Integrative Analyses of Saturation CRISPR Protein Scan

饱和 CRISPR 蛋白质扫描的综合分析

• 批准号: 10058930
• 负责人: Chun-Wei David Chen
• 金额: $ 13.2万
• 依托单位: BECKMAN RESEARCH INSTITUTE/CITY OF HOPE
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-04-01 至 2022-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10058930
• 关键词: 3-Dimensional; ART protein; Achievement; Acute leukemia; Alleles; Award; Bioconductor; Chromatin; Clinical; Clustered Regularly Interspaced Short Palindromic Repeats; Data; Data Analyses; Data Set; Databases; Development; Disease; Docking; Elements; Environment; Epigenetic Process; Funding; Fusion Oncogene Proteins; Future; Gene Expression; Gene Rearrangement; Genetic Screening; Genetic Transcription; Genomics; Goals; Histone H3; Histones; Human; KDM1A gene; Knowledge; Lead; Ligands; Lysine; MLL gene; Malignant Neoplasms; Methods; Methyltransferase; NUP98 gene; Nature; Parents; Patients; Pharmacologic Substance; Phase I Clinical Trials; Phosphotransferases; Play; Proteins; Reader; Regimen; Research; Role; Scanning; Survival Rate; T-Cell Lymphoma; Tertiary Protein Structure; Therapeutic; Three-dimensional analysis; Treatment Efficacy; Validation; Work; analysis pipeline; base; cBioPortal; cancer type; chromatin modification; clinical database; clinically relevant; computational pipelines; density; experimental study; functional genomics; genome integrity; improved; informatics tool; inhibitor/antagonist; innovation; insight; leukemia; leukemogenesis; mutant; novel; novel therapeutics; outcome forecast; p38 Mitogen Activated Protein Kinase; programs; response; targeted treatment; therapeutic candidate; therapeutic development; therapeutic target; tool; trial design

PROJECT SUMMARY/ABSTRACT Epigenetic mechanisms play a critical role in controlling gene expression during normal development and are often altered in disease states, particularly in cancer. MLL-rearranged (MLL-r) leukemias account for 5-10% of human acute leukemia and is associated with poor prognosis. The unmet clinical needs and the lack of effective targeted therapy to the MLL-r leukemias emphasize the need for novel regimens. Recent cancer epigenetics studies discovered a central role for the histone H3 lysine 79 (H3K79) methyltransferase DOT1L in MLL-r leukemogenesis. Important clinical responses have been noted with DOT1L inhibitor treatment as a single agent, however, it is expected that combination treatments will be necessary. Our preliminary studies proposed in the parent award R01 CA236626 based on a high-density CRISPR genetic screen of DOT1L have identified the potential of “saturation CRISPR protein scan” in de novo functional domain discovery. The objective of this Revision Application is to establish a computational pipeline to facilitate the data analyses of the saturation CRISPR protein scan. Our central hypothesis is that saturation CRISPR protein scan data harbor clinically impactful information that can be further explored through adaptation of the integrative informatics tools from the ITCR Program. We will (Aim 1) integrate the saturation CRISPR protein scan with cBioPortal (an integrative clinical genomic database; funded by ITCR) to identify clinically relevant alleles, and (Aim 2) streamline the saturation CRISPR protein scan with DINC 2.0 (a parallelized meta- docking method for the incremental docking of large ligands; funded by ITCR) to identify lead epigenetic ligands to the CRISPR defined hotspots. This study is innovative because (1) it introduces a novel concept of using saturation CRISPR genetic screens for epigenetic ligand discovery, and (2) it establishes an analysis pipeline for a novel field that bridges the functional genomics, protein domain identification, and therapeutics discovery. The impact of this research will be of significance because (1) it immediately provides novel therapeutic opportunities against the difficult-to-treat MLL-r leukemias, and (2) the computational pipeline established in this proposal and streamlined with the ITCR supported integrative informatics tools will help identify novel functional elements for future pharmaceutical targeting in multiple types of cancers.

项目总结/摘要 表观遗传机制在控制正常发育过程中的基因表达方面起着关键作用， 通常在疾病状态下改变，特别是在癌症中。MLL重排（MLL-r）白血病占5-10% 与人类急性白血病的预后不良有关。未满足的临床需求和缺乏 MLL-r白血病的有效靶向治疗强调了对新方案的需要。近期癌症 表观遗传学研究发现组蛋白H3赖氨酸79（H3 K79）甲基转移酶的核心作用 DOT 1 L在MLL-r白血病发生中的作用使用DOT 1 L抑制剂观察到重要的临床反应 然而，作为单一药剂治疗，预期将需要组合治疗。 我们在父母奖R 01 CA 236626中提出的基于高密度CRISPR的初步研究 DOT 1 L的遗传筛选已经确定了“饱和CRISPR蛋白扫描”在从头开始的潜力。 功能域发现。本修订版申请的目的是建立一个计算管道 以便于饱和CRISPR蛋白质扫描的数据分析。我们的核心假设是， CRISPR蛋白质扫描数据包含有临床影响力的信息，可以通过调整进一步探索 ITCR计划的综合信息学工具。我们将（目标1）整合饱和CRISPR 使用cBioPortal（一个综合性临床基因组数据库;由ITCR资助）进行蛋白质扫描， 相关等位基因，以及（目的2）用DINC 2.0（一种平行的Meta- 用于大配体的增量对接的对接方法;由ITCR资助），以鉴定领先的表观遗传配体 到CRISPR定义的热点。 这项研究具有创新性，因为（1）它引入了一种使用饱和CRISPR基因的新概念， 筛选表观遗传配体发现，以及（2）它为一个新领域建立了分析管道， 在功能基因组学、蛋白质结构域鉴定和治疗发现之间架起桥梁。 这项研究的影响将是有意义的，因为（1）它立即提供了新的治疗方法， 机会对难以治疗的MLL-r白血病，和（2）建立计算管道 在这个建议中，并与ITCR支持的综合信息学工具进行了简化，将有助于确定新的 在多种类型的癌症中用于未来药物靶向的功能元件。