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Richards T, Wilson P, Goggolidou P. Next generation sequencing identifies WNT signalling as a significant pathway in Autosomal Recessive Polycystic Kidney Disease (ARPKD) manifestation and may be linked to disease severity. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167309. [PMID: 38885798 DOI: 10.1016/j.bbadis.2024.167309] [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: 12/19/2023] [Revised: 05/28/2024] [Accepted: 06/11/2024] [Indexed: 06/20/2024]
Abstract
INTRODUCTION Autosomal Recessive Polycystic Kidney Disease (ARPKD) is a rare paediatric disease primarily caused by sequence variants in PKHD1. ARPKD presents with considerable clinical variability relating to the type of PKHD1 sequence variant, but not its position. Animal models of Polycystic Kidney Disease (PKD) suggest a complex genetic landscape, with genetic modifiers as a potential cause of disease variability. METHODS To investigate in an unbiased manner the molecular mechanisms of ARPKD and identify potential indicators of disease severity, Whole Exome Sequencing (WES) and RNA-Sequencing (RNA-Seq) were employed on human ARPKD kidneys and age-matched healthy controls. RESULTS WES confirmed the clinical diagnosis of ARPKD in our patient cohort consisting of ten ARPKD kidneys. Sequence variant type, nor position of PKHD1 sequence variants, was linked to disease severity. Sequence variants in genes associated with other ciliopathies were detected in the ARPKD cohort, but only PKD1 could be linked to disease severity. Transcriptomic analysis on a subset of four ARPKD kidneys representing severe and moderate ARPKD, identified a significant number of genes relating to WNT signalling, cellular metabolism and development. Increased expression of WNT signalling-related genes was validated by RT-qPCR in severe and moderate ARPKD kidneys. Two individuals in our cohort with the same PKHD1 sequence variants but different rates of kidney disease progression, with displayed transcriptomic differences in the expression of WNT signalling genes. CONCLUSION ARPKD kidney transcriptomics highlights changes in WNT signalling as potentially significant in ARPKD manifestation and severity, providing indicators for slowing down the progression of ARPKD.
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Affiliation(s)
- Taylor Richards
- School of Biomedical Science and Physiology, Faculty of Science and Engineering, University of Wolverhampton, Wulfruna Street, Wolverhampton WV1 1LY, UK
| | - Patricia Wilson
- Centre for Nephrology, UCL Medical School, Royal Free Campus, Rowland Hill, London NW3 2PF, UK
| | - Paraskevi Goggolidou
- School of Biomedical Science and Physiology, Faculty of Science and Engineering, University of Wolverhampton, Wulfruna Street, Wolverhampton WV1 1LY, UK.
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2
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Chen C, Gao J, Lv Q, Xu C, Xia Y, Du A. Retinitis pigmentosa and molar tooth sign caused by novel AHI1 compound heterozygote pathogenic variants. BMC Med Genomics 2021; 14:242. [PMID: 34627237 PMCID: PMC8502301 DOI: 10.1186/s12920-021-01089-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 09/23/2021] [Indexed: 11/30/2022] Open
Abstract
Background Joubert syndrome (JS) is a group of rare congenital disorders characterized by cerebellar vermis dysplasia, developmental delay, and retina dysfunctions. Herein, we reported a Chinese patient carrying a new variant in the AHI1 gene with mild JS, and the 3D structure of the affected Jouberin protein was also predicted. Case presentation The patient was a 31-year-old male, who presented difficulty at finding toys at the age of 2 years, night blindness from age of 5 years, intention tremor and walking imbalance from 29 years of age. Tubular visual field and retina pigmentation were observed on ophthalmology examinations, as well as molar tooth sign on brain magnetic resonance imaging (MRI). Whole exome sequence revealed two compound heterozygous variants at c.2105C>T (p.T702M) and c.1330A>T (p.I444F) in AHI1 gene. The latter one was a novel mutation. The 3D protein structure was predicted using I-TASSER and PyMOL, showing structural changes from functional β-sheet and α-helix to non-functional D-loop, respectively. Conclusions Mild JS due to novel variants at T702M and I444F in the AHI1 gene was reported. The 3D-structural changes in Jouberin protein might underlie the pathogenesis of JS.
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Affiliation(s)
- Chunyan Chen
- Department of Neurology, Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200336, China
| | - Jiong Gao
- WuXiDiagnostice, No. 31 Yiwei Road Waigaoqiao Pilot Free Trade Zone, Shanghai, 200131, China
| | - Qing Lv
- Department of Neurology, Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200336, China
| | - Chen Xu
- Department of Neurology, Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200336, China
| | - Yu Xia
- Department of Neurology, Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200336, China
| | - Ailian Du
- Department of Neurology, Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200336, China.
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3
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Neissi M, Mabudi H, Mohammadi‐Asl J. AHI1 gene mutation in a consanguineous Iranian family affected by Joubert syndrome: A case report. Clin Case Rep 2021; 9:e05002. [PMID: 34721863 PMCID: PMC8538011 DOI: 10.1002/ccr3.5002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/01/2021] [Accepted: 10/13/2021] [Indexed: 11/11/2022] Open
Abstract
This point of detected mutation could be considered as a novel mutational hotspot point that carried in patient ancestors. Moreover, the obtained results and family history suggest a precise genetic consulting and molecular prenatal evaluation for suspect individuals with a family history of mental and physical abnormalities.
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Affiliation(s)
- Mostafa Neissi
- Department of GeneticsKhuzestan Science and Research BranchIslamic Azad UniversityAhvazIran
- Department of GeneticsAhvaz BranchIslamic Azad UniversityAhvazIran
| | - Hadideh Mabudi
- Department of GeneticsAhvaz BranchIslamic Azad UniversityAhvazIran
| | - Javad Mohammadi‐Asl
- Department of GeneticsAhvaz BranchIslamic Azad UniversityAhvazIran
- Department of Medical GeneticsSchool of MedicineAhvaz Jundishapur University of Medical SciencesAhvazIran
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4
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Powell L, Olinger E, Wedderburn S, Ramakumaran VS, Kini U, Clayton-Smith J, Ramsden SC, Rice SJ, Barroso-Gil M, Wilson I, Cowley L, Johnson S, Harris E, Montgomery T, Bertoli M, Boltshauser E, Sayer JA. Identification of LAMA1 mutations ends diagnostic odyssey and has prognostic implications for patients with presumed Joubert syndrome. Brain Commun 2021; 3:fcab163. [PMID: 34423300 PMCID: PMC8374969 DOI: 10.1093/braincomms/fcab163] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/22/2021] [Accepted: 05/27/2021] [Indexed: 01/17/2023] Open
Abstract
Paediatric neurology syndromes are a broad and complex group of conditions with a large spectrum of clinical phenotypes. Joubert syndrome is a genetically heterogeneous neurological ciliopathy syndrome with molar tooth sign as the neuroimaging hallmark. We reviewed the clinical, radiological and genetic data for several families with a clinical diagnosis of Joubert syndrome but negative genetic analysis. We detected biallelic pathogenic variants in LAMA1, including novel alleles, in each of the four cases we report, thereby establishing a firm diagnosis of Poretti-Boltshauser syndrome. Analysis of brain MRI revealed cerebellar dysplasia and cerebellar cysts, associated with Poretti-Boltshauser syndrome and the absence of typical molar tooth signs. Using large UK patient cohorts, the relative prevalence of Joubert syndrome as a cause of intellectual disability was 0.2% and of Poretti-Boltshauser syndrome was 0.02%. We conclude that children with congenital brain disorders that mimic Joubert syndrome may have a delayed diagnosis due to poor recognition of key features on brain imaging and the lack of inclusion of LAMA1 on molecular genetic gene panels. We advocate the inclusion of LAMA1 genetic analysis on all intellectual disability and Joubert syndrome gene panels and promote a wider awareness of the clinical and radiological features of these syndromes.
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Affiliation(s)
- Laura Powell
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| | - Eric Olinger
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| | | | | | - Usha Kini
- Clinical Genetics, Oxford University Hospital, Oxford, UK
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WL, UK
| | - Simon C Ramsden
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester M13 9WL, UK
| | - Sarah J Rice
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| | - Miguel Barroso-Gil
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| | - Ian Wilson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| | - Lorraine Cowley
- Clinical Genetics, Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| | - Sally Johnson
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| | - Elizabeth Harris
- Clinical Genetics, Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| | - Tara Montgomery
- Clinical Genetics, Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| | - Marta Bertoli
- Clinical Genetics, Northern Genetics Service, Newcastle upon Tyne Hospitals NHS Foundation Trust, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| | | | - Eugen Boltshauser
- Paediatric Neurology (Emeritus), Children's University Hospital, Zürich, Switzerland
| | - John A Sayer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
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Karamzade A, Babaei M, Saberi M, Golchin N, Khalil Nejad Sani Banaei A, Eshaghkhani Y, Golchehre Z, Keramatipour M. Identification of a novel truncating variant in AHI1 gene and a brief review on mutations spectrum. Mol Biol Rep 2021; 48:5339-5345. [PMID: 34191236 DOI: 10.1007/s11033-021-06508-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 06/21/2021] [Indexed: 10/21/2022]
Abstract
Joubert syndrome (JS) is a rare inherited neurodevelopmental condition characterized by hypotonia, ataxia, developmental delay, abnormal eye movements, neonatal respiratory disturbance and unique midbrain-hindbrain malformation, known as the molar tooth sign. JS is a genetically heterogeneous disorder with nearly 35 ciliary genes are implicated in its pathogenesis. AHI1 gene is one of the most frequently mutated gene in JS patients which is accounted for 8-11% of cases, particularly in Arab population. AHI1 encodes a cilium-localized protein with a significant role in mediating vesicle trafficking, ciliogenesis and cell polarity. Here, we report a novel pathogenic variant in AHI1 gene and review previously published mutations in AHI1 gene briefly. Whole exome sequencing was employed to determine the causative mutation in an Iranian Arab family with JS from southwestern Iran. Segregation analysis of the candidate variant in the family members was performed using PCR-Sanger sequencing. This approach found a novel homozygous nonsense variant c.832C > T (p.Gln278Ter) in AHI1. Segregation analysis was consistent with individual's phenotype and an autosomal recessive pattern in the family. The variant residing in a relatively highly conserved region and fulfilled the criteria required to be classified as a pathogenic variant based on American College of Medical Genetics and Genomics guidelines. This study confirms the diagnosis of JS in this family and highlights the efficiency of next-generation sequencing-based technique to identify the genetic causes of hereditary disorders with locus heterogeneity.
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Affiliation(s)
- Arezou Karamzade
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Watson Genetic Laboratory, North Kargar street, Tehran, Iran
| | - Meisam Babaei
- Department of Pediatrics, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Mohammad Saberi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Neda Golchin
- Watson Genetic Laboratory, North Kargar street, Tehran, Iran
| | | | - Yeganeh Eshaghkhani
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Golchehre
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Keramatipour
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran. .,Watson Genetic Laboratory, North Kargar street, Tehran, Iran.
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6
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Zhang C, Sun Z, Xu L, Che F, Liu S. Novel compound heterozygous CPLANE1 variants identified in a Chinese family with Joubert syndrome. Int J Dev Neurosci 2021; 81:529-538. [PMID: 34091942 DOI: 10.1002/jdn.10135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/24/2021] [Accepted: 05/30/2021] [Indexed: 11/08/2022] Open
Abstract
Joubert syndrome (JS) and JS-related disorders (JSRD) are a group of neurodevelopmental diseases that share the "molar tooth sign" on axial brain magnetic resonance imaging (MRI), accompanied by cerebellar vermis hypoplasia, ataxia, hypotonia, and developmental delay. To identify variants responsible for the clinical symptoms of a Chinese family with JS and to explore the genotype-phenotype associations, we conducted a series of clinical examinations, including blood tests, brain MRI scans, ultrasound imaging, and ophthalmologic examination. Genomic DNA was extracted from the peripheral blood of the six-person family, and the pathogenic variants were detected by whole-exome sequencing (WES) and verified by Sanger sequencing. WES revealed two novel compound heterozygous variants in CPLANE1: c.1270C>T (p.Arg424*) in exon 10 and c.8901C>A (p.Tyr2967*) in exon 48 of one child, inherited from each parent. Both variants were absent in ethnically matched Chinese control individuals and were either absent or present at very low frequencies in public databases, suggesting that these variants could be the pathogenic triggers of the JS phenotype. Notably, these CPLANE1 sequence variants were related to the pathogenesis of autosomal recessive JS in this study. The newly discovered variants expand the mutation spectrum of CPLANE1, which assists in understanding the molecular mechanism underlying JS and improving the recognition of genetic counseling, particularly for families with a history of autosomal recessive JS.
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Affiliation(s)
- Cheng Zhang
- Department of Neurology, The Eleventh Clinical Medical College of Qingdao University, Linyi People's Hospital, Linyi, China.,Medical Genetic Department, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Zhenchao Sun
- Department of Neurology, The Eleventh Clinical Medical College of Qingdao University, Linyi People's Hospital, Linyi, China
| | - Lulu Xu
- Department of Geriatric Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Fengyuan Che
- Department of Neurology, The Eleventh Clinical Medical College of Qingdao University, Linyi People's Hospital, Linyi, China
| | - Shiguo Liu
- Medical Genetic Department, The Affiliated Hospital of Qingdao University, Qingdao, China
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7
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Petrović D, Čulić V, Swinderek-Alsayed Z. Three Cases of Joubert Syndrome in a Consanguineous Syrian Family and a Interesting Case of Multinational Collaboration. J Pediatr Genet 2021; 12:167-170. [PMID: 37090835 PMCID: PMC10118711 DOI: 10.1055/s-0040-1721826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 11/15/2020] [Indexed: 10/22/2022]
Abstract
AbstractJoubert syndrome (JS) is a rare congenital, autosomal recessive disorder characterized by a distinctive brain malformation, developmental delay, ocular motor apraxia, breathing abnormalities, and high clinical and genetic heterogeneity. We are reporting three siblings with JS from consanguineous parents in Syria. Two of them had the same homozygous c.2172delA (p.Trp725Glyfs*) AHI1 mutation and the third was diagnosed prenatally with magnetic resonance imaging. This pathogenic variant is very rare and described in only a few cases in the literature. Multinational collaboration could be of benefit for the patients from undeveloped, low-income countries that have a low-quality health care system, especially for the diagnosis of rare diseases.
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Affiliation(s)
- Davor Petrović
- Department of Pediatrics, University Hospital of Split, Split, Croatia
- University of Split School of Medicine, Split, Croatia
| | - Vida Čulić
- Department of Pediatrics, University Hospital of Split, Split, Croatia
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8
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Bryant L, Lozynska O, Maguire AM, Aleman TS, Bennett J. Prescreening whole exome sequencing results from patients with retinal degeneration for variants in genes associated with retinal degeneration. Clin Ophthalmol 2017; 12:49-63. [PMID: 29343940 PMCID: PMC5749571 DOI: 10.2147/opth.s147684] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Background Accurate clinical diagnosis and prognosis of retinal degeneration can be aided by the identification of the disease-causing genetic variant. It can confirm the clinical diagnosis as well as inform the clinician of the risk for potential involvement of other organs such as kidneys. It also aids in genetic counseling for affected individuals who want to have a child. Finally, knowledge of disease-causing variants informs laboratory investigators involved in translational research. With the advent of next-generation sequencing, identifying pathogenic mutations is becoming easier, especially the identification of novel pathogenic variants. Methods We used whole exome sequencing on a cohort of 69 patients with various forms of retinal degeneration and in whom screens for previously identified disease-causing variants had been inconclusive. All potential pathogenic variants were verified by Sanger sequencing and, when possible, segregation analysis of immediate relatives. Potential variants were identified by using a semi-masked approach in which rare variants in candidate genes were identified without knowledge of the clinical diagnosis (beyond "retinal degeneration") or inheritance pattern. After the initial list of genes was prioritized, genetic diagnosis and inheritance pattern were taken into account. Results We identified the likely pathogenic variants in 64% of the subjects. Seven percent had a single heterozygous mutation identified that would cause recessive disease and 13% had no obviously pathogenic variants and no family members available to perform segregation analysis. Eleven subjects are good candidates for novel gene discovery. Two de novo mutations were identified that resulted in dominant retinal degeneration. Conclusion Whole exome sequencing allows for thorough genetic analysis of candidate genes as well as novel gene discovery. It allows for an unbiased analysis of genetic variants to reduce the chance that the pathogenic mutation will be missed due to incomplete or inaccurate family history or analysis at the early stage of a syndromic form of retinal degeneration.
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Affiliation(s)
- Laura Bryant
- Center for Advanced Retinal and Ocular Therapeutics (CAROT), FM Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Olga Lozynska
- Center for Advanced Retinal and Ocular Therapeutics (CAROT), FM Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Albert M Maguire
- Center for Advanced Retinal and Ocular Therapeutics (CAROT), FM Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Ophthalmology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tomas S Aleman
- Center for Advanced Retinal and Ocular Therapeutics (CAROT), FM Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Ophthalmology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jean Bennett
- Center for Advanced Retinal and Ocular Therapeutics (CAROT), FM Kirby Center for Molecular Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Ophthalmology, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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9
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Leto K, Arancillo M, Becker EBE, Buffo A, Chiang C, Ding B, Dobyns WB, Dusart I, Haldipur P, Hatten ME, Hoshino M, Joyner AL, Kano M, Kilpatrick DL, Koibuchi N, Marino S, Martinez S, Millen KJ, Millner TO, Miyata T, Parmigiani E, Schilling K, Sekerková G, Sillitoe RV, Sotelo C, Uesaka N, Wefers A, Wingate RJT, Hawkes R. Consensus Paper: Cerebellar Development. CEREBELLUM (LONDON, ENGLAND) 2016; 15:789-828. [PMID: 26439486 PMCID: PMC4846577 DOI: 10.1007/s12311-015-0724-2] [Citation(s) in RCA: 256] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The development of the mammalian cerebellum is orchestrated by both cell-autonomous programs and inductive environmental influences. Here, we describe the main processes of cerebellar ontogenesis, highlighting the neurogenic strategies used by developing progenitors, the genetic programs involved in cell fate specification, the progressive changes of structural organization, and some of the better-known abnormalities associated with developmental disorders of the cerebellum.
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Affiliation(s)
- Ketty Leto
- Department of Neuroscience Rita Levi Montalcini, University of Turin, via Cherasco 15, 10026, Turin, Italy.
- Neuroscience Institute Cavalieri-Ottolenghi, University of Turin, Regione Gonzole 10, 10043, Orbassano, Torino, Italy.
| | - Marife Arancillo
- Departments of Pathology & Immunology and Neuroscience, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute of Texas Children's Hospital, 1250 Moursund Street, Suite 1325, Houston, TX, 77030, USA
| | - Esther B E Becker
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK
| | - Annalisa Buffo
- Department of Neuroscience Rita Levi Montalcini, University of Turin, via Cherasco 15, 10026, Turin, Italy
- Neuroscience Institute Cavalieri-Ottolenghi, University of Turin, Regione Gonzole 10, 10043, Orbassano, Torino, Italy
| | - Chin Chiang
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, 4114 MRB III, Nashville, TN, 37232, USA
| | - Baojin Ding
- Department of Microbiology and Physiological Systems and Program in Neuroscience, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605-2324, USA
| | - William B Dobyns
- Seattle Children's Research Institute, Center for Integrative Brain Research, Seattle, WA, USA
- Department of Pediatrics, Genetics Division, University of Washington, Seattle, WA, USA
| | - Isabelle Dusart
- Sorbonne Universités, Université Pierre et Marie Curie Univ Paris 06, Institut de Biologie Paris Seine, France, 75005, Paris, France
- Centre National de la Recherche Scientifique, CNRS, UMR8246, INSERM U1130, Neuroscience Paris Seine, France, 75005, Paris, France
| | - Parthiv Haldipur
- Seattle Children's Research Institute, Center for Integrative Brain Research, Seattle, WA, USA
| | - Mary E Hatten
- Laboratory of Developmental Neurobiology, The Rockefeller University, New York, NY, 10065, USA
| | - Mikio Hoshino
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-Higashi, Kodaira, Tokyo, 187-8502, Japan
| | - Alexandra L Joyner
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Masanobu Kano
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Daniel L Kilpatrick
- Department of Microbiology and Physiological Systems and Program in Neuroscience, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605-2324, USA
| | - Noriyuki Koibuchi
- Department of Integrative Physiology, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, Gunma, 371-8511, Japan
| | - Silvia Marino
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Salvador Martinez
- Department Human Anatomy, IMIB-Arrixaca, University of Murcia, Murcia, Spain
| | - Kathleen J Millen
- Seattle Children's Research Institute, Center for Integrative Brain Research, Seattle, WA, USA
| | - Thomas O Millner
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London, E1 2AT, UK
| | - Takaki Miyata
- Department of Anatomy and Cell Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Elena Parmigiani
- Department of Neuroscience Rita Levi Montalcini, University of Turin, via Cherasco 15, 10026, Turin, Italy
- Neuroscience Institute Cavalieri-Ottolenghi, University of Turin, Regione Gonzole 10, 10043, Orbassano, Torino, Italy
| | - Karl Schilling
- Anatomie und Zellbiologie, Anatomisches Institut, Rheinische Friedrich-Wilhelms-Universität, Bonn, Germany
| | - Gabriella Sekerková
- Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Roy V Sillitoe
- Departments of Pathology & Immunology and Neuroscience, Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute of Texas Children's Hospital, 1250 Moursund Street, Suite 1325, Houston, TX, 77030, USA
| | - Constantino Sotelo
- Institut de la Vision, UPMC Université de Paris 06, Paris, 75012, France
| | - Naofumi Uesaka
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Annika Wefers
- Center for Neuropathology, Ludwig-Maximilians-University, Munich, Germany
| | - Richard J T Wingate
- MRC Centre for Developmental Neurobiology, King's College London, London, UK
| | - Richard Hawkes
- Department of Cell Biology & Anatomy and Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, T2N 4NI, AB, Canada
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10
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Kang HG, Lee HK, Ahn YH, Joung JG, Nam J, Kim NKD, Ko JM, Cho MH, Shin JI, Kim J, Park HW, Park YS, Ha IS, Chung WY, Lee DY, Kim SY, Park WY, Cheong HI. Targeted exome sequencing resolves allelic and the genetic heterogeneity in the genetic diagnosis of nephronophthisis-related ciliopathy. Exp Mol Med 2016; 48:e251. [PMID: 27491411 PMCID: PMC5007639 DOI: 10.1038/emm.2016.63] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 02/29/2016] [Accepted: 03/11/2016] [Indexed: 01/02/2023] Open
Abstract
Nephronophthisis-related ciliopathy (NPHP-RC) is a common genetic cause of end-stage renal failure during childhood and adolescence and exhibits an autosomal recessive pattern of inheritance. Genetic diagnosis is quite limited owing to genetic heterogeneity in NPHP-RC. We designed a novel approach involving the step-wise screening of Sanger sequencing and targeted exome sequencing for the genetic diagnosis of 55 patients with NPHP-RC. First, five NPHP-RC genes were analyzed by Sanger sequencing in phenotypically classified patients. Known pathogenic mutations were identified in 12 patients (21.8%); homozygous deletions of NPHP1 in 4 juvenile nephronophthisis patients, IQCB1/NPHP5 mutations in 3 Senior–Løken syndrome patients, a CEP290/NPHP6 mutation in 1 Joubert syndrome patient, and TMEM67/MKS3 mutations in 4 Joubert syndrome patients with liver involvement. In the remaining undiagnosed patients, we applied targeted exome sequencing of 34 ciliopathy-related genes to detect known pathogenic mutations in 7 (16.3%) of 43 patients. Another 18 likely damaging heterozygous variants were identified in 13 NPHP-RC genes in 18 patients. In this study, we report a variety of pathogenic and candidate mutations identified in 55 patients with NPHP-RC in Korea using a step-wise application of two genetic tests. These results support the clinical utility of targeted exome sequencing to resolve the issue of allelic and genetic heterogeneity in NPHP-RC.
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Affiliation(s)
- Hee Gyung Kang
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Hyun Kyung Lee
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Yo Han Ahn
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Je-Gun Joung
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Jaeyong Nam
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Nayoung K D Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Jung Min Ko
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Min Hyun Cho
- Department of Pediatrics, Kyungpook National University School of Medicine, Daegu, Republic of Korea
| | - Jae Il Shin
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Joon Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Hye Won Park
- Department of Pediatrics, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Young Seo Park
- Department of Pediatrics, Asian Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Il-Soo Ha
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea
| | - Woo Yeong Chung
- Department of Pediatrics, College of Medicine, Inje University, Busan Paik Hospital, Busan, Republic of Korea
| | - Dae-Yeol Lee
- Department of Pediatrics, College of Medicine, Chonbuk National University, Jeonju, Republic of Korea
| | - Su Young Kim
- Department of Pediatrics, Pusan National University Children's Hospital, Pusan, Republic of Korea
| | - Woong Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Hae Il Cheong
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Republic of Korea
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11
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Heller R, Bolz HJ. The challenge of defining pathogenicity: the example of AHI1. Genet Med 2016; 17:508. [PMID: 26035799 DOI: 10.1038/gim.2015.46] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 02/05/2015] [Indexed: 01/21/2023] Open
Affiliation(s)
- Raoul Heller
- Institute of Human Genetics, University Hospital of Cologne, Cologne, Germany
| | - Hanno J Bolz
- 1] Institute of Human Genetics, University Hospital of Cologne, Cologne, Germany [2] Bioscientia Center for Human Genetics, Ingelheim, Germany
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12
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Chafai-Elalaoui S, Chalon M, Elkhartoufi N, Kriouele Y, Mansouri M, Attié-Bitach T, Sefiani A, Baala L. A homozygous AHI1 gene mutation (p.Thr304AsnfsX6) in a consanguineous Moroccan family with Joubert syndrome: a case report. J Med Case Rep 2015; 9:254. [PMID: 26541515 PMCID: PMC4635607 DOI: 10.1186/s13256-015-0732-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 10/08/2015] [Indexed: 12/31/2022] Open
Abstract
Introduction Joubert syndrome is a rare congenital disorder characterized by brain malformation, developmental delay with hypotonia, ocular motor apraxia, and breathing abnormalities. Joubert syndrome is a genetically highly heterogeneous ciliopathy disorder with 23 identified causative genes. The diagnosis is based on brain imaging showing the “molar tooth sign” with cerebellar vermis agenesis. We describe a consanguineous Moroccan family with three affected siblings (18-year-old boy, 13-year-old girl, and 10-year-old boy) showing typical signs of Joubert syndrome, and attempt to identify the underlying genetic defect in this family. Methods We performed genome-wide homozygosity mapping using a high-resolution array followed by targeted Sanger sequencing to identify the causative gene. Results This approach found three homozygous regions, one including the AHI1 gene. Direct sequencing of the 26 coding exons of AHI1 revealed a homozygous mutation (p.Thr304AsnfsX6) located in exon 7 present in the three Joubert syndrome-affected Moroccan siblings. Of more interest, this truncating mutation was previously reported in patients with compound heterozygous Joubert syndrome originating from Spain (one patient) and from the Netherlands (two patients), suggesting a possible founder effect or mutational hotspot. Conclusions Combined homozygosity mapping and targeted sequencing allowed the rapid detection of the disease-causing mutation in the AHI1 gene in this family affected with a highly genetically heterogeneous disorder. Carriers of the same truncating mutation (p.Thr304AsnfsX6), originating from Spain and the Netherlands, presented variable clinical characteristics, thereby corroborating the extreme heterogeneity of Joubert syndrome.
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Affiliation(s)
- Siham Chafai-Elalaoui
- Département de Génétique Médicale, Institut National d'Hygiène, Rabat, Maroc.,Centre de Génomique Humaine, Faculté de Médecine et de Pharmacie, Université Mohammed V Souissi, Rabat, Maroc
| | - Matthias Chalon
- Université d'Orléans & CNRS, INEM-UMR7355, Immunologie Expérimentale et Moléculaire & Neurogénétique, Orléans, France
| | - Nadia Elkhartoufi
- Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Yamna Kriouele
- Service de Pédiatrie IIA, Hôpital d'Enfants, Rabat, Maroc
| | - Maria Mansouri
- Département de Génétique Médicale, Institut National d'Hygiène, Rabat, Maroc.,Centre de Génomique Humaine, Faculté de Médecine et de Pharmacie, Université Mohammed V Souissi, Rabat, Maroc
| | - Tania Attié-Bitach
- Service d'Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfants Malades, AP-HP, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, France, Institut IMAGINE, Paris, France.,INSERM UMR1163, Paris Descartes - Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Abdelaziz Sefiani
- Département de Génétique Médicale, Institut National d'Hygiène, Rabat, Maroc.,Centre de Génomique Humaine, Faculté de Médecine et de Pharmacie, Université Mohammed V Souissi, Rabat, Maroc
| | - Lekbir Baala
- Université d'Orléans & CNRS, INEM-UMR7355, Immunologie Expérimentale et Moléculaire & Neurogénétique, Orléans, France. .,Centre Hospitalier Régional d'Orléans (CHRO), Pôle de Biopathologie, Orléans, France.
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13
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Knopp C, Rudnik-Schöneborn S, Eggermann T, Bergmann C, Begemann M, Schoner K, Zerres K, Ortiz Brüchle N. Syndromic ciliopathies: From single gene to multi gene analysis by SNP arrays and next generation sequencing. Mol Cell Probes 2015; 29:299-307. [DOI: 10.1016/j.mcp.2015.05.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 05/13/2015] [Accepted: 05/19/2015] [Indexed: 01/23/2023]
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14
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Hsu CCT, Kwan GNC, Bhuta S. High-Resolution Diffusion Tensor Imaging and Tractography in Joubert Syndrome: Beyond Molar Tooth Sign. Pediatr Neurol 2015; 53:47-52. [PMID: 25890865 DOI: 10.1016/j.pediatrneurol.2015.02.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 02/26/2015] [Accepted: 02/28/2015] [Indexed: 10/23/2022]
Abstract
BACKGROUND We undertook diffusion tensor imaging analysis of brainstem fiber tracts in two Joubert syndrome patients. METHODS Two Joubert syndrome patients underwent magnetic resonance imaging brain examination with diffusion tensor imaging. Imaging findings were compared with five age- and sex-matched control subjects with approval from the institutional ethic committee. The medical history and clinical examination findings in both patients were documented. RESULTS Diffusion tensor imaging analysis of the first patient demonstrated absence of the dorsal pontocerebellar tract and thinning of the middle cerebral peduncle. Diffusion tensor imaging analysis of the second child revealed thinning of the both the dorsal pontocerebellar and ventral pontocerebellar tract. Both patients exhibited thickened and horizontally oriented superior cerebellar peduncles. The superior cerebellar peduncles also failed to decussate in the mesencephalon. CONCLUSION Pontocerebellar tract abnormalities in Joubert syndrome patients have not been previously recognized. The difference in the pontocerebellar tract between the two Joubert syndrome patients suggests a spectrum of severity of pontine axonal migration abnormality.
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Affiliation(s)
- Charlie Chia-Tsong Hsu
- Department of Medical Imaging, Gold Coast University Hospital, Southport, Queensland, Australia
| | - Gigi Nga Chi Kwan
- Department of Medical Imaging, Gold Coast University Hospital, Southport, Queensland, Australia
| | - Sandeep Bhuta
- Department of Medical Imaging, Gold Coast University Hospital, Southport, Queensland, Australia; Griffith University, School of Medicine, Southport, Queensland, Australia.
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15
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Wang L, Yang Y, Song J, Mao L, Wei X, Sun Y, Yang S, Mu F, Wang H, Niu Y. Two novel mutations in the C-terminal region of centrosomal protein 290 (CEP290) result in classic Joubert syndrome. J Child Neurol 2015; 30:772-6. [PMID: 24850569 DOI: 10.1177/0883073814535488] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Accepted: 04/17/2014] [Indexed: 01/04/2023]
Abstract
Joubert syndrome is a neurologic disorder with a pathognomonic "molar tooth sign" on brain imaging. The purpose of this study was to identify potential mutations in a Chinese patient with Joubert syndrome by targeted massively parallel sequencing. Taking advantage of high-throughput DNA sequencing technologies, 18 Joubert-causing genes of a Chinese patient with classic Joubert syndrome were sequenced at a time, and 2 novel variants in the CEP290 gene (c.7323_7327delAGAAG and c.6012-2A>G) were identified in this patient. Sanger validation showed that 2 variants were inherited from each parents, respectively. Both variants are located in the C-terminal region of the CEP290 protein and are predicted to be deleterious. The results support that the combination of targeted genes enrichment and next-generation sequencing is valuable molecular diagnostic tool and suitable for clinical application.
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Affiliation(s)
- Lixia Wang
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | | | - Jieping Song
- Prenatal Diagnosis Center, Hubei Maternal and Child Health Hospital, China
| | | | | | - Yan Sun
- BGI-Shenzhen, Shenzhen, China
| | | | | | | | - Yanfeng Niu
- Department of Gastrointestinal Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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16
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Kroes HY, Monroe GR, van der Zwaag B, Duran KJ, de Kovel CG, van Roosmalen MJ, Harakalova M, Nijman IJ, Kloosterman WP, Giles RH, Knoers NVAM, van Haaften G. Joubert syndrome: genotyping a Northern European patient cohort. Eur J Hum Genet 2015; 24:214-20. [PMID: 25920555 DOI: 10.1038/ejhg.2015.84] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 02/09/2015] [Accepted: 03/25/2015] [Indexed: 11/09/2022] Open
Abstract
Joubert syndrome (JBS) is a rare neurodevelopmental disorder belonging to the group of ciliary diseases. JBS is genetically heterogeneous, with >20 causative genes identified to date. A molecular diagnosis of JBS is essential for prediction of disease progression and genetic counseling. We developed a targeted next-generation sequencing (NGS) approach for parallel sequencing of 22 known JBS genes plus 599 additional ciliary genes. This method was used to genotype a cohort of 51 well-phenotyped Northern European JBS cases (in some of the cases, Sanger sequencing of individual JBS genes had been performed previously). Altogether, 21 of the 51 cases (41%) harbored biallelic pathogenic mutations in known JBS genes, including 14 mutations not previously described. Mutations in C5orf42 (12%), TMEM67 (10%), and AHI1 (8%) were the most prevalent. C5orf42 mutations result in a purely neurological Joubert phenotype, in one case associated with postaxial polydactyly. Our study represents a population-based cohort of JBS patients not enriched for consanguinity, providing insight into the relative importance of the different JBS genes in a Northern European population. Mutations in C5orf42 are relatively frequent (possibly due to a Dutch founder mutation) and mutations in CEP290 are underrepresented compared with international cohorts. Furthermore, we report a case with heterozygous mutations in CC2D2A and B9D1, a gene associated with the more severe Meckel-Gruber syndrome that was recently published as a potential new JBS gene, and discuss the significance of this finding.
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Affiliation(s)
- Hester Y Kroes
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Glen R Monroe
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bert van der Zwaag
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Karen J Duran
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Carolien G de Kovel
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mark J van Roosmalen
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Magdalena Harakalova
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ies J Nijman
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Wigard P Kloosterman
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rachel H Giles
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Nine V A M Knoers
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Gijs van Haaften
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
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17
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Huang XF, Huang F, Wu KC, Wu J, Chen J, Pang CP, Lu F, Qu J, Jin ZB. Genotype–phenotype correlation and mutation spectrum in a large cohort of patients with inherited retinal dystrophy revealed by next-generation sequencing. Genet Med 2014; 17:271-8. [DOI: 10.1038/gim.2014.138] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 09/19/2014] [Indexed: 11/09/2022] Open
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18
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Brett M, McPherson J, Zang ZJ, Lai A, Tan ES, Ng I, Ong LC, Cham B, Tan P, Rozen S, Tan EC. Massively parallel sequencing of patients with intellectual disability, congenital anomalies and/or autism spectrum disorders with a targeted gene panel. PLoS One 2014; 9:e93409. [PMID: 24690944 PMCID: PMC3972136 DOI: 10.1371/journal.pone.0093409] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 03/04/2014] [Indexed: 12/27/2022] Open
Abstract
Developmental delay and/or intellectual disability (DD/ID) affects 1–3% of all children. At least half of these are thought to have a genetic etiology. Recent studies have shown that massively parallel sequencing (MPS) using a targeted gene panel is particularly suited for diagnostic testing for genetically heterogeneous conditions. We report on our experiences with using massively parallel sequencing of a targeted gene panel of 355 genes for investigating the genetic etiology of eight patients with a wide range of phenotypes including DD/ID, congenital anomalies and/or autism spectrum disorder. Targeted sequence enrichment was performed using the Agilent SureSelect Target Enrichment Kit and sequenced on the Illumina HiSeq2000 using paired-end reads. For all eight patients, 81–84% of the targeted regions achieved read depths of at least 20×, with average read depths overlapping targets ranging from 322× to 798×. Causative variants were successfully identified in two of the eight patients: a nonsense mutation in the ATRX gene and a canonical splice site mutation in the L1CAM gene. In a third patient, a canonical splice site variant in the USP9X gene could likely explain all or some of her clinical phenotypes. These results confirm the value of targeted MPS for investigating DD/ID in children for diagnostic purposes. However, targeted gene MPS was less likely to provide a genetic diagnosis for children whose phenotype includes autism.
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Affiliation(s)
- Maggie Brett
- KK Research Centre, KK Women's & Children's Hospital, Singapore, Singapore
| | | | | | - Angeline Lai
- Genetic Services, KK Women's & Children's Hospital, Singapore, Singapore
| | - Ee-Shien Tan
- Genetic Services, KK Women's & Children's Hospital, Singapore, Singapore
| | - Ivy Ng
- Genetic Services, KK Women's & Children's Hospital, Singapore, Singapore
| | - Lai-Choo Ong
- Universiti Malaya Medical Centre, Petaling Jaya, Malaysia
| | - Breana Cham
- Genetic Services, KK Women's & Children's Hospital, Singapore, Singapore
| | - Patrick Tan
- Duke-NUS Graduate Medical School, Singapore, Singapore
- National Cancer Centre, Singapore, Singapore
| | - Steve Rozen
- Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Ene-Choo Tan
- KK Research Centre, KK Women's & Children's Hospital, Singapore, Singapore
- * E-mail:
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19
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Tuz K, Hsiao YC, Juárez O, Shi B, Harmon EY, Phelps IG, Lennartz MR, Glass IA, Doherty D, Ferland RJ. The Joubert syndrome-associated missense mutation (V443D) in the Abelson-helper integration site 1 (AHI1) protein alters its localization and protein-protein interactions. J Biol Chem 2013; 288:13676-94. [PMID: 23532844 DOI: 10.1074/jbc.m112.420786] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Missense mutations in AHI1 result in the neurodevelopmental ciliopathy called Joubert syndrome. RESULTS Mutations in AHI1 decrease cilia formation, alter its localization and stability, and change its binding to HAP1 and NPHP1. CONCLUSION Mutations in AHI1 affect ciliogenesis, AHI1 protein localization, and AHI1-protein interactions. SIGNIFICANCE This study begins to describe how missense mutations in AHI1 can cause Joubert syndrome. Mutations in AHI1 cause Joubert syndrome (JBTS), a neurodevelopmental ciliopathy, characterized by midbrain-hindbrain malformations and motor/cognitive deficits. Here, we show that primary cilia (PC) formation is decreased in fibroblasts from individuals with JBTS and AHI1 mutations. Most missense mutations in AHI1, causing JBTS, occur in known protein domains, however, a common V443D mutation in AHI1 is found in a region with no known protein motifs. We show that cells transfected with AHI1-V443D, or a new JBTS-causing mutation, AHI1-R351L, have aberrant localization of AHI1 at the basal bodies of PC and at cell-cell junctions, likely through decreased binding of mutant AHI1 to NPHP1 (another JBTS-causing protein). The AHI1-V443D mutation causes decreased AHI1 stability because there is a 50% reduction in AHI1-V443D protein levels compared with wild type AHI1. Huntingtin-associated protein-1 (Hap1) is a regulatory protein that binds Ahi1, and Hap1 knock-out mice have been reported to have JBTS-like phenotypes, suggesting a role for Hap1 in ciliogenesis. Fibroblasts and neurons with Hap1 deficiency form PC with normal growth factor-induced ciliary signaling, indicating that the Hap1 JBTS phenotype is likely not through effects at PC. These results also suggest that the binding of Ahi1 and Hap1 may not be critical for ciliary function. However, we show that HAP1 has decreased binding to AHI1-V443D indicating that this altered binding could be responsible for the JBTS-like phenotype through an unknown pathway. Thus, these JBTS-associated missense mutations alter their subcellular distribution and protein interactions, compromising functions of AHI1 in cell polarity and cilium-mediated signaling, thereby contributing to JBTS.
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Affiliation(s)
- Karina Tuz
- Center for Neuropharmacology and Neuroscience, Albany Medical College, Albany, New York 12208, USA
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20
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Gill H, Muthusamy B, Atan D, Williams C, Ellis M. Joubert syndrome presenting with motor delay and oculomotor apraxia. Case Rep Pediatr 2012; 2011:262641. [PMID: 22606509 PMCID: PMC3350021 DOI: 10.1155/2011/262641] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2011] [Accepted: 12/25/2011] [Indexed: 01/09/2023] Open
Abstract
We describe two sisters who presented in early childhood with motor delay and unusual eye movements. Both demonstrated hypotonia and poor visual attention. The older girl at 14 weeks of age showed fine pendular horizontal nystagmus more pronounced on lateral gaze, but despite investigation with cranial MRI no diagnosis was reached. The birth of her younger sister four years later with a similar presentation triggered review of the sisters' visual behaviour. Each had developed an unusual but similar form of oculomotor apraxia (OMA) with head thrusts to maintain fixation rather than to change fixation. MRI of the older sibling demonstrated the characteristic "molar tooth sign" (MTS) of Joubert syndrome which was subsequently confirmed on MRI in the younger sibling. We discuss the genetically heterogeneous ciliopathies now grouped as Joubert syndrome and Related Disorders. Clinicians need to consider this group of disorders when faced with unusual eye movements in the developmentally delayed child.
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Affiliation(s)
- Harjinder Gill
- Community Paediatrics, The Children's Hospital, Oxford University Hospitals, Headley Way, Headington, Oxford OX3 9DU, UK
| | - Brinda Muthusamy
- Paediatric Ophthalmology and Adult Strabismus, The Wilmer Eye Institute at Johns Hopkins, 600 North Wolfe Street, Baltimore, MD 21287, USA
| | - Denize Atan
- Academic Department of Ophthalmology, School of Clinical Sciences, Bristol Eye Hospital, Lower Maudlin Street, Bristol BS1 2LX, UK
| | - Cathy Williams
- Centre for Child and Adolescent Health, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Matthew Ellis
- Centre for Child and Adolescent Health, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
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21
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Chaki M, Hoefele J, Allen SJ, Ramaswami G, Janssen S, Bergmann C, Heckenlively JR, Otto EA, Hildebrandt F. Genotype-phenotype correlation in 440 patients with NPHP-related ciliopathies. Kidney Int 2011; 80:1239-45. [PMID: 21866095 DOI: 10.1038/ki.2011.284] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Nephronophthisis (NPHP), an autosomal recessive cystic kidney disease, is the most frequent genetic cause for end-stage renal failure in the first three decades of life. Mutations in 13 genes (NPHP1-NPHP11, AHI1, and CC2D2A) cause NPHP with ubiquitous expression of the corresponding proteins consistent with the multiorgan involvement of NPHP-related diseases. The genotype-phenotype correlation in these ciliopathies can be explained by gene locus heterogeneity, allelism, and the impact of modifier genes. In some NPHP-related ciliopathies, the nature of the recessive mutations determines disease severity. In order to define the genotype-phenotype correlation more clearly, we evaluated a worldwide cohort of 440 patients from 365 families with NPHP-related ciliopathies, in whom both disease-causing alleles were identified. The phenotypes were ranked in the order of severity from degenerative to degenerative/dysplastic to dysplastic. A genotype of two null alleles caused a range of phenotypes, with an increasing order of severity of NPHP1, NPHP3, NPHP4, NPHP5, NPHP2, NPHP10, NPHP6, to AHI1. Only NPHP6 showed allelic influences on the phenotypes; the presence of two null mutations caused dysplastic phenotypes, whereas at least one missense allele rescued it to a milder degenerative phenotype. We also found nine novel mutations in the NPHP genes. Thus, our studies have important implications for genetic counseling and planning of renal replacement therapy.
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Affiliation(s)
- Moumita Chaki
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA
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22
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Coppieters F, Casteels I, Meire F, De Jaegere S, Hooghe S, van Regemorter N, Van Esch H, Matuleviciene A, Nunes L, Meersschaut V, Walraedt S, Standaert L, Coucke P, Hoeben H, Kroes HY, Vande Walle J, de Ravel T, Leroy BP, De Baere E. Genetic screening of LCA in Belgium: predominance of CEP290 and identification of potential modifier alleles in AHI1 of CEP290-related phenotypes. Hum Mutat 2011; 31:E1709-66. [PMID: 20683928 PMCID: PMC3048164 DOI: 10.1002/humu.21336] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Leber Congenital Amaurosis (LCA), the most severe inherited retinal dystrophy, is genetically heterogeneous, with 14 genes accounting for 70% of patients. Here, 91 LCA probands underwent LCA chip analysis and subsequent sequencing of 6 genes (CEP290, CRB1, RPE65, GUCY2D, AIPL1and CRX), revealing mutations in 69% of the cohort, with major involvement of CEP290 (30%). In addition, 11 patients with early-onset retinal dystrophy (EORD) and 13 patients with Senior-Loken syndrome (SLS), LCA-Joubert syndrome (LCA-JS) or cerebello-oculo-renal syndrome (CORS) were included. Exhaustive re-inspection of the overall phenotypes in our LCA cohort revealed novel insights mainly regarding the CEP290-related phenotype. The AHI1 gene was screened as a candidate modifier gene in three patients with the same CEP290 genotype but different neurological involvement. Interestingly, a heterozygous novel AHI1 mutation, p.Asn811Lys, was found in the most severely affected patient. Moreover, AHI1 screening in five other patients with CEP290-related disease and neurological involvement revealed a second novel missense variant, p.His758Pro, in one LCA patient with mild mental retardation and autism. These two AHI1 mutations might thus represent neurological modifiers of CEP290-related disease. © 2010 Wiley-Liss, Inc.
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Affiliation(s)
- Frauke Coppieters
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
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Is hearing loss a feature of Joubert syndrome, a ciliopathy? Int J Pediatr Otorhinolaryngol 2010; 74:1034-8. [PMID: 20591505 DOI: 10.1016/j.ijporl.2010.05.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Revised: 05/30/2010] [Accepted: 05/31/2010] [Indexed: 01/16/2023]
Abstract
OBJECTIVE To assess if hearing loss is a feature of Joubert syndrome (JBS), one of the ciliopathies and therefore possibly associated with hearing loss. DESIGN Retrospective case series. SETTING University Children's Hospital. PATIENTS Dutch patients with JBS. MAIN OUTCOME MEASURES Audiological data. RESULTS Data from 22 Dutch Joubert syndrome (JBS) cases (17 males, 5 females) aged 3-40 years were available. Audiological tests were successfully performed in 14 cases. Three cases (aged 17-26 years) showed very mild sensorineural hearing loss (SNHL) at different frequencies. Conductive hearing loss due to middle ear infections occurred frequently in young JBS children (6 out of 22 cases). In three cases (aged 3-13 years) the parents reported the child was hypersensitive to sound. CONCLUSION We found no evidence for significant hearing loss in Joubert syndrome patients. However, given the compromised speech development in JBS, conductive hearing loss due to middle ear infections should be treated vigorously. SNHL at a later age cannot be excluded on the basis of our data, given the sample size. Three of the older cases showed discretely increased hearing thresholds. Analogous to the ciliopathy Bardet-Biedl syndrome, where hearing thresholds were reported to be subclinically increased in a group of adolescents patients, we recommend follow-up of JBS patients in view of the possibility of progressive, late-onset SNHL.
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Brancati F, Dallapiccola B, Valente EM. Joubert Syndrome and related disorders. Orphanet J Rare Dis 2010; 5:20. [PMID: 20615230 PMCID: PMC2913941 DOI: 10.1186/1750-1172-5-20] [Citation(s) in RCA: 255] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Accepted: 07/08/2010] [Indexed: 12/22/2022] Open
Abstract
Joubert syndrome (JS) and related disorders (JSRD) are a group of developmental delay/multiple congenital anomalies syndromes in which the obligatory hallmark is the molar tooth sign (MTS), a complex midbrain-hindbrain malformation visible on brain imaging, first recognized in JS. Estimates of the incidence of JSRD range between 1/80,000 and 1/100,000 live births, although these figures may represent an underestimate. The neurological features of JSRD include hypotonia, ataxia, developmental delay, intellectual disability, abnormal eye movements, and neonatal breathing dysregulation. These may be associated with multiorgan involvement, mainly retinal dystrophy, nephronophthisis, hepatic fibrosis and polydactyly, with both inter- and intra-familial variability. JSRD are classified in six phenotypic subgroups: Pure JS; JS with ocular defect; JS with renal defect; JS with oculorenal defects; JS with hepatic defect; JS with orofaciodigital defects. With the exception of rare X-linked recessive cases, JSRD follow autosomal recessive inheritance and are genetically heterogeneous. Ten causative genes have been identified to date, all encoding for proteins of the primary cilium or the centrosome, making JSRD part of an expanding group of diseases called "ciliopathies". Mutational analysis of causative genes is available in few laboratories worldwide on a diagnostic or research basis. Differential diagnosis must consider in particular the other ciliopathies (such as nephronophthisis and Senior-Loken syndrome), distinct cerebellar and brainstem congenital defects and disorders with cerebro-oculo-renal manifestations. Recurrence risk is 25% in most families, although X-linked inheritance should also be considered. The identification of the molecular defect in couples at risk allows early prenatal genetic testing, whereas fetal brain neuroimaging may remain uninformative until the end of the second trimester of pregnancy. Detection of the MTS should be followed by a diagnostic protocol to assess multiorgan involvement. Optimal management requires a multidisciplinary approach, with particular attention to respiratory and feeding problems in neonates and infants. Cognitive and behavioral assessments are also recommended to provide young patients with adequate neuropsychological support and rehabilitation. After the first months of life, global prognosis varies considerably among JSRD subgroups, depending on the extent and severity of organ involvement.
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Affiliation(s)
- Francesco Brancati
- Mendel Laboratory, Casa Sollievo della Sofferenza Hospital, IRCCS, San Giovanni Rotondo, Italy
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Louie CM, Caridi G, Lopes VS, Brancati F, Kispert A, Lancaster MA, Schlossman AM, Otto EA, Leitges M, Gröne HJ, Lopez I, Gudiseva HV, O'Toole JF, Vallespin E, Ayyagari R, Ayuso C, Cremers FPM, den Hollander AI, Koenekoop RK, Dallapiccola B, Ghiggeri GM, Hildebrandt F, Valente EM, Williams DS, Gleeson JG. AHI1 is required for photoreceptor outer segment development and is a modifier for retinal degeneration in nephronophthisis. Nat Genet 2010; 42:175-80. [PMID: 20081859 PMCID: PMC2884967 DOI: 10.1038/ng.519] [Citation(s) in RCA: 143] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 12/03/2009] [Indexed: 12/13/2022]
Abstract
Photoreceptor degeneration is a common feature of ciliopathies, owing to the importance of the highly specialized ciliary structure of these cells. Absence of AHI1, which encodes a cilium-localized protein, has been shown to cause a form of Joubert syndrome highly penetrant for retinal degeneration1,2. We show that Ahi1 knockout mice fail to form outer segments (OS), and show abnormal distribution of opsin throughout photoreceptors. Apoptotic cell death occurs rapidly between 2-4 weeks of age and is significantly delayed by reduced dosage of opsin. This phenotype also displays dosage-sensitive genetic interactions with Nphp1, another ciliopathy gene. Although not a primary cause of retinal blindness in humans, an allele of AHI1 modifies the relative risk of retinal degeneration greater than 7 fold within a nephronophthisis cohort. Our data support context-specific roles for AHI1 as a contributor to retinopathy and may explain a proportion of the variability of retinal phenotypes observed in nephronophthisis.
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Affiliation(s)
- Carrie M Louie
- Howard Hughes Medical Institute, Department of Pediatrics, University of California, San Diego, La Jolla, USA
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Shi Z, Liang N, Xu W, Li K, Sheng G, Liu J, Xu A, Li XJ, Wu D. Expression, purification, crystallization and preliminary X-ray crystallographic analysis of the SH3 domain of human AHI1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:361-3. [PMID: 19342780 PMCID: PMC2664760 DOI: 10.1107/s174430910900774x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Accepted: 03/03/2009] [Indexed: 11/10/2022]
Abstract
The SH3 domain of human AHI1 was cloned and expressed in Escherichia coli. The protein was purified by affinity and size-exclusion chromatography and was crystallized using the sitting-drop vapour-diffusion method at 293 K. A complete data set was collected to 2.5 A resolution at 110 K. The crystal belonged to space group P4(1)2(1)2, with unit-cell parameters a = 67.377, b = 67.377, c = 98.549 A.
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Affiliation(s)
- Zhuliang Shi
- Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, People’s Republic of China
- Department of Life Sciences, University of Science and Technology of China, People’s Republic of China
| | - Ning Liang
- Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, People’s Republic of China
- Department of Life Sciences, University of Science and Technology of China, People’s Republic of China
| | - Wei Xu
- Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, People’s Republic of China
| | - Kuai Li
- Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, People’s Republic of China
- Department of Life Sciences, University of Science and Technology of China, People’s Republic of China
| | - Guoqing Sheng
- Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, People’s Republic of China
| | - Jinsong Liu
- Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, People’s Republic of China
| | - Aimin Xu
- Department of Medicine, The University of Hong Kong, Hong Kong
| | - Xiao-Jiang Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Donghai Wu
- Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences, People’s Republic of China
- Department of Life Sciences, University of Science and Technology of China, People’s Republic of China
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Abstract
Nephronophthisis (NPHP), a recessive cystic kidney disease, is the most frequent genetic cause of end-stage kidney disease in children and young adults. Positional cloning of nine genes (NPHP1 through 9) and functional characterization of their encoded proteins (nephrocystins) have contributed to a unifying theory that defines cystic kidney diseases as "ciliopathies." The theory is based on the finding that all proteins mutated in cystic kidney diseases of humans or animal models are expressed in primary cilia or centrosomes of renal epithelial cells. Primary cilia are sensory organelles that connect mechanosensory, visual, and other stimuli to mechanisms of epithelial cell polarity and cell-cycle control. Mutations in NPHP genes cause defects in signaling mechanisms that involve the noncanonical Wnt signaling pathway and the sonic hedgehog signaling pathway, resulting in defects of planar cell polarity and tissue maintenance. The ciliary theory explains the multiple organ involvement in NPHP, which includes retinal degeneration, cerebellar hypoplasia, liver fibrosis, situs inversus, and mental retardation. Positional cloning of dozens of unknown genes that cause NPHP will elucidate further signaling mechanisms involved. Nephrocystins are highly conserved in evolution, thereby allowing the use of animal models to develop future therapeutic approaches.
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Affiliation(s)
- Friedhelm Hildebrandt
- Department of Pediatrics, Howard Hughes Medical Institute, University of Michigan Health System, 8220C MSRB III, 1150 West Medical Center Drive, Ann Arbor, MI 48109-5646, USA.
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