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: 8175344
• 负责人: Mary N. Carrington
• 金额: $ 50.8万
• 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/8175344
• 关键词: 19q13.4; 3' Untranslated Regions; Accounting; Affect; African American; Attention; Autoimmunity; Binding; Binding Sites; Biology; Cell surface; Characteristics; Chinese American; Chromosomes; Collaborations; Complex; Copy Number Polymorphism; DNA; Data; Development; Disease; Disease Outcome; Drug Delivery Systems; Environment; Equilibrium; European; Event; Fred Hutchinson Cancer Research Center; Gene Cluster; Gene Duplication; Genes; Genetic; Genetic Crossing Over; Genetic Population Study; Genome; Goals; HLA Antigens; Haplotypes; Hematologic Neoplasms; Heterogeneity; Homologous Gene; Human; Human Genome; Hybrids; Immune Response Genes; Immune response; Immune system; Immunity; Immunoglobulins; Immunologic Surveillance; Individual; Infectious Agent; Killer Cells; Knowledge; Laboratories; Lead; Leukocytes; Link; Linkage Disequilibrium; Literature; Loss of Heterozygosity; Major Histocompatibility Complex; Malignant Neoplasms; Maternal-Fetal Exchange; Measures; Meiotic Recombination; MicroRNAs; Molecular Genetics; Molecular Profiling; Native Americans; Natural Selections; Nucleic Acid Regulatory Sequences; Nucleotides; Pathway interactions; Pattern; Pennsylvania; Physiological; Population; Post-Transcriptional Regulation; Predisposition; Process; Promoter Regions; Property; Proteins; Receptor Gene; Recording of previous events; Regulation; Reporting; Resistance; Role; Screening procedure; Site; South America; Structure; Surface; Time; Translations; Transplantation; Travel; Universities; Variant; base; expectation; homologous recombination; human disease; human leukocyte antigen gene; hybrid gene; interest; pathogen; population based; pressure; receptor; tumor

Copy number variation (CNV) is defined as a segment of DNA that is 1kb or larger and is present at a variable copy number in comparison with the reference genome and they are present abundantly in the human genome. Because of their homology and tandem arrangement on chromosome 19q13.4, KIR genes are susceptible to non-allelic homologous recombination, which causes deletions or duplications of genes. We are currently screening for KIR3DL1/3DS1 CNV and thus far we have accumulated data from 2798 subjects. In collaboration with Dr. Dan Geraghty (Fred Hutchinson Cancer Research Center), we have characterized KIR haplotypes in individuals with KIR3DL1/S1 CNV. Our preliminary results reveal 10 distinct deletion KIR haplotypes and 10 distinct duplication haplotypes. Interestingly, the deletion haplotypes consistently show deletion of KIR2DL4 and KIR3DL1/3DS1, while in duplication haplotypes, KIR2DL4 and KIR3DL1/3DS1 are both duplicated, suggesting that this region is a hotspot for unequal crossing over and that KIR2DL4 and KIR3DL1/3DS1 travel as a cassette. We have also identified hybrid KIR genes in some deletion haplotypes. In collaboration with Drs. Geraghty and Stephen Anderson, we aim to further characterize duplication/deletion haplotypes, define the break point of the unequal crossover events, identify hybrid genes and determine the expression pattern and function of hybrid genes. Post-transcriptional regulation of HLA may be an important factor in differential surface expression, which might be important for immune surveillance of infectious agents and tumors. We have identified a polymorphic microRNA (miRNA) target site in the 3 untranslated region (3UTR) of HLA-C that appears to differentially alter levels of expression of HLA-C allotypes on cell surfaces. The common SNPs in the miRNA-binding site regulate binding of miRNA and subsequent post-transcriptional processing resulting in high or low HLA-C expression. Preliminary evidence suggests that the HLA-B gene is subjected to post-transcriptional regulation through miRNA, as well. Currently, there are no reports in the literature that point to a role of miRNA in regulation of expression of the classical HLA class I or class II molecules. We will screen the 3UTR of each of these genes for miRNA binding sites, determine whether or not they are polymorphic, and if so, measure any potential effect of the variants on HLA expression. Characterization of this regulation pathway could lead to identification of drug targets that modulate HLA expression, thereby modulating the host response in human disease. Inferences regarding selection may provide relevant information about the functional importance of the regions analyzed. There is strong evidence that genes involved in the immune response are under natural selection. The evolutionarily recent geographic expansion of humans, and the even more recent development of large, relatively dense human settlements, has exposed our species to challenging new environments. Potentially lethal pathogens are likely to have exerted important selective pressures on the human genome, so immunity genes can be expected to show molecular signatures of the adaptation of human populations to these recent environments. Native American populations are of particular interest for studies of natural selection in genes of the immune system, since they are exposed to an extensive geographic territory with significant environmental heterogeneity. Studies of Native American populations can help in building human evolutionary history and with Dr. Diogo Meyer (University of Sao Paulo) we have begun to characterize allelic variability of the 3DL1/S1 and 2DL4 genes in Native American populations as well as the regulatory regions of these genes. Population genetic studies of cis-regulatory variation have now revealed rich and varied histories of adaptation for a number of loci, and have been able to link selective and phenotypic effects for a subset of these. HLA-G is a class Ib HLA gene expressed at the maternal-fetal interface. Since it was first described, this molecule has attracted attention due to its immunotolerogenic properties. Recent studies also suggest the relevance of HLA-G in physiological and pathological contexts, such as transplantation, autoimmunity, cancer and hematological malignancies. Evidence of balancing selection at the HLA-G promoter region has previously been found in the African American, European American and Chinese populations, suggesting that its expression may be under strong selective pressures and tight regulation. In this regard, we are investigating sequence variation and haplotype structure of the HLA-G promoter region in Native American populations. We have sequenced the 1320 bp region immediately upstream of the HLA-G translation start site in 24 Native American individuals distributed throughout North and South America. The preliminary results show high levels of nucleotide variation. Nucleotide diversity was 0.00641, which is about eight times as high as the human genome average. Indeed, a significant departure from the expectation of evolutionary neutrality was observed (TajimasD = 1.97) which is consistent with balancing selection at this locus. The fact that we found retention of a substantial amount of diversity, even in populations that have undergone loss of heterozygosity, as is the case in Native Americans, reinforces the importance of the promoter region of this gene in human evolutionary history. To confirm the hypothesis postulated with our preliminary results, we will extend our analyses to Native American populations of the Amazon region. Finally, we plan to continue to use population based approaches to identify patterns of association between the unlinked KIR and HLA loci that may have evolved due to selection pressures using newly acquired populations from several collaborators including Drs. Ken and Judy Kidd (Yale University) and Dr. Sara Tishkoff (University of Pennsylvania).

拷贝数变异（Copy number variation， CNV）被定义为DNA的一个片段，其长度为1kb或更大，与参考基因组相比，其拷贝数是可变的，并且在人类基因组中大量存在。由于KIR基因在染色体19q13.4上的同源性和串联排列，它们容易发生非等位基因同源重组，从而导致基因缺失或重复。我们目前正在筛选KIR3DL1/3DS1 CNV，到目前为止，我们已经收集了2798名受试者的数据。与Fred Hutchinson癌症研究中心的Dan Geraghty博士合作，我们在KIR3DL1/S1 CNV个体中表征了KIR单倍型。我们的初步结果揭示了10种不同的缺失KIR单倍型和10种不同的重复单倍型。有趣的是，缺失单倍型一致显示KIR2DL4和KIR3DL1/3DS1缺失，而在重复单倍型中，KIR2DL4和KIR3DL1/3DS1都是重复的，这表明该区域是不平等杂交的热点，KIR2DL4和KIR3DL1/3DS1作为一个磁带传播。我们还在一些缺失单倍型中发现了杂交KIR基因。在与博士合作。Geraghty和Stephen Anderson，我们的目标是进一步表征重复/缺失单倍型，确定不相等交叉事件的断点，鉴定杂交基因，确定杂交基因的表达模式和功能。HLA的转录后调控可能是差异表面表达的一个重要因素，这可能对感染因子和肿瘤的免疫监视很重要。我们已经在HLA-C的3非翻译区（3UTR）发现了一个多态性microRNA （miRNA）靶点，该靶点似乎不同地改变了HLA-C异体在细胞表面的表达水平。miRNA结合位点的常见snp调节miRNA的结合和随后的转录后加工，导致HLA-C的高或低表达。初步证据表明，HLA-B基因也受到miRNA转录后调控。目前，尚无文献报道指出miRNA在经典HLA I类或II类分子表达调控中的作用。我们将筛选这些基因的3UTR，以寻找miRNA结合位点，确定它们是否具有多态性，如果是，则测量这些变异对HLA表达的任何潜在影响。对这一调控途径的表征可能会导致鉴定出调节HLA表达的药物靶点，从而调节人类疾病中的宿主反应。关于选择的推论可以提供有关所分析区域功能重要性的相关信息。有强有力的证据表明，参与免疫反应的基因是在自然选择下产生的。最近人类在进化上的地理扩张，以及更近的大型、相对密集的人类定居点的发展，使我们这个物种暴露在具有挑战性的新环境中。潜在的致命病原体很可能对人类基因组施加了重要的选择压力，因此免疫基因有望显示出人类群体适应这些新环境的分子特征。美洲原住民群体对免疫系统基因自然选择的研究特别感兴趣，因为他们暴露在广阔的地理区域，具有显著的环境异质性。对美洲原住民群体的研究可以帮助建立人类进化史，与圣保罗大学的Diogo Meyer博士一起，我们已经开始表征美洲原住民群体中3DL1/S1和2DL4基因的等位基因变异性以及这些基因的调控区域。对顺式调控变异的群体遗传研究现在已经揭示了许多基因座丰富多样的适应历史，并且已经能够将其中一部分的选择效应和表型效应联系起来。HLA- g是在母胎界面表达的Ib类HLA基因。自首次被描述以来，该分子因其免疫耐受性而引起了人们的注意。最近的研究也表明HLA-G在生理和病理环境中的相关性，如移植、自身免疫、癌症和血液系统恶性肿瘤。此前在非裔美国人、欧裔美国人和中国人中发现了HLA-G启动子区域平衡选择的证据，这表明其表达可能受到强烈的选择压力和严格的调控。在这方面，我们正在研究美洲原住民HLA-G启动子区域的序列变异和单倍型结构。我们对分布在北美和南美的24个印第安人的HLA-G翻译起始位点上游1320bp区域进行了测序。初步结果显示核苷酸变异程度很高。核苷酸多样性为0.00641，约为人类基因组平均值的8倍。事实上，观察到与进化中性预期的显著偏离（TajimasD = 1.97），这与该位点的平衡选择是一致的。事实上，我们发现即使在杂合性丧失的人群中，也保留了大量的多样性，就像美洲原住民的情况一样，这加强了该基因的启动子区域在人类进化史上的重要性。为了证实我们的初步结果所假设的假设，我们将把我们的分析扩展到亚马逊地区的美洲原住民。最后，我们计划继续使用基于群体的方法来确定未链接的KIR和HLA位点之间的关联模式，这些位点可能是由于选择压力而进化而来的，使用来自几位合作者的新获得的群体，包括dr。肯·基德夫妇（耶鲁大学）和萨拉·蒂什科夫博士（宾夕法尼亚大学）。