American Association for Cancer Research
crc-23-0236_fig4.png (1.12 MB)

FIGURE 4 from Chromatin Accessibility Landscape of Human Triple-negative Breast Cancer Cell Lines Reveals Variation by Patient Donor Ancestry

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posted on 2023-10-05, 14:20 authored by Alexandra R. Harris, Gatikrushna Panigrahi, Huaitian Liu, Vishal N. Koparde, Maeve Bailey-Whyte, Tiffany H. Dorsey, Clayton C. Yates, Stefan Ambs

Hypoxia exacerbates donor ancestry-related differences in TF activity in cultured TNBC cell lines. A, Chromosome map showing the distribution of DARs between EA and AA TNBC cells when subjected to hypoxic conditions (FC > 2, FDR < 0.01). B, Differential digital footprinting in EA- and AA-derived TNBC lines was performed using TOBIAS to identify open chromatin regions and their TF binding sites. Shown are the top AA- or EA-associated TFs whose predicted binding activity increased by a defined magnitude of >0.05 under hypoxia. PPI network of TFs with differential binding capacities (DBS > 22.5, FDR < 0.01) that are up in EA (C) and AA (D) under hypoxia using the STRING database. Top 15 significantly enriched pathways (FDR < 0.01, Reactome-based) based on a TF network analysis.


Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research

Cancer Prevention Fellowship Program, National Cancer Institute, NIH



African American (AA) women have an excessive risk of developing triple-negative breast cancer (TNBC). We employed Assay for Transposase-Accessible Chromatin using sequencing to characterize differences in chromatin accessibility between nine commonly used TNBC cell lines derived from patients of European and African ancestry. Principal component and chromosome mapping analyses of accessibility peaks with the most variance revealed separation of chromatin profiles by patient group. Motif enrichment and footprinting analyses of disparate open chromatin regions revealed differences in transcription factor activity, identifying 79 with ancestry-associated binding patterns (FDR < 0.01). AA TNBC cell lines exhibited increased accessibility for 62 transcription factors associated with epithelial-to-mesenchymal transition, cancer stemness/chemotherapeutic resistance, proliferation, and aberrant p53 regulation, as well as KAISO, which has been previously linked to aggressive tumor characteristics in AA patients with cancer. Differential Assay for Transposase-Accessible Chromatin signal analysis identified 1,596 genes located within promoters of differentially open chromatin regions in AA-derived TNBC, identifying DNA methyltransferase 1 as the top upregulated gene associated with African ancestry. Pathway analyses with these genes revealed enrichment in several pathways, including hypoxia. Culturing cells under hypoxia showed ancestry-specific stress responses that led to the identification of a core set of AA-associated transcription factors, which included members of the Kruppel-like factor and Sp subfamilies, as well as KAISO, and identified ZDHHC1, a gene previously implicated in immunity and STING activation, as the top upregulated AA-specific gene under hypoxia. Together, these data reveal a differential chromatin landscape in TNBC associated with donor ancestry. The open chromatin structure of AA TNBC may contribute to a more lethal disease. We identify an ancestry-associated open chromatin landscape and related transcription factors that may contribute to aggressive TNBC in AA women. Furthermore, this study advocates for the inclusion of diversely sourced cell lines in experimental in vitro studies to advance health equity at all levels of scientific research.