Genome-Wide Analysis of Transcription Factor Function in Prostate Cancer

描述(申请人提供)：雄激素受体(AR)，一种配体依赖的转录因子，在前列腺癌的发生和发展中发挥关键作用，是治疗的靶点。令人惊讶的是，人们对AR结合、AR协同转录因子以及对人类基因组中AR靶基因的调控知之甚少。该方案的总体目标是从全基因组的角度研究雄激素依赖(AD)和非雄激素非依赖性(Al)前列腺癌细胞中AR及其协同转录因子对蛋白质编码基因和一类非编码基因(microRNA[miRNA])的组合转录调控。为了解决这些问题，我们将使用染色质免疫沉淀(ChIP)结合人类全基因组询问拼接微阵列(ChlP-on-Chip)来研究转录因子在AD和Al前列腺癌中的体内结合及其调控功能。我们的具体目标是：(1)确定AD和A1前列腺癌细胞中是否存在不同的AR结合、AR协同转录因子伙伴和AR靶基因。AR ChlP-on-Chip分析将在AD和A1前列腺癌细胞中进行。AR结合、协同转录因子和AR靶基因将通过生物信息学算法进行预测和实验验证。(2)研究AR及其协同转录因子对AD和A1前列腺癌细胞中AR靶基因的联合调控作用。协同转录因子ChlP-on-Chip将被执行，并与AR ChlP-on-Chip和基因表达谱相关联，以确定AD和A1前列腺癌细胞中AR靶基因的组合转录调控密码。(3)确定AR及其协同转录因子是否对AD和A1前列腺癌细胞中的miRNAs进行调控。RNA聚合酶II(PolII)ChlP-on-Chip将在AD和A1前列腺癌细胞中进行。POL II结合将与AR及其协同转录因子结合和miRNA表达谱相关联，以确定AD和A1前列腺癌细胞中差异转录因子调控的miRNA表达。综上所述，这些研究将在全基因组水平上加深我们对AR及其协同转录因子对靶基因编码和非编码基因转录调控的基础理解，从而为AD和A1前列腺癌的治疗干预提供新的分子靶点。

DESCRIPTION (provided by applicant): The androgen receptor (AR), a ligand-dependent transcription factor, plays a key role in the onset and progression of prostate cancer and is a therapeutic target. Surprisingly little is known of AR binding, AR collaborating transcription factors, and regulation of AR target genes in the human genome. The overall goal of this proposal is to investigate the combinatorial transcriptional regulation of protein-coding genes and a class of non-coding genes (microRNA [miRNA]) by AR and its collaborating transcription factors from a genome-wide view in androgen-dependent (AD) and -independent (Al) prostate cancer cells. To address these issues, we will use chromatin immunoprecipitation (ChIP) combined with human whole genome interrogating tiling microarrays (ChlP-on-chip) to study in vivo binding of transcription factors and their regulatory function in AD and Al prostate cancer. Our specific aims are to: (1) Determine whether distinct AR binding, AR collaborating transcription factor partners and AR target genes exist in AD and Al prostate cancer cells. AR ChlP-on-chip assays will be performed in AD and Al prostate cancer cells. AR binding, its collaborating transcription factors and AR target genes will be predicted by bioinformatics algorithms and experimentally validated. (2) Determine how AR and its collaborating transcription factors combinatorially regulate AR target genes in AD and Al prostate cancer cells. Collaborating transcription factors ChlP-on-chip will be performed and correlated with AR ChlP-on-chip and gene expression profiles to identify combinatorial transcriptional regulatory codes for AR target genes in AD and Al prostate cancer cells. (3) Determine whether AR and its collaborating transcription factors regulate miRNAs in AD versus Al prostate cancer cells. RNA polymerase II (pol II) ChlP-on-chip will be performed in AD and Al prostate cancer cells. Pol II binding will be correlated to AR and its collaborating transcription factors bindings and miRNA expression profiles to identify differential transcription factors-regulated miRNA expression in AD and Al prostate cancer cells. In summary, these studies will increase our fundamental understanding of differential transcriptional regulation of target coding and non-coding genes by AR and its collaborating transcription factors on a genome-wide level in AD and Al prostate cancer, which will lead to identification of new molecular targets for therapeutic intervention in AD and Al prostate cancer.