Novel Markers for Disease Outcome in Breast Cancer

Division Of Basic Sciences - Nci

Investigators

Linked publications, trials & patents

Abstract

Project 1: The mechanisms through which chronic stressors may be associated with tumor biologic characteristics, immune response, and health disparities remain insufficiently understood. Hence, we investigated the proteomic, transcriptomic, and genomic effects associated with multilevel chronic stressors (perceived stress, perceived inadequate social support, perceived racial and ethnic discrimination, and neighborhood deprivation) in 121 African American and European American women with breast cancer. In this clinical study, we gave breast cancer patients, who are scheduled for breast cancer surgery, a short survey evaluating their perceived stress and social isolation. We also collected frozen tumor and adjacent normal breast tissue and blood samples from these patients and evaluate whether the breast tissue or the blood samples have a biological signature related to their perceived stress and social isolation status. We then asked the question how stress-related factors might be associated with circulating immune-inflammation markers, immune profiles, and tumor biologic characteristics in women with breast cancer. We found that stress, inadequate social support, racial and ethnic discrimination, and neighborhood deprivation were associated with deleterious biologic and immunologic changes at the genomic, transcriptomic, and proteomic levels both systemically and within the tumor microenvironment in patients with breast cancer (JAMA Network Open; PMID: 39951265). Specifically, they were associated with suppression of the antitumor immune response, systemic inflammation, and deleterious tumor biologic characteristics. These outcomes were particularly pronounced in African American women. These findings suggest that chronic stressor-induced inflammation and immune dysfunction may be associated with increased breast cancer aggressiveness and cancer disparities in socially vulnerable and minoritized populations. Understanding biology as a possible mediator of cancer health disparities can inform prevention and public health interventions. Project 2: Breast cancer biology is influenced by ancestry and the environment with implications for disease outcome. Still, we lack the knowledge how non-cancerous cells within tumors are functionally altered by these factors at single-cell resolution. With this project, we undertook an ambitious study employing single-nucleus ATAC- and RNA-sequencing of frozen breast tumors to characterize chromatin accessibility and gene expression patterns with single-cell resolution in African American (n=33), Kenyan (n=25), and European American (n=24) women in relation to genetic ancestry, risk factor exposures, clinical characteristics, and 5-year survival. Current efforts focus on in-depth molecular characterization of ancestry- and disease risk factor-related differences in the tumor epithelium and microenvironment and distinct signatures present in lethal disease. We established a new protocol to successfully isolate intact, high-quality single nuclei from archival frozen breast tumor tissue through an optimized combination of enzymatic digestion and automated tissue homogenization. We performed single-nuclei Multiome sequencing of 82 tumors and established a new analytic pipeline for this dataset. Following filtering, normalization, peak calling, and integration, our dataset includes a total of 292,458 nuclei. Cancerous (163,419 nuclei) and non-cancerous (129,039 nuclei) cells were distinguished based on DNA copy number (CopyKat). Within the microenvironment, 11 major immune, epithelial, and stromal cell types were successfully annotated, exhibiting distinct patterns by population group (e.g. African American patient tumors showed markedly increased abundance of myeloid and T-cells, while Kenyan tumors showed increased abundance of pericytes and fibroblasts). After considerable effort, we were able to further complete detailed annotations of 26 immune cell subpopulations. Adjusting for confounders, we find that women of African descent distinctively possess pro-tumorigenic subpopulations of pericytes and vascular endothelial cells. They also exhibit a more immune-suppressive tumor microenvironment with impairment of dendritic cells and enrichment of tolerogenic B and regulatory T cells. Further, we describe gene signatures within the microenvironment that are predictive of survival. Together, we uncovered molecular characteristics of clinical significance in breast cancer of African ancestry women. A manuscript is currently drafted and will be submitted for publication in 2025.