The Developmental Genomics Section has been using a combination of zebrafish genetics and molecular embryology to study ear development and hearing regeneration. We have initiated research on hair cell regeneration in adult zebrafish. We exposed zebrafish to sound at sufficient decibels to cause significant, measurable hearing damage. We then measured the transcriptional changes in gene expression that occurred over the recovery period of four days and defined the mRNA genetic network needed for hair cell regeneration. We have identified over 2000 genes that are differentially regulated during hair cell regeneration, and we are in the process of systematically testing genes by gene inactivation and phenotyping of the mutant alleles for hair cell development and regeneration in early embryos. These experiments will define the nature of the stem cell niche and some of the conditions necessary to activate the regeneration response. The other major project of the lab """"""""Zebrafish insertional mutagenesis and functional genomics,"""""""" is generating thousands of mutations in the zebrafish genome and we will use mutants isolated from this work to identify other genes critical to proper hair cell regeneration. We have identified over 3,700 mutations by retroviral integration and approximately 200 of those genes are in our candidate lists from the sound exposure experiments. We will recover predicted mutations using in vitro fertilization and raise the mutant carriers to sexual maturity. We will then inbreed sibling carriers and screen the embryonic offspring using a variety of measures: 1) visual characterization of the morphology of the inner ear and lateral line in the first 5 days of development 2) efficacy of hair cell regeneration in the lateral line at 5 days post-fertilization 3) vigor of homozygous mutants raised to adult 4) efficacy of the startle response in adults 5) developmental and regeneration defects in embryos from homozygous mutant parents Initial pilot experiments have shown that 4 mutations out of 100 tested have detectable embyronic phenotypes that affect ear development. This is an approximately ten-fold enrichment over screening of genes at random. We have also identified two genes which have an impact on hair cell regeneration without having a significant impact on the normal development of the hair cells. One gene, MGAT5 increases the rate of hair cell regeneration, and a second gene, We will screen a minimum of 500 mutations, potentially yielding 50 new genes involved in hair cell development or regeneration. These genes will be prioritized based on the nature of the phenotypes, with highest priority going to genes that specifically impact hair cell regeneration. All mutations of interest will be freely distributed among the relevant research community for further study. Additionally we are performing pharmacological inhibition of candidate signaling pathways to determine which signals are involved in activation of neuromast hair cell regeneration after ototoxic exposure to copper. Recent experiments in the lab have shown that depending on which TGF-B receptor is inhibited, you can either prevent all hair cell regeneration after ablation in the case of inhibiting ALK3, or you can actually prevent hair cell death completely if you inhibit ALK5. In the next year we will determine which TGF-B ligands are involved in these processes and from which cells in the lateral line neuromasts are these signals coming from. This project is being phased out of the Developmental Genomics Section and will likely only be active for two more years.

Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
National Human Genome Research Institute
Zip Code
Vrljicak, Pavle; Tao, Shijie; Varshney, Gaurav K et al. (2016) Genome-Wide Analysis of Transposon and Retroviral Insertions Reveals Preferential Integrations in Regions of DNA Flexibility. G3 (Bethesda) 6:805-17
Pei, Wuhong; Xu, Lisha; Varshney, Gaurav K et al. (2016) Additive reductions in zebrafish PRPS1 activity result in a spectrum of deficiencies modeling several human PRPS1-associated diseases. Sci Rep 6:29946
Chandler, Randy J; LaFave, Matthew C; Varshney, Gaurav K et al. (2016) Genotoxicity in Mice Following AAV Gene Delivery: A Safety Concern for Human Gene Therapy? Mol Ther 24:198-201
Pei, Wuhong; Huang, Sunny C; Xu, Lisha et al. (2016) Loss of Mgat5a-mediated N-glycosylation stimulates regeneration in zebrafish. Cell Regen (Lond) 5:3
Pei, Wuhong; Tanaka, Katsuya; Huang, Sunny C et al. (2016) Extracellular HSP60 triggers tissue regeneration and wound healing by regulating inflammation and cell proliferation. NPJ Regen Med 1:
Planchart, Antonio; Mattingly, Carolyn J; Allen, David et al. (2016) Advancing toxicology research using in vivo high throughput toxicology with small fish models. ALTEX 33:435-452
Gallardo, Viviana E; Varshney, Gaurav K; Lee, Minnkyong et al. (2015) Phenotype-driven chemical screening in zebrafish for compounds that inhibit collective cell migration identifies multiple pathways potentially involved in metastatic invasion. Dis Model Mech 8:565-76
Marquart, Gregory D; Tabor, Kathryn M; Brown, Mary et al. (2015) A 3D Searchable Database of Transgenic Zebrafish Gal4 and Cre Lines for Functional Neuroanatomy Studies. Front Neural Circuits 9:78
Varshney, Gaurav K; Sood, Raman; Burgess, Shawn M (2015) Understanding and Editing the Zebrafish Genome. Adv Genet 92:1-52
Varshney, Gaurav K; Pei, Wuhong; LaFave, Matthew C et al. (2015) High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas9. Genome Res 25:1030-42

Showing the most recent 10 out of 18 publications