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Akbar W, Ullah A, Haider N, Suleman S, Khan FU, Shah AA, Sikandar MA, Basit S, Ahmad W. Identification of novel homozygous variants in FOXE3 and AP4M1 underlying congenital syndromic anophthalmia and microphthalmia. J Gene Med 2024; 26:e3601. [PMID: 37758467 DOI: 10.1002/jgm.3601] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/14/2023] [Accepted: 09/13/2023] [Indexed: 10/03/2023] Open
Abstract
BACKGROUND Anophthalmia and microphthalmia are severe developmental ocular disorders that affect the size of the ocular globe and can be unilateral or bilateral. The disease is found in syndromic as well as non-syndromic forms. It is genetically caused by chromosomal aberrations, copy number variations and single gene mutations, along with non-genetic factors such as viral infections, deficiency of vitamin A and an exposure to alcohol or drugs during pregnancy. To date, more than 30 genes having different modes of inheritance patterns are identified as causing anophthalmia and microphthalmia. METHODS In the present study, a clinical and genetic analysis was performed of six patients with anophthalmia and microphthalmia and/or additional phenotypes of intellectual disability, developmental delay and cerebral palsy from a large consanguineous Pakistani family. Whole exome sequencing followed by data analysis for variants prioritization and validation through Sanger sequencing was performed to identify the disease causing variant(s). American College of Medical Genetics and Genomics (ACMG) guidelines were applied to classify clinical interpretation of the prioritized variants. RESULTS Clinical investigations revealed that the affected individuals are afflicted with anophthalmia. Three of the patients showed additional phenotype of intellectual disability, developmental delays and other neurological symptoms. Whole exome sequencing of the DNA samples of the affected members in the family identified a novel homozygous stop gain mutation (NM_012186: c.106G>T: p.Glu36*) in Forkhead Box E3 (FOXE3) gene shared by all affected individuals. Moreover, patients segregating additional phenotypes of spastic paraplegia, intellectual disability, hearing loss and microcephaly showed an additional homozygous sequence variant (NM_004722: c.953G>A: p.Arg318Gln) in AP4M1. Sanger sequencing validated the correct segregation of the identified variants in the affected family. ACMG guidelines predicted the variants to be pathogenic. CONCLUSIONS We have investigated first case of syndromic anophthalmia caused by variants in the FOXE3 and AP4M1. The present findings are helpful for understanding pathological role of the mutations of the genes in syndromic forms of anophthalmia. Furthermore, the study signifies searching for the identification of second variant in families with patients exhibiting variable phenotypes. In addition, the findings will help clinical geneticists, genetic counselors and the affected family with respect to prenatal testing, family planning and genetic counseling.
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Affiliation(s)
- Warda Akbar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Asmat Ullah
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Nighat Haider
- Shaheed Zulfiqar Ali Bhutto Medical University, Department of Pediatrics, Pakistan Institute of Medical Sciences, Islamabad, Pakistan
| | - Sufyan Suleman
- Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Fati Ullah Khan
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Abid Ali Shah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | | | - Sulman Basit
- College of Medicine, Taibah University, Medina, Saudi Arabia
- Center for Genetics and Inherited Diseases, Taibah University, Medina, Saudi Arabia
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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Kuang L, Zhang M, Wang T, Huang T, Li J, Gan R, Yu M, Cao W, Yan X. The molecular genetics of anterior segment dysgenesis. Exp Eye Res 2023; 234:109603. [PMID: 37495069 DOI: 10.1016/j.exer.2023.109603] [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: 01/19/2023] [Revised: 07/19/2023] [Accepted: 07/22/2023] [Indexed: 07/28/2023]
Abstract
Anterior segment dysgenesis is a severe developmental eye disorder that leads to blindness in children. The exact mechanisms underlying this condition remain elusive. Recently, an increasing amount of studies have focused on genes and signal transduction pathways that affect anterior segment dysgenesis;these factors include transcription factors, developmental regulators, extracellular matrix genes, membrane-related proteins, cytoskeleton proteins and other associated genes. To date, dozens of gene variants have been found to cause anterior segment dysgenesis. However, there is still a lack of effective treatments. With a broader and deeper understanding of the molecular mechanisms underlying anterior segment development in the future, gene editing technology and stem cell technology may be new treatments for anterior segment dysgenesis. Further studies on the mechanisms of how different genes influence the onset and progression of anterior segment dysgenesis are still needed.
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Affiliation(s)
- Longhao Kuang
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, 518040, China
| | - Min Zhang
- School of Medicine, Anhui University of Science and Technology, Huainan, 232000, China
| | - Ting Wang
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, 518040, China
| | - Tao Huang
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, 518040, China
| | - Jin Li
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, 518040, China
| | - Run Gan
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, 518040, China
| | - Mingyu Yu
- Department of the Second Clinical Medical College, Jinan University (Shenzhen Eye Hospital), Shenzhen, 518020, China
| | - Wenchao Cao
- Department of the Second Clinical Medical College, Jinan University (Shenzhen Eye Hospital), Shenzhen, 518020, China
| | - Xiaohe Yan
- Shenzhen Eye Hospital, Jinan University, Shenzhen Eye Institute, Shenzhen, 518040, China.
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3
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Liu Z, Huang S, Zheng Y, Zhou T, Hu L, Xiong L, Li DWC, Liu Y. The lens epithelium as a major determinant in the development, maintenance, and regeneration of the crystalline lens. Prog Retin Eye Res 2023; 92:101112. [PMID: 36055924 DOI: 10.1016/j.preteyeres.2022.101112] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 07/28/2022] [Accepted: 08/02/2022] [Indexed: 02/01/2023]
Abstract
The crystalline lens is a transparent and refractive biconvex structure formed by lens epithelial cells (LECs) and lens fibers. Lens opacity, also known as cataracts, is the leading cause of blindness in the world. LECs are the principal cells of lens throughout human life, exhibiting different physiological properties and functions. During the embryonic stage, LECs proliferate and differentiate into lens fibers, which form the crystalline lens. Genetics and environment are vital factors that influence normal lens development. During maturation, LECs help maintain lens homeostasis through material transport, synthesis and metabolism as well as mitosis and proliferation. If disturbed, this will result in loss of lens transparency. After cataract surgery, the repair potential of LECs is activated and the structure and transparency of the regenerative tissue depends on postoperative microenvironment. This review summarizes recent research advances on the role of LECs in lens development, homeostasis, and regeneration, with a particular focus on the role of cholesterol synthesis (eg., lanosterol synthase) in lens development and homeostasis maintenance, and how the regenerative potential of LECs can be harnessed to develop surgical strategies and improve the outcomes of cataract surgery (Fig. 1). These new insights suggest that LECs are a major determinant of the physiological and pathological state of the lens. Further studies on their molecular biology will offer possibility to explore new approaches for cataract prevention and treatment.
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Affiliation(s)
- Zhenzhen Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Shan Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Yingfeng Zheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Tian Zhou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Leyi Hu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Lang Xiong
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - David Wan-Cheng Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China
| | - Yizhi Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, 510060, China; Research Unit of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, Beijing, 100085, China.
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4
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Wang X, Fan W, Xu Z, Zhang Q, Li N, Li R, Wang G, He S, Li W, Liao D, Zhang Z, Shu N, Huang J, Zhao C, Hou S. SOX2-positive retinal stem cells are identified in adult human pars plicata by single-cell transcriptomic analyses. MedComm (Beijing) 2022; 4:e198. [PMID: 36582303 PMCID: PMC9790047 DOI: 10.1002/mco2.198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 12/26/2022] Open
Abstract
Stem cell therapy is a promising strategy to rescue visual impairment caused by retinal degeneration. Previous studies have proposed controversial theories about whether in situ retinal stem cells (RSCs) are present in adult human eye tissue. Single-cell RNA sequencing (scRNA-seq) has emerged as one of the most powerful tools to reveal the heterogeneity of tissue cells. By using scRNA-seq, we explored the cell heterogeneity of different subregions of adult human eyes, including pars plicata, pars plana, retinal pigment epithelium (RPE), iris, and neural retina (NR). We identified one subpopulation expressing SRY-box transcription factor 2 (SOX2) as RSCs, which were present in the pars plicata of the adult human eye. Further analysis showed the identified subpopulation of RSCs expressed specific markers aquaporin 1 (AQP1) and tetraspanin 12 (TSPAN12). We, therefore, isolated this subpopulation using these two markers by flow sorting and found that the isolated RSCs could proliferate and differentiate into some retinal cell types, including photoreceptors, neurons, RPE cells, microglia, astrocytes, horizontal cells, bipolar cells, and ganglion cells; whereas, AQP1- TSPAN12- cells did not have this differentiation potential. In conclusion, our results showed that SOX2-positive RSCs are present in the pars plicata and may be valuable for treating human retinal diseases due to their proliferation and differentiation potential.
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Affiliation(s)
- Xiaotang Wang
- The First Affiliated Hospital of Chongqing Medical UniversityChongqingChina,Chongqing Key Laboratory of OphthalmologyChongqingChina,Chongqing Eye InstituteChongqingChina,Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular DiseasesChongqingChina
| | - Wei Fan
- The First Affiliated Hospital of Chongqing Medical UniversityChongqingChina,Chongqing Key Laboratory of OphthalmologyChongqingChina,Chongqing Eye InstituteChongqingChina,Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular DiseasesChongqingChina
| | - Zongren Xu
- The First Affiliated Hospital of Chongqing Medical UniversityChongqingChina,Chongqing Key Laboratory of OphthalmologyChongqingChina,Chongqing Eye InstituteChongqingChina,Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular DiseasesChongqingChina
| | - Qi Zhang
- The First Affiliated Hospital of Chongqing Medical UniversityChongqingChina,Chongqing Key Laboratory of OphthalmologyChongqingChina,Chongqing Eye InstituteChongqingChina,Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular DiseasesChongqingChina
| | - Na Li
- Department of Biochemistry and Molecular BiologyCollege of Basic MedicineChongqing Medical UniversityChongqingChina
| | - Ruonan Li
- The First Affiliated Hospital of Chongqing Medical UniversityChongqingChina,Chongqing Key Laboratory of OphthalmologyChongqingChina,Chongqing Eye InstituteChongqingChina,Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular DiseasesChongqingChina
| | - Guoqing Wang
- The First Affiliated Hospital of Chongqing Medical UniversityChongqingChina,Chongqing Key Laboratory of OphthalmologyChongqingChina,Chongqing Eye InstituteChongqingChina,Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular DiseasesChongqingChina
| | - Siyuan He
- The First Affiliated Hospital of Chongqing Medical UniversityChongqingChina,Chongqing Key Laboratory of OphthalmologyChongqingChina,Chongqing Eye InstituteChongqingChina,Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular DiseasesChongqingChina
| | - Wanqian Li
- The First Affiliated Hospital of Chongqing Medical UniversityChongqingChina,Chongqing Key Laboratory of OphthalmologyChongqingChina,Chongqing Eye InstituteChongqingChina,Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular DiseasesChongqingChina
| | - Dan Liao
- The First Affiliated Hospital of Chongqing Medical UniversityChongqingChina,Chongqing Key Laboratory of OphthalmologyChongqingChina,Chongqing Eye InstituteChongqingChina,Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular DiseasesChongqingChina
| | - Zhi Zhang
- The First Affiliated Hospital of Chongqing Medical UniversityChongqingChina,Chongqing Key Laboratory of OphthalmologyChongqingChina,Chongqing Eye InstituteChongqingChina,Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular DiseasesChongqingChina
| | - Nan Shu
- The First Affiliated Hospital of Chongqing Medical UniversityChongqingChina,Chongqing Key Laboratory of OphthalmologyChongqingChina,Chongqing Eye InstituteChongqingChina,Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular DiseasesChongqingChina
| | - Jiaxing Huang
- The First Affiliated Hospital of Chongqing Medical UniversityChongqingChina,Chongqing Key Laboratory of OphthalmologyChongqingChina,Chongqing Eye InstituteChongqingChina,Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular DiseasesChongqingChina
| | - Chenyang Zhao
- The First Affiliated Hospital of Chongqing Medical UniversityChongqingChina,Chongqing Key Laboratory of OphthalmologyChongqingChina,Chongqing Eye InstituteChongqingChina,Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular DiseasesChongqingChina
| | - Shengping Hou
- The First Affiliated Hospital of Chongqing Medical UniversityChongqingChina,Chongqing Key Laboratory of OphthalmologyChongqingChina,Chongqing Eye InstituteChongqingChina,Chongqing Branch (Municipality Division) of National Clinical Research Center for Ocular DiseasesChongqingChina
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5
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Multi-Faceted Roles of DNAJB Protein in Cancer Metastasis and Clinical Implications. Int J Mol Sci 2022; 23:ijms232314970. [PMID: 36499297 PMCID: PMC9737691 DOI: 10.3390/ijms232314970] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/28/2022] [Accepted: 11/28/2022] [Indexed: 12/02/2022] Open
Abstract
Heat shock proteins (HSPs) are highly conserved molecular chaperones with diverse cellular activities, including protein folding, assembly or disassembly of protein complexes, and maturation process under diverse stress conditions. HSPs also play essential roles in tumorigenesis, metastasis, and therapeutic resistance across cancers. Among them, HSP40s are widely accepted as regulators of HSP70/HSP90 chaperones and an accumulating number of biological functions as molecular chaperones dependent or independent of either of these chaperones. Despite large numbers of HSP40s, little is known about their physiologic roles, specifically in cancer progression. This article summarizes the multi-faceted role of DNAJB proteins as one subclass of the HSP40 family in cancer development and metastasis. Regulation and deregulation of DNAJB proteins at transcriptional, post-transcriptional, and post-translational levels contribute to tumor progression, particularly cancer metastasis. Furthermore, understanding differences in function and regulating mechanism between DNAJB proteins offers a new perspective on tumorigenesis and metastasis to improve therapeutic opportunities for malignant diseases.
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6
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A Novel Mutation in the FYCO1 Gene Causing Congenital Cataract: Case Study of a Chinese Family. DISEASE MARKERS 2022; 2022:5838104. [PMID: 36061348 PMCID: PMC9439885 DOI: 10.1155/2022/5838104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/14/2022] [Indexed: 11/17/2022]
Abstract
Congenital cataract is the most important global cause of visual impairment in children. Autosomal dominant and autosomal recessive inheritance account for the majority of the hereditary nonsyndromic congenital cataract. The function of FYCO1 gene is to guide the transport of the microtubule-directed vesicles. Mutations in the FYCO1 gene may cause cataracts. We reported a novel nonsense mutation in FYCO1 (c.1411C > T, P. R471 ∗), which could cause nonsyndrome autosomal recessive congenital cataract. We underwent an ophthalmology examination of all participants and collected blood samples from all participants and extracted genomic DNAs. By whole exome sequencing, we found that this family carried an unreported mutation in the FYCO1 gene: c.1411C > T, P. R471 ∗. Sanger sequencing was performed to verify the mutation. We used ITASSER and PYMOL to predict and compare the structure and function of the mutated proteins. Using SIFT software and referring to the relevant guidelines of ACMG, the mutation was determined to be pathogenic. The models suggested that the nonsense mutation p.R471∗ resulted in a profound disruption of the FYCO1 protein structure. This report expands the locus information of the FYCO1 mutations.
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7
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Demir E. The potential use of Drosophila as an in vivo model organism for COVID-19-related research: a review. Turk J Biol 2021; 45:559-569. [PMID: 34803454 PMCID: PMC8573831 DOI: 10.3906/biy-2104-26] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/13/2021] [Indexed: 01/08/2023] Open
Abstract
The world urgently needs effective antiviral approaches against emerging viruses, as shown by the coronavirus disease 2019 (COVID-19) pandemic, which has become an exponentially growing health crisis. Scientists from diverse backgrounds have directed their efforts towards identifying key features of SARS-CoV-2 and clinical manifestations of COVID-19 infection. Reports of more transmissible variants of SARS-CoV-2 also raise concerns over the possibility of an explosive trajectory of the pandemic, so scientific attention should focus on developing new weapons to help win the fight against coronaviruses that may undergo further mutations in the future. Drosophila melanogaster offers a powerful and potential in vivo model that can significantly increase the efficiency of drug screening for viral and bacterial infections. Thanks to its genes with functional human homologs, Drosophila could play a significant role in such gene-editing studies geared towards designing vaccines and antiviral drugs for COVID-19. It can also help rectify current drawbacks of CRISPR-based therapeutics like off-target effects and delivery issues, representing another momentous step forward in healthcare. Here I present an overview of recent literature and the current state of knowledge, explaining how it can open up new avenues for Drosophila in our battle against infectious diseases.
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Affiliation(s)
- Eşref Demir
- Medical Laboratory Techniques Program, Department of Medical Services and Techniques, Vocational School of Health Services, Antalya Bilim University, Antalya Turkey
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8
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Barashkov NA, Konovalov FA, Borisova TV, Teryutin FM, Solovyev AV, Pshennikova VG, Sapojnikova NV, Vychuzhina LS, Romanov GP, Gotovtsev NN, Morozov IV, Bondar AA, Platonov FA, Burtseva TE, Khusnutdinova EK, Posukh OL, Fedorova SA. Autosomal recessive cataract (CTRCT18) in the Yakut population isolate of Eastern Siberia: a novel founder variant in the FYCO1 gene. Eur J Hum Genet 2021; 29:965-976. [PMID: 33767456 PMCID: PMC8187664 DOI: 10.1038/s41431-021-00833-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/19/2020] [Accepted: 02/10/2021] [Indexed: 11/09/2022] Open
Abstract
Congenital autosomal recessive cataract with unknown genetic etiology is one of the most common Mendelian diseases among the Turkic-speaking Yakut population (Eastern Siberia, Russia). To identify the genetic cause of congenital cataract spread in this population, we performed whole-exome sequencing (Illumina NextSeq 500) in one Yakut family with three affected siblings whose parents had preserved vision. We have revealed the novel homozygous c.1621C>T transition leading to premature stop codon p.(Gln541*) in exon 8 of the FYCO1 gene (NM_024513.4). Subsequent screening of c.1621C>T p.(Gln541*) revealed this variant in a homozygous state in 25 out of 29 Yakut families with congenital cataract (86%). Among 424 healthy individuals from seven populations of Eastern Siberia (Russians, Yakuts, Evenks, Evens, Dolgans, Chukchi, and Yukaghirs), the highest carrier frequency of c.1621C>T p.(Gln541*) was found in the Yakut population (7.9%). DNA samples of 25 homozygous for c.1621C>T p.(Gln541*) patients with congenital cataract and 114 unaffected unrelated individuals without this variant were used for a haplotype analysis based on the genotyping of six STR markers (D3S3512, D3S3685, D3S3582, D3S3561, D3S1289, and D3S3698). The structure of the identified haplotypes indicates a common origin for all of the studied mutant chromosomes bearing c.1621C>T p.(Gln541*). The age of the с.1621C>T p.(Gln541*) founder haplotype was estimated to be approximately 260 ± 65 years (10 generations). These findings characterize Eastern Siberia as the region of the world with the most extensive accumulation of the unique variant c.1621C>T p.(Gln541*) in the FYCO1 gene as a result of the founder effect.
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Affiliation(s)
- Nikolay A Barashkov
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yakutsk, Russian Federation.
- Laboratory of Molecular Biology, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation.
| | | | - Tuyara V Borisova
- Laboratory of Molecular Biology, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
| | - Fedor M Teryutin
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yakutsk, Russian Federation
| | - Aisen V Solovyev
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yakutsk, Russian Federation
- Laboratory of Molecular Biology, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
| | - Vera G Pshennikova
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yakutsk, Russian Federation
| | - Nadejda V Sapojnikova
- Department of Ophthalmology, Republican Hospital #1 - National Centre of Medicine, Yakutsk, Russian Federation
| | - Lyubov S Vychuzhina
- Department of Ophthalmology, Republican Hospital #1 - National Centre of Medicine, Yakutsk, Russian Federation
| | - Georgii P Romanov
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yakutsk, Russian Federation
- Laboratory of Molecular Biology, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
| | - Nyurgun N Gotovtsev
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yakutsk, Russian Federation
| | - Igor V Morozov
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
- Novosibirsk State University, Novosibirsk, Russian Federation
| | - Alexander A Bondar
- SB RAS Genomics Core Facility, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Fedor A Platonov
- Medical Institute, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
| | - Tatiana E Burtseva
- Medical Institute, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
- Laboratory of the Children Health Monitoring and Medical-environmental Research, Yakut Science Centre of Complex Medical Problems, Yakutsk, Russian Federation
| | - Elza K Khusnutdinova
- Laboratory of Molecular Biology, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
- Laboratory of Human Molecular Genetics, Institute of Biochemistry and Genetics, Ufa Federal Research Center of Russian Academy of Sciences, Ufa, Russian Federation
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russian Federation
| | - Olga L Posukh
- Novosibirsk State University, Novosibirsk, Russian Federation
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Sardana A Fedorova
- Laboratory of Molecular Genetics, Yakut Science Centre of Complex Medical Problems, Yakutsk, Russian Federation
- Laboratory of Molecular Biology, M.K. Ammosov North-Eastern Federal University, Yakutsk, Russian Federation
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Reis LM, Sorokina EA, Dudakova L, Moravikova J, Skalicka P, Malinka F, Seese SE, Thompson S, Bardakjian T, Capasso J, Allen W, Glaser T, Levin AV, Schneider A, Khan A, Liskova P, Semina EV. Comprehensive phenotypic and functional analysis of dominant and recessive FOXE3 alleles in ocular developmental disorders. Hum Mol Genet 2021; 30:1591-1606. [PMID: 34046667 PMCID: PMC8369840 DOI: 10.1093/hmg/ddab142] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 11/16/2022] Open
Abstract
The forkhead transcription factor FOXE3 is critical for vertebrate eye development. Recessive and dominant variants cause human ocular disease but the full range of phenotypes and mechanisms of action for the two classes of variants are unknown. We identified FOXE3 variants in individuals with congenital eye malformations and carried out in vitro functional analysis on selected alleles. Sixteen new recessive and dominant families, including six novel variants, were identified. Analysis of new and previously reported genetic and clinical data demonstrated a broad phenotypic range with an overlap between recessive and dominant disease. Most families with recessive alleles, composed of truncating and forkhead-domain missense variants, had severe corneal opacity (90%; sclerocornea in 47%), aphakia (83%) and microphthalmia (80%), but some had milder features including isolated cataract. The phenotype was most variable for recessive missense variants, suggesting that the functional consequences may be highly dependent on the type of amino acid substitution and its position. When assessed, aniridia or iris hypoplasia were noted in 89% and optic nerve anomalies in 60% of recessive cases, indicating that these defects are also common and may be underrecognized. In dominant pedigrees, caused by extension variants, normal eye size (96%), cataracts (99%) and variable anterior segment anomalies were seen in most, but some individuals had microphthalmia, aphakia or sclerocornea, more typical of recessive disease. Functional studies identified variable effects on the protein stability, DNA binding, nuclear localization and transcriptional activity for recessive FOXE3 variants, whereas dominant alleles showed severe impairment in all areas and dominant-negative characteristics.
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Affiliation(s)
- Linda M Reis
- Department of Pediatrics and Children's Research Institute at the Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI 53226, USA
| | - Elena A Sorokina
- Department of Pediatrics and Children's Research Institute at the Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI 53226, USA
| | - Lubica Dudakova
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Jana Moravikova
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Pavlina Skalicka
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic.,Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Frantisek Malinka
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic.,Department of Computer Science, Czech Technical University in Prague, Prague, Czech Republic
| | - Sarah E Seese
- Department of Pediatrics and Children's Research Institute at the Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI 53226, USA
| | - Samuel Thompson
- Department of Pediatrics and Children's Research Institute at the Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI 53226, USA
| | - Tanya Bardakjian
- Department of Pediatrics, Albert Einstein Medical Center, Philadelphia, PA 19141, USA
| | - Jenina Capasso
- Pediatric Ophthalmology and Ocular Genetics, Flaum Eye Institute, Pediatric Genetics, Golisano Children's Hospital, University of Rochester, Rochester, NY 14534 USA
| | - William Allen
- Fullerton Genetics Center, Mission Hospitals, HCA, Asheville, NC, 28803 USA
| | - Tom Glaser
- Cell Biology and Human Anatomy Department, UC-Davis School of Medicine, Davis, CA 95616, USA
| | - Alex V Levin
- Pediatric Ophthalmology and Ocular Genetics, Flaum Eye Institute, Pediatric Genetics, Golisano Children's Hospital, University of Rochester, Rochester, NY 14534 USA
| | - Adele Schneider
- Department of Pediatrics, Albert Einstein Medical Center, Philadelphia, PA 19141, USA
| | - Ayesha Khan
- Pediatric Ophthalmology & Strabismus Unit, Al-Shifa Trust Eye Hospital, Rawalpindi, Pakistan.,Consultant Pediatric Ophthalmologist, Al Jalila Children's Specialty Hospital, United Arab Emirates
| | - Petra Liskova
- Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic.,Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital, Prague, Czech Republic
| | - Elena V Semina
- Department of Pediatrics and Children's Research Institute at the Medical College of Wisconsin and Children's Hospital of Wisconsin, Milwaukee, WI 53226, USA.,Departments of Ophthalmology and Cell Biology, Neurobiology and Anatomy at the Medical College of Wisconsin, Milwaukee, WI 53226, USA
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10
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Muchenditsi A, Talbot CC, Gottlieb A, Yang H, Kang B, Boronina T, Cole R, Wang L, Dev S, Hamilton JP, Lutsenko S. Systemic deletion of Atp7b modifies the hepatocytes' response to copper overload in the mouse models of Wilson disease. Sci Rep 2021; 11:5659. [PMID: 33707579 PMCID: PMC7952580 DOI: 10.1038/s41598-021-84894-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 02/09/2021] [Indexed: 02/03/2023] Open
Abstract
Wilson disease (WD) is caused by inactivation of the copper transporter Atp7b and copper overload in tissues. Mice with Atp7b deleted either globally (systemic inactivation) or only in hepatocyte recapitulate various aspects of human disease. However, their phenotypes vary, and neither the common response to copper overload nor factors contributing to variability are well defined. Using metabolic, histologic, and proteome analyses in three Atp7b-deficient mouse strains, we show that global inactivation of Atp7b enhances and specifically modifies the hepatocyte response to Cu overload. The loss of Atp7b only in hepatocytes dysregulates lipid and nucleic acid metabolisms and increases the abundance of respiratory chain components and redox balancing enzymes. In global knockouts, independently of their background, the metabolism of lipid, nucleic acid, and amino acids is inhibited, respiratory chain components are down-regulated, inflammatory response and regulation of chromosomal replication are enhanced. Decrease in glucokinase and lathosterol oxidase and elevation of mucin-13 and S100A10 are observed in all Atp7b mutant strains and reflect the extent of liver injury. The magnitude of proteomic changes in Atp7b-/- animals inversely correlates with the metallothioneins levels rather than liver Cu content. These findings facilitate identification of WD-specific metabolic and proteomic changes for diagnostic and treatment.
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Affiliation(s)
- Abigael Muchenditsi
- Department of Physiology, Johns Hopkins Medical Institutes, 725 N Wolfe street, Baltimore, MD, 21205, USA
| | - C Conover Talbot
- Core Analysis Unit, Johns Hopkins Medical Institutes, Baltimore, MD, 21205, USA
| | - Aline Gottlieb
- Department of Physiology, Johns Hopkins Medical Institutes, 725 N Wolfe street, Baltimore, MD, 21205, USA
| | - Haojun Yang
- Department of Physiology, Johns Hopkins Medical Institutes, 725 N Wolfe street, Baltimore, MD, 21205, USA
| | - Byunghak Kang
- Department of Molecular and Comparative Pathobiology, Johns Hopkins Medical Institutes, Baltimore, MD, 21205, USA
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Tatiana Boronina
- Mass Spectrometry and Proteomics Facility, Johns Hopkins Medical Institutes, Baltimore, MD, 21205, USA
| | - Robert Cole
- Mass Spectrometry and Proteomics Facility, Johns Hopkins Medical Institutes, Baltimore, MD, 21205, USA
| | - Li Wang
- Department of Physiology, Johns Hopkins Medical Institutes, 725 N Wolfe street, Baltimore, MD, 21205, USA
| | - Som Dev
- Department of Physiology, Johns Hopkins Medical Institutes, 725 N Wolfe street, Baltimore, MD, 21205, USA
| | - James P Hamilton
- Department of Medicine, Johns Hopkins Medical Institutes, Baltimore, MD, 21205, USA
| | - Svetlana Lutsenko
- Department of Physiology, Johns Hopkins Medical Institutes, 725 N Wolfe street, Baltimore, MD, 21205, USA.
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11
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A missense allele of PEX5 is responsible for the defective import of PTS2 cargo proteins into peroxisomes. Hum Genet 2021; 140:649-666. [PMID: 33389129 DOI: 10.1007/s00439-020-02238-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 11/07/2020] [Indexed: 11/27/2022]
Abstract
Peroxisomes, single-membrane intracellular organelles, play an important role in various metabolic pathways. The translocation of proteins from the cytosol to peroxisomes depends on peroxisome import receptor proteins and defects in peroxisome transport result in a wide spectrum of peroxisomal disorders. Here, we report a large consanguineous family with autosomal recessive congenital cataracts and developmental defects. Genome-wide linkage analysis localized the critical interval to chromosome 12p with a maximum two-point LOD score of 4.2 (θ = 0). Next-generation exome sequencing identified a novel homozygous missense variant (c.653 T > C; p.F218S) in peroxisomal biogenesis factor 5 (PEX5), a peroxisome import receptor protein. This missense mutation was confirmed by bidirectional Sanger sequencing. It segregated with the disease phenotype in the family and was absent in ethnically matched control chromosomes. The lens-specific knockout mice of Pex5 recapitulated the cataractous phenotype. In vitro import assays revealed a normal capacity of the mutant PEX5 to enter the peroxisomal Docking/Translocation Module (DTM) in the presence of peroxisome targeting signal 1 (PTS1) cargo protein, be monoubiquitinated and exported back into the cytosol. Importantly, the mutant PEX5 protein was unable to form a stable trimeric complex with peroxisomal biogenesis factor 7 (PEX7) and a peroxisome targeting signal 2 (PTS2) cargo protein and, therefore, failed to promote the import of PTS2 cargo proteins into peroxisomes. In conclusion, we report a novel missense mutation in PEX5 responsible for the defective import of PTS2 cargo proteins into peroxisomes resulting in congenital cataracts and developmental defects.
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12
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Liu Z, Wang R, Lin H, Liu Y. Lens regeneration in humans: using regenerative potential for tissue repairing. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1544. [PMID: 33313289 PMCID: PMC7729322 DOI: 10.21037/atm-2019-rcs-03] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The crystalline lens is an important optic element in human eyes. It is transparent and biconvex, refracting light and accommodating to form a clear retinal image. The lens originates from the embryonic ectoderm. The epithelial cells at the lens equator proliferate, elongate and differentiate into highly aligned lens fiber cells, which are the structural basis for maintaining the transparency of the lens. Cataract refers to the opacity of the lens. Currently, the treatment of cataract is to remove the opaque lens and implant an intraocular lens (IOL). This strategy is inappropriate for children younger than 2 years, because a developing eyeball is prone to have severe complications such as inflammatory proliferation and secondary glaucoma. On the other hand, the absence of the crystalline lens greatly affects visual function rehabilitation. The researchers found that mammalian lenses possess regenerative potential. We identified lens stem cells through linear tracking experiments and designed a minimally invasive lens-content removal surgery (MILS) to remove the opaque lens material while preserving the lens capsule, stem cells and microenvironment. In infants with congenital cataract, functional lens regeneration in situ can be observed after MILS, and the prognosis of visual function is better than that of traditional surgery. Because of insufficient regenerative ability in humans, the morphology and volume of the regenerated lens cannot reach the level of a normal lens. The activation, proliferation and differentiation of lens stem cells and the alignment of lens fibers are regulated by epigenetic factors, growth factors, transcription factors, immune system and other signals and their interactions. The construction of appropriate microenvironment can accelerate lens regeneration and improve its morphology. The therapeutic concept of MILS combined with microenvironment manipulation to activate endogenous stem cells for functional regeneration of organs in situ can be extended to other tissues and organs with strong self-renewal and repair ability.
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Affiliation(s)
- Zhenzhen Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Ruixin Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Haotian Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yizhi Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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13
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Sun L, Song F, Liu H, Wang C, Tang X, Li Z, Ge H, Liu P. The novel mutation P36R in LRP5L contributes to congenital membranous cataract via inhibition of laminin γ1 and c-MAF. Graefes Arch Clin Exp Ophthalmol 2020; 258:2737-2751. [PMID: 32789677 DOI: 10.1007/s00417-020-04846-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 07/01/2020] [Accepted: 07/13/2020] [Indexed: 12/20/2022] Open
Abstract
PURPOSE The present study investigated a pathogenic mutation and its mechanism on membranous cataract in a congenital membranous cataract family. METHODS An autosomal dominant four-generation Chinese congenital membranous cataract family was recruited and whole-exome sequencing was performed to screen for sequence variants. Candidate variants were validated using polymerase chain reaction and Sanger sequencing. Wild-type and mutant low-density lipoprotein receptor-related protein 5-like (LRP5L) plasmids were constructed and transfected into human lens epithelial cells (HLE B-3) and human anterior lens capsules. The cell lysates, nuclear and cytoplasmic proteins, and basement membrane components of HLE B-3 cells were harvested. LRP5L and laminin γ1 were knocked down in HLE B-3 cells using specific small-interfering RNA. The protein expression levels of LRP5L, laminin γ1, and c-MAF were detected using immunoblotting and immunofluorescence. RESULTS We identified a novel suspected pathogenic mutation in LRP5L (c.107C > G, p.P36R) in the congenital membranous cataract family. This mutation was absent in 300 normal controls and 300 age-related cataract patients. Bioinformatics analysis with PolyPhen-2 and SIFT suggested that LRP5L-P36R was pathogenic. LRP5L upregulated laminin γ1 expression in the cytoplasmic proteins of HLE B-3 cells and human anterior lens capsules, and LRP5L-P36R inhibited the effects of LRP5L. LRP5L upregulated c-MAF expression in the nucleus and cytoplasm of HLE B-3 cells, and LRP5L-P36R inhibited c-MAF expression via inhibition of laminin γ1. CONCLUSION Our study identified a novel gene, LRP5L, associated with congenital membranous cataract, and its mutant LRP5L-P36R contributed to membranous cataract development via inhibition of laminin γ1 and c-MAF.
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Affiliation(s)
- Liyao Sun
- Eye Hospital, First Affiliated Hospital, Harbin Medical University, 23 Youzheng Street, Harbin, 150001, China
| | - Fanqian Song
- Eye Hospital, First Affiliated Hospital, Harbin Medical University, 23 Youzheng Street, Harbin, 150001, China
| | - Hanruo Liu
- Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Beijing Ophthalmology & Visual Science Key Laboratory, Capital Medical University, Beijing, 100000, China
| | - Chao Wang
- Eye Hospital, First Affiliated Hospital, Harbin Medical University, 23 Youzheng Street, Harbin, 150001, China
| | - Xianling Tang
- Eye Hospital, First Affiliated Hospital, Harbin Medical University, 23 Youzheng Street, Harbin, 150001, China
| | - Zhijian Li
- Eye Hospital, First Affiliated Hospital, Harbin Medical University, 23 Youzheng Street, Harbin, 150001, China
| | - Hongyan Ge
- Eye Hospital, First Affiliated Hospital, Harbin Medical University, 23 Youzheng Street, Harbin, 150001, China.
| | - Ping Liu
- Eye Hospital, First Affiliated Hospital, Harbin Medical University, 23 Youzheng Street, Harbin, 150001, China.
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14
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Nadeem R, Kabir F, Li J, Gradstein L, Jiao X, Rauf B, Naeem MA, Assir MZ, Riazuddin S, Ayyagari R, Hejtmancik JF, Riazuddin SA. Mutations in CERKL and RP1 cause retinitis pigmentosa in Pakistani families. Hum Genome Var 2020; 7:14. [PMID: 32411380 PMCID: PMC7217820 DOI: 10.1038/s41439-020-0100-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 03/11/2020] [Accepted: 03/15/2020] [Indexed: 12/31/2022] Open
Abstract
This study was conducted to identify the genetic basis of retinal dystrophies in consanguineous Pakistani families. We recruited two families with retinitis pigmentosa (RP) displaying visual difficulties, including nyctalopia and constricted visual fields. Linkage analysis and Sanger sequencing resulted in the identification of a previously reported nonsense mutation, c.847C > T, in exon 5 of CERKL in one family and a novel four-base pair deletion in exon 4 of RP1, c.delAGAA4218_4221, leading to premature protein termination in the second family. Here, we report two RP-causing mutations extending the genetic heterogeneity of the disease.
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Affiliation(s)
- Raheela Nadeem
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700 Pakistan
| | - Firoz Kabir
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
| | - Jiali Li
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD 20892 USA
- Department of Ophthalmology, Zhujiang Hospital, Southern Medical University, Guangzhou, 515282 China
| | - Libe Gradstein
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Xiaodong Jiao
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Bushra Rauf
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700 Pakistan
| | - Muhammad Asif Naeem
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700 Pakistan
| | - Muhammad Zaman Assir
- Allama Iqbal Medical College, University of Health Sciences, Lahore, 54550 Pakistan
| | - Sheikh Riazuddin
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700 Pakistan
- Allama Iqbal Medical College, University of Health Sciences, Lahore, 54550 Pakistan
| | - Radha Ayyagari
- Shiley Eye Institute, University of California San Diego, La Jolla, CA 92093 USA
| | - J. Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - S. Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
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15
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Ali M, Kabir F, Raskar S, Renuse S, Na CH, Delannoy M, Khan SY, Riazuddin SA. Generation and proteome profiling of PBMC-originated, iPSC-derived lentoid bodies. Stem Cell Res 2020; 46:101813. [PMID: 32474394 DOI: 10.1016/j.scr.2020.101813] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/18/2020] [Accepted: 04/09/2020] [Indexed: 01/13/2023] Open
Abstract
Here, we report proteome profiling of peripheral blood mononuclear cell (PBMC)-originated, induced pluripotent stem cell (iPSC)-derived, lens-like organoids termed lentoid bodies at two differentiation time points. A small aliquot of the blood sample was ascertained to collect PBMCs that were reprogrammed to iPSCs. The PBMC-originated, iPSCs were differentiated to lentoid bodies employing the "fried egg" method. Quantitative real-time PCR (qRT-PCR) analysis revealed increased expression levels of lens-associated markers in lentoid bodies while transmission electron microscopy identified closely packed lens epithelial- and differentiating fiber-like cells in lentoid bodies. Total cellular protein was extracted from lentoid bodies at differentiation day 25 and mass spectrometry identified a total of 9,473 proteins. The low counts of crystallin proteins at differentiation day 25 prompted us to re-examine the proteome at differentiation day 35 as we reasoned that 10 additional days of differentiation will increase the crystallin count. However, we did not detect any substantial increase in crystallin protein counts at differentiation day 35. In conclusion, we report generation and proteome profiles of PBMC-originated, iPSC-derived lentoid bodies at multiple differentiation time points.
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Affiliation(s)
- Muhammad Ali
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Firoz Kabir
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Snehal Raskar
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Santosh Renuse
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Chan Hyun Na
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Michael Delannoy
- Department of Cell Biology and Imaging Facility, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shahid Y Khan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - S Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
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16
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Iqbal H, Khan SY, Zhou L, Irum B, Ali M, Ahmed MR, Shahzad M, Ali MH, Naeem MA, Riazuddin S, Hejtmancik JF, Riazuddin SA. Mutations in FYCO1 identified in families with congenital cataracts. Mol Vis 2020; 26:334-344. [PMID: 32355443 PMCID: PMC7190580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 04/26/2020] [Indexed: 11/04/2022] Open
Abstract
Purpose This study was designed to identify the pathogenic variants in three consanguineous families with congenital cataracts segregating as a recessive trait. Methods Consanguineous families with multiple individuals manifesting congenital cataracts were ascertained. All participating members underwent an ophthalmic examination. A small aliquot of the blood sample was collected from all participating individuals, and genomic DNAs were extracted. Homozygosity-based linkage analysis was performed using short tandem repeat (STR) markers. The haplotypes were constructed with alleles of the STR markers, and the two-point logarithm of odds (LOD) scores were calculated. The candidate gene was sequenced bidirectionally to identify the disease-causing mutations. Results Linkage analysis localized the disease interval to chromosome 3p in three families. Subsequently, bidirectional Sanger sequencing identified two novel mutations-a single base deletion resulting in a frameshift (c.3196delC; p.His1066IlefsTer10) mutation and a single base substitution resulting in a nonsense (c.4270C>T; p.Arg1424Ter) mutation-and a known missense (c.4127T>C, p.Leu1376Pro) mutation in FYCO1. All three mutations showed complete segregation with the disease phenotype and were absent in 96 ethnically matched control individuals. Conclusions We report two novel mutations and a previously reported mutation in FYCO1 in three large consanguineous families. Taken together, mutations in FYCO1 contribute nearly 15% to the total genetic load of autosomal recessive congenital cataracts in this cohort.
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Affiliation(s)
- Hira Iqbal
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Shahid Y. Khan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Lin Zhou
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD
| | - Bushra Irum
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Ali
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Mariya R. Ahmed
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Mohsin Shahzad
- Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan
| | | | - Muhammad Asif Naeem
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Sheikh Riazuddin
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan,Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan
| | - J. Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD
| | - S. Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD
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17
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George A, Cogliati T, Brooks BP. Genetics of syndromic ocular coloboma: CHARGE and COACH syndromes. Exp Eye Res 2020; 193:107940. [PMID: 32032630 DOI: 10.1016/j.exer.2020.107940] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 02/07/2023]
Abstract
Optic fissure closure defects result in uveal coloboma, a potentially blinding condition affecting between 0.5 and 2.6 per 10,000 births that may cause up to 10% of childhood blindness. Uveal coloboma is on a phenotypic continuum with microphthalmia (small eye) and anophthalmia (primordial/no ocular tissue), the so-called MAC spectrum. This review gives a brief overview of the developmental biology behind coloboma and its clinical presentation/spectrum. Special attention will be given to two prominent, syndromic forms of coloboma, namely, CHARGE (Coloboma, Heart defect, Atresia choanae, Retarded growth and development, Genital hypoplasia, and Ear anomalies/deafness) and COACH (Cerebellar vermis hypoplasia, Oligophrenia, Ataxia, Coloboma, and Hepatic fibrosis) syndromes. Approaches employed to identify genes involved in optic fissure closure in animal models and recent advances in live imaging of zebrafish eye development are also discussed.
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Affiliation(s)
- Aman George
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health. Bethesda, Maryland, 20892, USA
| | - Tiziana Cogliati
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health. Bethesda, Maryland, 20892, USA
| | - Brian P Brooks
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health. Bethesda, Maryland, 20892, USA.
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18
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Wang H, Yang T, Yuan Y, Sun X. Identification of FOXE3 transcription factor as a potent oncogenic factor in triple-negative breast cancer. Biochem Biophys Res Commun 2019; 523:78-85. [PMID: 31831170 DOI: 10.1016/j.bbrc.2019.12.034] [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: 11/20/2019] [Accepted: 12/06/2019] [Indexed: 10/25/2022]
Abstract
Triple-negative breast cancer (TNBC) represents a unique subgroup of breast cancers (BCa) with potential to be highly proliferative and invasive. Patient with TNBC are prone to developing resistance to chemotherapy. Therefore, TNBC usually has a poor clinical outcome. The key factors driving these malignant features remain poorly understood. In this study, we report for the first time that expression levels of FOXE3, a recently identified lens-specific transcription factor, were preferentially upregulated in TNBC tissues compared to non-TNBC tissues, and this upregulation correlated well to a poor overall/recurrence-free survival in patients. Depletion of FOXE3 in TNBC cell lines promoted cell death, cell cycle arrest, and potentiated sensitivity to docetaxel (DTX), a first-line chemotherapeutic drug for TNBC treatment. These alterations in cell growth/survival properties were accompanied by induction of CDKN1B, a gene encoding the tumor suppressor p27. We further provided the molecular evidence that FOXE3 could directly bind to the CDKN1B promoter and negatively regulate its transcription in TNBC cells. Importantly, knockdown of combined p27 and FOXE3 reversed the DTX-induced cell growth inhibition observed upon FOXE3 knockdown, indicating that the FOXE3's effects on TNBC progression were mediated mainly through transcriptional regulation of the p27 signaling. Together, our findings suggest that FOXE3 may function as a potent oncogene during the progression of TNBC, likely affecting cell proliferation, invasion and chemosensitivity, and functioning at least in part through transcriptional repression of p27 signaling.
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Affiliation(s)
- Hua Wang
- Department of Medical Oncology, Baoji Center Hospital, Baoji, 721008, China
| | - Tian Yang
- Department of Immunology, Fourth Military Medical University, Xi'an, 710032, China
| | - Yiyi Yuan
- Department of Histology and Embryology, Fourth Military Medical University, Xi'an, 710032, China
| | - Xiaomian Sun
- Department of Clinical Immunology, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, China.
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19
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Comparative transcriptome analysis of hESC- and iPSC-derived lentoid bodies. Sci Rep 2019; 9:18552. [PMID: 31811247 PMCID: PMC6898283 DOI: 10.1038/s41598-019-54258-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 10/26/2019] [Indexed: 01/18/2023] Open
Abstract
The ocular lens serves as an excellent system to investigate the intricate details of development and differentiation. Generation of lentoid bodies or lens-like structures using pluripotent stem cells is important for understanding the processes critical for lens morphogenesis and the mechanism of cataractogenesis. We previously reported the generation of peripheral blood mononuclear cell (PBMC)-originated, induced pluripotent stem cells (iPSCs). Here, we report generation of lentoid bodies from human embryonic stem cells (hESCs) and (PBMC)-originated, iPSCs employing the “fried egg” method with brief modifications. The ultrastructure analysis of hESC- and iPSC-derived lentoid bodies identified closely packed lens epithelial- and differentiating fiber-like cells. In addition, we performed RNA sequencing (RNA-Seq) based transcriptome profiling of hESC- and iPSC-derived lentoid bodies at differentiation day 25. Next-generation RNA sequencing (RNA-Seq) of hESC- and iPSC-derived lentoid bodies detected expression (≥0.659 RPKM) of 13,975 and 14,003 genes, respectively. Comparative transcriptome analysis of hESC- and iPSC-derived lentoid bodies revealed 13,563 (>96%) genes common in both datasets. Among the genes common in both transcriptome datasets, 12,856 (~95%) exhibited a quantitatively similar expression profile. Next, we compared the mouse lens epithelial and fiber cell transcriptomes with hESC- and iPSC-derived lentoid bodies transcriptomes and identified > 96% overlap with lentoid body transcriptomes. In conclusion, we report first-time comparative transcriptome analysis of hESC- and iPSC-derived lentoid bodies at differentiation day 25.
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20
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Wang Y, Ding X, Liu B, Li M, Chang Y, Shen H, Xie SM, Xing L, Li Y. ETV4 overexpression promotes progression of non-small cell lung cancer by upregulating PXN and MMP1 transcriptionally. Mol Carcinog 2019; 59:73-86. [PMID: 31670855 DOI: 10.1002/mc.23130] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 10/09/2019] [Accepted: 10/17/2019] [Indexed: 12/29/2022]
Abstract
ETS variant 4 (ETV4), together with ETV1 and ETV5, constitute the PEA3 subfamily of ETS transcription factors, which are implicated in the progression of many cancers. However, the clinicopathologic significance and molecular events regulated by ETV4 in lung cancer are still poorly understood, especially in squamous cell carcinoma of the lung. Here, we aimed to identify functional targets involved in ETV4-driven lung tumorigenesis. Microarray analysis and validation data revealed that ETV4 was the most preponderant PEA3 factor, which was significantly related to the advanced stage, lymph node metastasis, and poor prognosis of non-small cell lung cancers (NSCLCs; all P < .001). Reduced ETV4 expression suppressed the growth and metastasis of NSCLC both in vivo and in vitro. Microarray, gain, or loss of function and luciferase report assays revealed the direct regulatory effect of ETV4 on the expression of focal adhesion gene PXN and matrix metalloproteinase 1 (MMP1), and PXN and/or MMP1 inhibition partially abolished cell proliferation and migration induced by ETV4. Kaplan-Meier analysis indicated that ETV4 and PXN or MMP1 co-overexpression is associated with poor prognosis in human NSCLCs. In conclusion, the ETV4-PXN and ETV4-MMP1 axes are useful biomarkers of tumor progression and worse outcomes in NSCLCs.
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Affiliation(s)
- Yan Wang
- Department of Pathology, Hebei Medical University, Shijiazhuang, Hebei, China
| | - Xiaosong Ding
- Department of Pathology, Hebei Medical University, Shijiazhuang, Hebei, China
| | - Bei Liu
- Department of Pathology, Hebei Medical University, Shijiazhuang, Hebei, China
| | - Minglei Li
- Department of Pathology, Hebei Medical University, Shijiazhuang, Hebei, China
| | - Ying Chang
- Department of Pathology, Hebei Medical University, Shijiazhuang, Hebei, China
| | - Haitao Shen
- Department of Pathology, Hebei Medical University, Shijiazhuang, Hebei, China.,Center of Metabolic Diseases and Cancer Research, Institute of Medical and Health Science, Hebei Medical University, Shijiazhuang, Hebei, China
| | - Shelly M Xie
- Department of Pathology, Hebei Medical University, Shijiazhuang, Hebei, China
| | - Lingxiao Xing
- Department of Pathology, Hebei Medical University, Shijiazhuang, Hebei, China.,Center of Metabolic Diseases and Cancer Research, Institute of Medical and Health Science, Hebei Medical University, Shijiazhuang, Hebei, China
| | - Yuehong Li
- Department of Pathology, Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
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21
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Ali M, Khan SY, Vasanth S, Ahmed MR, Chen R, Na CH, Thomson JJ, Qiu C, Gottsch JD, Riazuddin SA. Generation and Proteome Profiling of PBMC-Originated, iPSC-Derived Corneal Endothelial Cells. Invest Ophthalmol Vis Sci 2019; 59:2437-2444. [PMID: 29847650 PMCID: PMC5957521 DOI: 10.1167/iovs.17-22927] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Purpose Corneal endothelial cells (CECs) are critical in maintaining clarity of the cornea. This study was initiated to develop peripheral blood mononuclear cell (PBMC)-originated, induced pluripotent stem cell (iPSC)-derived CECs. Methods We isolated PBMCs and programmed the mononuclear cells to generate iPSCs, which were differentiated to CECs through the neural crest cells (NCCs). The morphology of differentiating iPSCs was examined at regular intervals by phase contrast microscopy. In parallel, the expression of pluripotent and corneal endothelium (CE)-associated markers was investigated by quantitative real-time PCR (qRT-PCR). The molecular architecture of the iPSC-derived CECs and human corneal endothelium (hCE) was examined by mass spectrometry–based proteome sequencing. Results The PBMC-originated, iPSC-derived CECs were tightly adherent, exhibiting a hexagonal-like shape, one of the cardinal characteristics of CECs. The CE-associated markers expressed at significantly higher levels in iPSC-derived CECs at days 13, 20, and 30 compared with their respective levels in iPSCs. It is of importance that only residual expression levels of pluripotency markers were detected in iPSC-derived CECs. Cryopreservation of iPSC-derived CECs did not affect the tight adherence of CECs and their hexagonal-like shape while expressing high levels of CE-associated markers. Mass spectrometry–based proteome sequencing identified 10,575 proteins in the iPSC-derived CEC proteome. In parallel, we completed proteome profiling of the hCE identifying 6345 proteins. Of these, 5763 proteins were identified in the iPSC-derived CECs, suggesting that 90.82% of the hCE proteome overlaps with the iPSC-derived CEC proteome. Conclusions We have successfully developed a personalized approach to generate CECs that closely mimic the molecular architecture of the hCE. To the best of our knowledge, this is the first report describing the development of PBMC-originated, iPSC-derived CECs.
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Affiliation(s)
- Muhammad Ali
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Shahid Y Khan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Shivakumar Vasanth
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Mariya R Ahmed
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Ruiqiang Chen
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Chan Hyun Na
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Jason J Thomson
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut, United States
| | - Caihong Qiu
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut, United States
| | - John D Gottsch
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - S Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
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22
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Genetics of anophthalmia and microphthalmia. Part 1: Non-syndromic anophthalmia/microphthalmia. Hum Genet 2019; 138:799-830. [PMID: 30762128 DOI: 10.1007/s00439-019-01977-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 01/30/2019] [Indexed: 12/22/2022]
Abstract
Eye formation is the result of coordinated induction and differentiation processes during embryogenesis. Disruption of any one of these events has the potential to cause ocular growth and structural defects, such as anophthalmia and microphthalmia (A/M). A/M can be isolated or occur with systemic anomalies, when they may form part of a recognizable syndrome. Their etiology includes genetic and environmental factors; several hundred genes involved in ocular development have been identified in humans or animal models. In humans, around 30 genes have been repeatedly implicated in A/M families, although many other genes have been described in single cases or families, and some genetic syndromes include eye anomalies occasionally as part of a wider phenotype. As a result of this broad genetic heterogeneity, with one or two notable exceptions, each gene explains only a small percentage of cases. Given the overlapping phenotypes, these genes can be most efficiently tested on panels or by whole exome/genome sequencing for the purposes of molecular diagnosis. However, despite whole exome/genome testing more than half of patients currently remain without a molecular diagnosis. The proportion of undiagnosed cases is even higher in those individuals with unilateral or milder phenotypes. Furthermore, even when a strong gene candidate is available for a patient, issues of incomplete penetrance and germinal mosaicism make diagnosis and genetic counseling challenging. In this review, we present the main genes implicated in non-syndromic human A/M phenotypes and, for practical purposes, classify them according to the most frequent or predominant phenotype each is associated with. Our intention is that this will allow clinicians to rank and prioritize their molecular analyses and interpretations according to the phenotypes of their patients.
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23
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Phenotype–genotype correlations and emerging pathways in ocular anterior segment dysgenesis. Hum Genet 2018; 138:899-915. [DOI: 10.1007/s00439-018-1935-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 09/10/2018] [Indexed: 12/11/2022]
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24
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Khan SY, Kabir F, M'Hamdi O, Jiao X, Naeem MA, Khan SN, Riazuddin S, Hejtmancik JF, Riazuddin SA. Whole genome sequencing data for two individuals of Pakistani descent. Sci Data 2018; 5:180174. [PMID: 30204152 PMCID: PMC6137601 DOI: 10.1038/sdata.2018.174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 07/11/2018] [Indexed: 12/30/2022] Open
Abstract
Here we report next-generation based whole genome sequencing of two individuals (H1 and H2) from a family of Pakistani descent. The genomic DNA was used to prepare paired-end libraries for whole-genome sequencing. Deep sequencing yielded 706.49 and 778.12 million mapped reads corresponding to 70.64 and 77.81 Gb sequence data and 23× and 25× average coverage for H1 and H2, respectively. Notably, a total of 448,544 and 470,683 novel variants, not present in the single nucleotide polymorphism database (dbSNP), were identified in H1 and H2, respectively. Comparative analysis identified 2,415,852 variants common in both genomes including 240,181 variants absent in the dbSNP. Principal component analysis linked the ancestry of both genomes with South Asian populations. In conclusion, we report whole genome sequences of two individuals from a family of Pakistani descent.
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Affiliation(s)
- Shahid Y Khan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Firoz Kabir
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Oussama M'Hamdi
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiaodong Jiao
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Muhammad Asif Naeem
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | - Shaheen N Khan
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | - Sheikh Riazuddin
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 53700, Pakistan
| | - J Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - S Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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25
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Reis LM, Semina EV. Genetic landscape of isolated pediatric cataracts: extreme heterogeneity and variable inheritance patterns within genes. Hum Genet 2018; 138:847-863. [PMID: 30187164 DOI: 10.1007/s00439-018-1932-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 08/29/2018] [Indexed: 12/12/2022]
Abstract
Pediatric cataract represents an important cause of pediatric visual impairment. While both genetic and environmental causes for pediatric cataract are known, a large proportion remains idiopathic. The purpose of this review is to discuss genes involved in isolated pediatric cataract, with a focus on variable inheritance patterns within genes. Mutations in over 52 genes are known to cause isolated pediatric cataract, with a major contribution from genes encoding for crystallins, transcription factors, membrane proteins, and cytoskeletal proteins. Interestingly, both dominant and recessive inheritance patterns have been reported for mutations in 13 different cataract genes. For some genes, dominant and recessive alleles represent distinct types of mutations, but for many, especially missense variants, there are no clear patterns to distinguish between dominant and recessive alleles. Further research into the functional effects of these mutations, as well as additional data on the frequency of the identified variants, is needed to clarify variant pathogenicity. Exome sequencing continues to be successful in identifying novel genes associated with congenital cataract but is hindered by the extreme genetic heterogeneity of this condition. The large number of idiopathic cases suggests that more genes and potentially novel mechanisms of gene disruption remain to be identified.
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Affiliation(s)
- Linda M Reis
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Elena V Semina
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin, Milwaukee, WI, 53226, USA. .,Department of Ophthalmology, Medical College of Wisconsin, Milwaukee, WI, 53226, USA.
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26
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Khan SY, Ali M, Kabir F, Renuse S, Na CH, Talbot CC, Hackett SF, Riazuddin SA. Proteome Profiling of Developing Murine Lens Through Mass Spectrometry. Invest Ophthalmol Vis Sci 2018; 59:100-107. [PMID: 29332127 PMCID: PMC5769801 DOI: 10.1167/iovs.17-21601] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Purpose We previously completed a comprehensive profile of the mouse lens transcriptome. Here, we investigate the proteome of the mouse lens through mass spectrometry–based protein sequencing at the same embryonic and postnatal time points. Methods We extracted mouse lenses at embryonic day 15 (E15) and 18 (E18) and postnatal day 0 (P0), 3 (P3), 6 (P6), and 9 (P9). The lenses from each time point were preserved in three distinct pools to serve as biological replicates for each developmental stage. The total cellular protein was extracted from the lens, digested with trypsin, and labeled with isobaric tandem mass tags (TMT) for three independent TMT experiments. Results A total of 5404 proteins were identified in the mouse ocular lens in at least one TMT set, 4244 in two, and 3155 were present in all three TMT sets. The majority of the proteins exhibited steady expression at all six developmental time points; nevertheless, we identified 39 proteins that exhibited an 8-fold differential (higher or lower) expression during the developmental time course compared to their respective levels at E15. The lens proteome is composed of diverse proteins that have distinct biological properties and functional characteristics, including proteins associated with cataractogenesis and autophagy. Conclusions We have established a comprehensive profile of the developing murine lens proteome. This repository will be helpful in identifying critical components of lens development and processes essential for the maintenance of its transparency.
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Affiliation(s)
- Shahid Y Khan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Muhammad Ali
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Firoz Kabir
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Santosh Renuse
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Chan Hyun Na
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - C Conover Talbot
- Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Sean F Hackett
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - S Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
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27
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A zebrafish model of foxe3 deficiency demonstrates lens and eye defects with dysregulation of key genes involved in cataract formation in humans. Hum Genet 2018; 137:315-328. [PMID: 29713869 DOI: 10.1007/s00439-018-1884-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/16/2018] [Indexed: 12/14/2022]
Abstract
The Forkhead box E3 (FOXE3) gene encodes a transcription factor with a forkhead/winged helix domain that is critical for development of the lens and anterior segment of the eye. Monoallelic and biallelic deleterious sequence variants in FOXE3 cause aphakia, cataracts, sclerocornea and microphthalmia in humans. We used clustered regularly interspaced short palindromic repeats/Cas9 injections to target the foxe3 transcript in zebrafish in order to create an experimental model of loss of function for this gene. Larvae that were homozygous for an indel variant, c.296_300delTGCAG, predicting p.(Val99Alafs*2), demonstrated severe eye defects, including small or absent lenses and microphthalmia. The lenses of the homozygous foxe3 indel mutants showed more intense staining with zl-1 antibody compared to control lenses, consistent with increased lens fiber cell differentiation. Whole genome transcriptome analysis (RNA-Seq) on RNA isolated from wildtype larvae and larvae with eye defects that were putative homozygotes for the foxe3 indel variant found significant dysregulation of genes expressed in the lens and eye whose orthologues are associated with cataracts in human patients, including cryba2a, cryba1l1, mipa and hsf4. Comparative analysis of this RNA-seq data with iSyTE data identified several lens-enriched genes to be down-regulated in foxe3 indel mutants. We also noted upregulation of lgsn and crygmxl2 and downregulation of fmodb and cx43.4, genes that are expressed in the zebrafish lens, but that are not yet associated with an eye phenotype in humans. These findings demonstrate that this new zebrafish foxe3 mutant model is highly relevant to the study of the gene regulatory networks conserved in vertebrate lens and eye development.
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28
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Outcome of optical iridectomy in Peters anomaly. Graefes Arch Clin Exp Ophthalmol 2018; 256:1679-1683. [DOI: 10.1007/s00417-018-4000-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 04/17/2018] [Accepted: 04/20/2018] [Indexed: 11/25/2022] Open
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29
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Anand D, Agrawal SA, Slavotinek A, Lachke SA. Mutation update of transcription factor genes FOXE3, HSF4, MAF, and PITX3 causing cataracts and other developmental ocular defects. Hum Mutat 2018; 39:471-494. [PMID: 29314435 PMCID: PMC5839989 DOI: 10.1002/humu.23395] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 12/19/2017] [Accepted: 12/22/2017] [Indexed: 02/06/2023]
Abstract
Mutations in the transcription factor genes FOXE3, HSF4, MAF, and PITX3 cause congenital lens defects including cataracts that may be accompanied by defects in other components of the eye or in nonocular tissues. We comprehensively describe here all the variants in FOXE3, HSF4, MAF, and PITX3 genes linked to human developmental defects. A total of 52 variants for FOXE3, 18 variants for HSF4, 20 variants for MAF, and 19 variants for PITX3 identified so far in isolated cases or within families are documented. This effort reveals FOXE3, HSF4, MAF, and PITX3 to have 33, 16, 18, and 7 unique causal mutations, respectively. Loss-of-function mutant animals for these genes have served to model the pathobiology of the associated human defects, and we discuss the currently known molecular function of these genes, particularly with emphasis on their role in ocular development. Finally, we make the detailed FOXE3, HSF4, MAF, and PITX3 variant information available in the Leiden Online Variation Database (LOVD) platform at https://www.LOVD.nl/FOXE3, https://www.LOVD.nl/HSF4, https://www.LOVD.nl/MAF, and https://www.LOVD.nl/PITX3. Thus, this article informs on key variants in transcription factor genes linked to cataract, aphakia, corneal opacity, glaucoma, microcornea, microphthalmia, anterior segment mesenchymal dysgenesis, and Ayme-Gripp syndrome, and facilitates their access through Web-based databases.
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Affiliation(s)
- Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
| | - Smriti A. Agrawal
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
| | - Anne Slavotinek
- Department of Pediatrics, Division of Genetics, University of California, UCSF Benioff Children’s Hospital, San Francisco, CA 19716 USA
| | - Salil A. Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711 USA
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30
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Plaisancié J, Ragge N, Dollfus H, Kaplan J, Lehalle D, Francannet C, Morin G, Colineaux H, Calvas P, Chassaing N. FOXE3
mutations: genotype-phenotype correlations. Clin Genet 2018; 93:837-845. [DOI: 10.1111/cge.13177] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 01/25/2023]
Affiliation(s)
- J. Plaisancié
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse; Toulouse France
- INSERM U1056; Université Toulouse III; Toulouse France
| | - N.K. Ragge
- Faculty of Health and Life Sciences; Oxford Brookes University; Oxford UK
- West Midlands Regional Genetics Service; Birmingham Women and Children’s NHS Foundation Trust; Birmingham UK
| | - H. Dollfus
- Centre de Référence pour les affections rares en génétique ophtalmologique; CARGO, Filière SENSGENE, Hôpitaux Universitaires de Strasbourg; Strasbourg France
| | - J. Kaplan
- INSERM U1163; Génétique Ophtalmologique; Paris France
| | - D. Lehalle
- Centre de Génétique et Centre de Référence "Anomalies du Développement et Syndromes Malformatifs; Hôpital d'Enfants; Dijon France
| | - C. Francannet
- Service de Génétique Médicale; CHU Estaing; Clermont-Ferrand France
| | - G. Morin
- Service de génétique; Hôpital nord d’Amiens; Amiens France
| | - H. Colineaux
- Department of Epidemiology, Health Economics and Public Health; Toulouse University Hospital; France
- LEASP UMR1027, INSERM; Université Toulouse III; Toulouse France
| | - P. Calvas
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse; Toulouse France
- INSERM U1056; Université Toulouse III; Toulouse France
| | - N. Chassaing
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse; Toulouse France
- INSERM U1056; Université Toulouse III; Toulouse France
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Wada K, Saito J, Yamaguchi M, Seki Y, Furugori M, Takahashi G, Nishito Y, Matsuda H, Shitara H, Kikkawa Y. Pde6b rd1 mutation modifies cataractogenesis in Foxe3 rct mice. Biochem Biophys Res Commun 2018; 496:231-237. [PMID: 29317205 DOI: 10.1016/j.bbrc.2018.01.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 01/04/2018] [Indexed: 11/27/2022]
Abstract
The Foxe3rct mutation, which causes early-onset cataracts, is a recessive mutation found in SJL/J mice. A previous study reported that cataract phenotypes are modified by the genetic background of mouse inbred strains and that the Pde6brd1 mutation, which induced degeneration of the photoreceptor cells, is a strong candidate genetic modifier to accelerate the severity of cataractogenesis of Foxe3rct mice. We created congenic mice by transferring a genomic region including the Foxe3rct mutation to the B6 genetic background, which does not carry the Pde6brd1 mutation. In the congenic mice, the cataract phenotypes became remarkably mild, and the development of cataracts was suppressed for a long time. Moreover, we created transgenic mice by injecting BAC clones including the wild-type Pde6b gene into the eggs of SJL-Foxe3rct mice. Although the resistant effect for cataract phenotypes in transgenic mice was less than that in congenic mice, the severity and onset time of cataract phenotypes were clearly improved and delayed, respectively, compared with the phenotypes of the original SJL-Foxe3rct mice. These results clearly show that the development of early-onset cataracts requires at least two mutant alleles of Foxe3rct and Pde6brd1, and another modifier associated with the severity of cataract phenotypes in Foxe3rct mice underlies the genetic backgrounds in mice.
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Affiliation(s)
- Kenta Wada
- Graduate School of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido, 099-2493, Japan; Mammalian Genetics Project, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Junichi Saito
- Mammalian Genetics Project, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, 156-8506, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Midori Yamaguchi
- Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Yuta Seki
- Mammalian Genetics Project, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Masamune Furugori
- Graduate School of Bioindustry, Tokyo University of Agriculture, Abashiri, Hokkaido, 099-2493, Japan
| | - Gou Takahashi
- Regenerative Medicine Project, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Yasumasa Nishito
- Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Hiroshi Matsuda
- Division of Animal Life Science, Institute of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Hiroshi Shitara
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan; Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Yoshiaki Kikkawa
- Mammalian Genetics Project, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo, 156-8506, Japan.
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32
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Ullah I, Kabir F, Gottsch CBS, Naeem MA, Guru AA, Ayyagari R, Khan SN, Riazuddin S, Akram J, Riazuddin SA. Mutations in phosphodiesterase 6 identified in familial cases of retinitis pigmentosa. Hum Genome Var 2016; 3:16036. [PMID: 27917291 PMCID: PMC5112436 DOI: 10.1038/hgv.2016.36] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Revised: 08/24/2016] [Accepted: 09/08/2016] [Indexed: 11/10/2022] Open
Abstract
To delineate the genetic determinants associated with retinitis pigmentosa (RP), a hereditary retinal disorder, we recruited four large families manifesting cardinal symptoms of RP. We localized these families to regions on the human genome harboring the α and β subunits of phosphodiesterase 6 and identified mutations that were absent in control chromosomes. Our data suggest that mutations in PDE6A and PDE6B are responsible for the retinal phenotype in these families.
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Affiliation(s)
- Inayat Ullah
- National Centre of Excellence in Molecular Biology, University of the Punjab , Lahore, Pakistan
| | - Firoz Kabir
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Clare Brooks S Gottsch
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine , Baltimore, MD, USA
| | - Muhammad Asif Naeem
- National Centre of Excellence in Molecular Biology, University of the Punjab , Lahore, Pakistan
| | - Aditya A Guru
- Shiley Eye Institute, University of California San Diego , La Jolla, CA, USA
| | - Radha Ayyagari
- Shiley Eye Institute, University of California San Diego , La Jolla, CA, USA
| | - Shaheen N Khan
- National Centre of Excellence in Molecular Biology, University of the Punjab , Lahore, Pakistan
| | - Sheikh Riazuddin
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan; Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan; National Centre for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Javed Akram
- Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan; National Centre for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - S Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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A spectrum of CYP1B1 mutations associated with primary congenital glaucoma in families of Pakistani descent. Hum Genome Var 2016; 3:16021. [PMID: 27508083 PMCID: PMC4972894 DOI: 10.1038/hgv.2016.21] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/31/2016] [Accepted: 03/27/2016] [Indexed: 11/25/2022] Open
Abstract
Glaucoma is the second leading cause of blindness, affecting ~65 million people worldwide. We identified and ascertained a large cohort of inbred families with multiple individuals manifesting cardinal symptoms of primary congenital glaucoma (PCG) to investigate the etiology of the disease at a molecular level. Ophthalmic examinations, including slit-lamp microscopy and applanation tonometry, were performed to characterize the causal phenotype and confirm that affected individuals fulfilled the diagnostic criteria for PCG. Subsequently, exclusion analysis was completed with fluorescently labeled short tandem repeat markers, followed by Sanger sequencing to identify pathogenic variants. Exclusion analysis suggested linkage to the CYP1B1 locus, with positive two-point logarithm of odds scores in 23 families, while Sanger sequencing identified a total of 11 variants, including two novel mutations, in 23 families. All mutations segregated with the disease phenotype in their respective families. These included the following seven missense mutations: p.Y81N, p.E229K, p.R368H, p.R390H, p.W434R, p.R444Q and p.R469W, as well as one nonsense mutation, p.Q37*, and three frameshift mutations, p.W246Lfs81*, p.T404Sfs30* and p.P442Qfs15*. In conclusion, we identified a total of 11 mutations, reconfirming the genetic heterogeneity of CYP1B1 in the pathogenesis of PCG. To the best of our knowledge, this is the largest study investigating the contribution of CYP1B1 to the pathogenesis of PCG in the Pakistani population.
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