Integrated chromatin accessibility and gene expression landscape of human triple-negative breast cancer cell lines reveals variation by patient donor ancestry [RNA-seq]. Integrated chromatin accessibility and gene expression landscape of human triple-negative breast cancer cell lines reveals variation by patient donor ancestry [RNA-seq]

African American (AA) women are at increased risk of developing and dying from Triple-Negative Breast Cancer (TNBC), an aggressive breast cancer subtype, compared to European American (EA) women in the United States. In addition to social determinants, further investigation into biologic factors that contribute to these disparities is needed to fully understand this multi-factorial problem. In particular, the epigenetics of racial/population diversity and its influence on breast cancer incidence and outcomes remains underexplored. Using ATAC-sequencing and RNA-sequencing, we characterized differences in chromatin accessibility and gene expression between EA-derived versus AA-derived TNBC cell lines (N=9). Our analyses revealed significant differences in transcription factor binding and downstream gene expression associated with cancer stemness, resistance, and epithelial to mesenchymal transition. Differences were exacerbated under conditions of hypoxia. Together, these data suggest a differential chromatin and transcriptomic landscape that may contribute to worsened TNBC biology in women of African ancestry. Additionally, as many of these cell lines are used routinely in biomedical research, these findings also indicate that the ancestral origin of patient derived cell lines matters and may contribute to biologic variation in experimental data, suggesting that inclusion of diversely sourced cell lines should be considered in experimental design. Overall design: RNA was isolated from breast cancer cell lines (n = 8 normoxia and n = 8 hypoxia) using TRIzol method. The mRNA profiles of the above breast cancel cell lines were generated by deep sequencing using Illumina NextSeq 2000 P2.

在美国，相较于欧裔美国（European American, EA）女性，非裔美国（African American, AA）女性罹患三阴性乳腺癌（Triple-Negative Breast Cancer, TNBC，一种侵袭性乳腺癌亚型）并因此死亡的风险更高。除社会决定因素外，为全面理解这一多因素问题，仍需进一步探究造成这种健康差异的生物学机制。其中，种族/人群多样性的表观遗传学特征及其对乳腺癌发病率与预后的影响仍未得到充分探索。本研究通过ATAC测序（ATAC-sequencing）与RNA测序（RNA-sequencing），对欧裔来源与非裔来源的三阴性乳腺癌细胞系（N=9）之间的染色质开放性与基因表达差异进行了系统表征。分析结果显示，与癌症干细胞特性、肿瘤耐药性及上皮间质转化相关的转录因子结合事件与下游基因表达均存在显著差异。在缺氧培养条件下，上述差异会进一步放大。综合上述数据可知，染色质与转录组景观的差异可能加剧了非洲血统女性的三阴性乳腺癌恶性生物学行为。此外，鉴于这类细胞系在生物医学研究中被常规应用，本研究结果亦提示：患者来源细胞系的祖先起源会对实验结果产生影响，可能导致实验数据出现生物学层面的变异，这意味着实验设计中应考虑纳入来源多样化的细胞系。总体实验设计：采用TRIzol法从乳腺癌细胞系（常氧组n=8，缺氧组n=8）中分离总RNA。上述乳腺癌细胞系的mRNA表达谱通过Illumina NextSeq 2000 P2平台完成深度测序获取。