Long noncoding RNA regulations in breast cancer among African-American women

摘要 非洲裔美国人（AA）女性的乳腺癌发病率继续上升，并可能进一步扩大乳房。 AA女性经历的癌症差异，她们更有可能发展为侵袭性肿瘤类型， 预后更差这些差异的生物学原因在很大程度上仍然未知。最近全基因组， 高通量研究强调了长非编码RNA（lncRNA）作为一类新的 癌症中的调节分子。lncRNA在整体基因表达中形成重要的调控层， 越来越多的证据表明，特异性lncRNA的异常表达可能与乳腺癌有关， 致癌和进展。然而，迄今为止的研究都只针对EA女性，尚未 常用的高通量下一代测序（NGS），以提供无偏倚的全面 分析，并且大多不包括严格的正常组织对照。基于这些研究空白， 局限性，我们最近完成了一项在正常人和正常人中全基因组lncRNA表达谱的初步研究， 来自AA和EA妇女的肿瘤乳腺组织。LncRNA表达数据显示明确的组织-和亚型- 特定的表达模式。重要的是，我们注意到AA和AA之间存在大量差异丰度的lncRNA。 雌激素受体（ER）状态。这些结果表明，有独特的lncRNA， 我们假设AA肿瘤中的表达模式有助于侵袭性肿瘤生物学和高表达。 乳腺癌相关死亡率。我们提出了一个具有成本效益的研究，在一个良好的特点队列AA乳腺癌 妇女健康圈研究（WCHS）中的癌症患者，该研究有可用的肿瘤组织块， 关于肿瘤特征、临床结果、接受的治疗、生活方式因素和基因组的广泛数据- DNA甲基化。因此，我们的具体目标是：1）使用以下方法进行组织lncRNA表达谱分析： 总RNA测序（来自WCHS的1181例AA病例和来自科门组织库的100例AA对照）， 确定乳腺癌和ER亚型特异性的lncRNA（肿瘤，ER+，ER-vs.正常）和那些 与临床病理因素相关（例如，2）检查lncRNA表达水平与 乳腺癌生存率，并使用机器学习方法来识别一组组合的lncRNA 与乳腺癌生存相关;并进一步进行计算预测和体外功能研究。 分析以确定它们的生物学相关性;以及3）整合关于lncRNA表达和DNA序列的配对数据。 甲基化，以确定这些癌症和乳腺癌相关的lncRNA中的哪一个由DNA调节 甲基化，并探讨饮食，肥胖和其他生活方式相关因素是否与异常甲基化有关。 DNA甲基化这项工作是新颖的，预计这些发现将促进我们对分子生物学的理解。 在AA女性中观察到的导致侵袭性肿瘤生物学和癌症预后不良的机制， 可以转化为预防和治疗的靶向策略的发展。

ABSTRACT Breast cancer rates among African-American (AA) women continue to rise and may further widen breast cancer disparities experienced by AA women, who are more likely to develop aggressive tumor types with a worse prognosis. The biological reasons for these differences remain largely unknown. Recent genome-wide, high-throughput studies highlight an emerging role of long noncoding RNAs (lncRNAs) as a novel class of regulatory molecules in cancer. LncRNAs form an important regulatory layer in global gene expression, and increasing evidence indicates that abnormal expression of specific lncRNAs can contribute to breast cancer carcinogenesis and progression. Studies to date, however, are focused exclusively on EA women, have not commonly used high-throughput next generation sequencing (NGS) to provide unbiased comprehensive profiling, and mostly do not incorporate rigorous normal tissue controls. Motivated by these research gaps and limitations, we recently completed a pilot study of genome-wide lncRNA expression profiling in normal and tumor breast tissues from AA and EA women. LncRNA expression data showed clear tissue- and subtype- specific expression patterns. Importantly, we noted a number of differentially abundant lncRNAs between AA and EA women by estrogen receptor (ER) status. These results indicate that there are unique lncRNA expression patterns in AA tumors, which we hypothesize contributes to aggressive tumor biology and high breast cancer-related mortality. We propose a cost-effective study in a well-characterized cohort of AA breast cancer patients in the Women’s Circle of Health Study (WCHS), which has available tumor tissue blocks, and extensive data on tumor characteristics, clinical outcomes, treatments received, lifestyle factors, and genome- wide DNA methylation. As such, our Specific Aims are: 1) Perform tissue lncRNA expression profiling using total RNA sequencing (1181 AA cases from WCHS and 100 AA controls from Komen Tissue Bank) to determine lncRNAs that are breast cancer- and ER subtype- specific (tumor, ER+, ER- vs. normal) and those associated with clinico-pathological factors (e.g., grade); 2) Examine associations of lncRNA expression levels with breast cancer survival, and use a machine learning approach to identify a combined panel of lncRNAs associated with breast cancer survival; and further perform computational prediction and in vitro functional assays to determine their biological relevance; and 3) Integrate paired data on lncRNA expression and DNA methylation to determine which of these cancer- and prognosis-relevant lncRNAs are regulated by DNA methylation, and explore whether diet, obesity and other lifestyle-related factors are associated with aberrant DNA methylation. This work is novel and findings are anticipated to advance our understanding of molecular mechanisms contributing to aggressive tumor biology and poor cancer prognosis observed in AA women that can be translated into the development of targeted strategies for prevention and therapeutics.