Transcriptomic profiling and functional characterization of fusion genes in recurrent ovarian cancer

复发性卵巢癌融合基因的转录组分析和功能表征

基本信息

批准号：
9307549
负责人：
Nolan Priedigkeit
金额：
$ 4.9万
依托单位：
UNIVERSITY OF PITTSBURGH AT PITTSBURGH
依托单位国家：
美国
项目类别：
财政年份：
2016
资助国家：
美国
起止时间：
2016-07-01 至 2020-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9307549
关键词：
ABCB1 gene ANK3 gene Base Pairing Bioinformatics Biological Biological Assay Biological Markers CCDC6 gene CRISPR/Cas technology Cancer Etiology Cancer Model Cancer Relapse Cancer cell line Cell Line Cell Proliferation Cessation of life Chronic Myeloid Leukemia Clinical Clinical Trials Computer Simulation Custom Data Data Set Detection Diagnosis Disease Drug Efflux Drug Targeting Early Diagnosis Engineering Environment Epithelial Event FGFR2 gene Gene Fusion Generations Genes Genome Genomics Gleevec Goals Imatinib mesylate Institution Maintenance Malignant Female Reproductive System Neoplasm Malignant Neoplasms Malignant neoplasm of ovary Mediator of activation protein Messenger RNA Methods Mission Molecular Mutation National Cancer Institute Neoplasm Metastasis Oncogenic Ovarian Serous Cystadenocarcinoma Pathogenicity Patient-Focused Outcomes Patients Phenotype Physicians Plasma Play Prevalence Primary Neoplasm Probability Production RNA Recurrence Recurrent disease Recurrent tumor Regimen Relapse Reporting Resistance Reverse Transcriptase Polymerase Chain Reaction Role Sampling Scientist Serous Solid Solid Neoplasm Survival Rate TOP2A gene Techniques Technology Testing The Cancer Genome Atlas Training Transcript Tumor Cell Line Variant Woman Work bcr-abl Fusion Proteins burden of illness cancer recurrence cancer type cell motility clinically actionable clinically relevant cohort drug sensitivity efflux pump fusion gene gain of function human tissue improved in vitro Model inhibitor/antagonist knock-down malignant phenotype migration nano-string new therapeutic target next generation sequencing novel outcome forecast overexpression personalized medicine precision oncology response structural genomics success targeted biomarker therapeutic biomarker therapeutic target therapy development transcriptome sequencing transcriptomics treatment response tumor tumor DNA tumor progression

项目摘要

PROJECT SUMMARY Ovarian serous cystadenocarcinoma (OvCa) accounts for 90% of ovarian cancers and is most often detected in its later stages, has limited therapies and carries a poor prognosis—the 5-year survival rate for patients with late stage disease is less than 50%. Counterintuitively, OvCa is exquisitely sensitive to initial therapies with most patients achieving a complete clinical response. 80% of patients; however, will eventually relapse with metastases and an acquired tumor chemoresistance. Patients diagnosed with relapsed disease consequently have a tragic average survival of 12 to 18 months. Maintenance regimens to improve the overall survival of recurrent disease show limited success. The Cancer Genome Atlas (TCGA) has sequenced hundreds of primary OvCa tumors to improve our understanding of the disease. Results thus far have been humbling—very few recurrent base pair mutations are observed. Nevertheless, what has been appreciated is a remarkable degree of genomic structural variation. This instability creates a prime environment for the production of fusion genes and OvCa has been shown to harbor more transcript fusions per tumor than most other TCGA-analyzed cancers. Given the inherently unstable OvCa genome and the fact that acquired structural variation has been observed in recurrent OvCa, we hypothesize that fusion genes play a role in the enhanced malignancy observed in relapsed disease. To test this hypothesis, we will analyze massively parallel RNA sequencing (RNA-seq) on patient-matched primary / recurrent tumor pairs. Fusion genes will be detected and prevalence of fusions will be compared between primary and recurrent tumor samples using a customized bioinformatics pipeline. Preliminary work has identified multiple RT-PCR validated, in-frame, relapse-specific fusion transcripts involving known cancer modulators. Additionally, some fusions were found in multiple samples and cell lines suggesting a selection of particular fusion RNA drivers. Next, we will screen for recurrence of discovered fusion genes using a high-throughput NanoString fusion assay. Clinical associations (patient overall survival, therapy responses, etc.) will be made to determine if fusion gene presence, or overexpression of fusion gene partners, are clinically informative biomarkers. Lastly, we will define the biological effects of discovered fusions using in vitro models. Cancer cell lines will be engineered to harbor gene fusions and we will assess for increases in malignant phenotypes such as cellular proliferation, drug sensitivity, and cellular migration / invasion. The ultimate goals of this study will be (1) to increase our understanding of the role fusions genes play in cancer, beyond primary disease and (2) to identify novel therapeutic targets and biomarkers for OvCa , in accordance with the National Cancer Institute (NCI) mission statement.

项目概要卵巢浆液性囊腺癌 (OvCa) 占卵巢癌的 90%，最常被发现到了晚期，治疗方法有限，预后较差——患者的 5 年生存率与直觉相反的是，晚期疾病的发生率低于 50%，OvCa 对初始治疗极其敏感。大多数患者达到完全临床缓解，但 80% 的患者最终会复发。转移和获得性肿瘤化疗耐药性因此被诊断为疾病复发。维持治疗方案可提高总体生存期，平均生存期为 12 至 18 个月。复发性疾病的成功有限。癌症基因组图谱 (TCGA) 已对数百个原发性 OvCa 肿瘤进行了测序，以改善我们的研究迄今为止，人们对这种疾病的了解令人震惊——很少有复发的碱基对突变。然而，人们已经注意到基因组结构的显着程度。这种不稳定性为融合基因的产生创造了良好的环境，OvCa 已被证实。与大多数其他 TCGA 分析的癌症相比，每个肿瘤具有更多的转录融合。鉴于 OvCa 基因组本质上不稳定以及已观察到获得性结构变异的事实在复发性 OvCa 中，我们发现融合基因在观察到的恶性程度增强中发挥了作用。为了检验这一假设，我们将分析大规模并行 RNA 测序 (RNA-seq)。将检测患者匹配的原发性/复发性肿瘤对的融合基因，并确定融合的发生率。使用定制的生物信息学流程对原发性和复发性肿瘤样本进行比较。初步工作已鉴定出多个经过 RT-PCR 验证的框内复发特异性融合转录本此外，在多个样本和细胞系中发现了一些融合。建议选择特定的融合 RNA 驱动程序。接下来，我们将使用高通量 NanoString 融合筛选发现的融合基因的复发将进行临床关联（患者总体生存率、治疗反应等）以确定是否存在。融合基因的存在或融合基因伴侣的过度表达是临床信息丰富的生物标志物。最后，我们将使用体外癌细胞系定义所发现的融合的生物学效应。被设计为包含基因融合，我们将评估恶性表型的增加，例如细胞增殖、药物敏感性和细胞迁移/侵袭。这项研究的最终目标是（1）加深我们对融合基因在癌症，超越原发性疾病，以及 (2) 确定 OvCa 的新治疗靶点和生物标志物，根据美国国家癌症研究所 (NCI) 的使命宣言。