Defining Variation in the Natural Killer Cell Receptome in Human Populations

摘要 这个项目的总体目标是开发一张全面的层序和结构变化图 人类祖先不同群体中的NK(自然杀伤)细胞受体。两个基因组编码区域 NK细胞受体，白细胞受体复合体(LRC)和自然杀伤复合体(NKC)，容纳了90多个 在NK细胞对感染细胞和癌细胞的杀伤作用中起重要作用的基因。复杂的结构 这些区域内基因之间的变异和高度的序列同一性一直是阻碍 以前的全基因组关联和测序研究中的综合分析。凭借我们的专业知识和 在研究复杂基因组变异方面的经验，我们将开发出最全面的序列图谱 以及人群中LRC和NKC的结构变异。在具体目标1中，我们将进行一次高- 吞吐量研究需要使用我们新颖且经过验证的NEXT对这两个复合体进行完整测序- 世代排序方法。来自18个种群的2150个样本的DNA样本，包括原住民 美国人和来自南美洲、非洲人、欧洲美国人和非洲人的混血儿 美国人。序列数据将使用我们定制设计的生物信息学管道进行分析。我们将专注于 不仅是具有已知拷贝数结构变异的基因家族，如KIR(杀伤细胞 免疫球蛋白样受体)和LILR(白细胞免疫球蛋白样受体)，但将分析所有常见的 所有90个NKC和LRC基因的变异，以表征其变异的全部程度。与此协同 方法，在特定的目标2，我们将执行一个强大的单细胞表达数量性状基因座(EQTL) 外周血NK细胞单细胞转录本测序定位LRC和NKC 40例健康人的单个核细胞。我们将确定与差异表达水平相关的变体 用于对新出现的功能假说进行初步评估。我们将确定任何常见的变种 在与eQTL效应相关的LRC和NKC内，导致了对 到目前为止，NK受体在群体中的遗传变异。这一探索性项目将为下一步 功能研究，并可能最终导致发现NK细胞免疫治疗的新靶点。

ABSTRACT The overall goal of this project is to develop a comprehensive map of sequence and structural variation of the NK (natural killer) cell receptome in ancestrally diverse human populations. The two genomic regions encoding NK cell receptors, leukocyte receptor complex (LRC) and natural killer complex (NKC), house more than 90 genes with an essential role in NK cell cytotoxicity against infected and cancer cells. The complex structural variation and the high degree of sequence identity among genes within these regions have served as barriers to a comprehensive analysis in former genome-wide association and sequencing studies. With our expertise and experience in studying complex genomic variation, we will develop the most comprehensive map of sequence and structural variation of the LRC and NKC in human populations. In Specific Aim 1, we will conduct a high- throughput study entailing the complete sequencing of these two complexes using our novel and validated next- generation sequencing approach. DNA samples from 2150 samples from 18 populations, including Native Americans and admixed populations from South America, Africans, European Americans, and African Americans. Sequence data will be analyzed with our custom-designed bioinformatics pipelines. We will focus not only on gene families with a known structural variation of copy number, such as KIR (killer-cell immunoglobulin-like receptor) and LILR (leukocyte immunoglobulin-like receptors) but will analyze all common variants in all 90 NKC and LRC genes to characterize the full extent of their variation. Synergized with this approach, in Specific Aim 2, we will perform a powerful single-cell expression quantitative trait loci (eQTL) mapping of LRC and NKC by sequencing the single-cell transcriptomes of NK cells from peripheral blood mononuclear cells of 40 healthy individuals. We will identify variants associated with differential expression levels in NK cells for the initial assessment of emerging functional hypotheses. We will identify any common variants within the LRC and NKC that are associated with eQTL effects, resulting in the most comprehensive study of the NK receptome genetic variation in populations to date. This exploratory project will lay the basis for further functional studies and may ultimately lead to discovering new targets for NK cell immunotherapies.