Molecular origins and impact of APOBEC3 mutagenesis in cancer

APOBEC3 突变的分子起源和对癌症的影响

• 批准号: 10693177
• 负责人: JOHN MACIEJOWSKI
• 金额: $ 40.94万
• 依托单位: SLOAN-KETTERING INST CAN RESEARCH
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-01 至 2027-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10693177
• 关键词: Address; B-Cell Lymphomas; Bioinformatics; Biological Assay; Biological Markers; Biological Models; Breast Cancer cell line; Cancer Etiology; Cancer Model; Cancer cell line; Cell Line; Cell model; Cells; Characteristics; Clinical; Cytidine; Cytosine deaminase; Data; Deaminase; Detection; Dimensions; Disease; Engineering; Enzymes; Etiology; Evolution; Exposure to; Family; Gene Mutation; Genome; Goals; High Prevalence; Human; Immune; Individual; Knock-out; Link; Lung Adenocarcinoma; Malignant Neoplasms; Malignant neoplasm of lung; Malignant neoplasm of urinary bladder; Measures; Metastatic Carcinoma; Modeling; Molecular; Monitor; Mus; Mutagenesis; Mutation; Mutation Analysis; Neoplasm Metastasis; Outcome; Patient Selection; Pattern; Physiological; Play; Polymerase; Process; RNA Viruses; Reagent; Regulation; Resistance; Retroelements; Rodent; Role; Sensitivity and Specificity; Single base substitution; Single-Stranded DNA; Site; Source; Surrogate Markers; System; Testing; Therapeutic; Transgenes; Treatment Efficacy; Tyrosine Kinase Inhibitor; Xenograft procedure; biomarker validation; cancer cell; cancer genome; cancer prevention; cancer therapy; cancer type; carcinogenesis; experimental study; genome sequencing; human disease; imprint; insight; lung cancer cell; malignant breast neoplasm; member; mutant; novel strategies; overexpression; paralogous gene; preference; prognostic; reconstitution; recruit; scaffold; targeted treatment; therapeutic target; therapy resistant; tumorigenesis; whole genome

PROJECT SUMMARY Mutations arise as a result of exogenous and endogenous processes that leave characteristic imprints or signatures upon the genome. Systematic analysis of these mutational signatures led to the identification of >50 distinct types of single base substitutions (SBS) in human cancer genomes. Revealing the origins of individual signatures is critical for understanding cancer etiology, with potential implications for cancer prevention and therapy. Two of the most prevalent mutational signatures in cancer, termed SBS2 and SBS13, are present in >78% of cancer types and 56% of all cancer genomes, with a particular prominence in breast, bladder, and lung cancers. SBS2 and SBS13 are proposed to be caused by the endogenous APOBEC3 (A3) enzymes, which target ssDNA and RNA of viruses and retroelements as part of the innate immune defense. Correlations between A3 expression, driver gene mutations in A3-preferred contexts, and clinical outcomes suggest that A3 mutagenesis may play important roles in cancer etiology and evolution. Thus, there is strong rationale to understand the mechanisms of A3 activity. However, reliance on engineered model systems and correlative data have caused links between A3 enzymes, mutations in cancer, and cancer etiology to be poorly understood. We have identified human cancer cell lines with endogenous A3 mutagenesis and developed a workflow that enables us to quantify contributions of individual A3 members to mutations. Here, we propose to leverage this workflow to accomplish the following goals: 1) Identify A3 mutator enzymes in cancer types where A3 mutagenesis is prevalent and find biomarkers of their activity; 2) Investigate mechanisms modulating A3 mutagenesis; 3) Determine the functional relevance of A3 mutagenesis in therapy resistance and metastasis. Aim 1 will expand upon our characterization of human cancer cells with active A3 mutagenesis to identify A3 mutators in breast, bladder, and lung cancers. In parallel, we will directly assess the unknown specificity and sensitivity of assays to measure activities of individual A3 enzymes. These experiments may further confirm the speculative A3-etiology of a large number of cancer mutations and quantify contributions of individual A3 enzymes, thus nominating them as putative targets for therapeutic pursuit. Aim 2 builds on our preliminary data to investigate proposed modulators of A3 mutagenesis. These experiments have the potential to broaden the scope of therapeutic opportunities focused on cancer cell evolution. Aim 3 will assess the links between A3 enzymes, therapy resistance and metastasis in breast, bladder, and lung cancer cell lines. These experiments will test predictions from multi-dimensional associations that A3-mutagenesis is a disease-modifying process that can be therapeutically exploited at various stages of cancer evolution. Taken together, these studies will define the etiologies of highly prevalent mutational processes and identify strategies to elicit more durable clinical benefits to targeted therapies and curb metastasis.

项目摘要 突变是外源性和内源性过程的结果，这些过程会留下特征性印记， 基因组上的签名。对这些突变标记的系统分析导致鉴定出>50个突变标记。 人类癌症基因组中不同类型的单碱基取代（SBS）。揭示个体的起源 签名对于理解癌症病因至关重要，对癌症预防具有潜在意义， 疗法癌症中最常见的两种突变标记，称为SBS 2和SBS 13，存在于 >78%的癌症类型和56%的所有癌症基因组，特别突出的是乳腺癌，膀胱癌， 肺癌SBS 2和SBS 13被认为是由内源性APOBEC 3（A3）酶引起的， 其靶向病毒的ssDNA和RNA以及作为先天免疫防御的一部分的逆转录因子。相关性 A3表达、A3偏好背景下的驱动基因突变和临床结果之间的关系表明，A3 突变可能在癌症病因学和进化中起重要作用。因此，有很强的理由 了解A3活性的机制。然而，依赖工程模型系统和相关的 数据表明，A3酶、癌症突变和癌症病因之间的联系很差， 明白我们已经鉴定了具有内源性A3突变的人癌细胞系，并开发了一种新的抗A3突变的方法。 工作流程，使我们能够量化单个A3成员对突变的贡献。在此，我们建议 利用该工作流程来实现以下目标：1）鉴定癌症类型中的A3突变酶， A3突变是普遍存在的，并发现其活性的生物标志物; 2）研究调节A3的机制 3）确定A3诱变在治疗抗性和转移中的功能相关性。 目的1将扩展我们对具有活性A3诱变的人癌细胞的表征，以鉴定A3 乳腺癌、膀胱癌和肺癌中的突变体。同时，我们将直接评估未知的特异性， 测定单个A3酶活性的测定灵敏度。这些实验可以进一步证实 大量癌症突变的推测性A3病因学和个体A3的量化贡献 酶，从而提名它们作为治疗追求的假定目标。目标2建立在我们的初步数据基础上 以研究提出的A3诱变的调节剂。这些实验有可能扩大 治疗机会的范围集中在癌细胞的演变。目标3将评估A3与 在乳腺癌、膀胱癌和肺癌细胞系中的酶、治疗抗性和转移。这些实验 将测试来自多维关联的预测，即A3诱变是一种疾病修饰过程 可以在癌症发展的各个阶段进行治疗。这些研究将 确定高度流行的突变过程的病因，并确定策略，以引起更持久的 靶向治疗和抑制转移的临床益处。