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Charng WL, Nikolov M, Shrestha I, Seeley MA, Josyula NS, Justice AE, Dobbs MB, Gurnett CA. Exome sequencing of 1190 non-syndromic clubfoot cases reveals HOXD12 as a novel disease gene. J Med Genet 2024; 61:699-706. [PMID: 38663984 DOI: 10.1136/jmg-2024-109846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/20/2024] [Indexed: 06/13/2024]
Abstract
BACKGROUND Clubfoot, presenting as a rigid inward and downward turning of the foot, is one of the most common congenital musculoskeletal anomalies. The aetiology of clubfoot is poorly understood and variants in known clubfoot disease genes account for only a small portion of the heritability. METHODS Exome sequence data were generated from 1190 non-syndromic clubfoot cases and their family members from multiple ethnicities. Ultra-rare variant burden analysis was performed comparing 857 unrelated clubfoot cases with European ancestry with two independent ethnicity-matched control groups (1043 in-house and 56 885 gnomAD controls). Additional variants in prioritised genes were identified in a larger cohort, including probands with non-European ancestry. Segregation analysis was performed in multiplex families when available. RESULTS Rare variants in 29 genes were enriched in clubfoot cases, including PITX1 (a known clubfoot disease gene), HOXD12, COL12A1, COL9A3 and LMX1B. In addition, rare variants in posterior HOX genes (HOX9-13) were enriched overall in clubfoot cases. In total, variants in these genes were present in 8.4% (100/1190) of clubfoot cases with both European and non-European ancestry. Among these, 3 are de novo and 22 show variable penetrance, including 4 HOXD12 variants that segregate with clubfoot. CONCLUSION We report HOXD12 as a novel clubfoot disease gene and demonstrate a phenotypic expansion of known disease genes (myopathy gene COL12A1, Ehlers-Danlos syndrome gene COL9A3 and nail-patella syndrome gene LMX1B) to include isolated clubfoot.
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Affiliation(s)
- Wu-Lin Charng
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, Missouri, USA
| | - Momchil Nikolov
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, Missouri, USA
| | - Isabel Shrestha
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, Missouri, USA
| | - Mark A Seeley
- Department of Orthopaedics, Geisinger Medical Center, Danville, Pennsylvania, USA
| | | | - Anne E Justice
- Department of Population Health Sciences, Geisinger, Danville, PA, USA
| | - Matthew B Dobbs
- Paley Orthopedic & Spine Institute, West Palm Beach, Florida, USA
| | - Christina A Gurnett
- Department of Neurology, Washington University in Saint Louis School of Medicine, Saint Louis, Missouri, USA
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Hayman T, Millo T, Hendler K, Chowers I, Gross M, Banin E, Sharon D. Whole exome sequencing of 491 individuals with inherited retinal diseases reveals a large spectrum of variants and identification of novel candidate genes. J Med Genet 2024; 61:224-231. [PMID: 37798099 DOI: 10.1136/jmg-2023-109482] [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: 06/27/2023] [Accepted: 09/14/2023] [Indexed: 10/07/2023]
Abstract
BACKGROUND Inherited retinal diseases (IRDs) include a range of vision loss conditions caused by variants in different genes. The clinical and genetic heterogeneity make identification of the genetic cause challenging. Here, a cohort of 491 unsolved cases from our cohort of Israeli and Palestinian families with IRDs underwent whole exome sequencing (WES), including detection of CNVs as well as single nucleotide variants (SNVs). METHODS All participants underwent clinical examinations. Following WES on DNA samples by 3 billion, initial SNV analysis was performed by 3 billion and SNV and CNV analysis by Franklin Genoox. The CNVs indicated by the programme were confirmed by PCR followed by gel electrophoresis. RESULTS WES of 491 IRD cases revealed the genetic cause of disease in 51% of cases, of which 11% were due wholly or in part to CNVs. In two cases, we clarified previously incorrect or unclear clinical diagnoses. This analysis also identified ESRRB and DNM1 as potential novel genes. CONCLUSION This analysis is the most extensive one to include CNVs to examine IRD causing genes in the Israeli and Palestinian populations. It has allowed us to identify the causative variant of many patients with IRDs including ones with unclear diagnoses and potential novel genes.
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Affiliation(s)
- Tamar Hayman
- Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Talya Millo
- Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Karen Hendler
- Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Itay Chowers
- Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Menachem Gross
- Otolaryngology/Head and Neck Surgery, Hadassah Medical Center, Jerusalem, Jerusalem, Israel
| | - Eyal Banin
- Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dror Sharon
- Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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3
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Pressé MT, Malgrange B, Delacroix L. The cochlear matrisome: Importance in hearing and deafness. Matrix Biol 2024; 125:40-58. [PMID: 38070832 DOI: 10.1016/j.matbio.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 11/20/2023] [Accepted: 12/06/2023] [Indexed: 02/12/2024]
Abstract
The extracellular matrix (ECM) consists in a complex meshwork of collagens, glycoproteins, and proteoglycans, which serves a scaffolding function and provides viscoelastic properties to the tissues. ECM acts as a biomechanical support, and actively participates in cell signaling to induce tissular changes in response to environmental forces and soluble cues. Given the remarkable complexity of the inner ear architecture, its exquisite structure-function relationship, and the importance of vibration-induced stimulation of its sensory cells, ECM is instrumental to hearing. Many factors of the matrisome are involved in cochlea development, function and maintenance, as evidenced by the variety of ECM proteins associated with hereditary deafness. This review describes the structural and functional ECM components in the auditory organ and how they are modulated over time and following injury.
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Affiliation(s)
- Mary T Pressé
- Developmental Neurobiology Unit, GIGA-Neurosciences, University of Liège, 15 avenue Hippocrate - CHU - B36 (1st floor), Liège B-4000, Belgium
| | - Brigitte Malgrange
- Developmental Neurobiology Unit, GIGA-Neurosciences, University of Liège, 15 avenue Hippocrate - CHU - B36 (1st floor), Liège B-4000, Belgium
| | - Laurence Delacroix
- Developmental Neurobiology Unit, GIGA-Neurosciences, University of Liège, 15 avenue Hippocrate - CHU - B36 (1st floor), Liège B-4000, Belgium.
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Acke FRE, De Leenheer EMR. Hearing Loss in Stickler Syndrome: An Update. Genes (Basel) 2022; 13:genes13091571. [PMID: 36140739 PMCID: PMC9498449 DOI: 10.3390/genes13091571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/25/2022] [Accepted: 08/30/2022] [Indexed: 11/24/2022] Open
Abstract
Stickler syndrome is a connective tissue disorder characterized by ocular, skeletal, orofacial and auditory manifestations. Its main symptoms are high myopia, retinal detachment, joint hypermobility, early osteoarthritis, cleft palate, midfacial hypoplasia, micrognathia and hearing loss. Large phenotypical variability is apparent and partly explained by the underlying genetic heterogeneity, including collagen genes (COL2A1, COL11A1, COL11A2, COL9A1, COL9A2, COL9A3) and non-collagen genes (BMP4, LRP2, LOXL3). The most frequent type of Stickler syndrome (COL2A1) is characterized by a rather mild high-frequency sensorineural hearing loss in about half of the patients. COL11A1- and COL11A2-related Stickler syndrome results in more frequent hearing loss, being moderate and involving all frequencies. Hearing loss in the rarer types of Stickler syndrome depends on the gene expression in the cochlea, with moderate to severe downsloping hearing loss for Stickler syndrome caused by biallelic type IX collagen gene mutations and none or mild hearing loss for the non-collagen genes. Inherent to the orofacial manifestations, middle ear problems and temporary conductive hearing loss, especially at young age, are also prevalent. Consequently, hearing loss should be actively sought for and adequately treated in Stickler syndrome patients given its high prevalence and the concomitant visual impairment in most patients.
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Autosomal Recessive Stickler Syndrome. Genes (Basel) 2022; 13:genes13071135. [PMID: 35885918 PMCID: PMC9324312 DOI: 10.3390/genes13071135] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 02/04/2023] Open
Abstract
Stickler syndrome (SS) is a genetic disorder with manifestations in the eye, ear, joints, face and palate. Usually inherited in a dominant fashion due to heterozygous pathogenic variants in the collagen genes COL2A1 and COL11A1, it can rarely be inherited in a recessive fashion from variants in COL9A1, COL9A2, and COL9A3, COL11A1, as well as the non-collagen genes LRP2, LOXL3 and GZF1. We review the published cases of recessive SS, which comprise 40 patients from 23 families. Both homozygous and compound heterozygous pathogenic variants are found. High myopia is near-universal, and sensorineural hearing loss is very common in patients with variants in genes for type IX or XI collagen, although hearing appears spared in the LRP2 and LOXL3 patients and is variable in GZF1. Cleft palate is associated with type XI collagen variants, as well as the non-collagen genes, but is so far unreported with type IX collagen variants. Retinal detachment has occurred in 18% of all cases, and joint pain in 15%. However, the mean age of this cohort is 11 years old, so the lifetime incidence of both problems may be underestimated. This paper reinforces the importance of screening for SS in congenital sensorineural hearing loss, particularly when associated with myopia, and the need to warn patients and parents of the warning signs of retinal detachment, with regular ophthalmic review.
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Rad A, Najafi M, Suri F, Abedini S, Loum S, Karimiani EG, Daftarian N, Murphy D, Doosti M, Moghaddasi A, Ahmadieh H, Sabbaghi H, Rajati M, Hashemi N, Vona B, Schmidts M. Identification of three novel homozygous variants in COL9A3 causing autosomal recessive Stickler syndrome. Orphanet J Rare Dis 2022; 17:97. [PMID: 35241111 PMCID: PMC8892745 DOI: 10.1186/s13023-022-02244-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 02/10/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Stickler syndrome (STL) is a rare, clinically and molecularly heterogeneous connective tissue disorder. Pathogenic variants occurring in a variety of genes cause STL, mainly inherited in an autosomal dominant fashion. Autosomal recessive STL is ultra-rare with only four families with biallelic COL9A3 variants reported to date. RESULTS Here, we report three unrelated families clinically diagnosed with STL carrying different novel biallelic loss of function variants in COL9A3. Further, we have collected COL9A3 genotype-phenotype associations from the literature. CONCLUSION Our report substantially expands the molecular genetics and clinical basis of autosomal recessive STL and provides an overview about allelic COL9A3 disorders.
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Affiliation(s)
- Aboulfazl Rad
- Department of Otolaryngology, Head and Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University, 72076, Tübingen, Germany
| | - Maryam Najafi
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen, The Netherlands.,Pediatric Genetics Division, Center for Pediatrics and Adolescent Medicine, University Hospital Freiburg, Freiburg University Faculty of Medicine, Mathildenstrasse 1, 79106, Freiburg, Germany
| | - Fatemeh Suri
- Ophthalmic Research Center, Research Institute for Ophthalmology and Vision Science, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soheila Abedini
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashad University of Medical Science, Mashad, Iran.,Department of Molecular Genetics, Next Generation Genetic Polyclinic, Mashhad, Iran
| | - Stephen Loum
- Department of Otolaryngology, Head and Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University, 72076, Tübingen, Germany
| | | | - Narsis Daftarian
- Ocular Tissue Engineering Research Center, Research Institute for Ophthalmology and Vision Science, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - David Murphy
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashad University of Medical Science, Mashad, Iran
| | - Mohammad Doosti
- Pediatric Genetics Division, Center for Pediatrics and Adolescent Medicine, University Hospital Freiburg, Freiburg University Faculty of Medicine, Mathildenstrasse 1, 79106, Freiburg, Germany
| | - Afrooz Moghaddasi
- Ophthalmic Research Center, Research Institute for Ophthalmology and Vision Science, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Ahmadieh
- Ophthalmic Research Center, Research Institute for Ophthalmology and Vision Science, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamideh Sabbaghi
- Ophthalmic Epidemiology Research Center, Research Institute for Ophthalmology and Vision Science, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohsen Rajati
- Department of Otorhinolaryngology, School of Medicine, Ghaem Hospital, Sinus and Surgical Endoscopic Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Narges Hashemi
- Department of Pediatric Neurology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Barbara Vona
- Department of Otolaryngology, Head and Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University, 72076, Tübingen, Germany.,Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany.,Institute for Auditory Neuroscience and InnerEar Lab, University Medical Center Göttingen, Göttingen, Germany
| | - Miriam Schmidts
- Genome Research Division, Human Genetics Department, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen, The Netherlands. .,Pediatric Genetics Division, Center for Pediatrics and Adolescent Medicine, University Hospital Freiburg, Freiburg University Faculty of Medicine, Mathildenstrasse 1, 79106, Freiburg, Germany. .,CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany.
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7
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Vaclavik V, Tiab L, Sun YJ, Mahajan VB, Moulin A, Allaman-Pillet N, Munier FL, Schorderet DF. New COL6A6 Variant Causes Autosomal Dominant Retinitis Pigmentosa in a Four-Generation Family. Invest Ophthalmol Vis Sci 2022; 63:23. [PMID: 35333290 PMCID: PMC8963667 DOI: 10.1167/iovs.63.3.23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To report that variants in the gene for a large lamina basal component protein, COL6A6 (collagen type VI alpha 6 chain, Col6α6), linked to chromosome 3p22.1 causes retinitis pigmentosa (RP) in patients with autosomal dominant transmission (adRP). Methods A positional-cloning approach, whole exome sequencing, and modeling were used. The proband and several affected family members have been phenotyped and followed for over 12 years. Results A heterozygous missense variant, c.509C>G (p. Ser170Cys) in exon 2 of COL6A6 (comprised of 36 exons and 2236 amino acids), was observed in a four- generation family and is likely to cause the adRP phenotype. It was identified in 10 affected members. All affected family members had a distinct phenotype: late-onset rod cone dystrophy, with good retained visual acuity, until their late 70s. Immunohistochemistry of human retina showed a dot-like signal at the base of the inner segments of photoreceptors and outer plexiform layer (OPL). The structural modeling of the N7 domain of Col6α6 suggests that the mutant might result in the abnormal cellular localization of collagen VI or malformation of collagen fibers resulting in the loss of its unique filament structure. Conclusions COL6A6 is widely expressed in human tissues and evolutionary conserved. It is thought to interact with a range of extracellular matrix components. Our findings suggest that this form of RP has long-term useful central visual acuity and a mild progression, which are important considerations for patient counseling.
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Affiliation(s)
- Veronika Vaclavik
- Jules-Gonin Eye Hospital, University of Lausanne, Lausanne, Switzerland.,Department of Ophthalmology, Hospital Cantonal, Fribourg, Switzerland
| | - Leila Tiab
- Institute for Research in Ophthalmology, Sion, Switzerland
| | - Young Joo Sun
- Molecular Surgery Laboratory, Byers Eye Institute, Stanford University, Palo Alto, California, United States
| | - Vinit B Mahajan
- Molecular Surgery Laboratory, Byers Eye Institute, Stanford University, Palo Alto, California, United States.,Veterans Affairs Palo Alto Health Care System, Palo Alto, California, United States
| | - Alexandre Moulin
- Jules-Gonin Eye Hospital, University of Lausanne, Lausanne, Switzerland
| | | | - Francis L Munier
- Jules-Gonin Eye Hospital, University of Lausanne, Lausanne, Switzerland
| | - Daniel F Schorderet
- Institute for Research in Ophthalmology, Sion, Switzerland.,Faculty of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
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8
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Wu Q, Liu H, Yang Q, Wei B, Wang L, Tang Q, Wang J, Xi Y, Han C, Wang J, Li L. Developmental Transcriptome Profiling of the Tibial Reveals the Underlying Molecular Basis for Why Newly Hatched Quails Can Walk While Newly Hatched Pigeons Cannot. Front Cell Dev Biol 2022; 10:745129. [PMID: 35198553 PMCID: PMC8858812 DOI: 10.3389/fcell.2022.745129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/12/2022] [Indexed: 11/13/2022] Open
Abstract
Birds can be classified into altricial and precocial species. The hatchlings of altricial birds cannot stand, whereas precocial birds can walk and run soon after hatching. It might be owing to the development of the hindlimb bones in the embryo stage, but the molecular regulatory basis underlying the divergence is unclear. To address this issue, we chose the altricial pigeon and the precocial Japanese quail as model animals. The data of tibia weight rate, embryonic skeletal staining, and tibia tissues paraffin section during the embryonic stage showed that the Japanese quail and pigeon have similar skeletal development patterns, but the former had a faster calcification rate. We utilized the comparative transcriptome approach to screen the genes and pathways related to this heterochronism. We separately analyzed the gene expression of tibia tissues of quail and pigeon at two consecutive time points from an inability to stand to be able to stand. There were 2910 differentially expressed genes (DEGs) of quail, and 1635 DEGs of pigeon, respectively. A total of 409 DEGs in common in the quail and pigeon. On the other hand, we compared the gene expression profiles of pigeons and quails at four time points, and screened out eight pairs of expression profiles with similar expression trends but delayed expression in pigeons. By screening the common genes in each pair of expression profiles, we obtained a gene set consisting of 152 genes. A total of 79 genes were shared by the 409 DEGs and the 152 genes. Gene Ontology analysis of these common genes showed that 21 genes including the COL gene family (COL11A1, COL9A3, COL9A1), IHH, MSX2, SFRP1, ATP6V1B1, SRGN, CTHRC1, NOG, and GDF5 involved in the process of endochondral ossification. These genes were the candidate genes for the difference of tibial development between pigeon and quail. This is the first known study on the embryo skeletal staining in pigeon. It provides some new insights for studying skeletal development mechanisms and locomotor ability of altricial and precocial bird species.
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Naravane AV, Belin PJ, Pierce B, Quiram PA. Risk and Prevention of Retinal Detachments in Patients with Stickler Syndrome. Ophthalmic Surg Lasers Imaging Retina 2022; 53:7-11. [PMID: 34982001 DOI: 10.3928/23258160-20211213-02] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND AND OBJECTIVE To report the impact of prophylactic laser retinopexy in the prevention of retinal detachments (RDs) in patients with Stickler syndrome. PATIENTS AND METHODS This was a retrospective, comparative case series of patients with Stickler syndrome from the year 2000 to 2019. We compared the rate of RDs between individuals who did and did not receive prophylactic laser therapy. In patients with an RD, we compared the rate of RD in the fellow eye with and without prophylactic laser treatment. RESULTS A total of 95 eyes were identified. Fifty-four percent of the overall population was female. The RD rate was 26.7% among eyes without previous prophylactic laser retinopexy and 4.6% among eyes with previous prophylactic laser retinopexy. A Cox proportional model revealed that laser prophylaxis treatment had a statistically significant effect on the risk of RD or retinal tear during the 25-year survival period from birth (P = .034). Eyes receiving treatment were 70% less likely to experience RD or retinal tear (hazard ratio, 0.297; 95% CI, 0.097 to 0.913). CONCLUSIONS This study's results suggest a potential role for prophylactic laser retinopexy in the prevention of rhegmatogenous RD among patients with a clinical diagnosis of Stickler syndrome. [Ophthalmic Surg Lasers Imaging Retina. 2022;53:7-11.].
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10
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Alexander P, Gomersall P, Stancel-Lewis J, Fincham GS, Poulson A, Richards A, McNinch A, Baguley DM, Snead M. Auditory dysfunction in type 2 Stickler Syndrome. Eur Arch Otorhinolaryngol 2021; 278:2261-2268. [PMID: 32901364 PMCID: PMC8165062 DOI: 10.1007/s00405-020-06306-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/18/2020] [Indexed: 11/24/2022]
Abstract
PURPOSE To present the extent and site of lesion of auditory dysfunction in a large cohort of individuals with type 2 Stickler Syndrome. Type 2 Stickler Syndrome results from a mutation in the gene coding for α-1 type XI pro-collagen, which has been identified in the human vitreous, cartilage and the cochlea of the mouse. The condition is characterised by classic ocular abnormalities, auditory dysfunction, osteoarthropathy and oro-facial dysplasia. METHODS This is a population study which used a combination of audiometric, tympanometric, and self-report measures on a series of 65 individuals (mean age 29.2 years, range 3-70, female 63.1%) with genetically confirmed type 2 Stickler Syndrome. RESULTS Hearing impairment was identified in at least one ear for 69% of individuals. Analysis against age-matched normative data showed that reduced hearing sensitivity was present across all test frequencies. Sensorineural hearing loss was most common (77% of ears), with conductive (3%), mixed (7%) and no hearing loss (13%), respectively. The proportion of hypermobile tympanic membranes (24%) was less than previously documented in type 1 Stickler Syndrome. When present, this appears to arise as a direct result of collagen abnormalities in the middle ear. Self-report measures of speech and spatial hearing in sound were comparable to a non-syndromic cohort with similar audiometric thresholds. CONCLUSIONS Auditory impairment in type 2 Stickler Syndrome is predominantly associated with cochlear hearing loss of varying severities across affected individuals. The impact on hearing thresholds can be seen across the frequency range, suggesting a contribution of defective collagen throughout the cochlea. Self-report questionnaires showed that difficulties understanding speech, and spatial information in sound (such as that used for localisation), were worse than a young, normal-hearing population but comparable to a non-syndromic cohort with similar audiometric thresholds. Therefore, it is likely that hearing loss in type 2 Stickler Syndrome arises in the auditory periphery, without significant central processing deficits.
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Affiliation(s)
- Philip Alexander
- Vitreoretinal Service, Box 41, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ, UK
- NHS England Stickler Syndrome Diagnostic Service, Box 153, Cambridge University NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ, UK
| | - Philip Gomersall
- Ear, Nose and Throat (ENT) West Wing, Oxford Auditory Implant Programme, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Jack Stancel-Lewis
- NHS England and NHS Improvement, Wellington House 33-155 Waterloo Road, London, SE1 8UG, UK
| | - Gregory Scott Fincham
- Vitreoretinal Service, Box 41, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ, UK
- NHS England Stickler Syndrome Diagnostic Service, Box 153, Cambridge University NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ, UK
| | - Arabella Poulson
- Vitreoretinal Service, Box 41, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ, UK
- NHS England Stickler Syndrome Diagnostic Service, Box 153, Cambridge University NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ, UK
| | - Allan Richards
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
- Regional Molecular Genetics Laboratory, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ, UK
| | - Annie McNinch
- NHS England Stickler Syndrome Diagnostic Service, Box 153, Cambridge University NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ, UK
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
- Regional Molecular Genetics Laboratory, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ, UK
| | - David M Baguley
- National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham, NG1 5DU, UK.
- Hearing Sciences, Division of Clinical Neuroscience, School of Medicine, University of Nottingham, Nottingham, NG7 2UH, UK.
- Nottingham Audiology Services, Nottingham University NHS Trust, Nottingham, NG1 3DU, UK.
- Nottingham Biomedical Research Centre, Ropewalk House, 113 Ropewalk, Nottingham, NG1 5DU, UK.
| | - Martin Snead
- Vitreoretinal Service, Box 41, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ, UK
- NHS England Stickler Syndrome Diagnostic Service, Box 153, Cambridge University NHS Foundation Trust, Hills Road, Cambridge, CB2 0QQ, UK
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Khan AO, AlAbdi L, Patel N, Helaby R, Hashem M, Abdulwahab F, AlBadr FB, Alkuraya FS. Genetic testing results of children suspected to have Stickler syndrome type collagenopathy after ocular examination. Mol Genet Genomic Med 2021; 9:e1628. [PMID: 33951325 PMCID: PMC8172201 DOI: 10.1002/mgg3.1628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 02/10/2021] [Accepted: 02/10/2021] [Indexed: 12/04/2022] Open
Abstract
Purpose Stickler syndrome is a collagenopathy that is typically COL2A1‐related (autosomal dominant) and less commonly related to other collagen gene mutations. Diagnosis is straightforward when a child has myopia or retinal detachment in the setting of classic diagnostic criteria such as hearing impairment, midfacial hypoplasia, and arthropathy. However, some children have primarily ocular disease with mild or no extraocular features. Such children can remain undiagnosed unless suspicion is raised by the ophthalmologist. Methods Retrospective consecutive case series (2014–2016) of children (<12 years old) suspected to have Stickler syndrome type collagenopathy by a single ophthalmologist and able to complete genetic testing for this possibility. Suspicion was based on vitreous abnormalities and myopia or lens opacities in the setting of prior retinal detachment, hearing impairment, or facial flatness. Results Average age of the 12 identified children was 8 years old (range 3–11; five boys). Average spherical equivalent for phakic eyes was −13 (range −3.5 to −30). Nine children had lens opacities or aphakia; two with aphakia also had lens subluxation or iridodonesis. Other recurrent clinical features included flat facies (12/12), hearing impairment (5/12), and prior retinal detachment (4/12). Pathogenic variants for collagenopathy were uncovered in 10/12 children: COL11A1 (heterozygous) in six, COL2A1 (heterozygous) in two, and COL9A1 (homozygous) in two. One child was homozygous for pathogenic variation in LRPAP1. One child had no detectable gene mutations. Conclusions Taken together, these clinical features (particularly vitreous abnormality, myopia, and lens opacity) had a high molecular yield for collagen gene mutation. Ophthalmologists who see such children should suspect Stickler syndrome, even in the absence of overt systemic disease. COL11A1‐related rather than COL2A1‐related autosomal dominant disease may be more common when undiagnosed children are identified based on ocular examination. Biallelic mutations in LRPAP1 can result in a phenotype that may resemble Stickler syndrome.
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Affiliation(s)
- Arif O Khan
- Department of Genetics, KFSHRC, Riyadh, Saudi Arabia.,Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates.,Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine of Case Western University, Cleveland, OH, USA
| | - Lama AlAbdi
- Department of Genetics, KFSHRC, Riyadh, Saudi Arabia.,College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Nisha Patel
- Department of Genetics, KFSHRC, Riyadh, Saudi Arabia
| | - Rana Helaby
- Department of Genetics, KFSHRC, Riyadh, Saudi Arabia
| | - Mais Hashem
- Department of Genetics, KFSHRC, Riyadh, Saudi Arabia
| | | | - Fahad B AlBadr
- Department of Radiology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, KFSHRC, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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12
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Markova T, Sparber P, Borovikov A, Nagornova T, Dadali E. Clinical and genetic characterization of autosomal recessive stickler syndrome caused by novel compound heterozygous mutations in the COL9A3 gene. Mol Genet Genomic Med 2021; 9:e1620. [PMID: 33570243 PMCID: PMC8104176 DOI: 10.1002/mgg3.1620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 01/31/2021] [Indexed: 12/05/2022] Open
Abstract
Background Stickler syndrome (STL) is a clinically variable and genetically heterogeneous collagenopathy characterized by ophthalmic, auditory, skeletal, and orofacial abnormalities. STL is mainly inherited in an autosomal dominant pattern with mutations in the COL2A1, COL11A1, and COL11A2 genes. Autosomal recessive forms are rare. However, 19 patients have been reported to date, with STL caused by homozygous or compound heterozygous mutations in genes that encode for the three chains of type IX collagen: COL9A1, COL9A2, and COL9A3. Methods Genetic analysis was performed using the next‐generation sequencing of 166 genes associated with skeletal disorders and sequenced on an Ion Torrent S5 system with a minimum coverage of 100X. The two variants in the COL9A3 gene identified in the proband and the parents were confirmed by Sanger sequencing on an ABI3130xl sequencer. Results We describe a novel case of autosomal recessive Stickler syndrome caused by two undescribed mutations in the COL9A3 gene: c.268C>T (p.Arg90Ter) and c.1729C>T (p.Arg577Ter). The clinical features included severe sensorineural hearing loss, high myopia, vitreoretinal degeneration, and early‐onset arthropathy of the lower limbs. Radiography revealed mild spondyloepiphyseal dysplasia. Conclusion This case further expands the mutational and phenotypic spectrum of COL9A‐associated STL with a more severe presentation.
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Affiliation(s)
| | - Peter Sparber
- Research Centre for Medical Genetics, Moscow, Russia
| | | | | | - Elena Dadali
- Research Centre for Medical Genetics, Moscow, Russia
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13
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Salazar-Silva R, Dantas VLG, Alves LU, Batissoco AC, Oiticica J, Lawrence EA, Kawafi A, Yang Y, Nicastro FS, Novaes BC, Hammond C, Kague E, Mingroni-Netto RC. NCOA3 identified as a new candidate to explain autosomal dominant progressive hearing loss. Hum Mol Genet 2021; 29:3691-3705. [PMID: 33326993 PMCID: PMC7823111 DOI: 10.1093/hmg/ddaa240] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 09/21/2020] [Accepted: 10/15/2020] [Indexed: 12/27/2022] Open
Abstract
Hearing loss is a frequent sensory impairment in humans and genetic factors account for an elevated fraction of the cases. We have investigated a large family of five generations, with 15 reported individuals presenting non-syndromic, sensorineural, bilateral and progressive hearing loss, segregating as an autosomal dominant condition. Linkage analysis, using SNP-array and selected microsatellites, identified a region of near 13 cM in chromosome 20 as the best candidate to harbour the causative mutation. After exome sequencing and filtering of variants, only one predicted deleterious variant in the NCOA3 gene (NM_181659, c.2810C > G; p.Ser937Cys) fit in with our linkage data. RT-PCR, immunostaining and in situ hybridization showed expression of ncoa3 in the inner ear of mice and zebrafish. We generated a stable homozygous zebrafish mutant line using the CRISPR/Cas9 system. ncoa3-/- did not display any major morphological abnormalities in the ear, however, anterior macular hair cells showed altered orientation. Surprisingly, chondrocytes forming the ear cartilage showed abnormal behaviour in ncoa3-/-, detaching from their location, invading the ear canal and blocking the cristae. Adult mutants displayed accumulation of denser material wrapping the otoliths of ncoa3-/- and increased bone mineral density. Altered zebrafish swimming behaviour corroborates a potential role of ncoa3 in hearing loss. In conclusion, we identified a potential candidate gene to explain hereditary hearing loss, and our functional analyses suggest subtle and abnormal skeletal behaviour as mechanisms involved in the pathogenesis of progressive sensory function impairment.
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Affiliation(s)
- R Salazar-Silva
- Centro de Pesquisas sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, Brazil
| | - Vitor Lima Goes Dantas
- Centro de Pesquisas sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, Brazil
| | - Leandro Ucela Alves
- Centro de Pesquisas sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, Brazil
| | - Ana Carla Batissoco
- Centro de Pesquisas sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, Brazil
- Laboratório de Otorrinolaringologia/LIM32 –Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo , 01246-903, São Paulo, Brazil
| | - Jeanne Oiticica
- Laboratório de Otorrinolaringologia/LIM32 –Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo , 01246-903, São Paulo, Brazil
| | - Elizabeth A Lawrence
- School of Pharmacology, Physiology and Neuroscience, University of Bristol, Bristol, BS8 1TD, United Kingdom
| | - Abdelwahab Kawafi
- School of Pharmacology, Physiology and Neuroscience, University of Bristol, Bristol, BS8 1TD, United Kingdom
| | - Yushi Yang
- School of Physics, University of Bristol, Bristol, BS8 1TL, United Kingdom
- Centre for Nanoscience and Quantum Information, University of Bristol, Bristol, BS8 1FD, United Kingdom
- Bristol Centre for Functional Nanomaterials, University of Bristol, Bristol, BS8 1FD, United Kingdom
| | - Fernanda Stávale Nicastro
- Divisão de Educação e Reabilitação dos Distúrbios da Comunicação da Pontifícia Universidade Católica de São Paulo, 04022-040, São Paulo, Brazil
| | - Beatriz Caiuby Novaes
- Divisão de Educação e Reabilitação dos Distúrbios da Comunicação da Pontifícia Universidade Católica de São Paulo, 04022-040, São Paulo, Brazil
| | - Chrissy Hammond
- School of Pharmacology, Physiology and Neuroscience, University of Bristol, Bristol, BS8 1TD, United Kingdom
| | - Erika Kague
- Centro de Pesquisas sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, Brazil
- School of Pharmacology, Physiology and Neuroscience, University of Bristol, Bristol, BS8 1TD, United Kingdom
| | - R C Mingroni-Netto
- Centro de Pesquisas sobre o Genoma Humano e Células-Tronco, Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, 05508-090, São Paulo, Brazil
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14
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Kjellström U, Martell S, Brobeck C, Andréasson S. Autosomal recessive Stickler syndrome associated with homozygous mutations in the COL9A2 gene. Ophthalmic Genet 2020; 42:161-169. [PMID: 33356723 DOI: 10.1080/13816810.2020.1861309] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Background: Stickler syndrome is a hereditary disorder of collagen tissues causing ocular, auditory, orofacial, and joint manifestations. Ocular findings typically include vitreous degeneration, high myopia, retinal detachment, and cataract. Many subjects demonstrate sensorineural or conductive hearing loss. The inheritance is autosomal dominant with mutations in COL2A1, COL11A1, or COL11A2 or autosomal recessive due to mutations in COL9A1, COL9A2, or COL9A3. We describe a family with Stickler syndrome caused by homozygous loss-of-function mutations in COL9A2.Methods: Two brothers from a consanguineous family were examined with genetic testing, visual acuity, Goldmann perimetry, full-field and multifocal electroretinography (ffERG, mERG), optical coherence tomography (OCT), fundus autofluorescence (FAF), fundus photography, and pure-tone audiograms.Results: Both subjects were homozygous for the mutation c.1332del in COL9A2. Their parents were heterozygous for the same mutation. The boys demonstrated reduced visual acuity, vitreous changes and myopia. The proband was operated for retinal detachment and cataract in one eye. FfERG revealed reduced function of both rods and cones and mERG showed reduced macular function. No morphological macular changes were found by OCT or FAF. Both brothers have severe sensorineural hearing loss with down-sloping audiograms but only subtle midface hypoplasia and no, or mild joint problems.Conclusion: Only a few families with Stickler syndrome caused by COL9A2 mutations have been reported. We confirm previous descriptions with a severe ocular and auditory phenotype but mild orofacial and joint manifestations. Moreover, we demonstrate reduced macular and overall retinal function explaining the reduced visual acuity in patients with Stickler syndrome also without retinal complications.
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Affiliation(s)
- Ulrika Kjellström
- Department of Clinical Sciences Lund, Ophthalmology, Lund University, Skane University Hospital, Lund, Sweden
| | - Susanne Martell
- Department of Oto-Rhino-Laryngology, Helsingborg Hospital, Helsingborg, Sweden
| | - Cecilia Brobeck
- Department of Oto-Rhino-Laryngology, Helsingborg Hospital, Helsingborg, Sweden
| | - Sten Andréasson
- Department of Clinical Sciences Lund, Ophthalmology, Lund University, Skane University Hospital, Lund, Sweden
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15
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Boothe M, Morris R, Robin N. Stickler Syndrome: A Review of Clinical Manifestations and the Genetics Evaluation. J Pers Med 2020; 10:jpm10030105. [PMID: 32867104 PMCID: PMC7564399 DOI: 10.3390/jpm10030105] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/05/2020] [Accepted: 08/07/2020] [Indexed: 01/17/2023] Open
Abstract
Stickler Syndrome (SS) is a multisystem collagenopathy frequently encountered by ophthalmologists due to the high rate of ocular complications. Affected individuals are at significantly increased risk for retinal detachment and blindness, and early detection and diagnosis are critical in improving visual outcomes for these patients. Systemic findings are also common, with craniofacial, skeletal, and auditory systems often involved. SS is genotypically and phenotypically heterogenous, which can make recognizing and correctly diagnosing individuals difficult. Molecular genetic testing should be considered in all individuals with suspected SS, as diagnosis not only assists in treatment and management of the patient but may also help identify other at-risk family members. Here we review common clinical manifestation of SS and genetic tests frequently ordered as part of the SS evaluation.
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Affiliation(s)
- Megan Boothe
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA;
| | - Robert Morris
- Retina Specialists of Alabama, Birmingham, AL 35233, USA;
| | - Nathaniel Robin
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA;
- Correspondence:
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16
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Mutation Spectrum and De Novo Mutation Analysis in Stickler Syndrome Patients with High Myopia or Retinal Detachment. Genes (Basel) 2020; 11:genes11080882. [PMID: 32756486 PMCID: PMC7464315 DOI: 10.3390/genes11080882] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 07/16/2020] [Accepted: 07/30/2020] [Indexed: 02/08/2023] Open
Abstract
Stickler syndrome is a connective tissue disorder that affects multiple systems, including the visual system. Seven genes were reported to cause Stickler syndrome in patients with different phenotypes. In this study, we aimed to evaluate the mutation features of the phenotypes of high myopia and retinal detachment. Forty-two probands diagnosed with Stickler syndrome were included. Comprehensive ocular examinations were performed. A targeted gene panel test or whole exome sequencing was used to detect the mutations, and Sanger sequencing was conducted for verification and segregation analysis. Among the 42 probands, 32 (76%) presented with high myopia and 29 (69%), with retinal detachment. Pathogenic mutations were detected in 35 (83%) probands: 27 (64%) probands had COL2A1 mutations, and eight (19%) probands had COL11A1 mutations. Truncational mutations in COL2A1 were present in 21 (78%) probands. Missense mutations in COL2A1 were present in six probands, five of which presented with retinal detachment. De novo COL2A1 mutations were detected in 10 (37%) probands, with a mean paternal childbearing age of 29.64 ± 4.97 years old. The mutation features of probands with high myopia or retinal detachment showed that the probands had a high prevalence of COL2A1 mutations, truncational mutations, and de novo mutations.
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17
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Nixon T, Richards AJ, Lomas A, Abbs S, Vasudevan P, McNinch A, Alexander P, Snead MP. Inherited and de novo biallelic pathogenic variants in COL11A1 result in type 2 Stickler syndrome with severe hearing loss. Mol Genet Genomic Med 2020; 8:e1354. [PMID: 32578940 PMCID: PMC7507023 DOI: 10.1002/mgg3.1354] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 12/11/2022] Open
Abstract
Background Type 2 Stickler syndrome is usually a dominant disorder resulting from pathogenic variants in COL11A1 encoding the alpha 1 chain of type XI collagen. Typical molecular changes result in either substitution of an obligate glycine within the Gly‐Xaa‐Yaa amino acid sequence repeat region of the molecule, mRNA missplicing or deletions/duplications that typically leaves the message in‐frame. Clinical features include myopia, retinal detachment, craniofacial, joint, and hearing problems. Fibrochondrogenesis is also a COL11A1 related disorder, but here disease‐associated variants are recessive and may be either null alleles or substitutions of glycine, and the condition is usually lethal in infancy. Methods The patient was assessed in the NHS England Stickler syndrome diagnostic service. DNA from the patient and family were analyzed with Next Generation Sequencing on a panel of genes known to cause Stickler Syndrome. The effect of sequence variants was assessed using minigene analysis. Allele‐specific RT‐PCR was performed. Results This patient had clinical type 2 Stickler syndrome but with severe hearing loss and severe ocular features including retinal atrophy and retinal tears in childhood. We identified a de novo in frame deletion of COL11A1 (c.4109_4126del) consistent with dominantly inherited Stickler syndrome but also a second inherited variant (c.1245+2T>C), on the other allele, affecting normal splicing of COL11A1 exon 9. Conclusion Exon 9 of COL11A1 is alternatively expressed and disease causing changes affecting only this exon modify the phenotype resulting from biallelic COL11A1 disease‐associated variants and, instead of fibrochondrogenesis, produce a form of Stickler syndrome with severe hearing loss. Disease phenotypes from de novo pathogenic variants can be modified by inherited recessive variants on the other allele. This highlights the need for functional and family analysis to confirm the mode of inheritance in COL11A1‐related disorders, particularly for those variants that may alter normal pre‐mRNA splicing.
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Affiliation(s)
- Thomas Nixon
- School of Clinical Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.,Vitreoretinal Service, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Allan J Richards
- Department of Pathology, University of Cambridge, Cambridge, UK.,East Midlands and East of England NHS Genomic Laboratory Hub, Addenbrooke's Treatment Centre, Cambridge, UK
| | - Adrian Lomas
- East Midlands and East of England NHS Genomic Laboratory Hub, Addenbrooke's Treatment Centre, Cambridge, UK
| | - Stephen Abbs
- East Midlands and East of England NHS Genomic Laboratory Hub, Addenbrooke's Treatment Centre, Cambridge, UK
| | - Pradeep Vasudevan
- Department of Clinical Genetics, University Hospitals of Leicester NHS Trust, Infirmary Square, Leicester, UK
| | - Annie McNinch
- Vitreoretinal Service, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.,Department of Pathology, University of Cambridge, Cambridge, UK
| | - Philip Alexander
- School of Clinical Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.,Vitreoretinal Service, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Martin P Snead
- School of Clinical Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.,Vitreoretinal Service, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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18
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Ichikawa S, Prockop S, Cunningham-Rundles C, Sifers T, Conner BR, Wu S, Karam R, Walsh MF, Fiala E. Reticular dysgenesis caused by an intronic pathogenic variant in AK2. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005017. [PMID: 32532877 PMCID: PMC7304357 DOI: 10.1101/mcs.a005017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 03/23/2020] [Indexed: 01/25/2023] Open
Abstract
Reticular dysgenesis is a form of severe combined immunodeficiency (SCID) caused by biallelic pathogenic variants in AK2. Here we present the case of a boy diagnosed with SCID following a positive newborn screen (NBS). Genetic testing revealed a homozygous variant: AK2 c.330 + 5G > A. In silico analyses predicted weakened native donor splice site. However, this variant was initially classified as a variant of uncertain significance (VUS) given lack of direct evidence. To determine the impact on splicing, we analyzed RNA from the proband and his parents, using massively parallel RNA-seq of cloned RT-PCR products. Analysis showed that c.330 + 5G > A results in exon 3 skipping, which encodes a critical region of the AK2 protein. With these results, the variant was upgraded to pathogenic, and the patient was given a diagnosis of reticular dysgenesis. Interpretation of VUS at noncanonical splice site nucleotides presents a challenge. RNA sequencing provides an ideal platform to perform qualitative and quantitative assessment of intronic VUS, which can lead to reclassification if a significant impact on mRNA is observed. Genetic disorders of hematopoiesis and immunity represent fruitful areas to apply RNA-based analysis for variant interpretation given the high expression of RNA in blood.
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Affiliation(s)
- Shoji Ichikawa
- Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, California 92656, USA
| | - Susan Prockop
- MSK Kids, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,MSK Kids, Stem Cell Transplant and Cellular Therapy, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Charlotte Cunningham-Rundles
- Division of Clinical Immunology, Departments of Medicine and Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Travis Sifers
- Division of Clinical Immunology, Departments of Medicine and Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Blair R Conner
- Department of Research and Development, Ambry Genetics, Aliso Viejo, California 92656, USA
| | - Sitao Wu
- Department of Bioinformatics and Computational Biology, Ambry Genetics, Aliso Viejo, California 92656, USA
| | - Rachid Karam
- Department of Research and Development, Ambry Genetics, Aliso Viejo, California 92656, USA
| | - Michael F Walsh
- MSK Kids, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
| | - Elise Fiala
- MSK Kids, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
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19
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Mayer AK, Balousha G, Sharkia R, Mahajnah M, Ayesh S, Schulze M, Buchert R, Zobor D, Azem A, Schöls L, Bauer P, Wissinger B. Unraveling the genetic cause of hereditary ophthalmic disorders in Arab societies from Israel and the Palestinian Authority. Eur J Hum Genet 2020; 28:742-753. [PMID: 31896775 DOI: 10.1038/s41431-019-0566-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 11/12/2019] [Accepted: 12/10/2019] [Indexed: 11/09/2022] Open
Abstract
Visual impairment due to inherited ophthalmic disorders is amongst the most common disabilities observed in populations practicing consanguineous marriages. Here we investigated the molecular genetic basis of an unselected broad range of ophthalmic disorders in 20 consanguineous families from Arab villages of Israel and the Palestinian Authority. Most patients had little or very poor prior clinical workup and were recruited in a field study. Homozygosity mapping followed by candidate gene sequencing applying conventional Sanger sequencing or targeted next generation sequencing was performed in six families. In the remaining 14 families, one affected subject per family was chosen for whole exome sequencing. We discovered likely disease-causing variants, all homozygous, in 19 of 20 independent families (95%) including a previously reported novel disease gene for congenital nystagmus associated with foveal hypoplasia. Moreover, we found a family in which disease-causing variants for two collagenopathies - Stickler and Knobloch syndrome - segregate within a large sibship. Nine of the 19 distinct variants observed in this study were novel. Our study demonstrated a very high molecular diagnostic yield for a highly diverse spectrum of rare ophthalmic disorders in Arab patients from Israel and the Palestinian Authority, even with very limited prior clinical investigation. We conclude that 'genetic testing first' may be an economic way to direct clinical care and to support proper genetic counseling and risk assessment in these families.
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Affiliation(s)
- Anja K Mayer
- Institute for Ophthalmic Research, Molecular Genetics Laboratory, Tuebingen, Germany.,Praxis fuer Humangenetik Tuebingen, Tuebingen, Germany
| | - Ghassan Balousha
- Department of Pathology and Histology, Al-Quds University, Eastern Jerusalem, Palestinian Authority, Jerusalem, Israel
| | - Rajech Sharkia
- The Triangle Regional Research and Development Center, Kfar Qari', Israel.,Beit-Berl Academic College, Beit-Berl, Israel
| | - Muhammad Mahajnah
- Child Neurology and Development Center, Hillel-Yaffe Medical Center, Hadera, Israel.,The Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Suhail Ayesh
- Molecular Genetic Laboratory, Al-Makassed Islamic Charitable Society Hospital, Jerusalem, Israel
| | - Martin Schulze
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany.,Praxis fuer Humangenetik Tuebingen, Tuebingen, Germany
| | - Rebecca Buchert
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Ditta Zobor
- University Eye Hospital, University of Tuebingen, Tuebingen, Germany
| | - Abdussalam Azem
- The School of Neurobiology, Biochemistry and Biophysics, George S. Wise faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ludger Schöls
- Hertie Institute for Brain Research, University of Tuebingen, Tuebingen, Germany.,German Center of Neurodegenerative Diseases (DZNE), Tuebingen, Germany
| | - Peter Bauer
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Bernd Wissinger
- Institute for Ophthalmic Research, Molecular Genetics Laboratory, Tuebingen, Germany.
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