Systematic ocular phenotyping of 8,707 knockout mouse lines identifies genes associated with abnormal corneal phenotypes
Authors: Vo Peter , Imai-Leonard Denise M. , Yang Benjamin , Briere Andrew , Shao Andy , Casanova M. Isabel , Adams David , Amano Takanori , Amarie Oana , Berberovic Zorana , Bower Lynette , Braun Robert , Brown Steve , Burrill Samantha , Cho Soo Young , Clementson-Mobbs Sharon , D’Souza Abigail , Dickinson Mary , Eskandarian Mohammad , Flenniken Ann M. , Fuchs Helmut , Gailus-Durner Valerie , Heaney Jason , Hérault Yann , Angelis Martin Hrabe de , Hsu Chih-Wei , Jin Shundan , Joynson Russell , Kang Yeon Kyung , Kim Haerim , Masuya Hiroshi , Meziane Hamid , Murray Steve , Nam Ki-Hoan , Noh Hyuna , Nutter Lauryl M. J. , Palkova Marcela , Prochazka Jan , Raishbrook Miles Joseph , Riet Fabrice , Ryan Jennifer , Salazar Jason , Seavey Zachery , Seavitt John Richard , Sedlacek Radislav , Selloum Mohammed , Seo Kyoung Yul , Seong Je Kyung , Shin Hae-Sol , Shiroishi Toshihiko , Stewart Michelle , Svenson Karen , Tamura Masaru , Tolentino Heather , Udensi Uchechukwu , Wells Sara , White Jacqueline , Willett Amelia , Wotton Janine , Wurst Wolfgang , Yoshiki Atsushi ,   The International Mouse Phenotyping Consortium, Lanoue Louise , Lloyd K. C. Kent , Leonard Brian C. , Roux Michel J. , McKerlie Colin , Moshiri Ala 
Published: January 2025

Abstract

Purpose
Corneal dysmorphologies (CDs) are typically classified as either regressive degenerative corneal dystrophies (CDtrs) or defective growth and differentiation-driven corneal dysplasias (CDyps). Both eye disorders have multifactorial etiologies. While previous work has elucidated many aspects of CDs, such as presenting symptoms, epidemiology, and pathophysiology, the genetic mechanisms remain incompletely understood. The purpose of this study was to analyze phenotype data from 8,707 knockout mouse lines to identify new genes associated with the development of CDs in humans.

Methods
8,707 knockout mouse lines phenotyped by the International Mouse Phenotyping Consortium were queried for genes associated with statistically significant (P < 0.0001) abnormal cornea morphology to identify candidate CD genes. Corneal abnormalities were investigated by histopathology. A literature search was used to determine the proportion of candidate genes previously associated with CDs in mice and humans. Phenotypes of human orthologues of mouse candidate genes were compared with known human CD genes to identify protein-protein interactions and molecular pathways using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING), Protein Analysis Through Evolutionary Relationships (PANTHER), and Kyoto Encyclopedia of Genes and Genomes.

Results
Analysis of data from 8,707 knockout mouse lines identified 213 candidate CD genes. Of these, 37 (17%) genes were previously known to be associated with CD, including 14 in the mouse, 16 in humans, and 7 in both. The remaining 176 (83%) genes have not been previously implicated in CD. We also searched publicly available RNAseq data and found that 131 of the total 213 (61.5%) were expressed in adult human corneal tissue. STRING analysis showed several interactions within and between candidate and established CD proteins. All cellular pathways of the established genes were found in the PANTHER analysis of the candidate genes. Several of the candidate genes were implicated in corneal disease, such as TGF-ß signaling. We also identified other possible underappreciated mechanisms relevant to the human cornea.

Conclusions
We identified 213 mouse genes that resulted in statistically significant abnormal corneal phenotypes in knockout mice, many of which have not previously been implicated in corneal pathology. Bioinformatic analyses implicated candidate genes in several signaling pathways which are potential therapeutic targets.