10)(11)(12)(13). These results suggest that aggressive breast cancer subtypes may be related to altered gene methylation, and that methylation patterns may differ by ancestry.…”