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: 9119770
• 负责人: Thomas Paul Stricker
• 金额: $ 15.34万
• 依托单位: VANDERBILT UNIVERSITY MEDICAL CENTER
• 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/9119770
• 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; Estrogen receptor positive; Funding; Gene Expression; Genes; Genetic Transcription; Genetic Variation; Genomics; Genotype; Goals; Grant; Growth; Human; Inherited; Institutes; Knowledge; Lead; Learning; Malignant Neoplasms; Measures; Medical; Medical center; Mentors; Modeling; Molecular; Molecular Abnormality; 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 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; cancer subtypes; career; chemotherapy; clinically relevant; design; disease heterogeneity; 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 sequencing; novel; outcome forecast; promoter; protein function; rare variant; skills; subtype-specific therapies; symposium; targeted treatment; therapy development; tool; transcriptome sequencing; 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独立的医师科学家，专注于应用基因组技术以更好地了解癌症。该建议描述了一项为期5年的培训计划，以开发基因组学，癌症和解剖病理学的学术生涯。通过该培训计划，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（Kevin White）博士是该领域的领导者兼基因组和系统生物学研究所主任，他将指导我的科学发展。乳腺癌研究的公认领导者Olufunmilayo I. Olopade博士将担任该项目的征收者。她是芝加哥大学医学中心临床癌症遗传学与全球健康中心主任。此外，由备受瞩目的医学科学家组成的咨询委员会将提供科学和职业建议。我设计的项目并不是白色或Olopade实验室中现有项目的扩展；相反，我已经开发了新型技术和怀特实验室的专业知识，以生成和分析大型数据集，并将其与我对癌症和疾病的了解合并，以建立独立的研究线。我计划使用基因组技术在我自己的独立实验室中广泛研究人类肿瘤，因此我在白人实验室训练的指导阶段将为我提供一个关键的额外训练期，以学习如何将最先进的基因组技术应用于癌症。我提出了一个5年的培训期，在此期间我将获得技能 通过与我的导师的互动并参与正式教学，国家会议和会议，成为独立的医师科学家所必需的。我将通过追求病理学和基因组学和系统生物学独特的跨学科研究培训计划来进一步发展自己的科学技能。除了扩大自己的科学技能外，我还将获得成为成功的独立研究人员所需的其他技能经验，例如赠款写作，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，以使R01资金具有竞争力。这项培训将使ME带到具有深入了解癌症的独立研究人员的位置，因此我可以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，可以分为多种亚型，具有不同的生物学行为，对治疗敏感性和生存。这些行为和治疗敏感性的差异表明，亚型特异性疗法的发展将导致更有效的治疗方法。但是，对不同亚型之间的基因表达，生物学行为和最终结果的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测序来鉴定这些分子畸变。 RNA-seq将使我们能够分析几个过程，包括同工型特异性表达，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使用，替代剪接，染色体重排以及遗传和获得的遗传变异在乳腺癌中疾病异质性中的作用。但是，与大多数癌症测序研究不同，我们将不仅关注获得的突变。鉴于遗传变体在癌症中的已知作用以及稀有等位基因在复杂疾病中的可疑作用，我们认为遗传和获得的变体具有兴趣。实际上，我们的初步研究（请参阅目标1和2）强烈表明，我们可以根据罕见有害等位基因中包含的共同遗传变异来区分乳腺癌的两个亚型，其中包括突变和遗传变异。此外，我们的初步数据表明，我们不仅可以基于基因表达，而且还可以仅通过同工型使用来区分乳腺癌亚型。在鉴定出区分乳腺癌亚型的同工型和遗传变异体后，我们将确定这些同工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作用。因此，通过这项工作，我们希望更好地了解乳腺癌亚型内共享表型行为的机制。我们在这里的贡献预计将是区分ERBC和TNBC的分子机制，途径和过程的鉴定。这些机制代表了亚型特异性疾病驱动因素，因此是治疗干预的潜在靶标。通过识别和靶向这些机制，我们将能够为乳腺癌设计更有效的亚型特异性疗法。此外，这项工作将在我们对生物学基本疾病异质性的理解方面带来重要的进步。这里了解的是关于替代剪接，融合创建，罕见，遗传变体和疾病异质性的躯体突变的贡献的经验教训，适用于许多疾病。

项目成果

MLL3 is a de novo cause of endocrine therapy resistance.

• DOI: 10.1002/cam4.4285
• 发表时间: 2021-11
• 期刊: Cancer medicine
• 影响因子: 4
• 作者: Stauffer KM;Elion DL;Cook RS;Stricker T
• 通讯作者: Stricker T

Correction: Association of FGFR1 with ERα Maintains Ligand-Independent ER Transcription and Mediates Resistance to Estrogen Deprivation in ER+ Breast Cancer.

更正：FGFR1 与 ERα 的关联维持配体独立的 ER 转录并介导 ER 乳腺癌对雌激素剥夺的抵抗力。

• DOI: 10.1158/1078-0432.ccr-18-4268
• 发表时间: 2019
• 期刊: Clinical cancer research : an official journal of the American Association for Cancer Research
• 作者: Formisano,Luigi;Stauffer,KimberlyM;Young,ChristianD;Bhola,NeilE;Guerrero-Zotano,AngelL;Jansen,ValerieM;Estrada,MónicaM;Hutchinson,KatherineE;Giltnane,JenniferM;Schwarz,LuisJ;Lu,Yao;Balko,JustinM;Deas,Olivier;Cairo,Stef
• 通讯作者: Cairo,Stef