Targeting APOBEC3A-induced genetic heterogeneity and drug resistance in bladder cancer

靶向 APOBEC3A 诱导的膀胱癌遗传异质性和耐药性

基本信息

批准号：
10798615
负责人：
Bishoy Morris Faltas
金额：
$ 51.6万
依托单位：
WEILL MEDICAL COLL OF CORNELL UNIV
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：
2023-09-20 至 2028-08-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10798615
关键词：
Bar Codes Cell Line Cells Cessation of life Characteristics Clinical Trials Cytidine Cytidine Deaminase DNA Double Strand Break Data Deamination Decision Making Development Diagnosis Drug resistance Evolution FGFR3 gene Family Future Genes Genetic Genetic Heterogeneity Genetic Induction Genomics Goals Human In Vitro Induced Mutation Knowledge Laboratories Malignant Epithelial Cell Malignant Neoplasms Malignant neoplasm of urinary bladder Mediating Mediator Methods Modeling Mutagenesis Mutation Organoids Pathway interactions Patient-Focused Outcomes Patients Phenotype Phosphotransferases Phylogenetic Analysis Polymerase Proto-Oncogene Proteins c-akt Public Health Publishing Relapse Reporting Research Resistance Resistance development Role Sampling Signal Transduction Specific qualifier value System Systemic Therapy Testing Therapeutic Transitional Cell Carcinoma Tumor Bank United States Urothelium Work Xenograft procedure biomarker identification cancer cell clinical biomarkers clinical risk co-clinical trial de novo mutation improved improved outcome in vivo inhibitor innovation insertion/deletion mutation novel novel strategies novel therapeutic intervention pharmacologic precision medicine pressure prevent refractory cancer repaired response biomarker standard of care success targeted treatment therapeutically effective therapy resistant tumor tumor heterogeneity

项目摘要

PROJECT SUMMARY/ ABSTRACT Every five minutes, a new patient is diagnosed with urothelial carcinoma (UC) in the United States, resulting in the death of 18,000 patients annually. Nearly all patients with advanced UC will develop resistance to systemic treatment. Intratumoral heterogeneity (ITH) is a major contributor to treatment resistance by increasing the chance for resistant subclones to emerge. However, genetic ITH is currently not druggable and not considered in therapeutic decision-making, thus worsening drug-resistant patient phenotypes. The fundamental knowledge gap regarding genetic drivers of ITH impedes the development of effective therapeutic strategies to prevent and eliminate drug resistance. Our long-term goal is to define targetable mechanisms of ITH and treatment resistance to develop an effective precision strategy to achieve cures in patients with advanced UC. The overall objective is to define targetable mechanisms by which APOBEC3A-mediated ITH drives drug resistance and identify strategies to eliminate UC cells with APOBEC3A activity. Our central hypothesis is that APOBEC3A-induced cytidine deamination drives genetic ITH leading to the emergence of therapy-resistant UC clones and, in so doing, simultaneously creating unique targetable vulnerabilities. This hypothesis was formulated based on our published work and strong preliminary data showing that APOBEC3A expression in isogenic UC cell lines and patient-derived organoids drives genetic ITH. We found that APOBEC3A-induced, de novo mutations in the PIKC3A-AKT-MTOR signaling hub drive the resistance to erdafitinib, an FGFR3-inhibitor (FGFR3i) approved for UC treatment. Our preliminary data also revealed that APOBEC3A-induced double-stranded DNA breaks are preferentially repaired by the microhomology-mediated end-joining (MMEJ) pathway and that targeting the critical MMEJ mediator, polymerase theta (Polθ), is synthetically lethal in APOBEC3A-expressing clones. The rationale is that identifying targetable mechanisms by which APOBEC3A-induced ITH drives drug resistance and developing strategies to eliminate APOBEC3A-expressing UC cells will improve cure rates for patients. We will test our hypothesis by pursuing two specific Aims. Aim 1: Identify targetable mechanisms by which APOBEC3A- induced mutational ITH drives treatment resistance in UC. Aim 2: Identify synthetic lethal strategies to target UC tumors with APOBEC3A-induced DNA double-strand breaks. Aim 1 will use longitudinal clonal barcoding and in vitro and in vivo laboratory evolution to identify targetable APOBEC3A-driven kinase hubs that mediate FGFR3i resistance and validate them in patient samples from FGFR3i clinical trials. Aim 2 will use genetic and pharmacologic inhibition of Polθ in APOBEC3A-expressing UC models and a co-clinical trial of patient-derived UC organoids and xenografts to identify clinical biomarkers of response to APOBEC3A-MMEJ synthetic lethality. The approach is conceptually and technically innovative, creating a new paradigm for eliminating treatment- resistant cancers. Impact: Completion of the proposed research will establish APOBEC3A as a genetic driver of treatment resistance and enable synthetic lethal approaches to increase cure rates.

项目摘要/摘要每五分钟，一名新患者在美国被诊断出患有尿路上皮癌（UC），导致每年18,000名患者死亡。几乎所有具有晚期UC的患者都会产生对系统性的抗性治疗。肿瘤内异质性（ITH）是通过增加治疗耐药性的主要因素耐药子克隆出现的机会。但是，遗传ITH目前不可吸毒，也不考虑在热决策中，因此令人担忧的是耐药的患者表型。基本知识关于ITH遗传驱动因素的缺口阻碍了有效的治疗策略来预防和消除耐药性。我们的长期目标是定义ITH的目标机制和治疗耐药性制定有效的精确策略以实现晚期UC患者的治疗方法。总体目标是为了定义apobec3a介导的ITH驱动耐药性并识别的可靶向机制消除具有APOBEC3A活性的UC细胞的策略。我们的中心假设是apobec3a诱导的胞苷死亡驱动基因ITH导致耐药UC克隆的出现，并在因此，仅创建独特的目标漏洞。该假设是基于关于我们发表的工作和强大的初步数据，表明apobec3a在等源性UC细胞系中的表达患者衍生的类器官驱动基因ITH。我们发现apobec3a引起的，从头突变 PIKC3A-AKT-MTOR信号轮毂驱动对Erdafitinib的阻力，Erdafitinib是批准的FGFR3抑制剂（FGFR3I） UC治疗。我们的初步数据还显示，Apobec3a诱导的双链DNA断裂是通过微学介导的最终连接（MMEJ）途径优先修复临界MMEJ介体，聚合酶theta（polθ），在表达ApoBec3a的克隆中是致命的。这理由是识别ApoBec3a诱导的ITH驱动耐药性和制定消除表达APOBEC3A的UC细胞的策略将改善患者的治疗率。我们将通过追求两个具体目标来检验我们的假设。 AIM 1：确定APOBEC3A-的目标机制诱导的突变ITH驱动UC中的治疗耐药性。目标2：确定靶向UC的合成致命策略具有APOBEC3A诱导的DNA双链断裂的肿瘤断裂。 AIM 1将使用纵向克隆条形码和体内和体内实验室进化，以鉴定介导FGFR3I的靶向APOBEC3A驱动的激酶轮毂在FGFR3I临床试验中的患者样品中抗性并验证它们。 AIM 2将使用遗传和在表达APOBEC3A的UC模型中对POLθ的药理抑制作用和患者衍生的共同临床试验 UC类器官和异种移植物，以鉴定对APOBEC3A-MMEJ合成致死性反应的临床生物标志物。该方法在概念上和技术上都是创新的，创造了一种消除治疗的新范式 - 抗性癌症。影响：拟议研究的完成将确定APOBEC3A作为遗传驱动治疗耐药性并实现合成的致命方法，以提高治愈率。