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Munir A, Afsar S, Rehman AU. A systematic review of inherited retinal dystrophies in Pakistan: updates from 1999 to April 2023. BMC Ophthalmol 2024; 24:55. [PMID: 38317096 PMCID: PMC10840256 DOI: 10.1186/s12886-024-03319-7] [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: 06/01/2023] [Accepted: 01/19/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Inherited retinal degenerations (IRDs) are a group of rare genetic conditions affecting retina of the eye that range in prevalence from 1 in 2000 to 1 in 4000 people globally. This review is based on a retrospective analysis of research articles reporting IRDs associated genetic findings in Pakistani families between 1999 and April 2023. METHODS Articles were retrieved through survey of online sources, notably, PubMed, Google Scholar, and Web of Science. Following a stringent selection criterion, a total of 126 research articles and conference abstracts were considered. All reported variants were cross-checked and validated for their correct genomic nomenclature using different online resources/databases, and their pathogenicity scores were explained as per ACMG guidelines. RESULTS A total of 277 unique sequence variants in 87 distinct genes, previously known to cause IRDs, were uncovered. In around 70% cases, parents of the index patient were consanguineously married, and approximately 88.81% of the detected variants were found in a homozygous state. Overall, more than 95% of the IRDs cases were recessively inherited. Missense variants were predominant (41.88%), followed by Indels/frameshift (26.35%), nonsense (19.13%), splice site (12.27%) and synonymous change (0.36%). Non-syndromic IRDs were significantly higher than syndromic IRDs (77.32% vs. 22.68%). Retinitis pigmentosa (RP) was the most frequently observed IRD followed by Leber's congenital amaurosis (LCA). Altogether, mutations in PDE6A gene was the leading cause of IRDs in Pakistani families followed by mutations in TULP1 gene. CONCLUSION In summary, Pakistani families are notable in expressing recessively inherited monogenic disorders including IRDs likely due to the highest prevalence of consanguinity in the country that leads to expression of rare pathogenic variants in homozygous state.
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Affiliation(s)
- Asad Munir
- Department of Zoology, Faculty of Biological and Health Sciences, Hazara University, Mansehra, 21300, Khyber Pakhtunkhwa, Pakistan
| | - Salma Afsar
- Department of Zoology, Faculty of Biological and Health Sciences, Hazara University, Mansehra, 21300, Khyber Pakhtunkhwa, Pakistan
| | - Atta Ur Rehman
- Department of Zoology, Faculty of Biological and Health Sciences, Hazara University, Mansehra, 21300, Khyber Pakhtunkhwa, Pakistan.
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Li Z, Cheng W, Zi F, Wang J, Huang X, Sheng X, Rong W. Four different gene-related cone-rod dystrophy: clinical and genetic findings in six Chinese families with diverse modes of inheritance. Front Genet 2023; 14:1157156. [PMID: 38028590 PMCID: PMC10652761 DOI: 10.3389/fgene.2023.1157156] [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: 02/02/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
Purpose: To investigate pathogenic variants in six families with cone-rod dystrophy (CORD) presenting various inheritance patterns by using whole-exome sequencing (WES) and analyzing phenotypic features. Methods: A total of six families with CORD were enrolled in Ningxia Eye Hospital for this study. The probands and their family members received comprehensive ophthalmic examinations, and DNA was abstracted from patients and family members. Whole-exome sequencing was performed on probands to screen the causative variants, and all suspected pathogenic variants were determined via Sanger sequencing. Furthermore, co-segregation analysis was performed on available family members. The pathogenicity of novel variants was predicted using in silico analysis and evaluated according to the American College of Medical Genetics and Genomics (ACMG) guidelines. Results: Of the six families, two families were assigned as X-linked recessive (XL), two families were assigned as autosomal recessive (AR), and two families were assigned as autosomal dominant (AD). Pathogenic variants were detected in CACNA1F in two X-linked recessive probands, among which family 1 had a hemizygous frameshift variant c.2201del (p.Val734Glyfs*17) and family 2 had a hemizygous missense variant c.245G>A (p.Arg82Gln). Both probands had high myopia, with fundus tessellation accompanied by abnormalities in the outer structure of the macular area. The homozygous splice variant c.2373 + 5G>T in PROM1 and the homozygous nonsense variant c.604C>T (p.Arg202Ter) in ADAM9 were detected in two autosomal recessive families of the probands. Both probands showed different degrees of atrophy in the macular area, and the lesions showed hypofluorescence changes in autofluorescence. The heterozygous variation in CRX c.682C>T (p.Gln228Ter) was detected in two autosomal dominant families. The onset age of the two probands was late, with better vision and severe macular atrophy. According to ACMG guidelines and the analysis of online in silico tools, all variations were labeled as potentially harmful or pathogenic. Conclusion: Pathogenic variants in CACNA1F, PROM1, ADAM9, and CRX genes were identified in six families affected by the diverse inheritance patterns of CORD. Furthermore, the potential impact of the nonsense-mediated decay (NMD) mechanism on the manifestation of CORD phenotypes was examined and addressed. Simultaneously, the spectrum of pathogenic variants and clinical phenotypes associated with the CORD gene was extended.
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Affiliation(s)
- Zhen Li
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Wanyu Cheng
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Feiyin Zi
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Juan Wang
- Department of Ophthalmology, Qingdao West Coast New District Central Hospital, Qingdao, China
| | - Xiaoyu Huang
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | | | - Weining Rong
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
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3
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Ren X, Léveillard T. Modulating antioxidant systems as a therapeutic approach to retinal degeneration. Redox Biol 2022; 57:102510. [PMID: 36274523 PMCID: PMC9596747 DOI: 10.1016/j.redox.2022.102510] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 11/21/2022] Open
Abstract
The human retina is facing a big challenge of reactive oxygen species (ROS) from endogenous and exogenous sources. Excessive ROS can cause damage to DNA, lipids, and proteins, triggering abnormal redox signaling, and ultimately lead to cell death. Thus, oxidative stress has been observed in inherited retinal diseases as a common hallmark. To counteract the detrimental effect of ROS, cells are equipped with various antioxidant defenses. In this review, we will focus on the antioxidant systems in the retina and how they can protect retina from oxidative stress. Both small antioxidants and antioxidant enzymes play a role in ROS removal. Particularly, the thioredoxin and glutaredoxin systems, as the major antioxidant systems in mammalian cells, exert functions in redox signaling regulation via modifying cysteines in proteins. In addition, the thioredoxin-like rod-derived cone viability factor (RdCVFL) and thioredoxin interacting protein (TXNIP) can modulate metabolism in photoreceptors and promote their survival. In conclusion, elevating the antioxidant capacity in retina is a promising therapy to curb the progress of inherited retinal degeneration.
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Affiliation(s)
- Xiaoyuan Ren
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France; Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, 17177, Sweden.
| | - Thierry Léveillard
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France.
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Retinitis Pigmentosa'nın Genetik ve Klinik Değerlendirilmesi. JOURNAL OF CONTEMPORARY MEDICINE 2022. [DOI: 10.16899/jcm.1131536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Background: The aim of this study was to evaluate the most common underlying genetic and clinical etiologies of retinitis pigmentosa (RP) disease in our geographical area.
Material and Method: In our archive, there are about 3000 patients who applied to our clinic between the years 2015-2021. The files of approximately 700 patients with a definitive genetic diagnosis were retrospectively scanned. A definitive genetic diagnosis was made in 22 of these patients. During our research, we collected some clinical parameters including the prenatal, natal, and postnatal history of the patients, history of surgery and seizures, and family history. In family history, we did a detailed pedigree with at least 3 generational analyses, questioned parental kinship, looked for similar members in families, and identified inheritance patterns of their disorder. We draw 3 generations pedigree and we collected peripheral venous blood samples from patients and sent them to a commercial lab for gene panels or WES. After obtaining the definitive genetic diagnosis of all patients, we compiled a table with the other parameters we questioned.
Results: As a result of our WES analysis in patients 1 and 2, homozygous c.1331_1332 dupAG/p. Thr445ArgfsTer10 Class 2 variant was detected in the POC1B gene of patient #2.In the RP panel 1 reports of patients 3 and 4, the genomic alteration of c.2254dupA (p.Ser752Lysfs*14) was detected in exon 15 of the ABCA4 (NM_000350) gene. Patient 5, EYS c.4964T>C heterozygous. Patient 6. SEMA4A C.1168A>G (heterozygous). Patient 7, SEMA4A C.1168A>G (heterozygous), RP1 c.5402C>T (heterozygous), CGNB1 c.1382C>T (heterozygous).Patient #8, . Heterozygous variation of p.Thr390Ala (c.1168A>G) in the SEMA4A gene is present.As a result of our WES analysis, a homozygous c.2021C>A/p.Pro674His Class 2 variant was detected in the RPGRIP1 gene of patient #9. Heterozygous c.119-2A>C Class 1 mutation was detected in the NR2E3 gene of patient 10. Homozygous c.271C>T/p.Gln91* Class 1 mutation was detected in the MFRP gene in patient 11. Patient #12 was diagnosed at the age of 7-8 years. When we look at the exome sequencing results, a homozygous mutation in the CNGB1 gene c.413-1G> of patient 13 was detected. Heterozygous p.Ser361Tyr (c.1082C>A) change detected in the ABCA4 gene of patient #14 was detected. The heterozygous p.Glu150Lys (c.448G>A) change detected in the RHO gene of patient #15 was pathogenic according to ClinVar database and in silico analysis. rated as. Prediagnosis was Bardet-Biedle Syndrome in patient 16. P.Gly244Asp change was detected in RPE65 gene of patients 17 and 18. Automated DNA sequencing of patient #19 and patient #20 results in a homozygous sequence variation in the coding sequence of the NR2E3 genes, a homozygous CGG>CAG nucleotide substitution, and an amino acid replacement of Arg311Gln. Heterozygous mutation was detected in the same gene region in patient 21 (fathers). Variation in NR2E3 is the most likely cause of these patients' eye condition, as it is a complete genotype and is strongly associated with RP in many published families. Genetic results on an allele of the BBS1 gene of patient 22 (chr11:66.278.121-66.291.364 (13.2kb)/ISCN: seq [GRCH37]11q13.2(66.278).121-66.291.364)x1). The other allele has a heterozygous point mutation (c.1424dupT p.Ser476fs-rs886039798).
Conclusıons: As determined in our study, the disease can be encountered with many different genetic etiologies. In this regard, patients undergoing genetic testing should be carefully examined for both SNP (single nucleotide polymorphism) and CNV (copy number variation).In addition, before genetic tests are performed, it should be well determined whether there is an isolated RP or an accompanying RP. In this respect, patients should be evaluated by making a detailed anamnesis and physical examination and drawing a pedigree containing at least 3 generations. Therefore, it was concluded that accompanying abnormalities should also be examined in the evaluation of retinitis pigmentosa anomalies.
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Nojima S. Class IV semaphorins in disease pathogenesis. Pathol Int 2022; 72:471-487. [PMID: 36066011 DOI: 10.1111/pin.13270] [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: 05/16/2022] [Accepted: 08/16/2022] [Indexed: 12/01/2022]
Abstract
Semaphorins are a large family of secreted and/or transmembrane proteins, originally identified as proteins that function in axon guidance during neuronal development. However, semaphorins play crucial roles in other physiological and pathological processes, including immune responses, angiogenesis, maintenance of tissue homeostasis, and cancer progression. Class IV semaphorins may be present as transmembrane and soluble forms and are implicated in the pathogenesis of various diseases. This review discusses recent progress on the roles of class IV semaphorins determined by clinical and experimental pathology studies.
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Affiliation(s)
- Satoshi Nojima
- Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan.,Department of Immunopathology, World Premier International Research Center Initiative (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
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6
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Rafati M, Mohamadhashem F, Jalilian K, Hoseininasab F, Fakhri L, Hoseini A, Amiri H, Barati Z, Darzi Ramandi S, Mostofinezhad N, Mahmoudi AH, Ghaffari SR. Identification of a novel de novo variant in OTX2 in a patient with congenital microphthalmia using targeted next-generation sequencing followed by prenatal diagnosis. Ophthalmic Genet 2021; 43:262-267. [PMID: 34791963 DOI: 10.1080/13816810.2021.2002915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
BACKGROUND Next-generation sequencing has been proven to be a reliable method for the detection of genetic causes in heterogeneous ocular disorders. In this report an NGS-based diagnostic approach was taken to uncover the genetic etiology in a patient with coloboma and microphthalmia, a highly heterogeneous disease with intrafamilial phenotypic variability. MATERIALS AND METHODS Next generation sequencing using a targeted panel of 316 genes, was carried out in the proband. Prioritized variants were then identified and confirmed using Sanger sequencing. Prenatal diagnosis of the detected variant was then performed in the family. RESULTS A novel de novo frameshift variant c.157_164delTTCACTCG (p.Phe53fs) in OTX2, leading to a truncated protein, was identified. Prenatal diagnosis identified the same variant in the fetus. CONCLUSIONS This report demonstrates the importance of genetic counseling and underscores the efficiency and effectiveness of targeted NGS as a means of detecting variants in inherited eye disorders.
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Affiliation(s)
- Maryam Rafati
- Comprehensive Genetic Center, Hope Generation Foundation, Tehran, Iran.,Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran.,Department of Genomics Gene Clinic, Tehran, Iran
| | - Faezeh Mohamadhashem
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Koosha Jalilian
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Fatemeh Hoseininasab
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Laya Fakhri
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran
| | - Azadeh Hoseini
- Comprehensive Genetic Center, Hope Generation Foundation, Tehran, Iran
| | - Hosna Amiri
- Comprehensive Genetic Center, Hope Generation Foundation, Tehran, Iran
| | - Zeinab Barati
- Comprehensive Genetic Center, Hope Generation Foundation, Tehran, Iran
| | | | | | | | - Saeed Reza Ghaffari
- Comprehensive Genetic Center, Hope Generation Foundation, Tehran, Iran.,Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, Iran.,Department of Genomics Gene Clinic, Tehran, Iran
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Olkinuora AP, Peltomäki PT, Aaltonen LA, Rajamäki K. From APC to the genetics of hereditary and familial colon cancer syndromes. Hum Mol Genet 2021; 30:R206-R224. [PMID: 34329396 PMCID: PMC8490010 DOI: 10.1093/hmg/ddab208] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/01/2021] [Accepted: 07/05/2021] [Indexed: 11/12/2022] Open
Abstract
Hereditary colorectal cancer (CRC) syndromes attributable to high penetrance mutations represent 9-26% of young-onset CRC cases. The clinical significance of many of these mutations is understood well enough to be used in diagnostics and as an aid in patient care. However, despite the advances made in the field, a significant proportion of familial and early-onset cases remains molecularly uncharacterized and extensive work is still needed to fully understand the genetic nature of CRC susceptibility. With the emergence of next-generation sequencing and associated methods, several predisposition loci have been unraveled, but validation is incomplete. Individuals with cancer-predisposing mutations are currently enrolled in life-long surveillance, but with the development of new treatments, such as cancer vaccinations, this might change in the not so distant future for at least some individuals. For individuals without a known cause for their disease susceptibility, prevention and therapy options are less precise. Herein, we review the progress achieved in the last three decades with a focus on how CRC predisposition genes were discovered. Furthermore, we discuss the clinical implications of these discoveries and anticipate what to expect in the next decade.
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Affiliation(s)
- Alisa P Olkinuora
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00014 Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, 00014 Helsinki, Finland
| | - Päivi T Peltomäki
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00014 Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, 00014 Helsinki, Finland
| | - Lauri A Aaltonen
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00014 Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, 00014 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, 00014 Helsinki, Finland
| | - Kristiina Rajamäki
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, 00014 Helsinki, Finland
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, 00014 Helsinki, Finland
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8
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Pappalardo J, Heath Jeffery RC, Thompson JA, Charng J, Chelva ES, Constable IJ, McLaren TL, Lamey TM, De Roach JN, Chen FK. Progressive sector retinitis pigmentosa due to c.440G>T mutation in SAG in an Australian family. Ophthalmic Genet 2020; 42:62-70. [PMID: 33047631 DOI: 10.1080/13816810.2020.1832533] [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] [Indexed: 10/23/2022]
Abstract
BACKGROUND Heterozygous c.440 G > T mutation in the S-antigen visual arrestin (SAG) gene has been described as a cause of autosomal dominant retinitis pigmentosa (adRP) in a series of patients of Hispanic origin. This study presents the early and late clinical features and disease progression rates in an Australian family with SAG adRP. MATERIALS AND METHODS An observational case series of four family members with adRP. They were examined clinically, with multi-modal retinal imaging and electroretinography (ERG) to ascertain phenotype. Disease progression rate was measured using optical coherence tomography (OCT) and fundus autofluorescence (FAF). A retinal dystrophy panel was used for the proband and cascade testing with targeted Sanger sequencing was conducted in other available family members. RESULTS The proband presented at 36 years of age with profoundly reduced full-field ERG responses despite a sector RP phenotype. This progressed to a classic RP pattern over several decades leaving a small residual island of central visual field. The horizontal span of the residual outer nuclear layer and the area of hyperautofluorescent ring contracted at a rate of 8-11% and 9-14% per year, respectively. DNA sequencing confirmed the segregation of SAG c.440 G > T mutation with disease. CONCLUSION SAG adRP presents with a reduced full-field ERG response consistent with a rod-cone dystrophy in mid-life despite a sector RP phenotype. Centripetal progression of the disease into the macula can be tracked by OCT and FAF imaging.
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Affiliation(s)
- Juanita Pappalardo
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia , Nedlands, Australia
| | - Rachael C Heath Jeffery
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia , Nedlands, Australia
| | - Jennifer A Thompson
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Perth, Australia
| | - Jason Charng
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia , Nedlands, Australia
| | - Enid S Chelva
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Perth, Australia
| | - Ian J Constable
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia , Nedlands, Australia
| | - Terri L McLaren
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia , Nedlands, Australia.,Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Perth, Australia
| | - Tina M Lamey
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia , Nedlands, Australia.,Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Perth, Australia
| | - John N De Roach
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia , Nedlands, Australia.,Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Perth, Australia
| | - Fred K Chen
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia , Nedlands, Australia.,Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Perth, Australia.,Department of Ophthalmology, Royal Perth Hospital , Perth, Australia.,Department of Ophthalmology, Perth Children's Hospital , Nedlands, Australia
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Cirino AL, Cuddy S, Lakdawala NK. Deletion of entire LMNA gene as a cause of cardiomyopathy. HeartRhythm Case Rep 2020; 6:395-397. [PMID: 32695585 PMCID: PMC7360979 DOI: 10.1016/j.hrcr.2020.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
| | - Sarah Cuddy
- Brigham and Women's Hospital, Boston, Massachusetts
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Paraoan L, Sharif U, Carlsson E, Supharattanasitthi W, Mahmud NM, Kamalden TA, Hiscott P, Jackson M, Grierson I. Secretory proteostasis of the retinal pigmented epithelium: Impairment links to age-related macular degeneration. Prog Retin Eye Res 2020; 79:100859. [PMID: 32278708 DOI: 10.1016/j.preteyeres.2020.100859] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/24/2020] [Accepted: 03/26/2020] [Indexed: 12/19/2022]
Abstract
Secretory proteostasis integrates protein synthesis, processing, folding and trafficking pathways that are essential for efficient cellular secretion. For the retinal pigment epithelium (RPE), secretory proteostasis is of vital importance for the maintenance of the structural and functional integrity of apical (photoreceptors) and basal (Bruch's membrane/choroidal blood supply) sides of the environment it resides in. This integrity is achieved through functions governed by RPE secreted proteins, which include extracellular matrix modelling/remodelling, angiogenesis and immune response modulation. Impaired RPE secretory proteostasis affects not only the extracellular environment, but leads to intracellular protein aggregation and ER-stress with subsequent cell death. Ample recent evidence implicates dysregulated proteostasis as a key factor in the development of age-related macular degeneration (AMD), the leading cause of blindness in the developed world, and research aiming to characterise the roles of various proteins implicated in AMD-associated dysregulated proteostasis unveiled unexpected facets of the mechanisms involved in degenerative pathogenesis. This review analyses cellular processes unveiled by the study of the top 200 transcripts most abundantly expressed by the RPE/choroid in the light of the specialised secretory nature of the RPE. Functional roles of these proteins and the mechanisms of their impaired secretion, due to age and genetic-related causes, are analysed in relation to AMD development. Understanding the importance of RPE secretory proteostasis in relation to maintaining retinal health and how it becomes impaired in disease is of paramount importance for the development and assessment of future therapeutic advancements involving gene and cell therapies.
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Affiliation(s)
- Luminita Paraoan
- Department of Eye and Vision Science, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, United Kingdom.
| | - Umar Sharif
- Department of Eye and Vision Science, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, United Kingdom
| | - Emil Carlsson
- Department of Eye and Vision Science, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, United Kingdom
| | - Wasu Supharattanasitthi
- Department of Eye and Vision Science, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, United Kingdom; Department of Physiology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Nur Musfirah Mahmud
- Department of Eye and Vision Science, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, United Kingdom
| | - Tengku Ain Kamalden
- Eye Research Centre, Department of Ophthalmology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Paul Hiscott
- Department of Eye and Vision Science, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, United Kingdom
| | - Malcolm Jackson
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, United Kingdom
| | - Ian Grierson
- Department of Eye and Vision Science, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, United Kingdom
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Blond F, Léveillard T. Functional Genomics of the Retina to Elucidate its Construction and Deconstruction. Int J Mol Sci 2019; 20:E4922. [PMID: 31590277 PMCID: PMC6801968 DOI: 10.3390/ijms20194922] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 10/01/2019] [Indexed: 12/20/2022] Open
Abstract
The retina is the light sensitive part of the eye and nervous tissue that have been used extensively to characterize the function of the central nervous system. The retina has a central position both in fundamental biology and in the physiopathology of neurodegenerative diseases. We address the contribution of functional genomics to the understanding of retinal biology by reviewing key events in their historical perspective as an introduction to major findings that were obtained through the study of the retina using genomics, transcriptomics and proteomics. We illustrate our purpose by showing that most of the genes of interest for retinal development and those involved in inherited retinal degenerations have a restricted expression to the retina and most particularly to photoreceptors cells. We show that the exponential growth of data generated by functional genomics is a future challenge not only in terms of storage but also in terms of accessibility to the scientific community of retinal biologists in the future. Finally, we emphasize on novel perspectives that emerge from the development of redox-proteomics, the new frontier in retinal biology.
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Affiliation(s)
- Frédéric Blond
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France.
| | - Thierry Léveillard
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France.
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12
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Brommage R, Powell DR, Vogel P. Predicting human disease mutations and identifying drug targets from mouse gene knockout phenotyping campaigns. Dis Model Mech 2019; 12:dmm038224. [PMID: 31064765 PMCID: PMC6550044 DOI: 10.1242/dmm.038224] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Two large-scale mouse gene knockout phenotyping campaigns have provided extensive data on the functions of thousands of mammalian genes. The ongoing International Mouse Phenotyping Consortium (IMPC), with the goal of examining all ∼20,000 mouse genes, has examined 5115 genes since 2011, and phenotypic data from several analyses are available on the IMPC website (www.mousephenotype.org). Mutant mice having at least one human genetic disease-associated phenotype are available for 185 IMPC genes. Lexicon Pharmaceuticals' Genome5000™ campaign performed similar analyses between 2000 and the end of 2008 focusing on the druggable genome, including enzymes, receptors, transporters, channels and secreted proteins. Mutants (4654 genes, with 3762 viable adult homozygous lines) with therapeutically interesting phenotypes were studied extensively. Importantly, phenotypes for 29 Lexicon mouse gene knockouts were published prior to observations of similar phenotypes resulting from homologous mutations in human genetic disorders. Knockout mouse phenotypes for an additional 30 genes mimicked previously published human genetic disorders. Several of these models have helped develop effective treatments for human diseases. For example, studying Tph1 knockout mice (lacking peripheral serotonin) aided the development of telotristat ethyl, an approved treatment for carcinoid syndrome. Sglt1 (also known as Slc5a1) and Sglt2 (also known as Slc5a2) knockout mice were employed to develop sotagliflozin, a dual SGLT1/SGLT2 inhibitor having success in clinical trials for diabetes. Clinical trials evaluating inhibitors of AAK1 (neuropathic pain) and SGLT1 (diabetes) are underway. The research community can take advantage of these unbiased analyses of gene function in mice, including the minimally studied 'ignorome' genes.
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Affiliation(s)
- Robert Brommage
- Department of Metabolism Research, Lexicon Pharmaceuticals, 8800 Technology Forest Place, The Woodlands, TX 77381, USA
| | - David R Powell
- Department of Metabolism Research, Lexicon Pharmaceuticals, 8800 Technology Forest Place, The Woodlands, TX 77381, USA
| | - Peter Vogel
- St. Jude Children's Research Hospital, Pathology, MS 250, Room C5036A, 262 Danny Thomas Place, Memphis, TN 38105, USA
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Hanany M, Sharon D. Allele frequency analysis of variants reported to cause autosomal dominant inherited retinal diseases question the involvement of 19% of genes and 10% of reported pathogenic variants. J Med Genet 2019; 56:536-542. [PMID: 30910914 DOI: 10.1136/jmedgenet-2018-105971] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 02/18/2019] [Accepted: 03/03/2019] [Indexed: 12/22/2022]
Abstract
BACKGROUND Next generation sequencing (NGS) generates a large amount of genetic data that can be used to better characterise disease-causing variants. Our aim was to examine allele frequencies of sequence variants reported to cause autosomal dominant inherited retinal diseases (AD-IRDs). METHODS Genetic information was collected from various databases, including PubMed, the Human Genome Mutation Database, RETNET and gnomAD. RESULTS We generated a database of 1223 variants reported in 58 genes, including their allele frequency in gnomAD that contains NGS data of over 138 000 individuals. While the majority of variants are not represented in gnomAD, 138 had an allele count of >1 and were examined carefully for various aspects including cosegregation and functional analyses. The analysis revealed 122 variants that were reported pathogenic but unlikely to cause AD-IRDs. Interestingly, in some cases, these unlikely pathogenic variants were the only ones reported to cause disease in AD inheritance pattern for a particular gene, therefore raising doubt regarding the involvement of 11 (19%) of the genes in AD-IRDs. CONCLUSION We predict that these data are not limited to a specific disease or inheritance pattern since non-pathogenic variants were mistakenly reported as pathogenic in various diseases. Our results should serve as a warning sign for geneticists, variant database curators and sequencing panels' developers not to automatically accept reported variants as pathogenic but cross-reference the information with large databases.
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Affiliation(s)
- Mor Hanany
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Dror Sharon
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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14
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Liu X, Sun Y, Tian W, Wang F, Lv X, Wang M, Sun T, Zhang J, Wang L, Han M. Sema4A Responds to Hypoxia and Is Involved in Breast Cancer Progression. Biol Pharm Bull 2018; 41:1791-1796. [PMID: 30270262 DOI: 10.1248/bpb.b18-00423] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Semaphorin4A (Sema4A) is a family member of semaphorins expressed in immune cells and is also related with disease progression of tumor disease. In this study, we investigate the expression and pathological role of Sema4A in breast cancer (BCa). Our data showed that the expression of Sema4A increased in the tissues and serum of BCa patients when compared with normal controls. The expression of Sema4A in BCa cells could be induced by hypoxic treatment, whereas silencing hypoxia-inducible factor (HIF)-1α could attenuate the above induced. Furthermore, chromatin immunoprecipitation (ChIP) analysis demonstrated that HIF-1α could regulate the expression of Sema4A through directly binding to the promoter of Sema4A gene, whose enrichment could be further enhanced by hypoxic stimulation. In addition, silencing Sema4A could inhibit the proliferation, vascular endothelial growth factor (VEGF) production and the phosphorylation of Akt, extracellular signal-regulated kinase (ERK)1/2 mitogen-activated protein kinase (MAPK) and signal transduction and activator of transcription (STAT)3, but induce apoptosis of BCa cells in the presence of hypoxia. In contrast, recombinant human Sema4A treatment showed the opposite effects. Taken together, these results suggest that Sema4A could promote progression of BCa in the presence of hypoxia and it may hold potential for treatment target for BCa.
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Affiliation(s)
- Xiao Liu
- Cancer Therapy and Research Center, Shandong Provincial Hospital affiliated to Shandong University.,Zibo Central Hospital
| | | | | | | | | | | | | | - Jingjing Zhang
- Clinical Test Department of Shandong Qianfoshan Hospital
| | - Lin Wang
- Research Center for Medicinal Biotechnology, Key Laboratory for Rare & Uncommon Diseases of Shandong Province, Shandong Academy of Medicinal Sciences
| | - Mingyong Han
- Cancer Therapy and Research Center, Shandong Provincial Hospital affiliated to Shandong University
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15
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Wan L, Deng B, Wu Z, Chen X. Exome sequencing study of 20 patients with high myopia. PeerJ 2018; 6:e5552. [PMID: 30245926 PMCID: PMC6148412 DOI: 10.7717/peerj.5552] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 08/07/2018] [Indexed: 02/05/2023] Open
Abstract
Background High myopia is a common ocular disease worldwide. To expand our current understanding of the genetic basis of high myopia, we carried out a whole exome sequencing (WES) study to identify potential causal gene mutations. Methods A total of 20 individuals with high myopia were exome sequenced. A novel filtering strategy combining phenotypes and functional impact of variants was applied to identify candidate genes by multi-step bioinformatics analyses. Network and enrichment analysis were employed to examine the biological pathways involved in the candidate genes. Results In 16 out of 20 patients, we identified 20 potential pathogenic gene variants for high myopia. A total of 18 variants were located in myopia-associated chromosomal regions. In addition to the novel mutations found in five known myopia genes (ADAMTS18, CSMD1, P3H2, RPGR, and SLC39A5), we also identified pathogenic variants in seven ocular disease genes (ABCA4, CEP290, HSPG2, PCDH15, SAG, SEMA4A, and USH2A) as novel candidate genes. The biological processes associated with vision were significantly enriched in our candidate genes, including visual perception, photoreceptor cell maintenance, retinoid metabolic process, and cellular response to zinc ion starvation. Discussion Systematic mutation analysis of candidate genes was performed using WES data, functional interaction (FI) network, Gene Ontology and pathway enrichment. FI network analysis revealed important network modules and regulator linker genes (EP300, CTNNB1) potentially related to high myopia development. Our study expanded the list of candidate genes associated with high myopia, which increased the genetic screening performance and provided implications for future studies on the molecular genetics of myopia.
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Affiliation(s)
- Ling Wan
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,Department of Ophthalmology, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital and Affiliated Hospital of University of Electronic Science and Technology, Chengdu, Sichuan, China
| | - Boling Deng
- Department of Ophthalmology, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital and Affiliated Hospital of University of Electronic Science and Technology, Chengdu, Sichuan, China
| | - Zhengzheng Wu
- Department of Ophthalmology, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital and Affiliated Hospital of University of Electronic Science and Technology, Chengdu, Sichuan, China
| | - Xiaoming Chen
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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16
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Clinical and genetic characteristics of 251 consecutive patients with macular and cone/cone-rod dystrophy. Sci Rep 2018; 8:4824. [PMID: 29555955 PMCID: PMC5859282 DOI: 10.1038/s41598-018-22096-0] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 02/16/2018] [Indexed: 12/14/2022] Open
Abstract
Macular and cone/cone-rod dystrophies (MD/CCRD) demonstrate a broad genetic and phenotypic heterogeneity, with retinal alterations solely or predominantly involving the central retina. Targeted next-generation sequencing (NGS) is an efficient diagnostic tool for identifying mutations in patient with retinitis pigmentosa, which shows similar genetic heterogeneity. To detect the genetic causes of disease in patients with MD/CCRD, we implemented a two-tier procedure consisting of Sanger sequencing and targeted NGS including genes associated with clinically overlapping conditions. Disease-causing mutations were identified in 74% of 251 consecutive MD/CCRD patients (33% of the variants were novel). Mutations in ABCA4, PRPH2 and BEST1 accounted for 57% of disease cases. Further mutations were identified in CDHR1, GUCY2D, PROM1, CRX, GUCA1A, CERKL, MT-TL1, KIF11, RP1L1, MERTK, RDH5, CDH3, C1QTNF5, CRB1, JAG1, DRAM2, POC1B, NPHP1 and RPGR. We provide detailed illustrations of rare phenotypes, including autofluorescence and optical coherence tomography imaging. Targeted NGS also identified six potential novel genotype-phenotype correlations for FAM161A, INPP5E, MERTK, FBLN5, SEMA4A and IMPDH1. Clinical reassessment of genetically unsolved patients revealed subgroups with similar retinal phenotype, indicating a common molecular disease cause in each subgroup.
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17
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Lu Y, Zhou D, King R, Zhu S, Simpson CL, Jones BC, Zhang W, Geisert EE, Lu L. The genetic dissection of Myo7a gene expression in the retinas of BXD mice. Mol Vis 2018; 24:115-126. [PMID: 29430167 PMCID: PMC5802760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 01/31/2018] [Indexed: 11/16/2022] Open
Abstract
Purpose Usher syndrome (US) is characterized by a loss of vision due to retinitis pigmentosa (RP) and deafness. US has three clinical subtypes, but even within each subtype, the severity varies. Myosin VIIA, coded by Myo7a, has been identified as one of the causal genes of US. This study aims to identify pathways and other genes through which Myo7a interacts to affect the presentation of US symptoms. Methods In this study, we used the retinal tissue of BXD recombinant inbred (RI) mice to examine the expression of Myo7a and perform genetic mapping. Expression quantitative trait locus (eQTL), single nucleotide polymorphism (SNP), and gene correlation analysis were performed using GeneNetwork. Gene set enrichment analysis was performed using WebGestalt, and gene network construction was performed using the Gene Cohesion Analysis Tool. Results We found Myo7a to be cis-regulated, with varied levels of expression across BXD strains. Here, we propose a genetic network with 40 genes whose expression is highly correlated with Myo7a. Among these genes, six have been linked to retinal diseases, three to deafness, and five share a transcription factor with Myo7a. Gene ontology and pathway analysis revealed a strong connection among ion channel activity, Myo7a, and US. Conclusions Although Myo7a is a causal gene of US type I, this gene works with many other genes and pathways to affect the severity of US. Many of the genes found in the genetic network, pathways, and gene ontology categories of Myo7a are related to either deafness or blindness. Further investigation is needed to examine the specific relationships between these genes, which may assist in the treatment of US.
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Affiliation(s)
- Ye Lu
- Department of Ophthalmology, The First Affiliated Hospital, Zhejiang University College of Medicine, Hangzhou, China
| | - Diana Zhou
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN
| | - Rebecca King
- Department of Ophthalmology and Emory Eye Center, Emory University, Atlanta, GA
| | - Shuang Zhu
- Department of Ophthalmology & Visual Sciences, University of Texas Medical Branch, Galveston, TX
| | - Claire L. Simpson
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN
| | - Byron C. Jones
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN
| | - Wenbo Zhang
- Department of Ophthalmology & Visual Sciences, University of Texas Medical Branch, Galveston, TX
| | - Eldon E. Geisert
- Department of Ophthalmology and Emory Eye Center, Emory University, Atlanta, GA
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN
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18
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Bryant L, Lozynska O, Han G, Morgan JIW, Gai X, Maguire AM, Aleman T, Bennett J. On variants and disease-causing mutations: Case studies of a SEMA4A variant identified in inherited blindness. Ophthalmic Genet 2017; 39:144-146. [PMID: 28805479 DOI: 10.1080/13816810.2017.1354384] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The p.R713Q variant of the semaphorin-4a-encoding gene, SEMA4a, has been reported to cause autosomal dominant retinitis pigmentosa. Here we show three families with retinal degeneration in which unaffected family members are either homozygous or heterozygous for the variant. The p.R713Q variant in SEMA4A is insufficient to cause either autosomal recessive or autosomal dominant retinitis pigmentosa and is unlikely to be pathogenic.
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Affiliation(s)
- Laura Bryant
- a Center for Advanced Retinal and Ocular Therapeutics (CAROT) and F.M. Kirby Center for Molecular Ophthalmology , Scheie Eye Institute, University of Pennsylvania , Philadelphia , Pennsylvania , USA.,b Department of Ophthalmology , Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine , Philadelphia , Pennsylvania , USA
| | - Olga Lozynska
- a Center for Advanced Retinal and Ocular Therapeutics (CAROT) and F.M. Kirby Center for Molecular Ophthalmology , Scheie Eye Institute, University of Pennsylvania , Philadelphia , Pennsylvania , USA.,b Department of Ophthalmology , Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine , Philadelphia , Pennsylvania , USA
| | - Grace Han
- a Center for Advanced Retinal and Ocular Therapeutics (CAROT) and F.M. Kirby Center for Molecular Ophthalmology , Scheie Eye Institute, University of Pennsylvania , Philadelphia , Pennsylvania , USA.,b Department of Ophthalmology , Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine , Philadelphia , Pennsylvania , USA
| | - Jessica I W Morgan
- a Center for Advanced Retinal and Ocular Therapeutics (CAROT) and F.M. Kirby Center for Molecular Ophthalmology , Scheie Eye Institute, University of Pennsylvania , Philadelphia , Pennsylvania , USA.,b Department of Ophthalmology , Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine , Philadelphia , Pennsylvania , USA
| | - Xiaowu Gai
- c Department of Pathology and Laboratory Medicine , Children's Hospital Los Angeles , Los Angeles , California , USA
| | - Albert M Maguire
- a Center for Advanced Retinal and Ocular Therapeutics (CAROT) and F.M. Kirby Center for Molecular Ophthalmology , Scheie Eye Institute, University of Pennsylvania , Philadelphia , Pennsylvania , USA.,b Department of Ophthalmology , Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine , Philadelphia , Pennsylvania , USA
| | - Tomas Aleman
- a Center for Advanced Retinal and Ocular Therapeutics (CAROT) and F.M. Kirby Center for Molecular Ophthalmology , Scheie Eye Institute, University of Pennsylvania , Philadelphia , Pennsylvania , USA.,b Department of Ophthalmology , Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine , Philadelphia , Pennsylvania , USA
| | - Jean Bennett
- a Center for Advanced Retinal and Ocular Therapeutics (CAROT) and F.M. Kirby Center for Molecular Ophthalmology , Scheie Eye Institute, University of Pennsylvania , Philadelphia , Pennsylvania , USA.,b Department of Ophthalmology , Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine , Philadelphia , Pennsylvania , USA
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19
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Genetic characterization and disease mechanism of retinitis pigmentosa; current scenario. 3 Biotech 2017; 7:251. [PMID: 28721681 DOI: 10.1007/s13205-017-0878-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 07/10/2017] [Indexed: 12/21/2022] Open
Abstract
Retinitis pigmentosa is a group of genetically transmitted disorders affecting 1 in 3000-8000 individual people worldwide ultimately affecting the quality of life. Retinitis pigmentosa is characterized as a heterogeneous genetic disorder which leads by progressive devolution of the retina leading to a progressive visual loss. It can occur in syndromic (with Usher syndrome and Bardet-Biedl syndrome) as well as non-syndromic nature. The mode of inheritance can be X-linked, autosomal dominant or autosomal recessive manner. To date 58 genes have been reported to associate with retinitis pigmentosa most of them are either expressed in photoreceptors or the retinal pigment epithelium. This review focuses on the disease mechanisms and genetics of retinitis pigmentosa. As retinitis pigmentosa is tremendously heterogeneous disorder expressing a multiplicity of mutations; different variations in the same gene might induce different disorders. In recent years, latest technologies including whole-exome sequencing contributing effectively to uncover the hidden genesis of retinitis pigmentosa by reporting new genetic mutations. In future, these advancements will help in better understanding the genotype-phenotype correlations of disease and likely to develop new therapies.
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20
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de Pedro-Cuesta J, Martínez-Martín P, Rábano A, Alcalde-Cabero E, José García López F, Almazán-Isla J, Ruiz-Tovar M, Medrano MJ, Avellanal F, Calero O, Calero M. Drivers: A Biologically Contextualized, Cross-Inferential View of the Epidemiology of Neurodegenerative Disorders. J Alzheimers Dis 2016; 51:1003-22. [PMID: 26923014 PMCID: PMC4927850 DOI: 10.3233/jad-150884] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Background: Sutherland et al. (2011) suggested that, instead of risk factors for single neurodegenerative disorders (NDDs), there was a need to identify specific “drivers”, i.e., risk factors with impact on specific deposits, such as amyloid-β, tau, or α-synuclein, acting across entities. Objectives and Methods: Redefining drivers as “neither protein/gene- nor entity-specific features identifiable in the clinical and general epidemiology of conformational NDDs (CNDDs) as potential footprints of templating/spread/transfer mechanisms”, we conducted an analysis of the epidemiology of ten CNDDs, searching for patterns. Results: We identified seven potential drivers, each of which was shared by at least two CNDDs: 1) an age-at-exposure-related susceptibility to Creutzfeldt-Jakob disease (CJD) and several late-life CNDDs; 2) a relationship between age at onset, survival, and incidence; 3) shared genetic risk factors for CJD and late-life CNNDs; 4) partly shared personal (diagnostic, educational, behavioral, and social risk factors) predating clinical onset of late-life CNDDs; 5) two environmental risk factors, namely, surgery for sporadic CJD and amyotrophic lateral sclerosis, and Bordetella pertussis infection for Parkinson’s disease; 6) reticulo-endothelial system stressors or general drivers (andropause or premenopausal estrogen deficiency, APOEɛ4, and vascular risk factors) for late-life CNDDs such as dementia/Alzheimer’s disease, type-2 diabetes mellitus, and some sporadic cardiac and vascular degenerative diseases; and 7) a high, invariant incidence ratio of sporadic to genetic forms of mid- and late-life CNDDs, and type-2 diabetes mellitus. Conclusion: There might be a systematic epidemiologic pattern induced by specific proteins (PrP, TDP-43, SOD1, α-synuclein, amyloid-β, tau, Langerhans islet peptide, and transthyretin) or established combinations of these.
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Affiliation(s)
- Jesús de Pedro-Cuesta
- Department of Applied Epidemiology, National Center for Epidemiology, Carlos III Institute of Health, Madrid, Spain.,Consortium for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Pablo Martínez-Martín
- Department of Applied Epidemiology, National Center for Epidemiology, Carlos III Institute of Health, Madrid, Spain.,Consortium for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Alberto Rábano
- Consortium for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain.,Alzheimer Disease Research Unit, CIEN Foundation, Queen Sofia Foundation Alzheimer Center, Madrid, Spain
| | - Enrique Alcalde-Cabero
- Department of Applied Epidemiology, National Center for Epidemiology, Carlos III Institute of Health, Madrid, Spain.,Consortium for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Fernando José García López
- Department of Applied Epidemiology, National Center for Epidemiology, Carlos III Institute of Health, Madrid, Spain.,Consortium for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Javier Almazán-Isla
- Department of Applied Epidemiology, National Center for Epidemiology, Carlos III Institute of Health, Madrid, Spain.,Consortium for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - María Ruiz-Tovar
- Department of Applied Epidemiology, National Center for Epidemiology, Carlos III Institute of Health, Madrid, Spain.,Consortium for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Maria-José Medrano
- Department of Applied Epidemiology, National Center for Epidemiology, Carlos III Institute of Health, Madrid, Spain
| | - Fuencisla Avellanal
- Department of Applied Epidemiology, National Center for Epidemiology, Carlos III Institute of Health, Madrid, Spain.,Consortium for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Olga Calero
- Consortium for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain.,Chronic Disease Programme, Carlos III Institute of Health, Madrid, Spain
| | - Miguel Calero
- Consortium for Biomedical Research in Neurodegenerative Diseases (CIBERNED), Madrid, Spain.,Alzheimer Disease Research Unit, CIEN Foundation, Queen Sofia Foundation Alzheimer Center, Madrid, Spain.,Chronic Disease Programme, Carlos III Institute of Health, Madrid, Spain
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Ito D, Kumanogoh A. The role of Sema4A in angiogenesis, immune responses, carcinogenesis, and retinal systems. Cell Adh Migr 2016; 10:692-699. [PMID: 27736304 PMCID: PMC5160039 DOI: 10.1080/19336918.2016.1215785] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Semaphorins were originally identified as axon guidance cues that regulate the functional activity of axons in the nervous system. In addition, accumulating evidence indicates that semaphorins have multiple functions in physiological and pathogenic processes, including vascular development, tumor progression, and immune responses. Sema4A is a semaphorin expressed in immune cells, and is thus termed an “immune semaphorin.” Sema4A has 4 types of receptors: Plexin D family, Plexin B family, Tim-2, and Nrp-1. Recent studies suggest that Sema4A plays critical roles in many processes including cell–cell interactions, immune-cell activation, differentiation, and migration. In other studies, Sema4A is also associated with carcinogenesis and retinal systems. In this review, we summarize current knowledge regarding the biology of Sema4A in relation to angiogenesis, immune responses, colorectal cancer, and the retina.
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Affiliation(s)
- Daisuke Ito
- a Department of Respiratory Medicine , Allergy and Rheumatic Disease, Osaka University Graduate School of Medicine , Suita , Osaka , Japan
| | - Atsushi Kumanogoh
- a Department of Respiratory Medicine , Allergy and Rheumatic Disease, Osaka University Graduate School of Medicine , Suita , Osaka , Japan
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22
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Ullah I, Kabir F, Iqbal M, Gottsch CBS, Naeem MA, Assir MZ, Khan SN, Akram J, Riazuddin S, Ayyagari R, Hejtmancik JF, Riazuddin SA. Pathogenic mutations in TULP1 responsible for retinitis pigmentosa identified in consanguineous familial cases. Mol Vis 2016; 22:797-815. [PMID: 27440997 PMCID: PMC4947966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 07/14/2016] [Indexed: 11/16/2022] Open
Abstract
PURPOSE To identify pathogenic mutations responsible for autosomal recessive retinitis pigmentosa (arRP) in consanguineous familial cases. METHODS Seven large familial cases with multiple individuals diagnosed with retinitis pigmentosa were included in the study. Affected individuals in these families underwent ophthalmic examinations to document the symptoms and confirm the initial diagnosis. Blood samples were collected from all participating members, and genomic DNA was extracted. An exclusion analysis with microsatellite markers spanning the TULP1 locus on chromosome 6p was performed, and two-point logarithm of odds (LOD) scores were calculated. All coding exons along with the exon-intron boundaries of TULP1 were sequenced bidirectionally. We constructed a single nucleotide polymorphism (SNP) haplotype for the four familial cases harboring the K489R allele and estimated the likelihood of a founder effect. RESULTS The ophthalmic examinations of the affected individuals in these familial cases were suggestive of RP. Exclusion analyses confirmed linkage to chromosome 6p harboring TULP1 with positive two-point LOD scores. Subsequent Sanger sequencing identified the single base pair substitution in exon14, c.1466A>G (p.K489R), in four families. Additionally, we identified a two-base deletion in exon 4, c.286_287delGA (p.E96Gfs77*); a homozygous splice site variant in intron 14, c.1495+4A>C; and a novel missense variation in exon 15, c.1561C>T (p.P521S). All mutations segregated with the disease phenotype in the respective families and were absent in ethnically matched control chromosomes. Haplotype analysis suggested (p<10(-6)) that affected individuals inherited the causal mutation from a common ancestor. CONCLUSIONS Pathogenic mutations in TULP1 are responsible for the RP phenotype in seven familial cases with a common ancestral mutation responsible for the disease phenotype in four of the seven 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
| | - Muhammad Iqbal
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | | | - Muhammad Asif Naeem
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Zaman Assir
- Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan,National Centre for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Shaheen N. Khan
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 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
| | - 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
| | - Radha Ayyagari
- Shiley Eye Institute, University of California, San Diego, CA
| | - 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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23
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Gurrapu S, Tamagnone L. Transmembrane semaphorins: Multimodal signaling cues in development and cancer. Cell Adh Migr 2016; 10:675-691. [PMID: 27295627 DOI: 10.1080/19336918.2016.1197479] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Semaphorins constitute a large family of membrane-bound and secreted proteins that provide guidance cues for axon pathfinding and cell migration. Although initially discovered as repelling cues for axons in nervous system, they have been found to regulate cell adhesion and motility, angiogenesis, immune function and tumor progression. Notably, semaphorins are bifunctional cues and for instance can mediate both repulsive and attractive functions in different contexts. While many studies focused so far on the function of secreted family members, class 1 semaphorins in invertebrates and class 4, 5 and 6 in vertebrate species comprise around 14 transmembrane semaphorin molecules with emerging functional relevance. These can signal in juxtacrine, paracrine and autocrine fashion, hence mediating long and short range repulsive and attractive guidance cues which have a profound impact on cellular morphology and functions. Importantly, transmembrane semaphorins are capable of bidirectional signaling, acting both in "forward" mode via plexins (sometimes in association with receptor tyrosine kinases), and in "reverse" manner through their cytoplasmic domains. In this review, we will survey known molecular mechanisms underlying the functions of transmembrane semaphorins in development and cancer.
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Affiliation(s)
- Sreeharsha Gurrapu
- a Department of Oncology , University of Torino c/o IRCCS , Candiolo ( TO ), Italy.,b Candiolo Cancer Institute, IRCCS-FPO , Candiolo ( TO ), Italy
| | - Luca Tamagnone
- a Department of Oncology , University of Torino c/o IRCCS , Candiolo ( TO ), Italy.,b Candiolo Cancer Institute, IRCCS-FPO , Candiolo ( TO ), Italy
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24
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Kabir F, Ullah I, Ali S, Gottsch AD, Naeem MA, Assir MZ, Khan SN, Akram J, Riazuddin S, Ayyagari R, Hejtmancik JF, Riazuddin SA. Loss of function mutations in RP1 are responsible for retinitis pigmentosa in consanguineous familial cases. Mol Vis 2016; 22:610-25. [PMID: 27307693 PMCID: PMC4901054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 06/08/2016] [Indexed: 10/31/2022] Open
Abstract
PURPOSE This study was undertaken to identify causal mutations responsible for autosomal recessive retinitis pigmentosa (arRP) in consanguineous families. METHODS Large consanguineous families were ascertained from the Punjab province of Pakistan. An ophthalmic examination consisting of a fundus evaluation and electroretinography (ERG) was completed, and small aliquots of blood were collected from all participating individuals. Genomic DNA was extracted from white blood cells, and a genome-wide linkage or a locus-specific exclusion analysis was completed with polymorphic short tandem repeats (STRs). Two-point logarithm of odds (LOD) scores were calculated, and all coding exons and exon-intron boundaries of RP1 were sequenced to identify the causal mutation. RESULTS The ophthalmic examination showed that affected individuals in all families manifest cardinal symptoms of RP. Genome-wide scans localized the disease phenotype to chromosome 8q, a region harboring RP1, a gene previously implicated in the pathogenesis of RP. Sanger sequencing identified a homozygous single base deletion in exon 4: c.3697delT (p.S1233Pfs22*), a single base substitution in intron 3: c.787+1G>A (p.I263Nfs8*), a 2 bp duplication in exon 2: c.551_552dupTA (p.Q185Yfs4*) and an 11,117 bp deletion that removes all three coding exons of RP1. These variations segregated with the disease phenotype within the respective families and were not present in ethnically matched control samples. CONCLUSIONS These results strongly suggest that these mutations in RP1 are responsible for the retinal phenotype in affected individuals of all four consanguineous families.
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Affiliation(s)
- Firoz Kabir
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Inayat Ullah
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Shahbaz Ali
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | | | - Muhammad Asif Naeem
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Zaman Assir
- Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan,National Centre for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Shaheen N. Khan
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 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
| | - 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
| | - Radha Ayyagari
- Shiley Eye Institute, University of California, San Diego, CA
| | - 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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25
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Rose AM, Bhattacharya SS. Variant haploinsufficiency and phenotypic non-penetrance in PRPF31-associated retinitis pigmentosa. Clin Genet 2016; 90:118-26. [PMID: 26853529 DOI: 10.1111/cge.12758] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Revised: 02/02/2016] [Accepted: 02/03/2016] [Indexed: 11/30/2022]
Abstract
Retinitis pigmentosa (RP) is a genetically heterogenous group of inherited disorders, characterized by death of the retinal photoreceptor cells, leading to progressive visual impairment. One form of RP is caused by mutations in the ubiquitously expressed splicing factor, PRPF31, this form being known as RP11. An intriguing feature of RP11 is the presence of non-penetrance, which has been observed in the majority of PRPF31 mutation-carrying families. In contrast to variable expressivity, which is highly pervasive, true non-penetrance is a very rare phenomenon in Mendelian disorders. In this article, the molecular mechanisms underlying phenotypic non-penetrance in RP11 are explored. It is an elegant example of how our understanding of monogenic disorders has evolved from studying only the disease gene, to considering a mutation on the genetic background of the individual - the logical evolution in this genomic era.
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Affiliation(s)
- A M Rose
- Department of Genetics, UCL Institute of Ophthalmology, London, UK
| | - S S Bhattacharya
- Department of Genetics, UCL Institute of Ophthalmology, London, UK
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26
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Next-generation sequencing-based molecular diagnosis of 12 inherited retinal disease probands of Uyghur ethnicity. Sci Rep 2016; 6:21384. [PMID: 26856745 PMCID: PMC4746660 DOI: 10.1038/srep21384] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 01/22/2016] [Indexed: 01/10/2023] Open
Abstract
Inherited retinal disease (IRD) is a category of genetic disorders affecting retina. Understanding the molecular basis of IRD is vital for clinical and genetic classification of patients. Uyghur people is an isolated ethnic group mainly residing in northwestern China with genetic admixture from Europeans and East Asians. The genetic etiology of IRD in this specific population still remains unknown. Here, by next-generation sequencing (NGS), we screened mutations in over 200 known retinal disease genes in a cohort of 12 unrelated Uyghur IRD probands. Out of the 12 probands, six are solved with high confidence, two with low confidence, while the remaining four are unsolved. We identified known disease-causing alleles in this cohort that suggest ancient Uyghur migration and also discovered eight novel disease-associated variants. Our results showed NGS-based mutation screening as a reliable approach for molecular diagnosis. In addition, this approach can also be applied to reveal the genetic history of a specific ethnic group.
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27
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Lu QK, Zhao N, Lv YS, Gong WK, Wang HY, Tong QH, Lai XM, Liu RR, Fang MY, Zhang JG, Du ZF, Zhang XN. A novel CRX mutation by whole-exome sequencing in an autosomal dominant cone-rod dystrophy pedigree. Int J Ophthalmol 2015; 8:1112-7. [PMID: 26682157 DOI: 10.3980/j.issn.2222-3959.2015.06.06] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 03/30/2015] [Indexed: 11/02/2022] Open
Abstract
AIM To identify the disease-causing gene mutation in a Chinese pedigree with autosomal dominant cone-rod dystrophy (adCORD). METHODS A southern Chinese adCORD pedigree including 9 affected individuals was studied. Whole-exome sequencing (WES), coupling the Agilent whole-exome capture system to the Illumina HiSeq 2000 DNA sequencing platform was used to search the specific gene mutation in 3 affected family members and 1 unaffected member. After a suggested variant was found through the data analysis, the putative mutation was validated by Sanger DNA sequencing of samples from all available family members. RESULTS The results of both WES and Sanger sequencing revealed a novel nonsense mutation c.C766T (p.Q256X) within exon 5 of CRX gene which was pathogenic for adCORD in this family. The mutation could affect photoreceptor-specific gene expression with a dominant-negative effect and resulted in loss of the OTX tail, thus the mutant protein occupies the CRX-binding site in target promoters without establishing an interaction and, consequently, may block transactivation. CONCLUSION All modes of Mendelian inheritance in CORD have been observed, and genetic heterogeneity is a hallmark of CORD. Therefore, conventional genetic diagnosis of CORD would be time-consuming and labor-intensive. Our study indicated the robustness and cost-effectiveness of WES in the genetic diagnosis of CORD.
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Affiliation(s)
- Qin-Kang Lu
- Ophthalmology Center, Yinzhou People's Hospital, Yinzhou Hospital Affiliated to Medical School of Ningbo University, Ningbo 315040, Zhejiang Province, China
| | - Na Zhao
- Ophthalmology Center, Yinzhou People's Hospital, Yinzhou Hospital Affiliated to Medical School of Ningbo University, Ningbo 315040, Zhejiang Province, China
| | - Ya-Su Lv
- Department of Cell Biology and Medical Genetics, Research Center for Molecular Medicine, Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang Province, China
| | - Wei-Kun Gong
- Ophthalmology Center, Yinzhou People's Hospital, Yinzhou Hospital Affiliated to Medical School of Ningbo University, Ningbo 315040, Zhejiang Province, China
| | - Hui-Yun Wang
- Ophthalmology Center, Yinzhou People's Hospital, Yinzhou Hospital Affiliated to Medical School of Ningbo University, Ningbo 315040, Zhejiang Province, China
| | - Qi-Hu Tong
- Ophthalmology Center, Yinzhou People's Hospital, Yinzhou Hospital Affiliated to Medical School of Ningbo University, Ningbo 315040, Zhejiang Province, China
| | - Xiao-Ming Lai
- Ophthalmology Center, Yinzhou People's Hospital, Yinzhou Hospital Affiliated to Medical School of Ningbo University, Ningbo 315040, Zhejiang Province, China
| | - Rong-Rong Liu
- Department of Cell Biology and Medical Genetics, Research Center for Molecular Medicine, Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang Province, China
| | - Ming-Yan Fang
- BGI-Shenzhen, Shenzhen 518083, Guangdong Province, China
| | - Jian-Guo Zhang
- BGI-Shenzhen, Shenzhen 518083, Guangdong Province, China
| | - Zhen-Fang Du
- Department of Cell Biology and Medical Genetics, Research Center for Molecular Medicine, Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang Province, China
| | - Xian-Ning Zhang
- Department of Cell Biology and Medical Genetics, Research Center for Molecular Medicine, Institute of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang Province, China
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28
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Boulanger-Scemama E, El Shamieh S, Démontant V, Condroyer C, Antonio A, Michiels C, Boyard F, Saraiva JP, Letexier M, Souied E, Mohand-Saïd S, Sahel JA, Zeitz C, Audo I. Next-generation sequencing applied to a large French cone and cone-rod dystrophy cohort: mutation spectrum and new genotype-phenotype correlation. Orphanet J Rare Dis 2015; 10:85. [PMID: 26103963 PMCID: PMC4566196 DOI: 10.1186/s13023-015-0300-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 06/15/2015] [Indexed: 12/21/2022] Open
Abstract
Background Cone and cone-rod dystrophies are clinically and genetically heterogeneous inherited retinal disorders with predominant cone impairment. They should be distinguished from the more common group of rod-cone dystrophies (retinitis pigmentosa) due to their more severe visual prognosis with early central vision loss. The purpose of our study was to document mutation spectrum of a large French cohort of cone and cone-rod dystrophies. Methods We applied Next-Generation Sequencing targeting a panel of 123 genes implicated in retinal diseases to 96 patients. A systematic filtering approach was used to identify likely disease causing variants, subsequently confirmed by Sanger sequencing and co-segregation analysis when possible. Results Overall, the likely causative mutations were detected in 62.1 % of cases, revealing 33 known and 35 novel mutations. This rate was higher for autosomal dominant (100 %) than autosomal recessive cases (53.8 %). Mutations in ABCA4 and GUCY2D were responsible for 19.2 % and 29.4 % of resolved cases with recessive and dominant inheritance, respectively. Furthermore, unexpected genotype-phenotype correlations were identified, confirming the complexity of inherited retinal disorders with phenotypic overlap between cone-rod dystrophies and other retinal diseases. Conclusions In summary, this time-efficient approach allowed mutation detection in the most important cohort of cone-rod dystrophies investigated so far covering the largest number of genes. Association of known gene defects with novel phenotypes and mode of inheritance were established. Electronic supplementary material The online version of this article (doi:10.1186/s13023-015-0300-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elise Boulanger-Scemama
- INSERM, U968, Paris, F-75012, France.,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France.,CNRS, UMR_7210, Paris, F-75012, France
| | - Said El Shamieh
- INSERM, U968, Paris, F-75012, France.,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France.,CNRS, UMR_7210, Paris, F-75012, France
| | - Vanessa Démontant
- INSERM, U968, Paris, F-75012, France.,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France.,CNRS, UMR_7210, Paris, F-75012, France
| | - Christel Condroyer
- INSERM, U968, Paris, F-75012, France.,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France.,CNRS, UMR_7210, Paris, F-75012, France
| | - Aline Antonio
- INSERM, U968, Paris, F-75012, France.,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France.,CNRS, UMR_7210, Paris, F-75012, France.,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU ViewMaintain, INSERM-DHOS CIC 1423, Paris, F-75012, France
| | - Christelle Michiels
- INSERM, U968, Paris, F-75012, France.,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France.,CNRS, UMR_7210, Paris, F-75012, France
| | - Fiona Boyard
- INSERM, U968, Paris, F-75012, France.,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France.,CNRS, UMR_7210, Paris, F-75012, France
| | - Jean-Paul Saraiva
- IntegraGen SA, Genopole CAMPUS 1 bat G8 FR-91030 EVRY, Paris, France
| | - Mélanie Letexier
- IntegraGen SA, Genopole CAMPUS 1 bat G8 FR-91030 EVRY, Paris, France
| | - Eric Souied
- Centre Hospitalier Intercommunal de Créteil, Department of Ophthalmology, Université Paris-Est Créteil, 94000, Créteil, France
| | - Saddek Mohand-Saïd
- INSERM, U968, Paris, F-75012, France.,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France.,CNRS, UMR_7210, Paris, F-75012, France.,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU ViewMaintain, INSERM-DHOS CIC 1423, Paris, F-75012, France
| | - José-Alain Sahel
- INSERM, U968, Paris, F-75012, France.,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France.,CNRS, UMR_7210, Paris, F-75012, France.,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU ViewMaintain, INSERM-DHOS CIC 1423, Paris, F-75012, France.,Fondation Ophtalmologique Adolphe de Rothschild, 75019, Paris, France.,Académie des Sciences-Institut de France, 75006, Paris, France.,University College London Institute of Ophthalmology, 11-43 Bath Street, London, EC1V 9EL, UK
| | - Christina Zeitz
- INSERM, U968, Paris, F-75012, France. .,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France. .,CNRS, UMR_7210, Paris, F-75012, France.
| | - Isabelle Audo
- INSERM, U968, Paris, F-75012, France. .,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France. .,CNRS, UMR_7210, Paris, F-75012, France. .,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU ViewMaintain, INSERM-DHOS CIC 1423, Paris, F-75012, France. .,University College London Institute of Ophthalmology, 11-43 Bath Street, London, EC1V 9EL, UK.
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29
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Nash BM, Wright DC, Grigg JR, Bennetts B, Jamieson RV. Retinal dystrophies, genomic applications in diagnosis and prospects for therapy. Transl Pediatr 2015; 4:139-63. [PMID: 26835369 PMCID: PMC4729094 DOI: 10.3978/j.issn.2224-4336.2015.04.03] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Retinal dystrophies (RDs) are degenerative diseases of the retina which have marked clinical and genetic heterogeneity. Common presentations among these disorders include night or colour blindness, tunnel vision and subsequent progression to complete blindness. The known causative disease genes have a variety of developmental and functional roles with mutations in more than 120 genes shown to be responsible for the phenotypes. In addition, mutations within the same gene have been shown to cause different disease phenotypes, even amongst affected individuals within the same family highlighting further levels of complexity. The known disease genes encode proteins involved in retinal cellular structures, phototransduction, the visual cycle, and photoreceptor structure or gene regulation. This review aims to demonstrate the high degree of genetic complexity in both the causative disease genes and their associated phenotypes, highlighting the more common clinical manifestation of retinitis pigmentosa (RP). The review also provides insight to recent advances in genomic molecular diagnosis and gene and cell-based therapies for the RDs.
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Affiliation(s)
- Benjamin M Nash
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
| | - Dale C Wright
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
| | - John R Grigg
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
| | - Bruce Bennetts
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
| | - Robyn V Jamieson
- 1 Eye Genetics Research Group, Children's Medical Research Institute, University of Sydney, The Children's Hospital at Westmead and Save Sight Institute, Sydney, NSW, Australia ; 2 Sydney Genome Diagnostics, The Children's Hospital at Westmead, Sydney, NSW, Australia ; 3 Discipline of Paediatrics and Child Health, Sydney Medical School, University of Sydney, NSW, Australia
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30
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Ravesh Z, El Asrag ME, Weisschuh N, McKibbin M, Reuter P, Watson CM, Baumann B, Poulter JA, Sajid S, Panagiotou ES, O’Sullivan J, Abdelhamed Z, Bonin M, Soltanifar M, Black GC, Din MAU, Toomes C, Ansar M, Inglehearn CF, Wissinger B, Ali M. Novel C8orf37 mutations cause retinitis pigmentosa in consanguineous families of Pakistani origin. Mol Vis 2015; 21:236-43. [PMID: 25802487 PMCID: PMC4357040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 03/05/2015] [Indexed: 11/28/2022] Open
Abstract
PURPOSE To investigate the molecular basis of retinitis pigmentosa in two consanguineous families of Pakistani origin with multiple affected members. METHODS Homozygosity mapping and Sanger sequencing of candidate genes were performed in one family while the other was analyzed with whole exome next-generation sequencing. A minigene splicing assay was used to confirm the splicing defects. RESULTS In family MA48, a novel homozygous nucleotide substitution in C8orf37, c.244-2A>C, that disrupted the consensus splice acceptor site of exon 3 was found. The minigene splicing assay revealed that this mutation activated a cryptic splice site within exon 3, causing a 22 bp deletion in the transcript that is predicted to lead to a frameshift followed by premature protein truncation. In family MA13, a novel homozygous null mutation in C8orf37, c.555G>A, p.W185*, was identified. Both mutations segregated with the disease phenotype as expected in a recessive manner and were absent in 8,244 unrelated individuals of South Asian origin. CONCLUSIONS In this report, we describe C8orf37 mutations that cause retinal dystrophy in two families of Pakistani origin, contributing further data on the phenotype and the spectrum of mutations in this form of retinitis pigmentosa.
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Affiliation(s)
- Zeinab Ravesh
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan,Molecular Genetics Laboratory, Institute of Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Mohammed E. El Asrag
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, UK,Department of Zoology, Faculty of Science, Benha University, Benha, Egypt
| | - Nicole Weisschuh
- Molecular Genetics Laboratory, Institute of Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Martin McKibbin
- The Eye Department, St. James’s University Hospital, Leeds, UK
| | - Peggy Reuter
- Molecular Genetics Laboratory, Institute of Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | | | - Britta Baumann
- Molecular Genetics Laboratory, Institute of Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - James A. Poulter
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, UK
| | - Sundus Sajid
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Evangelia S. Panagiotou
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, UK
| | - James O’Sullivan
- Manchester Centre for Genomic Medicine, University of Manchester, St Mary's Hospital, Manchester, UK
| | - Zakia Abdelhamed
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, UK
| | - Michael Bonin
- Department of Medical Genetics, Angewandte Genomik, University of Tübingen, Tübingen, Germany
| | - Mehdi Soltanifar
- Department of Ophthalmology, Pakistan Institute of Medical Sciences, Islamabad, Pakistan
| | - Graeme C.M. Black
- Manchester Centre for Genomic Medicine, University of Manchester, St Mary's Hospital, Manchester, UK
| | | | - Carmel Toomes
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, UK
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Chris F. Inglehearn
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, UK
| | - Bernd Wissinger
- Molecular Genetics Laboratory, Institute of Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Manir Ali
- Section of Ophthalmology and Neuroscience, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, UK
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31
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Masuda T, Taniguchi M. Congenital diseases and semaphorin signaling: overview to date of the evidence linking them. Congenit Anom (Kyoto) 2015; 55:26-30. [PMID: 25385160 DOI: 10.1111/cga.12095] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 10/31/2014] [Indexed: 12/12/2022]
Abstract
Semaphorins and their receptors, neuropilins and plexins, were initially characterized as a modulator of axonal guidance during development, but are now recognized as a regulator of a wide range of developmental events including morphogenesis and angiogenesis, and activities of the immune system. Owing to the development of next-generation sequencing technologies together with other useful DNA assays, it has also become clear that semaphorin signaling plays a crucial role in many congenital diseases such as retinal degeneration and congenital heart defects. This review summarizes the recent knowledge about the relationship between a variety of congenital diseases and semaphorin signaling.
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Affiliation(s)
- Tomoyuki Masuda
- Department of Neurobiology, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
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32
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Ko JA, Hirata J, Yamane K, Sonoda KH, Kiuchi Y. Up-regulation of semaphorin 4A expression in human retinal pigment epithelial cells by PACAP released from cocultured neural cells. Cell Biochem Funct 2014; 33:29-36. [PMID: 25515530 DOI: 10.1002/cbf.3082] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 11/04/2014] [Accepted: 11/05/2014] [Indexed: 01/01/2023]
Abstract
Development and homeostasis of multicellular organisms require interactions between neighbouring cells. We recently established an in vitro model of cell-cell interaction based on a collagen vitrigel membrane. We have now examined the role of neural cells in retinal homeostasis by coculture of human retinal pigment epithelial (RPE) cells and neural cells on opposite sides of such a membrane. The neural cells (differentiated PC12 cells) induced up-regulation of semaphorin 4A (Sema4A), a member of the semaphorin family of neural guidance proteins, in RPE (ARPE19) cells. This effect of the neural cells was mimicked by the neuropeptide pituitary adenylate cyclase-activating polypeptide (PACAP) and was abolished by the PACAP antagonist PACAP(6-38). Coculture with neural cells or stimulation with PACAP also induced the phosphorylation of extracellular-signal-regulated kinase in ARPE19 cells, and this effect of the neural cells was inhibited by PACAP(6-38). Finally, among various cytokines examined, only the amount of interleukin-6 released by cocultures of ARPE19 and neural cells differed from that released by ARPE19 cells cultured alone. Interleukin-6 was not detected in culture supernatants of neural cells, and the reduction in the amount of interleukin-6 released by the cocultures compared with that released by ARPE19 cells alone was prevented by PACAP(6-38). Our findings suggest that PACAP released from retinal neural cells (photoreceptors or optic nerve cells) may regulate Sema4A expression in RPE cells and thereby contribute to the maintenance of retinal structure and function. Development and homeostasis of multicellular organisms require interactions between neighbouring cells. With the use of a coculture system based on a collagen vitrigel membrane, we have now shown that neural cells induce up-regulation of the neural guidance protein Sema4A in RPE cells. This effect of neural cells appears to be mediated by the neuropeptide PACAP. PACAP released from retinal neural cells (photoreceptors or optic nerve cells) may thus regulate Sema4A expression in RPE cells and thereby contribute to the maintenance of retinal structure and function.
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Affiliation(s)
- Ji-Ae Ko
- Department of Ophthalmology, Hiroshima University Graduate School of Biomedical Sciences, Hiroshima City, Hiroshima, Japan
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Germline variants in the SEMA4A gene predispose to familial colorectal cancer type X. Nat Commun 2014; 5:5191. [PMID: 25307848 PMCID: PMC4214414 DOI: 10.1038/ncomms6191] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 09/08/2014] [Indexed: 12/21/2022] Open
Abstract
Familial colorectal cancer type X (FCCTX) is characterized by clinical features of hereditary non-polyposis colorectal cancer with a yet undefined genetic background. Here we identify the SEMA4A p.Val78Met germline mutation in an Austrian kindred with FCCTX, using an integrative genomics strategy. Compared with wild-type protein, SEMA4A(V78M) demonstrates significantly increased MAPK/Erk and PI3K/Akt signalling as well as cell cycle progression of SEMA4A-deficient HCT-116 colorectal cancer cells. In a cohort of 53 patients with FCCTX, we depict two further SEMA4A mutations, p.Gly484Ala and p.Ser326Phe and the single-nucleotide polymorphism (SNP) p.Pro682Ser. This SNP is highly associated with the FCCTX phenotype exhibiting increased risk for colorectal cancer (OR 6.79, 95% CI 2.63 to 17.52). Our study shows previously unidentified germline variants in SEMA4A predisposing to FCCTX, which has implications for surveillance strategies of patients and their families.
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Khan MI, Azam M, Ajmal M, Collin RWJ, den Hollander AI, Cremers FPM, Qamar R. The molecular basis of retinal dystrophies in pakistan. Genes (Basel) 2014; 5:176-95. [PMID: 24705292 PMCID: PMC3978518 DOI: 10.3390/genes5010176] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 02/14/2014] [Accepted: 02/14/2014] [Indexed: 12/23/2022] Open
Abstract
The customary consanguineous nuptials in Pakistan underlie the frequent occurrence of autosomal recessive inherited disorders, including retinal dystrophy (RD). In many studies, homozygosity mapping has been shown to be successful in mapping susceptibility loci for autosomal recessive inherited disease. RDs are the most frequent cause of inherited blindness worldwide. To date there is no comprehensive genetic overview of different RDs in Pakistan. In this review, genetic data of syndromic and non-syndromic RD families from Pakistan has been collected. Out of the 132 genes known to be involved in non-syndromic RD, 35 different genes have been reported to be mutated in families of Pakistani origin. In the Pakistani RD families 90% of the mutations causing non-syndromic RD and all mutations causing syndromic forms of the disease have not been reported in other populations. Based on the current inventory of all Pakistani RD-associated gene defects, a cost-efficient allele-specific analysis of 11 RD-associated variants is proposed, which may capture up to 35% of the genetic causes of retinal dystrophy in Pakistan.
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Affiliation(s)
- Muhammad Imran Khan
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad 45600, Pakistan.
| | - Maleeha Azam
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad 45600, Pakistan.
| | - Muhammad Ajmal
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad 45600, Pakistan.
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, The Netherlands.
| | - Anneke I den Hollander
- Department of Human Genetics, Radboud University Medical Center, Nijmegen 6500 HB, The Netherlands.
| | - Frans P M Cremers
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad 45600, Pakistan.
| | - Raheel Qamar
- Department of Biosciences, Faculty of Science, COMSATS Institute of Information Technology, Islamabad 45600, Pakistan.
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Nong E, Lee W, Merriam JE, Allikmets R, Tsang SH. Disease progression in autosomal dominant cone-rod dystrophy caused by a novel mutation (D100G) in the GUCA1A gene. Doc Ophthalmol 2013; 128:59-67. [PMID: 24352742 DOI: 10.1007/s10633-013-9420-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 12/05/2013] [Indexed: 11/30/2022]
Abstract
PURPOSE To document longitudinal fundus autofluorescence (FAF) and electroretinogram (ERG) findings in a family with cone-rod dystrophy (CRD) caused by a novel missense mutation (D100G) in the GUCA1A gene. METHODS Observational case series. RESULTS Three family members 26-49 years old underwent complete clinical examinations. In all patients, funduscopic findings showed intraretinal pigment migration, loss of neurosensory retinal pigment epithelium, and macular atrophy. FAF imaging revealed the presence of a progressive hyperautofluorescent ring around a hypoautofluorescent center corresponding to macular atrophy. Full-field ERGs showed a more severe loss of cone than rod function in each patient. Thirty-hertz flicker responses fell far below normal limits. Longitudinal FAF and ERG findings in one patient suggested progressive CRD. Two more advanced patients exhibited reduced rod response consistent with disease stage. Direct sequencing of the GUCA1A gene revealed a new missense mutation, p.Asp100Gly (D100G), in each patient. CONCLUSION Patients with autosomal dominant CRD caused by a D100G mutation in GUCA1A exhibit progressive vision loss early within the first decade of life identifiable by distinct ERG characteristics and subsequent genetic testing.
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Affiliation(s)
- Eva Nong
- Department of Ophthalmology, Columbia University, New York, NY, USA
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36
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Hofmann K, Zweier M, Sticht H, Zweier C, Wittmann W, Hoyer J, Uebe S, van Haeringen A, Thiel CT, Ekici AB, Reis A, Rauch A. Biallelic SEMA3A defects cause a novel type of syndromic short stature. Am J Med Genet A 2013; 161A:2880-9. [PMID: 24124006 DOI: 10.1002/ajmg.a.36250] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 08/30/2013] [Indexed: 12/14/2022]
Abstract
Chromosomal microarray testing is commonly used to identify disease causing de novo copy number variants in patients with developmental delay and multiple congenital anomalies. In such a patient we now observed an 150 kb deletion on chromosome 7q21.11 affecting the first exon of the axon guidance molecule gene SEMA3A (sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A). This deletion was inherited from the healthy father, but considering the function of SEMA3A and phenotypic similarity to the knock-out mice, we still assumed a pathogenic relevance and tested for a recessive second defect. Sequencing of SEMA3A in the patient indeed revealed the de novo in-frame mutation p.Phe316_Lys317delinsThrSerSerAsnGlu. Cloning of the mutated allele in combination with two informative SNPs confirmed compound heterozygosity in the patient. While the altered protein structure was predicted to be benign, aberrant splicing resulting in a premature stop codon was proven by RT-PCR to occur in about half of the transcripts from this allele. Expression profiling in human fetal and adult cDNA panels, confirmed a high expression of SEMA3A in all brain regions as well as in adult and fetal heart and fetal skeletal muscle. Normal intellectual development in the patient was surprising but may be explained by the remaining 20% of SEMA3A expression level demonstrated by quantitative RT-PCR. We therefore report a novel autosomal recessive syndrome characterized by postnatal short stature with relative macrocephaly, camptodactyly, septal heart defect and several minor anomalies caused by biallelic mutations in SEMA3A.
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Affiliation(s)
- Kristin Hofmann
- Institute of Human Genetics, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
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Nojima S, Toyofuku T, Kamao H, Ishigami C, Kaneko J, Okuno T, Takamatsu H, Ito D, Kang S, Kimura T, Yoshida Y, Morimoto K, Maeda Y, Ogata A, Ikawa M, Morii E, Aozasa K, Takagi J, Takahashi M, Kumanogoh A. A point mutation in Semaphorin 4A associates with defective endosomal sorting and causes retinal degeneration. Nat Commun 2013; 4:1406. [PMID: 23360997 PMCID: PMC3562463 DOI: 10.1038/ncomms2420] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 12/20/2012] [Indexed: 12/25/2022] Open
Abstract
Semaphorin 4A (Sema4A) has an essential role in photoreceptor survival. In humans, mutations in Sema4A are thought to contribute to retinal degenerative diseases. Here we generate a series of knock-in mouse lines with corresponding mutations (D345H, F350C or R713Q) in the Sema4A gene and find that Sema4AF350C causes retinal degeneration phenotypes. The F350C mutation results in abnormal localization of the Sema4A protein, leading to impaired endosomal sorting of molecules indispensable for photoreceptor survival. Additionally, protein structural modelling reveals that the side chain of the 350th amino acid is critical to retain the proper protein conformation. Furthermore, Sema4A gene transfer successfully prevents photoreceptor degeneration in Sema4AF350C/F350C and Sema4A−/− mice. Thus, our findings not only indicate the importance of the Sema4A protein conformation in human and mouse retina homeostasis but also identify a novel therapeutic target for retinal degenerative diseases. Semaphorin 4A is implicated in photoreceptor survival. Nojima and colleagues generate transgenic mice with different mutations in the Sema4A gene and find that point mutation of F350 causes severe degeneration in photoreceptor cells, which can be rescued by virus-mediated gene therapy.
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Affiliation(s)
- Satoshi Nojima
- Department of Immunopathology, WPI Immunology Frontier Research Center, Osaka University, Suita City, Osaka 565-0871, Japan
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Huang L, Zhang Q, Li S, Guan L, Xiao X, Zhang J, Jia X, Sun W, Zhu Z, Gao Y, Yin Y, Wang P, Guo X, Wang J, Zhang Q. Exome sequencing of 47 chinese families with cone-rod dystrophy: mutations in 25 known causative genes. PLoS One 2013; 8:e65546. [PMID: 23776498 PMCID: PMC3679152 DOI: 10.1371/journal.pone.0065546] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 04/25/2013] [Indexed: 11/19/2022] Open
Abstract
Objective The goal of this study was to identify mutations in 25 known causative genes in 47 unrelated Chinese families with cone-rod dystrophy (CORD). Methods Forty-seven probands from unrelated families with CORD were recruited. Genomic DNA prepared from leukocytes was analyzed by whole exome sequencing. Variants in the 25 genes were selected and then validated by Sanger sequencing. Results Fourteen potential pathogenic mutations, including nine novel and five known, were identified in 10 of the 47 families (21.28%). Homozygous, compound heterozygous, and hemizygous mutations were detected in three, four, or three families, respectively. The 14 mutations in the 10 families were distributed among CNGB3 (three families), PDE6C (two families), ABCA4 (one family), RPGRIP1 (one family), RPGR (two families), and CACNA1F (one family). Conclusions This study provides a brief view on mutation spectrum of the 25 genes in a Chinese cohort with CORD. Identification of novel mutations enriched our understanding of variations in these genes and their associated phenotypes. To our knowledge, this is the first systemic exome-sequencing analysis of all of the 25 CORD-associated genes.
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Affiliation(s)
- Li Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong, China
| | | | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong, China
| | | | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong, China
| | | | - Xiaoyun Jia
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong, China
| | | | - Yang Gao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ye Yin
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Panfeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiangming Guo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, Guangdong, China
- * E-mail: (QJZ); (JW)
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong, China
- * E-mail: (QJZ); (JW)
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Huang L, Li S, Xiao X, Jia X, Wang P, Guo X, Zhang Q. Screening for variants in 20 genes in 130 unrelated patients with cone-rod dystrophy. Mol Med Rep 2013; 7:1779-85. [PMID: 23563732 DOI: 10.3892/mmr.2013.1415] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 03/07/2013] [Indexed: 11/05/2022] Open
Abstract
Cone-rod dystrophy (CORD) is a hereditary retinal disorder with primary cone impairment and subsequent rod involvement. To date, mutations responsible for CORD have been reported in 24 genes. However, the systemic evaluation of variants in these genes in a cohort of patients is rare, particularly in East Asia. In this study, 58 coding exons from 20 CORD genes, including 35 exons with previously identified mutations in 17 genes and all 23 coding exons for the other 3 genes (GUCY2D, PRPH2 and KCNV2), were analyzed by cycle sequencing on 130 unrelated probands with CORD. Four heterozygous mutations, 1 novel and 3 known, were detected in 4/130 patients, including c.259G>A (p.Asp87Asn) in UNC119, c.2512C>T (p.Arg838Cys) and c.2513G>A (p.Arg838His) in GUCY2D and c.946T>G (p.Trp316Gly) in PRPH2. The result implies a comparatively low rate of mutations in these exons in Chinese patients. These data suggest that in Chinese patients, CORD may be caused by mutations in exons that have not yet been screened or in genes that have yet to be identified. Further analysis of these patients may provide clarification.
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Affiliation(s)
- Li Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, Guangdong 510060, P.R. China
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Chang S, Vaccarella L, Olatunji S, Cebulla C, Christoforidis J. Diagnostic challenges in retinitis pigmentosa: genotypic multiplicity and phenotypic variability. Curr Genomics 2012; 12:267-75. [PMID: 22131872 PMCID: PMC3131734 DOI: 10.2174/138920211795860116] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 04/06/2011] [Accepted: 04/15/2011] [Indexed: 12/03/2022] Open
Abstract
Retinitis pigmentosa (RP) is a heterogeneous group of inherited retinal disorders. Diagnosis can be challenging as more than 40 genes are known to cause non-syndromic RP and phenotypic expression can differ significantly resulting in variations in disease severity, age of onset, rate of progression, and clinical findings. We describe the clinical manifestations of RP, the more commonly known causative gene mutations, and the genotypic-phenotypic correlation of RP.
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Affiliation(s)
- Susie Chang
- Retina Division, Havener Eye Institute, The Ohio State University College of Medicine, Columbus, Ohio, USA
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Toyofuku T, Nojima S, Ishikawa T, Takamatsu H, Tsujimura T, Uemura A, Matsuda J, Seki T, Kumanogoh A. Endosomal sorting by Semaphorin 4A in retinal pigment epithelium supports photoreceptor survival. Genes Dev 2012; 26:816-29. [PMID: 22465952 DOI: 10.1101/gad.184481.111] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Photoreceptor cell death is the hallmark of a group of human inherited retinal degeneration. Although the causative genetic mutations are often known, the mechanisms leading to photoreceptor degeneration remain poorly defined. Here, we show that Semaphorin 4A (Sema4A), a member of axonal guidance molecule semaphorin, plays a role in Rab11/FIP2-mediated endosomal sorting in retinal pigment epithelial cells to support photoreceptor function. In response to oxidative stress, Sema4A switches the endosomal sorting of the lysosomal precursor protein prosaposin from the lysosome to the exosomal release, which prevents light-induced photoreceptor apoptosis. In the absence of oxidative stress, Sema4A sorts retinoid-binding proteins with retinoids between the cell surface and endoplasmic reticulum, by which 11-cis-retinal, a chromophore for phototransduction, is regenerated and transported back to photoreceptors. Owing to defects in these processes, Sema4A-deficient mice exhibit marked photoreceptor degeneration. Our findings therefore indicate that Sema4A regulates two distinct endosomal-sorting pathways that are critical for photoreceptor survival and phototransduction during the transition between daylight and darkness.
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Affiliation(s)
- Toshihiko Toyofuku
- World Premier International Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan.
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Tsuruma K, Tanaka Y, Shimazawa M, Mashima Y, Hara H. Unoprostone reduces oxidative stress- and light-induced retinal cell death, and phagocytotic dysfunction, by activating BK channels. Mol Vis 2011; 17:3556-65. [PMID: 22219651 PMCID: PMC3250378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 12/27/2011] [Indexed: 11/01/2022] Open
Abstract
PURPOSE Unoprostone isopropyl (unoprostone) is a docosanoid currently used as an antiglaucoma agent. Unoprostone is known to have neuroprotective effects and to activate large conductance Ca²⁺-activated K⁺ (BK) channels. Recently, unoprostone has been tested in clinical studies as a therapeutic agent for retinitis pigmentosa (RP) and studies have demonstrated an improvement in retinal sensitivity and in the protection of central retinal sensitivity with its use. However, the mechanism of action underlying unoprostone's protective effect in RP is not fully known. It is well known that the pathogenesis of RP can be accelerated by oxidative stress or light irradiation. Therefore, the current study investigated the effects and the underlying mechanism of action of unoprostone on oxidative stress- and light irradiation-induced damage in photoreceptor and retinal pigment epithelial cultures. METHODS The study used the mouse retinal cone-cell line 661W to investigate the effects of unoprostone and its major metabolite, unoprostone-free acid (M1), on oxidative stress- or light irradiation-induced cell death, and a human retinal pigment epithelial cell line (ARPE-19), was used to investigate the effects on light-induced disruption of phagocytotic function in a latex bead assay. Additionally, we examined whether the effects of unoprostone and M1 were mediated by BK channels using iberiotoxin, a selective inhibitor of BK channels. RESULTS Unoprostone and M1 protected against light- or H₂O₂-induced cell death in 661W cells, and against light-induced phagocytotic dysfunction in ARPE-19 cells. Additionally, iberiotoxin inhibited the protective effects of unoprostone and M1. CONCLUSIONS These findings indicate that unoprostone has protective effects on oxidative stress- and light irradiation-induced damage in vitro and that these effects are mediated by activation of BK channels. This confirms that unoprostone represents a promising therapeutic agent for the treatment of RP and other retinal diseases.
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Affiliation(s)
- Kazuhiro Tsuruma
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, Gifu, Japan
| | - Yuka Tanaka
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, Gifu, Japan
| | - Masamitsu Shimazawa
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, Gifu, Japan
| | - Yukihiko Mashima
- Department of Ophthalmology, Keio University School of Medicine, 35 Shinano-machi, Shinjuku-ku, Tokyo, Japan
| | - Hideaki Hara
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, Gifu, Japan
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Yuan Y, Zhou X, Wang F, Yan M, Ding F. Evidence for a novel autosomal dominant retinitis pigmentosa linked to chromosome 1p22.1-q12 in a Chinese family. Curr Eye Res 2011; 36:154-67. [PMID: 21281067 DOI: 10.3109/02713683.2010.511393] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
PURPOSE To identify the causative genetic locus in a Chinese autosomal dominant retinitis pigmentosa (adRP) family that contained seven affected members in three generations. METHODS After clinical diagnosis and exclusion of all mapped genes and loci, the SLINK program was used to simulate the maximum logarithm of the likelihood ratio (LOD) score for a linkage study in this small family. A genome-wide scan was performed using microsatellite markers at 10 cM intervals. Two-point and multipoint LOD scores were calculated, and haplotypes were constructed. RESULTS The H11 family clinical presentation included an early onset of night blindness, a progressive loss of the peripheral visual field, typical retinitis pigmentosa (RP) fundus changes, and a cataract complication. A maximum two-point LOD score of 2.54 (θ = 0) was found at markers D1S2739, D1S457, D1S187, D1S189, and D1S305, and multipoint linkage analysis yielded a maximum LOD score of 2.54 for marker D1S187. These LOD scores were the closest to the maximum simulated LOD score. Haplotype analysis revealed that this form of adRP segregates with a 38.25 cM region that spanned 50 Mb on chromosome 1p22.1-q12. CONCLUSIONS Although this locus overlaps the RP19 locus caused by mutations in ABCA4 and the RP32 locus, both are inherited in an autosomal recessive mode rather than the autosomal dominant mode of inheritance found in the H11 family. The identification of this potential new locus for adRP further confirms the high level of heterogeneity for RP.
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Affiliation(s)
- Yuan Yuan
- Center for Gene Diagnosis, Zhongnan Hospital, Wuhan University, Wuhan, China
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45
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Garcia-Hoyos M, Auz-Alexandre CL, Almoguera B, Cantalapiedra D, Riveiro-Alvarez R, Lopez-Martinez MA, Gimenez A, Blanco-Kelly F, Avila-Fernandez A, Trujillo-Tiebas MJ, Garcia-Sandoval B, Ramos C, Ayuso C. Mutation analysis at codon 838 of the Guanylate Cyclase 2D gene in Spanish families with autosomal dominant cone, cone-rod, and macular dystrophies. Mol Vis 2011; 17:1103-9. [PMID: 21552474 PMCID: PMC3087450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Accepted: 04/25/2011] [Indexed: 10/27/2022] Open
Abstract
PURPOSE Heterozygous mutations around codon 838 of the guanylate cyclase 2D (GUCY2D) gene have recently been associated with more than a third of autosomal dominant macular dystrophy patients. The aim of our study was to evaluate the prevalence of these mutations in Spanish families with autosomal dominant cone, cone-rod, and macular dystrophies. METHODS Mutation analysis was performed by PCR amplification of exon 13 of GUCY2D and subsequent restriction analysis. To confirm the results, automatic sequencing analysis was also performed. RESULTS Among the 22 unrelated Spanish families included in the study, we found two associated disease mutations at codon 838 of the GUCY2D gene, one of which had not been previously described (p.R838P). This novel mutation exhibited phenotypic variability. CONCLUSIONS The prevalence of mutations around codon 838 of GUCY2D in our group of families (9.09%) is lower than that previously reported in other populations. However, the discovery of a novel mutation at codon 838 further suggests that this locus is a mutation hotspot within the GUCY2D gene, and confirms the importance of analyzing this codon to characterize molecularly these autosomal dominant retinal disorders.
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Affiliation(s)
- Maria Garcia-Hoyos
- Genetics Department, Instituto de Investigacion Sanitaria-Fundacion Jimenez Diaz (IIS-FJD), Madrid, Spain,Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Carmen Laura Auz-Alexandre
- Genetics Department, Instituto de Investigacion Sanitaria-Fundacion Jimenez Diaz (IIS-FJD), Madrid, Spain,Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Berta Almoguera
- Genetics Department, Instituto de Investigacion Sanitaria-Fundacion Jimenez Diaz (IIS-FJD), Madrid, Spain,Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Diego Cantalapiedra
- Genetics Department, Instituto de Investigacion Sanitaria-Fundacion Jimenez Diaz (IIS-FJD), Madrid, Spain,Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Rosa Riveiro-Alvarez
- Genetics Department, Instituto de Investigacion Sanitaria-Fundacion Jimenez Diaz (IIS-FJD), Madrid, Spain,Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Miguel Angel Lopez-Martinez
- Genetics Department, Instituto de Investigacion Sanitaria-Fundacion Jimenez Diaz (IIS-FJD), Madrid, Spain,Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Ascension Gimenez
- Genetics Department, Instituto de Investigacion Sanitaria-Fundacion Jimenez Diaz (IIS-FJD), Madrid, Spain,Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Fiona Blanco-Kelly
- Genetics Department, Instituto de Investigacion Sanitaria-Fundacion Jimenez Diaz (IIS-FJD), Madrid, Spain,Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Almudena Avila-Fernandez
- Genetics Department, Instituto de Investigacion Sanitaria-Fundacion Jimenez Diaz (IIS-FJD), Madrid, Spain,Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Maria Jose Trujillo-Tiebas
- Genetics Department, Instituto de Investigacion Sanitaria-Fundacion Jimenez Diaz (IIS-FJD), Madrid, Spain,Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Blanca Garcia-Sandoval
- Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain,Ophthalmology, Instituto de Investigacion Sanitaria-Fundacion Jimenez Diaz (IIS-FJD), Madrid, Spain
| | - Carmen Ramos
- Genetics Department, Instituto de Investigacion Sanitaria-Fundacion Jimenez Diaz (IIS-FJD), Madrid, Spain,Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
| | - Carmen Ayuso
- Genetics Department, Instituto de Investigacion Sanitaria-Fundacion Jimenez Diaz (IIS-FJD), Madrid, Spain,Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain
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Berger W, Kloeckener-Gruissem B, Neidhardt J. The molecular basis of human retinal and vitreoretinal diseases. Prog Retin Eye Res 2010; 29:335-75. [PMID: 20362068 DOI: 10.1016/j.preteyeres.2010.03.004] [Citation(s) in RCA: 394] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
During the last two to three decades, a large body of work has revealed the molecular basis of many human disorders, including retinal and vitreoretinal degenerations and dysfunctions. Although belonging to the group of orphan diseases, they affect probably more than two million people worldwide. Most excitingly, treatment of a particular form of congenital retinal degeneration is now possible. A major advantage for treatment is the unique structure and accessibility of the eye and its different components, including the vitreous and retina. Knowledge of the many different eye diseases affecting retinal structure and function (night and colour blindness, retinitis pigmentosa, cone and cone rod dystrophies, photoreceptor dysfunctions, as well as vitreoretinal traits) is critical for future therapeutic development. We have attempted to present a comprehensive picture of these disorders, including biological, clinical, genetic and molecular information. The structural organization of the review leads the reader through non-syndromic and syndromic forms of (i) rod dominated diseases, (ii) cone dominated diseases, (iii) generalized retinal degenerations and (iv) vitreoretinal disorders, caused by mutations in more than 165 genes. Clinical variability and genetic heterogeneity have an important impact on genetic testing and counselling of affected families. As phenotypes do not always correlate with the respective genotypes, it is of utmost importance that clinicians, geneticists, counsellors, diagnostic laboratories and basic researchers understand the relationships between phenotypic manifestations and specific genes, as well as mutations and pathophysiologic mechanisms. We discuss future perspectives.
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Affiliation(s)
- Wolfgang Berger
- Division of Medical Molecular Genetics and Gene Diagnostics, Institute of Medical Genetics, University of Zurich, Schorenstrasse 16, CH-8603 Schwerzenbach, Switzerland.
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Gautier M, Flori L, Riebler A, Jaffrézic F, Laloé D, Gut I, Moazami-Goudarzi K, Foulley JL. A whole genome Bayesian scan for adaptive genetic divergence in West African cattle. BMC Genomics 2009; 10:550. [PMID: 19930592 PMCID: PMC2784811 DOI: 10.1186/1471-2164-10-550] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Accepted: 11/21/2009] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The recent settlement of cattle in West Africa after several waves of migration from remote centres of domestication has imposed dramatic changes in their environmental conditions, in particular through exposure to new pathogens. West African cattle populations thus represent an appealing model to unravel the genome response to adaptation to tropical conditions. The purpose of this study was to identify footprints of adaptive selection at the whole genome level in a newly collected data set comprising 36,320 SNPs genotyped in 9 West African cattle populations. RESULTS After a detailed analysis of population structure, we performed a scan for SNP differentiation via a previously proposed Bayesian procedure including extensions to improve the detection of loci under selection. Based on these results we identified 53 genomic regions and 42 strong candidate genes. Their physiological functions were mainly related to immune response (MHC region which was found under strong balancing selection, CD79A, CXCR4, DLK1, RFX3, SEMA4A, TICAM1 and TRIM21), nervous system (NEUROD6, OLFM2, MAGI1, SEMA4A and HTR4) and skin and hair properties (EDNRB, TRSP1 and KRTAP8-1). CONCLUSION The main possible underlying selective pressures may be related to climatic conditions but also to the host response to pathogens such as Trypanosoma(sp). Overall, these results might open the way towards the identification of important variants involved in adaptation to tropical conditions and in particular to resistance to tropical infectious diseases.
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Affiliation(s)
- Mathieu Gautier
- INRA, UMR de Génétique Animale et Biologie Intégrative, 78350 Jouy-en-Josas, France
| | - Laurence Flori
- INRA, UMR de Génétique Animale et Biologie Intégrative, 78350 Jouy-en-Josas, France
| | - Andrea Riebler
- University of Zurich, Institute of Social and Preventive Medicine, Zurich, Switzerland
| | - Florence Jaffrézic
- INRA, UMR de Génétique Animale et Biologie Intégrative, 78350 Jouy-en-Josas, France
| | - Denis Laloé
- INRA, UMR de Génétique Animale et Biologie Intégrative, 78350 Jouy-en-Josas, France
| | - Ivo Gut
- CEA, Centre National de Génotypage, 91057 Evry, France
| | | | - Jean-Louis Foulley
- INRA, UMR de Génétique Animale et Biologie Intégrative, 78350 Jouy-en-Josas, France
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Li N, Mei H, MacDonald IM, Jiao X, Hejtmancik JF. Mutations in ASCC3L1 on 2q11.2 are associated with autosomal dominant retinitis pigmentosa in a Chinese family. Invest Ophthalmol Vis Sci 2009; 51:1036-43. [PMID: 19710410 DOI: 10.1167/iovs.09-3725] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To localize and identify the gene and mutations causing autosomal dominant retinitis pigmentosa in a Chinese Family. METHODS Families were ascertained and patients underwent complete ophthalmic examinations. Blood samples were collected and DNA was extracted. A linkage scan of genomic regions containing known candidate genes was performed by using 34 polymorphic microsatellite markers on genomic DNA from affected and unaffected family members, and lod scores were calculated. Candidate genes were sequenced and mutations analyzed. RESULTS A genome-wide scan yielded a lod score of 3.5 at theta = 0 for D2S2333 and 3.46 at theta = 0 for D2S2216. This region harbors the ASCC3L1 gene. Sequencing of ASCC3L1 in an affected family member showed a heterozygous single-base-pair change; c.3269G-->T, predicted to result in an Arg1090Leu amino acid change. CONCLUSIONS The results provide strong evidence that mutations in ASCC3L1 have resulted in autosomal dominant retinitis pigmentosa in this Chinese family.
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Ayub Q, Tyler-Smith C. Genetic variation in South Asia: assessing the influences of geography, language and ethnicity for understanding history and disease risk. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2009; 8:395-404. [DOI: 10.1093/bfgp/elp015] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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