Transcriptional Signatures of Homologous Recombination Deficiency for Targeted Ch

目标 Ch 同源重组缺陷的转录特征

• 批准号: 8424340
• 负责人: Robert W Sobol
• 金额: $ 24.35万
• 依托单位: UNIVERSITY OF PITTSBURGH AT PITTSBURGH
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-11-15 至 2014-10-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8424340
• 关键词: Address; Aging; BRCA1 gene; Base Excision Repairs; Biological Markers; Bromouridine; Cell Line; Cell physiology; Cells; Cisplatin; Code; DNA Repair; DNA Repair Disorder; DNA Repair Gene; DNA Repair Pathway; DNA repair protein; DNA-PKcs; Defect; Development; Disease; Epigenetic Process; Epithelial; Epithelial Cells; Excision Repair; Exposure to; Gene Expression; Gene Expression Profile; Genes; Genetic; Genetic Transcription; Genome; Genome Stability; Genotoxic Stress; Germ Lines; Glioma; Goals; Growth; Human; Ionizing radiation; Knowledge; Label; Lentivirus Vector; Libraries; MLH1 gene; Maintenance; Malignant Neoplasms; Measures; Mediating; Messenger RNA; MicroRNAs; Modeling; Molecular; Nonhomologous DNA End Joining; Normal Cell; Nucleotide Excision Repair; Pathway interactions; Phenotype; Physiologic pulse; Proteins; RNA; RNA Degradation; RNA Stability; RNA chemical synthesis; Radiation; Regimen; Role; SHFM1 gene; Sampling; Seeds; Single Strand Break Repair; Somatic Mutation; Stress; Techniques; Technology; Tumor-Derived; XPA gene; XRCC1 gene; base; cancer cell; chemotherapeutic agent; expectation; genome-wide; homologous recombination; improved; inhibitor/antagonist; neoplastic cell; new technology; next generation sequencing; novel strategies; public health relevance; repaired; response; small hairpin RNA; stable cell line; tool; transcriptome sequencing; transcriptomics; treatment planning; tumor; vector

DESCRIPTION (provided by applicant): DNA repair pathways maintain the integrity of the genome and it is therefore not surprising that many cancer cells are defective in some aspect of DNA repair. Fortunately, these cancer-specific DNA repair defects offer novel approaches for tumor-selective therapy such as the synthetic lethality of PARP1 inhibitors with BRCA-deficient or homologous recombination (HR)-deficient tumors. An important goal and challenge is thus to identify which tumors are defective in the various specific pathways of DNA repair. It is understood that changes in DNA repair capacity will impact cellular functions both at baseline and in response to genotoxic stress. Further, it has been suggested that these changes in DNA repair capacity may reprogram the cellular transcriptional landscape. Recent evidence suggests that this reprogramming occurs at multiple levels, including changes in the synthesis and stability of specific RNAs, suggesting that DNA repair deficiency may provide unique transcriptional signatures. It is our expectation that the RNA synthesis and stability signature associated with a defect in HR will be unique and may be useful in identifying HR defects without knowledge of any underlying gene defect. We have developed a genome-wide approach for identifying such a signature, termed "BrU-Seq", in which BromoUridine pulse-labeling of nascent RNAs is combined with RNA-Seq in a manner that reveals a remarkably large number of influences on gene expression with a clarity and efficiency not allowed by standard microarray or RNA-Seq approaches. To advance our understanding of the impact of a sudden (somatic) DNA repair defect in a normal cell, we propose to comprehensively evaluate the dynamic status of all coding and regulatory RNAs in the model non-tumorigenic epithelial cell line, MCF-10A, following loss of expression of DNA repair genes across each DNA repair pathway. We hypothesize that DNA repair defects will impact mRNA/microRNA expression and stability with DNA repair pathway-specific signatures that can be used to predict response to certain chemotherapeutic agents. Specifically, we will use BrU-Seq technology to (1) measure the synthesis, stability and structural content of all coding and regulatory RNA species in isogenic MCF-10A cell lines deficient in a key gene in each of the six major DNA repair pathways and (2) evaluate genotoxic stress-induced alterations in the transcriptional profile of the same cells in response to ionizing radiation and the chemotherapeutics temozolimide, cisplatin and PARP inhibitors. These studies will be a critical first step towards identifying signatures associated with specific DNA repair pathway defects in tumor samples that may be used as biomarkers to predict response to targeted chemotherapeutic agents.

描述（由申请人提供）：DNA修复途径保持基因组的完整性，因此毫不奇怪，许多癌细胞在DNA修复的某些方面都有缺陷。幸运的是，这些特异性DNA修复缺陷为肿瘤选择疗法提供了新的方法，例如具有BRCA缺乏或同源重组（HR）缺陷型肿瘤的PARP1抑制剂的合成致死性。因此，一个重要的目标和挑战是确定哪些肿瘤在DNA修复的各种特定途径中有缺陷。可以理解，DNA修复能力的变化将影响基线和响应遗传毒性应激的细胞功能。此外，已经提出，DNA修复能力中的这些变化可能会重新编程细胞转录局势。最近的证据表明，这种重编程发生在多个级别上，包括特定RNA的合成和稳定性的变化，表明DNA修复缺乏可能会提供独特的转录特征。我们期望与人力资源缺陷相关的RNA合成和稳定性签名将是独特的，并且可能在识别HR缺陷的情况下可能有用，而无需了解任何潜在的基因缺陷。我们已经开发了一种全基因组的方法，用于识别这种名为“ bru-seq”的特征，其中新生RNA的溴化脉冲标记与RNA-SEQ结合了RNA-SEQ，以一种非常明显的影响，以明确的和标准的微段或RNA-SEQ方法允许对基因表达的影响很大。为了促进我们对正常细胞中突然（体细胞）DNA修复缺陷的影响的理解，我们建议在模型非肿瘤上皮细胞系MCF-10A中全面评估所有编码和调节性RNA的动态状态，MCF-10A（MCF-10A），在每个DNA修复途径中DNA修复基因的表达丧失之后。我们假设DNA修复缺陷将用DNA修复途径特异性特异性特异性特异性特异性特异性的特异性特异性影响mRNA/microRNA的表达和稳定性，这些特异性可用于预测对某些化学治疗剂的反应。 Specifically, we will use BrU-Seq technology to (1) measure the synthesis, stability and structural content of all coding and regulatory RNA species in isogenic MCF-10A cell lines deficient in a key gene in each of the six major DNA repair pathways and (2) evaluate genotoxic stress-induced alterations in the transcriptional profile of the same cells in response to ionizing radiation and the chemotherapeutics temozolimide,顺铂和PARP抑制剂。这些研究将是识别与肿瘤样品中特定DNA修复途径缺陷相关的特征的关键第一步，这些特征可以用作预测对靶向化学治疗剂的反应的生物标志物。