FEN1 Endonuclease as a Synthetic Lethal Target for Cancer Therapy

FEN1 核酸内切酶作为癌症治疗的合成致死靶点

基本信息

批准号：
10294863
负责人：
Olivier Harismendy
金额：
$ 63.95万
依托单位：
UNIVERSITY OF CALIFORNIA, SAN DIEGO
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-08-15 至 2026-07-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10294863
关键词：
Ablation Affect Antineoplastic Agents BRCA1 Mutation BRCA1 gene BRCA2 Mutation BRCA2 gene Base Excision Repairs Biological Assay Biological Models Breast Cancer cell line Breast Cancer therapy Cancer cell line Cell Line Cells Chromosomal Rearrangement Chromosome Breakage Chromosomes Clustered Regularly Interspaced Short Palindromic Repeats Colorectal Cancer DNA DNA biosynthesis DNA replication fork DNA sequencing Data Defect Dependence Development Diploid Cells Double Strand Break Repair Dropout Drug Targeting Engineering Epigenetic Process Essential Genes Evaluation Evolution Frequencies Genes Genetic Genetic study Genomic DNA Genomic Instability Genomics Germ-Line Mutation Goals Guide RNA Hereditary Breast and Ovarian Cancer Syndrome Homologous Gene Human Human Genome Hypersensitivity In Vitro Informatics Inherited Knock-out Knowledge Laboratories Lethal Genes Libraries Maintenance Therapy Malignant - descriptor Malignant Neoplasms Malignant neoplasm of ovary Measures Metaphase Mining Mus Mutate Mutation Okazaki fragments PARP inhibition Pathway Analysis Pharmacology Process Progression-Free Survivals RTH-1 Nuclease Research Resistance Screening Result Small Interfering RNA Specificity Suppressor Genes Testing Therapeutic Agents Validation Yeasts base brca gene cancer cell cancer genome cancer genomics cancer therapy cancer type candidate selection candidate validation endonuclease genome integrity genome-wide homologous recombination improved in silico in vivo inhibitor/antagonist knock-down malignant breast neoplasm mutant nuclease predictive signature recombinational repair replication stress resistance mechanism response small molecule targeted cancer therapy therapeutic development therapeutic target therapy design transcriptomics tumor xenograft validation studies yeast genetics yeast genome

项目摘要

PROJECT SUMMARY Gross chromosomal rearrangements (GCRs), a type of genome instability, are often seen in inherited and sporadic cancers and are an important driver of malignant progression. For example, hereditary breast and ovarian cancers resulting from BRCA1 and BRCA2 germline mutations suffer from homologous recombination repair (HRR) defects that increase GCRs in model systems. Our previous studies have established a comprehensive network of genome instability suppressor (GIS) genes in yeast and demonstrated in silico that human homologs of these yeast GIS genes are genetically and/or epigenetically altered across many cancer types. From yeast genetic studies, we have also identified and rank-ordered synthetic lethal (SL) partners of non-essential GIS genes. The feasibility of targeting SL genetic interactions for rational cancer therapy has been supported by the application of PARP inhibitors for maintenance therapy of breast and ovarian cancers with BRCA1 or BRCA2 defects. To exploit additional SL interactions for cancer therapy, this proposal aims to leverage the wealth of knowledge on GIS genes and their SL partners developed in yeast to guide the development of therapeutics that target human GIS gene defects that cause GCRs in cancer. Specifically, the proposed studies will focus on the human Flap Endonuclease 1 (FEN1), the homolog of yeast RAD27, which has the highest number of SL-interactions with GIS genes of a variety of functions. FEN1 processes Okazaki fragments during lagging strand DNA synthesis and acts in long-patch base excision repair but is itself non- essential. To develop this nuclease as a target for treating cancers with defects in BRCA1, BRCA2 and other FEN1-SL partner GIS genes, we propose to carry out the following lines of research: AIM 1) To expand ongoing CRISPR-dropout screens and validation studies in cell lines and mice to (a) identify human genes in which defects cause sensitivity to our proprietary FEN1-inhibitors of highly potency and specificity and (b) define FEN1 SL-partner genes as well as cancer omics signatures that can be targeted with FEN1 inhibitors to induce SL; AIM 2) To combine informatics and cell-based validation approaches for a deep-dive into cancer omics and gene essentiality data to identify the spectrum and signatures of cancers amenable to therapeutic targeting with FEN1 inhibitors; AIM 3) To apply an array of genetics-based approaches to investigate mechanisms for acquired resistance to FEN1 inhibitors and to compare resistance to FEN1 versus PARP inhibitors; and, AIM 4) To determine the effects of FEN1 inhibition on DNA replication, fork stability, and chromosome integrity in BRCA1 and BRCA2 mutant cells to test the hypothesis that FEN1 inhibitors induce irreparable damage to replication forks in HRR-deficient cancer cells to cause lethality. These mechanistic studies will be extended to other validated FEN1-SL partner genes. These projects will greatly accelerate the development of FEN1 inhibitors to target cancer genome instability and will establish an experimental platform for evaluation and development of other potential therapeutic targets to be identified by the proposed research.

项目概要染色体总重排 (GCR) 是一种基因组不稳定性，常见于遗传性和遗传性疾病中。散发性癌症，是恶性进展的重要驱动因素。例如，遗传性乳房 BRCA1 和 BRCA2 种系突变引起的卵巢癌会遭受同源重组修复（HRR）缺陷，增加模型系统中的 GCR。我们之前的研究已经建立了酵母中基因组不稳定性抑制（GIS）基因的综合网络，并通过计算机证明这些酵母 GIS 基因的人类同源物在许多癌症中都发生了遗传和/或表观遗传改变类型。从酵母遗传学研究中，我们还鉴定了酵母的合成致死 (SL) 伴侣并对其进行了排序非必需 GIS 基因。针对 SL 基因相互作用进行合理癌症治疗的可行性得到PARP抑制剂在乳腺癌和卵巢癌维持治疗中应用的支持患有 BRCA1 或 BRCA2 缺陷。为了利用额外的 SL 相互作用进行癌症治疗，该提案旨在利用 GIS 基因及其在酵母中开发的 SL 伙伴的丰富知识来指导开发针对导致癌症 GCR 的人类 GIS 基因缺陷的疗法。具体来说，拟议的研究将集中于人类 Flap 核酸内切酶 1 (FEN1)，它是酵母 RAD27 的同源物，它与各种功能的 GIS 基因具有最多数量的 SL 相互作用。 FEN1 处理冈崎滞后链 DNA 合成过程中的片段，并在长补丁碱基切除修复中发挥作用，但其本身是非基本的。开发这种核酸酶作为治疗 BRCA1、BRCA2 和其他缺陷癌症的靶点 FEN1-SL伙伴GIS基因，我们建议开展以下研究方向： AIM 1) 扩展正在进行的 CRISPR-dropout 筛选和细胞系和小鼠验证研究，目的是 (a) 识别人类基因哪些缺陷导致对我们专有的高效力和特异性 FEN1 抑制剂敏感，以及 (b) 定义 FEN1 SL 伙伴基因以及癌症组学特征，可使用 FEN1 抑制剂靶向这些特征诱发 SL；目标 2) 结合信息学和基于细胞的验证方法来深入研究癌症组学和基因必要性数据，以确定适合治疗的癌症的谱和特征 FEN1 抑制剂靶向；目标 3) 应用一系列基于遗传学的方法进行研究 FEN1 抑制剂获得性耐药机制以及比较 FEN1 与 PARP 的耐药性抑制剂；目的 4) 确定 FEN1 抑制对 DNA 复制、叉稳定性和 BRCA1 和 BRCA2 突变细胞中的染色体完整性，以检验 FEN1 抑制剂诱导的假设 HRR 缺陷的癌细胞中的复制叉受到不可修复的损伤，从而导致死亡。这些机制研究将扩展到其他经过验证的 FEN1-SL 伙伴基因。这些项目将大大加速开发FEN1抑制剂以针对癌症基因组不稳定性并将建立实验平台用于评估和开发拟议研究确定的其他潜在治疗靶点。