Genetics of Complex Diseases and Health Disparities

APOL1的编码变异体可预防非洲人类锥虫病，但却造成了肾脏、子痫前期和心血管疾病方面的重大健康差异，这些疾病对非洲血统人群的影响不成比例。我们已经建立了一个广泛的校内和校外国际合作网络，以调查APOL1肾脏风险变异与先兆子痫（产妇和胎儿死亡的主要原因）、心血管疾病和慢性肾脏疾病的关系。我们还与NIDDK的研究人员合作，了解APOL1变异蛋白在子痫前期和肾脏疾病中的病理生理学。一个主要的目标是了解影响APOL1外显率的环境和遗传因素——只有20%携带APOL1高风险基因型的个体会发展为慢性肾脏疾病，这可能是因为APOL1需要第二次撞击才会出现肾损伤。然而，我们也发现APOL1外显率在遗传祖先和地理区域之间差异很大。我们正在测试一种假设，即欧洲血统染色体上的遗传变异加剧了APOL1外显率，导致非洲与欧洲混合人群（即非洲与欧洲混合人群）肾脏和肾脏疾病的风险增加。非裔美国人或拉丁裔黑人)，而非洲血统染色体上的遗传因素可能会减弱APOL1外显率。研究成果：1)APOL1风险变异作为心血管疾病（CVD）危险因素的独立作用在研究中存在矛盾。我们提供了我们实验室生成的10,000多名非裔美国人的数据，用于APOL1与心血管疾病事件（包括冠心病、心肌梗死、中风和心力衰竭）关联的荟萃分析。在9年的随访中，16,216名在研究入组时没有心血管疾病的参与者中发生了2076例心血管疾病事件。携带两种APOL1风险变体的个体与没有或只有一种APOL1风险变体的个体相比，患CVD的风险相似。心衰、心肌梗死、冠心病、中风和全因死亡的风险也与APOL1基因型相似。这项研究是迄今为止对APOL1肾脏风险变异与CVD或死亡的独立关联进行的最大规模的研究，表明APOL1肾脏风险变异与CVD风险增加无关，与肾脏疾病无关（Grams等，JASN, 2019）。3)先兆子痫对黑人女性的影响尤为严重，是医学上指示的早产的主要原因，也是未来高血压和慢性肾脏疾病（CKD）的风险。在生命历程框架下，考虑到子痫前期和CKD之间的紧密联系，我们询问母体和胎儿的APOL1肾脏风险等位基因是否会共同影响子痫前期的风险。我们与约翰霍普金斯大学的研究人员在波士顿出生队列中对426对黑人母婴（其中213对患有子痫前期）进行了纵向队列研究，进一步探讨了APOL1-子痫前期关联的潜在修饰因素。当按母国分层时，在隐性模型下，胎儿APOL1风险等位基因与非海地黑人先兆子痫风险增加相关（OR=3.2, 95% CI=1.2-9.1， P=0.025），但在海地黑人中没有。该研究进一步支持了胎儿APOL1肾风险等位基因与子痫前期风险增加相关的观察，并强调需要更好地了解母胎相互作用及其遗传和环境因素是子痫前期和随后CKD的种族差异的因素。4)血清尿酸升高是癌症、进行性肾脏疾病和全因死亡率的生物标志物，而血清尿酸水平极低是肾结石（肾结石）和运动引起的急性肾损伤的危险因素。我们使用全外显子组测序（WES）来评估遗传诊断的可行性。我们从韩国城市队列中选取了179,381名无基础疾病的极端低尿酸血症患者。进行WES是为了发现低尿酸血症的罕见致病变异。我们在31名受试者中的24人（77.4%）中发现了SLC22A12的两个已知隐性变异（p.Trp258*, pArg90His）。在一个独立的队列中，我们确定了50名低尿酸血症患者，并对p.Trp258*和p.g r90his变体进行了基因分型；50例低尿酸血症病例中有47例（94%）仅由两种突变解释。这是第一个在临床环境中显示低尿酸血症基因诊断筛查价值的研究。仅筛查两种种族特异性变异就确定了87.7%（71/81）的韩国单基因低尿酸血症患者（Cha等）。科学代表，2019)。早期基因鉴定构成性低尿酸血症可以通过避免脱水和过度运动来预防急性肾损伤。血清尿酸水平升高会引起痛风，并与多种疾病有关，包括某些癌症。我们对近7000名韩国人的血清尿酸水平进行了GWAS，并计算了多基因风险评分。我们在3194个人中验证了低频变异和多基因风险评分与SUA水平的关联，从而确定了与SUA相关的两种低频变异和六种常见的独立变异（Cho等）。科学代表，2020)。6) APOL1高危基因型也被证明可引起与covid -19相关的肾病，其组织学特征与HIVAN相似，HIVAN是一种快速进展的局灶节段性肾小球硬化症，几乎只在未经治疗的非洲血统HIV患者中发现，近80%的HIVAN患者携带APOL1高危基因型。在一系列病例研究中，在两个APOL1风险等位基因的携带者中发现了covid -19相关肾病。我们现在正在启动病例对照研究，以确定患有轻度至重度COVID-19的非洲裔美国人和非洲人的长期肾脏结局；我们的基本假设是APOL1高危基因型与肾损伤（蛋白尿）和肾功能下降有关。7)局灶节段性肾小球硬化（FSGS）的诊断需要肾活检，这在儿童和一些成人中可能是有问题的。此外，FSGS的机制和对治疗的反应是多种多样的。我们使用单细胞rna测序（scRNA-seq）来探索FSGS受试者尿液中与疾病相关的细胞特征。通过对来自12名FSGS受试者的23份尿液样本进行单细胞转录组学分析，我们鉴定出免疫细胞（主要是单核细胞）和肾上皮细胞（包括足细胞）。进一步分析发现两种亚型与M1和M2单核细胞一致。我们在先前发表的黑色素瘤、头颈癌和肾移植排斥反应的单核/巨噬细胞的单细胞转录组数据中发现了类似的M1和M2单核细胞的转录特征。尿足细胞高表达上皮-间质转化（EMT）标记基因。我们从免疫细胞中选择了17个高表达基因，从尿足细胞中选择了10个高表达的EMT基因。利用来自肾病综合征研究网络（NEPTUNE）的肾活检组织的转录组学数据，我们发现这些尿细胞免疫和EMT特征基因在FSGS活检组织中的表达水平高于最小变化活检组织。FSGS受试者尿液样本中单核细胞亚群和足细胞表达特征的鉴定表明，尿细胞谱分析可以作为肾病综合征的诊断工具。此外，这种方法可能有助于开发新的FSGS生物标志物，并确定针对免疫细胞和足细胞中特定分子途径的个性化治疗。

Coding variants in APOL1 protect against human African trypanosomiasis, but are responsible for major health disparities for kidney, preeclampsia and cardiovascular diseases that disproportionally affect people with African ancestry. We have developed an extensive network of intramural and extramural international collaborations to investigate the association of APOL1 renal risk variants with preeclampsia, a major cause of maternal and fetal death), cardiovascular disease, and chronic kidney disease. We are also collaborating with researchers at the NIDDK to understand the pathophysiology of APOL1 variant protein in preeclampsia and kidney disease. A major goal is to understand the environmental and genetic factors that affect penetrance of APOL1-only 20% of individuals carrying APOL1 high risk genotypes develop chronic kidney disease, likely because APOL1 requires a second hit for renal injury to manifest. However, we also find that APOL1 penetrance varies widely by genetic ancestry and across geographic regions. We are testing the hypothesis that genetic variants on European ancestry chromosomes exacerbate APOL1 penetrance, causing increased risk of renal and kidney disease in African x European admixed populations (ie. African Americans or black Latinos) while genetic factors on African ancestry chromosomes may attenuate APOL1 penetrance. Accomplishments: 1) The independent role of APOL1 risk variants as a risk factor for cardiovascular disease (CVD) is conflicted among studies. We contributed data generated by our laboratory in over 10,000 African Americans for a meta-analysis of APOL1 associations with incident CVD events, including coronary heart disease, myocardial infarction, stroke, and heart failure. Over 9 years of follow-up, 2076 incident cardiovascular disease events occurred in the 16,216 participants who did not have CVD at study enrollment. Individuals carrying two APOL1 risk variants had similar risk of CVD compared to individuals with zero or one variant. The risk of heart failure, myocardial infarction, coronary heart disease, stroke, and all-cause death considered individually was also similar by APOL1 genotype. This study, the largest conducted to date on the independent association of APOL1 kidney risk variants on CVD or death, suggests that APOL1 kidney risk variants are not associated with increased risk of CVD, independent of kidney disease (Grams et al, JASN, 2019). 3) Preeclampsia, disproportionately affecting Black women, is a leading cause of medically-indicated preterm delivery and risk for future hypertension and chronic kidney disease (CKD). Under a life-course framework, given the strong link between preeclampsia and CKD, we asked whether maternal and fetal APOL1 renal risk alleles can jointly influence preeclampsia risk. We further explored potential modifiers on APOL1- preeclampsia association in a longitudinal cohort study of 426 Black mother-infant pairs (213 with preeclampsia) from the Boston Birth Cohort with investigators at the Johns Hopkins University. When stratified by maternal country of origin, fetal APOL1 risk alleles were associated with an increased risk of preeclampsia among non-Haitian Blacks under recessive (OR=3.2, 95% CI=1.2-9.1, P=0.025) models, but not in Haitian Blacks. This study lends further support to the observation that fetal APOL1 renal risk alleles are associated with an increased risk of preeclampsia and underscores the need to better understand maternal-fetal interaction and their genetic and environmental factors as contributors to ethnic disparities in preeclampsia and subsequent CKD. 4) Elevated serum uric acid is a biomarker for cancer, progressive kidney disease, and all-cause mortality, while carriage of extremely low levels of serum uric acid is a risk factor for nephrolithiasis (kidney stones) and exercise-induced acute kidney injury. We used whole-exome sequencing (WES) to assess the feasibility for genetic diagnosis. We selected cases with extreme hypouricemia from a Korean urban cohort of 179,381 subjects without underlying conditions. WES were performed for the discovery of rare causal variants for hypouricemia. We identified two known recessive variants within SLC22A12 (p.Trp258*, pArg90His) in 24 out of 31 subjects (77.4%). In an independent cohort, we identified 50 individuals with hypouricemia and genotyped the p.Trp258* and p.Arg90His variants; 47 of the 50 (94%) hypouricemia cases were explained by only two mutations. This is the first study to show the value of genetic diagnostic screening for hypouricemia in the clinical setting. Screening of just two ethnic-specific variants identified 87.7% (71/81) of Korean patients with monogenic hypouricemia (Cha et al. Sci Rep, 2019). Early genetic identification of constitutive hypouricemia may prevent acute kidney injury by avoidance of dehydration and excessive exercise. Increased serum uric acid levels cause gout and are associated with multiple diseases, including certain cancers. We performed a GWAS for serum uric acid levels in nearly 7000 Koreans and calculated polygenic risk scores. We validated the association of low-frequency variants and the polygenic risk score with SUA levels in 3,194 individuals thereby identifying two low-frequency and six common independent variants associated with SUA (Cho et al. Sci Rep, 2020). 6) APOL1 high-risk genotypes have also been shown to cause COVID-19-associated nephropathy, with similar histological features to HIVAN, a rapidly progressive form of focal segmental glomerulosclerosis identified nearly exclusively in individuals with untreated HIV of African ancestry-nearly 80% of individuals with HIVAN carry APOL1 high-risk genotypes. In a series of case studies, COVID-19-associated nephropathy has been identified in carriers of two APOL1 risk alleles. We are now initiating case-control studies to identify long-term renal outcomes in African Americans and Africans who experienced mild to severe COVID-19; our underlying hypothesis is that APOL1 high-risk genotypes will be associated with renal injury (proteinuria) and decline in kidney function. 7) The diagnosis of focal segmental glomerulosclerosis (FSGS) requires a renal biopsy which can be problematic in children and in some adults. Further, the mechanisms of FSGS and response to therapy are diverse. We used single cell RNA-sequencing (scRNA-seq) to explore the disease-related cellular signatures in the urine of FSGS subjects. Using single cell transcriptomic analysis of 23 urine samples from 12 FSGS subjects, we identified immune cells, predominantly monocytes, and renal epithelial cells, including podocytes. Further analysis revealed two subtypes consistent with M1 and M2 monocytes. We found similar transcriptional signatures of M1 and M2 monocytes in the single cell transcriptomic data of monocytes/macrophages from the previously published studies of melanoma, head and neck cancer and kidney allograft rejection. Urine podocytes showed high expression of marker genes for epithelial-to-mesenchymal transition (EMT). We selected the 17 most highly expressed genes from immune cells and 10 most highly expressed EMT genes from urine podocytes. Using transcriptomic data from kidney biopsies from the Nephrotic Syndrome Study Network (NEPTUNE), we found that these urine cell immune and EMT signature genes showed higher expression levels in FSGS biopsies compared to minimal change biopsies. The identification of monocyte subsets and podocyte expression signatures in FSGS subjects' urine samples suggests that urine cell profiling can serve as a diagnostic tool in the context of nephrotic syndrome. Further, this approach may aid in the development of novel biomarkers for FSGS and for identifying personalized therapies targeting particular molecular pathways in immune cells and podocytes.