Abstract C085: A pilot study to identify DNA methylation biomarkers associated with African ancestry in Latin-American breast cancers

Abstract Women of African descent suffer from higher breast cancer mortality globally. Few studies have explored the experiences of these breast cancer patients in Latin-America. In countries like Brazil, breast cancer mortality of women of African descent is the highest after adjusting for age, level of education and stage at diagnosis. Research on African American and African breast cancer cancer patients has pointed to specific molecular signatures associated with genetic African ancestry. Here, we set out to identify DNA methylation markers associated with African ancestry in Afro-brazilian breast cancers by analyzing 48 frozen tumor DNAs from women treated at the National Cancer Institute Breast Cancer Hospital in Rio de Janeiro, Brazil. We used Illumina MethylationEPIC (850K) and Infinium genotyping arrays. We estimated the proportions of European, African and Indigenous American ancestries for each study participant using populations from the 1000 Genomes Project as reference. Ancestry estimates were generated on Admixture software under an unsupervised model, setting k=3. Using linear regression, we identified differentially DNA methylated positions (DMPs) between the highest (AFR=64±18%) and lowest (AFR=25±7%) African ancestry tertiles. Previous studies have shown West African ancestry is associated with triple negative breast cancer (TNBC), which is characterized by absence of expression of estrogen/progesterone receptors and overexpression of the HER2 protein. The breast cancer subtype proportions differ in the high and low African ancestry tertiles. The most common subtypes per African ancestry category were TNBC with 43.7% of the breast cancers in the high, and Luminal B with 56.2% in the low African ancestry tertile (Fisher exact t-test p=0.015). To account for this difference, we identified DMPs associated only with high African ancestry by removing DMPs specific to TNBC when compared to other subtypes using an adjusted p=0.01. A final set of 18,885 DMPs were identified to be exclusively associated with high African ancestry. 66.2% of these DMPs had higher DNA methylation levels in the highest African ancestry tertile versus the lowest, suggesting a prevalence of hypermethylated positions that could lead to downregulation of relevant breast cancer genes. We performed Gene Set Enrichment Analysis (GSEA) on African ancestry-associated DMPs in breast cancer tumor tissues, utilizing the KEGG and Gene Ontology (GO) databases. The GO analysis revealed enrichment in pathways related to the regulation of cell communication (1,451 genes, FDR=1.6x10-6), signaling (1,448 genes, FDR=1.6x10-6), and signal transduction (1,271 genes, FDR=2.8x10-6) in the top ten relevant pathways. While this study has a small sample, it provides preliminary evidence that specific DNA methylation biomarkers might exist in Afro-descendant breast cancers from Latin-American women. It also adds to the current knowledge on these populations that can benefit from the identification of molecular markers that can ultimately identify those at greater risk of mortality. Citation Format: Lissette Delgado-Cruzata, Andre Luiz da Silva. Christianes, Cynthia C. Cardoso, Stephanie-Marie Flowers, Diego J. Gomes de Paula, Tatiana A. Simão, Jennifer Vieira Gomes, Leonor Gusmão, Sheila C. Soares-Lima. A pilot study to identify DNA methylation biomarkers associated with African ancestry in Latin-American breast cancers abstract. In: Proceedings of the 18th AACR Conference on the Science of Cancer Health Disparities; 2025 Sep 18-21; Baltimore, MD. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2025;34(9 Suppl):Abstract nr C085.