PROJECT II: CHARACTERIZATION OF MOUSE MODELS TO VALIDATE NOVEL CDH GENES AND IDENTIFY CLINICALLY RELEVANT TARGETS FOR TREATMENT OF PULMONARY DEFECTS OF CDH PATIENTS. ABSTRACT: This proposal reflects an ongoing collaboration by a multidisciplinary team of scientists from The Jackson Laboratory (JAX) and the Massachusetts General Hospital (MGH) to make discoveries that could address the medical needs of Congenital Diaphragmatic Hernia (CDH) patients. As a team, we bring together expertise in genomics, bioinformatics, mouse models, and clinical experience in the care of these patients with this lethal human condition in which a small increase in respiratory function could lead to survival and normal life expectancy. To address the current gaps in knowledge about the underlying genetic etiology of CDH, we have sequenced human exomes of CDH patients, prioritized the variants as candidate genes through computational integration of human genetic data with developmental expression data from mouse lung and diaphragm tissue, and then linked those prioritized candidates into molecular pathways using protein-protein interaction data. Candidate genes emanating from these integrative analyses will be evaluated in in vitro assays of alveologenesis and for subsequent functional validation in mouse models. If these prioritization steps are favorable and if current models are unavailable, new models will be generated by gene editing in the CRISPR/Cas9 pipeline at the JAX. We will also leverage ongoing unbiased phenotype screens underway at JAX as part of the second phase of the Knockout Mouse Project (KOMP2) to identify novel genes associated with diaphragm and lung defects, one of which (SVEP1) is already under evaluation (see Fig. 4 ). Mutant mice will be phenotyped directly by microCT imaging of E15.5 or E18.5 embryos and postnatal pups at the JAX, and with histological analyses, lung morphometrics, and expression of cell lineage specific markers at the MGH. Our top priority will be on phenotypic evaluation of genes manifesting as pulmonary hypoplasia with alveolar simplification or failure of septation, with the hypothesis that such gene defects can be improved therapeutically after birth. Bioinformatics will be used to incorporate candidate gene variants prioritized by expression in lung and diaphragm transcriptomes, into molecular pathways from which to impute therapeutic targets. The most appropriate cell based, organ culture, and postnatal mouse models that respond to therapeutics selected from small molecule screens in Project III and inferred from drug discovery algorithms, will be carefully studied to demonstrate rescue of function in in vitro, ex vivo and, eventually, in vivo knockout mouse models generated from this Project.
PROJECT II: CHARACTERIZATION OF MOUSE MODELS TO VALIDATE NOVEL CDH GENES AND IDENTIFY CLINICALLY RELEVANT TARGETS FOR TREATMENT OF PULMONARY DEFECTS OF CDH PATIENTS. NARRATIVE: Congenital Diaphragmatic Hernia (CDH) is a common and highly lethal birth defect in which we have found pathogenic de novo gene variants present after whole exome sequencing in cohorts of affected probands but not present in unaffected parents. To prioritize these pathogenic variants for further study, we have screened each for expression in normal diaphragms and lungs during development. These high priority candidate gene variants will be used to create animal models of CDH using CRISPR/Cas9 gene editing. Additional new genes causing CDH were found by screening embryos and newborns for diaphragm and lung defects after systematically disabling all cell mouse genes by CRISPR/Cas9 editing in the KOMP2 (Knockout Mouse Program) at The Jackson Laboratories. We will also use novel bioinformatic algorithms to detect protein interactors of these candidate genes to uncover molecular pathways or networks from which we can impute molecular targets for future therapeutics aimed at improving alveolarization in these CDH patients after birth. We will rescue aberrant phenotypes observed in our new mouse models created by gene editing using small molecules from screens customized to identify molecules which improve alveolarization (Project III).
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