Brian C. Schutte - US grants

Cleft lip and palate (CL/P) is a major congenital structural anomaly that is notable for significant lifelong morbidity and complex etiology.. The extensive psychological, surgical, speech and dental involvement emphasize the importance of understanding the underlying causes. For the investigator, cleft lip and palate, like other complex diseases, provides a challenge in determining the multiple genetic, environmental and stochastic factors that lead to its phenotype. In this proposal, we will pursue the complex causes of cleft lip and palate through our investigations of a genetically simple form of clefting, Van der Woude syndrome (VDWS). VDWS is the most frequent syndromic form of cleft lip and palate and the form we fell is best suited to contribute to an increased understanding of the more common non-syndromic form of cleft lip and palate and the form we feel is best suited to contribute to an increased understanding of the more common non-syndromic form. Specific goals in this project will include: 1) identification of the VDWS gene. A genetic screen for disease-causing micro-deletions will be used to further restrict the region that contains the VDWS gene. Powerful gene-finding techniques, including the sequence analysis of the entire critical region, will be used to identify transcriptional units. Mutation screens will then be used to find disease causing changes in the DNA. Extensive mutation screens will be performed to search for functional domains. 2) characterization of the VDWS gene and its mouse homolog, including complete cDNA and genomic sequence analysis, the study of temporal and tissue-specific expression to identify developmental pathways that require the VDWS gene functional and screens for gene homologs which may function in the same pathway. 3) identification of sequences that regulate VDWS gene expression and the development of transgenic mouse models, including a mouse knockout that will be used in 4) long-term studies that will include complementation experiments to identify other genes in the pathway and investigate the effects of environmental factors on the VDWS gene and other genes in the same pathway. The impact of this project is that studies of CL/P are valuable, both for the importance of the defect itself as a contributor to morbidity and for providing a model for a complex human birth defect. The identification of the VDWS and VDWS-like genes will immediately provide for better risk counseling, and their characterization under environmental stresses hold the promise for contribution to preventative strategies and improved therapeutics. In addition, the identification of the VDWS gene is relevant to studies of CL/P because of its similarities to the more frequent non-syndromic forms of CL/P and because it will provide a foothold into the earliest steps of craniofacial development.

The goal of Project 0003 is to discover the genes that contribute to isolated cleft lip and palate, a common disorder with complex etiology. This project will study IRF6, a gene that encodes the transcription factor Interferon Regulatory Factor 6. Mutations in IRF6 cause Van der Woude syndrome (VWS). VWS is an outstanding clinical model for isolated cleft lip and palate because the phenotypes of VWS and isolated cleft lip and palate are similar. It is also an outstanding genetic model, since alleles of IRF6 are highly associated with isolated cleft lip and palate in nine geographically distinct populations. These results prove that IRF6 is a key component of a critical pathway in palate development. In this proposal we use mouse models to identify the IRF6 pathway and other genes therein. There are two main hypotheses, 1) IRF6 is a mediator of Tgfb signaling and 2) IRF6 gene targets are essential for palate development. There are three Specific Aims. Specific Aim 1 will determine which cell-type expresses Irf6 in the palate. This basic information will immediately suggest Irf6 pathways and gene targets. Specific Aim 2 will determine which pathways require Irf6 for palate development. The Tgfb3 signaling pathway is essential for palate development and Tgfb3 is expressed at about the same time and place as Irf6. Knockout mice will be used to test the hypotheses that Tgfb3 is essential for expression of Irf6 in the palate shelves. Specific Aim 3 will use microarray analysis to identify the target genes for Irf6 during palate development. In addition, if Irf6 is a mediator for Tgfb3, then gene expression in the palate will be similar in Tgfb3-/- and Irf6-/- mice. Addressing these aims will advance our understanding of Irf6, a gene that is essential in craniofacial development. Further, the IRF6 pathways and targets, discovered in this proposal, will be assessed for their involvement in cleft lip and palate in Project 0001 and in palate development in Project 0004 and Cores 9003 and 9004. This aggregate knowledge will enhance our ability to determine the causes of, and develop preventive interventions for, orofacial clefts.

Our understanding of the pathogenic mechanisms for orofacial clefting (OFC) is limited by the fact that less than half of the heritable risk for this disorder has been assigned to specific genes. Towards identifying pathological sequence variants among the many irrelevant ones detected in exomes and whole genomes of patients with this disorder, an understanding of the gene regulatory networks (GRNs) that govern the development of relevant tissues, including the oral periderm, is essential. We propose a systems biology approach to analyzing the periderm GRN. Using this approach in the past enabled us to identify three novel OFC risk genes. We will utilize two model organisms, zebrafish and mouse, because the periderm differentiation GRN appears to be highly conserved. In zebrafish, the periderm differentiates very early in embryogenesis, greatly facilitating the execution and interpretation of genetic perturbation analyses. Mouse, on the other hand, has the advantage that its craniofacial anatomy is more similar to that of humans. In Aim 1, we will determine the zebrafish periderm differentiation GRN using a state-of-the-art network inference algorithm, NetProphet 2. This tool carries out both a coexpression analysis and a differential expression analysis. Input data sets will include RNA-seq expression profiles we will generate from loss-of-function (LOF) embryos for 4 key transcription factors (TF) known to participate in this GRN. We will also identify the direct gene linkages of these key TFs in the periderm GRN. Finally, we will test a novel candidate member of the periderm GRN, Tead, by carrying out LOF tests in zebrafish, thereby exploiting the strength of this model system. In Aim 2 we will deduce the murine oral periderm differentiation GRN, also using the NetProphet algorithm. Input datasets will include expression profiles of periderm isolated from the palate shelves of wild-type mouse embryos, and from heterozygous mutants of three key TFs: Irf6, Grhl3 and Tfap2a. For each of the mutant genotypes there is evidence of abnormal periderm differentiation. We will also identify murine periderm enhancer candidates by sorting GFP-positive and -negative cells from Krt17-gfp transgenic embryos, performing ATAC-seq on both populations, and H3K27Ac ChIP-seq on cells from palate shelves and the nasal cavity. As in Aim 1, we will also identify the direct gene linkages of the key TFs. We will train a machine learning algorithm on palate periderm enhancers, and use the resulting scoring function to prioritize OFC-associated SNPs near genes that are expressed in periderm for those that are likely to directly affect risk for OFC. Finally, we will perform allele- specific reporter assays on the top candidate SNPs from each of three loci. The expected outcome is a deeper understanding of the specific TFs and cis-regulatory elements that control differentiation of the periderm. This will have a broad impact because it will enable human geneticists to prioritize candidate risk variants that emerge from whole-exome and -genome sequencing analyses of OFC.