Genomic Prediction of Doxorubicin-Induced Cardiotoxicity

阿霉素引起的心脏毒性的基因组预测

基本信息

批准号：
10456312
负责人：
Paul W. Burridge
金额：
$ 33.23万
依托单位：
NORTHWESTERN UNIVERSITY AT CHICAGO
依托单位国家：
美国
项目类别：
财政年份：
2018
资助国家：
美国
起止时间：
2018-09-13 至 2023-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10456312
关键词：
Affect Age Algorithms Anthracycline Attenuated Biochemical Bioinformatics Biological Biological Assay Biopsy Blastoma CRISPR/Cas technology Cancer Patient Candidate Disease Gene Cardiac Myocytes Cardiomyopathies Cardiotonic Agents Cardiotoxicity Cells Clinical Clinical Data Clustered Regularly Interspaced Short Palindromic Repeats Complication Correlation Studies Data Disadvantaged Dose Doxorubicin Etiology Exposure to Gene Expression Genes Genetic Genetic Markers Genetic study Genome Genomics Genotype Heart Transplantation Heart failure Human In Vitro Individual Knock-out Knowledge Lead Malignant Childhood Neoplasm Maps Mediating Metabolism Methodology Modality Molecular Mutation Oncologist Organ Pathway interactions Patients Pediatric cohort Pharmaceutical Preparations Phenotype Physiological Population Predisposition Process Quantitative Trait Loci RARG gene Reproducibility Research Research Personnel Resistance Role Route Single Nucleotide Polymorphism Solid Neoplasm Time Translating Untranslated RNA Validation Variant Work alternative treatment base cancer diagnosis cardioprotection chemotherapy clinical application cohort differential expression experience gene discovery genetic variant genome editing genome wide association study genomic tools human model induced pluripotent stem cell derived cardiomyocytes innovation interest leukemia/lymphoma lymphoblastoid cell line novel patient response pediatric patients prevent recruit response sarcoma screening sex side effect tool transcriptome transcriptome sequencing whole genome

项目摘要

Project Summary The anthracycline doxorubicin used in approximately 60% of pediatric cancer patients with metastatic solid tumors (sarcomas), blastomas, leukemia, and lymphoma. Treatments using doxorubicin are complicated by its well-established cardiotoxic side effect, which affects approximately 16% of pediatric patients, can lead to heart failure requiring heart transplant, and limits doxorubicin’s clinical utilization. Despite more than 50 years of research in this field, there is still, at present, little potential for either predicting or preventing cardiotoxicity. There is an obvious need for novel and innovative approaches to overcome this hurdle. Candidate gene association studies and genome–wide association studies (GWAS) have identified many single nucleotide polymorphisms (SNPs) that are statistically correlated with doxorubicin–induced cardiotoxicity (DIC), yet experimental validation of these SNPs has not been feasible due to the difficulty in isolating and culturing human cardiomyocytes in vitro. In our recent work, we showed that patient–specific human induced pluripotent stem cell–derived cardiomyocytes (hiPSC–CM) are efficient predictors of a patient’s likelihood of developing DIC, confirming for the first time that there is a genomic basis to DIC. Although GWAS has proven to be a powerful methodology for informing such genomic bases, it detects correlation rather than causation, and identified SNPs commonly fail to be replicated in subsequent studies. Here, we hypothesize that hiPSC-CMs can be utilized in three different modalities to study genetic variants associated with DIC: firstly, to discover novel predictive SNPs; secondly, to validate SNPs; and thirdly, to examine the modulated pathways and determine genotype-specific cardioprotective methodologies. In Aim 1, we will recruit 100 pediatric cancer patients who were exposed to doxorubicin and assess the response of patient-derived hiPSC-CM to doxorubicin in vitro to validate our previous findings in a large pediatric cohort with diverse biological covariates to verify the power of this tool. In Aim 2, we will use these 100 patient-specific lines to identify drug response differential expression quantitative trait loci (deQTL), assessing biological covariates such as dose, age, sex, SF, and cancer diagnosis both individually and combined. We will then validate these variants with genome editing, and mechanistically examine pathways causative to DIC susceptibility concentrating on genes with known roles in cardiomyopathy, cardioprotection, and doxorubicin metabolism. In Aim 3, we will interrogate the rigor and reproducibility of >40 existing DIC SNP studies, using CRISPR/Cas9 to edit the gene of interest in control isogenic hiPSC lines then assess the response of hiPSC-CM to doxorubicin. We will then use the discoveries above to discover/repurpose genome-informed cardioprotective drugs to prevent DIC in a genotype-specific manner. In summary, this work will deliver us the genetic rationale for why patients experience DIC and provide 1, fully human validated SNP data for clinical application, and 2, novel cardioprotective drugs to attenuate DIC.

项目概要大约 60% 的患有转移性实体瘤的儿科癌症患者使用蒽环类阿霉素肿瘤（肉瘤）、母细胞瘤、白血病和淋巴瘤的治疗因其使用阿霉素而变得复杂。已证实的心脏毒性副作用影响约 16% 的儿科患者，可导致心脏病失败需要心脏移植，并限制了阿霉素的临床应用，尽管已有 50 多年的历史。尽管该领域的研究目前在预测或预防心脏毒性方面的潜力仍然很小。显然需要新颖和创新的方法来克服这一障碍。研究和全基因组关联研究（GWAS）已经鉴定出许多单核苷酸多态性 (SNP) 与阿霉素诱导的心脏毒性 (DIC) 具有统计相关性，但尚未得到实验验证由于在体外分离和培养人类心肌细胞的困难，这些 SNP 的研究还不可行。在我们最近的工作中，我们表明患者特异性的人类诱导多能干细胞衍生心肌细胞 (hiPSC-CM) 是患者发生 DIC 可能性的有效预测因子，证实了尽管 GWAS 已被证明是一种强大的方法，但 DIC 首次具有基因组基础。告知此类基因组碱基，它检测的是相关性而不是因果关系，并且识别的 SNP 通常会失败在这里，我们追求 hiPSC-CM 可用于三种不同的情况。研究与 DIC 相关的遗传变异的方法：首先，发现新的预测 SNP；其次，验证 SNP；第三，检查调节途径并确定基因型特异性在目标 1 中，我们将招募 100 名接触过的儿童癌症患者。阿霉素并评估患者来源的 hiPSC-CM 在体外对阿霉素的反应，以验证我们之前的研究在具有不同生物协变量的大型儿科队列中的研究结果，我们在目标 2 中验证了该工具的功效。将使用这 100 个患者特异性品系来识别药物反应差异表达数量性状位点 (deQTL)，评估生物协变量，例如剂量、年龄、性别、SF 和癌症诊断，无论是单独还是然后，我们将通过基因组编辑验证这些变异，并机械地检查路径。导致 DIC 易感性的基因集中在已知在心肌病、心脏保护、在目标 3 中，我们将询问 > 40 个现有 DIC SNP 的严谨性和重现性。研究中，使用 CRISPR/Cas9 编辑对照同基因 hiPSC 系中的目的基因，然后评估反应然后，我们将利用上述发现来发现/重新利用基因组信息。心脏保护药物以基因型特异性方式预防 DIC 总而言之，这项工作将为我们带来以下成果。解释患者为何会经历 DIC 的遗传原理，并为临床提供 1 个完全经人体验证的 SNP 数据 2、减轻DIC的新型心脏保护药物的应用。