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Functional Interrogation of T2D-associated genes in human stem cell-derived models and mice

人类干细胞衍生模型和小鼠中 T2D 相关基因的功能研究

基本信息

批准号：
10649538
负责人：
Struan F A Grant
金额：
$ 174.17万
依托单位：
UNIVERSITY OF PENNSYLVANIA
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-08-20 至 2025-06-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10649538
关键词：
ATAC-seq Ablation Adipocytes Affect Animals Area Biological Biological Process Biology Biometry Blindness Candidate Disease Gene Cardiovascular Diseases Cause of Death Cell model Cells Chronic Collaborations Collection Communities Complex Data Data Set Diabetes Mellitus Diabetic mouse Disease Disease model Disease susceptibility Engineering Functional disorder Funding Genes Genetic Genetic Engineering Genetic Predisposition to Disease Genetic study Genomic approach Genomics Goals Health Hepatocyte Heterogeneity Human Human Genetics Hyperglycemia Individual Insulin Resistance Investigation Kidney Failure Knowledge Liver Malignant Neoplasms Maps Metabolic Methods Modeling Molecular Mus Muscle Fibers Mutant Strains Mice Neuropathy Non-Insulin-Dependent Diabetes Mellitus Obesity Pancreas Pathway Analysis Pathway interactions Patients Pediatric Hospitals Pennsylvania Phenotype Philadelphia Physiological Population Genetics Positioning Attribute Predisposition Prevalence Process Regulation Research Resources Role Skeletal Muscle Source Structure of beta Cell of islet System Testing Therapeutic Tissues Transcript United States National Institutes of Health Universities Untranslated RNA Variant Veterans biobank bioinformatics pipeline candidate identification causal variant cell type chromosome conformation capture clinical translation computational pipelines conditional mutant diabetes pathogenesis follow-up functional genomics gain of function gene interaction gene network gene regulatory network genome wide association study genome-wide genomic data genomic locus human stem cells human tissue in vivo induced pluripotent stem cell loss of function molecular phenotype mouse model multidisciplinary multiple data sources mutant mutant mouse model new therapeutic target novel therapeutics programs stem cell model stem cells therapeutic target trait transcriptome sequencing

项目摘要

Functional Interrogation of T2D-associated genes in human stem cell-derived models and mice Type 2 Diabetes (T2D) is one of the fastest-growing diseases and a leading cause of death throughout the world. A better understanding of the disease process, including characterization of both the genetic etiology and the contribution of different cell types to disease initiation, progression and heterogeneity promises to reveal new therapeutic targets. Large-scale genome-wide association studies (GWAS) of this common complex trait have driven the rapid identification of hundreds of T2D-associated loci. However, the mechanism(s) through which most of these loci influence disease susceptibility remain poorly understood. Our interdisciplinary team at Penn brings together experts in population genetics, T2D GWAS, biostatistics, metabolic tissue biology, human cellular disease modeling and T2D pathophysiology to tackle this critical knowledge gap. In collaboration with other Consortium groups, we aim to accomplish the following goals. (1) Provide the diabetes research community with a robust pipeline for mapping T2D GWAS variants to effector genes and target tissues. (2) Identify new genes and biological pathways that modulate susceptibility to T2D. (3) Define gene regulatory networks relevant to T2D with the goal of uncovering therapeutic ‘entry points’ for developing new treatments. For (1), we will prioritize “candidate effector transcripts” for downstream functional analyses by integrating multiple sources of data to gain a ‘confluence of evidence’ as to their disease relevance and tissue of action. These sources include publically available datasets, a unique collection of internal resources from the Million Veteran Program, and our own functional genomics (RNA-seq, ATAC-seq, chromatin conformation capture etc.) data generated from stem cell-derived T2D relevant cell types. For (2), we will examine the biological function of prioritized T2D-effector transcripts in human cell models of T2D-relevant tissue types using gain- and loss-of- function methods combined with a battery of physiological, metabolic, molecular phenotyping and genomic approaches. These studies include the use of induced pluripotent stem cell (iPSC) models for pancreatic b cells, hepatocytes, adipocytes and skeletal muscle cells, enabling precise genetic engineering and establishment of multiple cell types in the same genetic background. Through this process, we will identify 10 high priority candidate effector genes, which we will advance for comprehensive in vivo analyses in conditional mutant mouse models. For (3), we will perform network analyses through the integration of our multiple data sources to identify molecular memberships in broader pathways and search for pathway components that are potentially amenable for therapeutic targeting.

人干细胞衍生模型和小鼠中T2 D相关基因的功能研究 2型糖尿病（T2 D）是世界上增长最快的疾病之一，也是导致死亡的主要原因。更好地了解疾病过程，包括遗传病因学和不同细胞类型对疾病发生、进展和异质性的贡献有望揭示新的治疗目标对这种常见复杂性状的大规模全基因组关联研究（GWAS）推动了数百个T2 D相关基因座的快速鉴定。然而，通过这种机制，大多数影响疾病易感性的基因座仍然知之甚少。我们在宾夕法尼亚大学的跨学科团队汇集了群体遗传学、T2 D GWAS、生物统计学、代谢组织生物学、人类细胞疾病建模和T2 D病理生理学，以解决这一关键的知识差距。协同其他我们的目标是实现以下目标。 (1)为糖尿病研究社区提供一个强大的管道，用于映射T2 D GWAS变体，效应基因和靶组织。 (2)确定调节T2 D易感性的新基因和生物学途径。 (3)定义与T2 D相关的基因调控网络，目的是发现治疗的“入口” 开发新的治疗方法。对于（1），我们将通过整合用于下游功能分析的“候选效应转录物”，多个数据来源，以获得关于其疾病相关性和作用组织的“证据汇合”。这些来源包括可供使用的数据集，这是来自百万富翁的内部资源的独特集合 Veteran Program和我们自己的功能基因组学（RNA-seq，ATAC-seq，染色质构象捕获等）从干细胞衍生的T2 D相关细胞类型产生的数据。对于（2），我们将研究优先T2 D效应转录物在T2 D相关组织类型的人细胞模型中使用获得和损失的T2 D效应转录物，功能方法结合一系列生理、代谢、分子表型和基因组学方法，接近。这些研究包括使用胰腺B细胞的诱导多能干细胞（iPSC）模型，肝细胞，脂肪细胞和骨骼肌细胞，使精确的基因工程和建立同一基因背景下的多种细胞类型。通过这一过程，我们将确定10个高度优先事项候选效应基因，我们将在条件突变小鼠中进行全面的体内分析模型对于（3），我们将通过集成多个数据源来执行网络分析，以确定分子成员在更广泛的途径和寻找途径的组成部分，用于治疗靶向。

项目成果

期刊论文数量（8）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Genomics and phenomics of body mass index reveals a complex disease network.

DOI：
10.1038/s41467-022-35553-2
发表时间：
2022-12-29
期刊：
NATURE COMMUNICATIONS
影响因子：
16.6
作者：
Huang, Jie;Huffman, Jennifer E.;Huang, Yunfeng;Do Valle, Italo;Assimes, Themistocles L.;Raghavan, Sridharan;Voight, Benjamin F.;Liu, Chang;Barabasi, Albert-Laszlo;Huang, Rose D. L.;Hui, Qin;Nguyen, Xuan-Mai T.;Ho, Yuk-Lam;Djousse, Luc;Lynch, Julie A.;Vujkovic, Marijana;Tcheandjieu, Catherine;Tang, Hua;Damrauer, Scott M.;Reaven, Peter D.;Miller, Donald;Phillips, Lawrence S.;Ng, Maggie C. Y.;Graff, Mariaelisa;Haiman, Christopher A.;Loos, Ruth J. F.;North, Kari E.;Yengo, Loic;Smith, George Davey;Saleheen, Danish;Gaziano, J. Michael;Rader, Daniel J.;Tsao, Philip S.;Cho, Kelly;Chang, Kyong-Mi;Wilson, Peter W. F.;Sun, Yan, V;O'Donnell, Christopher J.
通讯作者：
O'Donnell, Christopher J.

Multi-phenotype analyses of hemostatic traits with cardiovascular events reveal novel genetic associations.

DOI：
10.1111/jth.15698
发表时间：
2022-06
期刊：
Journal of thrombosis and haemostasis : JTH
影响因子：
0
作者：
通讯作者：

Dietary Vitamin E Intake Is Associated With a Reduced Risk of Developing Digestive Diseases and Nonalcoholic Fatty Liver Disease.

DOI：
10.14309/ajg.0000000000001726
发表时间：
2022-06-01
期刊：
The American journal of gastroenterology
影响因子：
0
作者：
通讯作者：

The Diabetes Syndrome - A Collection of Conditions with Common, Interrelated Pathophysiologic Mechanisms.

DOI：
10.2147/ijgm.s305156
发表时间：
2021
期刊：
International journal of general medicine
影响因子：
2.3
作者：
Rachfal AW;Grant SFA;Schwartz SS
通讯作者：
Schwartz SS

Variant-to-gene-mapping analyses reveal a role for pancreatic islet cells in conferring genetic susceptibility to sleep-related traits.

变异基因图谱分析揭示了胰岛细胞在赋予睡眠相关特征遗传易感性方面的作用。

DOI：
10.1093/sleep/zsac109
发表时间：
2022
期刊：
Sleep
影响因子：
5.6
作者：
Lasconi,Chiara;Pahl,MatthewC;Pippin,JamesA;Su,Chun;Johnson,MatthewE;Chesi,Alessandra;Boehm,Keith;Manduchi,Elisabetta;Ou,Kristy;Golson,MariaL;Wells,AndrewD;Kaestner,KlausH;Grant,StruanFA
通讯作者：
Grant,StruanFA