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）：基因融合已被认为是肿瘤形成的标志。基因融合的研究为许多癌症诊断和治疗奠定了理论背景。最近，我们和其他人报道了前列腺癌中涉及两个邻近基因 SLC45A3 和 ELK4 的嵌合融合 RNA。嵌合RNA表达水平与前列腺癌进展相关。此外，沉默嵌合体会导致速度减慢 雄激素依赖性和去势抵抗性前列腺癌细胞中的增殖和更高水平的 CDKN1A 表达。有趣的是，我们发现SLC45A3-ELK4是通过相邻基因顺式剪接（cis-SAGe）/通读机制产生的，而不是染色体重排。尽管SLC45A3-ELK4具有生物学和临床意义，但cis-SAGe的机制尚未阐明，也未鉴定出cis-SAGe的其他实例。在我们的初步研究中，我们假设并积累了多种证据，即锌指蛋白 CTCF 与两个相邻基因之间的绝缘体位点的结合在 SLC45A3 和 ELK4 之间顺式 SAGe 的生成中发挥着重要作用。我们还假设通过操纵 CTCF 水平可以识别更多的 cis-SAGe 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的机制。我们推断 cis-SAGe 本质上是穿过基因边界的连续转录本的选择性剪接。我们假设SLC45A3和ELK4之间发生顺式SAGe事件必须满足三个因素：5'SLC45A3基因的激活、减少CTCF与两个基因之间的绝缘体区域的结合以及增强的选择性剪接。在目标 1 中，我们将首先在 LNCaP 前列腺癌细胞系中研究所有三个调节因素，然后在其他细胞系和临床样本中进行研究；在 Aim2 中，我们将操纵 CTCF 水平并使用配对末端转录组测序来识别其他 cis-SAGe 融合体。我们使用 LNCaP 细胞的初步研究已经产生了许多融合候选物供研究。我们将进一步验证这些候选者是否为真正的 cis-SAGe 事件，并扩展到其他细胞系。在 Aim3 中，我们将研究新发现的 cis-SAGe 融合体的生物学和临床意义。拟议的研究将阐明 cis-SAGe 的机制并发现新的癌症相关嵌合转录本。新的融合基因产物可能是新疾病生物标志物和/或治疗靶点的潜在候选者。同样的方法可以很容易地应用于其他癌症类型。