Genetics of adipose cell-type expression and cardiometabolic traits

摘要 全球肥胖症的流行正在推动心脏代谢性疾病患病率的迅速增加 疾病(CMD)，包括高甘油三酯血症、2型糖尿病(T2D)、高血压和非酒精性脂肪 肝病(NAFLD)。人群和性别在CMD易感性上存在差异；然而， 这些差异背后的生物学机制还没有被很好地理解。以前的大规模全基因组 关联研究(GWAS)已经在多个群体中可靠地确定了与CMD相关的变体；然而， 对GWA变异体生物学机制的功能理解仍然具有挑战性。一大专业 障碍是对相关细胞类型的有限了解，在这些细胞类型中，GWA型变体影响基因表达。散装 存在CMD相关组织的组织基因表达数据，例如皮下脂肪，但这些数据 表现出相当大的异质性，包括每种细胞类型内的细胞类型和细胞状态。皮下 脂肪是CMDs重要的人体内分泌组织，采集高质量的脂肪组织是可能的 样本来自健康的个体。然而，许多脂肪基因对CMD和CMD性状的贡献 人们对此仍然知之甚少。目前缺乏细胞类型的表达参考数据集限制了精细区域 GWA型变异效应的转录评估。此外，局部表达数量性状基因座(cis- EQTL)的分析因细胞类型的特定表达差异而混乱，这阻碍了复制努力 跨独立的批量RNA测序(RNA-seq)队列。要解决这些知识差距并确定 基因对脂肪细胞类型基因表达的影响，我们将进行单核RNA测序(SnRNA-Sequence)。 在来自300个特征良好的个体的冷冻皮下脂肪组织活检样本中，产生了 对细胞类型比例的精细估计，确定研究范围内和个性化的细胞类型特定差异 与心脏代谢性状水平相对应，并通过实验测试GWA型变异体对细胞的等位基因效应 类型特定的表达式。我们假设，通过阐明300个人的脂肪组织细胞类型的表达 对于现有的冷冻脂肪活检，我们可以利用现有的GWAS和脂肪批量RNA-SEQ数据(n=3,230； 45%的女性)来自不同的人群，以确定数百个CMD基因的相关细胞类型。在我们的 初步研究，我们已经成功地在冰冻的人类皮下脂肪组织中进行了SnRNA-seq 活组织检查并进行多组学研究，将GWAS结果与大宗脂肪RNA-SEQ数据相结合，确定 数百个共同定位的CMD性状基因座。我们的方法将利用现有的丰富信息 在GWAs和Bulk Adpose RNA-Seq队列中可用来阐明基本上未知的生物细胞类型 脂肪组织中驱动CMD的机制。拟议研究的成功将大大改善 了解关键人类CMD疾病和特征的细胞类型特异性转录机制 新陈代谢组织。

Abstract A global obesity epidemic is driving the concomitant rapid increase in the prevalence of cardiometabolic disorders (CMDs), including hypertriglyceridemia, type 2 diabetes (T2D), hypertension, and non-alcoholic fatty liver disease (NAFLD). Population- and sex-specific differences in CMD predisposition exist; however, the biological mechanisms underlying these differences are not well understood. Previous large-scale genome-wide association studies (GWAS) have reliably identified CMD-associated variants in multiple populations; however, functional understanding of the biological mechanisms of the GWAS variants remains challenging. One major obstacle is the limited knowledge of the relevant cell types in which GWAS variants affect gene expression. Bulk tissue gene expression data exist for CMD-relevant tissues, such as subcutaneous adipose, but these data exhibit considerable heterogeneity, including both cell type and cell state within each cell type. Subcutaneous adipose is an important human endocrine tissue for CMDs, and it is possible to collect high-quality adipose tissue samples from healthy individuals. However, the contributions of many adipose genes to CMDs and CMD traits are still poorly understood. The current lack of cell-type expression reference data sets limits fine-scale regional transcriptional assessment of GWAS variant effects. In addition, local expression quantitative trait locus (cis- eQTL) analyses are confounded by cell-type-specific expression differences, which hamper replication efforts across independent bulk RNA-sequenced (RNA-seq) cohorts. To address these knowledge gaps and identify genetic effects on adipose cell-type gene expression, we will perform single nucleus RNA-sequencing (snRNA- seq) in frozen subcutaneous adipose tissue biopsy samples from 300 well-characterized individuals, generate fine-scale estimates of cell-type proportions, identify study-wide and personalized cell-type-specific differences corresponding to cardiometabolic trait levels, and experimentally test GWAS variants for allelic effects on cell- type-specific expression. We hypothesize that by elucidating adipose tissue cell-type expression from 300 existing frozen adipose biopsies, we can leverage available GWAS and adipose bulk RNA-seq data (n=3,230; 45% female) from diverse populations to identify the relevant cell types for hundreds of CMD genes. In our preliminary studies, we have successfully performed snRNA-seq in frozen human subcutaneous adipose tissue biopsies and performed multi-omic studies integrating GWAS results with bulk adipose RNA-seq data, identifying hundreds of colocalized loci for CMD traits. Our approach will leverage the existing wealth of information available in GWAS and bulk adipose RNA-seq cohorts to elucidate the largely unknown cell types of biological mechanisms in the adipose tissue that drive CMDs. Success of the proposed study will substantially improve understanding of cell-type-specific transcriptional mechanisms of CMD diseases and traits in a key human metabolic tissue.