Breast cancer (BC) is the most prevalent cancer globally for women, contributing to 11.7% of all cancers in 2020. As a heterogeneous disease, BC is influenced by factors such as sex, age, and hormones. Although a number of genetic variants are linked to BC, roughly 90-95% of BC cases have an unknown hereditary link. Estrogen is critically related to BC, and genes within the estrogen pathway have been heavily studied. However, whether variations in the breast tissue microbiome are associated with genetic variation in estrogen receptor genes is currently unknown. We hypothesized that the genetic variation in and the expression of estrogen-related genes are associated with variations in local breast tissue microbes. To test our hypothesis, we conducted 30X whole genome sequencing on 60 breast tissue samples (healthy (n=15), pre-diagnostic (n=15), tumors (n=15), and adjacent normal (n=15)) donated by women to the Susan G. Komen and Indiana University Simon Cancer Center Tissue Banks. These same samples were previously analyzed for microbiome composition and function (mSystems, 2022).Following sequence pre-processing, variant calling, and alternate allele frequency calculation by the UC Davis Bioinformatics Core, we selected high and moderate variants with a quality score≥55 for further analysis. We ran generalized linear models to select variants with differences in frequency among tissue types (H, PD, AN, T, p≤0.2). Alternate allele frequencies and genotypes of the genes (BCL2L10, FOSL2-AS2, RAF1, and MAPK10) that passed this filter were then associated with bacterial ASVs deemed differentially abundant relative to the H tissue type (mSystems, 2022) using MaAsLin2. We also analyzed beta diversity (PC2) among the 60 tissues and conducted associations with variant frequencies and genotypes. We identified an association between the mut/mut genotype of MAPK10 and the genus Streptococcus (ASV415 q≤0.001, p≤0.001 and ASV7 q≤0.001, p≤0.001) and mut/mut genotype of BCL2L10 was also associated with the genus Proteus (mut/mut q=0.073, p≤0.001). Further, frequency of RAF1 was negatively associated with the genus Oceanobacillus (ASV916 q=0.806, p=0.010 and ASV10 q=0.806, p=0.011). For beta diversity, we observed the frequency of RAF1 (q=0.204, p=0.031) positively associated with PC2, while FOSL2-AS1 (q=0.204, p=0.059) and MAPK10 (q=0.204, p=0.055) frequency to be negatively associated with PC2.In conclusion, we highlight the identification of various associations between certain estrogen pathway genes with breast bacteria, suggesting that there is a relationship between breast tissue microbiome and the host genome. Next steps for this work involve analysis of transcription of MAPK10, RAF1, and BCL210 via qPCR to determine if the microbiome is associated with transcriptional alterations in these genes. This knowledge may be implemented as a predictive tool in assessing risk of BC development by using microbes as biomarkers for variation in host estrogen genetics and/or BC.

Citation Format: Rachel Jiang, Ariana McCaw, Lindsey Marian, Leah T Stiemsma. Association between Estrogen-Related Genetic and Microbial Factors in Breast Tissue: Implications for Breast Cancer Risk [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr A011.