Molecular genetics and population studies of the KIR and HLA gene complexes

KIR 和 HLA 基因复合物的分子遗传学和群体研究

• 批准号: 8763222
• 负责人: Mary N. Carrington
• 金额: $ 25.2万
• 依托单位: DIVISION OF BASIC SCIENCES - NCI
• 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/8763222
• 关键词: Accounting; Affect; Biology; Caucasians; Caucasoid Race; Cell surface; Characteristics; Chromosomes, Human, Pair 19; Complex; Copy Number Polymorphism; Cytoplasmic Tail; Data; Diploidy; Disease; Disease Outcome; Event; Evolution; Exhibits; Extracellular Domain; Gene Cluster; Gene Deletion; Gene Dosage; Gene Duplication; Genes; Genetic; Genetic Epistasis; Genetic Polymorphism; Genetic Population Study; Genetic Recombination; Genome; Genomics; Goals; HLA Antigens; Haplotypes; Homologous Gene; Human; Human Chromosomes; ITAM; Immune Response Genes; Immunoglobulins; Individual; Killer Cells; Knowledge; Laboratories; Leukocytes; Ligands; Ligation; Linkage Disequilibrium; Maintenance; Major Histocompatibility Complex; Measures; Mediating; Meiotic Recombination; Methods; Minor; Molecular Genetics; Pattern; Phase; Predisposition; Property; Proteins; Receptor Gene; Recombinants; Reporting; Resistance; Signal Transduction; Site; Sorting - Cell Movement; Structure; Time; Tyrosine; Ursidae Family; Variant; base; genetic analysis; homologous recombination; human disease; human leukocyte antigen gene; immune function; insertion/deletion mutation; interest; mRNA Expression; monocyte; population based; pressure; receptor

Leukocyte immunoglobulin-like receptor (LILR) B3 and LILRA6 represent a pair of inhibitory/activating receptors with identical extracellular domains and unknown ligands. LILRB3 can mediate inhibitory signaling via immunoreceptor tyrosine-based inhibition motifs (ITIMs) in its cytoplasmic tail whereas LILRA6 can signal through association with an activating adaptor molecule, FcRgamma, which bears a cytoplasmic tail with an immunoreceptor tyrosine-based activation motif (ITAM). The receptors are encoded by two highly polymorphic neighboring genes within the Leukocyte Receptor Complex (LRC) on human chromosome 19. We undertook a comprehensive genetic analysis of the LILRB3/A6 locus and investigated gene-specific expression. The data confirm the presence of high levels of non-synonymous variation in both genes with the majority of polymorphic sites being identical. In addition, the LILRA6 gene exhibits copy number variation (CNV) whereas LILRB3 does not. A screen of healthy Caucasians indicated that 32% of the subjects possessed more than 2 copies of LILRA6, whereas 4% have only one copy of the gene per diploid genome. Thus it is apparent that this locus has been subjected to non-allelic homologous recombination (NAHR) over time, resulting in variable copy numbers of the activating LILRA6 gene, but maintenance of a single fixed copy of the inhibitory LILRB3 gene.. Analysis of mRNA expression in the major fractions of PBMCs showed that LILRA6 is primarily expressed in monocytes, similarly to LILRB3, and its expression level correlates with copy number of the gene. We suggest that the LILRA6 CNV may influence the level of the activating receptor on the cell surface, potentially affecting signaling upon LILRB3/A6 ligation. The human KIR genes are arranged in at least six major gene-content haplotypes, all of which are combinations of four centromeric and two telomeric motifs. Several less frequent or minor haplotypes also exist, including insertions, deletions, and hybridization of KIR genes derived from the major haplotypes. These haplotype structures and their concomitant linkage disequilibrium among KIR genes suggest that more meaningful correlative data from studies of KIR genetics and complex disease may be achieved by measuring haplotypes of the KIR region in total. Previous studies of the KIR region have yielded detailed information about KIR haplotype structures derived uniquely from complete phased genomic sequences, revealing substructures of known haplotypes and further defined linkage among the KIR genes. Taking into account the many reported correlations between KIR polymorphism and disease, there is some imperative to incorporate KIR haplotype structures, including potential intraregion epistasis, into the association studies so that causative variation at KIR can be identified. In addition, the repetitive gene content structure of the KIR region may contribute to rapid evolution through aberrant recombination mechanisms, possibly driven by the immune function of KIR and providing further impetus towards understanding overall genomic region variation. Towards that end, a KIR haplotyping method developed by our collaborators that reports unambiguous combinations of KIR gene-content haplotypes, including both phase and copy number for each KIR was utilized. A total of 37 different gene content haplotypes were detected from 4,512 individuals and new sequence data was derived from haplotypes where the detailed structure was not previously available. An additional 10 haplotypes were detected in single copy but were not confirmed by sequencing. The 37 KIR haplotypes were sorted into 10 types of structural alterations, including gene deletions, insertions, and hybridizations, which together suggest a number of recombination events that might have occurred during KIR evolution. These new structures suggest a number of specific recombinant events during the course of KIR evolution, and add to an expanding diversity ofpotential new KIR haplotypes derived from gene duplication, deletion, and hybridization. The data provide important information regarding KIR genetic factors that may contribute to disease outcome.

白细胞免疫球蛋白样受体（LILR） B3和LILRA6是一对具有相同胞外结构域和未知配体的抑制/激活受体。LILRB3可以通过其胞质尾部的免疫受体酪氨酸基抑制基序（ITIMs）介导抑制信号，而LILRA6可以通过与激活接头分子FcRgamma的关联来介导信号，FcRgamma的胞质尾部带有免疫受体酪氨酸基激活基序（ITAM）。这些受体是由人类第19号染色体上的两个高度多态性的邻近基因编码的。我们对LILRB3/A6位点进行了全面的遗传分析，并研究了基因特异性表达。这些数据证实了两个基因中存在高水平的非同义变异，大多数多态性位点是相同的。此外，LILRA6基因表现出拷贝数变异（CNV），而LILRB3基因则没有。对健康高加索人的筛查表明，32%的受试者拥有2个以上的LILRA6拷贝，而4%的受试者每个二倍体基因组只有一个拷贝。因此，很明显，随着时间的推移，该位点受到非等位基因同源重组（NAHR）的影响，导致激活LILRA6基因的拷贝数变化，但抑制LILRB3基因的拷贝数保持不变。对PBMCs主要部位的mRNA表达分析表明，LILRA6主要表达于单核细胞，与LILRB3相似，其表达水平与基因拷贝数相关。我们认为LILRA6 CNV可能影响细胞表面激活受体的水平，潜在地影响LILRB3/A6连接的信号传导。人类KIR基因至少有6个主要的基因含量单倍型，所有这些单倍型都是4个着丝粒和2个端粒基序的组合。一些不太常见或次要的单倍型也存在，包括插入、缺失和来自主要单倍型的KIR基因杂交。这些单倍型结构及其伴随的KIR基因间连锁不平衡表明，通过测量KIR区域的总单倍型，可以获得更有意义的KIR遗传学与复杂疾病研究的相关数据。先前对KIR区域的研究已经获得了KIR单倍型结构的详细信息，这些结构来源于完整的基因组序列，揭示了已知单倍型的亚结构，并进一步确定了KIR基因之间的连锁关系。考虑到许多报道的KIR多态性与疾病之间的相关性，有必要将KIR单倍型结构，包括潜在的区域内显性，纳入关联研究，以便确定KIR的致病变异。此外，KIR区域的重复基因含量结构可能通过异常重组机制促进快速进化，这可能是由KIR的免疫功能驱动的，并为理解整体基因组区域变异提供了进一步的动力。为此，我们的合作者开发了一种KIR单倍型方法，该方法报告了KIR基因含量单倍型的明确组合，包括每个KIR的阶段和拷贝数。从4512个个体中共检测到37种不同的基因含量单倍型，并从先前未获得详细结构的单倍型中获得新的序列数据。在单个拷贝中检测到另外10个单倍型，但未通过测序证实。37个KIR单倍型被分为10种类型的结构改变，包括基因缺失、插入和杂交，它们共同表明在KIR进化过程中可能发生了许多重组事件。这些新的结构表明，在KIR进化过程中发生了许多特定的重组事件，并增加了来自基因复制、缺失和杂交的潜在新的KIR单倍型的多样性。这些数据提供了有关可能影响疾病结局的KIR遗传因素的重要信息。