title: Novel cardiovascular gene functions revealed via systematic phenotype prediction in zebrafish.
abstract: Comprehensive functional annotation of vertebrate genomes is fundamental to biological discovery. Reverse genetic screening has been highly useful for determination of gene function, but is untenable as a systematic approach in vertebrate model organisms given the number of surveyable genes and observable phenotypes. Unbiased prediction of gene-phenotype relationships offers a strategy to direct finite experimental resources towards likely phenotypes, thus maximizing de novo discovery of gene functions. Here we prioritized genes for phenotypic assay in zebrafish through machine learning, predicting the effect of loss of function of each of 15,106 zebrafish genes on 338 distinct embryonic anatomical processes. Focusing on cardiovascular phenotypes, the learning procedure predicted known knockdown and mutant phenotypes with high precision. In proof-of-concept studies we validated 16 high-confidence cardiac predictions using targeted morpholino knockdown and initial blinded phenotyping in embryonic zebrafish, confirming a significant enrichment for cardiac phenotypes as compared with morpholino controls. Subsequent detailed analyses of cardiac function confirmed these results, identifying novel physiological defects for 11 tested genes. Among these we identified tmem88a, a recently described attenuator of Wnt signaling, as a discrete regulator of the patterning of intercellular coupling in the zebrafish cardiac epithelium. Thus, we show that systematic prioritization in zebrafish can accelerate the pace of developmental gene function discovery.
authors.affiliation: Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Musso
authors.forename: Murat
authors.initials: M
authors.lastname: Tasan
authors.forename: Christian
authors.initials: C
authors.lastname: Mosimann
authors.forename: John E
authors.initials: JE
authors.lastname: Beaver
authors.forename: Eva
authors.initials: E
authors.lastname: Plovie
authors.forename: Logan A
authors.initials: LA
authors.lastname: Carr
authors.forename: Hon Nian
authors.initials: HN
authors.lastname: Chua
authors.forename: Julie
authors.initials: J
authors.lastname: Dunham
authors.forename: Khalid
authors.initials: K
authors.lastname: Zuberi
authors.forename: Harold
authors.initials: H
authors.lastname: Rodriguez
authors.forename: Quaid
authors.initials: Q
authors.lastname: Morris
authors.forename: Leonard
authors.initials: L
authors.lastname: Zon
authors.forename: Frederick P
authors.initials: FP
authors.lastname: Roth
authors.forename: Calum A
authors.initials: CA
authors.lastname: MacRae
mesh_terms: D000818:Animals; D004625:Embryo, Nonmammalian / Q000378:metabolism; D018507:Gene Expression Regulation, Developmental; D055785:Gene Knockdown Techniques; D006321:Heart / Q000196:embryology*; D008565:Membrane Proteins / Q000235:genetics / Q000378:metabolism*; D060172:Morpholinos / Q000235:genetics; D009206:Myocardium / Q000166:cytology*; D010641:Phenotype; D060449:Wnt Signaling Pathway / Q000235:genetics; D015027:Zebrafish / Q000196:embryology* / Q000235:genetics*; D029961:Zebrafish Proteins / Q000235:genetics / Q000378:metabolism*
chemical_list: D008565:Membrane Proteins; D060172:Morpholinos; C584121:Tmem88a protein, zebrafish; D029961:Zebrafish Proteins
keywords: Cardiovascular; Systems biology; Zebrafish; tmem88a