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Tevar A, Aroca-Aguilar JD, Bonet-Fernández JM, Atienzar-Aroca R, Campos-Mollo E, Méndez-Hernández C, Morales-Fernández L, Leal Palmer I, Coca-Prados M, Martinez-de-la-Casa JM, Garcia-Feijoo J, Escribano J. The Increased Burden of Rare Variants in Four Matrix Metalloproteinase-Related Genes in Childhood Glaucoma Suggests a Complex Genetic Inheritance of the Disease. Int J Mol Sci 2024; 25:5757. [PMID: 38891949 PMCID: PMC11171635 DOI: 10.3390/ijms25115757] [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: 03/13/2024] [Revised: 05/17/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024] Open
Abstract
Childhood glaucoma encompasses congenital and juvenile primary glaucoma, which are heterogeneous, uncommon, and irreversible optic neuropathies leading to visual impairment with a poorly understood genetic basis. Our goal was to identify gene variants associated with these glaucoma types by assessing the mutational burden in 76 matrix metalloproteinase-related genes. We studied 101 childhood glaucoma patients with no identified monogenic alterations using next-generation sequencing. Gene expression was assessed through immunohistochemistry. Functional analysis of selected gene variants was conducted in cultured cells and in zebrafish. Patients presented a higher proportion of rare variants in four metalloproteinase-related genes, including CPAMD8 and ADAMTSL4, compared to controls. ADAMTSL4 protein expression was observed in the anterior segment of both the adult human and zebrafish larvae's eye, including tissues associated with glaucoma. In HEK-293T cells, expression of four ADAMTSL4 variants identified in this study showed that two variants (p.Arg774Trp and p.Arg98Trp) accumulated intracellularly, inducing endoplasmic reticulum stress. Additionally, overexpressing these ADAMTSL4 variants in zebrafish embryos confirmed partial loss-of-function effects for p.Ser719Leu and p.Arg1083His. Double heterozygous functional suppression of adamtsl4 and cpamd8 zebrafish orthologs resulted in reduced volume of both the anterior eye chamber and lens within the chamber, supporting a genetic interaction between these genes. Our findings suggest that accumulation of partial functional defects in matrix metalloproteinase-related genes may contribute to increased susceptibility to early-onset glaucoma and provide further evidence supporting the notion of a complex genetic inheritance pattern underlying the disease.
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Affiliation(s)
- Angel Tevar
- Área de Genética, Facultad de Medicina de Albacete, Universidad de Castilla-La Mancha, 02006 Albacete, Spain; (A.T.); (J.-D.A.-A.); (J.-M.B.-F.); (R.A.-A.)
- Biomedicine Institute, Universidad de Castilla-La Mancha, 02006 Albacete, Spain
- Cooperative Research Network on Age-Related Ocular Pathology, Visual and Life Quality (OFTARED), Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.C.-M.); (C.M.-H.); (L.M.-F.); (J.-M.M.-d.-l.-C.); (J.G.-F.)
| | - José-Daniel Aroca-Aguilar
- Área de Genética, Facultad de Medicina de Albacete, Universidad de Castilla-La Mancha, 02006 Albacete, Spain; (A.T.); (J.-D.A.-A.); (J.-M.B.-F.); (R.A.-A.)
- Biomedicine Institute, Universidad de Castilla-La Mancha, 02006 Albacete, Spain
- Cooperative Research Network on Age-Related Ocular Pathology, Visual and Life Quality (OFTARED), Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.C.-M.); (C.M.-H.); (L.M.-F.); (J.-M.M.-d.-l.-C.); (J.G.-F.)
| | - Juan-Manuel Bonet-Fernández
- Área de Genética, Facultad de Medicina de Albacete, Universidad de Castilla-La Mancha, 02006 Albacete, Spain; (A.T.); (J.-D.A.-A.); (J.-M.B.-F.); (R.A.-A.)
- Biomedicine Institute, Universidad de Castilla-La Mancha, 02006 Albacete, Spain
- Cooperative Research Network on Age-Related Ocular Pathology, Visual and Life Quality (OFTARED), Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.C.-M.); (C.M.-H.); (L.M.-F.); (J.-M.M.-d.-l.-C.); (J.G.-F.)
| | - Raquel Atienzar-Aroca
- Área de Genética, Facultad de Medicina de Albacete, Universidad de Castilla-La Mancha, 02006 Albacete, Spain; (A.T.); (J.-D.A.-A.); (J.-M.B.-F.); (R.A.-A.)
- Biomedicine Institute, Universidad de Castilla-La Mancha, 02006 Albacete, Spain
- Cooperative Research Network on Age-Related Ocular Pathology, Visual and Life Quality (OFTARED), Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.C.-M.); (C.M.-H.); (L.M.-F.); (J.-M.M.-d.-l.-C.); (J.G.-F.)
| | - Ezequiel Campos-Mollo
- Cooperative Research Network on Age-Related Ocular Pathology, Visual and Life Quality (OFTARED), Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.C.-M.); (C.M.-H.); (L.M.-F.); (J.-M.M.-d.-l.-C.); (J.G.-F.)
- Servicio de Oftalmología, Hospital Virgen de los Lirios, 03804 Alcoy, Spain;
| | - Carmen Méndez-Hernández
- Cooperative Research Network on Age-Related Ocular Pathology, Visual and Life Quality (OFTARED), Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.C.-M.); (C.M.-H.); (L.M.-F.); (J.-M.M.-d.-l.-C.); (J.G.-F.)
- Servicio de Oftalmología, Hospital Clínico San Carlos, 28040 Madrid, Spain
- Instituto de Investigación Sanitaria del Hospital Clínico San Carlos, 28040 Madrid, Spain
- Instituto de Investigaciones Oftalmológicas Ramón Castroviejo, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Laura Morales-Fernández
- Cooperative Research Network on Age-Related Ocular Pathology, Visual and Life Quality (OFTARED), Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.C.-M.); (C.M.-H.); (L.M.-F.); (J.-M.M.-d.-l.-C.); (J.G.-F.)
- Servicio de Oftalmología, Hospital Clínico San Carlos, 28040 Madrid, Spain
- Instituto de Investigación Sanitaria del Hospital Clínico San Carlos, 28040 Madrid, Spain
- Instituto de Investigaciones Oftalmológicas Ramón Castroviejo, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Iñaki Leal Palmer
- Servicio de Oftalmología, Hospital Virgen de los Lirios, 03804 Alcoy, Spain;
| | - Miguel Coca-Prados
- Department of Ophthalmology and Visual Science, Yale University Medical School, New Haven, CT 06510, USA;
| | - Jose-Maria Martinez-de-la-Casa
- Cooperative Research Network on Age-Related Ocular Pathology, Visual and Life Quality (OFTARED), Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.C.-M.); (C.M.-H.); (L.M.-F.); (J.-M.M.-d.-l.-C.); (J.G.-F.)
- Servicio de Oftalmología, Hospital Clínico San Carlos, 28040 Madrid, Spain
- Instituto de Investigación Sanitaria del Hospital Clínico San Carlos, 28040 Madrid, Spain
- Instituto de Investigaciones Oftalmológicas Ramón Castroviejo, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Julian Garcia-Feijoo
- Cooperative Research Network on Age-Related Ocular Pathology, Visual and Life Quality (OFTARED), Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.C.-M.); (C.M.-H.); (L.M.-F.); (J.-M.M.-d.-l.-C.); (J.G.-F.)
- Servicio de Oftalmología, Hospital Clínico San Carlos, 28040 Madrid, Spain
- Instituto de Investigación Sanitaria del Hospital Clínico San Carlos, 28040 Madrid, Spain
- Instituto de Investigaciones Oftalmológicas Ramón Castroviejo, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Julio Escribano
- Área de Genética, Facultad de Medicina de Albacete, Universidad de Castilla-La Mancha, 02006 Albacete, Spain; (A.T.); (J.-D.A.-A.); (J.-M.B.-F.); (R.A.-A.)
- Biomedicine Institute, Universidad de Castilla-La Mancha, 02006 Albacete, Spain
- Cooperative Research Network on Age-Related Ocular Pathology, Visual and Life Quality (OFTARED), Instituto de Salud Carlos III, 28029 Madrid, Spain; (E.C.-M.); (C.M.-H.); (L.M.-F.); (J.-M.M.-d.-l.-C.); (J.G.-F.)
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2
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Al-Saei O, Malka S, Owen N, Aliyev E, Vempalli FR, Ocieczek P, Al-Khathlan B, Fakhro K, Moosajee M. Increasing the diagnostic yield of childhood glaucoma cases recruited into the 100,000 Genomes Project. BMC Genomics 2024; 25:484. [PMID: 38755526 PMCID: PMC11097485 DOI: 10.1186/s12864-024-10353-8] [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: 12/22/2023] [Accepted: 04/25/2024] [Indexed: 05/18/2024] Open
Abstract
Childhood glaucoma (CG) encompasses a heterogeneous group of genetic eye disorders that is responsible for approximately 5% of childhood blindness worldwide. Understanding the molecular aetiology is key to improving diagnosis, prognosis and unlocking the potential for optimising clinical management. In this study, we investigated 86 CG cases from 78 unrelated families of diverse ethnic backgrounds, recruited into the Genomics England 100,000 Genomes Project (GE100KGP) rare disease cohort, to improve the genetic diagnostic yield. Using the Genomics England/Genomic Medicine Centres (GE/GMC) diagnostic pipeline, 13 unrelated families were solved (13/78, 17%). Further interrogation using an expanded gene panel yielded a molecular diagnosis in 7 more unrelated families (7/78, 9%). This analysis effectively raises the total number of solved CG families in the GE100KGP to 26% (20/78 families). Twenty-five percent (5/20) of the solved families had primary congenital glaucoma (PCG), while 75% (15/20) had secondary CG; 53% of this group had non-acquired ocular anomalies (including iris hypoplasia, megalocornea, ectopia pupillae, retinal dystrophy, and refractive errors) and 47% had non-acquired systemic diseases such as cardiac abnormalities, hearing impairment, and developmental delay. CYP1B1 was the most frequently implicated gene, accounting for 55% (11/20) of the solved families. We identified two novel likely pathogenic variants in the TEK gene, in addition to one novel pathogenic copy number variant (CNV) in FOXC1. Variants that passed undetected in the GE100KGP diagnostic pipeline were likely due to limitations of the tiering process, the use of smaller gene panels during analysis, and the prioritisation of coding SNVs and indels over larger structural variants, CNVs, and non-coding variants.
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Affiliation(s)
- Omayma Al-Saei
- Institute of Ophthalmology, University College London, London, EC1V 9EL, UK
- Department of Human Genetics, Sidra Medicine, PO Box 26999, Doha, Qatar
| | - Samantha Malka
- Moorfields Eye Hospital NHS Foundation Trust, London, EC1V 2PD, UK
| | - Nicholas Owen
- Institute of Ophthalmology, University College London, London, EC1V 9EL, UK
| | - Elbay Aliyev
- Department of Human Genetics, Sidra Medicine, PO Box 26999, Doha, Qatar
| | | | - Paulina Ocieczek
- Moorfields Eye Hospital NHS Foundation Trust, London, EC1V 2PD, UK
| | | | - Khalid Fakhro
- Department of Human Genetics, Sidra Medicine, PO Box 26999, Doha, Qatar
| | - Mariya Moosajee
- Institute of Ophthalmology, University College London, London, EC1V 9EL, UK.
- Moorfields Eye Hospital NHS Foundation Trust, London, EC1V 2PD, UK.
- The Francis Crick Institute, London, NW1 1AT, UK.
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Carstens N, Goolam S, Hulley M, Brandenburg JT, Ramsay M, Williams SEI. Exome-based mutation screening in South African children with primary congenital glaucoma. Eye (Lond) 2023; 37:362-368. [PMID: 35094026 PMCID: PMC9873788 DOI: 10.1038/s41433-022-01941-7] [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: 03/24/2021] [Revised: 01/03/2022] [Accepted: 01/14/2022] [Indexed: 01/29/2023] Open
Abstract
OBJECTIVES To identify pathogenic variants in a cohort of 23 black South African children with sporadic primary congenital glaucoma (PCG) using an exome-based approach. METHODS Children with PCG were recruited from two Paediatric Ophthalmology Clinics in Johannesburg, South Africa. Whole exome sequencing was performed on genomic DNA. Of the 23 children, 19 were male and 19 had bilateral PCG. A variant prioritization strategy was employed whereby variants in known PCG genes (CYP1B1, LTBP2 and TEK) were evaluated first, followed by the identification of putative disease-causing variants in other genes related to eye diseases and phenotypes. RESULTS Validated pathogenic variants in the CYP1B1 gene (c.1169 G>A; p.Arg390His) and TEK gene (c.922 G>A; p.Gly308Arg) were identified in one child each. No LTBP2 mutations were identified in this cohort. In silico predictions identified potentially damaging rare variants in genes previously associated with eye development phenotypes or glaucoma in a further 12 children. CONCLUSIONS This study demonstrates the value of whole exome sequencing in identifying disease-causing variants in African children with PCG. It is the first report of a TEK disease-causing variant in an African PCG patient. Potential causative variants detected in PCG candidate genes warrant further investigation.
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Affiliation(s)
- Nadia Carstens
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Saadiah Goolam
- Division of Ophthalmology, Department of Neurosciences, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michaella Hulley
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jean-Tristan Brandenburg
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michele Ramsay
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Susan Eileen Isabella Williams
- Division of Ophthalmology, Department of Neurosciences, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
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Shen R, Li VSW, Wong MOM, Chan PPM. Pediatric Glaucoma-From Screening, Early Detection to Management. CHILDREN (BASEL, SWITZERLAND) 2023; 10:children10020181. [PMID: 36832310 PMCID: PMC9954748 DOI: 10.3390/children10020181] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/10/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023]
Abstract
Pediatric glaucoma (PG) covers a rare and heterogeneous group of diseases with variable causes and presentations. Delayed diagnosis of PG could lead to blindness, bringing emotional and psychological burdens to patients' caregivers. Recent genetic studies identified novel causative genes, which may provide new insight into the etiology of PG. More effective screening strategies could be beneficial for timely diagnosis and treatment. New findings on clinical characteristics and the latest examination instruments have provided additional evidence for diagnosing PG. In addition to IOP-lowering therapy, managing concomitant amblyopia and other associated ocular pathologies is essential to achieve a better visual outcome. Surgical treatment is usually required although medication is often used before surgery. These include angle surgeries, filtering surgeries, minimally invasive glaucoma surgeries, cyclophotocoagulation, and deep sclerectomy. Several advanced surgical therapies have been developed to increase success rates and decrease postoperative complications. Here, we review the classification and diagnosis, etiology, screening, clinical characteristics, examinations, and management of PG.
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Affiliation(s)
- Ruyue Shen
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Venice S. W. Li
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Eye Hospital, Kowloon, Hong Kong, China
| | - Mandy O. M. Wong
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Eye Hospital, Kowloon, Hong Kong, China
| | - Poemen P. M. Chan
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Hong Kong Eye Hospital, Kowloon, Hong Kong, China
- Lam Kin Chung. Jet King-Shing Ho Glaucoma Treatment and Research Centre, Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Department of Ophthalmology and Visual Sciences, The Prince of Wales Hospital, Hong Kong, China
- Correspondence: ; Tel.: +852-3943-5807
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5
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Zamani M, Sedighzadeh S, Seifi T, Negahdari S, Zeighami J, Sedaghat A, Shariati G, Galehdari H. Whole-exome sequencing deciphers the genetic profile of visual impairments in patients from Southwest Iran. Mol Genet Genomics 2022; 297:1289-1300. [PMID: 35754085 DOI: 10.1007/s00438-022-01917-y] [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: 09/04/2021] [Accepted: 05/27/2022] [Indexed: 10/17/2022]
Abstract
Genetic ocular diseases are heterogeneous disorders. Recent advances have led to a paradigm shift in the discovery of eye disease-associated genetic variants from linkage and genome-wide association studies to next-generation sequencing-based genome studies. The aim of the current study was to investigate the spectrum of possible vision impairment-related variants in 66 Iranian patients. Whole-exome sequencing (WES) technology followed by bioinformatics analysis, Sanger validation, and co-segregation study were done to find eye disease-causing variants in the patients with vision impairments from Southwest Iran. WES revealed disease-causing variants in 82% of the enrolled cases. WES of understudied cohorts presented an effective strategy for determining pathogenic variants in heterogeneous eye diseases and demonstrated the distribution of causative genetic mutations in Iranian patients. The present data could provide the potential to accelerate genetic screening and a reference for treatment modalities for patients with different types of eye disorders from Southwest Iran.
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Affiliation(s)
- Mina Zamani
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran.,Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran
| | - Sahar Sedighzadeh
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran.,Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran
| | - Tahereh Seifi
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran.,Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran
| | - Samira Negahdari
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran.,Legal Medicine Research Center, Legal Medicine Organization, Ahvaz, Iran
| | - Jawaher Zeighami
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran
| | - Alireza Sedaghat
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran.,Diabetes Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Gholamreza Shariati
- Narges Medical Genetics and Prenatal Diagnosis Laboratory, Ahvaz, Iran. .,Department of Medical Genetics, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Hamid Galehdari
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran.
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Animal Model Contributions to Primary Congenital Glaucoma. J Ophthalmol 2022; 2022:6955461. [PMID: 35663518 PMCID: PMC9162845 DOI: 10.1155/2022/6955461] [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: 01/29/2022] [Accepted: 05/12/2022] [Indexed: 11/17/2022] Open
Abstract
Primary congenital glaucoma (PCG) is an ocular disease characterized by congenital anterior segmental maldevelopment with progressive optic nerve degeneration. Certain genes, such as cytochrome P450 family 1 subfamily B member 1 and latent TGF-β-binding protein 2, are involved in the pathogenesis of PCG, but the exact pathogenic mechanism has not yet been fully elucidated. There is an urgent need to determine the etiology and pathophysiology of PCG and develop new therapeutic methods to stop disease progression. Animal models can simulate PCG and are essential to study the pathogenesis and treatment of PCG. Various animal species have been used in the study of PCG, including rabbits, rats, mice, cats, zebrafish, and quails. These models are formed spontaneously or by combining with genetic engineering technology. The focus of the present study is to review the characteristics and potential applications of animal models in PCG and provide new approaches to understand the mechanism and develop new treatment strategies for patients with PCG.
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Wang E, Guo Y, Gao S, Zhou Y, Liu B, Dissanayaka WL, Zheng Y, Zhou Q, Zhai J, Gao Z, Zhang B, Liu R, Zhang K. Long Non-Coding RNAs MALAT1 and NEAT1 in Non-syndromic Orofacial Clefts. Oral Dis 2022; 29:1668-1679. [PMID: 35255186 DOI: 10.1111/odi.14177] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 02/25/2022] [Accepted: 03/01/2022] [Indexed: 11/27/2022]
Abstract
Long non-coding RNAs (lncRNAs) are thought to play important roles in non-syndromic orofacial clefts (NSOFC). Clinical diagnosis was categorized as either non-syndromic cleft lip with or without cleft palate (NSCL/P), or non-syndromic cleft palate-only (NSCPO). Tissues excised from the trimmed wound edge were reserved as experimental samples; adjacent normal control was used as a positive control, and tissue from healthy individuals was used as a blank control. Target lncRNAs in the collected tissues were identified using microarrays and quantitative reverse transcription PCR (RT-qPCR). Immunohistochemical (IHC) staining and RT-qPCR were used to verify the target mRNAs. Pathway, gene ontology (GO) enrichment, and TargetScan predictions were employed to construct competing endogenous RNA networks (ceRNA networks) and explore their potential functions. RNA-Seq revealed 24 upregulated and 43 downregulated lncRNAs; MALAT1 and NEAT1 were screened and validated using RT-qPCR. Common NSOFC risk factors were positively correlated with MALAT1 and NEAT1 expression. Bioinformatics predicted four ceRNA networks; GO enrichment focused on their potential functions. RT-qPCR and IHC data were consistent with respect to expression levels of proteins and the mRNAs that encode them. As MALAT1 and NEAT1 are associated with the severity of NSOFC, they represent potential therapeutic targets and prognostic biomarkers.
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Affiliation(s)
- Errui Wang
- School of Stomatology, Lanzhou University, Lanzhou, 730000, China
| | - Yumeng Guo
- School of Stomatology, Lanzhou University, Lanzhou, 730000, China
| | - Shuting Gao
- Applied Oral Sciences & Community Dental Care, Faculty of Dentistry, The University of Hong Kong, Hong Kong, China
| | - Ying Zhou
- School of Stomatology, Lanzhou University, Lanzhou, 730000, China
| | - Bin Liu
- School of Stomatology, Lanzhou University, Lanzhou, 730000, China.,Gansu Province Key Lab of Maxillofacial Reconstruction and Intelligent Manufacturing, Lanzhou, 730000, China
| | - Waruna Lakmal Dissanayaka
- Applied Oral Sciences & Community Dental Care, Faculty of Dentistry, The University of Hong Kong, Hong Kong, China
| | - Yayuan Zheng
- School of Stomatology, Lanzhou University, Lanzhou, 730000, China
| | - Qiaozhen Zhou
- School of Stomatology, Lanzhou University, Lanzhou, 730000, China
| | - Junkai Zhai
- School of Stomatology, Lanzhou University, Lanzhou, 730000, China
| | - Zhengkun Gao
- School of Stomatology, Lanzhou University, Lanzhou, 730000, China
| | - Baoping Zhang
- School of Stomatology, Lanzhou University, Lanzhou, 730000, China.,Gansu Province Key Lab of Maxillofacial Reconstruction and Intelligent Manufacturing, Lanzhou, 730000, China.,Institute of Biomechanics and Medical Engineering, Lanzhou University, Key Laboratory of Mechanics on Disaster and Environment in Western China, Ministry of Education, Lanzhou University, Lanzhou, 730000, China
| | - Ruimin Liu
- Gansu Province Hospital, Department of Oral and Maxillofacial Surgery, Lanzhou, 730000, China
| | - Kailiang Zhang
- School of Stomatology, Lanzhou University, Lanzhou, 730000, China.,Gansu Province Key Lab of Maxillofacial Reconstruction and Intelligent Manufacturing, Lanzhou, 730000, China
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8
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Genetics in primary congenital glaucoma: Implications in disease management and counseling. Eur J Med Genet 2021; 65:104378. [PMID: 34748994 DOI: 10.1016/j.ejmg.2021.104378] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 06/10/2021] [Accepted: 11/02/2021] [Indexed: 11/21/2022]
Abstract
Primary congenital glaucoma is an important cause of visual impairment in children. It can develop both pre- and postnatally. Angle surgery is the first line treatment modality. If the disease remains untreated or if the diagnosis is delayed, it can lead to irreversible visual loss and blindness. The genetics of primary congenital glaucoma are complex and not yet entirely understood. At present multiple disease-causing genes have been identified. CYP1B1 is the most well known gene causing autosomal recessive congenital glaucoma. Other genes have been found to play a role through recessive, dominant or polygenic mechanisms. Here we provide an overview of the known genes and mechanisms described in patients with PCG. Furthermore, we provide a practical counseling and follow-up guideline for relatives of a proband.
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9
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Gupta V, Somarajan BI, Kaur G, Gupta S, Singh R, Pradhan D, Singh H, Kaur P, Sharma A, Chawla B, Pahuja A, Ramachandran R, Sharma A. Exome sequencing identifies procollagen-lysine 2-oxoglutarate 5-dioxygenase 2 mutations in primary congenital and juvenile glaucoma. Indian J Ophthalmol 2021; 69:2710-2716. [PMID: 34571620 PMCID: PMC8597539 DOI: 10.4103/ijo.ijo_1750_21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/10/2021] [Accepted: 08/23/2021] [Indexed: 01/11/2023] Open
Abstract
PURPOSE To report the association of procollagen-lysine 2-oxoglutarate 5-dioxygenase 2 (PLOD2) mutations with bilateral primary congenital glaucoma (PCG) in monozygotic twins and with nondominant juvenile-onset primary open-angle glaucoma (JOAG). METHODS We utilized family-based whole-exome sequencing to detect disease-causing mutations in a pair of monozygotic twins with de-novo PCG and compared its existence in 50 nonfamilial cases of JOAG and 30 healthy controls. To validate the identified mutations, direct Sanger sequencing was performed. For further evaluation of gene expression in the ocular tissues, we performed whole-mount in situ hybridization in zebrafish embryos. RESULTS We identified a novel missense mutation (c.1925A>G, p.Tyr642Cys) in the PLOD2 gene in the monozygotic twin pair with PCG and another missense mutation (c.1880G>A, p.Arg627Gln) in one JOAG patient. Both mutations identified were heterozygous. Neither the parents of the twins nor the parents of the JOAG patient harbored the mutation and it was probably a de-novo change. The zebrafish in situ hybridization revealed expression of the PLOD2 gene during embryogenesis of the eye. CONCLUSION We observed an association of PLOD2 mutations with PCG and with nonfamilial JOAG. This new gene needs to be further investigated for its role in pathways associated with glaucoma pathogenesis.
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Affiliation(s)
- Viney Gupta
- Dr Rajendra Prasad Centre for Ophthalmic Sciences, New Delhi, India
| | | | - Gagandeep Kaur
- Public Health Foundation of India (PHFI), New Delhi, India
| | - Shikha Gupta
- Dr Rajendra Prasad Centre for Ophthalmic Sciences, New Delhi, India
| | - Renu Singh
- Dr Rajendra Prasad Centre for Ophthalmic Sciences, New Delhi, India
| | - Dibyabhaba Pradhan
- Division of Biomedical Informatics, Indian Council of Medical Research, Mohali, Punjab, India
| | - Harpreet Singh
- Division of Biomedical Informatics, Indian Council of Medical Research, Mohali, Punjab, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, Mohali, Punjab, India
| | - Anshul Sharma
- Department of Anatomy, All India Institute of Medical Sciences, Mohali, Punjab, India
| | - Bindia Chawla
- Department of Biology, Indian Institute of Scientific and Educational Research (IISER), Mohali, Punjab, India
| | - Anisha Pahuja
- Department of Biology, Indian Institute of Scientific and Educational Research (IISER), Mohali, Punjab, India
| | - Rajesh Ramachandran
- Department of Biology, Indian Institute of Scientific and Educational Research (IISER), Mohali, Punjab, India
| | - Arundhati Sharma
- Department of Anatomy, All India Institute of Medical Sciences, Mohali, Punjab, India
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10
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Hong Y, Luo Y. Zebrafish Model in Ophthalmology to Study Disease Mechanism and Drug Discovery. Pharmaceuticals (Basel) 2021; 14:ph14080716. [PMID: 34451814 PMCID: PMC8400593 DOI: 10.3390/ph14080716] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/16/2021] [Accepted: 07/21/2021] [Indexed: 12/14/2022] Open
Abstract
Visual impairment and blindness are common and seriously affect people’s work and quality of life in the world. Therefore, the effective therapies for eye diseases are of high priority. Zebrafish (Danio rerio) is an alternative vertebrate model as a useful tool for the mechanism elucidation and drug discovery of various eye disorders, such as cataracts, glaucoma, diabetic retinopathy, age-related macular degeneration, photoreceptor degeneration, etc. The genetic and embryonic accessibility of zebrafish in combination with a behavioral assessment of visual function has made it a very popular model in ophthalmology. Zebrafish has also been widely used in ocular drug discovery, such as the screening of new anti-angiogenic compounds or neuroprotective drugs, and the oculotoxicity test. In this review, we summarized the applications of zebrafish as the models of eye disorders to study disease mechanism and investigate novel drug treatments.
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Affiliation(s)
| | - Yan Luo
- Correspondence: ; Tel.: +86-020-87335931
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11
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Alexandre-Moreno S, Bonet-Fernández JM, Atienzar-Aroca R, Aroca-Aguilar JD, Escribano J. Null cyp1b1 Activity in Zebrafish Leads to Variable Craniofacial Defects Associated with Altered Expression of Extracellular Matrix and Lipid Metabolism Genes. Int J Mol Sci 2021; 22:ijms22126430. [PMID: 34208498 PMCID: PMC8234340 DOI: 10.3390/ijms22126430] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/11/2021] [Accepted: 06/12/2021] [Indexed: 12/13/2022] Open
Abstract
Simple Summary CYP1B1 is a cytochrome P450 monooxygenase involved in oxidative metabolism of different endogenous lipids and drugs. The loss of function (LoF) of this gene underlies many cases of recessive primary congenital glaucoma (PCG), an infrequent disease and a common cause of infantile loss of vision in children. To the best of our knowledge, this is the first study to generate a cyp1b1 knockout zebrafish model. The zebrafish line did not exhibit glaucoma-related phenotypes; however, adult mutant zebrafish presented variable craniofacial alterations, including uni- or bilateral craniofacial alterations with incomplete penetrance and variable expressivity. Transcriptomic analyses of seven-dpf cyp1b1-KO zebrafish revealed differentially expressed genes related to extracellular matrix and cell adhesion, cell growth and proliferation, lipid metabolism and inflammation. Overall, this study provides evidence for the complexity of the phenotypes and molecular pathways associated with cyp1b1 LoF, as well as for the dysregulation of extracellular matrix gene expression as one of the mechanisms underlying cyp1b1 disruption-associated pathogenicity. Abstract CYP1B1 loss of function (LoF) is the main known genetic alteration present in recessive primary congenital glaucoma (PCG), an infrequent disease characterized by delayed embryonic development of the ocular iridocorneal angle; however, the underlying molecular mechanisms are poorly understood. To model CYP1B1 LoF underlying PCG, we developed a cyp1b1 knockout (KO) zebrafish line using CRISPR/Cas9 genome editing. This line carries the c.535_667del frameshift mutation that results in the 72% mRNA reduction with the residual mRNA predicted to produce an inactive truncated protein (p.(His179Glyfs*6)). Microphthalmia and jaw maldevelopment were observed in 23% of F0 somatic mosaic mutant larvae (144 hpf). These early phenotypes were not detected in cyp1b1-KO F3 larvae (144 hpf), but 27% of adult (four months) zebrafish exhibited uni- or bilateral craniofacial alterations, indicating the existence of incomplete penetrance and variable expressivity. These phenotypes increased to 86% in the adult offspring of inbred progenitors with craniofacial defects. No glaucoma-related phenotypes were observed in cyp1b1 mutants. Transcriptomic analyses of the offspring (seven dpf) of cyp1b1-KO progenitors with adult-onset craniofacial defects revealed functionally enriched differentially expressed genes related to extracellular matrix and cell adhesion, cell growth and proliferation, lipid metabolism (retinoids, steroids and fatty acids and oxidation–reduction processes that include several cytochrome P450 genes) and inflammation. In summary, this study shows the complexity of the phenotypes and molecular pathways associated with cyp1b1 LoF, with species dependency, and provides evidence for the dysregulation of extracellular matrix gene expression as one of the mechanisms underlying the pathogenicity associated with cyp1b1 disruption.
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Affiliation(s)
- Susana Alexandre-Moreno
- Área de Genética, Facultad de Medicina de Albacete, Instituto de Investigación en Discapacidades Neurológicas (IDINE), Universidad de Castilla-La Mancha, 02006 Albacete, Spain; (S.A.-M.); (J.-M.B.-F.); (R.A.-A.)
- Cooperative Research Network on Age-Related Ocular Pathology, Visual and Life Quality (OFTARED), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Juan-Manuel Bonet-Fernández
- Área de Genética, Facultad de Medicina de Albacete, Instituto de Investigación en Discapacidades Neurológicas (IDINE), Universidad de Castilla-La Mancha, 02006 Albacete, Spain; (S.A.-M.); (J.-M.B.-F.); (R.A.-A.)
- Cooperative Research Network on Age-Related Ocular Pathology, Visual and Life Quality (OFTARED), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Raquel Atienzar-Aroca
- Área de Genética, Facultad de Medicina de Albacete, Instituto de Investigación en Discapacidades Neurológicas (IDINE), Universidad de Castilla-La Mancha, 02006 Albacete, Spain; (S.A.-M.); (J.-M.B.-F.); (R.A.-A.)
- Cooperative Research Network on Age-Related Ocular Pathology, Visual and Life Quality (OFTARED), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - José-Daniel Aroca-Aguilar
- Área de Genética, Facultad de Medicina de Albacete, Instituto de Investigación en Discapacidades Neurológicas (IDINE), Universidad de Castilla-La Mancha, 02006 Albacete, Spain; (S.A.-M.); (J.-M.B.-F.); (R.A.-A.)
- Cooperative Research Network on Age-Related Ocular Pathology, Visual and Life Quality (OFTARED), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence: (J.-D.A.-A.); (J.E.)
| | - Julio Escribano
- Área de Genética, Facultad de Medicina de Albacete, Instituto de Investigación en Discapacidades Neurológicas (IDINE), Universidad de Castilla-La Mancha, 02006 Albacete, Spain; (S.A.-M.); (J.-M.B.-F.); (R.A.-A.)
- Cooperative Research Network on Age-Related Ocular Pathology, Visual and Life Quality (OFTARED), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence: (J.-D.A.-A.); (J.E.)
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12
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Identification of candidate genes and pathways in retinopathy of prematurity by whole exome sequencing of preterm infants enriched in phenotypic extremes. Sci Rep 2021; 11:4966. [PMID: 33654115 PMCID: PMC7925531 DOI: 10.1038/s41598-021-83552-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 02/01/2021] [Indexed: 01/05/2023] Open
Abstract
Retinopathy of prematurity (ROP) is a vasoproliferative retinal disease affecting premature infants. In addition to prematurity itself and oxygen treatment, genetic factors have been suggested to predispose to ROP. We aimed to identify potentially pathogenic genes and biological pathways associated with ROP by analyzing variants from whole exome sequencing (WES) data of premature infants. As part of a multicenter ROP cohort study, 100 non-Hispanic Caucasian preterm infants enriched in phenotypic extremes were subjected to WES. Gene-based testing was done on coding nonsynonymous variants. Genes showing enrichment of qualifying variants in severe ROP compared to mild or no ROP from gene-based tests with adjustment for gestational age and birth weight were selected for gene set enrichment analysis (GSEA). Mean BW of included infants with pre-plus, type-1 or type 2 ROP including aggressive posterior ROP (n = 58) and mild or no ROP (n = 42) were 744 g and 995 g, respectively. No single genes reached genome-wide significance that could account for a severe phenotype. GSEA identified two significantly associated pathways (smooth endoplasmic reticulum and vitamin C metabolism) after correction for multiple tests. WES of premature infants revealed potential pathways that may be important in the pathogenesis of ROP and in further genetic studies.
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13
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Knockout of myoc Provides Evidence for the Role of Myocilin in Zebrafish Sex Determination Associated with Wnt Signalling Downregulation. BIOLOGY 2021; 10:biology10020098. [PMID: 33573230 PMCID: PMC7912607 DOI: 10.3390/biology10020098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/16/2022]
Abstract
Myocilin is a secreted glycoprotein with a poorly understood biological function and it is mainly known as the first glaucoma gene. To explore the normal role of this protein in vivo we developed a myoc knockout (KO) zebrafish line using CRISPR/Cas9 genome editing. This line carries a homozygous variant (c.236_239delinsAAAGGGGAAGGGGA) that is predicted to result in a loss-of-function of the protein because of a premature termination codon p.(V75EfsX60) that resulted in a significant reduction of myoc mRNA levels. Immunohistochemistry showed the presence of myocilin in wild-type embryonic (96 h post-fertilization) anterior segment eye structures and caudal muscles. The protein was also detected in different adult ocular and non-ocular tissues. No gross macroscopic or microscopic alterations were identified in the KO zebrafish, but, remarkably, we observed absence of females among the adult KO animals and apoptosis in the immature juvenile gonad (28 dpf) of these animals, which is characteristic of male development. Transcriptomic analysis showed that adult KO males overexpressed key genes involved in male sex determination and presented differentially expressed Wnt signalling genes. These results show that myocilin is required for ovary differentiation in zebrafish and provides in vivo support for the role of myocilin as a Wnt signalling pathway modulator. In summary, this myoc KO zebrafish line can be useful to investigate the elusive function of this protein, and it provides evidence for the unexpected function of myocilin as a key factor in zebrafish sex determination.
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14
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Li M, Liu C, Xu X, Liu Y, Jiang Z, Li Y, Lv Y, Lu S, Hu C, Mao H. Grass carp (Ctenopharyngodon idella) GPATCH3 initiates IFN 1 expression via the activation of STING-IRF7 signal axis. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 112:103781. [PMID: 32645337 DOI: 10.1016/j.dci.2020.103781] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 06/24/2020] [Accepted: 06/24/2020] [Indexed: 06/11/2023]
Abstract
GPATCH3, a protein with G-patch domain, is known to participate in innate immune response and organ development in mammals. However, there are few reports on GPATCH3 in fish. Here the cDNA sequence of GPATCH3 was cloned from Ctenopharyngodon idella (CiGPATCH3, MN149902) and was determined its character. A cDNA sequence of CiGPATCH3 is 1646 bp and contains an ORF of 1221 bp translating a protein of 407 amino acids. Phylogenetic analysis uncovered that CiGPATCH3 possesses a relatively high degree of homology with Cyprinus carpio GPATCH3. The mRNA level of CiGPATCH3 was increased following the intracellular stimulation of poly (I:C) into CIK cells. In vivo, over-expression of CiGPATCH3 can significantly up-regulate IFN 1 and ISG15 expression at mRNA and protein levels. To investigate the molecular mechanism by which GPATCH3 initiates the innate immune response in fish, co-IP experiments were performed to analyze the substrates of CiGPATCH3. The results showed that CiGPATCH3 directly interacted with CiSTING, but not with CiIRF3, CiIRF7, CiTBK1 or CiIPS-1. As compared with the single transfection of CO cells with either CiGPATCH3 or CiSTING, the expression of IFN 1 was more significantly up-regulated in cells under treatment with dual transfection of CiGPATCH3 and CiSTING. Knockdown of CiGPATCH3 inhibited STING-mediated IFN 1 expression in fish cells. Over-expression of CiGPATCH3 and CiSTING facilitated the phosphorylation and cytoplasmic-to-nuclear translocation of CiIRF7. These results explicitly showed that CiGPATCH3 up-regulates IFN 1 and ISG15 expression via the activation of STING-IRF7 signal axis in vivo.
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Affiliation(s)
- Meifeng Li
- Department of Bioscience, School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Changxin Liu
- Department of Bioscience, School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Xiaowen Xu
- Department of Bioscience, School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Yapeng Liu
- Department of Bioscience, School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Zeying Jiang
- Department of Bioscience, School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Yinping Li
- Department of Bioscience, School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Yangfeng Lv
- Department of Bioscience, School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Shina Lu
- Department of Bioscience, School of Life Science, Nanchang University, Nanchang, 330031, China
| | - Chengyu Hu
- Department of Bioscience, School of Life Science, Nanchang University, Nanchang, 330031, China.
| | - Huiling Mao
- Department of Bioscience, School of Life Science, Nanchang University, Nanchang, 330031, China.
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15
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Qiao C, Jia H, Zhang H, Wang H, Liang J, Song J, Li L, Duan X, Cao K, Hu J. Coding Variants in HOOK2 and GTPBP3 May Contribute to Risk of Primary Angle Closure Glaucoma. DNA Cell Biol 2020; 39:949-957. [PMID: 32397755 DOI: 10.1089/dna.2019.5079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Primary angle closure glaucoma (PACG) is a major cause of blindness worldwide. This study proposed to screen candidate PACG-associated variants in Chinese Han people. Whole exome sequencing was applied to five confirmed PACG patients and two primary angle closure suspect individuals within a PACG-enriched Chinese Han family. A series of bioinformatics analyses were implemented to obtain high-risk single nucleotide variant (SNV) loci for PACG, which were subsequently used for linkage analysis for identifying linkage genome regions. In addition, MassARRAY SNV genotyping was applied to high-risk PACG loci as well as those within linkage regions in another independent cohort including 251 PACG and 251 normal samples to further screen high-confidence SNVs. A total of 27 loci in 19 genes remained after linkage analysis. The 19 genes were significantly enriched in biological processes tightly related to PACG, including retinol metabolism and salmonella infection. Two nonsynonymous SNV loci, rs897804 in exon15 of HOOK2 and rs3745193 in exon7 of GTPBP3, were recognized with higher variant frequency in PACG samples than that in control samples after association analysis of MassARRAY SNV genotyping data. This study sheds new light on the understanding of PACG incidence among Chinese Han people.
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Affiliation(s)
- Chunyan Qiao
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, P.R. China.,Beijing Ophthalmology and Visual Science Key Lab, Beijing, P.R. China
| | - Hongyan Jia
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, P.R. China.,Beijing Ophthalmology and Visual Science Key Lab, Beijing, P.R. China
| | - Hui Zhang
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, P.R. China.,Beijing Ophthalmology and Visual Science Key Lab, Beijing, P.R. China
| | - Hui Wang
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, P.R. China.,Beijing Ophthalmology and Visual Science Key Lab, Beijing, P.R. China
| | - Jing Liang
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, P.R. China.,Beijing Ophthalmology and Visual Science Key Lab, Beijing, P.R. China
| | - Jing Song
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, P.R. China.,Beijing Ophthalmology and Visual Science Key Lab, Beijing, P.R. China
| | - Liang Li
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, P.R. China.,Beijing Ophthalmology and Visual Science Key Lab, Beijing, P.R. China
| | - Xiaoming Duan
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, P.R. China.,Beijing Ophthalmology and Visual Science Key Lab, Beijing, P.R. China
| | - Kai Cao
- Beijing Ophthalmology and Visual Science Key Lab, Beijing, P.R. China.,Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, P.R. China
| | - Jianping Hu
- Beijing Ophthalmology and Visual Science Key Lab, Beijing, P.R. China.,Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, P.R. China
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16
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Role of GUCA1C in Primary Congenital Glaucoma and in the Retina: Functional Evaluation in Zebrafish. Genes (Basel) 2020; 11:genes11050550. [PMID: 32422965 PMCID: PMC7288452 DOI: 10.3390/genes11050550] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/06/2020] [Accepted: 05/12/2020] [Indexed: 12/29/2022] Open
Abstract
Primary congenital glaucoma (PCG) is a heterogeneous, inherited, and severe optical neuropathy caused by apoptotic degeneration of the retinal ganglion cell layer. Whole-exome sequencing analysis of one PCG family identified two affected siblings who carried a low-frequency homozygous nonsense GUCA1C variant (c.52G > T/p.Glu18Ter/rs143174402). This gene encodes GCAP3, a member of the guanylate cyclase activating protein family, involved in phototransduction and with a potential role in intraocular pressure regulation. Segregation analysis supported the notion that the variant was coinherited with the disease in an autosomal recessive fashion. GCAP3 was detected immunohistochemically in the adult human ocular ciliary epithelium and retina. To evaluate the ocular effect of GUCA1C loss-of-function, a guca1c knockout zebrafish line was generated by CRISPR/Cas9 genome editing. Immunohistochemistry demonstrated the presence of GCAP3 in the non-pigmented ciliary epithelium and retina of adult wild-type fishes. Knockout animals presented up-regulation of the glial fibrillary acidic protein in Müller cells and evidence of retinal ganglion cell apoptosis, indicating the existence of gliosis and glaucoma-like retinal damage. In summary, our data provide evidence for the role of GUCA1C as a candidate gene in PCG and offer new insights into the function of this gene in the ocular anterior segment and the retina.
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17
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CPAMD8 loss-of-function underlies non-dominant congenital glaucoma with variable anterior segment dysgenesis and abnormal extracellular matrix. Hum Genet 2020; 139:1209-1231. [PMID: 32274568 DOI: 10.1007/s00439-020-02164-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/03/2020] [Indexed: 01/08/2023]
Abstract
Abnormal development of the ocular anterior segment may lead to a spectrum of clinical phenotypes ranging from primary congenital glaucoma (PCG) to variable anterior segment dysgenesis (ASD). The main objective of this study was to identify the genetic alterations underlying recessive congenital glaucoma with ASD (CG-ASD). Next-generation DNA sequencing identified rare biallelic CPAMD8 variants in four patients with CG-ASD and in one case with PCG. CPAMD8 is a gene of unknown function and recently associated with ASD. Bioinformatic and in vitro functional evaluation of the variants using quantitative reverse transcription PCR and minigene analysis supported a loss-of-function pathogenic mechanism. Optical and electron microscopy of the trabeculectomy specimen from one of the CG-ASD cases revealed an abnormal anterior chamber angle, with altered extracellular matrix, and apoptotic trabecular meshwork cells. The CPAMD8 protein was immunodetected in adult human ocular fluids and anterior segment tissues involved in glaucoma and ASD (i.e., aqueous humor, non-pigmented ciliary epithelium, and iris muscles), as well as in periocular mesenchyme-like cells of zebrafish embryos. CRISPR/Cas9 disruption of this gene in F0 zebrafish embryos (96 hpf) resulted in varying degrees of gross developmental abnormalities, including microphthalmia, pharyngeal maldevelopment, and pericardial and periocular edemas. Optical and electron microscopy examination of these embryos showed iridocorneal angle hypoplasia (characterized by altered iris stroma cells, reduced anterior chamber, and collagen disorganized corneal stroma extracellular matrix), recapitulating some patients' features. Our data support the notion that CPAMD8 loss-of-function underlies a spectrum of recessive CG-ASD phenotypes associated with extracellular matrix disorganization and provide new insights into the normal and disease roles of this gene.
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18
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Dapas M, Sisk R, Legro RS, Urbanek M, Dunaif A, Hayes MG. Family-Based Quantitative Trait Meta-Analysis Implicates Rare Noncoding Variants in DENND1A in Polycystic Ovary Syndrome. J Clin Endocrinol Metab 2019; 104:3835-3850. [PMID: 31038695 PMCID: PMC6660913 DOI: 10.1210/jc.2018-02496] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 04/17/2019] [Indexed: 02/07/2023]
Abstract
CONTEXT Polycystic ovary syndrome (PCOS) is among the most common endocrine disorders of premenopausal women, affecting 5% to15% of this population depending on the diagnostic criteria applied. It is characterized by hyperandrogenism, ovulatory dysfunction, and polycystic ovarian morphology. PCOS is highly heritable, but only a small proportion of this heritability can be accounted for by the common genetic susceptibility variants identified to date. OBJECTIVE The objective of this study was to test whether rare genetic variants contribute to PCOS pathogenesis. DESIGN, PATIENTS, AND METHODS We performed whole-genome sequencing on DNA from 261 individuals from 62 families with one or more daughters with PCOS. We tested for associations of rare variants with PCOS and its concomitant hormonal traits using a quantitative trait meta-analysis. RESULTS We found rare variants in DENND1A (P = 5.31 × 10-5, adjusted P = 0.039) that were significantly associated with reproductive and metabolic traits in PCOS families. CONCLUSIONS Common variants in DENND1A have previously been associated with PCOS diagnosis in genome-wide association studies. Subsequent studies indicated that DENND1A is an important regulator of human ovarian androgen biosynthesis. Our findings provide additional evidence that DENND1A plays a central role in PCOS and suggest that rare noncoding variants contribute to disease pathogenesis.
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Affiliation(s)
- Matthew Dapas
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Ryan Sisk
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Richard S Legro
- Department of Obstetrics and Gynecology, Penn State College of Medicine, Hershey, Pennsylvania
| | - Margrit Urbanek
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Center for Reproductive Science, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Andrea Dunaif
- Division of Endocrinology, Diabetes, and Bone Disease, Icahn School of Medicine at Mount Sinai, New York, New York
| | - M Geoffrey Hayes
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Department of Anthropology, Northwestern University, Evanston, Illinois
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19
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Medina-Trillo C, Aroca-Aguilar JD, Ferre-Fernández JJ, Alexandre-Moreno S, Morales L, Méndez-Hernández CD, García-Feijoo J, Escribano J. Role of FOXC2 and PITX2 rare variants associated with mild functional alterations as modifier factors in congenital glaucoma. PLoS One 2019; 14:e0211029. [PMID: 30657791 PMCID: PMC6338360 DOI: 10.1371/journal.pone.0211029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 01/07/2019] [Indexed: 11/19/2022] Open
Abstract
Congenital glaucoma (CG) is a severe and inherited childhood optical neuropathy that leads to irreversible visual loss and blindness in children. CG pathogenesis remains largely unexplained in most patients. Herein we have extended our previous studies to evaluate the role of FOXC2 and PITX2 variants in CG. Variants of the proximal promoter and transcribed sequence of these two genes were analyzed by Sanger sequencing in a cohort of 133 CG families. To investigate possible oligogenic inheritance involving FOXC2 or PITX2 and CYP1B1, we also analyzed FOXC2 and PITX2 variants in a group of 25 CG cases who were known to carry CYP1B1 glaucoma-associated genotypes. The functional effect of three identified variants was assessed by transactivation luciferase reporter assays, protein stability and subcellular localization analyses. We found eight probands (6.0%) who carried four rare FOXC2 variants in the heterozygous state. In addition, we found an elevated frequency (8%) of heterozygous and rare PITX2 variants in the group of CG cases who were known to carry CYP1B1 glaucoma-associated genotypes, and one of these PITX2 variants arose de novo. To the best of our knowledge, two of the identified variants (FOXC2: c.1183C>A, p.(H395N); and PITX2: c.535C>A, p.(P179T)) have not been previously identified. Examination of the genotype-phenotype correlation in this group suggests that the presence of the infrequent PITX2 variants increase the severity of the phenotype. Transactivation reporter analyses showed partial functional alteration of three identified amino acid substitutions (FOXC2: p.(C498R) and p.(H395N); PITX2: p.(P179T)). In summary, the increased frequency in PCG patients of rare FOXC2 and PITX2 variants with mild functional alterations, suggests they play a role as putative modifier factors in this disease further supporting that CG is not a simple monogenic disease and provides novel insights into the complex pathological mechanisms that underlie CG.
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Affiliation(s)
- Cristina Medina-Trillo
- Área de Genética, Facultad de Medicina, Universidad de Castilla-La Mancha, Albacete, SPAIN
- Instituto de Investigación en Discapacidades Neurológicas (IDINE), Universidad de Castilla-La Mancha, Albacete, SPAIN
- Cooperative Research Network on Prevention, Early Detection and Treatment of Prevalent Degenerative and Chronic Ocular Pathology (OftaRed), Instituto de Salud Carlos III, Madrid, SPAIN
| | - José-Daniel Aroca-Aguilar
- Área de Genética, Facultad de Medicina, Universidad de Castilla-La Mancha, Albacete, SPAIN
- Instituto de Investigación en Discapacidades Neurológicas (IDINE), Universidad de Castilla-La Mancha, Albacete, SPAIN
- Cooperative Research Network on Prevention, Early Detection and Treatment of Prevalent Degenerative and Chronic Ocular Pathology (OftaRed), Instituto de Salud Carlos III, Madrid, SPAIN
| | - Jesús-José Ferre-Fernández
- Área de Genética, Facultad de Medicina, Universidad de Castilla-La Mancha, Albacete, SPAIN
- Instituto de Investigación en Discapacidades Neurológicas (IDINE), Universidad de Castilla-La Mancha, Albacete, SPAIN
- Cooperative Research Network on Prevention, Early Detection and Treatment of Prevalent Degenerative and Chronic Ocular Pathology (OftaRed), Instituto de Salud Carlos III, Madrid, SPAIN
| | - Susana Alexandre-Moreno
- Área de Genética, Facultad de Medicina, Universidad de Castilla-La Mancha, Albacete, SPAIN
- Instituto de Investigación en Discapacidades Neurológicas (IDINE), Universidad de Castilla-La Mancha, Albacete, SPAIN
- Cooperative Research Network on Prevention, Early Detection and Treatment of Prevalent Degenerative and Chronic Ocular Pathology (OftaRed), Instituto de Salud Carlos III, Madrid, SPAIN
| | - Laura Morales
- Cooperative Research Network on Prevention, Early Detection and Treatment of Prevalent Degenerative and Chronic Ocular Pathology (OftaRed), Instituto de Salud Carlos III, Madrid, SPAIN
- Servicio de Oftalmología, Hospital San Carlos, Madrid, SPAIN
- Instituto de Investigación Sanitaria del Hospital Clínico San Carlos, Madrid, SPAIN
| | - Carmen-Dora Méndez-Hernández
- Cooperative Research Network on Prevention, Early Detection and Treatment of Prevalent Degenerative and Chronic Ocular Pathology (OftaRed), Instituto de Salud Carlos III, Madrid, SPAIN
- Servicio de Oftalmología, Hospital San Carlos, Madrid, SPAIN
- Instituto de Investigación Sanitaria del Hospital Clínico San Carlos, Madrid, SPAIN
| | - Julián García-Feijoo
- Cooperative Research Network on Prevention, Early Detection and Treatment of Prevalent Degenerative and Chronic Ocular Pathology (OftaRed), Instituto de Salud Carlos III, Madrid, SPAIN
- Servicio de Oftalmología, Hospital San Carlos, Madrid, SPAIN
- Instituto de Investigación Sanitaria del Hospital Clínico San Carlos, Madrid, SPAIN
| | - Julio Escribano
- Área de Genética, Facultad de Medicina, Universidad de Castilla-La Mancha, Albacete, SPAIN
- Instituto de Investigación en Discapacidades Neurológicas (IDINE), Universidad de Castilla-La Mancha, Albacete, SPAIN
- Cooperative Research Network on Prevention, Early Detection and Treatment of Prevalent Degenerative and Chronic Ocular Pathology (OftaRed), Instituto de Salud Carlos III, Madrid, SPAIN
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Gupta S, Chatterjee S, Mukherjee A, Mutsuddi M. Whole exome sequencing: Uncovering causal genetic variants for ocular diseases. Exp Eye Res 2017; 164:139-150. [PMID: 28844620 DOI: 10.1016/j.exer.2017.08.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 08/22/2017] [Accepted: 08/22/2017] [Indexed: 01/23/2023]
Abstract
Identification of causal genetic defects for human diseases took a significant leap when the first generation DNA sequencing technologies enabled biologists extract sequence-based genetic information from living beings. However, these sequencing methods had unavoidable constraints of throughput, scalability, rapidity, and resolution. In this direction, next-generation sequencing (NGS) since the time of its advent has revolutionized the process of gene discovery for both monogenic and multifactorial genetic diseases. Among several variations of NGS, whole exome sequencing (WES) has emerged as a smart strategy that enables identification of disease causing variants present within the coding region of the human genome. The current review focuses primarily on the application of WES in identification of causal variants for ocular diseases. WES has successfully revealed pathogenic variants in a variety of ocular diseases such as retinal degenerations, refractive errors, lens diseases, corneal dystrophies, and developmental ocular defects. It has demonstrated immense potential for molecular diagnosis of genetic ocular diseases. WES has been extensively used in Mendelian and complex cases, familial and sporadic cases, simplex and multiplex cases, and syndromic and non-syndromic cases of ocular diseases. Although many such ocular diseases have been investigated using WES, reports indicate that it has been employed overwhelmingly for heterogeneous retinal degenerations. WES, within a short period of time, has proved to be a cost-effective and promising approach for understanding the genetic basis of ocular diseases.
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Affiliation(s)
- Shashank Gupta
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Souradip Chatterjee
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Ashim Mukherjee
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Mousumi Mutsuddi
- Department of Molecular and Human Genetics, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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