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Fernández-Suárez E, González-Del Pozo M, Méndez-Vidal C, Martín-Sánchez M, Mena M, de la Morena-Barrio B, Corral J, Borrego S, Antiñolo G. Long-read sequencing improves the genetic diagnosis of retinitis pigmentosa by identifying an Alu retrotransposon insertion in the EYS gene. Mob DNA 2024; 15:9. [PMID: 38704576 PMCID: PMC11069205 DOI: 10.1186/s13100-024-00320-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Biallelic variants in EYS are the major cause of autosomal recessive retinitis pigmentosa (arRP) in certain populations, a clinically and genetically heterogeneous disease that may lead to legal blindness. EYS is one of the largest genes (~ 2 Mb) expressed in the retina, in which structural variants (SVs) represent a common cause of disease. However, their identification using short-read sequencing (SRS) is not always feasible. Here, we conducted targeted long-read sequencing (T-LRS) using adaptive sampling of EYS on the MinION sequencing platform (Oxford Nanopore Technologies) to definitively diagnose an arRP family, whose affected individuals (n = 3) carried the heterozygous pathogenic deletion of exons 32-33 in the EYS gene. As this was a recurrent variant identified in three additional families in our cohort, we also aimed to characterize the known deletion at the nucleotide level to assess a possible founder effect. RESULTS T-LRS in family A unveiled a heterozygous AluYa5 insertion in the coding exon 43 of EYS (chr6(GRCh37):g.64430524_64430525ins352), which segregated with the disease in compound heterozygosity with the previously identified deletion. Visual inspection of previous SRS alignments using IGV revealed several reads containing soft-clipped bases, accompanied by a slight drop in coverage at the Alu insertion site. This prompted us to develop a simplified program using grep command to investigate the recurrence of this variant in our cohort from SRS data. Moreover, LRS also allowed the characterization of the CNV as a ~ 56.4kb deletion spanning exons 32-33 of EYS (chr6(GRCh37):g.64764235_64820592del). The results of further characterization by Sanger sequencing and linkage analysis in the four families were consistent with a founder variant. CONCLUSIONS To our knowledge, this is the first report of a mobile element insertion into the coding sequence of EYS, as a likely cause of arRP in a family. Our study highlights the value of LRS technology in characterizing and identifying hidden pathogenic SVs, such as retrotransposon insertions, whose contribution to the etiopathogenesis of rare diseases may be underestimated.
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Affiliation(s)
- Elena Fernández-Suárez
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC, University of Seville, Seville, Spain
- Center for Biomedical Network Research On Rare Diseases (CIBERER), Seville, Spain
| | - María González-Del Pozo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC, University of Seville, Seville, Spain
- Center for Biomedical Network Research On Rare Diseases (CIBERER), Seville, Spain
| | - Cristina Méndez-Vidal
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC, University of Seville, Seville, Spain
- Center for Biomedical Network Research On Rare Diseases (CIBERER), Seville, Spain
| | - Marta Martín-Sánchez
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC, University of Seville, Seville, Spain
- Center for Biomedical Network Research On Rare Diseases (CIBERER), Seville, Spain
| | - Marcela Mena
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC, University of Seville, Seville, Spain
- Center for Biomedical Network Research On Rare Diseases (CIBERER), Seville, Spain
| | - Belén de la Morena-Barrio
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, Murcia, Spain
| | - Javier Corral
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Pascual Parrilla, CIBERER-ISCIII, Murcia, Spain
| | - Salud Borrego
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC, University of Seville, Seville, Spain.
- Center for Biomedical Network Research On Rare Diseases (CIBERER), Seville, Spain.
| | - Guillermo Antiñolo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío/CSIC, University of Seville, Seville, Spain.
- Center for Biomedical Network Research On Rare Diseases (CIBERER), Seville, Spain.
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2
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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.
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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
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3
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Karam A, Delvallée C, Estrada-Cuzcano A, Geoffroy V, Lamouche JB, Leuvrey AS, Nourisson E, Tarabeux J, Stoetzel C, Scheidecker S, Porter LF, Génin E, Redon R, Sandron F, Boland A, Deleuze JF, Le May N, Dollfus H, Muller J. WGS Revealed Novel BBS5 Pathogenic Variants, Missed by WES, Causing Ciliary Structure and Function Defects. Int J Mol Sci 2023; 24:8729. [PMID: 37240074 PMCID: PMC10218572 DOI: 10.3390/ijms24108729] [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: 03/31/2023] [Revised: 04/18/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Bardet-Biedl syndrome (BBS) is an autosomal recessive ciliopathy that affects multiple organs, leading to retinitis pigmentosa, polydactyly, obesity, renal anomalies, cognitive impairment, and hypogonadism. Until now, biallelic pathogenic variants have been identified in at least 24 genes delineating the genetic heterogeneity of BBS. Among those, BBS5 is a minor contributor to the mutation load and is one of the eight subunits forming the BBSome, a protein complex implied in protein trafficking within the cilia. This study reports on a European BBS5 patient with a severe BBS phenotype. Genetic analysis was performed using multiple next-generation sequencing (NGS) tests (targeted exome, TES and whole exome, WES), and biallelic pathogenic variants could only be identified using whole-genome sequencing (WGS), including a previously missed large deletion of the first exons. Despite the absence of family samples, the biallelic status of the variants was confirmed. The BBS5 protein's impact was confirmed on the patient's cells (presence/absence and size of the cilium) and ciliary function (Sonic Hedgehog pathway). This study highlights the importance of WGS and the challenge of reliable structural variant detection in patients' genetic explorations as well as functional tests to assess a variant's pathogenicity.
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Affiliation(s)
- Adella Karam
- Laboratoire de Génétique Médicale, UMR_S INSERM U1112, Institut de Génétique Médicale d’Alsace (IGMA), Faculté de Médecine FMTS, Université de Strasbourg, 67000 Strasbourg, France
| | - Clarisse Delvallée
- Laboratoire de Génétique Médicale, UMR_S INSERM U1112, Institut de Génétique Médicale d’Alsace (IGMA), Faculté de Médecine FMTS, Université de Strasbourg, 67000 Strasbourg, France
| | - Alejandro Estrada-Cuzcano
- Laboratoire de Génétique Médicale, UMR_S INSERM U1112, Institut de Génétique Médicale d’Alsace (IGMA), Faculté de Médecine FMTS, Université de Strasbourg, 67000 Strasbourg, France
| | - Véronique Geoffroy
- Laboratoire de Génétique Médicale, UMR_S INSERM U1112, Institut de Génétique Médicale d’Alsace (IGMA), Faculté de Médecine FMTS, Université de Strasbourg, 67000 Strasbourg, France
| | - Jean-Baptiste Lamouche
- Laboratoire de Génétique Médicale, UMR_S INSERM U1112, Institut de Génétique Médicale d’Alsace (IGMA), Faculté de Médecine FMTS, Université de Strasbourg, 67000 Strasbourg, France
| | - Anne-Sophie Leuvrey
- Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France (E.N.)
| | - Elsa Nourisson
- Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France (E.N.)
| | - Julien Tarabeux
- Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France (E.N.)
| | - Corinne Stoetzel
- Laboratoire de Génétique Médicale, UMR_S INSERM U1112, Institut de Génétique Médicale d’Alsace (IGMA), Faculté de Médecine FMTS, Université de Strasbourg, 67000 Strasbourg, France
| | - Sophie Scheidecker
- Laboratoire de Génétique Médicale, UMR_S INSERM U1112, Institut de Génétique Médicale d’Alsace (IGMA), Faculté de Médecine FMTS, Université de Strasbourg, 67000 Strasbourg, France
- Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France (E.N.)
| | - Louise Frances Porter
- Laboratoire de Génétique Médicale, UMR_S INSERM U1112, Institut de Génétique Médicale d’Alsace (IGMA), Faculté de Médecine FMTS, Université de Strasbourg, 67000 Strasbourg, France
- Centre de Référence Pour les Affections Rares en Génétique Ophtalmologique (CARGO), Institut de Génétique Médicale d’Alsace (IGMA), Filière SENSGENE, Hôpitaux Universitaires de Strasbourg, 67091 Strasbourg, France
| | - Emmanuelle Génin
- Inserm, Université de Brest, EFS, UMR 1078, GGB, F-29200 Brest, France
| | - Richard Redon
- CHU Nantes, CNRS, INSERM, L’institut du Thorax, Nantes Université, 44000 Nantes, France
| | - Florian Sandron
- CEA, Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, 91057 Evry, France
| | - Anne Boland
- CEA, Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, 91057 Evry, France
| | - Jean-François Deleuze
- CEA, Centre National de Recherche en Génomique Humaine, Université Paris-Saclay, 91057 Evry, France
| | - Nicolas Le May
- Laboratoire de Génétique Médicale, UMR_S INSERM U1112, Institut de Génétique Médicale d’Alsace (IGMA), Faculté de Médecine FMTS, Université de Strasbourg, 67000 Strasbourg, France
| | - Hélène Dollfus
- Laboratoire de Génétique Médicale, UMR_S INSERM U1112, Institut de Génétique Médicale d’Alsace (IGMA), Faculté de Médecine FMTS, Université de Strasbourg, 67000 Strasbourg, France
- Centre de Référence Pour les Affections Rares en Génétique Ophtalmologique (CARGO), Institut de Génétique Médicale d’Alsace (IGMA), Filière SENSGENE, Hôpitaux Universitaires de Strasbourg, 67091 Strasbourg, France
- Service de Génétique Médicale, Institut de Génétique Médicale d’Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France
| | - Jean Muller
- Laboratoire de Génétique Médicale, UMR_S INSERM U1112, Institut de Génétique Médicale d’Alsace (IGMA), Faculté de Médecine FMTS, Université de Strasbourg, 67000 Strasbourg, France
- Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France (E.N.)
- Unité Fonctionnelle de Bioinformatique Médicale Appliquée au Diagnostic (UF7363), Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France
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4
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Delvallée C, Dollfus H. Retinal Degeneration Animal Models in Bardet-Biedl Syndrome and Related Ciliopathies. Cold Spring Harb Perspect Med 2023; 13:13/1/a041303. [PMID: 36596648 PMCID: PMC9808547 DOI: 10.1101/cshperspect.a041303] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Retinal degeneration due to photoreceptor ciliary-related proteins dysfunction accounts for more than 25% of all inherited retinal dystrophies. The cilium, being an evolutionarily conserved and ubiquitous organelle implied in many cellular functions, can be investigated by way of many models from invertebrate models to nonhuman primates, all these models have massively contributed to the pathogenesis understanding of human ciliopathies. Taking the Bardet-Biedl syndrome (BBS) as an emblematic example as well as other related syndromic ciliopathies, the contribution of a wide range of models has enabled to characterize the role of the BBS proteins in the archetypical cilium but also at the level of the connecting cilium of the photoreceptors. There are more than 24 BBS genes encoding for proteins that form different complexes such as the BBSome and the chaperone proteins complex. But how they lead to retinal degeneration remains a matter of debate with the possible accumulation of proteins in the inner segment and/or accumulation of unwanted proteins in the outer segment that cannot return in the inner segment machinery. Many BBS proteins (but not the chaperonins for instance) can be modeled in primitive organisms such as Paramecium, Chlamydomonas reinardtii, Trypanosoma brucei, and Caenorhabditis elegans These models have enabled clarifying the role of a subset of BBS proteins in the primary cilium as well as their relations with other modules such as the intraflagellar transport (IFT) module, the nephronophthisis (NPHP) module, or the Meckel-Gruber syndrome (MKS)/Joubert syndrome (JBTS) module mostly involved with the transition zone of the primary cilia. Assessing the role of the primary cilia structure of the connecting cilium of the photoreceptor cells has been very much studied by way of zebrafish modeling (Danio rerio) as well as by a plethora of mouse models. More recently, large animal models have been described for three BBS genes and one nonhuman primate model in rhesus macaque for BBS7 In completion to animal models, human cell models can now be used notably thanks to gene editing and the use of induced pluripotent stem cells (iPSCs). All these models are not only important for pathogenesis understanding but also very useful for studying therapeutic avenues, their pros and cons, especially for gene replacement therapy as well as pharmacological triggers.
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Affiliation(s)
- Clarisse Delvallée
- Laboratoire de Génétique Médicale UMRS1112, Centre de Recherche Biomédicale de Strasbourg, CRBS, Institut de Génétique Médicale d'Alsace, IGMA, Strasbourg 67000, France
| | - Hélène Dollfus
- Laboratoire de Génétique Médicale UMRS1112, Centre de Recherche Biomédicale de Strasbourg, CRBS, Institut de Génétique Médicale d'Alsace, IGMA, Strasbourg 67000, France
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5
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Vezain M, Thauvin-Robinet C, Vial Y, Coutant S, Drunat S, Urtizberea JA, Rolland A, Jacquin-Piques A, Fehrenbach S, Nicolas G, Lecoquierre F, Saugier-Veber P. Retrotransposon insertion as a novel mutational cause of spinal muscular atrophy. Hum Genet 2023; 142:125-138. [PMID: 36138164 DOI: 10.1007/s00439-022-02473-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/15/2022] [Indexed: 01/18/2023]
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder resulting from biallelic alterations of the SMN1 gene: deletion, gene conversion or, in rare cases, intragenic variants. The disease severity is mainly influenced by the copy number of SMN2, a nearly identical gene, which produces only low amounts of full-length (FL) mRNA. Here we describe the first example of retrotransposon insertion as a pathogenic SMN1 mutational event. The 50-year-old patient is clinically affected by SMA type III with a diagnostic odyssey spanning nearly 30 years. Despite a mild disease course, he carries a single SMN2 copy. Using Exome Sequencing and Sanger sequencing, we characterized a SINE-VNTR-Alu (SVA) type F retrotransposon inserted in SMN1 intron 7. Using RT-PCR and RNASeq experiments on lymphoblastoid cell lines, we documented the dramatic decrease of FL transcript production in the patient compared to subjects with the same SMN1 and SMN2 copy number, thus validating the pathogenicity of this SVA insertion. We described the mutant FL-SMN1-SVA transcript characterized by exon extension and showed that it is subject to degradation by nonsense-mediated mRNA decay. The stability of the SMN-SVA protein may explain the mild course of the disease. This observation exemplifies the role of retrotransposons in human genetic disorders.
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Affiliation(s)
- Myriam Vezain
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - Christel Thauvin-Robinet
- INSERM UMR1231 GAD-Génétique des Anomalies du Développement, Bourgogne Franche-Comté University, F-21000 , Dijon, France.,Genetics Center, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Dijon-Burgundy University Hospital, F-21000, Dijon, France
| | - Yoann Vial
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France.,Genetics Department, AP-HP, Robert-Debré University Hospital, 48 boulevard Sérurier, 75019 , Paris, France
| | - Sophie Coutant
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - Séverine Drunat
- INSERM UMR 1141, PROTECT, Paris University, F-75019, Paris, France.,Genetics Department, AP-HP, Robert-Debré University Hospital, F-75019, Paris, France
| | - Jon Andoni Urtizberea
- Myology Institute, AP-HP Pitié-Salpêtrière University Hospital, F-75013, Paris, France
| | - Anne Rolland
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Pediatrics Department, Valence Hospital, 179 boulevard du Maréchal Juin, 26000, Valence, France
| | - Agnès Jacquin-Piques
- Department of Neurology, Clinical Neurophysiology, Competence Center of Neuromuscular Diseases, Dijon-Burgundy University Hospital, F-21000, Dijon, France
| | - Séverine Fehrenbach
- Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - Gaël Nicolas
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - François Lecoquierre
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - Pascale Saugier-Veber
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France. .,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France. .,Laboratoire de Génétique Moléculaire, UFR-Santé, 22 boulevard Gambetta, 76183, Rouen, France.
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6
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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.
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7
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Kõks S, Pfaff AL, Singleton LM, Bubb VJ, Quinn JP. Non-reference genome transposable elements (TEs) have a significant impact on the progression of the Parkinson's disease. Exp Biol Med (Maywood) 2022; 247:1680-1690. [PMID: 36000172 PMCID: PMC9597212 DOI: 10.1177/15353702221117147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The pathophysiology of Parkinson's disease (PD) is a complex process of the interaction between genetic and environmental factors. Studies on the genetic component of PD have predominantly focused on single nucleotide polymorphisms (SNPs) using a cross-sectional case-control design in large genome-wide association studies. This approach while giving insight into a significant portion of the genetics of PD does not fully account for all the genetic components resulting in missing heritability. In this study, we approached this problem by focusing on the non-reference genome transposable elements (TEs) and their impact on the progression of PD using a longitudinal study design within the Parkinson's progression markers initiative (PPMI) cohort. We analyzed 2886 Alu repeats, 360 LINE1 and 128 SINE-VNTR-Alus (SVAs) that were called from the whole-genome sequence data which are not within the reference genome. The presence or absence of these non-reference TE variants is known as a retrotransposon insertion polymorphism, and measuring this polymorphism describes the impact of TEs on the traits. The variations for the presence or absence of the non-reference TE elements were modeled to align with the changes in the 114 outcome measures during the five-year follow-up period of the PPMI cohort. Linear mixed-effects models were used, and many TEs were found to have a highly significant effect on the longitudinal changes in the clinically important PD outcomes such as UPDRS subscale II, UPDRS total scores, and modified Schwab and England ADL scale. In addition, the progression of several imaging and functional measures, including the Caudate/Putamen ratio and levodopa equivalent daily dose (LEDD) were also significantly affected by the TEs. In conclusion, this study identified the overwhelming effect of the non-reference TEs on the progression of PD and is a good example of the impact the variations in the "junk DNA" have on complex diseases.
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Affiliation(s)
- Sulev Kõks
- Perron Institute for Neurological and
Translational Science, Perth, WA 6009, Australia,Centre for Molecular Medicine and
Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia,Sulev Kõks.
| | - Abigail L Pfaff
- Perron Institute for Neurological and
Translational Science, Perth, WA 6009, Australia,Centre for Molecular Medicine and
Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - Lewis M Singleton
- Perron Institute for Neurological and
Translational Science, Perth, WA 6009, Australia
| | - Vivien J Bubb
- Department of Pharmacology and
Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of
Liverpool, Liverpool L69 3BX, UK
| | - John P Quinn
- Department of Pharmacology and
Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of
Liverpool, Liverpool L69 3BX, UK
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8
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Pfaff AL, Singleton LM, Kõks S. Mechanisms of disease-associated SINE-VNTR-Alus. Exp Biol Med (Maywood) 2022; 247:756-764. [PMID: 35387528 DOI: 10.1177/15353702221082612] [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: 01/02/2023] Open
Abstract
SINE-VNTR-Alus (SVAs) are the youngest retrotransposon family in the human genome. Their ongoing mobilization has generated genetic variation within the human population. At least 24 insertions to date, detailed in this review, have been associated with disease. The predominant mechanisms through which this occurs are alterations to normal splicing patterns, exonic insertions causing loss-of-function mutations, and large genomic deletions. Dissecting the functional impact of these SVAs and the mechanism through which they cause disease provides insight into the consequences of their presence in the genome and how these elements could influence phenotypes. Many of these disease-associated SVAs have been difficult to characterize and would not have been identified through routine analyses. However, the number identified has increased in recent years as DNA and RNA sequencing data became more widely available. Therefore, as the search for complex structural variation in disease continues, it is likely to yield further disease-causing SVA insertions.
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Affiliation(s)
- Abigail L Pfaff
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - Lewis M Singleton
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia
| | - Sulev Kõks
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
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9
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Primary Cilia and Their Role in Acquired Heart Disease. Cells 2022; 11:cells11060960. [PMID: 35326411 PMCID: PMC8946116 DOI: 10.3390/cells11060960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 12/10/2022] Open
Abstract
Primary cilia are non-motile plasma membrane extrusions that display a variety of receptors and mechanosensors. Loss of function results in ciliopathies, which have been strongly linked with congenital heart disease, as well as abnormal development and function of most organ systems. Adults with congenital heart disease have high rates of acquired heart failure, and usually die from a cardiac cause. Here we explore primary cilia’s role in acquired heart disease. Intraflagellar Transport 88 knockout results in reduced primary cilia, and knockout from cardiac endothelium produces myxomatous degeneration similar to mitral valve prolapse seen in adult humans. Induced primary cilia inactivation by other mechanisms also produces excess myocardial hypertrophy and altered scar architecture after ischemic injury, as well as hypertension due to a lack of vascular endothelial nitric oxide synthase activation and the resultant left ventricular dysfunction. Finally, primary cilia have cell-to-cell transmission capacity which, when blocked, leads to progressive left ventricular hypertrophy and heart failure, though this mechanism has not been fully established. Further research is still needed to understand primary cilia’s role in adult cardiac pathology, especially heart failure.
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10
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Fröhlich A, Pfaff AL, Bubb VJ, Koks S, Quinn JP. Characterisation of the Function of a SINE-VNTR-Alu Retrotransposon to Modulate Isoform Expression at the MAPT Locus. Front Mol Neurosci 2022; 15:815695. [PMID: 35370538 PMCID: PMC8965460 DOI: 10.3389/fnmol.2022.815695] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/10/2022] [Indexed: 11/30/2022] Open
Abstract
SINE-VNTR-Alu retrotransposons represent one class of transposable elements which contribute to the regulation and evolution of the primate genome and have the potential to be involved in genetic instability and disease progression. However, these polymorphic elements have not been extensively analysed when addressing the missing heritability of neurodegenerative diseases, including Parkinson’s disease (PD) and amyotrophic lateral sclerosis (ALS). SVA_67, a retrotransposon insertion polymorphism, is located in a 1.8 Mb region of high linkage disequilibrium, called the MAPT locus, which is known to contribute to increased risk of developing PD, frontotemporal dementia and other tauopathies. To investigate the role of SVA_67 in directing differential gene expression at this locus, we characterised the impact of SVA_67 allele dosage on isoform expression of several genes in the MAPT locus using the datasets from both the Parkinson’s Progression Markers Initiative and New York Genome Center Consortium Target ALS cohort. The Parkinson’s data was from gene expression in the blood and the ALS data from a variety of CNS regions and allowed us to demonstrate that SVA_67 presence or absence correlated with both isoform- and tissue-specific expression of multiple genes at this locus. This study highlights the importance of addressing SVA polymorphism in disease genetics to gain insight into a better understanding of the role of these regulatory domains to a variety of neurodegenerative diseases.
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Affiliation(s)
- Alexander Fröhlich
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- *Correspondence: Alexander Fröhlich,
| | - Abigail L. Pfaff
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
| | - Vivien J. Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Sulev Koks
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
| | - John P. Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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11
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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: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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.
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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
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12
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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: 29] [Impact Index Per Article: 9.7] [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.
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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
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13
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Geoffroy V, Guignard T, Kress A, Gaillard JB, Solli-Nowlan T, Schalk A, Gatinois V, Dollfus H, Scheidecker S, Muller J. AnnotSV and knotAnnotSV: a web server for human structural variations annotations, ranking and analysis. Nucleic Acids Res 2021; 49:W21-W28. [PMID: 34023905 PMCID: PMC8262758 DOI: 10.1093/nar/gkab402] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/16/2021] [Accepted: 04/29/2021] [Indexed: 11/13/2022] Open
Abstract
With the dramatic increase of pangenomic analysis, Human geneticists have generated large amount of genomic data including millions of small variants (SNV/indel) but also thousands of structural variations (SV) mainly from next-generation sequencing and array-based techniques. While the identification of the complete SV repertoire of a patient is getting possible, the interpretation of each SV remains challenging. To help identifying human pathogenic SV, we have developed a web server dedicated to their annotation and ranking (AnnotSV) as well as their visualization and interpretation (knotAnnotSV) freely available at the following address: https://www.lbgi.fr/AnnotSV/. A large amount of annotations from >20 sources is integrated in our web server including among others genes, haploinsufficiency, triplosensitivity, regulatory elements, known pathogenic or benign genomic regions, phenotypic data. An ACMG/ClinGen compliant prioritization module allows the scoring and the ranking of SV into 5 SV classes from pathogenic to benign. Finally, the visualization interface displays the annotated SV in an interactive way including popups, search fields, filtering options, advanced colouring to highlight pathogenic SV and hyperlinks to the UCSC genome browser or other public databases. This web server is designed for diagnostic and research analysis by providing important resources to the user.
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Affiliation(s)
- Véronique Geoffroy
- Laboratoire de Génétique Médicale, U1112, INSERM, IGMA, FMTS, Université de Strasbourg, Strasbourg, France
| | | | - Arnaud Kress
- Complex Systems and Translational Bioinformatics, ICube, UMR 7357, University of Strasbourg, CNRS, FMTS, Strasbourg, France
| | | | - Tor Solli-Nowlan
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Audrey Schalk
- Laboratoires de Diagnostic Génétique, IGMA, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | | | - Hélène Dollfus
- Laboratoire de Génétique Médicale, U1112, INSERM, IGMA, FMTS, Université de Strasbourg, Strasbourg, France
- Centre de référence pour les Affections Rares en Génétique Ophtalmologique, Filière SENSGENE, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Sophie Scheidecker
- Laboratoire de Génétique Médicale, U1112, INSERM, IGMA, FMTS, Université de Strasbourg, Strasbourg, France
- Laboratoires de Diagnostic Génétique, IGMA, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Jean Muller
- Laboratoire de Génétique Médicale, U1112, INSERM, IGMA, FMTS, Université de Strasbourg, Strasbourg, France
- Laboratoires de Diagnostic Génétique, IGMA, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- Unité Fonctionnelle de Bioinformatique Médicale appliquée au diagnostic (UF7363), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
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14
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In Silico identification of a common mobile element insertion in exon 4 of RP1. Sci Rep 2021; 11:13381. [PMID: 34183725 PMCID: PMC8238996 DOI: 10.1038/s41598-021-92834-4] [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: 01/22/2021] [Accepted: 06/14/2021] [Indexed: 11/18/2022] Open
Abstract
Mobile element insertions (MEIs) typically exceed the read lengths of short-read sequencing technologies and are therefore frequently missed. Recently, a founder Alu insertion in exon 4 of RP1 has been detected in Japanese patients with macular dystrophy by PCR and gel electrophoresis. We aimed to develop a grep search program for the detection of the Alu insertion in exon 4 of RP1 using unprocessed short reads. Among 494 unrelated Korean patients with inherited eye diseases, 273 patients with specific retinal phenotypes who were previously genotyped by targeted panel or whole exome sequencing were selected. Five probands had a single heterozygous truncating RP1 variant, and one of their unaffected parents also carry this variant. To find a hidden genetic variant, whole genome sequencing was performed in two patients, and it revealed AluY c.4052_4053ins328/p.(Tyr1352Alafs*9) insertion in RP1 exon 4. This AluY insertion was additionally identified in other 3 families, which was confirmed by PCR and gel electrophoresis. We developed simplified grep search program to detect this AluY insertion in RP1 exon 4. The simple grep search revealed a median variant allele frequency of 0.282 (interquartile range, 0.232–0.383), with no false-positive results using 120 control samples. The MEI in RP1 exon 4 was a common founder mutation in Korean, occurring in 1.8% of our cohort. The RP1-Alu grep program efficiently detected the AluY insertion, without the preprocessing of raw data or complex installation processes.
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15
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Next-Generation Sequencing Applications for Inherited Retinal Diseases. Int J Mol Sci 2021; 22:ijms22115684. [PMID: 34073611 PMCID: PMC8198572 DOI: 10.3390/ijms22115684] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 12/12/2022] Open
Abstract
Inherited retinal diseases (IRDs) represent a collection of phenotypically and genetically diverse conditions. IRDs phenotype(s) can be isolated to the eye or can involve multiple tissues. These conditions are associated with diverse forms of inheritance, and variants within the same gene often can be associated with multiple distinct phenotypes. Such aspects of the IRDs highlight the difficulty met when establishing a genetic diagnosis in patients. Here we provide an overview of cutting-edge next-generation sequencing techniques and strategies currently in use to maximise the effectivity of IRD gene screening. These techniques have helped researchers globally to find elusive causes of IRDs, including copy number variants, structural variants, new IRD genes and deep intronic variants, among others. Resolving a genetic diagnosis with thorough testing enables a more accurate diagnosis and more informed prognosis and should also provide information on inheritance patterns which may be of particular interest to patients of a child-bearing age. Given that IRDs are heritable conditions, genetic counselling may be offered to help inform family planning, carrier testing and prenatal screening. Additionally, a verified genetic diagnosis may enable access to appropriate clinical trials or approved medications that may be available for the condition.
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16
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Reference SVA insertion polymorphisms are associated with Parkinson's Disease progression and differential gene expression. NPJ Parkinsons Dis 2021; 7:44. [PMID: 34035310 PMCID: PMC8149882 DOI: 10.1038/s41531-021-00189-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 04/23/2021] [Indexed: 12/20/2022] Open
Abstract
The development of Parkinson's disease (PD) involves a complex interaction of genetic and environmental factors. Genome-wide association studies using extensive single nucleotide polymorphism datasets have identified many loci involved in disease. However much of the heritability of Parkinson's disease is still to be identified and the functional elements associated with the risk to be determined and understood. To investigate the component of PD that may involve complex genetic variants we characterised the hominid specific retrotransposon SINE-VNTR-Alus (SVAs) in the Parkinson's Progression Markers Initiative cohort utilising whole genome sequencing. We identified 81 reference SVAs polymorphic for their presence/absence, seven of which were associated with the progression of the disease and with differential gene expression in whole blood RNA sequencing data. This study highlights the importance of addressing SVA variants and potentially other types of retrotransposons in PD genetics, furthermore, these SVA elements should be considered as regulatory domains that could play a role in disease progression.
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17
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Ascari G, Rendtorff ND, De Bruyne M, De Zaeytijd J, Van Lint M, Bauwens M, Van Heetvelde M, Arno G, Jacob J, Creytens D, Van Dorpe J, Van Laethem T, Rosseel T, De Pooter T, De Rijk P, De Coster W, Menten B, Rey AD, Strazisar M, Bertelsen M, Tranebjaerg L, De Baere E. Long-Read Sequencing to Unravel Complex Structural Variants of CEP78 Leading to Cone-Rod Dystrophy and Hearing Loss. Front Cell Dev Biol 2021; 9:664317. [PMID: 33968938 PMCID: PMC8097100 DOI: 10.3389/fcell.2021.664317] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/08/2021] [Indexed: 11/13/2022] Open
Abstract
Inactivating variants as well as a missense variant in the centrosomal CEP78 gene have been identified in autosomal recessive cone-rod dystrophy with hearing loss (CRDHL), a rare syndromic inherited retinal disease distinct from Usher syndrome. Apart from this, a complex structural variant (SV) implicating CEP78 has been reported in CRDHL. Here we aimed to expand the genetic architecture of typical CRDHL by the identification of complex SVs of the CEP78 region and characterization of their underlying mechanisms. Approaches used for the identification of the SVs are shallow whole-genome sequencing (sWGS) combined with quantitative polymerase chain reaction (PCR) and long-range PCR, or ExomeDepth analysis on whole-exome sequencing (WES) data. Targeted or whole-genome nanopore long-read sequencing (LRS) was used to delineate breakpoint junctions at the nucleotide level. For all SVs cases, the effect of the SVs on CEP78 expression was assessed using quantitative PCR on patient-derived RNA. Apart from two novel canonical CEP78 splice variants and a frameshifting single-nucleotide variant (SNV), two SVs affecting CEP78 were identified in three unrelated individuals with CRDHL: a heterozygous total gene deletion of 235 kb and a partial gene deletion of 15 kb in a heterozygous and homozygous state, respectively. Assessment of the molecular consequences of the SVs on patient's materials displayed a loss-of-function effect. Delineation and characterization of the 15-kb deletion using targeted LRS revealed the previously described complex CEP78 SV, suggestive of a recurrent genomic rearrangement. A founder haplotype was demonstrated for the latter SV in cases of Belgian and British origin, respectively. The novel 235-kb deletion was delineated using whole-genome LRS. Breakpoint analysis showed microhomology and pointed to a replication-based underlying mechanism. Moreover, data mining of bulk and single-cell human and mouse transcriptional datasets, together with CEP78 immunostaining on human retina, linked the CEP78 expression domain with its phenotypic manifestations. Overall, this study supports that the CEP78 locus is prone to distinct SVs and that SV analysis should be considered in a genetic workup of CRDHL. Finally, it demonstrated the power of sWGS and both targeted and whole-genome LRS in identifying and characterizing complex SVs in patients with ocular diseases.
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Affiliation(s)
- Giulia Ascari
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Nanna D Rendtorff
- The Kennedy Center, Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Marieke De Bruyne
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Julie De Zaeytijd
- Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium
| | - Michel Van Lint
- Department of Ophthalmology, Antwerp University Hospital, Antwerp, Belgium
| | - Miriam Bauwens
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Mattias Van Heetvelde
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Gavin Arno
- Great Ormond Street Hospital, London, United Kingdom.,Moorfields Eye Hospital, London, United Kingdom.,UCL Institute of Ophthalmology, London, United Kingdom
| | - Julie Jacob
- Department of Ophthalmology, University Hospitals Leuven, Leuven, Belgium
| | - David Creytens
- Department of Pathology, Ghent University Hospital, Ghent, Belgium.,Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University Hospital, Ghent, Belgium.,Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Thalia Van Laethem
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Toon Rosseel
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Tim De Pooter
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.,Neuromics Support Facility, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Peter De Rijk
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.,Neuromics Support Facility, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Wouter De Coster
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.,Applied and Translational Neurogenomics Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Björn Menten
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Alfredo Dueñas Rey
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Mojca Strazisar
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.,Neuromics Support Facility, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Mette Bertelsen
- The Kennedy Center, Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Ophthalmology, Rigshospitalet-Glostrup, University of Copenhagen, Glostrup, Denmark
| | - Lisbeth Tranebjaerg
- The Kennedy Center, Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Elfride De Baere
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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Duong Phu M, Bross S, Burkhalter MD, Philipp M. Limitations and opportunities in the pharmacotherapy of ciliopathies. Pharmacol Ther 2021; 225:107841. [PMID: 33771583 DOI: 10.1016/j.pharmthera.2021.107841] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/11/2021] [Indexed: 01/10/2023]
Abstract
Ciliopathies are a family of rather diverse conditions, which have been grouped based on the finding of altered or dysfunctional cilia, potentially motile, small cellular antennae extending from the surface of postmitotic cells. Cilia-related disorders include embryonically arising conditions such as Joubert, Usher or Kartagener syndrome, but also afflictions with a postnatal or even adult onset phenotype, i.e. autosomal dominant polycystic kidney disease. The majority of ciliopathies are syndromic rather than affecting only a single organ due to cilia being found on almost any cell in the human body. Overall ciliopathies are considered rare diseases. Despite that, pharmacological research and the strive to help these patients has led to enormous therapeutic advances in the last decade. In this review we discuss new treatment options for certain ciliopathies, give an outlook on promising future therapeutic strategies, but also highlight the limitations in the development of therapeutic approaches of ciliopathies.
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Affiliation(s)
- Max Duong Phu
- Department of Experimental and Clinical Pharmacology and Pharmacogenomics, Section of Pharmacogenomics, Eberhard-Karls-University of Tübingen, 72074 Tübingen, Germany
| | - Stefan Bross
- Department of Experimental and Clinical Pharmacology and Pharmacogenomics, Section of Pharmacogenomics, Eberhard-Karls-University of Tübingen, 72074 Tübingen, Germany
| | - Martin D Burkhalter
- Department of Experimental and Clinical Pharmacology and Pharmacogenomics, Section of Pharmacogenomics, Eberhard-Karls-University of Tübingen, 72074 Tübingen, Germany
| | - Melanie Philipp
- Department of Experimental and Clinical Pharmacology and Pharmacogenomics, Section of Pharmacogenomics, Eberhard-Karls-University of Tübingen, 72074 Tübingen, Germany.
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Dormegny L, Velizarova R, Schroder CM, Kilic-Huck U, Comtet H, Dollfus H, Bourgin P, Ruppert E. Sleep-Disordered Breathing, Quality of Sleep and Chronotype in a Cohort of Adult Patients with Bardet-Biedl Syndrome. Nat Sci Sleep 2021; 13:1913-1919. [PMID: 34720600 PMCID: PMC8550541 DOI: 10.2147/nss.s320660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/16/2021] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVE/BACKGROUND Bardet-Biedl syndrome (BBS) is a rare but well-recognized ciliopathy with high genetic and phenotypic heterogeneity. Cardinal features include obesity, diabetes and high blood pressure (HBP), which are often associated with sleep-disordered breathing. Also, the high prevalence of blindness due to retinal dystrophy could affect circadian sleep-wake rhythms. We characterized in this cohort of adult BBS patients sleep-disordered breathing, sleep quality, daytime sleepiness and chronotype. PATIENTS AND METHODS Thirty-two patients with genetically confirmed BBS were included in this observational single center study. Overnight respiratory polygraphy was performed for sleep apnea syndrome (SAS) in 30 patients. Quality of sleep, daytime sleepiness, fatigue and chronotype were assessed in 25 patients using Pittsburgh sleep quality index (PSQI), 14-day sleep diary (SD), Epworth sleepiness scale (ESS), Pichot fatigue scale (PFS) and Horne and Ostberg morningness-eveningness questionnaire (MEQ). RESULTS Patients' mean age was 32±11 years and mean BMI 32.6±7.7 kg/m2. Eleven (35%) patients had HBP and 7 (22%) diabetes. Moderate to severe sleep apnea syndrome (SAS) was present in 5 (17%) and was not associated with altered sleep, daytime sleepiness or fatigue. Most of the patients (63%) evaluated their sleep as of good quality (PSQI ≤ 5). Median scores of sleep quality, daytime sleepiness and fatigue were normal (PSQI of 3.0 [2.0-6.0], ESS of 9.0 [6.0-13.0] and PFS of 8.0 [3.0-13.0], respectively). Predominant chronotypes according to MEQ were either "intermediate" (57%) or "moderate morning" (29%). None had a free running sleep-wake cycle. 14-day SD revealed overall few awakenings at night and low daytime napping. CONCLUSIONS Given the cardiovascular risk factors, systematic screening for SAS should be considered in BBS patients, regardless of sleep and daytime vigilance complaints. None of these highly visually impaired patients had a circadian sleep-wake rhythm disorder. Further objective assessments are needed to better characterize sleep and circadian rhythms in BBS patients.
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Affiliation(s)
- Léa Dormegny
- Centre des Troubles du Sommeil - CIRCSom, Hôpital Civil, University of Strasbourg, Strasbourg, 67091, France.,Department of Ophthalmology, Hôpital Civil, University of Strasbourg, Strasbourg, 67091, France
| | - Reana Velizarova
- Centre des Troubles du Sommeil - CIRCSom, Hôpital Civil, University of Strasbourg, Strasbourg, 67091, France
| | - Carmen M Schroder
- Centre des Troubles du Sommeil - CIRCSom, Hôpital Civil, University of Strasbourg, Strasbourg, 67091, France.,Institute for Cellular and Integrative Neurosciences, CNRS - UPR 3212, Strasbourg, 67000, France
| | - Ulker Kilic-Huck
- Centre des Troubles du Sommeil - CIRCSom, Hôpital Civil, University of Strasbourg, Strasbourg, 67091, France.,Institute for Cellular and Integrative Neurosciences, CNRS - UPR 3212, Strasbourg, 67000, France
| | - Henri Comtet
- Centre des Troubles du Sommeil - CIRCSom, Hôpital Civil, University of Strasbourg, Strasbourg, 67091, France.,Institute for Cellular and Integrative Neurosciences, CNRS - UPR 3212, Strasbourg, 67000, France
| | - Hélène Dollfus
- Centre des Affections Rares en Génétique Ophtalmologique (CARGO), University of Strasbourg, Strasbourg, 67091, France
| | - Patrice Bourgin
- Centre des Troubles du Sommeil - CIRCSom, Hôpital Civil, University of Strasbourg, Strasbourg, 67091, France.,Institute for Cellular and Integrative Neurosciences, CNRS - UPR 3212, Strasbourg, 67000, France
| | - Elisabeth Ruppert
- Centre des Troubles du Sommeil - CIRCSom, Hôpital Civil, University of Strasbourg, Strasbourg, 67091, France.,Institute for Cellular and Integrative Neurosciences, CNRS - UPR 3212, Strasbourg, 67000, France
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Santoni M, Piva F, Cimadamore A, Giulietti M, Battelli N, Montironi R, Cosmai L, Porta C. Exploring the Spectrum of Kidney Ciliopathies. Diagnostics (Basel) 2020; 10:E1099. [PMID: 33339422 PMCID: PMC7766105 DOI: 10.3390/diagnostics10121099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 11/30/2022] Open
Abstract
Ciliopathies are a group of multi-organ diseases caused by the disruption of the primary cilium. This event leads to a variety of kidney disorders, including nephronophthisis, renal cystic dysplasia, and renal cell carcinoma (RCC). Primary cilium contributes to the regulation of the cell cycle and protein homeostasis, that is, the balance between protein synthesis and degradation by acting on the ubiquitin-proteasome system, autophagy, and mTOR signaling. Many proteins are involved in renal ciliopathies. In particular, fibrocystin (PKHD1) is involved in autosomal recessive polycystic kidney disease (ARPKD), while polycystin-1 (PKD1) and polycystin-2 (PKD2) are implicated in autosomal dominant polycystic kidney disease (ADPKD). Moreover, primary cilia are associated with essential signaling pathways, such as Hedgehog, Wnt, and Platelet-Derived Growth Factor (PDGF). In this review, we focused on the ciliopathies associated with kidney diseases, exploring genes and signaling pathways associated with primary cilium and the potential role of cilia as therapeutic targets in renal disorders.
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Affiliation(s)
- Matteo Santoni
- Oncology Unit, Macerata Hospital, 62100 Macerata, Italy;
| | - Francesco Piva
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60126 Ancona, Italy; (F.P.); (M.G.)
| | - Alessia Cimadamore
- Section of Pathological Anatomy, School of Medicine, United Hospitals, Polytechnic University of the Marche Region, 60126 Ancona, Italy;
| | - Matteo Giulietti
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60126 Ancona, Italy; (F.P.); (M.G.)
| | | | - Rodolfo Montironi
- Section of Pathological Anatomy, School of Medicine, United Hospitals, Polytechnic University of the Marche Region, 60126 Ancona, Italy;
| | - Laura Cosmai
- Division of Nephrology and Dialysis, ASST Fatebenefratelli-Sacco, Fatebenefratelli Hospital, 20121 Milan, Italy;
| | - Camillo Porta
- Chair of Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari ‘A. Moro’, 70121 Bari, Italy;
- Division of Medical Oncology, A.O.U. ConsorzialePoliclinico di Bari, 70124 Bari, Italy
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