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

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.

项目概要/摘要了解癌症基因组的进展促进了新型疗法的发展针对癌症 DNA 蛋白质产物的独特改变。由此产生的靶向治疗，连同蛋白质靶向免疫疗法使癌症患者的生存率取得了显着进步。然而，并非所有患者从这些新疗法中受益，许多癌症继续接受 DNA 双酶治疗链断裂（DSB）产生的放射疗法和化学疗法。 CRISPR-Cas9 系统等核酸靶向方法现在能够研究一种新的实验性癌症治疗方法：直接靶向 DNA 而不是其蛋白质产物。这提案旨在对该模式进行初步调查和评估。假设：在多个重排连接处定向诱导 DNA DSB，特定于癌症基因组，可以导致癌细胞特异性细胞毒性并避免对健康组织造成损害。具体目标 1. 描述癌症特异性 Cas9 靶向基因组位点的概况癌症和癌细胞系。为此，将开发一个计算管道来表征频谱跨癌细胞系百科全书的 Cas9 可靶向基因组改变和泛癌症分析包含 300 多种癌细胞系和 2500 个癌症基因组的全基因组数据库。序列的特点是可能会影响癌症治疗中靶点有效性的特征，包括靶点克隆性、靶点拷贝数量以及跨癌症类型的可靶向基因组改变的分布。这条管道将成为公开可用的工具，用于生成 Cas9 可靶向重排断点列表，以供未来研究使用。目标 2. 开发使用针对癌症特异性的 Cas9 在癌细胞中诱导细胞毒性的方法 DNA 重排断点。在一系列原理验证实验中，该目标将评估 Cas9 是否可以通过将 DNA 断裂靶向单个高度扩增的位点或多个位点来诱导靶向细胞死亡癌症新基因组中的独特位点以及这是否会在健康组织中产生毒性。目标 3. 确定对 Cas9 介导的 DNA 损伤具有抵抗力或敏感性的蛋白质因子：该目标将包括 CRISPR 敲除筛选，以发现影响细胞对多种 Cas9 敏感性的蛋白质诱导DNA断裂。该提案将在癌症基因组学和靶向治疗的指导下提供培训丹纳法伯癌症研究所的 Matthew Meyerson 教授在这两个领域都有丰富的经验。此外实验和计算研究，申请人将在会议上展示结果，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领域的同事和导师互动字段。计划中的研究旨在最终在同行评审期刊上发表。最终，这培训应该为申请人在美国研究机构担任研究教员做好准备。