Statistical Genetics of Dose Response Traits

剂量反应特征的统计遗传学

• 批准号: 10928611
• 负责人: Alison Motsinger-Reif
• 金额: $ 13.17万
• 依托单位: NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10928611
• 关键词: African; Antineoplastic Agents; B-Cell Activation; B-Lymphocytes; Biological Markers; Biological Models; Brain Neoplasms; Cancer Center; Candidate Disease Gene; Cell Line; Cells; Characteristics; Chemoresistance; Clinical; Collaborations; Colorectal Cancer; Data; Data Set; Development; Disease; Dose; Ethnic Origin; Flow Cytometry; Follow-Up Studies; Gene Expression; Gene Expression Profiling; Genes; Genetic; Genetic Polymorphism; Genetic Predisposition to Disease; Genetic Variation; Genotype; Glioblastoma; Glioma; Goals; Heterogeneity; Immunoglobulin Class Switching; Immunoglobulin G; Lymphocyte; MGMT gene; MS4A1 gene; Malignant Neoplasms; Measures; Mediating; Methodology; Modeling; Monoclonal Antibody CD20; Monoclonal Antibody Therapy; North Carolina; Patient-Focused Outcomes; Patients; Pharmaceutical Preparations; Pharmacogenomics; Phenotype; Phosphotransferases; Prognostic Marker; Progression-Free Survivals; Regression Analysis; Research; Resistance; Source; Stratification; Surface Immunoglobulins; The Cancer Genome Atlas; Therapeutic; Toxicogenomics; Transcript; Universities; Validation; Variant; Work; anti-CD20; chemotherapy; cohort; colon cancer cell line; cost effectiveness; cytotoxic; doctoral student; ethnic diversity; genetic variant; genome wide association study; glioma cell line; high throughput screening; improved; in vivo; knock-down; lymphoblastoid cell line; mutant; novel; oxaliplatin; patient response; patient variability; prednisolone; prognostic; receptor; response; response biomarker; rituximab; small hairpin RNA; survival prediction; temozolomide; tool; trait; tumor

Dissecting the genetic etiology of cancer drug response using a lymphoblastoid cell line model has been a longstanding research goal. The use of ex-vivo model systems to provide a level of forecasting for in-vivo characteristics remains an important need for cancer therapeutics. The use of lymphoblastoid cell lines (LCLs) is an attractive approach for pharmacogenomics and toxicogenomics, due to their scalability, efficiency, and cost-effectiveness. In previous years of the project, we used LCLs to conduct genome-wide association studies for numerous anti-cancer drugs. The GWAS analyses identified a number of significant findings, and this year the project was focused on functional follow up studies to confirm associations and begin to understand the functional consequences of genetic variation in this context. Summaries of these studies are below. Oxaliplatin (OXAL) is a commonly used chemotherapy for treating colorectal cancer (CRC). A recent genome wide association study (GWAS) showed that a genetic variant (rs11006706) in the lncRNA gene MKX-AS1 and partnered sense gene MKX could impact the response of genetically varied cell lines to OXAL treatment. This study found that the expression levels of MKX-AS1 and MKX in lymphocytes (LCLs) and CRC cell lines differed between the rs11006706 genotypes, indicating that this gene pair could play a role in OXAL response. Further analysis of patient survival data from the Cancer Genome Atlas (TCGA) and other sources showed that patients with high MKX-AS1 expression status had significantly worse overall survival (HR = 3.2; 95%CI = (1.179); p = 0.024) compared to cases with low MKX-AS1 expression status. Alternatively, high MKX expression status had significantly better overall survival (HR = 0.22; 95%CI = (0.070.7); p = 0.01) compared to cases with low MKX expression status. These results suggest an association between MKX-AS1 and MKX expression status that could be useful as a prognostic marker of response to OXAL and potential patient outcomes in CRC. Temozolomide (TMZ) chemotherapy is an important tool in the treatment of glioma brain tumors. However, variable patient response and chemo-resistance remain exceptionally challenging. Our previous genome-wide association study (GWAS) identified a suggestively significant association of SNP rs4470517 in the RYK (receptor-like kinase) gene with TMZ drug response. Functional validation of RYK using lymphocytes and glioma cell lines resulted in gene expression analysis indicating differences in expression status between genotypes of the cell lines and TMZ dose response. We conducted univariate and multivariate Cox regression analyses using publicly available TCGA and GEO datasets to investigate the impact of RYK gene expression status on glioma patient overall (OS) and progression-free survival (PFS). Our results indicated that in IDH mutant gliomas, RYK expression and tumor grade were significant predictors of survival. In IDH wildtype glioblastomas (GBM), MGMT status was the only significant predictor. Despite this result, we revealed a potential benefit of RYK expression in IDH wildtype GBM patients. We found that a combination of RYK expression and MGMT status could serve as an additional biomarker for improved survival. Overall, our findings suggest that RYK expression may serve as an important prognostic or predictor of TMZ response and survival for glioma patients. Monoclonal antibody (mAb) therapy directed against CD20 is an important tool in the treatment of B cell disorders. However, variable patient response and acquired resistance remain important clinical challenges. To identify genetic factors that may influence sensitivity to treatment, the cytotoxic activity of three CD20 mAbs: rituximab; ofatumumab; and obinutuzumab, were screened in high-throughput assays using 680 ethnically diverse lymphoblastoid cell lines (LCLs) followed by a pharmacogenomic assessment. GWAS analysis identified several novel gene candidates. The most significant SNP, rs58600101, in the gene MKL1 displayed ethnic stratification, with the variant being significantly more prevalent in the African cohort and resulting in reduced transcript levels as measured by qPCR. Functional validation of MKL1 by shRNA-mediated knockdown of MKL1 resulted in a more resistant phenotype. Gene expression analysis identified the developmentally associated TGFB1I1 as the most significant gene associated with sensitivity. qPCR among a panel of sensitive and resistant LCLs revealed immunoglobulin class-switching as well as differences in the expression of B cell activation markers. Flow cytometry showed heterogeneity within some cell lines relative to surface Ig isotype with a shift to more IgG+ cells among the resistant lines. Pretreatment with prednisolone could partly reverse the resistant phenotype. Results suggest that the efficacy of anti-CD20 mAb therapy may be influenced by B cell developmental status as well as polymorphism in the MKL1 gene

使用淋巴母细胞系模型剖析癌症药物反应的遗传病因学一直是一个长期的研究目标。使用体外模型系统来提供体内特征的预测水平仍然是癌症治疗学的重要需求。淋巴母细胞系(LCLS)的使用是药物基因组学和毒理基因组学的一种有吸引力的方法，因为它们具有可扩展性、效率和成本效益。在该项目的前几年，我们使用LCLS对许多抗癌药物进行了全基因组关联研究。全球遗传多样性研究所的分析确定了一些重要的发现，今年该项目的重点是功能后续研究，以确认相关性并开始了解遗传变异在这一背景下的功能后果。这些研究的摘要如下。 奥沙利铂(OXAL)是治疗结直肠癌的常用化疗方案。最近的一项全基因组关联研究表明，lncRNA基因MKX-AS1及其合作的正义基因MKX的一个遗传变异(Rs11006706)可以影响不同的遗传细胞系对OXAL的反应。本研究发现MKX-AS1和MKX在淋巴细胞(LCLS)和结直肠癌细胞系中的表达水平在rs11006706基因之间存在差异，提示该基因对在OXAL反应中可能起作用。来自癌症基因组图谱和其他来源的患者生存数据的进一步分析显示，与MKX-AS1低表达状态的患者相比，高MKX-AS1表达状态的患者的总体生存率显著较差(HR=3.295%CI=1.179；p=0.024)。与低MKX表达状态相比，高MKX表达状态患者的总体生存率显著提高(HR=0.22；95%CI=0.070.7；p=0.01)。这些结果表明，MKX-AS1和MKX表达状态之间存在关联，可作为OXAL疗效和潜在的结直肠癌患者预后的预测标记物。 替莫唑胺(TMZ)化疗是治疗脑胶质瘤的重要手段。然而，变化无常的患者反应和化疗耐药性仍然具有极大的挑战性。我们先前的全基因组关联研究发现，RYK(受体样激酶)基因中的SNP rs4470517与TMZ的药物反应显著相关。使用淋巴细胞和胶质瘤细胞系对RYK进行功能验证后，进行了基因表达分析，表明不同类型细胞系和TMZ剂量反应的表达状态存在差异。我们使用公开可用的TCGA和GEO数据集进行单因素和多因素COX回归分析，以调查RYK基因表达状态对胶质瘤患者总体(OS)和无进展生存期(PFS)的影响。我们的结果表明，在IDH突变的胶质瘤中，RYK的表达和肿瘤分级是显著的生存预测因素。在IDH野生型胶质母细胞瘤中，MGMT状态是唯一有意义的预测因素。尽管如此，我们发现RYK在IDH野生型GBM患者中的表达有潜在的好处。我们发现，RYK的表达和MGMT状态的结合可以作为改善生存率的额外生物标志物。总体而言，我们的研究结果表明，RYK的表达可能是胶质瘤患者TMZ反应和生存的重要预后或预测指标。 针对CD20的单抗治疗是治疗B细胞疾病的重要手段。然而，不同的患者反应和获得性耐药性仍然是重要的临床挑战。为了确定可能影响治疗敏感性的遗传因素，使用680个不同种族的淋巴母细胞系(LCL)进行了高通量分析，然后进行了药物基因组学评估，以确定三种CD20单抗：美罗华、ofatumumab和obinutuzumab的细胞毒活性。Gwas分析确定了几个新的候选基因。MKL1基因中最显著的SNP rs58600101表现出种族分层，该变异在非洲队列中明显更普遍，并导致qPCR检测到的转录水平降低。通过shRNA介导的MKL1基因敲除MKL1的功能验证导致了更多的抗性表型。基因表达分析表明，与发育相关的TGFB1I1基因是与敏感性相关的最重要的基因。在一组敏感和耐药的LCLS中进行定量聚合酶链式反应，发现免疫球蛋白类型转换以及B细胞激活标志物的表达存在差异。流式细胞术显示某些细胞系在表面Ig亚型上具有异质性，并在耐药系中向更多的Ig+细胞转变。强的松龙可部分逆转耐药表型。结果提示，抗CD20单抗治疗的疗效可能受B细胞发育状态和MKL1基因多态性的影响