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Meng F, Ren S. Identification of hub genes and molecular pathways in keratoconus by integrating bioinformatics and literature mining at the RNA level. Int Ophthalmol 2024; 44:244. [PMID: 38904678 DOI: 10.1007/s10792-024-03071-3] [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: 07/11/2023] [Accepted: 02/16/2024] [Indexed: 06/22/2024]
Abstract
OBJECTIVE Keratoconus (KC) is a condition characterized by progressive corneal steepening and thinning. However, its pathophysiological mechanism remains vague. We mainly performed literature mining to extract bioinformatic and related data on KC at the RNA level. The objective of this study was to explore the potential pathological mechanisms of KC by identifying hub genes and key molecular pathways at the RNA level. METHODS We performed an exhaustive search of the PubMed database and identified studies that pertained to gene transcripts derived from diverse corneal layers in patients with KC. The identified differentially expressed genes were intersected, and overlapping genes were extracted for further analyses. Significantly enriched genes were screened using "Gene Ontology" (GO) and "Kyoto Encyclopedia of Genes and Genomes" (KEGG) analysis with the "Database for Annotation, Visualization, and Integrated Discovery" (DAVID) database. A protein-protein interaction (PPI) network was constructed for the significantly enriched genes using the STRING database. The PPI network was visualized using the Cytoscape software, and hub genes were screened via betweenness centrality values. Pathways that play a critical role in the pathophysiology of KC were discovered using the GO and KEGG analyses of the hub genes. RESULTS 68 overlapping genes were obtained. Fifty genes were significantly enriched in 67 biological processes, and 16 genes were identified in 7 KEGG pathways. Moreover, 14 nodes and 32 edges were identified via the PPI network constructed using the STRING database. Multiple analyses identified 4 hub genes, 12 enriched biological processes, and 6 KEGG pathways. GO enrichment analysis showed that the hub genes are mainly involved in the positive regulation of apoptotic process, and KEGG analysis showed that the hub genes are primarily associated with the interleukin-17 (IL-17) and tumor necrosis factor (TNF) pathways. Overall, the matrix metalloproteinase 9, IL-6, estrogen receptor 1, and prostaglandin-endoperoxide synthase 2 were the potential important genes associated with KC. CONCLUSION Four genes, matrix metalloproteinase 9, IL-6, estrogen receptor 1, and prostaglandin endoperoxide synthase 2, as well as IL-17 and TNF pathways, are critical in the development of KC. Inflammation and apoptosis may contribute to the pathogenesis of KC.
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Affiliation(s)
- Feiying Meng
- Henan Eye Hospital, Henan Provincial People's Hospital/People's Hospital of Zhengzhou University, Zhengzhou, 450003, China
- Eye Institute, Henan Academy of Innovations in Medical Science, Zhengzhou, China
| | - Shengwei Ren
- Henan Eye Hospital, Henan Provincial People's Hospital/People's Hospital of Zhengzhou University, Zhengzhou, 450003, China.
- Eye Institute, Henan Academy of Innovations in Medical Science, Zhengzhou, China.
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Vought R, Greenstein SA, Gelles J, Hersh PS. The Pathophysiology of Keratoconus. Cornea 2024:00003226-990000000-00572. [PMID: 38830186 DOI: 10.1097/ico.0000000000003585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 04/29/2024] [Indexed: 06/05/2024]
Abstract
PURPOSE Keratoconus is a progressive disease characterized by changes in corneal shape, resulting in loss of visual function. There remains a lack of comprehensive understanding regarding its underlying pathophysiology. This review aims to bridge this gap by exploring structural failures and inflammatory processes involved in the etiology and progression of keratoconus. METHODS A literature review was conducted using PubMed and Google Scholar databases, screening for articles published in English using the keyword combinations of "keratoconus" with "pathophysiology," "pathology," "metabolism," "inflammatory," "oxidative stress," "cytokines," "enzymes," "collagen," and "cornea." Articles published between January 1, 1970, and June 1, 2023, were queried and reviewed, with greater emphasis placed on more recent data. Fifty-six relevant studies were examined to develop a thorough review of the pathophysiological mechanisms at play in keratoconus. RESULTS Biomechanical structural failures in the cornea seem to be the primary militating factors in keratoconus etiology and progression. These include disruptions in the arrangement in the collagen lamellae, a decrease in collagen levels, a decrease in natural collagen crosslinking, and changes in lysosomal enzyme activity. Immunologic changes have also been identified in keratoconus, challenging the traditional view of the condition as noninflammatory. Elevated levels of proinflammatory cytokines like IL-1b, IL-6, IL-17, and TNF-α have been observed, along with increased apoptosis of keratocytes. Increased oxidative stress leads to the activation of collagenase and gelatinase enzymes. CONCLUSIONS Keratoconus is a complex condition influenced by both structural defects and inflammatory processes. Understanding these mechanisms can inform clinical management and potentially lead to more effective treatments.
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Affiliation(s)
- Rita Vought
- Institute of Ophthalmology and Visual Science, Rutgers New Jersey Medical School, Newark, NJ; and
| | - Steven A Greenstein
- Institute of Ophthalmology and Visual Science, Rutgers New Jersey Medical School, Newark, NJ; and
- Cornea and Laser Eye Institute, CLEI Center for Keratoconus, Teaneck, NJ
| | - John Gelles
- Institute of Ophthalmology and Visual Science, Rutgers New Jersey Medical School, Newark, NJ; and
- Cornea and Laser Eye Institute, CLEI Center for Keratoconus, Teaneck, NJ
| | - Peter S Hersh
- Institute of Ophthalmology and Visual Science, Rutgers New Jersey Medical School, Newark, NJ; and
- Cornea and Laser Eye Institute, CLEI Center for Keratoconus, Teaneck, NJ
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Nowak-Malczewska DM, Swierkowska J, Gajecka M. Differentially expressed microRNAs targeting genes in key pathways in keratoconus. Front Genet 2024; 15:1301676. [PMID: 38469119 PMCID: PMC10925626 DOI: 10.3389/fgene.2024.1301676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/12/2024] [Indexed: 03/13/2024] Open
Abstract
Introduction: Keratoconus (KTCN) is a corneal ectasia, characterized by a progressive thinning and protrusion of the cornea, with a complex etiology involving genetic, behavioral, lifestyle, and environmental factors. Previous studies indicated that microRNAs (miRNAs) could be involved in KTCN pathogenesis. This in silico study aimed to identify precursor microRNAs (pre-miRNAs) differentially expressed in KTCN corneas and to characterize mature miRNAs and their target genes. Materials and methods: Expression levels of pre-miRNAs were retrieved from our previously obtained RNA sequencing data of 25 KTCN and 25 non-KTCN human corneas (PMID:28145428, PMID:30994860). Differential expression with FDR ≤0.01 and ≥1.5-fold changes were considered significant. Lists of target genes (target score ≥90) of mature miRNAs were obtained from miRDB. Revealed up-/downregulated miRNAs and their target genes were assessed in databases and literature. Enrichment analyses were completed applying the DAVID database. Results: From a total of 47 pre-miRNAs, six were remarkably upregulated (MIR184, MIR548I1, MIR200A, MIR6728, MIR429, MIR1299) and four downregulated (MIR6081, MIR27B, MIR23B, MIR23A) in KTCN corneas. Out of the 1,409 target genes, 220 genes with decreased and 57 genes with increased expression levels in KTCN samples vs non-KTCN samples were found. The extracellular matrix (ECM) organization, response to mechanical stimulus, regulation of cell shape, and signal transduction processes/pathways were identified as distinctive in enrichment analyses. Also, processes associated with the regulation of transcription and DNA binding were listed. Conclusion: Indicated miRNAs and their target genes might be involved in KTCN pathogenesis via disruption of crucial molecular processes, including ECM organization and signal transduction.
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Affiliation(s)
- Dorota M. Nowak-Malczewska
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Marzena Gajecka
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
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Nowak-Wąs M, Wąs P, Czuba Z, Wojnicz R, Wyględowska-Promieńska D. Expression of Tissue Inhibitors of Metalloproteinases (TIMP-1, TIMP-2, TIMP-3, TIMP-4) in Blood Serum of Patients with Keratoconus. J Clin Med 2024; 13:1168. [PMID: 38398480 PMCID: PMC10889408 DOI: 10.3390/jcm13041168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/13/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND The etiology of keratoconus is unclear. Current evidence suggests that inflammatory and systemic mechanisms might play a role in its pathophysiology. The proper interaction of proteolytic enzymes-matrix metalloproteinases-and their specific tissue inhibitors (TIMPs) within the cornea is essential in maintaining its structure, transparency and healing processes. The aim of the study was to determine the concentration of the TIMPs TIMP-1, TIMP-2, TIMP-3, and TIMP-4 in the blood serum samples of patients with keratoconus compared to the control group. METHODS The study encompassed 132 patients, of which 83 people constituted the study group and 49 the control group. The concentration of selected TIMPs was determined using the Human Magnetic Luminex® Performance Assay method. RESULTS In the study group, the concentrations of TIMP-1 and TIMP-3 were statistically significantly reduced, and TIMP-2 and TIMP-4 increased compared to the control group. The analysis of individual TIMPs in terms of their usefulness as potential predictors of keratoconus showed high results of diagnostic sensitivity and specificity for all TIMPs, in particular for TIMP-1 and TIMP-2. CONCLUSION The above results may indicate systemic disturbances in the TIMPs regulation among keratoconus patients. High diagnostic sensitivity and specificity of all TIMPs, in particular TIMP-1 and TIMP-2, may confirm their participation in the etiopathogenesis of this disease.
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Affiliation(s)
- Marta Nowak-Wąs
- Department of Histology and Cell Pathology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 40-055 Katowice, Poland
- Department of Ophthalmology, Kornel Gibinski University Clinical Center, Medical University of Silesia, 40-055 Katowice, Poland
| | - Paweł Wąs
- Department of Ophthalmology, Megrez Provincial Specialist Hospital in Tychy, 43-100 Tychy, Poland
| | - Zenon Czuba
- Department of Microbiology and Immunology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 40-055 Katowice, Poland
| | - Romuald Wojnicz
- Department of Histology and Cell Pathology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 40-055 Katowice, Poland
| | - Dorota Wyględowska-Promieńska
- Department of Ophthalmology, Kornel Gibinski University Clinical Center, Medical University of Silesia, 40-055 Katowice, Poland
- Department of Ophthalmology, Faculty of Medical Sciences in Katowice, Medical University of Silesia, 40-055 Katowice, Poland
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Xu L, Yang K, Zhu M, Yin S, Gu Y, Fan Q, Wang Y, Pang C, Ren S. Trio-based exome sequencing broaden the genetic spectrum in keratoconus. Exp Eye Res 2023; 226:109342. [PMID: 36502923 DOI: 10.1016/j.exer.2022.109342] [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: 05/25/2022] [Revised: 11/09/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
Keratoconus (KC) is a complex corneal disorder with genetic factors involving in its pathogenesis. The genetic etiology of KC has not been fully elucidated. In this study, we aimed to expand the genetic spectrum in KC by trio-based exome sequencing. Trio-based exome sequencing was conducted in 20 patients with KC and their unaffected parents to broaden the genetic spectrum of the disease. With a series of filtering criteria, de novo, recessive homozygous, and compound heterozygous variants in candidate genes were identified, and the candidate genes were classified for further analysis. Finally, we identified 60 variants in 32 candidate genes through trio-based exome sequencing. Among the candidate genes, 10 genes (ARHGEF10, ARHGEF17, ASPM, FLNA, NDRG1, NEB, PLS3, STARD8, SYNE1, TTN) were classified as cytoskeleton-related genes, 4 genes (COL28A1, SDK1, STAB1, TENM2) were classified as cell adhesion-related genes, and 18 genes (APLP2, BCORL1, CCNB3, FOXN1, FUT8, GALNT10, HEPH, HHIP, HMGB3, HS6ST2, JADE3, KIAA0040, MCF2L, MYOF, QRICH2, RPS6KA6, SMARCA1, TNRC6A) were classified into other genes group. Additionally, the candidate rare deleterious variants in TTN were highly repeated in 25% trios. In conclusion, the study provided new insights into the genetic spectrum of KC which might underlie the genetic etiology for the disease. The findings would improve our understanding of pathogenesis in KC and provide critical clues to future functional validation.
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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, 450003, 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, 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, Henan University People's Hospital, Zhengzhou, 450003, 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, 450003, China
| | - Yawen Wang
- Henan University People's Hospital, Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institute, Zhengzhou, 450003, 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, Zhengzhou, 450003, 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, 450003, China; Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Henan Eye Hospital, Henan Eye Institution, Zhengzhou, 450003, China.
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Niazi S, Moshirfar M, Alizadeh F, Doroodgar F, Baradaran-Rafii A, Filutowski O, Niazi F, Ambrósio R. Association of 2 Lysyl Oxidase Gene Single Nucleotide Polymorphisms with Keratoconus: A Nationwide Registration Study. OPHTHALMOLOGY SCIENCE 2022; 3:100247. [PMID: 36748061 PMCID: PMC9898806 DOI: 10.1016/j.xops.2022.100247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/31/2022] [Accepted: 11/03/2022] [Indexed: 11/10/2022]
Abstract
Purpose Keratoconus (KC) is the most common primary ectatic corneal disease, characterized by progressive thinning of the cornea, affecting its shape and structure and leading to visual loss. Lysyl oxidase is an important component of the extracellular matrix and contributes to the homeostasis of corneal stromal extracellular matrix via enzymatic reaction. This nationwide registration study aims to examine the association of KC with 2 known single nucleotide polymorphisms, rs2956540 and rs10519694, in a population of Iranian descent. Design Case-control. Participants One hundred seventy-eight subjects with KC and 180 clinically healthy subjects participated in the study. Methods Genomic DNA was extracted from peripheral blood samples, and their genotypes were determined using tetra-primer amplification refractory mutation system-polymerase chain reaction. Main Outcome Measures Allele frequency for rs2956540 and rs10519694. Results Genotype frequency was significantly different between cases and controls for rs2956540 (P value = 0.019). The rs2956540 C allele carriers were significantly more frequent among KC cases than healthy controls (P valuechi-square = 0.015, P valueFisher exact = 0.017). There was a significant difference in genotype frequency between groups for rs10519694 (P value = 0.001). T allele carriers were significantly more frequent among KC patients (P valuechi-square = 0.002, P valueFisher exact = 0.001). Sex stratification revealed no significant differences in genotype frequency between males and females in cases and controls. Fitting the general linear model showed that rs10519694 could be considered a predictor for the development of KC (P value = 0.001); however, this was not observed for rs2956540 (P value = 0.323). Conclusions rs2956540 and rs10519694 are associated with KC in a population of Iranian descent. rs10519694 could potentially be used for KC risk prediction.
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Affiliation(s)
- Sana Niazi
- Ophthalmic Research Center, Research Institute for Ophthalmology and Vision Science, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Majid Moshirfar
- John A. Moran Eye Center, University of Utah, Salt Lake City, Utah
| | - Fatemeh Alizadeh
- Department of Genomic Psychiatry and Behavioral Genomics (DGPBG), Roozbeh Hospital, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Farideh Doroodgar
- Translational Ophthalmology Research Center, Tehran University of Medical Sciences, Tehran, Iran,Negah Specialty Ophthalmic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran,Correspondence: Farideh Doroodgar, MD; Address: Negah Specialty Ophthalmic Hospital and Research Center, No 3., Ketabi St., Shariati Ave., Tehran, Iran; Postal Code: 1544914599
| | - Alireza Baradaran-Rafii
- Ophthalmic Research Center, Research Institute for Ophthalmology and Vision Science, Shahid Beheshti University of Medical Sciences, Tehran, Iran,Department of Ophthalmology, Morsani College of Medicine, University of South Florida, Tampa, Florida
| | - Oliver Filutowski
- Department of Ophthalmology, Morsani College of Medicine, University of South Florida, Tampa, Florida
| | - Feizollah Niazi
- Clinical Research Development Center, Shahid Modarres Educational hospital, Shahid Behesht University of Medical Sciences, Tehran, Iran
| | - Renato Ambrósio
- Department of Ophthalmology, Federal University the State of Rio de Janeiro (UNIRIO), São Paulo, Brazil,Department of Ophthalmology, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil,Instituto de Olhos Renato Ambrósio, Rio de Janeiro, Brazil,Rio de Janeiro Corneal Tomography and Biomechanics Study Group, Rio de Janeiro, Brazil,BrAIN: Brazilian Artificial Intelligence Networking in Medicine, Rio de Janeiro & Maceió, Brazil
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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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Novel Mutations Identified in the Chinese Han Population with Keratoconus by Next-Generation Sequencing. J Ophthalmol 2022; 2022:9991910. [PMID: 35186329 PMCID: PMC8853779 DOI: 10.1155/2022/9991910] [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: 03/10/2021] [Revised: 08/29/2021] [Accepted: 12/10/2021] [Indexed: 11/17/2022] Open
Abstract
Aim. To identify novel mutations in keratoconus (KC) susceptibility genes in the Chinese Han population. Methods. A total of fifty-two patients with primary KC were recruited. Blood samples were collected, and genomic DNA was isolated from peripheral blood leukocytes. The entire coding region, intron-exon junctions, and promoter regions of sixteen known KC susceptibility genes were screened with next-generation sequencing technology. All identified variants were further confirmed using the Sanger sequencing technology. The Sorting Intolerant from Tolerant (SIFT), MutationTaster, and PolyPhen 2 programs were used to predict the effect of amino acid substitution on protein. Results. After removing twelve known SNPs (single nucleotide polymorphisms) and three variants predicted to be harmless, nine novel mutations were identified in eight of the fifty-two patients, including c.455C > T:p.P152L in FNDC3B; c.3636_3637del:p.R1212fs in COL4A4; c.5015G > T:p.R1672L, c.3798dupA:p.P1267fs, and c.28G > A:p.A10T in MPDZ; c.1940C > T:p.P647L in DOCK9; c.127_128insGGC:p.Q43delinsRQ in POLG; c.3019G > A:p.V1007I in IPO5; and c.624 + 7− > A in TGFBI. All nine mutations in the patients with KC were heterozygote. Conclusion. This study enlarged the gene profile of KC and should be further confirmed by well-powered, genome-wide association studies (GWAS) of Han Chinese patients.
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Hao XD, Gao H, Xu WH, Shan C, Liu Y, Zhou ZX, Wang K, Li PF. Systematically Displaying the Pathogenesis of Keratoconus via Multi-Level Related Gene Enrichment-Based Review. Front Med (Lausanne) 2022; 8:770138. [PMID: 35141241 PMCID: PMC8818795 DOI: 10.3389/fmed.2021.770138] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/31/2021] [Indexed: 01/20/2023] Open
Abstract
Keratoconus (KC) is an etiologically heterogeneous corneal ectatic disorder. To systematically display the pathogenesis of keratoconus (KC), this study reviewed all the reported genes involved in KC, and performed an enrichment analysis of genes identified at the genome, transcription, and protein levels respectively. Combined analysis of multi-level results revealed their shared genes, gene ontology (GO), and pathway terms, to explore the possible pathogenesis of KC. After an initial search, 80 candidate genes, 2,933 transcriptional differential genes, and 947 differential proteins were collected. The candidate genes were significantly enriched in extracellular matrix (ECM) related terms, Wnt signaling pathway and cytokine activities. The enriched GO/pathway terms of transcription and protein levels highlight the importance of ECM, cell adhesion, and inflammatory once again. Combined analysis of multi-levels identified 13 genes, 43 GOs, and 12 pathways. The pathogenic relationships among these overlapping factors maybe as follows. The gene mutations/variants caused insufficient protein dosage or abnormal function, together with environmental stimulation, leading to the related functions and pathways changes in the corneal cells. These included response to the glucocorticoid and reactive oxygen species; regulation of various signaling (P13K-AKT, MAPK and NF-kappaB), apoptosis and aging; upregulation of cytokines and collagen-related enzymes; and downregulation of collagen and other ECM-related proteins. These undoubtedly lead to a reduction of extracellular components and induction of cell apoptosis, resulting in the loosening and thinning of corneal tissue structure. This study, in addition to providing information about the genes involved, also provides an integrated insight into the gene-based etiology and pathogenesis of KC.
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Affiliation(s)
- Xiao-Dan Hao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
- *Correspondence: Xiao-Dan Hao
| | - Hua Gao
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Qingdao, China
- Shandong Eye Hospital, Shandong Eye Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Wen-Hua Xu
- Department of Inspection, The Medical Faculty of Qingdao University, Qingdao, China
| | - Chan Shan
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Ying Liu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Zhi-Xia Zhou
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Kun Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
- Kun Wang
| | - Pei-Feng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
- Pei-Feng Li
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Abstract
As a transparent avascular tissue located at the front of the eyeball, the cornea is an important barrier to external damage. Both epithelial and endothelial cells of the cornea harbor primary cilia, which sense changes in the external environment and regulate intracellular signaling pathways. Accumulating evidence suggests that the primary cilium regulates corneal development in several ways, including participation in corneal epithelial stratification and maintenance of corneal endothelial cell morphology. In addition, the primary cilium has been implicated in the pathogenesis of several corneal diseases. In this review, we discuss recent findings that demonstrate the critical role of the primary cilium in corneal development. We also discuss the link between ciliary dysfunction and corneal diseases, which suggests that the primary cilium could be targeted to treat these diseases.
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Affiliation(s)
- Ting Song
- Institute of Biomedical Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, China
| | - Jun Zhou
- Institute of Biomedical Sciences, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, China.,State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, China. E-mail:
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Bykhovskaya Y, Rabinowitz YS. Update on the genetics of keratoconus. Exp Eye Res 2020; 202:108398. [PMID: 33316263 DOI: 10.1016/j.exer.2020.108398] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/04/2020] [Accepted: 12/07/2020] [Indexed: 02/07/2023]
Abstract
In the past few years we have seen a great acceleration of discoveries in the field of keratoconus including new treatments, diagnostic tools, genomic and molecular determinants of disease risk. Recent genome-wide association studies (GWAS) of keratoconus cases and population wide studies of variation in central corneal thickness and in corneal biomechanical properties confirmed already identified genes and found many new susceptibility variants and biological pathways. Recent findings in genetic determinants of familial keratoconus revealed functionally important variants and established first mouse model of keratoconus. Latest transcriptomic and expression studies started assessing novel non-coding RNA targets in addition to identifying tissue specific effects of coding genes. First genomic insights into better prediction of treatment outcomes are bringing the advent of genomic medicine into keratoconus clinical practice.
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Affiliation(s)
- Yelena Bykhovskaya
- Cornea Genetic Eye Institute, Department of Surgery and Board of the Governors Regenerative Medicine Institute, Beverly Hills, Cedars-Sinai, Los Angeles, CA, United States.
| | - Yaron S Rabinowitz
- Cornea Genetic Eye Institute, Department of Surgery and Board of the Governors Regenerative Medicine Institute, Beverly Hills, Cedars-Sinai, Los Angeles, CA, United States
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12
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Hao XD, Chen XN, Zhang YY, Chen P, Wei C, Shi WY, Gao H. Multi-level consistent changes of the ECM pathway identified in a typical keratoconus twin's family by multi-omics analysis. Orphanet J Rare Dis 2020; 15:227. [PMID: 32867823 PMCID: PMC7457807 DOI: 10.1186/s13023-020-01512-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 08/13/2020] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Keratoconus (KC) is a common, degenerative disorder of the cornea, and genetic factors play a key role in its development. However, the genetic etiology of KC is still unclear. This study used the family of twins as material, using, for the first time, multi-omics analysis, to systematically display the changes in KC candidate factors in patients at the DNA, RNA, and protein levels. These can evaluate candidate pathogenic factors in depth and lock onto pathogenic targets. RESULTS The twins in this study presented classic phenotypes, clear diagnoses, complete case data, and clinical samples, which are excellent materials for genetically studying KC. Whole-exome sequencing was conducted on both the twins and their parents. Transcriptome sequencing was conducted on proband's and health individual's primary human corneal fibroblast cells. Quantitative Real-time PCR and western blot were used to validate the differential gene expressions between the proband and controls. By integrating genomics, transcriptome, and protein level data, multiple consecutive events of KC were systematically analyzed to help better understand the molecular mechanism and genetic basis of KC. The results showed that the accumulation of rare, micro-effect risk variants was the pathogenic factor in this Chinese KC family. Consistent changes in extracellular matrices (ECMs) at the DNA and RNA levels suggested that ECM related changes play a key role in KC pathogenesis. The major gene variants (WNT16, CD248, COL6A2, COL4A3 and ADAMTS3) may affect the expression of related collagens or ECM proteins, thus reducing the amount of ECM in corneas and resulting in KC. CONCLUSIONS This study, the first to explore the genetic etiology of KC via multi-omics analysis under the polygenetic model, has provided new insights into the genetic mechanisms underlying KC and an effective strategy for studying KC pathogenesis in the future.
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Affiliation(s)
- Xiao-Dan Hao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, China.,State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, 266071, China
| | - Xiu-Nian Chen
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266021, China.,State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, 266071, China
| | - Yang-Yang Zhang
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, 266071, China
| | - Peng Chen
- Department of Human Anatomy, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Chao Wei
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, 266071, China
| | - Wei-Yun Shi
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, 266071, China.,Shandong Eye Hospital, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250021, China
| | - Hua Gao
- State Key Laboratory Cultivation Base, Shandong Provincial Key Laboratory of Ophthalmology, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Qingdao, 266071, China. .,Shandong Eye Hospital, Shandong Eye Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250021, China.
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13
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Karolak JA, Ginter-Matuszewska B, Tomela K, Kabza M, Nowak-Malczewska DM, Rydzanicz M, Polakowski P, Szaflik JP, Gajecka M. Further evaluation of differential expression of keratoconus candidate genes in human corneas. PeerJ 2020; 8:e9793. [PMID: 32879808 PMCID: PMC7443321 DOI: 10.7717/peerj.9793] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/31/2020] [Indexed: 12/26/2022] Open
Abstract
Background Keratoconus (KTCN) is a progressive eye disease, characterized by changes in the shape and thickness of the cornea that results in loss of visual acuity. While numerous KTCN candidate genes have been identified, the genetic etiology of the disease remains undetermined. To further investigate and verify the contribution of particular genetic factors to KTCN, we assessed 45 candidate genes previously indicated as involved in KTCN etiology based on transcriptomic and genomic data. Methods The RealTime ready Custom Panel, covering 45 KTCN candidate genes and two reference transcripts, has been designed. Then, the expression profiles have been assessed using the RT-qPCR assay in six KTCN and six non-KTCN human corneas, obtained from individuals undergoing a penetrating keratoplasty procedure. Results In total, 35 genes exhibiting differential expression between KTCN and non-KTCN corneas have been identified. Among these genes were ones linked to the extracellular matrix formation, including collagen synthesis or the TGF-β, Hippo, and Wnt signaling pathways. The most downregulated transcripts in KTCN corneas were CTGF, TGFB3, ZNF469, COL5A2, SMAD7, and SPARC, while TGFBI and SLC4A11 were the most upregulated ones. Hierarchical clustering of expression profiles demonstrated almost clear separation between KTCN and non-KTCN corneas. The gene expression levels determined using RT-qPCR showed a strong correlation with previous RNA sequencing (RNA-Seq) results. Conclusions A strong correlation between RT-qPCR and earlier RNA-Seq data confirms the possible involvement of genes from collagen synthesis and the TGF-β, Hippo, and Wnt signaling pathways in KTCN etiology. Our data also revealed altered expression of several genes, such as LOX, SPARC, and ZNF469, in which single nucleotide variants have been frequently identified in KTCN. These findings further highlight the heterogeneous nature of KTCN.
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Affiliation(s)
- Justyna A Karolak
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland.,Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Barbara Ginter-Matuszewska
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Katarzyna Tomela
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland.,Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Michal Kabza
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Dorota M Nowak-Malczewska
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Piotr Polakowski
- Department of Ophthalmology, Medical University of Warsaw, Warsaw, Poland
| | - Jacek P Szaflik
- Department of Ophthalmology, Medical University of Warsaw, Warsaw, Poland
| | - Marzena Gajecka
- Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland.,Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
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14
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Xu X, Zhang X, Cui Y, Yang H, Ping X, Wu J, Yu X, Jin X, Huang X, Shentu X. Three novel variants identified within ECM-related genes in Chinese Han keratoconus patients. Sci Rep 2020; 10:5844. [PMID: 32246022 PMCID: PMC7125089 DOI: 10.1038/s41598-020-62572-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 03/04/2020] [Indexed: 12/24/2022] Open
Abstract
As the primary indication for corneal transplantation, the pathogenesis of keratoconus remains elusive. Aiming to identify whether any mutation from extracellular-matrix (ECM)-related genes contributes to the patients with sporadic cases of keratoconus (KC) from Chinese Han population, one hundred and fifty-three participants in total were enrolled in our study, including fifty-three KC patients and one hundred healthy controls. Mutational analysis of three ECM-related genes (LOX, COL5A1 and TIMP3) with next-generation sequencing and Sanger sequencing was performed. To further confirm the function of three ECM-related genes in the pathogenesis of keratoconus, we performed Real-time Quantitative PCR in vitro. Results showed that three new sequence variants (c.95 G > A in LOX, c.1372 C > T in COL5A1 and c.476 C > T in TIMP3) were identified in aforementioned ECM-related genes in KC patients without being detected among the healthy controls. According to the results of QPCR, we found that the expression levels of LOX and TIMP3 were decreased in the KC patients, while COL5A1 showed no significant difference of expression. This is the first time to screen so many ECM-related genes in Chinese keratoconus patients using next-generation sequencing. We find numerous underlying causal variants, enlarging lots of mutation spectrums and thus providing new sites for other investigators to replicate and for further research.
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Affiliation(s)
- Xiayan Xu
- Department of Ophthalmology, The Second Affiliated Hospital of Zhejiang University, College of Medicine, Hangzhou, Zhejiang, China
| | - Xin Zhang
- Department of Ophthalmology, The Second Affiliated Hospital of Zhejiang University, College of Medicine, Hangzhou, Zhejiang, China
| | - Yilei Cui
- Department of Ophthalmology, The Second Affiliated Hospital of Zhejiang University, College of Medicine, Hangzhou, Zhejiang, China
| | - Hao Yang
- Department of Ophthalmology, The Second Affiliated Hospital of Zhejiang University, College of Medicine, Hangzhou, Zhejiang, China
| | - Xiyuan Ping
- Department of Ophthalmology, The Second Affiliated Hospital of Zhejiang University, College of Medicine, Hangzhou, Zhejiang, China
| | - Jing Wu
- Department of Ophthalmology, The Second Affiliated Hospital of Zhejiang University, College of Medicine, Hangzhou, Zhejiang, China
| | - Xiaoning Yu
- Department of Ophthalmology, The Second Affiliated Hospital of Zhejiang University, College of Medicine, Hangzhou, Zhejiang, China
| | - Xiuming Jin
- Department of Ophthalmology, The Second Affiliated Hospital of Zhejiang University, College of Medicine, Hangzhou, Zhejiang, China
| | - Xiaodan Huang
- Department of Ophthalmology, The Second Affiliated Hospital of Zhejiang University, College of Medicine, Hangzhou, Zhejiang, China
| | - Xingchao Shentu
- Department of Ophthalmology, The Second Affiliated Hospital of Zhejiang University, College of Medicine, Hangzhou, Zhejiang, China.
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15
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Genome-wide association meta-analysis of corneal curvature identifies novel loci and shared genetic influences across axial length and refractive error. Commun Biol 2020; 3:133. [PMID: 32193507 PMCID: PMC7081241 DOI: 10.1038/s42003-020-0802-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 01/24/2020] [Indexed: 12/22/2022] Open
Abstract
Corneal curvature, a highly heritable trait, is a key clinical endophenotype for myopia - a major cause of visual impairment and blindness in the world. Here we present a trans-ethnic meta-analysis of corneal curvature GWAS in 44,042 individuals of Caucasian and Asian with replication in 88,218 UK Biobank data. We identified 47 loci (of which 26 are novel), with population-specific signals as well as shared signals across ethnicities. Some identified variants showed precise scaling in corneal curvature and eye elongation (i.e. axial length) to maintain eyes in emmetropia (i.e. HDAC11/FBLN2 rs2630445, RBP3 rs11204213); others exhibited association with myopia with little pleiotropic effects on eye elongation. Implicated genes are involved in extracellular matrix organization, developmental process for body and eye, connective tissue cartilage and glycosylation protein activities. Our study provides insights into population-specific novel genes for corneal curvature, and their pleiotropic effect in regulating eye size or conferring susceptibility to myopia.
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16
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Cao K, Sahebjada S, Richardson AJ, Baird PN. Do age-related macular degeneration genes show association with keratoconus? EYE AND VISION 2019; 6:38. [PMID: 31819893 PMCID: PMC6885317 DOI: 10.1186/s40662-019-0164-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 11/03/2019] [Indexed: 01/06/2023]
Abstract
Background Keratoconus (KC) is a common corneal condition with an unknown gender predominance. Although numerous studies have investigated the genetic component of KC, no specific genes have yet been attributed to the condition. We recently reported posterior segment changes occurring in the eyes of KC patients. However, it is not clear whether these changes are part of KC pathogenesis or reflect changes in anatomical features of the eye manifested by changes at the cornea. Given retinal changes represent the main characteristics observed in age-related macular degeneration (AMD) and that pleiotropy has been demonstrated between different eye diseases, we wished to assess if known AMD associated genes were also associated with KC. Methods A total of 248 KC subjects and 366 non-KC (control) subjects were recruited from public and private clinics in Melbourne for this analysis. Nineteen single nucleotide polymorphisms (SNPs) previously associated with AMD, including rs10490924 (ARMS2/HTRA1), rs10737680 (CFH), rs13278062 (TNFRSF10A), rs1864163 (CETP), rs2230199 (C3), rs3130783 (IER3/DDR1), rs334353 (TGFBR1), rs3812111 (COL10A1), rs429608 (C2/CFB), rs4420638 (APOE), rs4698775 (CFI), rs5749482 (TIMP3), rs6795735 (ADAMTS9), rs8017304 (RAD51B), rs8135665 (SLC16A8), rs920915 (LIPC), rs943080 (VEGFA), rs9542236 (B3GALTL) and rs13081855 (COL8A1/FILIP1L), were genotyped in this cohort. Logistic regression was applied to evaluate the association between these SNPs and KC on both genders together, as well as each gender separately. Linear regression was also applied to assess the association between SNPs and corneal curvature. Bonferroni correction was applied to adjust for multiple testing. Results Genotyping data were available for 18 SNPs. The SNP, rs6795735 (ADAMTS9) was significantly associated with KC (p = 3.5 × 10- 4) when both genders were assessed, whereas rs5749482 (TIMP3) was only associated in males (p = 7.7 × 10- 4) following Bonferroni multiple correction. However, when the covariates of age and gender were included, the associations became non-significant. In addition, none of the SNPs appeared significant for corneal curvature. Conclusions Our study suggested a potential association of rs6795735 in the ADAMTS9 gene and rs5749482 in the TIMP3 gene in KC and that different associations may be gender specific. Overall, SNPs initially identified as associated with AMD following multiple correction may be further impacted by other factors such as age or gender and further studies are needed to resolve this issue.
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Affiliation(s)
- Ke Cao
- 1Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Australia.,2Department of Surgery, Ophthalmology, The University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3000 Australia
| | - Srujana Sahebjada
- 1Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Australia.,2Department of Surgery, Ophthalmology, The University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3000 Australia
| | - Andrea J Richardson
- 1Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Australia
| | - Paul N Baird
- 2Department of Surgery, Ophthalmology, The University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3000 Australia
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17
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Sharif R, Khaled ML, McKay TB, Liu Y, Karamichos D. Transcriptional profiling of corneal stromal cells derived from patients with keratoconus. Sci Rep 2019; 9:12567. [PMID: 31467338 PMCID: PMC6715750 DOI: 10.1038/s41598-019-48983-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 08/16/2019] [Indexed: 12/03/2022] Open
Abstract
Keratoconus (KC) is a multi-factorial corneal ectasia with unknown etiology affecting approximately 1:2000 people worldwide. Dysregulated gene expression, using RNA-Seq technology, have been reported in KC corneal tissue. However, the differential expression of genes, in KC corneal stromal cells have been widely ignored. We utilized mRNA-Seq to analyze gene expression in primary human corneal stromal cells derived from five non-Keratoconus healthy (HCF) and four Keratoconus (HKC) donors. Selected genes were further validated using real time PCR (RT-PCR). We have identified 423 differentially expressed genes with 187 down- and 236 up-regulated in KC-affected corneal stromal cells. Gene ontology analysis using WebGestalt indicates the enrichment of genes involved in cell migration, extracellular matrix, adherens junction, and MAPK signaling. Our protein-protein interaction network analysis identified several network seeds, such as EGFR, NEDD4, SNTA1, LGALS3BP, HSPB1, SDC2, MME, and HIF1A. Our work provides an otherwise unknown information on the transcriptional changes in HKCs, and reveals critical mechanisms of the cellular compartment. It also highlights the importance of human-based in vitro studies on a disease that currently lacks strong biomarkers and animal models.
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Affiliation(s)
- Rabab Sharif
- Department of Cell Biology, University of Oklahoma Health science Center, Oklahoma City, Oklahoma, 73104, USA
| | - Mariam L Khaled
- Department of Cellular Biology & Anatomy, Augusta University, Augusta, GA, 30912, United States
| | - Tina B McKay
- Schepens Eye Research Institute and Department of Ophthalmology, Harvard Medical School, Boston, MA, 02114, USA
| | - Yutao Liu
- Department of Cellular Biology & Anatomy, Augusta University, Augusta, GA, 30912, United States.
| | - Dimitrios Karamichos
- Department of Cell Biology, University of Oklahoma Health science Center, Oklahoma City, Oklahoma, 73104, USA.
- Department of Ophthalmology/Dean McGee Eye Institute, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma, 73104, USA.
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18
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Sargazi S, Moudi M, Heidari Nia M, Saravani R, Malek Raisi H. Association of KIF26B and COL4A4 gene polymorphisms with the risk of keratoconus in a sample of Iranian population. Int Ophthalmol 2019; 39:2621-2628. [PMID: 31077021 DOI: 10.1007/s10792-019-01111-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 04/30/2019] [Indexed: 12/30/2022]
Abstract
PURPOSE Keratoconus (KTCN) is a congenital corneal eye disorder which correlates with abnormal distribution of the collagen fiber and causes loss of visual acuity. COLA4A gene has a substantive role in collagen synthesis, whereas KIF26B as a new candidate gene belonging to kinesin superfamily (KIFs) has been suggested to be associated with this disease. So, in this preliminary study, we simultaneously evaluated the effects of two single nucleotide polymorphisms, 222855rs7C/T and rs12407427C/T, on KTCN susceptibility in a sample of Iranian population. METHODS The present case-control study consists of 144 patients confirmed with KTCN and 153 healthy controls. The variants are genotyped by using amplification refractory mutation system-polymerase chain reaction method. RESULTS The findings disclosed that rs2228557C/T and rs12407427C/T polymorphisms significantly increased the risk of KTCN in measured (codominant1; p = 0.0001, codominant2; p = 0.0001, codominant3; p = 0.0006, dominant; p = 0.0001, over-dominant; p = 0.0005) and (codominant1; p = 0.0001, codominant3; p = 0.0005, recessive; p = 0.0001) inheritance patterns, respectively. CONCLUSION Our results did prove a statistical association of both rs2228557 and rs12407427 genotypes (TT and CT + CC) and allele (T) with KTCN susceptibility in Iranian population. Further studies in other ethnicities are required to verify our results.
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Affiliation(s)
- Saman Sargazi
- Department of Clinical Biochemistry, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.,Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mahdiyeh Moudi
- Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan, Iran.,Department of Medical Genetics, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Milad Heidari Nia
- Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan, Iran.,Department of Biology, Faculty of Science, Isfahan University, Isfahan, Iran
| | - Ramin Saravani
- Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan, Iran. .,Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran.
| | - Hamid Malek Raisi
- Infectious Diseases and Tropical Medicine Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
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19
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di Martino E, Ali M, Inglehearn CF. Matrix metalloproteinases in keratoconus - Too much of a good thing? Exp Eye Res 2019; 182:137-143. [PMID: 30910610 DOI: 10.1016/j.exer.2019.03.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 02/27/2019] [Accepted: 03/19/2019] [Indexed: 12/17/2022]
Abstract
Keratoconus (KC) is a progressive, early onset, and often bilateral eye condition, in which the cornea gradually weakens and bulges out, and in advanced cases may eventually become cone-shaped. The available evidence suggests that it is a multifactorial disease with environmental and genetic contributions. Matrix Metalloproteinases (MMPs) are a family of 24 zinc-dependent proteases with the ability to degrade collagen and other extracellular matrix (ECM) proteins, which are important components of the cornea. During the past two decades a growing body of literature has accumulated suggesting a link between MMPs and keratoconus. This article aims to summarize the current knowledge on the role of MMPs in the pathogenesis of KC. MMP-driven ECM remodelling is thought to be a necessary step for cornea healing, but a fine balance in the expression of MMPs is essential in maintaining the integrity and transparency of the cornea and for its correct healing, and an imbalance in this tightly regulated process may, in the long term, result in the progressive weakening of the cornea. There is extensive evidence that MMPs are upregulated in the corneal tissue and tears of KC patients, implicating dysregulated proteolysis in KC, with an increase in the level of some MMPs, particularly MMP-1 and MMP-9, confirmed in multiple independent studies. There is also evidence for a causative link between inflammation, which could result from the mechanical trauma due to contact lens wearing or/and eye rubbing, and the increased MMPs production observed in KC. However, the precise role of each MMP in the cornea is still unclear and the mechanisms causing their upregulation are mostly undiscovered. Further studies are required to verify the functional role of specific MMPs in KC development and assess the genetic association between common MMPs variants and risk of KC. As MMPs inhibitors are in development, this information could potentially drive the discovery of new treatments for KC.
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Affiliation(s)
- Erica di Martino
- Division of Primary Care, Public Health and Palliative Care, Leeds Institute of Health Sciences, University of Leeds, Worsley Building, Clarendon Way, Leeds, LS2 9NL, United Kingdom
| | - Manir Ali
- Section of Ophthalmology and Neuroscience, Leeds Institute of Medical Research, University of Leeds, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, United Kingdom
| | - Chris F Inglehearn
- Section of Ophthalmology and Neuroscience, Leeds Institute of Medical Research, University of Leeds, Wellcome Trust Brenner Building, Beckett Street, Leeds, LS9 7TF, United Kingdom.
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20
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Epigenetically dysregulated genes and pathways implicated in the pathogenesis of non-syndromic high myopia. Sci Rep 2019; 9:4145. [PMID: 30858441 PMCID: PMC6411983 DOI: 10.1038/s41598-019-40299-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 11/30/2018] [Indexed: 12/20/2022] Open
Abstract
Myopia, commonly referred to as nearsightedness, is one of the most common causes of visual disability throughout the world. It affects more people worldwide than any other chronic visual impairment condition. Although the prevalence varies among various ethnic groups, the incidence of myopia is increasing in all populations across globe. Thus, it is considered a pressing public health problem. Both genetics and environment play a role in development of myopia. To elucidate the epigenetic mechanism(s) underlying the pathophysiology of high-myopia, we conducted methylation profiling in 18 cases and 18 matched controls (aged 4–12 years), using Illumina MethylationEPIC BeadChips array. The degree of myopia was variable among subjects, ranging from −6 to −15D. We identified 1541 hypermethylated CpGs, representing 1745 genes (2.0-fold or higher) (false discovery rate (FDR) p ≤ 0.05), multiple CpGs were p < 5 × 10−8 with a receiver operating characteristic area under the curve (ROC-AUC) ≥ 0.75 in high-myopia subjects compared to controls. Among these, 48 CpGs had excellent correlation (AUC ≥ 0.90). Herein, we present the first genome-wide DNA methylation analysis in a unique high-myopia cohort, showing extensive and discrete methylation changes relative to controls. The genes we identified hold significant potential as targets for novel therapeutic intervention either alone, or in combination.
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21
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Panahi Y, Azimi A, Naderi M, Jadidi K, Sahebkar A. An analytical enrichment-based review of structural genetic studies on keratoconus. J Cell Biochem 2018; 120:4748-4756. [PMID: 30260013 DOI: 10.1002/jcb.27764] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 09/06/2018] [Indexed: 12/19/2022]
Abstract
Keratoconus is a progressive bilateral corneal protrusion that leads to irregular astigmatism and impairment of vision. Keratoconus is an etiologically heterogeneous corneal dystrophy and both environmental and genetic factors play a role in its etiopathogenesis. In this analytical review, we have studied all the genes that are structurally associated with keratoconus and have tried to explain the function of each gene and its association with other eye disorders in a concise way. In addition, using gene set enrichment analysis, it was attempted to find the most important impaired metabolic pathways in keratoconus. Several genetic studies have been carried out on keratoconus and several genes have been identified as risk factors involved in the etiology of the disease. In the current study, 16 studies, including nine association studies, five genome-wide association studies, one linkage study, and one meta-analysis, were reviewed and based on the 19 genes found, enrichment was performed and the most important metabolic pathways involved in the disease were identified. The enrichment results indicated that the two pathways, interleukin 1 processing and assembly of collagen fibrils, are significantly associated with the disease. Obviously, the results of this study, in addition to providing information about the genes involved in the disease, can provide an integrated insight into the gene-based etiology of keratoconus and therapeutic opportunities thereof.
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Affiliation(s)
- Yunes Panahi
- Chemical Injuries Research Center, System Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Azimi
- Department of Ophthalmology, Poostchi Eye Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mostafa Naderi
- Chemical Injuries Research Center, System Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Khosrow Jadidi
- Chemical Injuries Research Center, System Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,Neurogenic inflammation Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
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Khaled ML, Bykhovskaya Y, Yablonski SER, Li H, Drewry MD, Aboobakar IF, Estes A, Gao XR, Stamer WD, Xu H, Allingham RR, Hauser MA, Rabinowitz YS, Liu Y. Differential Expression of Coding and Long Noncoding RNAs in Keratoconus-Affected Corneas. Invest Ophthalmol Vis Sci 2018; 59:2717-2728. [PMID: 29860458 PMCID: PMC5984031 DOI: 10.1167/iovs.18-24267] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 04/23/2018] [Indexed: 12/22/2022] Open
Abstract
Purpose Keratoconus (KC) is the most common corneal ectasia. We aimed to determine the differential expression of coding and long noncoding RNAs (lncRNAs) in human corneas affected with KC. Methods From the corneas of 10 KC patients and 8 non-KC healthy controls, 200 ng total RNA was used to prepare sequencing libraries with the SMARTer Stranded RNA-Seq kit after ribosomal RNA depletion, followed by paired-end 50-bp sequencing with Illumina Sequencer. Differential analysis was done using TopHat/Cufflinks with a gene file from Ensembl and a lncRNA file from NONCODE. Pathway analysis was performed using WebGestalt. Using the expression level of differentially expressed coding and noncoding RNAs in each sample, we correlated their expression levels in KC and controls separately and identified significantly different correlations in KC against controls followed by visualization using Cytoscape. Results Using |fold change| ≥ 2 and a false discovery rate ≤ 0.05, we identified 436 coding RNAs and 584 lncRNAs with differential expression in the KC-affected corneas. Pathway analysis indicated the enrichment of genes involved in extracellular matrix, protein binding, glycosaminoglycan binding, and cell migration. Our correlation analysis identified 296 pairs of significant KC-specific correlations containing 117 coding genes enriched in functions related to cell migration/motility, extracellular space, cytokine response, and cell adhesion. Our study highlighted the potential roles of several genes (CTGF, SFRP1, AQP5, lnc-WNT4-2:1, and lnc-ALDH3A2-2:1) and pathways (TGF-β, WNT signaling, and PI3K/AKT pathways) in KC pathogenesis. Conclusions Our RNA-Seq-based differential expression and correlation analyses have identified many potential KC contributing coding and noncoding RNAs.
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Affiliation(s)
- Mariam Lofty Khaled
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, Georgia, United States
| | - Yelena Bykhovskaya
- Regenerative Medicine Institute and Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Sarah E. R. Yablonski
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, Georgia, United States
- STAR Program, Augusta University, Augusta, Georgia, United States
| | - Hanzhou Li
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, Georgia, United States
| | - Michelle D. Drewry
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, Georgia, United States
| | - Inas F. Aboobakar
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - Amy Estes
- Department of Ophthalmology, Augusta University, Augusta, Georgia, United States
| | - X. Raymond Gao
- Department of Ophthalmology and Visual Science, University of Illinois at Chicago, Chicago, Illinois, United States
| | - W. Daniel Stamer
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - Hongyan Xu
- Department of Population Health Sciences, Augusta University, Augusta, Georgia, United States
| | - R. Rand Allingham
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
| | - Michael A. Hauser
- Department of Ophthalmology, Duke University Medical Center, Durham, North Carolina, United States
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States
| | - Yaron S. Rabinowitz
- Regenerative Medicine Institute and Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Yutao Liu
- Department of Cellular Biology and Anatomy, Augusta University, Augusta, Georgia, United States
- James and Jean Culver Vision Discovery Institute, Medical College of Georgia, Augusta University, Augusta, Georgia, United States
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, Georgia, United States
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