Whole-genome bisulfite sequencing of cell-free DNA to investigate molecular contributors to racial survival differences in advanced-stage triple-negative breast cancer.

Abstract

3059 Background: Black women are twice as likely to be diagnosed with triple-negative breast cancer (TNBC), a highly aggressive and difficult-to-treat subtype with poor survival outcomes. While well-defined factors such as socioeconomic status have been recognized, the impact of genomic and molecular factors on the racial disparity in TNBC survival remains understudied. Liquid biopsy, a non-invasive and real-time method for studying the molecular landscape of tumors, has yet to be explored in the context of racial survival disparities in TNBC. Methods: Ten Black TNBC patients were matched with ten White TNBC patients based on age, family history, tumor stage, grade, and inflammatory breast cancer (IBC) status. Baseline blood samples were collected prior to the initiation of a new therapy. Cell-free DNA (cfDNA) was extracted from plasma, bisulfite-converted, and analyzed through whole-genome bisulfite sequencing (WGBS). After quality control, ichorCNA was used to identify copy number alterations (CNAs), and MethylKit was applied for methylome analysis. Associations between CNAs, differentially methylated regions (DMRs), and progression-free survival (PFS) were evaluated and compared between Black and White patients. Results: The Black-White pairs were well-matched across key clinical variables, including age (P = 0.99), family history (P = 1.00), tumor stage (P = 1.00), grade (P = 1.00), and IBC status (P = 0.37). Black TNBC patients had poorer PFS compared to their White counterparts. Significant CNAs were identified on chromosome 1 (chr1:20400000-23900000_p36.12 and chr1:7200000-9200000_p36.23), regions associated with known breast cancer prognosis genes such as EPHB2 and E2F2 . Thirteen DMRs were found to be significantly associated with the racial differences in PFS, with key genes such as CDH13 and TMEM132C identified in these regions. Notably, the methylation status of the CDH13 promoter has previously been associated with breast cancer risk. The predictive power for PFS was significantly enhanced in a model combining these 13 DMRs with race (Concordance Index [C-index] = 0.96), compared to a model using race alone (C-index = 0.75). Conclusions: In this pilot study utilizing WGBS of cfDNA, we identified significant CNAs and DMRs associated with the racial disparity in survival outcomes among advanced-stage TNBC patients. These findings provide insight into the genomic and molecular contributors to this disparity and highlight the potential of liquid biopsy for future studies. Larger studies are needed to validate these results and further investigate the underlying mechanisms.