Genetics of Complex Diseases and Health Disparities

慢性肾脏疾病（CKD），影响超过2600万美国人，经常导致肾衰竭。每年有超过10万人患上终末期肾病（ESKD），近50万人接受透析或肾脏移植，每年花费300亿美元。ESKD的三个主要病因是2型糖尿病、高血压和肾小球硬化。非裔美国人患晚期ESKD的可能性是白人的3-4倍。局灶节段性肾小球硬化（FSGS）是成人原发性肾病综合征的主要原因，也是儿童ESKD的主要原因。FSGS是一种综合征，包括特发性形式和与肾细胞数量减少、高血压和HIV-1感染相关的形式。在此之前，我们使用混合映射来定位22号染色体上与FSGS和hiv相关肾病（HIVAN）相关的区域。最强的信号集中在MYH9上，编码肌球蛋白IIA，这是一个可能的候选基因。随后，在编码载脂蛋白1 （APOL1）的APOL1基因中发现了包含2个绝对连锁不平衡错义变异（G1等位基因）和1个框内6碱基对缺失（G2等位基因）的编码变异。APOL1编码变体与FSGS的相关性比MYH9变体更强。ApoL1提供保护，防止感染布鲁氏锥虫；APOL1 G1和G2风险等位基因恢复了对罗得西亚锥虫（一种导致昏睡病的杂合子）的保护。最近，在包含MYH9/APOL1的区域内，APOL1 G1和G2等位基因正选择导致单倍型纯合。APOL1风险等位基因最近在撒哈拉以南非洲出现，但由于非洲侨民，在世界其他地区也发现了apo1风险等位基因。G1和G2等位基因的频率在非洲裔美国人中约为35%，在尼日利亚约鲁巴人中约为60%。这些等位基因几乎解释了非裔美国人患肾病的所有额外风险，从而为全球主要的健康差异提供了遗传基础。我们继续对这一遗传区域进行研究，以确定这些风险变异是否与其他非肾脏或肾脏表型相关。我们也正在确定供体或受体的APOL1变异是否与供体移植物存活有关。成就1。FSGS和萎陷性肾小球病变是肾病综合征的常见病因。超过20个基因的变异与足细胞肾小球病有关，包括对线粒体功能至关重要的基因。PDSS2是合成辅酶Q10的十烯丙基尾部所必需的。小鼠基因Pdss2在塌陷肾小球病的kd/kd小鼠模型中发生突变，这种组织学在人类hiv相关肾病中可见。在一项病例对照研究中，我们通过对377例原发性FSGS或肾小球坍缩症患者和900名对照者进行基因分型，对PDSS2基因的9个单核苷酸多态性（snp）进行了研究，验证了人类PDSS2多态性与FSGS或肾小球坍缩症相关的假设。在欧洲裔美国人（EA）中，一对代理snp与足细胞疾病显著相关，且一种PDSS2单倍型纯合子的患者患足细胞疾病的风险显著增加。相比之下，AA病例和对照组的PDSS2基因型和单倍型分布相似。因此，PDSS2单倍型在EA对照人群中频率为13%，纯合子频率为1.2%，与EA中FSGS和塌陷性肾小球病变的风险显著增加相关。来自FSGS患者的淋巴母细胞样细胞系（LCLs）的辅酶Q10明显低于来自对照组的细胞系；出乎意料的是，这一发现与PDSS2单倍型无关。这些结果表明，FSGS患者存在辅酶Q10缺乏症，并且这种缺乏症在患者源性lcl中表现出来。这项研究发表在《美国肾生理学杂志》上。一系列研究表明，非洲血统人群中最常见的慢性肾脏疾病发病率较高是由于非洲人类锥虫病（HAT）阳性选择下的APOL1变异。这些变异位于APOL1的血清耐药相关（SRA）相互作用结构域编码区或附近。为了探索APOL1潜在功能变异的分布，我们研究了187个个体的核苷酸变异，这些个体来自10个地理上和遗传上不同的非洲族群，暴露于导致HAT的两种布鲁氏锥虫亚种。我们观察到在编码裂解寄生虫所需的功能域的区域中异常高水平的非同义多态性。正如我们之前在人类基因组多样性项目的非洲样本中所显示的那样，G2等位基因频率在所有人群中相似（3%-8%），G1等位基因仅在约鲁巴人中常见（39%）。我们假设两种显示最近选择信号的新变异可能与HAT抗性有关，因为它们发生在锥虫裂解所需的结构域内。我们现在正在探索这些新变异与HAT耐药和CKD的关系。3)为了研究APOL1风险变异在非裔美国人高血压肾病中的作用，我们研究了APOL1等位基因与非裔美国人肾病和高血压研究（AASK）队列参与者肾脏终点的关系。在这个队列中，随机分为两个治疗组和两个血压目标，无论治疗组如何，都有持续进展到终末期肾脏疾病。为了更好地理解这一点，在一项包括675例AASK参与者病例和618例非肾病对照个体的研究中，我们评估了载脂蛋白L1 （APOL1）编码变异与高血压肾病和临床结果的关系。APOL1 G1和G2以及44个祖先信息标记进行基因分型，并通过logistic回归多变量模型进行分析。在隐性模型中，与对照组相比，APOL1风险变异在所有病例中与肾脏疾病显著相关，优势比为2.57。在病情较晚期的AASK病例中，这种关联得到加强，优势比为4.61-6.29。APOL1风险变异始终与肾脏疾病的进展相关，跨越药物类别和血压目标。4) A型血友病患者因子VIII抑制抗体的产生是一个复杂的过程，涉及多种遗传和环境因素，包括导致该缺陷的F8突变类型。为了研究抑制剂发展的遗传基础，我们建立了血友病抑制剂遗传学研究（HIGS）联合队列，包括来自3个独立队列的833名受试者：有和没有抑制剂病史的兄弟对和单胞胎，以及104对抑制剂状态不一致的兄弟对。利用Illumina iSelect平台，我们从1081个免疫应答和免疫修饰基因中设计了13 331个单核苷酸多态性。在对潜在混杂因素进行调整后，发现53个单核苷酸多态性是抑制剂状态的重要预测因子。在53个标志物中，13个具有meta P .001。在不一致的对中，53个中有8个是显著的预测因子。这些结果表明，基因对抑制剂发育的贡献是复杂的，可能涉及许多基因或途径。这项研究发表在《血液》杂志上。

Chronic kidney disease (CKD), affecting over 26 million Americans, frequently leads to kidney failure. More than 100,000 individuals develop end stage kidney disease (ESKD) annually and nearly 500,000 receive dialysis or kidney transplants at an annual cost of $30 billion dollars. The three leading causes of ESKD are type 2 diabetes, hypertension, and glomerulosclerosis. African Americans are 3-4 times more likely to develop end ESKD compared to their white counterparts. Focal segmental glomerulosclerosis (FSGS) is the leading cause of primary nephritic syndrome in adults and the leading cause of ESKD in children. FSGS represents a syndrome that includes idiopathic forms and forms associated with reduced nephron numbers, hypertension, and HIV-1 infection. Previously, we used admixture mapping to localize a region on chromosome 22 associated with FSGS and HIV-associated nephropathy (HIVAN). The strongest signal was centered on MYH9, encoding myosin IIA, a plausible candidate gene. Subsequently, coding variants comprising 2 missense variants (G1 allele) in absolute linkage disequlibrium and an inframe 6 basepair deletion (G2 allele) were identified in the APOL1 gene encoding apolipoprotein 1 (APOL1). The APOL1 coding variants were more strongly associated with FSGS than were the MYH9 variants. ApoL1 provides protection against infection with Trypanosoma brucei brucei; the APOL1 G1 and G2 risk alleles restore protection against T. b. rhodesiense, a cause of sleeping sickness in heterozygotes. APOL1 G1 and G2 alleles have been under recent positive selection resulting in haplotype homozygosity across the region comprising MYH9/APOL1. The APOL1 risk alleles emerged recently in sub-Saharan Africa, but are found in other regions of the world as a result of the African Diaspora. The frequencies of G1 and G2 alleles are approximately 35% in African Americans and 60% in Yoruba from Nigeria. These alleles explain nearly all the excess risk of kidney disease in African Americans, thus providing a genetic basis for a major global health disparity. We have continued our studies of this genetic region to determine if these risk variants are associated with other non-renal or renal phenotypes. We are also determining if APOL1 variants in the donor or recipient are associated with donor graft survival. Accomplishments 1. FSGS and collapsing glomerulopathy are common causes of nephrotic syndrome. Variants in over 20 genes have been associated with podocyte glomerulopathies, including genes critical for mitochondrial function. PDSS2 is required for synthesis of the decaprenyl tail of coenzyme Q10 in humans. The mouse gene Pdss2 is mutated in the kd/kd mouse model of collapsing glomerulopathy, a histology seen in HIV-associated nephropathy in humans. We examined the hypothesis that human PDSS2 polymorphisms are associated with FSGS or collapsing glomerulopathy by genotyping 377 cases with primary FSGS or collapsing glomerulopathy and 900 controls, for nine single nucleotide polymorphisms (SNPs) in the PDSS2 gene in a case-control study. Among European Americans (EA), a pair of proxy SNPs was significantly associated with podocyte disease, and patients homozygous for one PDSS2 haplotype had a strongly increased risk for podocyte disease. By contrast, the distribution of PDSS2 genotypes and haplotypes were similar in AA cases and controls. Thus, a PDSS2 haplotype, which has a frequency of 13% in the EA control population and a homozygote frequency of 1.2%, is associated with a significantly increased risk for FSGS and collapsing glomerulopathy in EA. Lymphoblastoid cell lines (LCLs) from FSGS patients had significantly less coenzyme Q10 than cell lines from controls; unexpectedly this finding was independent of PDSS2 haplotype. These results suggest that FSGS patients have coenzyme Q10 deficiency, and that this deficiency is manifested in patient-derived LCLs. This study was published in the American Journal of Renal Physiological. 2. A series of studies have shown that the higher rates of the most common causes of chronic kidney disease in persons of African ancestry is due to APOL1 variants that under positive selection by Human African Trypanosomiasis (HAT). These variants are found in or near the serum-resistance-associated (SRA)-interacting-domain-encoding region of APOL1. To explore the distribution of potential functional variation at APOL1, we studied nucleotide variation in 187 individuals across ten geographically and genetically diverse African ethnic groups with exposure to two Trypanosoma brucei subspecies that cause HAT. We observed unusually high levels of nonsynonymous polymorphism in the regions encoding the functional domains that are required for lysing parasites. As we previously showed in African samples from the human genome diversity project allele frequencies of G2 were similar across all populations (3%-8%), the G1 allele was only common in the Yoruba (39%). We hypothesized that two new variants that showed signals of recent selection might be associated with HAT resistance as they occurred within domains required for lysis of trypanosomes. We are now exploring the association of these new variants with HAT resistance and CKD. This study was published in the American Journal of Human Genetics. 3) To examine the role of APOL1 risk variants in African Americans with kidney disease attributed to hypertension, we studied the association of APOL1 alleles on renal end points in in participants of the African American Study of Kidney Disease and Hypertension (AASK) cohort. In this cohort, randomized to two treatment arms and to two blood pressure targets there was relentless progression to end stage renal disease regardless of treatment arm. To better understand this, coding variants in the apolipoprotein L1 (APOL1) was evaluated for an association with hypertension-attributed nephropathy and clinical outcomes in a study comprising 675 AASK participant cases and 618 non-nephropathy control individuals. APOL1 G1 and G2, along with 44 ancestry informative markers, were genotyped and analyzed by logistic regression multivariable models. In recessive models, APOL1 risk variants were significantly associated with kidney disease in all cases compared to controls with an odds ratio of 2.57. In AASK cases with more advanced disease, the association was strengthened with odds ratios of 4.61-6.29. APOL1 risk variants were consistently associated with renal disease progression across medication classes and blood pressure targets. This study was published in Kidney International. 4) The development of inhibitory antibodies to factor VIII in people with hemophilia A is a complex process involving multiple genetic and environmental factors, including the type of F8 mutation that causes the deficiency. To investigate the genetic basis for inhibitor development we developed the The Hemophilia Inhibitor Genetics Study (HIGS) Combined Cohort comprising 833 subjects from 3 independent cohorts: brother pairs and singletons with and without a history of inhibitors, as well as 104 brother pairs discordant for inhibitor status. Using the Illumina iSelect platform, we designed a panel of 13 331 single-nucleotide polymorphisms from 1081 immune response and immune modifier genes. After adjustment for potential confounders, 53 single-nucleotide polymorphisms were found to be significant predictors of inhibitor status. Of the 53 markers, 13 had meta P .001. Eight of the 53 were significant predictors among the discordant pairs. These results indicate that the genetic contribution to inhibitor development is complex and likely involves many genes or pathways. This study was published in Blood.