High-throughput Analysis of Mutations Identified by RNA-sequencing Triple Negativ

RNA 测序三阴性突变的高通量分析

• 批准号: 8242433
• 负责人: Thomas Paul Stricker
• 金额: $ 15.18万
• 依托单位: VANDERBILT UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-09-24 至 2017-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8242433
• 关键词: Accounting; Advisory Committees; Affect; Alleles; Ally; Alternative Splicing; American; Anatomy; Antibodies; Behavior; Behavior Therapy; Bioinformatics; Biological; Biological Markers; Biology; Breast Cancer Treatment; Cancer Etiology; Categories; Cell Line; Cessation of life; ChIP-seq; Chicago; Chromosomal Rearrangement; Clinical; Complex; Data; Data Set; Development; Disease; Estrogen Receptors; Funding; Gene Expression; Genes; Genetic Transcription; Genetic Variation; Genomics; Genotype; Goals; Grant; Growth; Heterogeneity; Human; Inherited; Institutes; Knowledge; Lead; Learning; Malignant Neoplasms; Measures; Medical; Medical center; Mentors; Modeling; Molecular; Molecular Profiling; Mutation; Outcome; Pathologic; Pathologist; Pathology; Pathway interactions; Pharmaceutical Preparations; Phase; Phenotype; Physicians; Positioning Attribute; Process; Progesterone Receptors; Program Development; Protein Isoforms; Public Health; Publishing; RNA; RNA Sequences; RNA Splicing; Research; Research Personnel; Research Training; Role; Sampling; Scientist; Somatic Mutation; Spliced Genes; Systems Biology; Techniques; Technology; Testing; Therapeutic Intervention; Time; Training; Training Programs; Tumor Tissue; Universities; Variant; Woman; Work; Writing; anticancer research; base; cancer genetics; cancer genomics; career; chemotherapy; clinically relevant; design; effective therapy; experience; fusion gene; genetic variant; global health; high throughput analysis; human disease; improved; interest; killings; malignant breast neoplasm; man; meetings; new technology; next generation; novel; outcome forecast; promoter; protein function; skills; symposium; therapy development; tool; triple-negative invasive breast carcinoma; tumor

DESCRIPTION (provided by applicant): My long-term career goal is to become an independent physician-scientist, focused on applying genomic technologies to better understand cancer. This proposal describes a 5 year training program for the development of an academic career in genomics, cancer and Anatomic Pathology. Through this training program, I will gain new skills in genomics and systems biology and their application to human disease. Dr. Kevin White, who is a leader in the field and Director of the Institute for Genomics and Systems Biology, will mentor my scientific development. Dr. Olufunmilayo I. Olopade, a recognized leader in the breast cancer research, will serve as a co-mentor on this project. She is the director of the Center for Clinical Cancer Genetics and Global Health at the University of Chicago Medical Center. In addition, an advisory committee of highly-regarded medical scientists will provide scientific and career advice. The project I have designed is not an extension of existing projects in the White or Olopade lab; rather I have taken the development of novel technologies and the White's labs expertise in generating and analyzing large datasets and merged it with my knowledge of cancer and disease to establish an independent line of research. I plan use genomic techniques to study human tumors extensively in my own independent lab, so the mentored phase of my training in the White lab will provide me with a critical additional training period in which to learn how to apply cutting edge genomic technologies to cancer. I have proposed a 5-year training period during which I will acquire skills necessary to become an independent physician-scientist through interactions with my mentors and participation in formal didactics, national meetings and conferences. I will further develop my scientific skills by pursuing a unique cross-disciplinary research training program in Pathology and Genomics and Systems Biology. In addition to expanding my scientific skill set, I will gain experience in other skills necessary to become a successful independent investigator, such as grant writing, mentoring, and lab management. Furthermore, this additional training will give me time to generate and publish enough data to be competitive for R01 funding. This training will propel the me to an independent investigator position with a deep knowledge of cancer, so that I can make valuable contributions to the cancer field. Breast cancer, the second leading cause of cancer death amongst American women, can be divided into multiple subtypes with different biological behaviors, sensitivity to therapy, and survival. These differences in behavior and treatment sensitivities suggest that the development of subtype-specific therapies will lead to more effective treatment. However, the molecular mechanisms responsible for differences in gene expression, biological behavior, and ultimately outcome, between the different subtypes are poorly understood. We hypothesize that clinically relevant differences between breast cancer subtypes are driven by subtype-specific molecular aberrations. We propose to use RNA sequencing to identify these molecular aberrations. RNA-seq will allow us to analyze several processes, including isoform-specific expression, novel fusion genes, and inherited and somatic genetic variants. Thus, RNA-sequencing will allow me to investigate the role of alternative promoter usage, alterative splicing, chromosomal rearrangements, and inherited and acquired genetic variants in disease heterogeneity in breast cancer. However, unlike most cancer sequencing studies, we will not focus solely on acquired mutations. Given the known role of inherited variants in cancer, and the suspected role of rare alleles in complex disease, we regard both inherited and acquired variants with interest. Indeed, our preliminary studies (see Aim 1 and 2) strongly suggest that we can differentiate two subtypes of breast cancer based on shared genetic variation contained largely in rare deleterious alleles, which include both mutations and inherited variants. Furthermore, our preliminary data suggests that we can differentiate breast cancer subtypes based not only by gene expression, but also by isoform usage alone. Having identified isoforms and genetic variants that distinguish breast cancer subtypes, we will determine if these isoforms or genetic variants alter protein function in cell line models. We will then correlate these effects in human tumor tissue. Thus, through this work we expect to develop a better understanding of the mechanisms underlying shared phenotypic behavior within subtypes of breast cancer. Our contribution here is expected to be the identification of molecular mechanisms, pathways, and processes that differentiate ERBC and TNBC. These mechanisms represent subtype-specific drivers of disease and thus potential targets for therapeutic intervention. By identifying and targeting these mechanisms, we will be able to design more effective, subtype-specific therapies for breast cancer. Furthermore, this work will provide important advances in our understanding of the biology underlying disease heterogeneity. The lessons learned here about the contribution of alternative splicing, fusion-genes, rare, inherited variants and somatic mutations to disease heterogeneity will be applicable to many diseases.

描述（由申请人提供）：我的长期职业目标是成为一名独立的医师科学家，专注于应用基因组技术来更好地了解癌症。该提案描述了一个为期 5 年的培训计划，旨在发展基因组学、癌症和解剖病理学方面的学术职业。通过这个培训计划，我将获得基因组学和系统生物学的新技能及其在人类疾病中的应用。凯文·怀特博士是该领域的领导者，也是基因组学和系统生物学研究所所长，他将指导我的科学发展。 Olufunmilayo I. Olopade 博士是乳腺癌研究领域公认的领导者，他将担任该项目的联合导师。她是芝加哥大学医学中心临床癌症遗传学和全球健康中心主任。此外，由备受推崇的医学科学家组成的咨询委员会将提供科学和职业建议。我设计的项目不是 White 或 Olopade 实验室现有项目的延伸；相反，我利用了新技术的发展以及怀特实验室在生成和分析大型数据集方面的专业知识，并将其与我对癌症和疾病的知识相结合，建立了一条独立的研究路线。我计划在我自己的独立实验室中使用基因组技术广泛研究人类肿瘤，因此我在 White 实验室的培训指导阶段将为我提供一个关键的额外培训期，让我学习如何将尖端基因组技术应用于癌症。我提出了一个为期 5 年的培训期，在此期间我将获得技能 通过与导师的互动以及参加正式的教学、全国会议和会议，成为一名独立的医师科学家是必要的。我将通过在病理学、基因组学和系统生物学方面进行独特的跨学科研究培训计划来进一步发展我的科学技能。除了扩展我的科学技能之外，我还将获得成为一名成功的独立研究者所需的其他技能的经验，例如资助写作、指导和实验室管理。此外，这种额外的培训将使我有时间生成和发布足够的数据，以便在 R01 资金方面具有竞争力。这次培训将推动我成为一名对癌症有深入了解的独立研究者，从而为癌症领域做出宝贵的贡献。乳腺癌是美国女性癌症死亡的第二大原因，可分为多种亚型，具有不同的生物学行为、对治疗的敏感性和生存率。这些行为和治疗敏感性的差异表明，亚型特异性疗法的开发将带来更有效的治疗。然而，人们对不同亚型之间基因表达、生物学行为和最终结果差异的分子机制知之甚少。我们假设乳腺癌亚型之间的临床相关差异是由亚型特异性分子畸变驱动的。我们建议使用 RNA 测序来识别这些分子畸变。 RNA-seq 将使我们能够分析多个过程，包括异构体特异性表达、新型融合基因以及遗传和体细胞遗传变异。因此，RNA 测序将使我能够研究替代启动子的使用、可变剪接、染色体重排以及遗传和获得性遗传变异在乳腺癌疾病异质性中的作用。然而，与大多数癌症测序研究不同，我们不会仅仅关注获得性突变。鉴于遗传变异在癌症中的已知作用，以及罕见等位基因在复杂疾病中的可疑作用，我们对遗传变异和获得性变异都感兴趣。事实上，我们的初步研究（参见目标 1 和 2）强烈表明，我们可以根据主要包含在罕见有害等位基因中的共享遗传变异（包括突变和遗传变异）来区分乳腺癌的两种亚型。此外，我们的初步数据表明，我们不仅可以根据基因表达，还可以单独根据异构体的使用来区分乳腺癌亚型。在确定了区分乳腺癌亚型的亚型和遗传变异后，我们将确定这些亚型或遗传变异是否会改变细胞系模型中的蛋白质功能。然后我们将在人类肿瘤组织中关联这些效应。因此，通过这项工作，我们希望更好地了解乳腺癌亚型内共有表型行为的机制。我们在这里的贡献预计是识别区分 ERBC 和 TNBC 的分子机制、途径和过程。这些机制代表了疾病的亚型特异性驱动因素，因此是治疗干预的潜在目标。通过识别和针对这些机制，我们将能够设计出更有效的、亚型特异性的乳腺癌疗法。此外，这项工作将为我们理解疾病异质性背后的生物学提供重要进展。这里学到的关于选择性剪接、融合基因、罕见遗传变异和体细胞突变对疾病异质性的贡献的经验教训将适用于许多疾病。