BACKGROUND: Microphthalmia, anophthalmia, and coloboma (MAC) spectrum disease encompasses a group of eye malformations which play a role in childhood visual impairment. Although the predominant cause of eye malformations is known to be heritable in nature, with 80% of cases displaying loss-of-function mutations in the ocular developmental genes OTX2 or SOX2, the genetic abnormalities underlying the remaining cases of MAC are incompletely understood. This study intended to identify the novel genes and pathways required for early eye development. Additionally, pathways involved in eye formation during embryogenesis are also incompletely understood. This study aims to identify the novel genes and pathways required for early eye development through systematic forward screening of the mammalian genome. RESULTS: Query of the International Mouse Phenotyping Consortium (IMPC) database (data release 17.0, August 01, 2022) identified 74 unique knockout lines (genes) with genetically associated eye defects in mouse embryos. The vast majority of eye abnormalities were small or absent eyes, findings most relevant to MAC spectrum disease in humans. A literature search showed that 27 of the 74 lines had previously published knockout mouse models, of which only 15 had ocular defects identified in the original publications. These 12 previously published gene knockouts with no reported ocular abnormalities and the 47 unpublished knockouts with ocular abnormalities identified by the IMPC represent 59 genes not previously associated with early eye development in mice. Of these 59, we identified 19 genes with a reported human eye phenotype. Overall, mining of the IMPC data yielded 40 previously unimplicated genes linked to mammalian eye development. Bioinformatic analysis showed that several of the IMPC genes colocalized to several protein anabolic and pluripotency pathways in early eye development. Of note, our analysis suggests that the serine-glycine pathway producing glycine, a mitochondrial one-carbon donator to folate one-carbon metabolism (FOCM), is essential for eye formation. CONCLUSIONS: Using genome-wide phenotype screening of single-gene knockout mouse lines, STRING analysis, and bioinformatic methods, this study identified genes heretofore unassociated with MAC phenotypes providing models to research novel molecular and cellular mechanisms involved in eye development. These findings have the potential to hasten the diagnosis and treatment of this congenital blinding disease.

CAM SU Genomic Resource Center Soochow University Suzhou China

Centre of Animal Biotechnology and Gene Therapy Universitat Autònoma de Barcelona Barcelona Spain

Czech Center for Phenogenomics Institute of Molecular Genetics of the Czech Academy of Sciences Vestec Czech Republic

Department of Laboratory Medicine and Pathobiology Faculty of Medicine University of Toronto Toronto ON Canada

Department of Molecular and Human Genetics Baylor College of Medicine Houston TX USA

Department of Ophthalmology and Vision Science School of Medicine University of California Davis Sacramento CA USA

Department of Surgery School of Medicine University of California Davis Sacramento CA USA

European Bioinformatics Institute Wellcome Genome Campus Hinxton Cambridgeshire UK

Faculty of Health Sciences PCDDP North West University Potchefstroom South Africa

German Mouse Clinic Institute of Experimental Genetics Helmholtz Zentrum München Neuherberg Germany

Indian Institutes of Science Education and Research Pune India

Institut de Génétique et de Biologie Moléculaire et Cellulaire Université de Strasbourg Illkirch France

Lunenfeld Tanenbaum Research Institute Sinai Health Toronto ON Canada

Medical Research Council Harwell Institute Mammalian Genetics Unit and Mary Lyon Centre Harwell Campus Oxfordshire UK

Monterotondo Mouse Clinic Italian National Research Council Monterotondo Scalo Italy

Mouse Biology Program University of California Davis Davis CA USA

Nanjing Biomedical Research Institute Nanjing University Nanjing China

National Laboratory Animal Center National Applied Research Laboratories Beijing China

National Laboratory Animal Center National Applied Research Laboratories Taipei City Taiwan

Oakland University William Beaumont School of Medicine Rochester MI USA

Ophthalmic Genetics and Visual Function Branch National Eye Institute NIH Bethesda MD 20892 USA

Phenomics Australia The John Curtin School of Medical Research Canberra Australia

Research Institute for Veterinary Science College of Veterinary Medicine Seoul National University Seoul South Korea

RIKEN BioResource Center Tsukuba Japan

The Centre for Phenogenomics Toronto ON Canada

The Hospital for Sick Children Toronto ON Canada

The Jackson Laboratory Bar Harbor ME USA

The Wellcome Trust Sanger Institute Wellcome Genome Campus Hinxton Cambridge UK

UC Davis Eye Center 4860 Y St Ste 2400 Sacramento CA 95817 USA

University of Miami Miller School of Medicine Miami FL USA

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