Integration of germline and tumor genomes in CLL

CLL 中种系和肿瘤基因组的整合

• 批准号: 10295177
• 负责人: Esteban Braggio
• 金额: $ 63.39万
• 依托单位: MAYO CLINIC ROCHESTER
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-12-06 至 2023-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10295177
• 关键词: Address; Affect; Apoptosis; B-Cell Neoplasm; B-Lymphocytes; Biological; Biology; CD19 gene; CISH gene; Cell Line; Characteristics; Chronic Lymphocytic Leukemia; DNA; Data; Development; Diagnosis; Disease; Epigenetic Process; Etiology; Evolution; Family member; Gene Expression; Gene Targeting; Genes; Genetic; Genetic Counseling; Genetic Transcription; Genome; Genomics; Genotype; Goals; Heterogeneity; Human Herpesvirus 4; In Vitro; Individual; Inherited; Joints; Knowledge; Location; Lymphocyte; Lymphocytosis; MicroRNAs; Mutate; Odds Ratio; Outcome; Patients; Predisposition; Prevention strategy; Public Health; Quantitative Trait Loci; RNA; Recurrence; Risk; Risk Factors; Role; Signal Transduction; Single Nucleotide Polymorphism; Somatic Mutation; Susceptibility Gene; Telomere Length Maintenance; Testing; Time; Validation; Variant; Weight; Whole Blood; Woman; base; cancer genome; cell type; chronic lymphocytic leukemia cell; driver mutation; early screening; exome sequencing; genetic variant; genome sequencing; genome wide association study; improved; insight; interest; leukemia; lymphoblastoid cell line; men; novel; novel marker; polygenic risk score; risk variant; targeted sequencing; targeted treatment; trait; transcriptome sequencing; transcriptomics; tumor; tumor DNA; whole genome

Project Summary: Chronic lymphocytic leukemia (CLL) is a neoplasm of B-cell lymphocytes. It has a strong genetic component with 45 inherited single nucleotide polymorphisms (SNPs) identified through genome-wide association studies (GWAS). Using these SNPs, we computed a polygenic risk score (PRS), which is a weighted average of the risk alleles across the SNPs with the weights being the log odds ratios from SNP associations, and found that individuals in the upper quintile had a ~3-fold increased risk of CLL compared to the middle quintile (P<0.0001), providing evidence that the combination of known and common CLL susceptibility variants is one of the strongest CLL risk factors. In addition, whole genome and exome sequencing studies have recently identified over 60 recurrent somatic CLL variants or copy number alterations (CNA) and found that 88-90% of CLL cases have at least one putative driver mutation and ~44% have at least three driver mutations. However, little is known about how the inherited genetic variants interact with the tumor (at DNA and RNA level) and their contribution to tumor evolution. This application proposes to address this knowledge gap. In preliminary data from our CLL GWAS, we have evidence that a number of the CLL GWAS-discovered SNPs influence the expression levels of genes in cis (within 1-Mb window around the SNP) using RNA from whole blood or lymphoblastoid cell lines (LCL). However, because whole blood is a composition of multiple cell types, of which B-cells make up ~5-10%, B-cell specific signals are most likely missed, and gene expression from cell lines may be altered by the Epstein Barr Virus transformation used to generate LCL. Aim 1 proposes to overcome these limitations by using RNA from sorted tumor B-cells, sorted B-cells of healthy controls, and sorted clonal B-cells from individuals with the precursor condition to CLL, monoclonal B-cell lymphocytosis (MBL), to perform expression quantitative trait locus (eQTL) analyses. Validation and experimental in vitro studies will be performed to confirm and evaluate the functional relevance of variants of interest. Next, little is known about the extent of inherited germline variants in the individuals with somatic driver mutations. Aim 2 will address this gap to assess the relationship between germline and tumor DNA variants and to assess their effect on CLL outcomes. Finally, CLL is a heterogeneous disease with ~20% of CLL cases having a 5-year overall survival of 15-19%. There are a number of somatic variants that drive aggressive CLL disease, yet little is known about the role of inherited variants. Aim 3 will address this gap by identifying novel inherited variants associated with CLL aggressiveness. Upon completion, we will have identified gene targets of the known CLL susceptibility SNPs, will have characterized those CLL cases with high or low burden of genomic variants and assessed the effects on CLL outcomes, and will have gained insight into the genetic contribution to aggressive CLL. Our results may provide the potential discovery of novel biomarkers for targeted therapies, reveal novel ways to subclassify CLL, and develop potential genetic counseling strategies for family members.

项目概要： 慢性淋巴细胞白血病（CLL）是B细胞淋巴细胞的肿瘤。它有很强的遗传成分 通过全基因组关联研究确定了45种遗传性单核苷酸多态性（SNP）， （GWAS）。使用这些SNP，我们计算了多基因风险评分（PRS），这是一个加权平均值， 风险等位基因的SNP的权重是从SNP关联的对数优势比，并发现， 与中间五分位数相比，上五分位数的个体患CLL的风险增加约3倍。 （P<0.0001），提供了已知和常见CLL易感性变异的组合是一种 最强的CLL风险因素。此外，全基因组和外显子组测序研究最近 鉴定了超过60种复发性体细胞CLL变异或拷贝数改变（CNA），并发现88-90%的 CLL病例至少有一个推定的驱动突变，约44%的病例至少有三个驱动突变。然而，在这方面， 关于遗传性遗传变异如何与肿瘤相互作用（在DNA和RNA水平）及其 对肿瘤演变的贡献。本申请旨在解决这一知识差距。初步数据显示， 从我们的CLL GWAS中，我们有证据表明，许多CLL GWAS发现的SNP影响了 使用来自全血的RNA的顺式基因表达水平（SNP周围1 Mb窗口内），或 类淋巴母细胞系（LCL）。然而，由于全血是多种细胞类型的组合物， 其中B细胞占~5- 10%，B细胞特异性信号最有可能丢失，并且来自细胞的基因表达 可以通过用于产生LCL的Epstein巴尔病毒转化来改变细胞系。目标1建议， 通过使用来自分选的肿瘤B细胞、健康对照的分选的B细胞的RNA克服这些限制， 从具有CLL前体条件的个体中分选克隆B细胞，单克隆B细胞淋巴细胞增多症 (MBL)进行表达数量性状基因座（eQTL）分析。验证和体外实验 将进行研究以确认和评价感兴趣的变体的功能相关性。下一篇：Little Is 已知在具有体细胞驱动突变的个体中遗传的种系变异的程度。目的2 将解决这一差距，以评估生殖系和肿瘤DNA变异之间的关系，并评估其 对CLL结果的影响。最后，CLL是一种异质性疾病，约20%的CLL病例具有5年的随访期。 总生存率为15- 19%。有许多体细胞变异导致侵袭性CLL疾病，但很少 是关于遗传变异的作用。AIM 3将通过识别新的遗传变异来解决这一差距 与CLL侵略性有关。完成后，我们将确定已知CLL的基因靶点 易感性SNP将表征具有高或低基因组变异负担的那些CLL病例， 评估了对CLL结果的影响，并将深入了解遗传因素对侵袭性 CLL。我们的研究结果可能为靶向治疗提供新的生物标志物的潜在发现， 对CLL进行细分的方法，并为家庭成员制定潜在的遗传咨询策略。