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.

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