Targeting the cancer neo-genome for destruction with CRISPR-Cas enzymes

使用 CRISPR-Cas 酶靶向破坏癌症新基因组

基本信息

批准号：
10678361
负责人：
Mitchell L Leibowitz
金额：
$ 6.91万
依托单位：
DANA-FARBER CANCER INST
依托单位国家：
美国
项目类别：
财政年份：
2023
资助国家：
美国
起止时间：
2023-07-01 至 2026-06-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10678361
关键词：
Affect Age Apoptosis Apoptotic Biological Assay Biological Markers CRISPR/Cas technology Cancer Patient Cancer cell line Cell Cycle Cell Death Cell Death Induction Cell Line Cell Survival Cells Cessation of life Chromosomal Duplication Chromosomes Clonality Clustered Regularly Interspaced Short Palindromic Repeats Coculture Techniques Complex Cytotoxic agent DNA DNA Damage DNA Double Strand Break DNA Repair DNA Sequence Alteration DNA Sequence Rearrangement Dana-Farber Cancer Institute Data Development Double Minutes Effectiveness Elements Encyclopedias Enzymes Evaluation Event Excision Future Gene Rearrangement Gene Targeting Genes Genome Genomics Guide RNA Hour Human Immunotherapy Institution Investigation Journals Knock-out Malignant Neoplasms Measures Mediating Medical Mentors Methods Modality Mutate Mutation Natural Killer Cells Normal Cell Nucleic Acids Operative Surgical Procedures Outcome Pathway interactions Patients Peer Review Predisposition Proteins Publications Radiation therapy Research Resistance Scientist Series Site Stains System Therapeutic Tissues Toxic effect Training United States Variant cancer cell cancer genome cancer genomics cancer therapy cancer type career cell killing cell type chemotherapy chromosome loss chromosome missegregation chromothripsis computational pipelines cytotoxic cytotoxicity data repository design experience experimental study genome database genome editing genomic locus improved new therapeutic target next generation novel novel therapeutics pan-genome professor repaired research faculty screening small molecule symposium targeted nucleases targeted treatment tool tumor whole genome

Affect Age Apoptosis Apoptotic Biological Assay Biological Markers CRISPR/Cas technology Cancer Patient Cancer cell line Cell Cycle Cell Death Cell Death Induction Cell Line Cell Survival Cells Cessation of life Chromosomal Duplication Chromosomes Clonality Clustered Regularly Interspaced Short Palindromic Repeats Coculture Techniques Complex Cytotoxic agent DNA DNA Damage DNA Double Strand Break DNA Repair DNA Sequence Alteration DNA Sequence Rearrangement Dana-Farber Cancer Institute Data Development Double Minutes Effectiveness Elements Encyclopedias Enzymes Evaluation Event Excision Future Gene Rearrangement Gene Targeting Genes Genome Genomics Guide RNA Hour Human Immunotherapy Institution Investigation Journals Knock-out Malignant Neoplasms Measures Mediating Medical Mentors Methods Modality Mutate Mutation Natural Killer Cells Normal Cell Nucleic Acids Operative Surgical Procedures Outcome Pathway interactions Patients Peer Review Predisposition Proteins Publications Radiation therapy Research Resistance Scientist Series Site Stains System Therapeutic Tissues Toxic effect Training United States Variant cancer cell cancer genome cancer genomics cancer therapy cancer type career cell killing cell type chemotherapy chromosome loss chromosome missegregation chromothripsis computational pipelines cytotoxic cytotoxicity data repository design experience experimental study genome database genome editing genomic locus improved new therapeutic target next generation novel novel therapeutics pan-genome professor repaired research faculty screening small molecule symposium targeted nucleases targeted treatment tool tumor whole genome

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项目摘要

Project Summary/Abstract Advances in understanding the cancer genome have led to the development of novel therapeutics that target distinct alterations in protein products of cancer DNA. The resulting targeted therapies, together with protein-targeting immunotherapies, have led to significant advances in cancer patient survival. However, not all patients benefit from these new therapies and instead many cancers continue to be treated with DNA double- strand break (DSB)-generating radio- and chemo- therapies. Nucleic acid targeting approaches such as the CRISPR-Cas9 system now enable investigation of a new modality for experimental cancer therapeutics: targeting DNA directly rather than its protein products. This proposal is aimed at the initial investigation and evaluation of this modality. Hypothesis: Targeted induction of DNA DSBs at multiple rearrangement junctions, specific to the cancer genome, can lead to cancer-cell specific cytotoxicity and spare damage to healthy tissue. Specific Aim 1. Characterize the landscape of cancer-specific Cas9-targetable genomic sites across cancers and cancer cell lines. In this aim, a computational pipeline will be developed to characterize the spectrum of Cas9-targetable genome alterations across the Cancer Cell Line Encyclopedia and Pan-Cancer Analysis of Whole Genomes databases of over 300 cancer cell lines and 2500 cancer genomes. Sequence features that may affect target effectiveness in cancer therapy will be characterized, including target clonality, target copy number, and the distribution of targetable genomic alterations across cancer types. This pipeline will become a publicly available tool to generate lists of Cas9-targetable rearrangement breakpoints for use in future studies. Aim 2. Develop methods to induce cytotoxicity in cancer cells using Cas9 targeted to cancer-specific DNA rearrangement breakpoints. In a series of proof-of-principle experiments, this aim will assess whether Cas9 can induce targeted cell death through targeting DNA breaks to either single highly amplified sites or several unique sites in the cancer neo-genome and whether this generates toxicity in healthy tissue. Aim 3. Identify protein factors responsible for resistance or sensitivity to Cas9-mediated DNA damage: This aim will comprise a CRISPR knockout screen to discover proteins that affect cell sensitivity to multiple Cas9- induced DNA breaks. This proposal will provide training in cancer genomics and targeted therapeutics under the guidance of Professor Matthew Meyerson at Dana-Farber Cancer Institute, who is experienced in both fields. In addition to experimental and computational research, the applicant will present results at conferences, train future scientists, and interact with colleagues and mentors in the cancer genomics, genome editing, and cancer therapeutics fields. The planned research is intended to culminate in publication in peer-reviewed journals. Ultimately, this training should prepare the applicant for a career as research faculty at a United States research institution.

项目摘要/摘要了解癌症基因组的进步导致了新型治疗剂的发展靶向癌症DNA蛋白质产物的不同变化。由此产生的靶向疗法以及靶向蛋白质的免疫疗法已导致癌症患者生存的重大进展。但是，不是全部患者受益于这些新疗法，相反，许多癌症继续接受DNA双重治疗链断裂（DSB） - 生成的射线和化学疗法。核酸靶向方法，例如CRISPR-CAS9系统，现在可以研究一种新的实验性癌症治疗剂的方式：直接靶向DNA而不是其蛋白质产物。这提案旨在对这种方式进行初步研究和评估。假设：针对多个重排连接处的DNA DSB的靶向诱导，特有的基因组可以导致癌症特异性细胞毒性和对健康组织的备用损害。特定目的1。表征整个癌症特异性Cas9的基因组位点的景观癌症和癌细胞系。在此目标中，将开发计算管道来表征频谱跨癌细胞系百科全书的CAS9靶向基因组改变和泛伴奏分析超过300个癌细胞系和2500个癌症基因组的全基因组数据库。序列特征是可能会影响癌症治疗中的目标有效性，包括目标克隆性，目标副本数量，以及在癌症类型中靶向基因组改变的分布。该管道将成为一个公开可用的工具，以生成可CAS9可靶向重排断点的列表，以在未来的研究中使用。目标2。开发使用针对癌症特异性的CAS9诱导癌细胞中细胞毒性的方法 DNA重排断点。在一系列原则实验中，此目标将评估CAS9是否可以通过靶向DNA断裂到单个高度扩增位点或几个来诱导靶向细胞死亡癌症新基因组中的独特部位以及这是否在健康组织中产生毒性。目标3。确定蛋白质因子负责抗性或对Cas9介导的DNA损伤的敏感性：该目标将包括一个CRIS敲除屏幕，以发现影响细胞对多个CAS9-的敏感性的蛋白质诱导的DNA断裂。该建议将在癌症基因组学和有针对性治疗的培训下在在这两个领域都经验丰富的达娜·弗伯（Dana-Farber）癌症研究所的马修·梅耶森（Matthew Meyerson）教授。此外实验和计算研究，申请人将在会议上介绍结果，培训未来的科学家，并与癌症基因组学，基因组编辑和癌症治疗的同事和导师互动字段。计划的研究旨在最终在同行评审期刊中出版。最终，这个培训应准备申请人在美国研究机构担任研究学院的职业。