PUBLICATION
Identification of 4 novel human ocular coloboma genes ANK3, BMPR1B, PDGFRA, and CDH4 through evolutionary conserved vertebrate gene analysis
- Authors
- Owen, N., Toms, M., Young, R.M., Eintracht, J., Sarkar, H., Brooks, B.P., Moosajee, M., Genomics England Research Consortium
- ID
- ZDB-PUB-220118-7
- Date
- 2022
- Source
- Genetics in medicine : official journal of the American College of Medical Genetics 24(5): 1073-1084 (Journal)
- Registered Authors
- Brooks, Brian P., Young, Rodrigo
- Keywords
- Coloboma, Congenital eye defects, Disease genetics, Genomic sequencing, Microphthalmia
- MeSH Terms
-
- Animals
- Ankyrins/genetics
- Ankyrins/metabolism
- Bone Morphogenetic Protein Receptors, Type I/genetics
- Bone Morphogenetic Protein Receptors, Type I/metabolism
- Coloboma*/genetics
- Genetic Testing
- Humans
- Mice
- Microphthalmos*/genetics
- Phenotype
- Zebrafish/genetics
- PubMed
- 35034853 Full text @ Genet. Med.
Citation
Owen, N., Toms, M., Young, R.M., Eintracht, J., Sarkar, H., Brooks, B.P., Moosajee, M., Genomics England Research Consortium (2022) Identification of 4 novel human ocular coloboma genes ANK3, BMPR1B, PDGFRA, and CDH4 through evolutionary conserved vertebrate gene analysis. Genetics in medicine : official journal of the American College of Medical Genetics. 24(5):1073-1084.
Abstract
Purpose Ocular coloboma arises from genetic or environmental perturbations that inhibit optic fissure (OF) fusion during early eye development. Despite high genetic heterogeneity, 70% to 85% of patients remain molecularly undiagnosed. In this study, we have identified new potential causative genes using cross-species comparative meta-analysis.
Methods Evolutionarily conserved differentially expressed genes were identified through in silico analysis, with in situ hybridization, gene knockdown, and rescue performed to confirm spatiotemporal gene expression and phenotype. Interrogation of the 100,000 Genomes Project for putative pathogenic variants was performed.
Results Nine conserved differentially expressed genes between zebrafish and mouse were identified. Expression of zebrafish ank3a, bmpr1ba/b, cdh4, and pdgfaa was localized to the OF, periocular mesenchyme cells, or ciliary marginal zone, regions traversed by the OF. Knockdown of ank3, bmpr1b, and pdgfaa revealed a coloboma and/or microphthalmia phenotype. Novel pathogenic variants in ANK3, BMPR1B, PDGFRA, and CDH4 were identified in 8 unrelated coloboma families. We showed BMPR1B rescued the knockdown phenotype but variant messenger RNAs failed, providing evidence of pathogenicity.
Conclusion We show the utility of cross-species meta-analysis to identify several novel coloboma disease-causing genes. There is a potential to increase the diagnostic yield for new and unsolved patients while adding to our understanding of the genetic basis of OF morphogenesis.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping