Abstract C044: Investigation of breast tumor biology and microenvironment in women of African descent using a single cell multiomic approach

• Published in: Cancer epidemiology, biomarkers & prevention biomarkers & prevention, 2023-12, Vol.32 (12_Supplement), p.C044-C044
• Main Authors: Harris, Alexandra R., Liu, Huaitian, Jenkins-Lord, Brittany, Makokha, Francis, Sayed, Shahin, Gierach, Gretchen, Ambs, Stefan
• Format: Article
• Language: English
• ISSN: 1538-7755; 1538-7755
• DOI: 10.1158/1538-7755.DISP23-C044

Women of African descent are at an increased risk of developing and dying from aggressive subtypes of breast cancer. A connection between aggressive disease and Western Sub-Saharan African ancestry has been postulated, but it remains largely unknown to what extent breast cancer in Africa is reminiscent of breast cancer in U.S. African American (AA) women who experience disproportionately high mortality rates. We performed ATAC- and RNA-sequencing on 9 human triple-negative breast cancer cell lines of U.S. origin and discovered that African ancestry influences the chromatin landscape, leading to disparate transcription factor activity and downstream gene expression patterns indicative of an aggressive tumor biology. Here, we describe an ambitious study that employs single-nucleus ATAC- and RNA-sequencing (snMultiome) of frozen breast tumors to characterize chromatin accessibility and gene expression patterns with single-cell resolution in AA (n=32), Kenyan (n=18), and European American (EA, n=20) women in relation to ancestry and risk factor exposure. In an initial pilot in 10 Kenyan women, we successfully isolated intact, high-quality single nuclei from frozen breast tumor tissue through an optimized combination of enzymatic digestion and an automated tissue homogenizer. We performed multiome sequencing on a total of 36525 nuclei across these 10 pilot tumors using the 10x Genomics platform. Following filtering, normalization (SCT for snRNA; LSI for snATAC), peak calling (MACS2), and integration (Seurat-v4 for snRNA; Harmony for snATAC), we characterized tumor, stromal, and immune cell populations (totaling 10 distinct cell types). We observed striking intra- and inter-tumoral heterogeneity across Kenyan women, with increased abundance of immune subpopulations (myeloid, T-cells, B-cells) in triple-negative subtypes. After demonstrating technical feasibility and success in this sample subset, we are now performing integration, cell type annotation, and downstream analyses in our larger cohort to characterize differences in both tumor biology and the tumor microenvironment in European American, African American, and Kenyan women at the single cell level. To date, 70 tumors spanning breast cancer subtypes have been sequenced. We are currently performing downstream analyses in this cohort to characterize ancestry- and risk factor-related differences in the tumor epithelium and microenvironment at the single-cell level. This project holds the potential to yield