Single nuclei chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry

Abstract Single nuclei analysis is allowing robust classification of cell types in an organ that helps to establish relationships between cell-type specific gene expression and chromatin accessibility status of gene regulatory regions. Using the institutional resource of breast tissues of healthy donors of various genetic ancestry, we have developed a comprehensive chromatin accessibility (snATAC-seq) and gene expression (snRNA-seq) atlas of human breast tissues. Our analyses included 51,367 nuclei with average sequence coverage of 1195 genes per nuclei. These nuclei were derived from 22 donors of Ashkenazi descent, 20 of European non-Ashkenazi ancestry, 10 of Asian ancestry, 10 Hispanic/Latina, 10 Native American, 6 from BRCA1 mutation carriers, and 5 from BRCA2 mutation carriers. Although tissues from 20 women of African Ancestry were included in sequencing, poor quality sequencing reads prevented inclusion of data from those samples in the final analysis. Integrated analysis revealed 10 distinct cell types in the healthy breast, which included three major epithelial cell subtypes (mature luminal, luminal progenitor, basal), two endothelial subtypes, two adipocyte subtypes, fibroblasts, T-cells, and macrophages. Mature luminal cells could be further divided into two distinct hormone sensitive subtypes, HSa and HSb, with HSa subtype expressing higher levels of Estrogen Receptor alpha (ESR1) and NEK10, a tyrosine kinase that controls p53 activity and limits cell proliferation. The luminal progenitors could be broadly classified into alveolar progenitors (AP) and basal-luminal hybrid progenitors (BL). AP cells expressed higher levels of ELF5, a known marker of alveolar cells, compared to BL cells. Basal cells could be classified into two subtypes with Basal-BAa cells being the most dominant and expressing higher levels of TP63 and NFIB compared to Basal-BAb cells. ESR1 expression pattern was distinctly different in tissues from Native Americans compared to the rest, with a high level of ESR1 expression extending to AP cells. In fact, overall AP cell numbers were ~3-fold higher in Native Americans compared to others (18.9% versus 1.5-8.8%). Furthermore, Ingenuity pathway analysis of differentially expressed genes revealed elevated Estrogen Receptor signaling in ML and AP cell types of Native Americans compared to those of other genetic ancestry. Despite significant differences in expression and activity in Native Americans compared to others, the chromatin accessibility map of the ESR1 gene regulatory regions in ML and LP cells did not show any genetic ancestry dependent variability. In general, cell subtype-specific gene expression did not correlate with chromatin accessibility differences, suggesting that transcriptional regulation independent of chromatin accessibility governs cell type-specific gene expression in the breast. Collectively, these results reveal complexities in gene expression in different cell types of the breast Citation Format: Poornima Bhat-Nakshatri, Duojiao Chen, Aditi Khatpe, Hongyu Gao, Yunlong Liu, Anna Maria Storniolo, Harikrishna Nakshatri. Single nuclei chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry [abstract]. In: Proceedings of the 15th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2022 Sep 16-19; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr IA024.