Effects of genetic polymorphism in MHC, KIR, and related loci on human disease

HLA I类（HLA-I）同种异体对tapasin （TAPBP）的依赖性差异很大，tapasin是肽装载复合物的一个组成部分，用于在细胞表面呈现肽。我们已经确定了全球人群（N = 250）中常见hla - 1同种异体的tapasin依赖性（TD）值，显示出HLA-A、HLA-B和HLA-C的连续值。这种变异在功能上是相关的，因为tapasin不依赖的同种异体显示出比tapasin依赖的同种异体更广泛的肽序列，并且tapasin不依赖赋予HIV-1疾病保护作用。鉴于tapasin在形成hla - 1肽库中的作用及其对疾病结局的影响，我们假设其表达水平的自然变化也可能影响疾病的发病机制和易感性。我们研究了在乌干达收集的大型纵向疟疾队列，以估计变异对疟疾疾病结局的免疫遗传学影响。其中一项研究发现两个snp rs111686073 （G或C）和rss59097151 （A或G）分别通过改变AP-2alpha转录因子和microRNA-4486结合位点来调节TAPBP mRNA的表达水平。具有高TAPBP mRNA水平的变异rs111686073G和rss59097151a与较低的恶性疟原虫流行率和较低的临床疟疾发病率相关，特别是在携带tapasin依赖性HLA I类同种异型的个体中。无论基因型如何，tapasin非依赖性同种异体在这两个snp上都具有相对的保护作用。这些数据表明，较高的tapasin表达水平可以提高tapasin依赖性同种异体的肽负荷，其程度与tapasin非依赖性同种异体相似，从而更好地控制恶性疟原虫。HLA I类等位基因与HIV疾病之间的关联早已为人所知。在黑人中已建立的关联包括B5702、B5703、B5801和B8101的保护性关联，以及B1801、B1802、B4501和B5802的易感关联。杨森疫苗2期临床试验研究了对马赛克抗原疫苗的免疫反应的许多方面；在平行猕猴疫苗试验中，对HIV抗原的ELISA和ELISpot反应可预测对HIV攻击的保护。报告疫苗反应的试验数据包括306名受试者，其中172名是非裔美国人或非洲黑人，因此我们将分析重点放在这一群体上。我们研究了HLA与HIV控制的关联是否也与疫苗接种后的不同gag/env反应相关。应答指标包括ELISA应答强度，测定抗体对5种不同Env蛋白的应答；ELISpot计数，测定t细胞对11种Env、Gag和Pol蛋白池的应答。此外，我们考虑了CD4和CD8 T细胞对10个Env、Gag和Pol蛋白池引发的细胞内染色（ICS）抗原反应水平，因为这些反应与ELISpot不同地评估了T细胞的功能，并且ICS反应在以前的疫苗试验中与保护有关。采用主成分分析（PCA）来降低ELISA和ELISpot分析中检测的多种HIV抗原的自由度；第一个主成分（PC）捕获整体反应的强度，而第二个主成分捕获对不同抗原的差异反应。在ELISA或ELISpot反应中，第一个PC与HLA I类或II类没有显著的关联，但在对测试的比较数进行校正后（FDR小于0.1），第二个PC对ELISpot反应的某些I类等位基因接近统计学意义。ELISpot数据的第二个PC主要是由T细胞对Gag和Env抗原的反应差异驱动的。在自然史研究中，已知对Gag的反应可以控制HIV，而对Env的反应则保护性较弱，因为编码Env的基因突变率极高。因此，我们假设在第二个PC中发现的HLA关联反映了这些等位基因对Gag和Env的差异反应。因此，我们为ELISpot和ICS定义了一个“Gag - Env”变量，从平均Gag反应中减去平均Env反应，并检测HLA I类与该变量的相关性。观察到几个显著的关联。HLA-B5703与CD8 ICS Gag - Env应答的相关性最强（5E-07的FDR）。值得注意的是，HLA-B在控制艾滋病毒方面表现出最强的效果。我们还观察到HLA-B等位基因对HIV病毒载量控制的影响（以平均HIV病毒载量随时间测量）与Gag - Env变量之间存在显著相关性。因此，在未经治疗的HIV-1感染者中赋予保护作用的HLA-B等位基因也可能赋予对含有HIV Gag插入物作为抗原的HIV疫苗的保护性CD8 T细胞反应。这些数据表明，疫苗效力可能适用于一部分接种疫苗的受试者。HLA等位基因多样性被认为是通过显性维持的，这是一种由等位基因杂合性决定的选择优势。杂合子优势可能是HLA呈现的多肽种类更广泛的结果，导致比纯合子个体更好的免疫监视，纯合子个体的多肽范围仅由一个等位基因决定。我们以前曾报道过这种对艾滋病毒进展的有害影响。这种分析的局限性来自于基因纯合子与杂合子个体之间的模糊区分。例如，由两个非常密切相关的等位基因组成的基因型可能与真正的基因纯合子结合的肽库一样有限。计算构成给定基因型的等位基因对之间的遗传距离是估计等位基因对之间功能相似性程度的一种手段，假设随着等位基因之间的遗传距离增加，肽库的独特性也应该增加。然而，遗传距离作为一个连续变量分析，在我们的血清转换者队列中没有显示出对艾滋病进展的影响。从各种常见的HLA I类同种异体中洗脱的肽的详细研究已经进行并公开提供。这些数据为更直接地量化等位基因杂合性对HLA肽库宽度的影响提供了手段。我们关注的是给定同种异体呈现的多肽的聚合特性，而不是多肽之间的微小差异。我们只保留那些位置熵低于0.1的氨基酸（即在给定位置上对一个氨基酸的高选择性），以减少在高熵位置上产生的噪声。由此产生的简化符号，称为亚基，允许紧凑的表示不同家族的肽，一个给定的同种异型可以呈现。该方法将95种不同HLA I类同种异体呈现的111,898个非聚合肽浓缩为382个不同的亚基。我们比较了给定基因型在每个位点上编码的同种异型对的亚基，并计算了这对同种异型之间不共享的亚基的比例，以量化同种异型之间的功能差异。使用新的亚基序度量，我们比较了每个基因座中功能差异最大的基因型个体和功能差异最小的基因型个体。每个位点的这种分类改善了与艾滋病进展的关联，远远超过了HLA-A （HR 2.63, p 3.5E-05）和HLA-B （HR 2.68, p 2.5E-05）的遗传合合性。我们计划将该指标或相关指标应用于其他人类疾病，包括其他传染病、癌症以及癌症免疫治疗和自身免疫性疾病的结果。

HLA class I (HLA-I) allotypes vary widely in their dependence on tapasin (TAPBP), an integral component of the peptide loading complex, to present peptides on the cell surface. We have determined tapasin dependence (TD) values for common HLA-I allotypes across worldwide populations (N = 250), which show a continuum of values for HLA-A, HLA-B and HLA-C. This variation is functionally relevant, as tapasin-independent allotypes were shown to present a broader array of peptides than tapasin-dependent allotypes, and tapasin independence conferred protection in HIV-1 disease. Given the role of tapasin in shaping the HLA-I peptide repertoire and its impact on disease outcome, we hypothesized that natural variation in its expression level could also affect disease pathogenesis and susceptibility. We have studied a large longitudinal malaria cohort collected in Uganda to estimate immunogenetic effects of variation on malarial disease outcome. One of these studies identified two SNPs, rs111686073 (G or C) and rs59097151 (A or G), that regulate TAPBP mRNA expression levels by altering AP-2alpha transcription factor and microRNA-4486 binding sites, respectively. The variants conferring high TAPBP mRNA level, rs111686073G and rs59097151A, associated with lower Plasmodium falciparum parasite prevalence and lower incidence of clinical malaria specifically among individuals carrying tapasin-dependent HLA class I allotypes. Tapasin-independent allotypes associated with relative protection regardless of the genotype at these two SNPs. These data suggest that higher tapasin expression levels can enhance peptide loading of tapasin-dependent allotypes to a similar extent displayed by tapasin-independent allotypes, resulting in better control of P. falciparum. Associations between HLA Class I alleles and HIV disease have long been known. Established associations in Blacks include protective associations for B5702, B5703, B5801, and B8101, and susceptible associations for B1801, B1802, B4501, and B5802. The Janssen vaccine phase 2 clinical trial studied many aspects of the immune response to a mosaic antigen vaccine; ELISA and ELISpot response to HIV antigens were predictive of protection against HIV challenge in the parallel macaque vaccine trial. Trial data with vaccine response reported includes 306 subjects, of which 172 are African Americans or Black Africans, thus we focused our analyses on this group. We investigated whether the association of HLA with HIV control also associated with differential gag/env response after vaccination. Response measures included the strength of ELISA responses, which measured antibody responses to five variant Env proteins, and ELISpot count, which measured T-cell responses to 11 Env, Gag, and Pol protein pools. In addition, we considered intra-cellular staining (ICS) antigen response levels elicited by both CD4 and CD8 T cells for 10 Env, Gag, and Pol protein pools, as these assess T cell functionality distinctly from ELISpot, and ICS responses were previously linked to protection in previous vaccine trials. A principal components analysis (PCA) was performed to reduce the degrees of freedom for the multiple HIV antigens tested in the ELISA and ELISpot analysis; the first principal component (PC) captured the strength of overall response, while the second PC captured differential response to different antigens. There were no significant associations for HLA class I or II in the first PC for ELISA or ELISpot responses, but the second PC for ELISpot response approached statistical significance for some class I alleles after correction for the number of comparisons tested (FDR less than 0.1). The second PC of the ELISpot data was primarily driven by the difference between the T cell responses to Gag vs. Env antigens. Responses to Gag are known to confer HIV control in natural history studies, whereas those to Env are less protective because of the extreme mutation rate of the gene encoding Env. Thus, we hypothesized that the HLA associations identified in the second PC reflected a differential response to Gag vs. Env by those alleles that showed significance. We therefore defined a "Gag - Env" variable for ELISpot and ICS by subtracting the mean Env response from the mean Gag response and tested for HLA class I associations with this variable. Several significant associations were observed. The strongest association was that of HLA-B5703 with the CD8 ICS Gag - Env response (FDR of 5E-07). Of note, HLA-B shows the strongest effects for control of HIV. We also observed a significant correlation between the effects of HLA-B alleles on HIV viral load control (measured as mean HIV viral load over time) and the Gag - Env variable. Thus, HLA-B alleles that confer protection in untreated HIV-1 infected subjects may also confer protective CD8 T cell responses to HIV vaccines that contain HIV Gag inserts as antigens. These data suggest that vaccine efficacy may apply to a proportion of subjects receiving the vaccine. HLA allelic diversity is thought to be maintained through overdominance, a selective advantage determined by allelic heterozygosity. Heterozygous advantage may be the result of a broader variety of peptides presented by HLA, resulting in a better immune surveillance than for homozygous individuals whose universe of peptides is determined by one allele only. We have previously reported this detrimental effect on HIV progression. A limitation of this analysis emanates from the blunt distinction between genetically homozygous vs. heterozygous individuals. A genotype composed of two alleles that are very closely related may for example, bind as limited a peptide repertoire as do true genetic homozygotes. Calculation of genetic distances between the pair of alleles composing a given genotype is one means for estimating the degree of functional similarity between pairs of alleles, assuming that as the genetic distance between alleles increases, so should the distinctiveness of the peptide repertoire. However, genetic distance, analyzed as a continuous variable, showed no effect on AIDS progression in our seroconverter cohort. Detailed studies of peptides eluted from various common HLA class I allotypes have been performed and made publicly available. These data provide the means to more directly quantitate the impact of allelic heterozygosity on the breadth of the HLA peptide repertoire. We focused on aggregate properties of the peptides presented by a given allotype rather than minor differences across peptides. We retained only those amino acids with a positional entropy lower than 0.1 (i.e. high selectivity for one amino acid at a given position) in order to reduce noise contributed at positions with high entropy. The resulting simplified logograms, termed submotifs, allow compact representation of the different families of peptides that a given allotype can present. This approach condensed a universe of 111,898 nonamer peptides presented by 95 different HLA class I allotypes into 382 distinct submotifs. We compared submotifs of the allotype pairs encoded by a given genotype at each locus, and calculated the proportion of submotifs that are not shared between that pair of allotypes in order to quantify the functional divergence between allotypes. Using the novel submotif metric, we compared, for each locus, individuals with the most functionally divergent genotypes to those with the least functionally divergent genotypes. This categorization at each locus improved the association with AIDS progression far beyond that observed for genetic zygosity at both HLA-A (HR 2.63, p 3.5E-05) and HLA-B (HR 2.68, p 2.5E-05). We plan to apply the metric, or related metrics to other human diseases including other infectious diseases, cancer and outcome to cancer immunotherapy and autoimmune diseases.