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Li X, Yao Y, Xing S, Zheng YH, Zhou Y, Yu X, Su J, Chen S, Jin ZB. Trio-based whole-exome sequencing of 200 Chinese patients with keratoconus. Exp Eye Res 2024; 248:110109. [PMID: 39326774 DOI: 10.1016/j.exer.2024.110109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Revised: 09/09/2024] [Accepted: 09/23/2024] [Indexed: 09/28/2024]
Abstract
Keratoconus (KC) is a complex corneal disorder with a well-recognized genetic component. In this study, we aimed to expand the genetic spectrum of 200 Chinese patients with keratoconus and their unaffected parents. Trio-based whole-exome sequencing was performed in 200 patients with sporadic keratoconus and their unaffected parents. The variants identified in candidate genes for keratoconus were analyzed using multiple bioinformatics tools. Finally, we identified 7 variants in 5 candidate genes for keratoconus in 5 patients. The c.T464C variant in the IMPDH1 gene was defined as likely pathogenic according to the guidelines of the American College of Medical Genetics and Genomics, and the remaining variants in candidate genes (TRANK1, SLC4A11, CERKL, IFT172) were defined as uncertain significance. Our results expand the genetic spectrum in KC, highlight the genetic heterogeneity of this disease and provide important clues for future functional validation.
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Affiliation(s)
- Xingyong Li
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; Taizhou Ophthalmology and Optometry Hospital, Taizhou 318001, China
| | - Yinghao Yao
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), The Eye Hospital, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Shilai Xing
- Institute of PSI Genomics, Wenzhou Global Eye & Vision Innovation Center, Wenzhou, 325024, Zhejiang, China
| | - Yi-Han Zheng
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China
| | - Yang Zhou
- Taizhou Ophthalmology and Optometry Hospital, Taizhou 318001, China
| | - Xiaoguang Yu
- Institute of PSI Genomics, Wenzhou Global Eye & Vision Innovation Center, Wenzhou, 325024, Zhejiang, China
| | - Jianzhong Su
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), The Eye Hospital, Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China.
| | - Shihao Chen
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; National Engineering Research Center of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China; State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou 325027, China; Taizhou Ophthalmology and Optometry Hospital, Taizhou 318001, China.
| | - Zi-Bing Jin
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China; Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology and Visual Sciences Key Laboratory, Beijing, 100005, China
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Song C, Li L, Liu C, Hu L, Bai J, Liang W, Zhao L, Song W, Li S. Whole-exome sequencing screening for candidate genes and variants associated with primary sporadic keratoconus in Chinese patients. Exp Eye Res 2024; 245:109978. [PMID: 38908538 DOI: 10.1016/j.exer.2024.109978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 04/29/2024] [Accepted: 06/19/2024] [Indexed: 06/24/2024]
Abstract
The pathogenesis of keratoconus (KC) is complex, and genetic factors play an important role. The purpose of this study was to screen and analyse candidate genes and variants in Chinese patients with primary sporadic KC. Whole-exome sequencing (WES) was performed to identify candidate genes and variants in 105 unrelated Chinese patients with primary sporadic KC. Through a series of screening processes, 54 candidate variants in 26 KC candidate genes were identified in 53 KC patients (53/105, 50.5%). These 54 candidate variants included 10 previously identified variants in 9 KC candidate genes and 44 novel variants in 20 KC candidate genes. The previously identified variants occurred in 25.7% (27/105) of patients. Of these, 4 variants (COL6A5, c.5014T > G; CAST, c.1814G > A; ZNF469, c.946G > A; and MPDZ, c.3836A > G) were identified for the first time in Chinese KC patients. The novel variants occurred in 33.3% (35/105) of patients. Of the 26 screened KC candidate genes, 11 KC candidate genes (CAT, COL12A1, FLG, HKDC1, HSPG2, PLOD1, ITGA2, TFAP2B, USH2A, WNT10A, and COL6A5) were found to be potentially pathogenic in Chinese KC patients for the first time. Gene Ontology (GO) biological process (BP) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed on the 26 KC candidate genes using the Database for Annotation, Visualization, and Integrated Discovery (DAVID). The results showed that the KC candidate genes were significantly enriched in biological processes such as collagen fibril organization and extracellular matrix (ECM) organization and in ECM-receptor interaction and protein digestion and absorption pathways. The results further expand the spectrum of KC candidate variants and provide a basis for further KC gene studies.
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Affiliation(s)
- Chunyuan Song
- Aier Eye Hospital, Jinan University, Guangzhou, 510071, China
| | - Ling Li
- Beijing Aier-Intech Eye Hospital, Beijing, 100021, China; Aier Corneal Institute, Beijing, 100021, China
| | - Chang Liu
- Beijing Aier-Intech Eye Hospital, Beijing, 100021, China; Aier Corneal Institute, Beijing, 100021, China
| | - Luping Hu
- Beijing Aier-Intech Eye Hospital, Beijing, 100021, China
| | - Jie Bai
- Beijing Aier-Intech Eye Hospital, Beijing, 100021, China; Aier Corneal Institute, Beijing, 100021, China
| | - Weiyan Liang
- Aier Eye Hospital of Anhui Medical University, Anhui, 230031, China; Tianjin Aier Eye Hospital, Tianjin, 300000, China
| | - Lin Zhao
- Beijing Aier-Intech Eye Hospital, Beijing, 100021, China; Aier Corneal Institute, Beijing, 100021, China
| | - Wenxiu Song
- Beijing Aier-Intech Eye Hospital, Beijing, 100021, China; Aier Corneal Institute, Beijing, 100021, China
| | - Shaowei Li
- Aier Eye Hospital, Jinan University, Guangzhou, 510071, China; Beijing Aier-Intech Eye Hospital, Beijing, 100021, China; Aier Corneal Institute, Beijing, 100021, China; Aier Eye Hospital of Anhui Medical University, Anhui, 230031, China; Tianjin University, Tianjin, 300072, China.
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Yang K, Liu X, Xu L, Gu Y, Fan Q, Yin S, Wang Y, Yuan Y, Chang A, Zang Y, Yin C, Pang C, Wang C, Ren S. The Chinese keratoconus (CKC) cohort study. Eur J Epidemiol 2024; 39:679-689. [PMID: 38703249 DOI: 10.1007/s10654-024-01128-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 04/17/2024] [Indexed: 05/06/2024]
Abstract
The Chinese keratoconus (CKC) cohort study is a population-based longitudinal prospective cohort study in the Chinese population involving a clinical database and biobanks. This ongoing study focuses on the prevention of KC progression and is the first to involve the effect of gene‒environment interactions on KC progression. The CKC cohort is hospital-based and dynamic and was established in Zhengzhou, China; KC patients (n = 1114) from a large geographical area were enrolled from January 2019 to June 2023, with a mean age of 22.23 years (6‒57 years). Demographic details, socioeconomic characteristics, lifestyle, disease history, surgical history, family history, and visual and social function data are being collected using questionnaires. General physical examination, eye examination, biological specimen collection, and first-degree relative data were collected and analyzed in the present study. The primary focus of the present study was placed on gene, environment and the effect of gene‒environment interactions on KC progression. The follow-up of the CKC cohort study is expected to include data collection at 3 months, 6 months, and 1 year after the initial examination and then at the annual follow-up examinations. The first follow-up of the CKC cohort study was recorded. A total of 918 patients completed the follow-up by June 1, 2023, with a response rate of 82.40%. Aside from the younger age of patients who were followed up, no significant differences were found between patients who were followed up and patients who were not.
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Affiliation(s)
- Kaili Yang
- Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institute, People's Hospital of Zhengzhou University, Henan University People's Hospital, 7 Weiwu Road, Zhengzhou, Henan, China
| | - Xiaotian Liu
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Liyan Xu
- Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institute, People's Hospital of Zhengzhou University, Henan University People's Hospital, 7 Weiwu Road, Zhengzhou, Henan, China
| | - Yuwei Gu
- Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institute, People's Hospital of Zhengzhou University, Henan University People's Hospital, 7 Weiwu Road, Zhengzhou, Henan, China
| | - Qi Fan
- Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institute, People's Hospital of Zhengzhou University, Henan University People's Hospital, 7 Weiwu Road, Zhengzhou, Henan, China
| | - Shanshan Yin
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institute, Zhengzhou, Henan, China
| | - Yifan Wang
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institute, Zhengzhou, Henan, China
| | - Yi Yuan
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institute, Zhengzhou, Henan, China
| | - Anqi Chang
- Henan University People's Hospital, Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institute, Zhengzhou, Henan, China
| | - Yonghao Zang
- Xinxiang Medical University, Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institute, Zhengzhou, Henan, China
| | - Chenchen Yin
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institute, Zhengzhou, Henan, China
| | - Chenjiu Pang
- Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institute, People's Hospital of Zhengzhou University, Henan University People's Hospital, 7 Weiwu Road, Zhengzhou, Henan, China
| | - Chongjian Wang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Shengwei Ren
- Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institute, People's Hospital of Zhengzhou University, Henan University People's Hospital, 7 Weiwu Road, Zhengzhou, Henan, China.
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González-Atienza C, Sánchez-Cazorla E, Villoldo-Fernández N, del Hierro A, Boto A, Guerrero-Carretero M, Nieves-Moreno M, Arruti N, Rodríguez-Solana P, Mena R, Rodríguez-Jiménez C, Rosa-Pérez I, Acal JC, Blasco J, Naranjo-Castresana M, Ruz-Caracuel B, Montaño VEF, Ortega Patrón C, Rubio-Martín ME, García-Fernández L, Rikeros-Orozco E, Gómez-Cano MDLÁ, Delgado-Mora L, Noval S, Vallespín E. Whole-Exome Sequencing of 24 Spanish Families: Candidate Genes for Non-Syndromic Pediatric Keratoconus. Genes (Basel) 2023; 14:1838. [PMID: 37895187 PMCID: PMC10606385 DOI: 10.3390/genes14101838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
Keratoconus is a corneal dystrophy that is one of the main causes of corneal transplantation and for which there is currently no effective treatment for all patients. The presentation of this disease in pediatric age is associated with rapid progression, a worse prognosis and, in 15-20% of cases, the need for corneal transplantation. It is a multifactorial disease with genetic variability, which makes its genetic study difficult. Discovering new therapeutic targets is necessary to improve the quality of life of patients. In this manuscript, we present the results of whole-exome sequencing (WES) of 24 pediatric families diagnosed at the University Hospital La Paz (HULP) in Madrid. The results show an oligogenic inheritance of the disease. Genes involved in the structure, function, cell adhesion, development and repair pathways of the cornea are proposed as candidate genes for the disease. Further studies are needed to confirm the involvement of the candidate genes described in this article in the development of pediatric keratoconus.
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Affiliation(s)
- Carmen González-Atienza
- Molecular Ophthalmology Section, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, Hospital Universitario La Paz, 28046 Madrid, Spain; (C.G.-A.); (E.S.-C.); (P.R.-S.); (R.M.); (C.R.-J.); (V.E.F.M.); (C.O.P.); (M.E.R.-M.); (L.G.-F.)
| | - Eloísa Sánchez-Cazorla
- Molecular Ophthalmology Section, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, Hospital Universitario La Paz, 28046 Madrid, Spain; (C.G.-A.); (E.S.-C.); (P.R.-S.); (R.M.); (C.R.-J.); (V.E.F.M.); (C.O.P.); (M.E.R.-M.); (L.G.-F.)
| | - Natalia Villoldo-Fernández
- Department of Pediatric Ophthalmology, IdiPaz, Hospital Universitario La Paz, 28046 Madrid, Spain; (N.V.-F.); (A.d.H.); (A.B.); (M.G.-C.); (N.A.); (I.R.-P.); (J.C.A.); (J.B.); (M.N.-C.); (S.N.)
| | - Almudena del Hierro
- Department of Pediatric Ophthalmology, IdiPaz, Hospital Universitario La Paz, 28046 Madrid, Spain; (N.V.-F.); (A.d.H.); (A.B.); (M.G.-C.); (N.A.); (I.R.-P.); (J.C.A.); (J.B.); (M.N.-C.); (S.N.)
- European Reference Network on Eye Diseases (ERN-EYE), Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Ana Boto
- Department of Pediatric Ophthalmology, IdiPaz, Hospital Universitario La Paz, 28046 Madrid, Spain; (N.V.-F.); (A.d.H.); (A.B.); (M.G.-C.); (N.A.); (I.R.-P.); (J.C.A.); (J.B.); (M.N.-C.); (S.N.)
- European Reference Network on Eye Diseases (ERN-EYE), Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Marta Guerrero-Carretero
- Department of Pediatric Ophthalmology, IdiPaz, Hospital Universitario La Paz, 28046 Madrid, Spain; (N.V.-F.); (A.d.H.); (A.B.); (M.G.-C.); (N.A.); (I.R.-P.); (J.C.A.); (J.B.); (M.N.-C.); (S.N.)
| | - María Nieves-Moreno
- Department of Pediatric Ophthalmology, IdiPaz, Hospital Universitario La Paz, 28046 Madrid, Spain; (N.V.-F.); (A.d.H.); (A.B.); (M.G.-C.); (N.A.); (I.R.-P.); (J.C.A.); (J.B.); (M.N.-C.); (S.N.)
- European Reference Network on Eye Diseases (ERN-EYE), Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Natalia Arruti
- Department of Pediatric Ophthalmology, IdiPaz, Hospital Universitario La Paz, 28046 Madrid, Spain; (N.V.-F.); (A.d.H.); (A.B.); (M.G.-C.); (N.A.); (I.R.-P.); (J.C.A.); (J.B.); (M.N.-C.); (S.N.)
- European Reference Network on Eye Diseases (ERN-EYE), Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Patricia Rodríguez-Solana
- Molecular Ophthalmology Section, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, Hospital Universitario La Paz, 28046 Madrid, Spain; (C.G.-A.); (E.S.-C.); (P.R.-S.); (R.M.); (C.R.-J.); (V.E.F.M.); (C.O.P.); (M.E.R.-M.); (L.G.-F.)
| | - Rocío Mena
- Molecular Ophthalmology Section, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, Hospital Universitario La Paz, 28046 Madrid, Spain; (C.G.-A.); (E.S.-C.); (P.R.-S.); (R.M.); (C.R.-J.); (V.E.F.M.); (C.O.P.); (M.E.R.-M.); (L.G.-F.)
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (B.R.-C.); (E.R.-O.); (L.D.-M.)
| | - Carmen Rodríguez-Jiménez
- Molecular Ophthalmology Section, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, Hospital Universitario La Paz, 28046 Madrid, Spain; (C.G.-A.); (E.S.-C.); (P.R.-S.); (R.M.); (C.R.-J.); (V.E.F.M.); (C.O.P.); (M.E.R.-M.); (L.G.-F.)
| | - Irene Rosa-Pérez
- Department of Pediatric Ophthalmology, IdiPaz, Hospital Universitario La Paz, 28046 Madrid, Spain; (N.V.-F.); (A.d.H.); (A.B.); (M.G.-C.); (N.A.); (I.R.-P.); (J.C.A.); (J.B.); (M.N.-C.); (S.N.)
| | - Juan Carlos Acal
- Department of Pediatric Ophthalmology, IdiPaz, Hospital Universitario La Paz, 28046 Madrid, Spain; (N.V.-F.); (A.d.H.); (A.B.); (M.G.-C.); (N.A.); (I.R.-P.); (J.C.A.); (J.B.); (M.N.-C.); (S.N.)
| | - Joana Blasco
- Department of Pediatric Ophthalmology, IdiPaz, Hospital Universitario La Paz, 28046 Madrid, Spain; (N.V.-F.); (A.d.H.); (A.B.); (M.G.-C.); (N.A.); (I.R.-P.); (J.C.A.); (J.B.); (M.N.-C.); (S.N.)
| | - Marta Naranjo-Castresana
- Department of Pediatric Ophthalmology, IdiPaz, Hospital Universitario La Paz, 28046 Madrid, Spain; (N.V.-F.); (A.d.H.); (A.B.); (M.G.-C.); (N.A.); (I.R.-P.); (J.C.A.); (J.B.); (M.N.-C.); (S.N.)
| | - Beatriz Ruz-Caracuel
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (B.R.-C.); (E.R.-O.); (L.D.-M.)
- Clinical Bioinformatics Section, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, CIBERER, Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Victoria E. F. Montaño
- Molecular Ophthalmology Section, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, Hospital Universitario La Paz, 28046 Madrid, Spain; (C.G.-A.); (E.S.-C.); (P.R.-S.); (R.M.); (C.R.-J.); (V.E.F.M.); (C.O.P.); (M.E.R.-M.); (L.G.-F.)
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (B.R.-C.); (E.R.-O.); (L.D.-M.)
| | - Cristina Ortega Patrón
- Molecular Ophthalmology Section, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, Hospital Universitario La Paz, 28046 Madrid, Spain; (C.G.-A.); (E.S.-C.); (P.R.-S.); (R.M.); (C.R.-J.); (V.E.F.M.); (C.O.P.); (M.E.R.-M.); (L.G.-F.)
| | - M. Esther Rubio-Martín
- Molecular Ophthalmology Section, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, Hospital Universitario La Paz, 28046 Madrid, Spain; (C.G.-A.); (E.S.-C.); (P.R.-S.); (R.M.); (C.R.-J.); (V.E.F.M.); (C.O.P.); (M.E.R.-M.); (L.G.-F.)
| | - Laura García-Fernández
- Molecular Ophthalmology Section, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, Hospital Universitario La Paz, 28046 Madrid, Spain; (C.G.-A.); (E.S.-C.); (P.R.-S.); (R.M.); (C.R.-J.); (V.E.F.M.); (C.O.P.); (M.E.R.-M.); (L.G.-F.)
| | - Emi Rikeros-Orozco
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (B.R.-C.); (E.R.-O.); (L.D.-M.)
- Clinical Genetics Section, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, CIBERER, Hospital Universitario La Paz, 28046 Madrid, Spain;
| | - María de Los Ángeles Gómez-Cano
- Clinical Genetics Section, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, CIBERER, Hospital Universitario La Paz, 28046 Madrid, Spain;
| | - Luna Delgado-Mora
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (B.R.-C.); (E.R.-O.); (L.D.-M.)
- Clinical Genetics Section, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, CIBERER, Hospital Universitario La Paz, 28046 Madrid, Spain;
| | - Susana Noval
- Department of Pediatric Ophthalmology, IdiPaz, Hospital Universitario La Paz, 28046 Madrid, Spain; (N.V.-F.); (A.d.H.); (A.B.); (M.G.-C.); (N.A.); (I.R.-P.); (J.C.A.); (J.B.); (M.N.-C.); (S.N.)
- European Reference Network on Eye Diseases (ERN-EYE), Hospital Universitario La Paz, 28046 Madrid, Spain
| | - Elena Vallespín
- Molecular Ophthalmology Section, Medical and Molecular Genetics Institute (INGEMM) IdiPaz, Hospital Universitario La Paz, 28046 Madrid, Spain; (C.G.-A.); (E.S.-C.); (P.R.-S.); (R.M.); (C.R.-J.); (V.E.F.M.); (C.O.P.); (M.E.R.-M.); (L.G.-F.)
- European Reference Network on Eye Diseases (ERN-EYE), Hospital Universitario La Paz, 28046 Madrid, Spain
- Biomedical Research Center in the Rare Diseases Network (CIBERER), Carlos II Health Institute (ISCIII), 28029 Madrid, Spain; (B.R.-C.); (E.R.-O.); (L.D.-M.)
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Ren S, Yang K, Fan Q, Wang Q, Zhu M, Yin S, Gu Y, Xu L. Bioinformatics analysis of key candidate genes and pathways in Chinese patients with keratoconus. Exp Eye Res 2023; 231:109488. [PMID: 37116607 DOI: 10.1016/j.exer.2023.109488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/10/2023] [Accepted: 04/19/2023] [Indexed: 04/30/2023]
Abstract
Keratoconus (KC) is a multifactorial disease in which genetic factors played important roles in its pathogenesis. The purpose of the current study was to identify the key candidate genes and pathways in Chinese patients with KC through bioinformatics analysis. Totally, we identified 71 candidate genes by analyzing the results of whole exome sequencing on 51 Chinese patients with KC, combining with previous reports on differential expression at transcription and protein levels in KC. Gene enrichment analysis with GeneCodis demonstrated that two significantly enriched terms including 21 genes in biological process (BP) were detected, and six significantly enriched terms containing 14 genes in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were discovered. The STRING was utilized to construct the protein-protein interaction (PPI) network of identified genes. The result showed that a PPI network consisted of 14 nodes with 14 edges was constructed, and two gene modules were obtained. Eight hub genes (LAMB3, LAMA3, LAMA1, ITGA6, ITGA3, COL6A3, COL6A2, and COL6A1) were identified as key candidate genes for KC by cytoHubba in Cytoscape. Functional enrichment analysis with ClueGO and CluePedia indicated that the ECM-receptor interaction was the key pathway accounted for KC. The findings might provide novel insights on the genetic basis of KC.
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Affiliation(s)
- Shengwei Ren
- Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institute, People's Hospital of Zhengzhou University, Zhengzhou, 450003, China; Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institution, Zhengzhou, 450003, China
| | - Kaili Yang
- Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institute, People's Hospital of Zhengzhou University, Zhengzhou, 450003, China
| | - Qi Fan
- Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institute, People's Hospital of Zhengzhou University, Zhengzhou, 450003, China
| | - Qing Wang
- Henan University People's Hospital, Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institute, Zhengzhou, 450003, China
| | - Meng Zhu
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institution, Zhengzhou, 450003, China
| | - Shanshan Yin
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institution, Zhengzhou, 450003, China
| | - Yuwei Gu
- Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institute, People's Hospital of Zhengzhou University, Zhengzhou, 450003, China
| | - Liyan Xu
- Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institute, People's Hospital of Zhengzhou University, Zhengzhou, 450003, China.
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Xu L, Yang K, Yin S, Gu Y, Fan Q, Wang Y, Zhao D, Ren S. Family-based exome sequencing identifies candidate genes related to keratoconus in Chinese families. Front Genet 2022; 13:988620. [PMID: 36118869 PMCID: PMC9478549 DOI: 10.3389/fgene.2022.988620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Keratoconus (KC) is a complex corneal disorder with a strong genetic component. The present study aimed to identify candidate genes related to KC in Chinese families.Methods: Family-based exome sequencing was performed in ten patients suffering from KC who belong to five families with two affected members in each. The candidate rare variants were identified with multi-step bioinformatics analysis. The STRING website was used to perform the protein interaction of the identified genes.Results: Our analyses identified 32 candidate rare variants in 13 genes by family-based exome sequencing. The molecular analyses of identified genes showed that EPCAM directly interacted with CTNNB1 of the Hippo signaling pathway and focal adhesion pathway, and directly interacted with CTNNB1, CDH1 of the WNT signaling pathway. SHROOM3 directly interacted with ROCK2, ROCK1 of the focal adhesion pathway. SYNE1 directly interacted with MUSK of the extracellular matrix organization pathway. TEK directly interacted with VEGFA, SHC1, PIK3R1, GRB2 of the focal adhesion pathway. TTN directly interacted with CAPN3 of the extracellular matrix organization pathway.Conclusion: The EPCAM, SHROOM3, SYNE1, TEK, and TTN genes were potential high-risk candidate pathogenic genes of familial KC. The findings might significantly improve our understanding of the genetic etiology of the disease, providing novel insights on KC pathogenesis.
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Affiliation(s)
- Liyan Xu
- Henan Provincial People’s Hospital, Henan Eye Hospital, Henan Eye Institute, People’s Hospital of Zhengzhou University, Henan University People’s Hospital, Zhengzhou, China
| | - Kaili Yang
- Henan Provincial People’s Hospital, Henan Eye Hospital, Henan Eye Institute, People’s Hospital of Zhengzhou University, Henan University People’s Hospital, Zhengzhou, China
| | - Shanshan Yin
- Zhengzhou University People’s Hospital, Henan Provincial People’s Hospital, Henan Eye Hospital, Henan Eye Institution, Zhengzhou, China
| | - Yuwei Gu
- Henan Provincial People’s Hospital, Henan Eye Hospital, Henan Eye Institute, People’s Hospital of Zhengzhou University, Henan University People’s Hospital, Zhengzhou, China
| | - Qi Fan
- Henan Provincial People’s Hospital, Henan Eye Hospital, Henan Eye Institute, People’s Hospital of Zhengzhou University, Henan University People’s Hospital, Zhengzhou, China
| | - Yawen Wang
- Henan University People’s Hospital, Henan Provincial People’s Hospital, Henan Eye Hospital, Henan Eye Institute, Zhengzhou, China
| | - Dongqing Zhao
- Henan Provincial People’s Hospital, Henan Eye Hospital, Henan Eye Institute, People’s Hospital of Zhengzhou University, Henan University People’s Hospital, Zhengzhou, China
| | - Shengwei Ren
- Henan Provincial People’s Hospital, Henan Eye Hospital, Henan Eye Institute, People’s Hospital of Zhengzhou University, Henan University People’s Hospital, Zhengzhou, China
- *Correspondence: Shengwei Ren,
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7
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Shinde V, Sobreira N, Wohler ES, Maiti G, Hu N, Silvestri G, George S, Jackson J, Chakravarti A, Willoughby CE, Chakravarti S. Pathogenic alleles in microtubule, secretory granule and extracellular matrix-related genes in familial keratoconus. Hum Mol Genet 2021; 30:658-671. [PMID: 33729517 DOI: 10.1093/hmg/ddab075] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 03/03/2021] [Accepted: 03/05/2021] [Indexed: 12/30/2022] Open
Abstract
Keratoconus is a common corneal defect with a complex genetic basis. By whole exome sequencing of affected members from 11 multiplex families of European ancestry, we identified 23 rare, heterozygous, potentially pathogenic variants in 8 genes. These include nonsynonymous single amino acid substitutions in HSPG2, EML6 and CENPF in two families each, and in NBEAL2, LRP1B, PIK3CG and MRGPRD in three families each; ITGAX had nonsynonymous single amino acid substitutions in two families and an indel with a base substitution producing a nonsense allele in the third family. Only HSPG2, EML6 and CENPF have been associated with ocular phenotypes previously. With the exception of MRGPRD and ITGAX, we detected the transcript and encoded protein of the remaining genes in the cornea and corneal cell cultures. Cultured stromal cells showed cytoplasmic punctate staining of NBEAL2, staining of the fibrillar cytoskeletal network by EML6, while CENPF localized to the basal body of primary cilia. We inhibited the expression of HSPG2, EML6, NBEAL2 and CENPF in stromal cell cultures and assayed for the expression of COL1A1 as a readout of corneal matrix production. An upregulation in COL1A1 after siRNA inhibition indicated their functional link to stromal cell biology. For ITGAX, encoding a leukocyte integrin, we assayed its level in the sera of 3 affected families compared with 10 unrelated controls to detect an increase in all affecteds. Our study identified genes that regulate the cytoskeleton, protein trafficking and secretion, barrier tissue function and response to injury and inflammation, as being relevant to keratoconus.
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Affiliation(s)
- Vishal Shinde
- Department of Ophthalmology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Nara Sobreira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Elizabeth S Wohler
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - George Maiti
- Department of Ophthalmology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Nan Hu
- Department of Ophthalmology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Giuliana Silvestri
- Department of Ophthalmology, Belfast Health and Social Care Trust, Belfast BT12 6BA UK
| | - Sonia George
- Department of Ophthalmology, Belfast Health and Social Care Trust, Belfast BT12 6BA UK
| | - Jonathan Jackson
- Department of Ophthalmology, Belfast Health and Social Care Trust, Belfast BT12 6BA UK
| | - Aravinda Chakravarti
- Center for Human Genetics and Genomics, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Colin E Willoughby
- Department of Ophthalmology, Belfast Health and Social Care Trust, Belfast BT12 6BA UK.,Genomic Medicine, Biomedical Sciences Research Institute, Ulster University, Coleraine BT52 1SA, UK
| | - Shukti Chakravarti
- Department of Ophthalmology, NYU Grossman School of Medicine, New York, NY 10016, USA.,Department of Pathology, NYU Grossman School of Medicine, New York, NY 10016, USA
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8
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Veerappa AM. Cascade of interactions between candidate genes reveals convergent mechanisms in keratoconus disease pathogenesis. Ophthalmic Genet 2021; 42:114-131. [PMID: 33554698 DOI: 10.1080/13816810.2020.1868013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Keratoconus is a progressive thinning, steepening and distortion of the cornea which can lead to loss of vision if left untreated. Keratoconus has a complex multifactorial etiology, with genetic and environmental components contributing to the disease pathophysiology. Studies have observed high concordance between monozygotic twins, discordance between dizygotic twins, and high familial segregation indicating the presence of a very strong genetic component in the pathogenesis of keratoconus. The use of genome-wide linkage studies on families and twins, genome-wide association studies (GWAS) on case-controls, next-generation sequencing (NGS)-based genomic screens on both familial and non-familial cohorts have led to the identification of keratoconus candidate genes with much greater success and increased resproducibility of genetic findings. This review focuses on candidate genes identified till date and attempts to understand their role in biological processes underlying keratoconus pathogenesis. In addition, using these genes I propose molecular pathways that could contribute to keratoconus pathogenesis. The pathways identified the presence of direct cross-talk between known candidate genes of keratoconus and remarkably, 28 known candidate genes have a direct relationship among themselves that involves direct protein-protein binding, regulatory activities such as activation and inhibition, chaperone, transcriptional activation/co-activation, and enzyme catalysis. This review attempts to describe these relationships and cross-talks in the context of keratoconus pathogenesis.
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Affiliation(s)
- Avinash M Veerappa
- Department of Ophthalmology, NYU Langone Medical Center, New York, New York, USA
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