We are proposing a Community Zebrafish Resource for Modeling GWAS Biology that will exploit existing expertise within our institutions in zebrafish genetics, bioinformatics, zebrafish assay development, genetic modeling and mechanistic studies. These studies will lay the foundation for exploration of the gene networks underlying common human disease phenotypes, and establish high-throughput biology in the zebrafish as a platform to complement GWAS across a broad range of traits. Importantly, this approach is readily adapted to drug response phenotypes and novel traits as they emerge.
The Specific Aims are;
Aim 1 -Initial feasibility assessment and assay development a) Bioinformatics-An initial evaluation of the traits to assess the feasibility of modeling in the zebrafish combined with bioinformatic identification of true orthologs, reagent design and where possible in silico prioritization of candidates. In addition we will specifically explore the relationships between candidate causal SNPs (identified from 1000 genomes data [26, 27]) and the latest tissue-specific ENCODE maps to define the transcription factor networks that may be impacted by the common variants [28, 29]. b) Assay design-We will build representative and quantitative assays for the phenotypes of interest, and anchor these to existing human genotypes and phenotypes using known manipulations of known Mendelian genes regulating the phenotype.
Aim 2 -Systematic evaluation of candidate genes and non-coding variants across multiple loci-Once the phenotypic assays have been validated, we will test in the zebrafish each of the candidate genes and regulatory sequences (where the orthologs can be identified) for their effects alone and in combination on the primary trait . Quantitative assessments will be generated for loss of function and gain of function alleles, using existing mutants, morpholinos and transient or stable transgenesis. We propose to study approximately 15-20 GWAS loci per year.
Aim 3 -Establishing zebrafish models for downstream discovery-Once we have established the causal genes underlying each GWAS locus, we will develop stable loss of function (using TALEN or zinc finger nuclease technology) or gain of function alleles for each gene [31 -33]. In addition, where relevant we will generate stable reporter strains for subsequent genetic or chemical screens. These lines will be made freely available to the community to accelerate the translation of completed and ongoing GWAS.
Modern human genetic studies generate new markers of disease much more rapidly than biologists can study the underlying mechanisms. We propose to generate a community resource to allow investigators to use new high-throughput techniques in the zebrafish to explore the mechanisms of their recent genetic results. This resource will identify the genes causing major common human diseases and will generate animal models to allow additional studies of disease mechanism or potentially drug discovery.
|Nissim, Sahar; Weeks, Olivia; Talbot, Jared C et al. (2016) Iterative use of nuclear receptor Nr5a2 regulates multiple stages of liver and pancreas development. Dev Biol 418:108-23|
|Cox, Andrew G; Tsomides, Allison; Kim, Andrew J et al. (2016) Selenoprotein H is an essential regulator of redox homeostasis that cooperates with p53 in development and tumorigenesis. Proc Natl Acad Sci U S A 113:E5562-71|
|Jain, Isha H; Zazzeron, Luca; Goli, Rahul et al. (2016) Hypoxia as a therapy for mitochondrial disease. Science 352:54-61|
|CHARGE Consortium Hematology Working Group (2016) Meta-analysis of rare and common exome chip variants identifies S1PR4 and other loci influencing blood cell traits. Nat Genet 48:867-76|
|(2016) Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function. Nat Commun 7:10023|
|Gorski, Mathias; Tin, Adrienne; Garnaas, Maija et al. (2015) Genome-wide association study of kidney function decline in individuals of European descent. Kidney Int 87:1017-29|
|TaÅŸan, Murat; Musso, Gabriel; Hao, Tong et al. (2015) Selecting causal genes from genome-wide association studies via functionally coherent subnetworks. Nat Methods 12:154-9|
|Musso, Gabriel; Tasan, Murat; Mosimann, Christian et al. (2014) Novel cardiovascular gene functions revealed via systematic phenotype prediction in zebrafish. Development 141:224-35|
|Deo, Rahul C; Musso, Gabriel; Tasan, Murat et al. (2014) Prioritizing causal disease genes using unbiased genomic features. Genome Biol 15:534|
|McMahon, Gearoid M; Olden, Matthias; Garnaas, Maija et al. (2014) Sequencing of LRP2 reveals multiple rare variants associated with urinary trefoil factor-3. J Am Soc Nephrol 25:2896-905|