1
|
Schultz LM, Knighton A, Huguet G, Saci Z, Jean-Louis M, Mollon J, Knowles EEM, Glahn DC, Jacquemont S, Almasy L. Copy-number variants differ in frequency across genetic ancestry groups. HGG ADVANCES 2024; 5:100340. [PMID: 39138864 PMCID: PMC11401192 DOI: 10.1016/j.xhgg.2024.100340] [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: 03/21/2024] [Revised: 08/07/2024] [Accepted: 08/07/2024] [Indexed: 08/15/2024] Open
Abstract
Copy-number variants (CNVs) have been implicated in a variety of neuropsychiatric and cognitive phenotypes. We found that deleterious CNVs are less prevalent in non-European ancestry groups than they are in European ancestry groups of both the UK Biobank (UKBB) and a US replication cohort (SPARK). We also identified specific recurrent CNVs that consistently differ in frequency across ancestry groups in both the UKBB and SPARK. These ancestry-related differences in CNV prevalence present in both an unselected community population and a family cohort enriched with individuals diagnosed with autism spectrum disorder (ASD) strongly suggest that genetic ancestry should be considered when probing associations between CNVs and health outcomes.
Collapse
Affiliation(s)
- Laura M Schultz
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Alexys Knighton
- School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Zohra Saci
- CHU Sainte-Justine, Montréal, QC, Canada
| | | | - Josephine Mollon
- Department of Psychiatry and Behavioral Sciences, Boston Children's Hospital, Boston, MA, USA; Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Emma E M Knowles
- Department of Psychiatry and Behavioral Sciences, Boston Children's Hospital, Boston, MA, USA; Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - David C Glahn
- Department of Psychiatry and Behavioral Sciences, Boston Children's Hospital, Boston, MA, USA; Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Sébastien Jacquemont
- CHU Sainte-Justine, Montréal, QC, Canada; Department of Pediatrics, Université de Montréal, Montréal, QC, Canada
| | - Laura Almasy
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
2
|
Orlova M, Gundorova P, Kadnikova V, Polyakov A. Spectrum of pathogenic variants and high prevalence of pathogenic BBS7 variants in Russian patients with Bardet-Biedl syndrome. Front Genet 2024; 15:1419025. [PMID: 39092430 PMCID: PMC11291329 DOI: 10.3389/fgene.2024.1419025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 06/05/2024] [Indexed: 08/04/2024] Open
Abstract
Introduction Bardet-Biedl syndrome is a rare condition characterized by obesity, retinitis pigmentosa, polydactyly, development delay, and structural kidney anomalies. This syndrome has an autosomal recessive type of inheritance. For the first time, molecular genetic testing has been provided for a large cohort of Russian patients with Bardet-Biedl syndrome. Materials and methods Genetic testing was provided to 61 unrelated patients using an MPS panel that includes coding regions and intronic areas of all genes (n = 21) currently associated with Bardet-Biedl syndrome. Results The diagnosis was confirmed for 41% of the patients (n = 25). Disease-causing variants were observed in BBS1, BBS4, BBS7, TTC8, BBS9, BBS10, BBS12, and MKKS genes. In most cases, pathogenic and likely pathogenic variants were localized in BBS1, BBS10, and BBS7 genes; recurrent variants were also observed in these genes. Discussion The frequency of pathogenic and likely pathogenic variants in the BBS1 and BBS10 genes among Russian patients matches the research data in other countries. The frequency of pathogenic variants in the BBS7 gene is about 1.5%-2% of patients with Bardet-Biedl syndrome, while in the cohort of Russian patients, the fraction is 24%. In addition, the recurrent pathogenic variant c.1967_1968delinsC was detected in the BBS7 gene. The higher frequency of this variant in the Russian population, as well as the lack of association of this pathogenic variant with Bardet-Biedl syndrome in other populations, suggests that the variant c.1967_1968delinsC in the BBS7 gene is major and has a founder effect in the Russian population. Results provided in this article show the significant role of pathogenic variants in the BBS7 gene for patients with Bardet-Biedl syndrome in the Russian population.
Collapse
Affiliation(s)
- M. Orlova
- DNA-diagnostics Laboratory, Research Centre for Medical Genetics, Moscow, Russia
| | - P. Gundorova
- University Children’s Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - V. Kadnikova
- DNA-diagnostics Laboratory, Research Centre for Medical Genetics, Moscow, Russia
| | - A. Polyakov
- DNA-diagnostics Laboratory, Research Centre for Medical Genetics, Moscow, Russia
| |
Collapse
|
3
|
Tomlinson JW. Bardet-Biedl syndrome: A focus on genetics, mechanisms and metabolic dysfunction. Diabetes Obes Metab 2024; 26 Suppl 2:13-24. [PMID: 38302651 DOI: 10.1111/dom.15480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/18/2024] [Accepted: 01/18/2024] [Indexed: 02/03/2024]
Abstract
Bardet-Biedl syndrome (BBS) is a rare, monogenic, multisystem disorder characterized by retinal dystrophy, renal abnormalities, polydactyly, learning disabilities, as well as metabolic dysfunction, including obesity and an increased risk of type 2 diabetes. It is a primary ciliopathy, and causative mutations in more than 25 different genes have been described. Multiple cellular mechanisms contribute to the development of the metabolic phenotype associated with BBS, including hyperphagia as a consequence of altered hypothalamic appetite signalling as well as alterations in adipocyte biology promoting adipocyte proliferation and adipogenesis. Within this review, we describe in detail the metabolic phenotype associated with BBS and discuss the mechanisms that drive its evolution. In addition, we review current approaches to the metabolic management of patients with BBS, including the use of weight loss medications and bariatric surgery. Finally, we evaluate the potential of targeting hypothalamic appetite signalling to limit hyperphagia and induce clinically significant weight loss.
Collapse
Affiliation(s)
- Jeremy W Tomlinson
- Oxford Centre for Diabetes, Endocrinology and Metabolism, NIHR Oxford Biomedical Research Centre, University of Oxford, Churchill Hospital, Oxford, UK
| |
Collapse
|
4
|
Schobers G, Derks R, den Ouden A, Swinkels H, van Reeuwijk J, Bosgoed E, Lugtenberg D, Sun SM, Corominas Galbany J, Weiss M, Blok MJ, Olde Keizer RACM, Hofste T, Hellebrekers D, de Leeuw N, Stegmann A, Kamsteeg EJ, Paulussen ADC, Ligtenberg MJL, Bradley XZ, Peden J, Gutierrez A, Pullen A, Payne T, Gilissen C, van den Wijngaard A, Brunner HG, Nelen M, Yntema HG, Vissers LELM. Genome sequencing as a generic diagnostic strategy for rare disease. Genome Med 2024; 16:32. [PMID: 38355605 PMCID: PMC10868087 DOI: 10.1186/s13073-024-01301-y] [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: 09/21/2023] [Accepted: 02/02/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND To diagnose the full spectrum of hereditary and congenital diseases, genetic laboratories use many different workflows, ranging from karyotyping to exome sequencing. A single generic high-throughput workflow would greatly increase efficiency. We assessed whether genome sequencing (GS) can replace these existing workflows aimed at germline genetic diagnosis for rare disease. METHODS We performed short-read GS (NovaSeq™6000; 150 bp paired-end reads, 37 × mean coverage) on 1000 cases with 1271 known clinically relevant variants, identified across different workflows, representative of our tertiary diagnostic centers. Variants were categorized into small variants (single nucleotide variants and indels < 50 bp), large variants (copy number variants and short tandem repeats) and other variants (structural variants and aneuploidies). Variant calling format files were queried per variant, from which workflow-specific true positive rates (TPRs) for detection were determined. A TPR of ≥ 98% was considered the threshold for transition to GS. A GS-first scenario was generated for our laboratory, using diagnostic efficacy and predicted false negative as primary outcome measures. As input, we modeled the diagnostic path for all 24,570 individuals referred in 2022, combining the clinical referral, the transition of the underlying workflow(s) to GS, and the variant type(s) to be detected. RESULTS Overall, 95% (1206/1271) of variants were detected. Detection rates differed per variant category: small variants in 96% (826/860), large variants in 93% (341/366), and other variants in 87% (39/45). TPRs varied between workflows (79-100%), with 7/10 being replaceable by GS. Models for our laboratory indicate that a GS-first strategy would be feasible for 84.9% of clinical referrals (750/883), translating to 71% of all individuals (17,444/24,570) receiving GS as their primary test. An estimated false negative rate of 0.3% could be expected. CONCLUSIONS GS can capture clinically relevant germline variants in a 'GS-first strategy' for the majority of clinical indications in a genetics diagnostic lab.
Collapse
Affiliation(s)
- Gaby Schobers
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboudumc, Nijmegen, Netherlands
| | - Ronny Derks
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
| | - Amber den Ouden
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
| | - Hilde Swinkels
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
| | - Jeroen van Reeuwijk
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboudumc, Nijmegen, Netherlands
| | - Ermanno Bosgoed
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
| | | | - Su Ming Sun
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Jordi Corominas Galbany
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboudumc, Nijmegen, Netherlands
| | - Marjan Weiss
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
| | - Marinus J Blok
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Richelle A C M Olde Keizer
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboudumc, Nijmegen, Netherlands
| | - Tom Hofste
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
| | - Debby Hellebrekers
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
| | - Alexander Stegmann
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | | | - Aimee D C Paulussen
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboudumc, Nijmegen, Netherlands
| | | | | | | | | | | | - Christian Gilissen
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboudumc, Nijmegen, Netherlands
| | | | - Han G Brunner
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboudumc, Nijmegen, Netherlands
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Marcel Nelen
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboudumc, Nijmegen, Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands.
- Research Institute for Medical Innovation, Radboudumc, Nijmegen, Netherlands.
| |
Collapse
|
5
|
Khan S, Focșa IO, Budișteanu M, Stoica C, Nedelea F, Bohîlțea L, Caba L, Butnariu L, Pânzaru M, Rusu C, Jurcă C, Chirita-Emandi A, Bănescu C, Abbas W, Sadeghpour A, Baig SM, Bălgrădean M, Davis EE. Exome sequencing in a Romanian Bardet-Biedl syndrome cohort revealed an overabundance of causal BBS12 variants. Am J Med Genet A 2023; 191:2376-2391. [PMID: 37293956 PMCID: PMC10524726 DOI: 10.1002/ajmg.a.63322] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/16/2023] [Accepted: 05/26/2023] [Indexed: 06/10/2023]
Abstract
Bardet-Biedl syndrome (BBS), is an emblematic ciliopathy hallmarked by pleiotropy, phenotype variability, and extensive genetic heterogeneity. BBS is a rare (~1/140,000 to ~1/160,000 in Europe) autosomal recessive pediatric disorder characterized by retinal degeneration, truncal obesity, polydactyly, cognitive impairment, renal dysfunction, and hypogonadism. Twenty-eight genes involved in ciliary structure or function have been implicated in BBS, and explain the molecular basis for ~75%-80% of individuals. To investigate the mutational spectrum of BBS in Romania, we ascertained a cohort of 24 individuals in 23 families. Following informed consent, we performed proband exome sequencing (ES). We detected 17 different putative disease-causing single nucleotide variants or small insertion-deletions and two pathogenic exon disruptive copy number variants in known BBS genes in 17 pedigrees. The most frequently impacted genes were BBS12 (35%), followed by BBS4, BBS7, and BBS10 (9% each) and BBS1, BBS2, and BBS5 (4% each). Homozygous BBS12 p.Arg355* variants were present in seven pedigrees of both Eastern European and Romani origin. Our data show that although the diagnostic rate of BBS in Romania is likely consistent with other worldwide cohorts (74%), we observed a unique distribution of causal BBS genes, including overrepresentation of BBS12 due to a recurrent nonsense variant, that has implications for regional diagnostics.
Collapse
Affiliation(s)
- Sheraz Khan
- Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
- Human Molecular Genetics Lab, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE-C), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Ina Ofelia Focșa
- University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania
- Cytogenomic Medical Laboratory, Bucharest, Romania
| | - Magdalena Budișteanu
- Psychiatry Research Laboratory, "Prof. Dr. Alexandru Obregia" Clinical Hospital of Psychiatry, Bucharest, Romania
- Medical Genetic Laboratory, "Victor Babeș" National Institute of Pathology, Bucharest, Romania
- Department of Medical Genetics, Faculty of Medicine, "Titu Maiorescu" University, Bucharest, Romania
| | - Cristina Stoica
- University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania
- Department of Pediatrics, Clinical Institute Fundeni, Bucharest, Romania
| | - Florina Nedelea
- University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania
- Genetics Department, Clinical Hospital Filantropia, Bucharest, Romania
| | | | - Lavinia Caba
- Department of Medical Genetics, "Grigore T. Popa" University of Medicine and Pharmacy, Iași, Romania
| | - Lăcrămioara Butnariu
- Department of Medical Genetics, "Grigore T. Popa" University of Medicine and Pharmacy, Iași, Romania
- Regional Medical Genetics Centre, "Sf. Maria" Children's Hospital, Iași, Romania
| | - Monica Pânzaru
- Department of Medical Genetics, "Grigore T. Popa" University of Medicine and Pharmacy, Iași, Romania
- Regional Medical Genetics Centre, "Sf. Maria" Children's Hospital, Iași, Romania
| | - Cristina Rusu
- Department of Medical Genetics, "Grigore T. Popa" University of Medicine and Pharmacy, Iași, Romania
- Regional Medical Genetics Centre, "Sf. Maria" Children's Hospital, Iași, Romania
| | - Claudia Jurcă
- Department of Genetics, Faculty of Medicine and Pharmacy, University of Oradea, Oradea, Romania
- Department of Pediatrics, "Dr. Gavril Curteanu" Municipal Clinical Hospital, Oradea, Romania
| | - Adela Chirita-Emandi
- Emergency Hospital for Children Louis Turcanu, Regional Center of Medical Genetics Timis, Timisoara, Romania
- Victor Babes University of Medicine and Pharmacy Timisoara, Department of Microscopic Morphology Genetics, Center for Genomic Medicine, Timisoara, Romania
| | - Claudia Bănescu
- "George Emil Palade" University of Medicine, Pharmacy, Sciences and Technology, Târgu Mureş, Romania
| | - Wasim Abbas
- Human Molecular Genetics Lab, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE-C), Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Azita Sadeghpour
- Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina, USA
- Duke Precision Medicine Program, Department of Medicine, Division of General Internal Medicine, Duke University Medical Center, Durham, NC, USA
| | - Shahid Mahmood Baig
- Pakistan Science Foundation (PSF), Islamabad, Pakistan
- Department of Biological and Biomedical Sciences, Agha Khan University Karachi, Karachi, Pakistan
| | - Mihaela Bălgrădean
- University of Medicine and Pharmacy "Carol Davila", Bucharest, Romania
- Department of Pediatrics and Pediatric Nephrology, Emergency Clinical Hospital for Children "Maria Skłodowska Curie", Bucharest, Romania
| | - Erica E Davis
- Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
- Department of Pediatrics and Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| |
Collapse
|
6
|
Leggatt GP, Seaby EG, Veighey K, Gast C, Gilbert RD, Ennis S. A Role for Genetic Modifiers in Tubulointerstitial Kidney Diseases. Genes (Basel) 2023; 14:1582. [PMID: 37628633 PMCID: PMC10454709 DOI: 10.3390/genes14081582] [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: 07/17/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
With the increased availability of genomic sequencing technologies, the molecular bases for kidney diseases such as nephronophthisis and mitochondrially inherited and autosomal-dominant tubulointerstitial kidney diseases (ADTKD) has become increasingly apparent. These tubulointerstitial kidney diseases (TKD) are monogenic diseases of the tubulointerstitium and result in interstitial fibrosis and tubular atrophy (IF/TA). However, monogenic inheritance alone does not adequately explain the highly variable onset of kidney failure and extra-renal manifestations. Phenotypes vary considerably between individuals harbouring the same pathogenic variant in the same putative monogenic gene, even within families sharing common environmental factors. While the extreme end of the disease spectrum may have dramatic syndromic manifestations typically diagnosed in childhood, many patients present a more subtle phenotype with little to differentiate them from many other common forms of non-proteinuric chronic kidney disease (CKD). This review summarises the expanding repertoire of genes underpinning TKD and their known phenotypic manifestations. Furthermore, we collate the growing evidence for a role of modifier genes and discuss the extent to which these data bridge the historical gap between apparently rare monogenic TKD and polygenic non-proteinuric CKD (excluding polycystic kidney disease).
Collapse
Affiliation(s)
- Gary P. Leggatt
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
- Wessex Kidney Centre, Queen Alexandra Hospital, Portsmouth Hospitals NHS Trust, Portsmouth PO6 3LY, UK
- Renal Department, University Hospital Southampton, Southampton SO16 6YD, UK
| | - Eleanor G. Seaby
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
| | - Kristin Veighey
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
- Renal Department, University Hospital Southampton, Southampton SO16 6YD, UK
| | - Christine Gast
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
- Wessex Kidney Centre, Queen Alexandra Hospital, Portsmouth Hospitals NHS Trust, Portsmouth PO6 3LY, UK
| | - Rodney D. Gilbert
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
- Department of Paediatric Nephrology, Southampton Children’s Hospital, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Sarah Ennis
- Human Genetics & Genomic Medicine, University of Southampton, Southampton SO16 6YD, UK; (E.G.S.); (K.V.); (C.G.); (R.D.G.); (S.E.)
| |
Collapse
|
7
|
Tian X, Zhao H, Zhou J. Organization, functions, and mechanisms of the BBSome in development, ciliopathies, and beyond. eLife 2023; 12:e87623. [PMID: 37466224 DOI: 10.7554/elife.87623] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023] Open
Abstract
The BBSome is an octameric protein complex that regulates ciliary transport and signaling. Mutations in BBSome subunits are closely associated with ciliary defects and lead to ciliopathies, notably Bardet-Biedl syndrome. Over the past few years, there has been significant progress in elucidating the molecular organization and functions of the BBSome complex. An improved understanding of BBSome-mediated biological events and molecular mechanisms is expected to help advance the development of diagnostic and therapeutic approaches for BBSome-related diseases. Here, we review the current literature on the structural assembly, transport regulation, and molecular functions of the BBSome, emphasizing its roles in cilium-related processes. We also provide perspectives on the pathological role of the BBSome in ciliopathies as well as how these can be exploited for therapeutic benefit.
Collapse
Affiliation(s)
- Xiaoyu Tian
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Huijie Zhao
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Jun Zhou
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan, China
- State Key Laboratory of Medicinal Chemical Biology, Haihe Laboratory of Cell Ecosystem, College of Life Sciences, Nankai University, Tianjin, China
| |
Collapse
|
8
|
Wen S, Wang M, Qian X, Li Y, Wang K, Choi J, Pennesi ME, Yang P, Marra M, Koenekoop RK, Lopez I, Matynia A, Gorin M, Sui R, Yao F, Goetz K, Porto FBO, Chen R. Systematic assessment of the contribution of structural variants to inherited retinal diseases. Hum Mol Genet 2023; 32:2005-2015. [PMID: 36811936 PMCID: PMC10244226 DOI: 10.1093/hmg/ddad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/03/2023] [Accepted: 02/11/2023] [Indexed: 02/24/2023] Open
Abstract
Despite increasing success in determining genetic diagnosis for patients with inherited retinal diseases (IRDs), mutations in about 30% of the IRD cases remain unclear or unsettled after targeted gene panel or whole exome sequencing. In this study, we aimed to investigate the contributions of structural variants (SVs) to settling the molecular diagnosis of IRD with whole-genome sequencing (WGS). A cohort of 755 IRD patients whose pathogenic mutations remain undefined were subjected to WGS. Four SV calling algorithms including include MANTA, DELLY, LUMPY and CNVnator were used to detect SVs throughout the genome. All SVs identified by any one of these four algorithms were included for further analysis. AnnotSV was used to annotate these SVs. SVs that overlap with known IRD-associated genes were examined with sequencing coverage, junction reads and discordant read pairs. Polymerase Chain Reaction (PCR) followed by Sanger sequencing was used to further confirm the SVs and identify the breakpoints. Segregation of the candidate pathogenic alleles with the disease was performed when possible. A total of 16 candidate pathogenic SVs were identified in 16 families, including deletions and inversions, representing 2.1% of patients with previously unsolved IRDs. Autosomal dominant, autosomal recessive and X-linked inheritance of disease-causing SVs were observed in 12 different genes. Among these, SVs in CLN3, EYS and PRPF31 were found in multiple families. Our study suggests that the contribution of SVs detected by short-read WGS is about 0.25% of our IRD patient cohort and is significantly lower than that of single nucleotide changes and small insertions and deletions.
Collapse
Affiliation(s)
- Shu Wen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Meng Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xinye Qian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Keqing Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jongsu Choi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mark E Pennesi
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Paul Yang
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Molly Marra
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Robert K Koenekoop
- McGill Ocular Genetics Laboratory and Centre, Department of Paediatric Surgery, Human Genetics, and Ophthalmology, McGill University Health Centre, Montreal, Quebec, H4A 3S5, Canada
| | - Irma Lopez
- McGill Ocular Genetics Laboratory and Centre, Department of Paediatric Surgery, Human Genetics, and Ophthalmology, McGill University Health Centre, Montreal, Quebec, H4A 3S5, Canada
| | - Anna Matynia
- Jules Stein Eye Institute, Los Angeles, CA 90095, USA
- Ophthalmology, University of California Los Angeles David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Michael Gorin
- Jules Stein Eye Institute, Los Angeles, CA 90095, USA
- Ophthalmology, University of California Los Angeles David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Ruifang Sui
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Fengxia Yao
- Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Kerry Goetz
- Office of the Director, National Eye Institute/National Institutes of Health, Bethesda, MD 20892, USA
| | - Fernanda Belga Ottoni Porto
- INRET Clínica e Centro de Pesquisa, Belo Horizonte, Minas Gerais, 30150270, Brazil
- Department of Ophthalmology, Santa Casa de Misericórdia de Belo Horizonte, Belo Horizonte, Minas Gerais, 30150221, Brazil
- Centro Oftalmológico de Minas Gerais, Belo Horizonte, Minas Gerais, 30180070, Brazil
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
9
|
Zhong F, Tan M, Gao Y. Novel multi-allelic variants, two BBS2 and one PKD1 variant, of renal ciliopathies: A case report and literature review. Eur J Med Genet 2023; 66:104753. [PMID: 37003573 DOI: 10.1016/j.ejmg.2023.104753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/04/2023] [Accepted: 03/26/2023] [Indexed: 04/03/2023]
Abstract
BACKGROUND Bardet-Biedl syndrome (BBS) and autosomal dominant polycystic kidney disease (ADPKD) are renal ciliopathies. BBS has 22 pathogenic genes, and ADPKD is mainly caused by PKD1 and PKD2 variants. Cases with tri-allelic variants of BBS and PKD1 are rare. CASE PRESENTATION The proband was an 11-year-old Chinese male with cysts in both kidneys, blurred vision, hyperopia, and short fingers and toes. The patient underwent a kidney transplant due to rapid deterioration of renal failure. During follow-up, a smaller field of vision, a slow increase in height, and a weight gain were observed. In addition, renal function and anemia were improved. High-throughput sequencing analysis showed two heterozygous variants in BBS2 (c.563delT (p.I188Tfs*13) inherited from the father and c.534+1G > t (splicing) from the mother) and one heterozygous variant in PKD1 (c.6223C > T (p.R2075C)) inherited from the mother. CONCLUSION This paper reported a ciliopathy patient with multi-allelic variants (two BBS2 variants and one PKD1 variant) that may lead to early symptoms and more rapid progression. An early genetic diagnosis may contribute to predicting disease progression and guiding management and follow-up.
Collapse
Affiliation(s)
- Fazhan Zhong
- Guangzhou Medical University Affiliated Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Mei Tan
- Guangzhou Medical University Affiliated Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Yan Gao
- Guangzhou Medical University Affiliated Guangzhou Women and Children's Medical Center, Guangzhou, China.
| |
Collapse
|
10
|
Wen S, Wang M, Qian X, Li Y, Wang K, Choi J, Pennesi ME, Yang P, Marra M, Koenekoop RK, Lopez I, Matynia A, Gorin M, Sui R, Yao F, Goetz K, Porto FBO, Chen R. Systematic assessment of the contribution of structural variants to inherited retinal diseases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.02.522522. [PMID: 36789417 PMCID: PMC9928032 DOI: 10.1101/2023.01.02.522522] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Despite increasing success in determining genetic diagnosis for patients with inherited retinal diseases (IRDs), mutations in about 30% of the IRD cases remain unclear or unsettled after targeted gene panel or whole exome sequencing. In this study, we aimed to investigate the contributions of structural variants (SVs) to settling the molecular diagnosis of IRD with whole-genome sequencing (WGS). A cohort of 755 IRD patients whose pathogenic mutations remain undefined was subjected to WGS. Four SV calling algorithms including include MANTA, DELLY, LUMPY, and CNVnator were used to detect SVs throughout the genome. All SVs identified by any one of these four algorithms were included for further analysis. AnnotSV was used to annotate these SVs. SVs that overlap with known IRD-associated genes were examined with sequencing coverage, junction reads, and discordant read pairs. PCR followed by Sanger sequencing was used to further confirm the SVs and identify the breakpoints. Segregation of the candidate pathogenic alleles with the disease was performed when possible. In total, sixteen candidate pathogenic SVs were identified in sixteen families, including deletions and inversions, representing 2.1% of patients with previously unsolved IRDs. Autosomal dominant, autosomal recessive, and X-linked inheritance of disease-causing SVs were observed in 12 different genes. Among these, SVs in CLN3, EYS, PRPF31 were found in multiple families. Our study suggests that the contribution of SVs detected by short-read WGS is about 0.25% of our IRD patient cohort and is significantly lower than that of single nucleotide changes and small insertions and deletions.
Collapse
|
11
|
Solarat C, Valverde D. Clinical and molecular diagnosis of Bardet-Biedl syndrome (BBS). Methods Cell Biol 2023; 176:125-137. [PMID: 37164534 DOI: 10.1016/bs.mcb.2022.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Bardet-Biedl syndrome (BBS) is a rare genetic disease of the group of ciliopathies, a group of pathologies characterized mainly by defects in the structure and/or function of primary cilia. The main features of this ciliopathy are retinal dystrophy, obesity, polydactyly, urogenital and renal abnormalities, and cognitive impairment, commonly accompanied by various secondary features, making clear the extensive clinical heterogeneity associated with this syndrome, which, together with the frequent overlapping phenotype with other ciliopathies, greatly complicates its diagnosis. Patients are mainly detected by their pediatrician at quite early ages, usually between 2 and 6years. The pediatrician, given the main symptoms they present, usually refers patients to a specialist. Personalized medicine brought diagnosis closer to many patients who lacked it. It usually presents an autosomal recessive mode of inheritance, but in recent years several authors have proposed more complex inheritance models to explain the frequent inter- and intra-familial clinical variability. The main molecular techniques used for diagnosis are gene panels, the clinical exome and, in certain cases, the patient's complete genome. Although numerous studies have contributed to defining the role of the different BBS genes and designing various strategies for the molecular diagnosis of BBS, as well as delving into the functions performed by these proteins, these advances have not been sufficient to develop a complete treatment for this syndrome. and to be able to offer patients some therapeutic options.
Collapse
|
12
|
Amore G, Spoto G, Scuderi A, Prato A, Dicanio D, Nicotera A, Farello G, Chimenz R, Ceravolo I, Salpietro V, Gitto E, Ceravolo G, Iapadre G, Rosa GD, Pironti E. Bardet–Biedl Syndrome: A Brief Overview on Clinics and Genetics. JOURNAL OF PEDIATRIC NEUROLOGY 2022. [DOI: 10.1055/s-0042-1759534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
AbstractBardet–Biedl syndrome is a genetically pleiotropic disorder characterized by high clinical heterogeneity with severe multiorgan impairment. Clinically, it encompasses primary and secondary manifestations, mainly including retinal dystrophy, mental retardation, obesity, polydactyly, hypogonadism in male, and renal abnormalities. At least 21 different genes have been identified, all involved into primary cilium structure or function. To date, genotype–phenotype correlation is still poor.
Collapse
Affiliation(s)
- Greta Amore
- Department of Human Pathology of the Adult and Developmental Age “Gaetano Barresi,” Unit of Child Neurology and Psychiatry, University of Messina, Messina, Italy
| | - Giulia Spoto
- Department of Human Pathology of the Adult and Developmental Age “Gaetano Barresi,” Unit of Child Neurology and Psychiatry, University of Messina, Messina, Italy
| | - Anna Scuderi
- Department of Human Pathology of the Adult and Developmental Age “Gaetano Barresi,” Unit of Child Neurology and Psychiatry, University of Messina, Messina, Italy
| | - Adriana Prato
- Department of Human Pathology of the Adult and Developmental Age “Gaetano Barresi,” Unit of Child Neurology and Psychiatry, University of Messina, Messina, Italy
| | - Daniela Dicanio
- Department of Human Pathology of the Adult and Developmental Age “Gaetano Barresi,” Unit of Child Neurology and Psychiatry, University of Messina, Messina, Italy
| | - Antonio Nicotera
- Department of Human Pathology of the Adult and Developmental Age “Gaetano Barresi,” Unit of Child Neurology and Psychiatry, University of Messina, Messina, Italy
| | - Giovanni Farello
- Pediatric Clinic–Department of Life, Health and Environmental Sciences–Piazzale Salvatore Tommasi 1, Coppito (AQ), Italy
| | - Roberto Chimenz
- Faculty of Medicine and Surgery, University of Messina, Messina, Italy
| | - Ida Ceravolo
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | | | - Eloisa Gitto
- Neonatal and Pediatric Intensive Care Unit, Department of Human Pathology in Adult and Developmental Age “Gaetano Barresi,” University of Messina, Messina, Italy
| | - Giorgia Ceravolo
- Department of Human Pathology of the Adult and Developmental Age “Gaetano Barresi,” Unit of Pediatric Emergency, University of Messina, Messina, Italy
| | - Giulia Iapadre
- Department of Pediatrics, University of L'Aquila, L'Aquila, Italy
| | - Gabriella Di Rosa
- Department of Human Pathology of the Adult and Developmental Age “Gaetano Barresi,” Unit of Child Neurology and Psychiatry, University of Messina, Messina, Italy
| | - Erica Pironti
- Department of Woman-Child, Unit of Child Neurology and Psychiatry, Ospedali Riuniti, University of Foggia, Foggia, Italy
| |
Collapse
|
13
|
Wang J, Thomas HR, Thompson RG, Waldrep SC, Fogerty J, Song P, Li Z, Ma Y, Santra P, Hoover JD, Yeo NC, Drummond IA, Yoder BK, Amack JD, Perkins B, Parant JM. Variable phenotypes and penetrance between and within different zebrafish ciliary transition zone mutants. Dis Model Mech 2022; 15:dmm049568. [PMID: 36533556 PMCID: PMC9844136 DOI: 10.1242/dmm.049568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 11/04/2022] [Indexed: 12/23/2022] Open
Abstract
Meckel syndrome, nephronophthisis, Joubert syndrome and Bardet-Biedl syndrome are caused by mutations in proteins that localize to the ciliary transition zone (TZ). The phenotypically distinct syndromes suggest that these TZ proteins have differing functions. However, mutations in a single TZ gene can result in multiple syndromes, suggesting that the phenotype is influenced by modifier genes. We performed a comprehensive analysis of ten zebrafish TZ mutants, including mks1, tmem216, tmem67, rpgrip1l, cc2d2a, b9d2, cep290, tctn1, nphp1 and nphp4, as well as mutants in ift88 and ift172. Our data indicate that variations in phenotypes exist between different TZ mutants, supporting different tissue-specific functions of these TZ genes. Further, we observed phenotypic variations within progeny of a single TZ mutant, reminiscent of multiple disease syndromes being associated with mutations in one gene. In some mutants, the dynamics of the phenotype became complex with transitory phenotypes that are corrected over time. We also demonstrated that multiple-guide-derived CRISPR/Cas9 F0 'crispant' embryos recapitulate zygotic null phenotypes, and rapidly identified ciliary phenotypes in 11 cilia-associated gene candidates (ankfn1, ccdc65, cfap57, fhad1, nme7, pacrg, saxo2, c1orf194, ttc26, zmynd12 and cfap52).
Collapse
Affiliation(s)
- Jun Wang
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Holly R. Thomas
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Robert G. Thompson
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Stephanie C. Waldrep
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Joseph Fogerty
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Ping Song
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Zhang Li
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, AL 35294, USA
| | - Yongjie Ma
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Peu Santra
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Jonathan D. Hoover
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Nan Cher Yeo
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| | - Iain A. Drummond
- Davis Center for Aging and Regeneration, Mount Desert Island Biological Laboratory, 159 Old Bar Harbor Road, Bar Harbor, ME 04609, USA
| | - Bradley K. Yoder
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, AL 35294, USA
| | - Jeffrey D. Amack
- Department of Cell and Developmental Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Brian Perkins
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - John M. Parant
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham School of Medicine, Birmingham, AL 35294, USA
| |
Collapse
|
14
|
Tao T, Liu J, Wang B, Pang J, Li X, Huang L. Novel mutations in BBS genes and clinical characterization of Chinese families with Bardet-Biedl syndrome. Eur J Ophthalmol 2022; 33:11206721221136324. [PMID: 36325687 DOI: 10.1177/11206721221136324] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
PURPOSE Bardet-Biedl syndrome (BBS) is a rare autosomal-recessive inherited disorder characterized by multisystem anomalies. The objective of this study was to detect and analyse pathogenic variants in four Chinese families with BBS. METHODS Comprehensive clinical examinations were performed to investigate and evaluate the phenotypes of the affected individuals from four families. Genomic DNA was extracted from peripheral blood. Next-generation sequencing (NGS) was performed for four families, and the presence of pathogenic variants was confirmed via Sanger sequencing. RESULTS There were two males and three females with a mean age of 16.00 years. All probands displayed the primary clinical features of BBS. Mutation screening demonstrated four novel mutations: c.613C>T; p.Q205* in the BBS5 gene, c.1391C>G; p.S464* in the BBS10 gene, and c.155delC; p.S52* and c.1584T>G; p.Y528* in the BBS12 gene. Two previously reported mutations were also identified, including c.534 + 1G>T in the BBS2 gene and c.539G>A; p.G180E in the BBS10 gene. The bioinformatic analysis revealed that all the detected mutations in BBS genes were disease causing. CONCLUSIONS This study identified four novel BBS gene mutations in these Chinese families and further expanded the genotypic spectrum of BBS, thus contributing to the literature and understanding of this multisystem disease.
Collapse
Affiliation(s)
- Tianchang Tao
- Department of Ophthalmology, 71185Peking University People's Hospital, Eye Diseases and Optometry Institute, Beijing, China
- Department of Ophthalmology, Peking University People's Hospital, Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, Beijing, China
- College of Optometry, Peking University Health Science Center, Beijing, China
| | - Jia Liu
- Department of Ophthalmology, 71185Peking University People's Hospital, Eye Diseases and Optometry Institute, Beijing, China
- Department of Ophthalmology, Peking University People's Hospital, Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, Beijing, China
- College of Optometry, Peking University Health Science Center, Beijing, China
| | - Bin Wang
- Eye Research Institute, 599608Xiamen Eye Center of Xiamen University, Xiamen, China
| | - Jijing Pang
- Eye Research Institute, 599608Xiamen Eye Center of Xiamen University, Xiamen, China
| | - Xiaoxin Li
- Department of Ophthalmology, 71185Peking University People's Hospital, Eye Diseases and Optometry Institute, Beijing, China
- Department of Ophthalmology, Peking University People's Hospital, Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, Beijing, China
- College of Optometry, Peking University Health Science Center, Beijing, China
- Eye Research Institute, 599608Xiamen Eye Center of Xiamen University, Xiamen, China
| | - Lvzhen Huang
- Department of Ophthalmology, 71185Peking University People's Hospital, Eye Diseases and Optometry Institute, Beijing, China
- Department of Ophthalmology, Peking University People's Hospital, Beijing Key Laboratory of Diagnosis and Therapy of Retinal and Choroid Diseases, Beijing, China
- College of Optometry, Peking University Health Science Center, Beijing, China
| |
Collapse
|
15
|
Chromosome 2q12.3-q13 copy number variants in patients with neurodevelopmental disorders: genotype-phenotype correlation and new hotspots. Psychiatr Genet 2022; 32:171-177. [PMID: 35837682 DOI: 10.1097/ypg.0000000000000319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
INTRODUCTION The complex structure of the chromosome 2q12.3-q13 region provides a high chance of recombination events between various low copy repeats (LCRs). Copy number variants (CNV) in this region are present in both healthy populations and individuals affected with developmental delay, autism and congenital anomalies. Variable expressivity, reduced penetrance and limited characterization of the affected genes have complicated the classification of the CNVs clinical significance. METHODS Chromosomal microarray analysis data were reviewed for 10 298 patients with neurodevelopmental disorders referred to the UPMC Medical Genetics and Genomics Laboratories. A genotype-phenotype correlation was performed among the patients harboring the 2q12.3-q13 CNVs with overlapping genomic intervals. RESULTS We identified 17 (1 in ~600) individuals with rare CNVs in the 2q12.3-q13 region, including nine patients with deletions, seven individuals with duplications and one patient who had both a deletion and a duplication. Likely pathogenic CNVs with the breakpoints between LCRs encompassing the potential dosage-sensitive genes BCL2L11, BUB1, FBLN7 and TMEM87B were the most common. CNVs were also observed between LCRs surrounding the RANBP2 and LIMS1 genes. CONCLUSION Our study provides evidence for pathogenic CNV hotspots within the chromosome 2q12.3-q13 region. We suggest CNV classification based on the affected interval and the involvement of potential dosage-sensitive genes in these patients.
Collapse
|
16
|
Belyaeva EO, Lebedev IN. Interloci CNV Interactions in Variability of the Phenotypes of Neurodevelopmental Disorders. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422100027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
17
|
Rusterholz TDS, Hofmann C, Bachmann-Gagescu R. Insights Gained From Zebrafish Models for the Ciliopathy Joubert Syndrome. Front Genet 2022; 13:939527. [PMID: 35846153 PMCID: PMC9280682 DOI: 10.3389/fgene.2022.939527] [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: 05/09/2022] [Accepted: 05/26/2022] [Indexed: 12/04/2022] Open
Abstract
Cilia are quasi-ubiquitous microtubule-based sensory organelles, which play vital roles in signal transduction during development and cell homeostasis. Dysfunction of cilia leads to a group of Mendelian disorders called ciliopathies, divided into different diagnoses according to clinical phenotype constellation and genetic causes. Joubert syndrome (JBTS) is a prototypical ciliopathy defined by a diagnostic cerebellar and brain stem malformation termed the “Molar Tooth Sign” (MTS), in addition to which patients display variable combinations of typical ciliopathy phenotypes such as retinal dystrophy, fibrocystic renal disease, polydactyly or skeletal dystrophy. Like most ciliopathies, JBTS is genetically highly heterogeneous with ∼40 associated genes. Zebrafish are widely used to model ciliopathies given the high conservation of ciliary genes and the variety of specialized cilia types similar to humans. In this review, we compare different existing JBTS zebrafish models with each other and describe their contributions to our understanding of JBTS pathomechanism. We find that retinal dystrophy, which is the most investigated ciliopathy phenotype in zebrafish ciliopathy models, is caused by distinct mechanisms according to the affected gene. Beyond this, differences in phenotypes in other organs observed between different JBTS-mutant models suggest tissue-specific roles for proteins implicated in JBTS. Unfortunately, the lack of systematic assessment of ciliopathy phenotypes in the mutants described in the literature currently limits the conclusions that can be drawn from these comparisons. In the future, the numerous existing JBTS zebrafish models represent a valuable resource that can be leveraged in order to gain further insights into ciliary function, pathomechanisms underlying ciliopathy phenotypes and to develop treatment strategies using small molecules.
Collapse
Affiliation(s)
- Tamara D. S. Rusterholz
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
- Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
| | - Claudia Hofmann
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
- Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
| | - Ruxandra Bachmann-Gagescu
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
- Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
- *Correspondence: Ruxandra Bachmann-Gagescu,
| |
Collapse
|
18
|
Khan K, Ahram DF, Liu YP, Westland R, Sampogna RV, Katsanis N, Davis EE, Sanna-Cherchi S. Multidisciplinary approaches for elucidating genetics and molecular pathogenesis of urinary tract malformations. Kidney Int 2022; 101:473-484. [PMID: 34780871 PMCID: PMC8934530 DOI: 10.1016/j.kint.2021.09.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/15/2021] [Accepted: 09/30/2021] [Indexed: 12/28/2022]
Abstract
Advances in clinical diagnostics and molecular tools have improved our understanding of the genetically heterogeneous causes underlying congenital anomalies of kidney and urinary tract (CAKUT). However, despite a sharp incline of CAKUT reports in the literature within the past 2 decades, there remains a plateau in the genetic diagnostic yield that is disproportionate to the accelerated ability to generate robust genome-wide data. Explanations for this observation include (i) diverse inheritance patterns with incomplete penetrance and variable expressivity, (ii) rarity of single-gene drivers such that large sample sizes are required to meet the burden of proof, and (iii) multigene interactions that might produce either intra- (e.g., copy number variants) or inter- (e.g., effects in trans) locus effects. These challenges present an opportunity for the community to implement innovative genetic and molecular avenues to explain the missing heritability and to better elucidate the mechanisms that underscore CAKUT. Here, we review recent multidisciplinary approaches at the intersection of genetics, genomics, in vivo modeling, and in vitro systems toward refining a blueprint for overcoming the diagnostic hurdles that are pervasive in urinary tract malformation cohorts. These approaches will not only benefit clinical management by reducing age at molecular diagnosis and prompting early evaluation for comorbid features but will also serve as a springboard for therapeutic development.
Collapse
Affiliation(s)
- Kamal Khan
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA.,Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA (current address)
| | - Dina F. Ahram
- Division of Nephrology, Columbia University, New York, USA
| | - Yangfan P. Liu
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA
| | - Rik Westland
- Division of Nephrology, Columbia University, New York, USA.,Department of Pediatric Nephrology, Amsterdam UMC- Emma Children’s Hospital, Amsterdam, NL
| | | | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA; Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA (current address); Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA; Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.
| | - Erica E. Davis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA.,Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA (current address).,Department of Pediatrics and Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.,To whom correspondence should be addressed: ADDRESS CORRESPONDENCE TO: Simone Sanna-Cherchi, MD, Division of Nephrology, Columbia University, College of Physicians and Surgeons, New York, NY 10032, USA; Phone: 212-851-4925; Fax: 212-851-5461; . Erica E. Davis, PhD, Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA; Phone: 312-503-7662; Fax: 312-503-7343; , Nicholas Katsanis, PhD, Stanley Manne Children’s Research Institute, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA; Phone: 312-503-7339; Fax: 312-503-7343;
| | - Simone Sanna-Cherchi
- Department of Medicine, Division of Nephrology, Columbia University Irving Medical Center, New York, New York, USA.
| |
Collapse
|
19
|
Focșa IO, Budișteanu M, Burloiu C, Khan S, Sadeghpour A, Bohîlțea LC, Davis EE, Bălgrădean M. A case of Bardet-Biedl syndrome caused by a recurrent variant in BBS12: A case report. Biomed Rep 2021; 15:103. [PMID: 34760276 PMCID: PMC8567465 DOI: 10.3892/br.2021.1479] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/29/2021] [Indexed: 12/30/2022] Open
Abstract
Bardet-Biedl syndrome (BBS) is a clinically and genetically heterogenous disorder that manifests as a result of primary cilia impairment. Cilia are present on most cell types, thus BBS is a multisystemic condition involving the majority of organ systems. The core features of the syndrome include retinal degeneration, obesity, polydactyly, cognitive impairment, renal anomalies and urogenital malformations. To date, pathogenic variants in 26 genes have been shown to be involved in the molecular basis of this rare ciliopathy. Of these causal loci, BBS12 accounts for ~8% of all cases. In this case report, an individual with BBS caused by a rare recurrent variant in BBS12 (NM_152618.3: c.1063C>T; p.Arg355*) is described and compared with others with the same DNA variant, placing this finding in the context of the current literature.
Collapse
Affiliation(s)
- Ina Ofelia Focșa
- Department of Medical Genetics, University of Medicine and Pharmacy 'Carol Davila', 021901 Bucharest, Romania
| | - Magdalena Budișteanu
- Department of Pediatric Neurology, 'Prof. Dr. Alexandru Obregia' Clinical Hospital of Psychiatry, 041914 Bucharest, Romania.,Medical Genetic Laboratory, 'Victor Babeș' National Institute of Pathology, 050096 Bucharest, Romania.,Department of Medical Genetics, Titu Maiorescu University, 040441 Bucharest, Romania
| | - Carmen Burloiu
- Department of Pediatric Neurology, 'Prof. Dr. Alexandru Obregia' Clinical Hospital of Psychiatry, 041914 Bucharest, Romania
| | - Sheraz Khan
- National Institute for Biotechnology and Genetic Engineering (NIBGE-C), Faisalabad, Pakistan Institute of Engineering and Applied Sciences, Islamabad 38000, Pakistan.,Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Azita Sadeghpour
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC 27701, USA.,Duke Center for Applied Genomics and Precision Medicine, Duke University, Durham, NC 27708, USA
| | - Laurențiu C Bohîlțea
- Department of Medical Genetics, University of Medicine and Pharmacy 'Carol Davila', 021901 Bucharest, Romania
| | - Erica E Davis
- Advanced Center for Translational and Genetic Medicine, Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA.,Departments of Pediatrics and Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Mihaela Bălgrădean
- Department of Pediatrics and Pediatric Nephrology, Emergency Clinical Hospital for Children 'Maria Skłodowska Curie', 077120 Bucharest, Romania.,Department of Pediatrics, University of Medicine and Pharmacy 'Carol Davila', 077120 Bucharest, Romania
| |
Collapse
|
20
|
Focșa IO, Budișteanu M, Bălgrădean M. Clinical and genetic heterogeneity of primary ciliopathies (Review). Int J Mol Med 2021; 48:176. [PMID: 34278440 PMCID: PMC8354309 DOI: 10.3892/ijmm.2021.5009] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 06/28/2021] [Indexed: 01/11/2023] Open
Abstract
Ciliopathies comprise a group of complex disorders, with involvement of the majority of organs and systems. In total, >180 causal genes have been identified and, in addition to Mendelian inheritance, oligogenicity, genetic modifications, epistatic interactions and retrotransposon insertions have all been described when defining the ciliopathic phenotype. It is remarkable how the structural and functional impairment of a single, minuscule organelle may lead to the pathogenesis of highly pleiotropic diseases. Thus, combined efforts have been made to identify the genetic substratum and to determine the pathophysiological mechanism underlying the clinical presentation, in order to diagnose and classify ciliopathies. Yet, predicting the phenotype, given the intricacy of the genetic cause and overlapping clinical characteristics, represents a major challenge. In the future, advances in proteomics, cell biology and model organisms may provide new insights that could remodel the field of ciliopathies.
Collapse
Affiliation(s)
- Ina Ofelia Focșa
- Department of Medical Genetics, University of Medicine and Pharmacy 'Carol Davila', 021901 Bucharest, Romania
| | - Magdalena Budișteanu
- Department of Pediatric Neurology, 'Prof. Dr. Alexandru Obregia' Clinical Hospital of Psychiatry, 041914 Bucharest, Romania
| | - Mihaela Bălgrădean
- Department of Pediatrics and Pediatric Nephrology, Emergency Clinical Hospital for Children 'Maria Skłodowska Curie', 077120 Bucharest, Romania
| |
Collapse
|
21
|
Suárez-González J, Seidel V, Andrés-Zayas C, Izquierdo E, Buño I. Novel biallelic variant in BBS9 causative of Bardet-Biedl syndrome: expanding the spectrum of disease-causing genetic alterations. BMC Med Genomics 2021; 14:91. [PMID: 33771153 PMCID: PMC7995718 DOI: 10.1186/s12920-021-00943-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 03/16/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Bardet-Biedl syndrome (BBS) is a rare autosomal recessive ciliopathy disorder. Many BBS disease-causing genetic variants have been identified due to the advancement of molecular diagnostic tools. We report on a novel pathogenic variant in a consanguineous Pakistani family with an affected child. CASE PRESENTATION Clinical exome sequencing was used to search for BBS causing variants in the affected individual and identified a novel homozygous splice-site variant in the BBS9 gene (c.702 + 1del). Sanger sequencing was performed for variant validation and segregation studies. Expression analysis using mRNA levels to assess the functional impact of the novel variant demonstrated skipping of exon 7 in the affected alleles, suggesting a truncating effect. Three-dimensional structural modelling was used to predict pathogenicity of the variant residue and the alteration leads to a partial deletion of the PHTB1_N domain and a total deletion of the PHTB1_C domain. CONCLUSION The study of this case expands the spectrum of biallelic variants in the BBS9 gene associated with BBS and increased the knowledge on the molecular consequences of splicing variation c.702 + 1del.
Collapse
Affiliation(s)
- Julia Suárez-González
- Genomics Unit, Gregorio Marañón General University Hospital, Gregorio Marañón Health Research Institute (IiSGM), C/Doctor Esquerdo 46, 28007, Madrid, Spain
- Gregorio Marañón Health Research Institute (IiSGM), Madrid, Spain
| | - Verónica Seidel
- Clinical Genetics, Department of Pediatrics, Gregorio Marañón General University Hospital, Madrid, Spain
| | - Cristina Andrés-Zayas
- Genomics Unit, Gregorio Marañón General University Hospital, Gregorio Marañón Health Research Institute (IiSGM), C/Doctor Esquerdo 46, 28007, Madrid, Spain
- Gregorio Marañón Health Research Institute (IiSGM), Madrid, Spain
| | - Elvira Izquierdo
- Pediatric Nephrology, Department of Pediatrics, Gregorio Marañón General University Hospital, Madrid, Spain
| | - Ismael Buño
- Genomics Unit, Gregorio Marañón General University Hospital, Gregorio Marañón Health Research Institute (IiSGM), C/Doctor Esquerdo 46, 28007, Madrid, Spain.
- Gregorio Marañón Health Research Institute (IiSGM), Madrid, Spain.
- Department of Hematology, Gregorio Marañón General University Hospital, Madrid, Spain.
- Department of Cell Biology, School of Medicine, Complutense University of Madrid, Madrid, Spain.
| |
Collapse
|
22
|
Tsyklauri O, Niederlova V, Forsythe E, Prasai A, Drobek A, Kasparek P, Sparks K, Trachtulec Z, Prochazka J, Sedlacek R, Beales P, Huranova M, Stepanek O. Bardet-Biedl Syndrome ciliopathy is linked to altered hematopoiesis and dysregulated self-tolerance. EMBO Rep 2021; 22:e50785. [PMID: 33426789 DOI: 10.15252/embr.202050785] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 12/04/2020] [Accepted: 12/09/2020] [Indexed: 12/19/2022] Open
Abstract
Bardet-Biedl Syndrome (BBS) is a pleiotropic genetic disease caused by the dysfunction of primary cilia. The immune system of patients with ciliopathies has not been investigated. However, there are multiple indications that the impairment of the processes typically associated with cilia may have influence on the hematopoietic compartment and immunity. In this study, we analyze clinical data of BBS patients and corresponding mouse models carrying mutations in Bbs4 or Bbs18. We find that BBS patients have a higher prevalence of certain autoimmune diseases. Both BBS patients and animal models have altered red blood cell and platelet compartments, as well as elevated white blood cell levels. Some of the hematopoietic system alterations are associated with BBS-induced obesity. Moreover, we observe that the development and homeostasis of B cells in mice is regulated by the transport complex BBSome, whose dysfunction is a common cause of BBS. The BBSome limits canonical WNT signaling and increases CXCL12 levels in bone marrow stromal cells. Taken together, our study reveals a connection between a ciliopathy and dysregulated immune and hematopoietic systems.
Collapse
Affiliation(s)
- Oksana Tsyklauri
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.,Faculty of Science, Charles University, Prague, Czech Republic
| | - Veronika Niederlova
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Elizabeth Forsythe
- Genetics and Genomic Medicine Programme, University College London Great Ormond Street Institute of Child Health, London, UK.,National Bardet-Biedl Syndrome Service, Department of Clinical Genetics, Great Ormond Street Hospital, London, UK
| | - Avishek Prasai
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ales Drobek
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Kasparek
- Laboratory of Transgenic Models of Diseases, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic.,Czech Centre for Phenogenomics, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Kathryn Sparks
- National Bardet-Biedl Syndrome Service, Department of Clinical Genetics, Great Ormond Street Hospital, London, UK
| | - Zdenek Trachtulec
- Laboratory of Germ Cell Development, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Prochazka
- Laboratory of Transgenic Models of Diseases, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic.,Czech Centre for Phenogenomics, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Radislav Sedlacek
- Laboratory of Transgenic Models of Diseases, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic.,Czech Centre for Phenogenomics, Division BIOCEV, Institute of Molecular Genetics of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Philip Beales
- Genetics and Genomic Medicine Programme, University College London Great Ormond Street Institute of Child Health, London, UK.,National Bardet-Biedl Syndrome Service, Department of Clinical Genetics, Great Ormond Street Hospital, London, UK
| | - Martina Huranova
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ondrej Stepanek
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| |
Collapse
|
23
|
Novel Compound Heterozygous BBS2 and Homozygous MKKS Variants Detected in Chinese Families with Bardet-Biedl Syndrome. J Ophthalmol 2021; 2021:6751857. [PMID: 33520300 PMCID: PMC7817241 DOI: 10.1155/2021/6751857] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 10/23/2020] [Accepted: 12/19/2020] [Indexed: 11/29/2022] Open
Abstract
Background Bardet–Biedl syndrome (BBS) is a rare multisystem developmental disorder. In this study, we report the genetic causes and clinical manifestations in two Chinese families with BBS. Materials and Methods Two families were recruited in this study. Family A was a four-generation family with four affected and 15 unaffected members participating in the study, and family B was a consanguineous family with one affected and three unaffected members participating. Whole exome sequencing was performed in the two families, followed by a multistep bioinformatics analysis. Sanger sequencing was used to verify the variants and to perform a segregation analysis. Comprehensive ocular and systemic examinations were also conducted. Results Novel compound heterozygous variants c.235T > G (p.T79P) and c.534 + 1G > T were detected in the BBS2 gene in family A, and known homozygous variant c.748G > A (p.G250R) was detected in the MKKS gene in family B. Both families presented with retinitis pigmentosa; however, except for polydactyly, all other systemic manifestations were different. All of the affected family members in family A were overweight with a high body mass index (range from 26.5 to 41.9) and high blood pressure. Family A also presented with a delay in the onset of secondary sex characteristics and genital anomalies, while other systemic abnormalities were absent in family B. Conclusions This study presents one family with two novel BBS2 variants, expanding the variant spectrum of BBS, and one family with a known homozygous MKKS variant. The different phenotypes seen between the families with BBS2 and MKKS variants will contribute to the literature and our overall understanding of BBS.
Collapse
|
24
|
Kousi M, Söylemez O, Ozanturk A, Mourtzi N, Akle S, Jungreis I, Muller J, Cassa CA, Brand H, Mokry JA, Wolf MY, Sadeghpour A, McFadden K, Lewis RA, Talkowski ME, Dollfus H, Kellis M, Davis EE, Sunyaev SR, Katsanis N. Evidence for secondary-variant genetic burden and non-random distribution across biological modules in a recessive ciliopathy. Nat Genet 2020; 52:1145-1150. [PMID: 33046855 PMCID: PMC8272915 DOI: 10.1038/s41588-020-0707-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 08/31/2020] [Indexed: 11/08/2022]
Abstract
The influence of genetic background on driver mutations is well established; however, the mechanisms by which the background interacts with Mendelian loci remain unclear. We performed a systematic secondary-variant burden analysis of two independent cohorts of patients with Bardet-Biedl syndrome (BBS) with known recessive biallelic pathogenic mutations in one of 17 BBS genes for each individual. We observed a significant enrichment of trans-acting rare nonsynonymous secondary variants in patients with BBS compared with either population controls or a cohort of individuals with a non-BBS diagnosis and recessive variants in the same gene set. Strikingly, we found a significant over-representation of secondary alleles in chaperonin-encoding genes-a finding corroborated by the observation of epistatic interactions involving this complex in vivo. These data indicate a complex genetic architecture for BBS that informs the biological properties of disease modules and presents a model for secondary-variant burden analysis in recessive disorders.
Collapse
Affiliation(s)
- Maria Kousi
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
| | - Onuralp Söylemez
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Aysegül Ozanturk
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, USA
| | - Niki Mourtzi
- Advanced Center for Translational and Genetic Medicine, Lurie Children's Hospital, Chicago, IL, USA
| | - Sebastian Akle
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Boston, MA, USA
| | - Irwin Jungreis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
| | - Jean Muller
- Laboratoire de Génétique Médicale, Institut de Génétique Médicale d'Alsace, INSERM U1112, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Laboratoire de Diagnostic Génétique, Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Christopher A Cassa
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Harrison Brand
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Program in Population and Medical Genetics and Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jill Anne Mokry
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Maxim Y Wolf
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
| | - Azita Sadeghpour
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, USA
| | - Kelsey McFadden
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, USA
| | - Richard A Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Ophthalmology, Baylor College of Medicine, Houston, TX, USA
| | - Michael E Talkowski
- Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Program in Population and Medical Genetics and Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Hélène Dollfus
- Laboratoire de Génétique Médicale, Institut de Génétique Médicale d'Alsace, INSERM U1112, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA
| | - Erica E Davis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, USA
- Advanced Center for Translational and Genetic Medicine, Lurie Children's Hospital, Chicago, IL, USA
| | - Shamil R Sunyaev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, USA.
- Advanced Center for Translational and Genetic Medicine, Lurie Children's Hospital, Chicago, IL, USA.
- Departments of Pediatrics and Cellular and Molecular Biology, Northwestern University School of Medicine, Chicago, IL, USA.
| |
Collapse
|
25
|
Abstract
Obesity represents a major health burden to both developed and developing countries. Furthermore, the incidence of obesity is increasing in children. Obesity contributes substantially to mortality in the United States by increasing the risk for type 2 diabetes, cardiovascular-related diseases, and other comorbidities. Despite environmental changes over past decades, including increases in high-calorie foods and sedentary lifestyles, there is very clear evidence of a genetic predisposition to obesity risk. Childhood obesity cases can be categorized in one of two ways: syndromic or non-syndromic. Syndromic obesity includes disorders such as Prader-Willi syndrome, Bardet-Biedl syndrome, and Alström syndrome. Non-syndromic cases of obesity can be further separated into rarer instances of monogenic obesity and much more common forms of polygenic obesity. The advent of genome-wide association studies (GWAS) and next-generation sequencing has driven significant advances in our understanding of the genetic contribution to childhood obesity. Many rare and common genetic variants have been shown to contribute to the heritability in obesity, although the molecular mechanisms underlying most of these variants remain unclear. An important caveat of GWAS efforts is that they do not strictly represent gene target discoveries, rather simply the uncovering of robust genetic signals. One clear example of this is with progress in understanding the key obesity signal harbored within an intronic region of the FTO gene. It has been shown that the non-coding region in which the variant actually resides in fact influences the expression of genes distal to FTO instead, specifically IRX3 and IRX5. Such discoveries suggest that associated non-coding variants can be embedded within or next to one gene, but commonly influence the expression of other, more distal effector genes. Advances in genetics and genomics are therefore contributing to a deeper understanding of childhood obesity, allowing for development of clinical tools and therapeutic agents.
Collapse
|
26
|
Deletion in the Bardet-Biedl Syndrome Gene TTC8 Results in a Syndromic Retinal Degeneration in Dogs. Genes (Basel) 2020; 11:genes11091090. [PMID: 32962042 PMCID: PMC7565673 DOI: 10.3390/genes11091090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/12/2020] [Accepted: 09/15/2020] [Indexed: 02/06/2023] Open
Abstract
In golden retriever dogs, a 1 bp deletion in the canine TTC8 gene has been shown to cause progressive retinal atrophy (PRA), the canine equivalent of retinitis pigmentosa. In humans, TTC8 is also implicated in Bardet–Biedl syndrome (BBS). To investigate if the affected dogs only exhibit a non-syndromic PRA or develop a syndromic ciliopathy similar to human BBS, we recruited 10 affected dogs to the study. The progression of PRA for two of the dogs was followed for 2 years, and a rigorous clinical characterization allowed a careful comparison with primary and secondary characteristics of human BBS. In addition to PRA, the dogs showed a spectrum of clinical and morphological signs similar to primary and secondary characteristics of human BBS patients, such as obesity, renal anomalies, sperm defects, and anosmia. We used Oxford Nanopore long-read cDNA sequencing to characterize retinal full-length TTC8 transcripts in affected and non-affected dogs, the results of which suggest that three isoforms are transcribed in the retina, and the 1 bp deletion is a loss-of-function mutation, resulting in a canine form of Bardet–Biedl syndrome with heterogeneous clinical signs.
Collapse
|
27
|
Exploring Key Challenges of Understanding the Pathogenesis of Kidney Disease in Bardet-Biedl Syndrome. Kidney Int Rep 2020; 5:1403-1415. [PMID: 32954066 PMCID: PMC7486190 DOI: 10.1016/j.ekir.2020.06.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/04/2020] [Accepted: 06/17/2020] [Indexed: 12/21/2022] Open
Abstract
Bardet–Biedl syndrome (BBS) is a rare pleiotropic inherited disorder known as a ciliopathy. Kidney disease is a cardinal clinical feature; however, it is one of the less investigated traits. This study is a comprehensive analysis of the literature aiming to collect available information providing mechanistic insights into the pathogenesis of kidney disease by analyzing clinical and basic science studies focused on this issue. The analysis revealed that the syndrome is either clinically and genetically heterogenous, with 24 genes discovered to date, but with 3 genes (BBS1, BBS2, and BBS10) accounting for almost 50% of diagnoses; genotype–phenotype correlation studies showed that patients with BBS1 mutations have a less severe renal phenotype than the other 2 most common loci; in addition, truncating rather than missense mutations are more likely to cause kidney disease. However, significant intrafamilial clinical variability has been described, with no clear explanation to date. In mice kidneys, Bbs genes have relative low expression levels, in contrast with other common affected organs, like the retina; surprisingly, Bbs1 is the only locus with basal overexpression in the kidney. In vitro studies indicate that signalling pathways involved in embryonic kidney development and repair are affected in the context of BBS depletion; in mice, kidney disease does not have a full penetrance; when present, it resembles human phenotype and shows an age-dependent progression. Data on the exact contribution of local versus systemic consequences of Bbs dysfunction are scanty and further investigations are required to get firm conclusions.
Collapse
|
28
|
Wang N, Zhu W, Han B, Wang H, Zhu H, Chen Y, Chen Y, Liu J, Liu Y, Zhao S, Song H, Qiao J. Inherited Missense Mutation Occurring in Arginine76 of the SRY Gene Does Not Account for Familial 46, XY Sex Reversal. J Clin Endocrinol Metab 2020; 105:5788229. [PMID: 32140723 DOI: 10.1210/clinem/dgaa109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 03/03/2020] [Indexed: 11/19/2022]
Abstract
BACKGROUND SRY (sex determining region of Y) is one of the important genes involved in the process of human sex determination. The disturbed sex determination caused by an SRY mutation accounts for 10% to 15% of cases with 46, XY sex reversal. Recently, 3 distal enhancers were identified upstream of the SOX9 gene. OBJECTIVES The purpose of this study was to investigate the molecular etiology of 46, XY sex reversal in 3 familial patients and a sporadic patient. DESIGN Next-generation sequencing was used to reveal the genotype and inherited pattern. Copy number variations and single nucleotide polymorphism haplotyping were analyzed to observe the alteration of enhancers of SOX9. Transcriptional activity of SRY mutation were assessed by a dual luciferase reporting system, and nuclear translocation was observed by confocal microscopy. RESULTS Two novel SRY gene mutations, p.Arg76Leu and p.Glu89flx15, were identified. In the pedigree with multiple patients, p.Arg76Leu mutation in SRY and p.Gly212Ser mutation in NR5A1 were identified in the proband. The heterozygous deletion far upstream of the SOX9 gene in chromosome 17 was identified in the 3 patients in this family, containing the distal enhancer eSR-A of SOX9 but not eSR-B and eALDI. The frameshift mutation p.Glu89flx15 was revealed to inhibit the transcriptional activity of the target gene, whereas the missense mutation p.Arg76Leu barely showed an effect. CONCLUSION In contrast to sporadic cases, inherited single nucleotide variations of SRY are not the main cause of the severe phenotype of 46, XY sex reversal, and the enhancers of SOX9 should be investigated carefully in such patients.
Collapse
Affiliation(s)
- Nan Wang
- Department of Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenjiao Zhu
- Department of Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bing Han
- Department of Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hao Wang
- Department of Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Zhu
- Department of Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingchao Chen
- Department of Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Chen
- Department of obstetrics and gynecology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianhua Liu
- Department of obstetrics and gynecology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yang Liu
- Department of Plastic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuangxia Zhao
- Research Centre for Clinical Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huaidong Song
- Research Centre for Clinical Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Qiao
- Department of Endocrinology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
29
|
Dupont MA, Humbert C, Huber C, Siour Q, Guerrera IC, Jung V, Christensen A, Pouliet A, Garfa-Traoré M, Nitschké P, Injeyan M, Millar K, Chitayat D, Shannon P, Girisha KM, Shukla A, Mechler C, Lorentzen E, Benmerah A, Cormier-Daire V, Jeanpierre C, Saunier S, Delous M. Human IFT52 mutations uncover a novel role for the protein in microtubule dynamics and centrosome cohesion. Hum Mol Genet 2020; 28:2720-2737. [PMID: 31042281 DOI: 10.1093/hmg/ddz091] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/24/2019] [Accepted: 04/25/2019] [Indexed: 12/26/2022] Open
Abstract
Mutations in genes encoding components of the intraflagellar transport (IFT) complexes have previously been associated with a spectrum of diseases collectively termed ciliopathies. Ciliopathies relate to defects in the formation or function of the cilium, a sensory or motile organelle present on the surface of most cell types. IFT52 is a key component of the IFT-B complex and ensures the interaction of the two subcomplexes, IFT-B1 and IFT-B2. Here, we report novel IFT52 biallelic mutations in cases with a short-rib thoracic dysplasia (SRTD) or a congenital anomaly of kidney and urinary tract (CAKUT). Combining in vitro and in vivo studies in zebrafish, we showed that SRTD-associated missense mutation impairs IFT-B complex assembly and IFT-B2 ciliary localization, resulting in decreased cilia length. In comparison, CAKUT-associated missense mutation has a mild pathogenicity, thus explaining the lack of skeletal defects in CAKUT case. In parallel, we demonstrated that the previously reported homozygous nonsense IFT52 mutation associated with Sensenbrenner syndrome [Girisha et al. (2016) A homozygous nonsense variant in IFT52 is associated with a human skeletal ciliopathy. Clin. Genet., 90, 536-539] leads to exon skipping and results in a partially functional protein. Finally, our work uncovered a novel role for IFT52 in microtubule network regulation. We showed that IFT52 interacts and partially co-localized with centrin at the distal end of centrioles where it is involved in its recruitment and/or maintenance. Alteration of this function likely contributes to centriole splitting observed in Ift52-/- cells. Altogether, our findings allow a better comprehensive genotype-phenotype correlation among IFT52-related cases and revealed a novel, extra-ciliary role for IFT52, i.e. disruption may contribute to pathophysiological mechanisms.
Collapse
Affiliation(s)
- Marie Alice Dupont
- Laboratory of Hereditary Kidney Diseases, INSERM, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Camille Humbert
- Laboratory of Hereditary Kidney Diseases, INSERM, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Céline Huber
- Laboratory of Molecular and Physiopathological bases of osteochondrodysplasia, INSERM, Paris, France.,Department of Genetics, Reference Centre for Skeletal Dysplasia, Assistance Publique - Hôpitaux de Paris, Necker-Enfants Malades Hospital, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Quentin Siour
- Laboratory of Molecular and Physiopathological bases of osteochondrodysplasia, INSERM, Paris, France.,Department of Genetics, Reference Centre for Skeletal Dysplasia, Assistance Publique - Hôpitaux de Paris, Necker-Enfants Malades Hospital, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Ida Chiara Guerrera
- Proteomics Platform 3P5-Necker, Paris Descartes-Sorbonne Paris Cité University, Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France
| | - Vincent Jung
- Proteomics Platform 3P5-Necker, Paris Descartes-Sorbonne Paris Cité University, Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS3633, Paris, France
| | - Anni Christensen
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Aurore Pouliet
- Genomics Core Facility, Imagine Institute and Structure Fédérative de Recherche Necker, INSERM UMR1163 and INSERM US24/CNRS UMS3633, Paris Descartes-Sorbonne Paris Cité University, Paris, France
| | - Meriem Garfa-Traoré
- Cell Imaging Platform UMS 24, Structure Fédérative de Recherche Necker, Inserm US24/CNRS UMS3633, Paris, France
| | - Patrick Nitschké
- Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France.,Bioinformatics Core Facility, Paris Descartes-Sorbonne Paris Cité University, Paris, France
| | - Marie Injeyan
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Kathryn Millar
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - David Chitayat
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada.,Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Patrick Shannon
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Katta Mohan Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India
| | - Charlotte Mechler
- Assistance Publique - Hôpitaux de Paris, Louis Mourier Hospital, Colombes, France
| | - Esben Lorentzen
- Department of Structural Cell Biology, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Alexandre Benmerah
- Laboratory of Hereditary Kidney Diseases, INSERM, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Valérie Cormier-Daire
- Laboratory of Molecular and Physiopathological bases of osteochondrodysplasia, INSERM, Paris, France.,Department of Genetics, Reference Centre for Skeletal Dysplasia, Assistance Publique - Hôpitaux de Paris, Necker-Enfants Malades Hospital, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Cécile Jeanpierre
- Laboratory of Hereditary Kidney Diseases, INSERM, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Sophie Saunier
- Laboratory of Hereditary Kidney Diseases, INSERM, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Marion Delous
- Laboratory of Hereditary Kidney Diseases, INSERM, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
| |
Collapse
|
30
|
Chakrabarty S, Savantre SB, Ramachandra Bhat C, Satyamoorthy K. Multiple genetic mutations implicate spectrum of phenotypes in Bardet-Biedl syndrome. Gene 2020; 725:144164. [PMID: 31639430 DOI: 10.1016/j.gene.2019.144164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 09/14/2019] [Accepted: 10/08/2019] [Indexed: 11/17/2022]
Abstract
Bardet-Biedl syndrome (BBS) is a clinically and genetically heterogeneous ciliopathy with several clinical features including retinitis pigmentosa, obesity, kidney dysfunction, postaxial polydactyly, behavioral dysfunction and hypogonadism with wide spectrum of additional features. With multiple phenotypes and heterogeneous distribution, it is unlikely that BBS is caused by single gene defect. We have performed clinical and genetic diagnosis of two individuals from an Indian family with classical BBS symptoms. Whole exome sequencing identified homozygous missense mutation in BBS10 gene, hemizygous missense AR and homozygous missense PDE6B mutations in the proband and affected sibling with BBS. Identification of BBS10 mutation along with AR and PDE6B gene mutation will expand the genetic and phenotypic spectrum in individuals with BBS.
Collapse
Affiliation(s)
- Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Swheta B Savantre
- Department of Medicine, K.V.G. Medical College & Hospital, Dakshina Kannada, Sullia 574327, India
| | - C Ramachandra Bhat
- Department of Medicine, K.V.G. Medical College & Hospital, Dakshina Kannada, Sullia 574327, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India.
| |
Collapse
|
31
|
Tsai IC, Adams KA, Tzeng JA, Shennib O, Tan PL, Katsanis N. Genome-wide suppressor screen identifies USP35/USP38 as therapeutic candidates for ciliopathies. JCI Insight 2019; 4:130516. [PMID: 31723061 DOI: 10.1172/jci.insight.130516] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 10/09/2019] [Indexed: 12/17/2022] Open
Abstract
The ciliopathies are a group of phenotypically overlapping disorders caused by structural or functional defects in the primary cilium. Although disruption of numerous signaling pathways and cellular trafficking events have been implicated in ciliary pathology, treatment options for affected individuals remain limited. Here, we performed a genome-wide RNAi (RNA interference) screen to identify genetic suppressors of BBS4, one of the genes mutated in Bardet-Biedl syndrome (BBS). We discovered 10 genes that, when silenced, ameliorate BBS4-dependent pathology. One of these encodes USP35, a negative regulator of the ubiquitin proteasome system, suggesting that inhibition of a deubiquitinase, and subsequent facilitation of the clearance of signaling components, might ameliorate BBS-relevant phenotypes. Testing of this hypothesis in transient and stable zebrafish genetic models showed this posit to be true; suppression or ablation of usp35 ameliorated hallmark ciliopathy defects including impaired convergent extension (CE), renal tubule convolution, and retinal degeneration with concomitant clearance of effectors such as β-catenin and rhodopsin. Together, our findings reinforce a direct link between proteasome-dependent degradation and ciliopathies and suggest that augmentation of this system might offer a rational path to novel therapeutic modalities.
Collapse
Affiliation(s)
- I-Chun Tsai
- Center for Human Disease Modeling, Duke University School of Medicine, Durham, North Carolina, USA
| | - Kevin A Adams
- Center for Human Disease Modeling, Duke University School of Medicine, Durham, North Carolina, USA
| | - Joyce A Tzeng
- Center for Human Disease Modeling, Duke University School of Medicine, Durham, North Carolina, USA
| | - Omar Shennib
- Center for Human Disease Modeling, Duke University School of Medicine, Durham, North Carolina, USA
| | - Perciliz L Tan
- Center for Human Disease Modeling, Duke University School of Medicine, Durham, North Carolina, USA.,Rescindo Therapeutics, Durham, North Carolina, USA
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University School of Medicine, Durham, North Carolina, USA.,Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA.,Departments of Pediatrics and Cellular and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| |
Collapse
|
32
|
Niederlova V, Modrak M, Tsyklauri O, Huranova M, Stepanek O. Meta-analysis of genotype-phenotype associations in Bardet-Biedl syndrome uncovers differences among causative genes. Hum Mutat 2019; 40:2068-2087. [PMID: 31283077 DOI: 10.1002/humu.23862] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 06/17/2019] [Accepted: 07/03/2019] [Indexed: 12/16/2022]
Abstract
Bardet-Biedl syndrome (BBS) is a recessive genetic disease causing multiple organ anomalies. Most patients carry mutations in genes encoding for the subunits of the BBSome, an octameric ciliary transport complex, or accessory proteins involved in the BBSome assembly or function. BBS proteins have been extensively studied using in vitro, cellular, and animal models. However, the molecular functions of particular BBS proteins and the etiology of the BBS symptoms are still largely elusive. In this study, we applied a meta-analysis approach to study the genotype-phenotype association in humans using our database of all reported BBS patients. The analysis revealed that the identity of the causative gene and the character of the mutation partially predict the clinical outcome of the disease. Besides their potential use for clinical prognosis, our analysis revealed functional differences of particular BBS genes in humans. Core BBSome subunits BBS2, BBS7, and BBS9 manifest as more critical for the function and development of kidneys than peripheral subunits BBS1, BBS4, and BBS8/TTC8, suggesting that incomplete BBSome retains residual function at least in the kidney.
Collapse
Affiliation(s)
- Veronika Niederlova
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Martin Modrak
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Oksana Tsyklauri
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Martina Huranova
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ondrej Stepanek
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| |
Collapse
|
33
|
Manara E, Paolacci S, D’Esposito F, Abeshi A, Ziccardi L, Falsini B, Colombo L, Iarossi G, Pilotta A, Boccone L, Guerri G, Monica M, Marta B, Maltese PE, Buzzonetti L, Rossetti L, Bertelli M. Mutation profile of BBS genes in patients with Bardet-Biedl syndrome: an Italian study. Ital J Pediatr 2019; 45:72. [PMID: 31196119 PMCID: PMC6567512 DOI: 10.1186/s13052-019-0659-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 05/16/2019] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Bardet-Biedl syndrome (BBS) is a rare inherited multisystemic disorder with autosomal recessive or complex digenic triallelic inheritance. There is currently no treatment for BBS, but some morbidities can be managed. Accurate molecular diagnosis is often crucial for the definition of appropriate patient management and for the development of a potential personalized therapy. METHODS We developed a next-generation-sequencing (NGS) protocol for the screening of the 18 most frequently mutated genes to define the genotype and clarify the mutation spectrum of a cohort of 20 BBS Italian patients. RESULTS We defined the causative variants in 60% of patients; four of those are novel. 33% of patients also harboured variants in additional gene/s, suggesting possible oligogenic inheritance. To explore the function of different genes, we looked for correlations between genotype and phenotype in our cohort. Hypogonadism was more frequently detected in patients with variants in BBSome proteins, while renal abnormalities in patients with variations in BBSome chaperonin genes. CONCLUSIONS NGS is a powerful tool that can help understanding BBS patients' phenotype through the identification of mutations that could explain differences in phenotype severity and could provide insights for the development of targeted therapy. Furthermore, our results support the existence of additional BBS loci yet to be identified.
Collapse
Affiliation(s)
| | | | - Fabiana D’Esposito
- Magi Euregio, Bolzano, Italy
- Imperial College Ophthalmic Research Unit, Western Eye Hospital, Imperial College Healthcare NHS Trust, London, UK
- Eye Clinic, Department of Neurosciences, Reproductive Sciences and Dentistry, Federico II University, Naples, Italy
| | | | | | - Benedetto Falsini
- Institute of Ophthalmology, Università Cattolica del Sacro Cuore, Rome, Italy
- Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Rome, Italy
| | - Leonardo Colombo
- Department of Ophthalmology, San Paolo Hospital, University of Milan, Milan, Italy
| | - Giancarlo Iarossi
- Department of Ophthalmology, Bambino Gesù IRCCS Children’s Hospital, Rome, Italy
| | - Alba Pilotta
- Special Unit of Auxoendocrinology, Diabetology and Pediatric Genetics, University of Brescia, Spedali Civili di Brescia, Brescia, Italy
| | - Loredana Boccone
- Microcitemic Regional Hospital, Brotzu Hospital, Cagliari, Italy
| | | | - Marica Monica
- Microcitemic Regional Hospital, Brotzu Hospital, Cagliari, Italy
| | - Balzarini Marta
- Microcitemic Regional Hospital, Brotzu Hospital, Cagliari, Italy
| | | | - Luca Buzzonetti
- Department of Ophthalmology, Bambino Gesù IRCCS Children’s Hospital, Rome, Italy
| | - Luca Rossetti
- Department of Ophthalmology, San Paolo Hospital, University of Milan, Milan, Italy
| | | |
Collapse
|
34
|
Outtandy P, Russell C, Kleta R, Bockenhauer D. Zebrafish as a model for kidney function and disease. Pediatr Nephrol 2019; 34:751-762. [PMID: 29502161 PMCID: PMC6424945 DOI: 10.1007/s00467-018-3921-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 12/12/2017] [Accepted: 12/12/2017] [Indexed: 12/31/2022]
Abstract
Kidney disease is a global problem with around three million people diagnosed in the UK alone and the incidence is rising. Research is critical to develop better treatments. Animal models can help to better understand the pathophysiology behind the various kidney diseases and to screen for therapeutic compounds, but the use especially of mammalian models should be minimised in the interest of animal welfare. Zebrafish are increasingly used, as they are genetically tractable and have a basic renal anatomy comparable to mammalian kidneys with glomerular filtration and tubular filtration processing. Here, we discuss how zebrafish have advanced the study of nephrology and the mechanisms underlying kidney disease.
Collapse
Affiliation(s)
- Priya Outtandy
- Centre for Nephrology, Royal Free Hospital/Medical School, University College London, 1. Floor, Room 1.7007, Rowland Hill Street, London, NW3 2PF, UK
- Department of Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, London, NW1 0TU, UK
| | - Claire Russell
- Department of Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, London, NW1 0TU, UK
| | - Robert Kleta
- Centre for Nephrology, Royal Free Hospital/Medical School, University College London, 1. Floor, Room 1.7007, Rowland Hill Street, London, NW3 2PF, UK.
| | - Detlef Bockenhauer
- Centre for Nephrology, Royal Free Hospital/Medical School, University College London, 1. Floor, Room 1.7007, Rowland Hill Street, London, NW3 2PF, UK
| |
Collapse
|
35
|
Salehi Karlslätt K, Pettersson M, Jäntti N, Szafranski P, Wester T, Husberg B, Ullberg U, Stankiewicz P, Nordgren A, Lundin J, Lindstrand A, Nordenskjöld A. Rare copy number variants contribute pathogenic alleles in patients with intestinal malrotation. Mol Genet Genomic Med 2019; 7:e549. [PMID: 30632303 PMCID: PMC6418355 DOI: 10.1002/mgg3.549] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/05/2018] [Accepted: 12/05/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Intestinal malrotation is a potentially life-threatening congenital anomaly due to the risk of developing midgut volvulus. The reported incidence is 0.2%-1% and both apparently hereditary and sporadic cases have been reported. Intestinal malrotation is associated with a few syndromes with known genotype but the genetic contribution in isolated intestinal malrotation has not yet been reported. Rare copy number variants (CNVs) have been implicated in many congenital anomalies, and hence we sought to investigate the potential contribution of rare CNVs in intestinal malrotation. METHODS Analysis of array comparative genomic hybridization (aCGH) data from 47 patients with symptomatic intestinal malrotation was performed. RESULTS We identified six rare CNVs in five patients. Five CNVs involved syndrome loci: 7q11.23 microduplication, 16p13.11 microduplication, 18q terminal deletion, HDAC8 (Cornelia de Lange syndrome type 5 and FOXF1) as well as one intragenic deletion in GALNT14, not previously implicated in human disease. CONCLUSION In the present study, we identified rare CNVs contributing pathogenic or potentially pathogenic alleles in five patients with syndromic intestinal malrotation, suggesting that CNV screening is indicated in intestinal malrotation with associated malformations or neurological involvements. In addition, we identified intestinal malrotation in two known syndromes (Cornelia de Lange type 5 and 18q terminal deletion syndrome) that has not previously been associated with gastrointestinal malformations.
Collapse
Affiliation(s)
- Karin Salehi Karlslätt
- Department of Women's and Children's Health and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Pediatrics, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Pettersson
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Nina Jäntti
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Tomas Wester
- Department of Pediatric Surgery, Karolinska University Hospital, Stockholm, Sweden.,Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Britt Husberg
- Department of General Surgery, Ersta Hospital, Stockholm, Sweden
| | - Ulla Ullberg
- Department of Pediatric Radiology, Karolinska University Hospital, Stockholm, Sweden
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Johanna Lundin
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Agneta Nordenskjöld
- Department of Women's and Children's Health and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Pediatric Surgery, Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
36
|
Khan TN, Khan K, Sadeghpour A, Reynolds H, Perilla Y, McDonald MT, Gallentine WB, Baig SM, Davis EE, Katsanis N. Mutations in NCAPG2 Cause a Severe Neurodevelopmental Syndrome that Expands the Phenotypic Spectrum of Condensinopathies. Am J Hum Genet 2019; 104:94-111. [PMID: 30609410 PMCID: PMC6323578 DOI: 10.1016/j.ajhg.2018.11.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 11/26/2018] [Indexed: 01/29/2023] Open
Abstract
The use of whole-exome and whole-genome sequencing has been a catalyst for a genotype-first approach to diagnostics. Under this paradigm, we have implemented systematic sequencing of neonates and young children with a suspected genetic disorder. Here, we report on two families with recessive mutations in NCAPG2 and overlapping clinical phenotypes that include severe neurodevelopmental defects, failure to thrive, ocular abnormalities, and defects in urogenital and limb morphogenesis. NCAPG2 encodes a member of the condensin II complex, necessary for the condensation of chromosomes prior to cell division. Consistent with a causal role for NCAPG2, we found abnormal chromosome condensation, augmented anaphase chromatin-bridge formation, and micronuclei in daughter cells of proband skin fibroblasts. To test the functional relevance of the discovered variants, we generated an ncapg2 zebrafish model. Morphants displayed clinically relevant phenotypes, such as renal anomalies, microcephaly, and concomitant increases in apoptosis and altered mitotic progression. These could be rescued by wild-type but not mutant human NCAPG2 mRNA and were recapitulated in CRISPR-Cas9 F0 mutants. Finally, we noted that the individual with a complex urogenital defect also harbored a heterozygous NPHP1 deletion, a common contributor to nephronophthisis. To test whether sensitization at the NPHP1 locus might contribute to a more severe renal phenotype, we co-suppressed nphp1 and ncapg2, which resulted in significantly more dysplastic renal tubules in zebrafish larvae. Together, our data suggest that impaired function of NCAPG2 results in a severe condensinopathy, and they highlight the potential utility of examining candidate pathogenic lesions beyond the primary disease locus.
Collapse
Affiliation(s)
- Tahir N Khan
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA
| | - Kamal Khan
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA; Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Azita Sadeghpour
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA
| | - Hannah Reynolds
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA; Furman University, Greenville, SC 29613, USA
| | - Yezmin Perilla
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA
| | - Marie T McDonald
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC 27710, USA
| | - William B Gallentine
- Department of Pediatrics, Division of Pediatric Neurology, Duke University Medical Center, Durham, NC 27710, USA
| | - Shahid M Baig
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Erica E Davis
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA.
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA.
| |
Collapse
|
37
|
Ladino LY, Galvis J, Yasnó D, Ramírez A, Beltrán OI. A pathogenic homozygous variant of the BBS10 gene in a patient with Bardet Biedl syndrome. BIOMEDICA : REVISTA DEL INSTITUTO NACIONAL DE SALUD 2018; 38:308-320. [PMID: 30335236 DOI: 10.7705/biomedica.v38i4.4199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 03/23/2018] [Accepted: 04/02/2018] [Indexed: 06/08/2023]
Abstract
The Bardet-Biedl syndrome is an autosomal recessive hereditary disorder with vast locus heterogeneity that belongs to the so-called ciliopathies, whose proteins are localized in the primary cilia and present functional deficiency. The multisystemic features of the disease include ocular, renal, cognitive, skeletal, as well as gonadal involvement and obesity, among others, with high inter- and intrafamilial variability. We describe the clinical case of an adolescent male patient with Bardet-Biedl syndrome, including the approach, the results from a 22-gene sequencing panel, and the analysis of updated scientific literature. We collected the clinical data of the patient and, after obtaining the informed consent, we conducted a multigenic sequencing panel oriented to known implicated genes. The patient was born to consanguineous parents and was the first affected member of the family. He presented with postaxial polydactyly, obesity, micropenis, retinitis pigmentosa, and learning disability. The multigenic panel allowed the identification of the homozygous pathogenic variant c.39_46del in the BBS10 gene and in other BBS genes variants associated with obesity. As the Bardet-Biedl syndrome is a rare disease, it is challenging to interpret its pleiotropism and gene/allelic heterogeneity. Its confirmation by molecular tests allows an adequate approach, follow-up, and genetic counseling of the patient and the family.
Collapse
Affiliation(s)
- Luz Yaqueline Ladino
- Departamento de Genética, Grupo de Investigación GenHOMI, Fundación Hospital Pediátrico La Misericordia-HOMI, Bogotá, D.C., Colombia Maestría en Genética Humana, Universidad Nacional de Colombia, Bogotá, D.C., Colombia.
| | | | | | | | | |
Collapse
|
38
|
Pettersson M, Vaz R, Hammarsjö A, Eisfeldt J, Carvalho CMB, Hofmeister W, Tham E, Horemuzova E, Voss U, Nishimura G, Klintberg B, Nordgren A, Nilsson D, Grigelioniene G, Lindstrand A. Alu-Alu mediated intragenic duplications in IFT81 and MATN3 are associated with skeletal dysplasias. Hum Mutat 2018; 39:1456-1467. [PMID: 30080953 DOI: 10.1002/humu.23605] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 07/09/2018] [Accepted: 08/02/2018] [Indexed: 01/22/2023]
Abstract
Skeletal dysplasias are a diverse group of rare Mendelian disorders with clinical and genetic heterogeneity. Here, we used targeted copy number variant (CNV) screening and identified intragenic exonic duplications, formed through Alu-Alu fusion events, in two individuals with skeletal dysplasia and negative exome sequencing results. First, we detected a homozygous tandem duplication of exon 9 and 10 in IFT81 in a boy with Jeune syndrome, or short-rib thoracic dysplasia (SRTD) (MIM# 208500). Western blot analysis did not detect any wild-type IFT81 protein in fibroblasts from the patient with the IFT81 duplication, but only a shorter isoform of IFT81 that was also present in the normal control samples. Complementary zebrafish studies suggested that loss of full-length IFT81 protein but expression of a shorter form of IFT81 protein affects the phenotype while being compatible with life. Second, a de novo tandem duplication of exons 2 to 5 in MATN3 was identified in a girl with multiple epiphyseal dysplasia (MED) type 5 (MIM# 607078). Our data highlights the importance of detection and careful characterization of intragenic duplication CNVs, presenting them as a novel and very rare genetic mechanism in IFT81-related Jeune syndrome and MATN3-related MED.
Collapse
Affiliation(s)
- Maria Pettersson
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet and Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Raquel Vaz
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anna Hammarsjö
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet and Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Wolfgang Hofmeister
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet and Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Eva Horemuzova
- Department of Women's and Children's Health, Karolinska Institutet and Paediatric Endocrinology Unit, Karolinska University Hospital, Stockholm, Sweden
| | - Ulrika Voss
- Department of Pediatric Radiology, Karolinska University Hospital, Stockholm, Sweden
| | - Gen Nishimura
- Intractable Disease Center, Saitama University Hospital, Saitama, Japan
| | - Bo Klintberg
- Department of Pediatrics, Visby Hospital, Visby, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet and Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet and Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
| | - Giedre Grigelioniene
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet and Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet and Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
39
|
Wang B, Zhang Y, Dong H, Gong S, Wei B, Luo M, Wang H, Wu X, Liu W, Xu X, Zheng Y, Sun M. Loss of Tctn3 causes neuronal apoptosis and neural tube defects in mice. Cell Death Dis 2018; 9:520. [PMID: 29725084 PMCID: PMC5938703 DOI: 10.1038/s41419-018-0563-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 03/23/2018] [Accepted: 04/03/2018] [Indexed: 12/18/2022]
Abstract
Tctn3 belongs to the Tectonic (Tctn) family and is a single-pass membrane protein localized at the transition zone of primary cilia as an important component of ciliopathy-related protein complexes. Previous studies showed that mutations in Tctn1 and Tctn2, two members of the tectonic family, have been reported to disrupt neural tube development in humans and mice, but the functions of Tctn3 in brain development remain elusive. In this study, Tctn3 knockout (KO) mice were generated by utilizing the piggyBac (PB) transposon system. We found that Tctn3 KO mice exhibited abnormal global development, including prenatal lethality, microphthalmia, polysyndactyly, and abnormal head, sternum, and neural tube, whereas Tctn3 heterozygous KO mice did not show abnormal development or behaviors. Further, we found that the mRNA levels of Gli1 and Ptch1, downstream signaling components of the Shh pathway, were significantly reduced. Likewise, neural tube patterning-related proteins, such as Shh, Foxa2, and Nkx2.2, were altered in their distribution. Interestingly, Tctn3 KO led to significant changes in apoptosis-related proteins, including Bcl-2, Bax, and cleaved PARP1, resulting in reduced numbers of neuronal cells in embryonic brains. Tctn3 KO inhibited the PI3K/Akt signaling pathway but not the mTOR-dependent pathway. The small molecule SC79, a specific Akt activator, blocked apoptotic cell death in primary mouse embryonic fibroblasts from Tctn3 KO mice. Finally, NPHP1, a protein with anti-apoptotic ability, was found to form a complex with Tctn3, and its levels were decreased in Tctn3 KO mice. In conclusion, our results show that Tctn3 KO disrupts the Shh signaling pathway and neural tube patterning, resulting in abnormal embryonic development, cellular apoptosis, and prenatal death in mice.
Collapse
Affiliation(s)
- Bin Wang
- Institute for Fetology, the First Affiliated Hospital of Soochow University, Suzhou City, 215006, Jiangsu, China.,Institute of Neuroscience, Soochow University, Suzhou City, 215123, Jiangsu, China
| | - Yingying Zhang
- Institute for Fetology, the First Affiliated Hospital of Soochow University, Suzhou City, 215006, Jiangsu, China
| | - Hongli Dong
- Department of Neurology, Suzhou Hospital of Traditional Chinese Medicine, Suzhou City, 215123, Jiangsu, China
| | - Siyi Gong
- Institute for Fetology, the First Affiliated Hospital of Soochow University, Suzhou City, 215006, Jiangsu, China.,Institute of Neuroscience, Soochow University, Suzhou City, 215123, Jiangsu, China
| | - Bin Wei
- Institute for Fetology, the First Affiliated Hospital of Soochow University, Suzhou City, 215006, Jiangsu, China
| | - Man Luo
- Institute of Neuroscience, Soochow University, Suzhou City, 215123, Jiangsu, China
| | - Hongyan Wang
- Obstetrics and Gynecology Hospital Research Center, Institute of Reproduction and Development, Fudan University, Shanghai, 200433, China.,State Key Laboratory of Genetic Engineering, MOE Key Laboratory of Contemporary Anthropology, and Collaborative Innovation Center for Genetics & Development, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Xiaohui Wu
- State Key Laboratory of Genetic Engineering, MOE Key Laboratory of Contemporary Anthropology, and Collaborative Innovation Center for Genetics & Development, School of Life Sciences, Fudan University, Shanghai, 200438, China.,Institute of Developmental Biology & Molecular Medicine, Fudan University, Shanghai, 200433, China
| | - Wei Liu
- Department of Pathology, the First Affiliated Hospital of Soochow University, Suzhou City, 215006, Jiangsu, China
| | - Xingshun Xu
- Institute of Neuroscience, Soochow University, Suzhou City, 215123, Jiangsu, China.
| | - Yufang Zheng
- Obstetrics and Gynecology Hospital Research Center, Institute of Reproduction and Development, Fudan University, Shanghai, 200433, China. .,State Key Laboratory of Genetic Engineering, MOE Key Laboratory of Contemporary Anthropology, and Collaborative Innovation Center for Genetics & Development, School of Life Sciences, Fudan University, Shanghai, 200438, China. .,Institute of Developmental Biology & Molecular Medicine, Fudan University, Shanghai, 200433, China.
| | - Miao Sun
- Institute for Fetology, the First Affiliated Hospital of Soochow University, Suzhou City, 215006, Jiangsu, China.
| |
Collapse
|
40
|
Hofmeister W, Pettersson M, Kurtoglu D, Armenio M, Eisfeldt J, Papadogiannakis N, Gustavsson P, Lindstrand A. Targeted copy number screening highlights an intragenic deletion of WDR63 as the likely cause of human occipital encephalocele and abnormal CNS development in zebrafish. Hum Mutat 2018; 39:495-505. [PMID: 29285825 DOI: 10.1002/humu.23388] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/21/2017] [Accepted: 12/15/2017] [Indexed: 02/04/2023]
Abstract
Congenital malformations affecting the neural tube can present as isolated malformations or occur in association with other developmental abnormalities and syndromes. Using high-resolution copy number screening in 66 fetuses with neural tube defects, we identified six fetuses with likely pathogenic mutations, three aneuploidies (one trisomy 13 and two trisomy 18) and three deletions previously reported in NTDs (one 22q11.2 deletion and two 1p36 deletions) corresponding to 9% of the cohort. In addition, we identified five rare deletions and two duplications of uncertain significance including a rare intragenic heterozygous in-frame WDR63 deletion in a fetus with occipital encephalocele. Whole genome sequencing verified the deletion and excluded known pathogenic variants. The deletion spans exons 14-17 resulting in the expression of a protein missing the third and fourth WD-repeat domains. These findings were supported by CRISPR/Cas9-mediated somatic deletions in zebrafish. Injection of two different sgRNA-pairs targeting relevant intronic regions resulted in a deletion mimicking the human deletion and a concomitant increase of abnormal embryos with body and brain malformations (41%, n = 161 and 62%, n = 224, respectively), including a sac-like brain protrusion (7% and 9%, P < 0.01). Similar results were seen with overexpression of RNA encoding the deleted variant in zebrafish (total abnormal; 46%, n = 255, P < 0.001) compared with the overexpression of an equivalent amount of wild-type RNA (total abnormal; 3%, n = 177). We predict the in-frame WDR63 deletion to result in a dominant negative or gain-of-function form of WDR63. These are the first findings supporting a role for WDR63 in encephalocele formation.
Collapse
Affiliation(s)
- Wolfgang Hofmeister
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maria Pettersson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Deniz Kurtoglu
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Miriam Armenio
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
| | - Nikos Papadogiannakis
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Huddinge, Sweden
| | - Peter Gustavsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Centre of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
41
|
Harel T, Lupski JR. Genomic disorders 20 years on-mechanisms for clinical manifestations. Clin Genet 2017; 93:439-449. [PMID: 28950406 DOI: 10.1111/cge.13146] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 09/01/2017] [Accepted: 09/21/2017] [Indexed: 12/18/2022]
Abstract
Genomic disorders result from copy-number variants (CNVs) or submicroscopic rearrangements of the genome rather than from single nucleotide variants (SNVs). Diverse technologies, including array comparative genomic hybridization (aCGH) and single nucleotide polymorphism (SNP) microarrays, and more recently, whole genome sequencing and whole-exome sequencing, have enabled robust genome-wide unbiased detection of CNVs in affected individuals and in reportedly healthy controls. Sequencing of breakpoint junctions has allowed for elucidation of upstream mechanisms leading to genomic instability and resultant structural variation, whereas studies of the association between CNVs and specific diseases or susceptibility to morbid traits have enhanced our understanding of the downstream effects. In this review, we discuss the hallmarks of genomic disorders as they were defined during the first decade of the field, including genomic instability and the mechanism for rearrangement defined as nonallelic homologous recombination (NAHR); recurrent vs nonrecurrent rearrangements; and gene dosage sensitivity. Moreover, we highlight the exciting advances of the second decade of this field, including a deeper understanding of genomic instability and the mechanisms underlying complex rearrangements, mechanisms for constitutional and somatic chromosomal rearrangements, structural intra-species polymorphisms and susceptibility to NAHR, the role of CNVs in the context of genome-wide copy number and single nucleotide variation, and the contribution of noncoding CNVs to human disease.
Collapse
Affiliation(s)
- T Harel
- Department of Genetic and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - J R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Texas Children's Hospital, Houston, Texas.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| |
Collapse
|
42
|
Abeshi A, Fanelli F, Beccari T, Dundar M, D’Esposito F, Bertelli M. Genetic testing for Bardet-Biedl syndrome. THE EUROBIOTECH JOURNAL 2017. [DOI: 10.24190/issn2564-615x/2017/s1.04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract
We studied the scientific literature and disease guidelines in order to summarize the clinical utility of genetic testing for Bardet- Biedl syndrome (BBS). The disease has autosomal recessive inheritance, a prevalence varying from one in 13 500 to one in 160 000, and is caused by mutations in the ARL6, BBIP1, BBS1, BBS2, BBS4, BBS5, BBS7, BBS9, BBS10, BBS12, CEP290, IFT172, IFT27, LZTFL1, MKKS, MKS1, NPHP1, SDCCAG8, TRIM32, TTC8 and WDPCP genes. The clinical diagnosis of BBS is based on four primary features or three primary features plus two secondary features. The genetic test is useful for confirming diagnosis, and for differential diagnosis, couple risk assessment and access to clinical trials.
Collapse
Affiliation(s)
- Andi Abeshi
- MAGI Balkans, Tirana , Albania
- MAGI’S Lab, Rovereto , Italy
| | | | - Tommaso Beccari
- Department of Pharmaceutical Sciences, University of Perugia, Perugia , Italy
| | - Munis Dundar
- Department of Medical Genetics, Erciyes University Medical School, Kayseri , Turkey
| | - Fabiana D’Esposito
- MAGI Euregio, Bolzano , Italy
- Head and Neck Department, School of Medicine and Surgery, University of Naples “Federico II”, Corso Umberto I, 40, 80138 Napoli NA, Italy
- ICORG (Imperial College Ophthalmology Research Group), Western Eye Hospital, London , UK
| | | |
Collapse
|
43
|
Bujakowska KM, Liu Q, Pierce EA. Photoreceptor Cilia and Retinal Ciliopathies. Cold Spring Harb Perspect Biol 2017; 9:cshperspect.a028274. [PMID: 28289063 DOI: 10.1101/cshperspect.a028274] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Photoreceptors are sensory neurons designed to convert light stimuli into neurological responses. This process, called phototransduction, takes place in the outer segments (OS) of rod and cone photoreceptors. OS are specialized sensory cilia, with analogous structures to those present in other nonmotile cilia. Deficient morphogenesis and/or dysfunction of photoreceptor sensory cilia (PSC) caused by mutations in a variety of photoreceptor-specific and common cilia genes can lead to inherited retinal degenerations (IRDs). IRDs can manifest as isolated retinal diseases or syndromic diseases. In this review, we describe the structure and composition of PSC and different forms of ciliopathies with retinal involvement. We review the genetics of the IRDs, which are monogenic disorders but genetically diverse with regard to causality.
Collapse
Affiliation(s)
- Kinga M Bujakowska
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts 02114
| | - Qin Liu
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts 02114
| | - Eric A Pierce
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts 02114
| |
Collapse
|
44
|
Priya S, Nampoothiri S, Sen P, Sripriya S. Bardet-Biedl syndrome: Genetics, molecular pathophysiology, and disease management. Indian J Ophthalmol 2017; 64:620-627. [PMID: 27853007 PMCID: PMC5151149 DOI: 10.4103/0301-4738.194328] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Primary cilia play a key role in sensory perception and various signaling pathways. Any defect in them leads to group of disorders called ciliopathies, and Bardet–Biedl syndrome (BBS, OMIM 209900) is one among them. The disorder is clinically and genetically heterogeneous, with various primary and secondary clinical manifestations, and shows autosomal recessive inheritance and highly prevalent in inbred/consanguineous populations. The disease mapped to at least twenty different genes (BBS1-BBS20), follow oligogenic inheritance pattern. BBS proteins localizes to the centerosome and regulates the biogenesis and functions of the cilia. In BBS, the functioning of various systemic organs (with ciliated cells) gets deranged and results in systemic manifestations. Certain components of the disease (such as obesity, diabetes, and renal problems) when noticed earlier offer a disease management benefit to the patients. However, the awareness of the disease is comparatively low and most often noticed only after severe vision loss in patients, which is usually in the first decade of the patient's age. In the current review, we have provided the recent updates retrieved from various types of scientific literature through journals, on the genetics, its molecular relevance, and the clinical outcome in BBS. The review in nutshell would provide the basic awareness of the disease that will have an impact in disease management and counseling benefits to the patients and their families.
Collapse
Affiliation(s)
- Sathya Priya
- SNONGC Department of Genetics and Molecular Biology, Kamal Nayan Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, Tamil Nadu; School of Chemical and Biotechnology, SASTRA University, Thanjavur, Tamil Nadu, India
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences and Research Center, Cochin, Kerala, India
| | - Parveen Sen
- Department of Vitreoretina Clinic, Medical Research Foundation, Chennai, Tamil Nadu, India
| | - S Sripriya
- SNONGC Department of Genetics and Molecular Biology, Kamal Nayan Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, Tamil Nadu, India
| |
Collapse
|
45
|
Genetic characterization and disease mechanism of retinitis pigmentosa; current scenario. 3 Biotech 2017; 7:251. [PMID: 28721681 DOI: 10.1007/s13205-017-0878-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 07/10/2017] [Indexed: 12/21/2022] Open
Abstract
Retinitis pigmentosa is a group of genetically transmitted disorders affecting 1 in 3000-8000 individual people worldwide ultimately affecting the quality of life. Retinitis pigmentosa is characterized as a heterogeneous genetic disorder which leads by progressive devolution of the retina leading to a progressive visual loss. It can occur in syndromic (with Usher syndrome and Bardet-Biedl syndrome) as well as non-syndromic nature. The mode of inheritance can be X-linked, autosomal dominant or autosomal recessive manner. To date 58 genes have been reported to associate with retinitis pigmentosa most of them are either expressed in photoreceptors or the retinal pigment epithelium. This review focuses on the disease mechanisms and genetics of retinitis pigmentosa. As retinitis pigmentosa is tremendously heterogeneous disorder expressing a multiplicity of mutations; different variations in the same gene might induce different disorders. In recent years, latest technologies including whole-exome sequencing contributing effectively to uncover the hidden genesis of retinitis pigmentosa by reporting new genetic mutations. In future, these advancements will help in better understanding the genotype-phenotype correlations of disease and likely to develop new therapies.
Collapse
|
46
|
Pettersson M, Viljakainen H, Loid P, Mustila T, Pekkinen M, Armenio M, Andersson-Assarsson JC, Mäkitie O, Lindstrand A. Copy Number Variants Are Enriched in Individuals With Early-Onset Obesity and Highlight Novel Pathogenic Pathways. J Clin Endocrinol Metab 2017; 102:3029-3039. [PMID: 28605459 DOI: 10.1210/jc.2017-00565] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 06/07/2017] [Indexed: 01/22/2023]
Abstract
CONTEXT Only a few genetic causes for childhood obesity have been identified to date. Copy number variants (CNVs) are known to contribute to obesity, both syndromic (15q11.2 deletions, Prader-Willi syndrome) and nonsyndromic (16p11.2 deletions) obesity. OBJECTIVE To study the contribution of CNVs to early-onset obesity and evaluate the expression of candidate genes in subcutaneous adipose tissue. DESIGN AND SETTING A case-control study in a tertiary academic center. PARTICIPANTS CNV analysis was performed on 90 subjects with early-onset obesity and 67 normal-weight controls. Subcutaneous adipose tissue from body mass index-discordant siblings was used for the gene expression analyses. MAIN OUTCOME MEASURES We used custom high-density array comparative genomic hybridization with exon resolution in 1989 genes, including all known obesity loci. The expression of candidate genes was assessed using microarray analysis of messenger RNA from subcutaneous adipose tissue. RESULTS We identified rare CNVs in 17 subjects (19%) with obesity and 2 controls (3%). In three cases (3%), the identified variant involved a known syndromic lesion (22q11.21 duplication, 1q21.1 deletion, and 16p11.2 deletion, respectively), although the others were not known. Seven CNVs in 10 families were inherited and segregated with obesity. Expression analysis of 37 candidate genes showed discordant expression for 10 genes (PCM1, EFEMP1, MAMLD1, ACP6, BAZ2B, SORBS1, KLF15, MACROD2, ATR, and MBD5). CONCLUSIONS Rare CNVs contribute possibly pathogenic alleles to a substantial fraction of children with early-onset obesity. The involved genes might provide insights into pathogenic mechanisms and involved cellular pathways. These findings highlight the importance of CNV screening in children with early-onset obesity.
Collapse
MESH Headings
- Abnormalities, Multiple/genetics
- Acid Phosphatase/genetics
- Adolescent
- Adult
- Ataxia Telangiectasia Mutated Proteins/genetics
- Autistic Disorder/genetics
- Autoantigens/genetics
- Case-Control Studies
- Cell Cycle Proteins/genetics
- Child
- Child, Preschool
- Chromosome Deletion
- Chromosome Disorders/genetics
- Chromosome Duplication/genetics
- Chromosomes, Human, Pair 1/genetics
- Chromosomes, Human, Pair 16/genetics
- Chromosomes, Human, Pair 22/genetics
- Comparative Genomic Hybridization
- DNA Copy Number Variations
- DNA Repair Enzymes/genetics
- DNA-Binding Proteins/genetics
- DiGeorge Syndrome/genetics
- Extracellular Matrix Proteins/genetics
- Female
- Humans
- Hydrolases/genetics
- Intellectual Disability/genetics
- Kruppel-Like Transcription Factors/genetics
- Male
- Megalencephaly/genetics
- Microfilament Proteins/genetics
- Nuclear Proteins/genetics
- Pediatric Obesity/genetics
- Proteins/genetics
- RNA, Messenger/metabolism
- Siblings
- Subcutaneous Fat/metabolism
- Transcription Factors/genetics
- Transcription Factors, General
- Transcriptome
- Young Adult
Collapse
Affiliation(s)
- Maria Pettersson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm 171 77, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Heli Viljakainen
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki FI-00029, Finland
| | - Petra Loid
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki FI-00029, Finland
| | - Taina Mustila
- Department of Pediatrics, Seinäjoki Central Hospital, Seinäjoki FI-60100, Finland
| | - Minna Pekkinen
- Folkhälsan Institute of Genetics, Helsinki FI-00290, Finland
| | - Miriam Armenio
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm 171 77, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Johanna C Andersson-Assarsson
- Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg 413 90, Sweden
| | - Outi Mäkitie
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm 171 77, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki FI-00029, Finland
- Folkhälsan Institute of Genetics, Helsinki FI-00290, Finland
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm 171 77, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm 171 77, Sweden
| |
Collapse
|
47
|
Jávorszky E, Morinière V, Kerti A, Balogh E, Pikó H, Saunier S, Karcagi V, Antignac C, Tory K. QMPSF is sensitive and specific in the detection of NPHP1 heterozygous deletions. ACTA ACUST UNITED AC 2017; 55:809-816. [DOI: 10.1515/cclm-2016-0819] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/08/2016] [Indexed: 11/15/2022]
Abstract
Abstract
Background:
Nephronophthisis, an autosomal recessive nephropathy, is responsible for 10% of childhood chronic renal failure. The deletion of its major gene, NPHP1, with a minor allele frequency of 0.24% in the general population, is the most common mutation leading to a monogenic form of childhood chronic renal failure. It is challenging to detect it in the heterozygous state. We aimed to evaluate the sensitivity and the specificity of the quantitative multiplex PCR of short fluorescent fragments (QMPSF) in its detection.
Methods:
After setting up the protocol of QMPSF, we validated it on 39 individuals diagnosed by multiplex ligation-dependent probe amplification (MLPA) with normal NPHP1 copy number (n=17), with heterozygous deletion (n=13, seven parents and six patients), or with homozygous deletion (n=9). To assess the rate of the deletions that arise from independent events, deleted alleles were haplotyped.
Results:
The results of QMPSF and MLPA correlated perfectly in the identification of 76 heterozygously deleted and 56 homozygously deleted exons. The inter-experimental variability of the dosage quotient obtained by QMPSF was low: control, 1.05 (median; range, 0.86−1.33, n = 102 exons); heterozygous deletion, 0.51 (0.42−0.67, n = 76 exons); homozygous deletion, 0 (0−0, n = 56 exons). All patients harboring a heterozygous deletion were found to carry a hemizygous mutation. At least 15 out of 18 deletions appeared on different haplotypes and one deletion appeared de novo.
Conclusions:
The cost- and time-effective QMPSF has a 100% sensitivity and specificity in the detection of NPHP1 deletion. The potential de novo appearance of NPHP1 deletions makes its segregation analysis highly recommended in clinical practice.
Collapse
|
48
|
Bujakowska KM, Fernandez-Godino R, Place E, Consugar M, Navarro-Gomez D, White J, Bedoukian EC, Zhu X, Xie HM, Gai X, Leroy BP, Pierce EA. Copy-number variation is an important contributor to the genetic causality of inherited retinal degenerations. Genet Med 2017; 19:643-651. [PMID: 27735924 PMCID: PMC6377944 DOI: 10.1038/gim.2016.158] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 08/30/2016] [Indexed: 11/10/2022] Open
Abstract
PURPOSE Despite substantial progress in sequencing, current strategies can genetically solve only approximately 55-60% of inherited retinal degeneration (IRD) cases. This can be partially attributed to elusive mutations in the known IRD genes, which are not easily identified by the targeted next-generation sequencing (NGS) or Sanger sequencing approaches. We hypothesized that copy-number variations (CNVs) are a major contributor to the elusive genetic causality of IRDs. METHODS Twenty-eight cases previously unsolved with a targeted NGS were investigated with whole-genome single-nucleotide polymorphism (SNP) and comparative genomic hybridization (CGH) arrays. RESULTS Deletions in the IRD genes were detected in 5 of 28 families, including a de novo deletion. We suggest that the de novo deletion occurred through nonallelic homologous recombination (NAHR) and we constructed a genomic map of NAHR-prone regions with overlapping IRD genes. In this article, we also report an unusual case of recessive retinitis pigmentosa due to compound heterozygous mutations in SNRNP200, a gene that is typically associated with the dominant form of this disease. CONCLUSIONS CNV mapping substantially increased the genetic diagnostic rate of IRDs, detecting genetic causality in 18% of previously unsolved cases. Extending the search to other structural variations will probably demonstrate an even higher contribution to genetic causality of IRDs.Genet Med advance online publication 13 October 2016.
Collapse
Affiliation(s)
- Kinga M Bujakowska
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
| | - Rosario Fernandez-Godino
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
| | - Emily Place
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
| | - Mark Consugar
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel Navarro-Gomez
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
| | - Joseph White
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
| | - Emma C Bedoukian
- Ophthalmic Genetics &Visual Electrophysiology, Division of Ophthalmology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Xiaosong Zhu
- Ophthalmic Genetics &Visual Electrophysiology, Division of Ophthalmology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Hongbo M Xie
- Department of BioMedical Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Xiaowu Gai
- Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Bart P Leroy
- Ophthalmic Genetics &Visual Electrophysiology, Division of Ophthalmology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Ophthalmology &Center for Medical Genetics, Ghent University Hospital &Ghent University, Ghent, Belgium
| | - Eric A Pierce
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
49
|
Mitchison HM, Valente EM. Motile and non-motile cilia in human pathology: from function to phenotypes. J Pathol 2017; 241:294-309. [PMID: 27859258 DOI: 10.1002/path.4843] [Citation(s) in RCA: 292] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 11/03/2016] [Accepted: 11/04/2016] [Indexed: 12/13/2022]
Abstract
Ciliopathies are inherited human disorders caused by both motile and non-motile cilia dysfunction that form an important and rapidly expanding disease category. Ciliopathies are complex conditions to diagnose, being multisystem disorders characterized by extensive genetic heterogeneity and clinical variability with high levels of lethality. There is marked phenotypic overlap among distinct ciliopathy syndromes that presents a major challenge for their recognition, diagnosis, and clinical management, in addition to posing an on-going task to develop the most appropriate family counselling. The impact of next-generation sequencing and high-throughput technologies in the last decade has significantly improved our understanding of the biological basis of ciliopathy disorders, enhancing our ability to determine the possible reasons for the extensive overlap in their symptoms and genetic aetiologies. Here, we review the diverse functions of cilia in human health and disease and discuss a growing shift away from the classical clinical definitions of ciliopathy syndromes to a more functional categorization. This approach arises from our improved understanding of this unique organelle, revealed through new genetic and cell biological insights into the discrete functioning of subcompartments of the cilium (basal body, transition zone, intraflagellar transport, motility). Mutations affecting these distinct ciliary protein modules can confer different genetic diseases and new clinical classifications are possible to define, according to the nature and extent of organ involvement. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Hannah M Mitchison
- Genetics and Genomic Medicine Programme, University College London, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London, WC1N 1EH, UK
| | - Enza Maria Valente
- Department of Medicine and Surgery, University of Salerno, Salerno, Italy.,Neurogenetics Unit, IRCCS Santa Lucia Foundation, Via del Fosso di Fiorano, 00143, Rome, Italy
| |
Collapse
|
50
|
Eisfeldt J, Vezzi F, Olason P, Nilsson D, Lindstrand A. TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data. F1000Res 2017; 6:664. [PMID: 28781756 DOI: 10.12688/f1000research.11168.1] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/05/2017] [Indexed: 01/07/2023] Open
Abstract
Reliable detection of large structural variation ( > 1000 bp) is important in both rare and common genetic disorders. Whole genome sequencing (WGS) is a technology that may be used to identify a large proportion of the genomic structural variants (SVs) in an individual in a single experiment. Even though SV callers have been extensively used in research to detect mutations, the potential usage of SV callers within routine clinical diagnostics is still limited. One well known, but not well-addressed problem is the large number of benign variants and reference errors present in the human genome that further complicates analysis. Even though there is a wide range of SV-callers available, the number of callers that allow detection of the entire spectra of SV at a low computational cost is still relatively limited.
Collapse
Affiliation(s)
- Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet Science Park, 171 21 Solna, Sweden
| | - Francesco Vezzi
- Science for Life Laboratory, Karolinska Institutet Science Park, 171 21 Solna, Sweden.,Department of Biochemistry and Biophysics, Stockholm University, 171 21 Stockholm, Sweden
| | - Pall Olason
- Science for Life Laboratory, Dept of Cell and Molecular Biology, Uppsala University, Husargatan 3, Uppsala, SE-752 37, Sweden
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet Science Park, 171 21 Solna, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| |
Collapse
|