Abstract PO-187: Identification of ancestry-specific gene expression profiles of African triple- negative breast tumors
Authors: Martini Rachel , Gebregzabher Endale , Dorsaint Princesca , Chu Timothy , Arora Kanika , Gibbs Lee , Manojlovic Zarko , Rovine Nicolas , Sboner Andrea , Elemento Olivier , Carpten John , Newman Lisa , Davis Melissa 
Published: December 2020

Women with shared West African ancestry suffer from disproportionately higher breast cancer (BC) mortality and are more frequently diagnosed with the most aggressive form of BC, triple negative BC (TNBC). We and others have shown a higher prevalence of TNBC in West African (Ghanaian) and AA women, compared to lower levels of TNBC in East African (Ethiopian) and White/European American (EA) women, and that higher levels of quantified West African ancestry are found among women with TNBC compared to non-TNBC breast tumors. To further understand the role of West African ancestry in the TNBC tumor microenvironment, we conducted RNA sequencing on a pilot cohort of archival FFPE tumor tissue obtained from Ghanaian (n = 19) and Ethiopian (n = 20) women with TNBC disease to study differences in gene expression profiles. SNV calls were obtained from the RNAseq data, and 1K Genome subpopulations were used as references to quantify ancestry of each patient. We observed that our Ghanaian samples have over 94% African ancestry (corresponding to West African populations), where our Ethiopian samples showed between 37-48% African ancestry (corresponding to East African populations). Quantified ancestry among our Ethiopian samples also revealed a significant proportion of European ancestry (30-49%), corresponding to Italian ancestry. Differentially expressed genes (DEGs) were identified by comparing self- reported ethnicity and correlations with genetic ancestry. We have identified over 600 DEGs between Ghanaian vs Ethiopian TNBC samples (p &lt; 0.01). We found over 900 genes that were associated with quantified African ancestry (p &lt; 0.01), using African ancestry as a continuous variable with linear regression methods.

Unsupervised hierarchical clustering of this gene set was able to separate Ghanaian and Ethiopian samples. We compared the output of both approaches, and found that only ~200 genes were shared, showing the distinct value of both approaches. We have begun to investigate the role of our differential gene lists in canonical pathways and gene networks using Ingenuity Pathway analysis methods. Using our overlapping differential gene list from both approaches, we observed differences such as quantity of T lymphocytes, where downregulation of genes may indicate differing levels this immune cell population in the TNBC tumor environment. In our ongoing analysis, we are using deconvolution methods, such as CIBERSORT and xCell, to validate and further characterize the presence of various immune cell populations in our TNBC tumors. This study shows that quantified genetic ancestry can be used to identify ancestry-specific gene regulation in African TNBC tumors. Specifically, with our ongoing analysis of the immune cell representation in our samples, we can define differences in tumor heterogeneity and immune response in an ancestry- specific manor.

Citation Format: Rachel Martini, Endale Gebregzabher, Princesca Dorsaint, Timothy Chu, Kanika Arora, Lee Gibbs, Zarko Manojlovic, Nicolas Rovine, Andrea Sboner, Olivier Elemento, John Carpten, Lisa Newman, Melissa Davis. Identification of ancestry-specific gene expression profiles of African triple- negative breast tumors [abstract]. In: Proceedings of the AACR Virtual Conference: Thirteenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2020 Oct 2-4. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(12 Suppl):Abstract nr PO-187.