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. 2025 Jan 20;26(1):48.
doi: 10.1186/s12864-025-11222-8.

Systematic ocular phenotyping of 8,707 knockout mouse lines identifies genes associated with abnormal corneal phenotypes

Peter Vo  1 , Denise M Imai-Leonard  2 , Benjamin Yang  3 , Andrew Briere  4 , Andy Shao  5 , M Isabel Casanova  6 , David Adams  7 , Takanori Amano  8 , Oana Amarie  9 , Zorana Berberovic  10 , Lynette Bower  11 , Robert Braun  12 , Steve Brown  13 , Samantha Burrill  12 , Soo Young Cho  14 , Sharon Clementson-Mobbs  15 , Abigail D'Souza  10 , Mary Dickinson  16 , Mohammad Eskandarian  10 , Ann M Flenniken  10 , Helmut Fuchs  9 , Valerie Gailus-Durner  9 , Jason Heaney  17 , Yann Hérault  18 , Martin Hrabe de Angelis  9 , Chih-Wei Hsu  16 , Shundan Jin  8 , Russell Joynson  15 , Yeon Kyung Kang  19 , Haerim Kim  20 , Hiroshi Masuya  8 , Hamid Meziane  18 , Steve Murray  12 , Ki-Hoan Nam  20 , Hyuna Noh  19 , Lauryl M J Nutter  21 , Marcela Palkova  22 , Jan Prochazka  22 , Miles Joseph Raishbrook  22 , Fabrice Riet  18 , Jennifer Ryan  12 , Jason Salazar  11 , Zachery Seavey  12 , John Richard Seavitt  17 , Radislav Sedlacek  22 , Mohammed Selloum  18 , Kyoung Yul Seo  23 , Je Kyung Seong  24 , Hae-Sol Shin  23 , Toshihiko Shiroishi  8 , Michelle Stewart  15 , Karen Svenson  12 , Masaru Tamura  8 , Heather Tolentino  11 , Uchechukwu Udensi  16 , Sara Wells  15 , Jacqueline White  12 , Amelia Willett  12 , Janine Wotton  12 , Wolfgang Wurst  25 , Atsushi Yoshiki  8 ; International Mouse Phenotyping Consortium; Louise Lanoue  11 , K C Kent Lloyd  11   26 , Brian C Leonard  6 , Michel J Roux  27 , Colin McKerlie  21   28 , Ala Moshiri  29   30
Affiliations

Systematic ocular phenotyping of 8,707 knockout mouse lines identifies genes associated with abnormal corneal phenotypes

Peter Vo et al. BMC Genomics. .

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.

Keywords: Corneal disease; Corneal dysmorphologies; Corneal dystrophies.

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Conflict of interest statement

Declarations. Ethics approval and consent to participate: All procedures at each IMPC center adhered to local, state, and national regulatory guidelines, based on the standards of Animal Research: Reporting of In Vivo Experiments guidelines, a list of recommendations to standardize and improve the quality and reproducibility of animal research. A Housing and Husbandry protocol was also followed, which contains a collection of mandatory and optional procedures to be used during international mouse experimentation.4,5 Guidelines can be accessed at https://www.mousephenotype.org/about-impc/animal-welfare/ . All procedures on live animals were reviewed and approved by associated institutional animal care and use committees (IACUC), animal care committees (ACC), or equivalent. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Example phenotypes of various knockout lines with corneal abnormalities documented by external color photography. Top Row: WT, Apmap−/−, Aurka+/−, Mir96−/− Bottom Row: Ubac1-/-, Vps26c+/-, Vwa5a-/-, Zbtb4-/-
Fig. 2
Fig. 2
The corneal plaques in Nfil3-deficient mice (A, magnified view in B) represented foci of mid-stromal mineralization (asterisk) that elicit a variable degree of granulomatous response (arrow). Control corneal tissue from WT mice is shown in panel C
Fig. 3
Fig. 3
Pax6-deficiency manifests in the eyes as (A, magnified view in B) microphthalmia with a central corneal defect (black arrow in A), subcapsular cataract (asterisk in C), persistent hyaloid vasculature, anterior and posterior synechiae, retinal detachment and pthisis bulbi. The corneal defect (B) is covered by corneal epithelial downgrowth
Fig. 4
Fig. 4
STRING analysis of protein-protein interactions between 210 out of the 213 candidate genes, with Organism set to Homo sapiens, and using the settings Network Type = full STRING network, Required score = high confidence (0.7) and FDR stringency = medium (5%). Two proteins (NGP, STRA6L) and one micro-RNA (MIR96) were omitted from this analysis since they were not included in the STRING tool
Fig. 5
Fig. 5
STRING analysis of protein-protein interactions between 210 Candidate genes (Purple) and 46 of the 48 gold standard genes (Green) (CNA1 was not present in STRING, nor the micro RNA miR-184), with Organism set to Homo sapiens, and using the settings Network Type = full STRING network, Required score = high confidence (0.7) and FDR stringency = medium (5%). PAX6, PITX2 and FOXE3, the three genes present in both lists, are represented in red. Nodes corresponding to genes for which there were PubMed reports of phenotypes in human, mouse or both are circled respectively in dark green, blue or dark red. Edges are color-coded in red when one node corresponds to one of the three common genes and in cyan when linking the two gene sets
Fig. 6
Fig. 6
Molecular pathways of 213 candidate genes and 48 gold standard genes using the PANTHER tool. All gold standard CD gene pathways were found within the candidate pathways chart (highlighted)
Fig. 7
Fig. 7
KEGG pathway for TGF-Beta signaling. Stars indicate genes from either the candidate CD list (purple), established CD gene list (green), or both (red)
See this image and copyright information in PMC

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