Characterizing noncoding GWAS variants in acute lymphoblastic leukemia treatment outcome

表征急性淋巴细胞白血病治疗结果中的非编码 GWAS 变异

基本信息

批准号：
10459411
负责人：
Daniel Savic
金额：
$ 48.18万
依托单位：
ST. JUDE CHILDREN'S RESEARCH HOSPITAL
依托单位国家：
美国
项目类别：
财政年份：
2019
资助国家：
美国
起止时间：
2019-08-01 至 2024-07-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10459411
关键词：
Acute Lymphocytic Leukemia Address Alleles Biological Assay Biology Bypass CRISPR/Cas technology Catalogs Cell Line Cellular biology Childhood Acute Lymphocytic Leukemia Chromatin Chromosome Mapping Clinic Clinical Clustered Regularly Interspaced Short Palindromic Repeats DNA Sequence Data Data Set Development Disease Outcome Drug resistance Enhancers Follow-Up Studies Gene Expression Regulation Genes Genetic Genetic Determinism Genetic Variation Genome Genomics Goals Human Inherited Knowledge Leukemic Cell Link Linkage Disequilibrium Location Malignant Childhood Neoplasm Maps Modeling Nature Newly Diagnosed Patients Pharmaceutical Preparations Phenotype Publishing Recurrent disease Regulator Genes Regulatory Element Relapse Reporter Research Proposals Residual Neoplasm Resistance Resources Role Saint Jude Children&apos s Research Hospital Sampling Site Survival Rate System Treatment Failure Treatment Protocols Treatment outcome Untranslated RNA Variant acute lymphoblastic leukemia cell antileukemic agent causal variant chemotherapeutic agent cohort follow-up functional genomics gene function genetic variant genome editing genome wide association study genomic data improved leukemia leukemia relapse mouse model novel novel therapeutics outcome prediction patient derived xenograft model personalized medicine precision medicine promoter relapse patients resistance mechanism response transcriptome treatment response treatment strategy

项目摘要

PROJECT SUMMARY Acute lymphoblastic leukemia (ALL) is the most prevalent childhood cancer, and although overall survival rates of ALL have substantially improved, resistance to antileukemic agents remains a major clinical problem. Antileukemic drug resistance is predictive of poor disease outcome and is commonly observed in ALL patients that have relapsed, who have a low overall survival rate of only 40%. The mechanisms that cause ALL relapse and drug resistance remain poorly understood. To address how inherited genomic variability contributes to these mechanisms, genome wide association studies (GWASs) have identified DNA sequence variation associated with ALL treatment outcome. However, since these variants are noncoding in nature, their connection to gene function, ALL biology and antileukemic drug resistance has been difficult to establish. Moreover, given that hundreds of variants are typically in strong linkage disequilibrium with the associated variant, pinpointing causal variants at GWAS loci has been challenging. To address these challenges, we have generated functional genomic maps of the ALL genome, including the precise locations of noncoding regulatory elements in >40 ALL samples. Through rigorous open chromatin-fine mapping using our ALL genome maps, and by integrating our results with drug resistance phenotypes from primary ALL cells obtained from patients at St. Jude (SJ), we identified 3229 variants at 125 GWAS loci associated with ALL treatment outcome that are predicted to have an impact on gene regulation, leukemic cell biology and antileukemic drug resistance. Using these fine-mapped variants, we propose an integrative strategy for identifying candidate causal variants associated with ALL treatment outcome, and a rational experimental system for functionally linking these variants and their target genes to antileukemic drug resistance. In Aim 1, we will perform massively parallel reporter assays (MPRAs) on >3200 fine-mapped variants to assess their gene regulatory activities and to identify allele-specific differences in activity. In Aim 2, we will employ a polygenomic strategy by integrating our MPRA results with diverse genomic datasets to prioritize and rank fine-mapped variants by their likelihood of being causal. For this effort, we will capitalize on the unique and rich resources available at SJ, including extensive genomic characterizations and drug resistance phenotypes from large ALL patient cohorts, as well as ongoing genomic characterizations for all new and/or relapsed patients. We will functionally validate the role of the top 20 ranked candidate causal variants on antileukemic drug resistance using CRISPR technology and chemotherapeutic drug viability assays in human ALL cell lines. We will also identify GWAS target genes and functionally assess their role in antileukemic drug resistance in human ALL cell lines and in patient-derived xenograft mouse models of pediatric ALL. Collectively, our proposal will uncover novel genomic mechanisms of antileukemic drug resistance. Ultimately, these data can inform approaches to circumvent resistance in the clinic, and be used to improve initial treatment, as well as guide therapy for relapsed disease through precision medicine and more personalized treatment regimens.

项目摘要急性淋巴细胞白血病（全部）是最普遍的儿童癌症，尽管总体生存率所有人都有显着改善，对抗白血病药物的抗性仍然是一个主要的临床问题。抗血症药物耐药性可以预测疾病不良的预后，并且在所有患者中通常都观察到复发，总生存率低40％。引起所有复发的机制耐药性仍然很少。解决遗传基因组变异性如何对这些变异机制，基因组广泛的关联研究（GWASS）已鉴定出与DNA序列变化相关与所有治疗结果。但是，由于这些变体本质上是不编码的，因此它们与基因的联系功能，所有生物学和抗白血病耐药性都很难建立。而且，鉴于这一点数百个变体通常与相关的变体不平衡地处于不平衡状态 GWAS基因座的变体一直具有挑战性。为了应对这些挑战，我们产生了功能所有基因组的基因组图，包括> 40的非编码调节元素的精确位置样品。通过使用我们的所有基因组图的严格开放染色质 - 绘制映射，并通过整合我们的来自来自圣裘德（SJ）患者获得的原发性细胞的耐药性表型的结果，我们确定了与所有治疗结果相关的125个GWAS基因座的3229个变体对基因调节，白血病细胞生物学和抗白血病耐药性的影响。使用这些精细映射变体，我们提出了一种综合策略，用于识别与所有人相关的候选因果变体治疗结果和合理的实验系统，用于在功能上连接这些变体及其目标基因抗抗血症药物的耐药性。在AIM 1中，我们将在AIM 1上进行大规模平行的记者测定法（MPRA） > 3200个精细映射变体，以评估其基因调节活动并确定等位基因特异性差异在活动中。在AIM 2中，我们将通过将MPRA结果与不同的基因组相结合来采用多基因组策略数据集优先级和对绘制的变体来确定其因果关系的可能性。为此，我们将利用SJ可用的独特而丰富的资源，包括广泛的基因组特征和来自大型所有患者队列的耐药性表型，以及所有的基因组表征新的和/或复发的患者。我们将在功能上验证排名最高的候选因果变体的作用使用CRISPR技术和化学治疗性药物生存能力测定的抗血清药物耐药性所有细胞系。我们还将确定GWAS靶基因并在功能上评估其在抗白血病药物中的作用人类所有细胞系的耐药性以及儿科衍生的异种移植小鼠模型中的抗性。共同我们的建议将揭示抗血症耐药性的新型基因组机制。最终，这些数据可以告知诊所中规避阻力的方法，并用于改善初始治疗通过精确医学和更多个性化治疗方案指导疾病的指导疗法。