Genetics of adipose cell-type expression and cardiometabolic traits

脂肪细胞类型表达和心脏代谢特征的遗传学

• 批准号: 10611492
• 负责人: KAREN L. MOHLKE
• 金额: $ 60.72万
• 依托单位: UNIVERSITY OF CALIFORNIA LOS ANGELES
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-05-01 至 2026-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10611492
• 关键词: Address; Adipocytes; Adipose tissue; Affect; Alleles; Automobile Driving; Biological; Biopsy; Biopsy Specimen; Cardiometabolic Disease; Cell Nucleus; Cell physiology; Cells; Communities; Data; Data Set; Detection; Disease; Endocrine; Exhibits; Female; Freezing; Gene Expression; Genes; Genetic; Genetic Transcription; Health; Heterogeneity; Human; Hypertension; Hypertriglyceridemia; Individual; Knowledge; Medical History; Metabolic; Non-Insulin-Dependent Diabetes Mellitus; Obesity Epidemic; Outcome; Phenotype; Population; Population Heterogeneity; Predisposition; Prevalence; Quantitative Trait Loci; RNA Sequences; Research; Resolution; Resources; Sampling; Sex Differences; Signal Transduction; Specificity; Testing; Tissue Sample; Tissues; Validation; Variant; cardiometabolism; cell type; cohort; data repository; disorder prevention; disorder risk; experience; genetic variant; genome wide association study; genome-wide; genome-wide analysis; improved; multiple omics; non-alcoholic fatty liver disease; obesogenic; phenotypic data; single nucleus RNA-sequencing; subcutaneous; success; trait; transcriptomics

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.

摘要 全球肥胖流行正在推动心血管代谢疾病患病率的随之迅速增加， 在一些实施方案中，糖尿病患者可以患有包括高血糖症、2型糖尿病（T2 D）、高血压和非酒精性脂肪性疾病（CMD）在内的多种疾病。 肝病（NAFLD）。CMD易感性存在人群和性别特异性差异;然而， 这些差异背后的生物学机制还不清楚。大规模全基因组 关联研究（GWAS）已经在多个群体中可靠地鉴定了CMD相关的变体;然而， 对GWAS变体的生物学机制的功能性理解仍然具有挑战性。一个主要 目前的障碍是对GWAS变异体影响基因表达的相关细胞类型的了解有限。散装 存在CMD相关组织如皮下脂肪的组织基因表达数据，但这些数据 表现出相当大的异质性，包括细胞类型和每种细胞类型内的细胞状态。皮下 脂肪是CMD的重要人体内分泌组织，并且可以收集高质量的脂肪组织 来自健康个体的样本。然而，许多脂肪基因对CMD和CMD性状的贡献 仍然知之甚少。目前缺乏细胞类型表达参考数据集，限制了精细尺度的区域表达。 GWAS变体效应的转录评估。此外，局部表达数量性状基因座（cis- eQTL）分析被细胞类型特异性表达差异混淆，这妨碍了复制努力 在独立的批量RNA测序（RNA-seq）队列中。为了弥补这些知识差距， 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- seq）在来自300个充分表征的个体的冷冻皮下脂肪组织活检样品中，产生 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异性差异 对应于心脏代谢特征水平，并实验测试GWAS变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例脂肪组织细胞类型表达， 现有的冷冻脂肪活检，我们可以利用可用的GWAS和脂肪批量RNA-seq数据（n= 3，230; 45%的女性），以确定数百个CMD基因的相关细胞类型。在我们 初步研究，我们已经成功地进行snRNA-seq在冷冻的人皮下脂肪组织 活组织检查并进行多组学研究，将GWAS结果与大量脂肪RNA-seq数据整合， 数百个CMD性状的共定位基因座。我们的方法将利用现有的丰富信息 在GWAS和大量脂肪RNA-seq队列中可用，以阐明生物学特性的大部分未知细胞类型。 脂肪组织中驱动CMD的机制。建议的研究若能成功， 了解CMD疾病和特征的细胞类型特异性转录机制， 代谢组织

项目成果

Isolation of Nuclei from Human Snap-frozen Liver Tissue for Single-nucleus RNA Sequencing.

从人速冻肝组织中分离细胞核进行单核 RNA 测序。

• DOI: 10.21769/bioprotoc.4601
• 发表时间: 2023
• 期刊: Bio-protocol
• 影响因子: 0.8
• 作者: Alvarez,Marcus;Benhammou,JihaneN;Rao,Shuyun;Mishra,Lopa;Pisegna,JosephR;Pajukanta,Päivi
• 通讯作者: Pajukanta,Päivi

Cross-tissue omics analysis discovers ten adipose genes encoding secreted proteins in obesity-related non-alcoholic fatty liver disease.

• DOI: 10.1016/j.ebiom.2023.104620
• 发表时间: 2023-06
• 期刊: EBIOMEDICINE
• 影响因子: 11.1
• 作者: Darci-Maher, Nicholas;Alvarez, Marcus;Arasu, Uma Thanigai;Selvarajan, Ilakya;Lee, Seung Hyuk T.;Pan, David Z.;Miao, Zong;Das, Sankha Subhra;Kaminska, Dorota;Ord, Tiit;Benhammou, Jihane N.;Wabitsch, Martin;Pisegna, Joseph R.;Mannisto, Ville;Pietilainen, Kirsi H.;Laakso, Markku;Sinsheimer, Janet S.;Kaikkonen, Minna U.;Pihlajamaki, Jussi;Pajukanta, Paivi
• 通讯作者: Pajukanta, Paivi