Race-specific transcriptome and Long non-coding RNA of ADT-resistant African-American prostate cancer cell models.. Race-specific transcriptome and Long non-coding RNA of ADT-resistant African-American prostate cancer cell models.

Purpose: The goals of this study are to compare NGS-derived Androgen Deprivation Therapy (ADT) resistant transcriptome to profiling (RNA-seq) to Androgen Deprivation Therapy (ADT) sensitive transcriptome in African American prostate cancer cells and validate by reverse transcription polymerase chain reaction (qRT–PCR) methods. Method: Total RNA was extracted from different CaP cell who were ADT sensitive and ADT resistance. Total RNA was subjected to whole transcriptome sequencing analysis. Sequence reads Results: We performed whole transcriptome RNA-Seq analysis through paired-end deep sequencing to systematically investigate the molecular features of different CaP cell models- RCC7/N, RCC7T/E, RCC7T/E-ADT, RCC7T/E-CD133, E006AA-hT and E006AA-hT-ADT We obtained an average of 23.85 million reads per sample, ranging from 22.86 to 24.93 million reads, with an average mapping rate of 98.29% to the reference human genome (UCSC version hg20). Next we performed Kal’s Z-test and generated Fold-Change (FC) values, p values and False Discovery Rate (FDR) values for measuring comparative gene expression profile. By applying stringent statistical threshold of greater than or equal to 2 FC, p value < 0.05 and FDR value < 1, we identified genes that were significantly differentially expressed in three different comparative groups. Conclusions: "Our study represents the first detailed analysis of African American ADT resistant transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions. " Overall design: Androgen resistant and Androgen sensitive mRNA profiles from African American prostate cancer of were generated by deep sequencing, in duplicate using Illumina HiSeq

研究目的：本研究旨在对比非洲裔美国前列腺癌细胞中，下一代测序（Next-Generation Sequencing，NGS）获得的雄激素剥夺治疗（Androgen Deprivation Therapy，ADT）耐药转录组与ADT敏感转录组的RNA测序（RNA-seq）谱，并通过实时定量逆转录聚合酶链式反应（qRT–PCR）方法进行验证。
方法：从不同株ADT敏感与ADT耐药的前列腺癌细胞（CaP细胞，CaP为前列腺癌Prostate Cancer的缩写）中提取总RNA，对总RNA开展全转录组测序分析。
测序读段与结果：本研究通过双端深度测序完成全转录组RNA测序分析，以系统探究不同前列腺癌细胞模型——RCC7/N、RCC7T/E、RCC7T/E-ADT、RCC7T/E-CD133、E006AA-hT及E006AA-hT-ADT的分子特征。所有样本的平均测序读段数为2385万，读段数范围为2286万至2493万，与参考人类基因组（UCSC版本hg20）的平均比对率为98.29%。随后采用Kal's Z检验计算折叠变化（Fold-Change，FC）值、p值及错误发现率（False Discovery Rate，FDR），以评估基因表达谱差异。通过设置严格的统计阈值：折叠变化≥2、p值<0.05且FDR<1，我们在三个对比组中筛选出了显著差异表达的基因。
结论：本研究首次借助RNA测序技术，通过生物学重复对非洲裔美国人群的ADT耐药转录组开展详细分析。本研究报道的优化数据分析流程，可为表达谱的对比研究提供参考框架。研究结果表明，NGS可实现对细胞或组织内mRNA含量更全面、准确的定量与定性评估。综上，基于RNA-seq的转录组表征可加速遗传网络分析，并助力解析复杂的生物学功能。
整体实验设计：通过Illumina HiSeq平台进行双份重复深度测序，获得非洲裔美国前列腺癌的雄激素耐药与雄激素敏感mRNA表达谱。