Mechanisms of Abnormal Diaphragm and Cardiac Development

膈肌异常和心脏发育的机制

• 批准号: 10613958
• 负责人: Daryl Armstrong Scott
• 金额: $ 44.84万
• 依托单位: BAYLOR COLLEGE OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-07-01 至 2025-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10613958
• 关键词: 8p23.1; Acceleration; Affect; Algorithms; Animal Model; Binding; Bioinformatics; Biological Assay; Birth; Candidate Disease Gene; Cardiac; Cardiovascular system; Child; Chromosome Deletion; Chromosomes; Clinical; Clinical Data; Clinical Research; Congenital Abnormality; Congenital diaphragmatic hernia; Cytogenetics; Data; Development; Diaphragmatic Hernia; Discipline; Disease; Embryo; Encyclopedias; Endocardium; Endothelium; Foundations; GATA4 gene; Genes; Genetic; Genetic Transcription; Genomic Segment; Genomics; Goals; Grant; Heart; Hernia; Human; In Situ Hybridization; Individual; Intervention; Knowledge; Laboratories; Learning; Life; LoxP-flanked allele; Luciferases; Maps; Mesenchymal; MicroRNAs; Modeling; Molecular; Morbidity - disease rate; Mus; Newborn Infant; Ontology; Pathogenicity; Pathway Analysis; Pathway interactions; Phenotype; Process; Proteins; Publishing; Recurrence; Research; Research Personnel; Respiratory Diaphragm; Role; SOX7 gene; Source; Syndrome; Techniques; Therapeutic Intervention; Training; United States National Institutes of Health; Update; Validation; WNT4 gene; Work; biochip; bioinformatics tool; cardiogenesis; congenital anomaly; data integration; data modeling; dosage; epigenomics; experimental study; gene discovery; gene interaction; genome database; human disease; innovation; large scale data; machine learning algorithm; malformation; microdeletion; molecular sequence database; mortality; mouse genome; mouse model; next generation sequencing; novel; prevent; preventive intervention; research study; septal defect; transcription factor; transcriptome sequencing; web based interface

Project Summary Congenital diaphragmatic hernia (CDH) is a life-threatening birth defect that accounts for 8% of all major congenital anomalies. In cases where CDH co-occurs with cardiovascular malformations (CVMs), mortality rates increase from 30 to 60%, and long-term morbidity is common. Our goal is to identify genes that cause CDH and CDH/CVM, and to discover the mechanism by which they control diaphragm and heart development. Correctly identifying genes that contribute to specific phenotypes from the large list of candidate genes data generated in research and clinical studies is a major obstacle to progress in this and other research fields. In Specific Aim #1, we will address this challenge by generating ranked CDH and CDH/CVM pathogenicity scores for all RefSeq genes using a machine-learning algorithm that integrates data from large-scale genomic knowledge sources. We will use these scores to identify novel CDH and CDH/CVM genes from cytogenetically defined critical regions and form large next-generation sequencing databases as part of our multifaceted approach to novel gene discovery. We will also accelerate the pace at which human disease genes are discovered by making these scores and our machine-learning algorithm freely available. 8p23.1 microdeletions that encompass GATA4 and SOX7 are among the most frequently identified causes of CDH/CVM. In RNA-seq studies, we identified several CDH-associated genes that are dysregulated in the E15.5 diaphragms of Gata4flox/flox;Prx1-Cre embryos. These embryos are an ideal model of the sac hernias that comprise 20% of human CDH cases. In Specific Aim #2, we will combine data from RNA-seq and BioChIP-seq analyses with the priority scores generated in Aim #1 to identify primary GATA4 target genes whose dysregulation contribute to the development of sac CDH. We will then determine if alterations in the expression of these target genes can cause CDH, or can modify the CDH phenotypes of GATA4-deficient mice. We have shown that SOX7 deficiency causes septal defects by decreasing endothelial-to-mesenchymal transition (EMT) in the developing heart. In RNA-seq and in situ hybridization studies we have shown that the expression of Wnt4—a key regulator of EMT in the endocardium—is severely decreased in E9.5 Sox7-/- hearts. In Specific Aim #3 we will determine if Wnt4 is a primary target of SOX7, and whether modulation of WNT4 or its downstream effectors can rescue SOX7-related cardiac phenotypes. Several lines of evidence suggset that WNT4 is a novel CDH/CVM gene in humans. To confirm this association, and learn more about the role of WNT4 in diaphragm and heart development, we will determine if WNT4 deficiency causes CDH/CVM in mice, if Sox7 and Wnt4 interact genetically in the development of CDH/CVM and if SOX7 regulates Wnt4 transcripition in the developing diaphragm. Through these studies we will identify novel CDH and CDH/CVM genes and pathways. The bioinformatic tools we develop in this grant will enhance gene discovery efforts across multiple research fields.

项目概要 先天性膈疝 (CDH) 是一种危及生命的出生缺陷，占所有重大出生缺陷的 8% 如果 CDH 与心血管畸形 (CVM) 同时发生，死亡率会降低。 发病率从 30% 增加到 60%，并且长期发病很常见。我们的目标是找出导致该病的基因。 CDH 和 CDH/CVM，并发现它们控制隔膜和心脏发育的机制。 从大量候选基因中正确识别有助于特定表型的基因 研究和临床研究中产生的数据是该领域和其他研究领域取得进展的主要障碍。 在具体目标 #1 中，我们将通过生成排名的 CDH 和 CDH/CVM 致病性来应对这一挑战 使用整合大规模基因组数据的机器学习算法对所有 RefSeq 基因进行评分 我们将使用这些分数从细胞遗传学中识别新的 CDH 和 CDH/CVM 基因。 定义关键区域并形成大型下一代测序数据库，作为我们多方面的一部分 我们还将加快发现人类疾病基因的步伐。 通过免费提供这些分数和我们的机器学习算法来发现。 包含 GATA4 和 SOX7 的 8p23.1 微缺失是最常见的原因之一 在 RNA-seq 研究中，我们发现了几个在 CDH/CVM 中失调的基因。 Gata4flox/flox 的 E15.5 隔膜；Prx1-Cre 胚胎这些胚胎是囊疝的理想模型。 占人类 CDH 病例的 20% 在特定目标 #2 中，我们将结合 RNA-seq 和 BioChIP-seq 的数据。 使用目标 #1 中生成的优先级分数进行分析，以确定主要 GATA4 靶基因，其 然后我们将确定表达是否发生改变。 这些靶基因的作用可以引起CDH，或者可以改变GATA4缺陷小鼠的CDH表型。 我们已经证明 SOX7 缺陷通过减少内皮间质细胞的形成而导致间隔缺损。 在RNA-seq和原位杂交研究中，我们已经证明了发育中心脏的转变（EMT）。 Wnt4（心内膜 EMT 的关键调节因子）的表达在 E9.5 Sox7-/- 心脏中严重降低。 在具体目标#3中，我们将确定 Wnt4 是否是 SOX7 的主要靶标，以及 WNT4 或 其下游效应器可以挽救 SOX7 相关的心脏表型。 多项证据表明 WNT4 是人类中的一种新型 CDH/CVM 基因，以证实这一点。 关联，并更多地了解 WNT4 在隔膜和心脏发育中的作用，我们将确定是否 如果 Sox7 和 Wnt4 在发育过程中存在遗传相互作用，WNT4 缺陷会导致小鼠 CDH/CVM CDH/CVM 和 if SOX7 调节发育隔膜中的 Wnt4 转录。 通过这些研究，我们将确定新的 CDH 和 CDH/CVM 基因和生物信息学通路。 我们在这笔赠款中开发的工具将加强多个研究领域的基因发现工作。

项目成果

Identifying phenotypic expansions for congenital diaphragmatic hernia plus (CDH+) using DECIPHER data.

• DOI: 10.1002/ajmg.a.62919
• 发表时间: 2022-10
• 期刊: AMERICAN JOURNAL OF MEDICAL GENETICS PART A
• 影响因子: 2
• 作者: Hardcastle, Amy;Berry, Aliska M.;Campbell, Ian M.;Zhao, Xiaonan;Liu, Pengfei;Gerard, Amanda E.;Rosenfeld, Jill A.;Sisoudiya, Saumya D.;Hernandez-Garcia, Andres;Loddo, Sara;Di Tommaso, Silvia;Novelli, Antonio;Dentici, Maria L.;Capolino, Rossella;Digilio, Maria C.;Graziani, Ludovico;Rustad, Cecilie F.;Neas, Katherine;Ferrero, Giovanni B.;Brusco, Alfredo;Di Gregorio, Eleonora;Wellesley, Diana;Beneteau, Claire;Joubert, Madeleine;Van den Bogaert, Kris;Boogaerts, Anneleen;McMullan, Dominic J.;Dean, John;Giuffrida, Maria G.;Bernardini, Laura;Varghese, Vinod;Shannon, Nora L.;Harrison, Rachel E.;Lam, Wayne W. K.;McKee, Shane;Turnpenny, Peter D.;Cole, Trevor;Morton, Jenny;Eason, Jacqueline;Jones, Marilyn C.;Hall, Rebecca;Wright, Michael;Horridge, Karen;Shaw, Chad A.;Chung, Wendy K.;Scott, Daryl A.
• 通讯作者: Scott, Daryl A.

Underlying genetic etiologies of congenital diaphragmatic hernia.

• DOI: 10.1002/pd.6099
• 发表时间: 2022-03
• 期刊: Prenatal diagnosis
• 影响因子: 3
• 作者: Scott DA;Gofin Y;Berry AM;Adams AD
• 通讯作者: Adams AD

Evidence-Based Genetic Testing for Individuals with Congenital Diaphragmatic Hernia.

• DOI: 10.1016/j.jpeds.2022.05.059
• 发表时间: 2022-09
• 期刊: JOURNAL OF PEDIATRICS
• 影响因子: 5.1
• 作者: Gofin, Yoel;Scott, Daryl A.
• 通讯作者: Scott, Daryl A.

Sox7-positive endothelial progenitors establish coronary arteries and govern ventricular compaction.

• DOI: 10.15252/embr.202255043
• 发表时间: 2023-10-09
• 期刊: EMBO reports
• 影响因子: 7.7

Evidence that FGFRL1 contributes to congenital diaphragmatic hernia development in humans.

• DOI: 10.1002/ajmg.a.62066
• 发表时间: 2021-03
• 期刊: American journal of medical genetics. Part A
• 作者: Gofin Y;Mackay LP;Machol K;Keswani S;Potocki L;Di Gregorio E;Naretto VG;Brusco A;Hernandez-Garcia A;Scott DA
• 通讯作者: Scott DA