Mechanisms of Abnormal Diaphragm and Cardiac Development

A molecular cause cannot be identified for most cases of congenital diaphragmatic hernia (CDH) and/or cardiovascular malformations (CVMs) due to an incomplete understanding of the genes that cause these common, life-threatening birth defects. Low-penetrance genes and unique variants are important sources of missing CDH/CVM heritability. They can be difficult to identify in conventional human genetic studies but are often essential for normal diaphragm and cardiac development as demonstrated in their associated mouse models. In this application, we will identify novel CDH/CVM low-penetrance genes and unique variants and determine the morphogenetic and molecular mechanisms by which they cause these defects. This will be accomplished using an innovative gene discovery pipeline that we have used to identify 52 genes and variants that cause CDH/CVM and other congenital anomalies in the past 5 years. In Specific Aim #1, we will identify and prioritize low-penetrance CDH/CVM genes and unique CDH/CVM-causing variants using a machine learning approach. We will use data from >3,000 individuals to identify novel CDH/CVM genes and unique variants. In some cases, existing data will be sufficient to prove that a candidate gene or variant is causative as was the case for 11 CDH/CVM genes that we identified in proof of principle studies. If current data are insufficient, we will use a machine learning approach to prioritize candidate genes for in-depth searches for additional CDH/CVM cases in humans (Aim #1) and CDH/CVM screening in a representative mouse model (Aim #2) as a means of confirming their association with CDH/CVM. In Specific Aim #2, we will screen up to 20 high-priority candidate genes and variants for CDH/CVM in mouse models. These studies will provide strong corroborating evidence of an association between candidate genes and unique variants and CDH/CVM. We will screen for CDH/CVM in existing mouse lines using a high-throughput micro-CT pipeline that we have previously used to identify CDH/CVM in mouse embryos. If a representative mouse line does not exist or is lethal prior to the completion of diaphragm muscularization and heart development (<E16.5), we will generate new mouse models for screening using advanced and novel techniques, including prime editing and N1 embryo screens. In Specific Aim #3, we will determine the morphogenic and molecular mechanisms by which select variants and genes contribute to the development of CDH/CVM. These studies will leverage mouse models for two CDH/CVM genes, CHAMP1 and WNT4, that were previously identified though our gene discovery pipeline and were subsequently shown to cause high-penetrance CVM and CDH in mice, respectively. The morphogenic assays we will use are well established and our proposed molecular studies include cutting-edge Multiomic snRNA-seq and snATAC-seq evaluations. The results of these studies will have an immediate impact on our ability to molecularly diagnose individuals with CDH/CVM and will lay the foundation from which new preventative and therapeutic interventions for CDH/CVM can be developed. Project Number: 2R01HD098458-06A1 | Fiscal Year: 2026 | NIH Institute/Center: Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) | Principal Investigator: Daryl Scott | Institution: BAYLOR COLLEGE OF MEDICINE, HOUSTON, TX | Award Amount: $480,000 | Activity Code: R01 | Study Section: Genetics of Health and Disease Study Section[GHD] View on NIH RePORTER: https://reporter.nih.gov/project-details/11360552