cis-splicing of adjacent genes in prostate cancer

前列腺癌中相邻基因的顺式剪接

• 批准号: 8930941
• 负责人: HUI LI
• 金额: $ 32.79万
• 依托单位: UNIVERSITY OF VIRGINIA
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-09-22 至 2019-08-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8930941
• 关键词: Alternative Splicing; Androgens; Apoptosis; Binding; Biological; Biological Markers; Biological Process; Breast Carcinoma; CCCTC-binding factor; CDKN1A gene; Cancer Biology; Cancer cell line; Cell Line; Cells; Chimera organism; Chromosomal RNA; Chromosomal Rearrangement; Clinical; Code; DNA; Data; Development; Diagnostic; Disease; Epigenetic Process; Event; Exons; Gene Fusion; Gene Mutation; Generations; Genes; Genetic; Genetic Transcription; Health; Iceberg; LNCaP; Light; Maintenance; Malignant - descriptor; Malignant Neoplasms; Malignant neoplasm of prostate; Modeling; Molecular; Neoplasms; Nucleic Acid Regulatory Sequences; Oncogenic; Outcome; Phenotype; Play; Process; Prognostic Marker; Prostate carcinoma; Proteins; RNA; RNA Sequence Analysis; RNA Splicing; Reading; Regulation; Relative (related person); Reporting; Role; Sampling; Site; Somatic Mutation; Staging; Testing; Therapeutic; Transcript; Tumor Biology; Work; Zinc Fingers; base; cancer cell; cancer diagnosis; cancer type; castration resistant prostate cancer; clinically significant; fusion gene; gene discovery; genome sequencing; lung Carcinoma; meetings; migration; novel; overexpression; programs; promoter; prostate cancer cell; prostate cancer cell line; theories; therapeutic target; transcriptome sequencing; tumor progression; tumorigenic

DESCRIPTION (provided by applicant): Gene fusions have been considered a hallmark of neoplasia. The study of gene fusions has founded the theoretical backgrounds for many cancer diagnosis and therapeutics. Recently, we and others reported a chimeric fusion RNA involving two neighboring genes, SLC45A3 and ELK4, in prostate cancer. The chimeric RNA expression level correlates with prostate cancer progression. In addition, silencing the chimera led to slower proliferation and higher levels of CDKN1A expression in both androgen-dependent and castration- resistant prostate cancer cells. Intriguingly, we found that SLC45A3-ELK4 is generated by a mechanism of cis- splicing of adjacent genes (cis-SAGe)/read-through, instead of chromosomal rearrangement. Despite the biological and clinical significance of SLC45A3-ELK4, neither has the mechanism of cis-SAGe been elucidated, nor have other examples of cis-SAGe been identified. In our preliminary studies we hypothesized, and have accumulated multiple lines of evidence, that the binding of the zinc finger protein CTCF to insulator sites in-between the two neighboring genes plays an important role in the generation of cis-SAGe between SLC45A3 and ELK4. We also hypothesize that more cis-SAGe events can be identified through manipulating CTCF level, with implications for both prostate cancer biology and tumor biology in general. We propose to provide more evidence for these hypotheses in three aims. In Aim1, we will investigate the mechanism of cis- SAGe using SLC45A3-ELK4 as a model. We reasoned that the cis-SAGe is essentially alternative splicing of a continuous transcript passing through gene boundaries. We hypothesized that three factors have to be met for the cis-SAGe event to happen between SLC45A3 and ELK4: activation of the 5' SLC45A3 gene, reduced CTCF binding to the insulator regions in-between two genes, and enhanced alternative splicing. In Aim1, we will investigate all three factors of regulation first in LNCaP prostate cancer cell line, then in other cell lines and in clinical samples; In Aim2, we will manipulate CTCF level and use paired-end transcriptome sequencing to identify additional cis-SAGe fusions. Our preliminary study using LNCaP cells already generated many fusion candidates for study. We will further validate these candidates as true cis-SAGe events and expand to other cell lines. In Aim3, we will investigate the biological and clinical significance o the newly identified cis-SAGe fusions. The proposed study will shed light on the mechanism of cis-SAGe and discover novel cancer- associated chimeric transcripts. The novel fusion gene products may be potential candidates for new disease biomarkers and/or therapeutic targets. The same approach can be easily adapted in other cancer types.

描述（由申请人提供）：基因融合被认为是肿瘤的标志。基因融合的研究建立了许多癌症诊断和治疗剂的理论背景。最近，我们和其他人报道了前列腺癌中涉及两个相邻基因SLC45A3和ELK4的嵌合融合RNA。嵌合RNA表达水平与前列腺癌的进展相关。此外，沉默的嵌合体导致较慢 在雄激素依赖性和castatration-耐药性前列腺癌细胞中，增殖和较高水平的CDKN1A表达。有趣的是，我们发现SLC45A3-ELK4是通过相邻基因（顺式）/读取的机制而不是染色体重排的。尽管SLC45A3-ELK4具有生物学和临床意义，但也没有阐明CIS-SAGE的机制，也没有发现其他顺式示例。在我们的初步研究中，我们假设并积累了多种证据，即在两个相邻基因之间的锌指蛋白CTCF与绝缘体位点的结合在SLC45A3和ELK4之间的顺式中发挥了重要作用。我们还假设可以通过操纵CTCF水平来识别更多的顺式 - 平衡事件，这对前列腺癌生物学和一般肿瘤生物学都有影响。我们建议在三个目标中为这些假设提供更多证据。在AIM1中，我们将使用SLC45A3-ELK4作为模型研究CIS-SAGE的机理。我们认为，顺式 - 基本上是通过基因边界的连续转录物的替代剪接。我们假设必须在SLC45A3和ELK4之间发生三个因素：5'SLC45A3基因的激活在两个基因之间与绝缘体区域的结合减少，从而减少了CTCF的结合，并增强了替代拼接。在AIM1中，我们将首先在LNCAP前列腺癌细胞系，然后在其他细胞系和临床样品中研究所有三个调节因素。在AIM2中，我们将操纵CTCF级别并使用配对的转录组测序来识别其他顺式融合。我们使用LNCAP细胞的初步研究已经产生了许多候选融合候选者。我们将进一步验证这些候选者为真实的顺式事件，并扩展到其他细胞系。在AIM3中，我们将研究新近鉴定的顺式融合的生物学和临床意义。拟议的研究将阐明顺式 - 含量的机理，并发现新型癌症相关的嵌合转录本。新型的融合基因产物可能是新疾病生物标志物和/或治疗靶标的潜在候选者。可以在其他癌症类型中轻松适应相同的方法。