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Ballios BG, Mandola A, Tayyib A, Tumber A, Garkaby J, Vong L, Heon E, Roifman CM, Vincent A. Deep phenotypic characterization of the retinal dystrophy in patients with RNU4ATAC-associated Roifman syndrome. Eye (Lond) 2023; 37:3734-3742. [PMID: 37225827 PMCID: PMC10697969 DOI: 10.1038/s41433-023-02581-1] [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: 12/30/2022] [Revised: 05/01/2023] [Accepted: 05/11/2023] [Indexed: 05/26/2023] Open
Abstract
PURPOSE To characterize the retinal phenotype in RNU4ATAC-associated Roifman syndrome. METHODS Ten patients (including 8 males) with molecularly confirmed Roifman syndrome underwent detailed ophthalmologic evaluation including fundus imaging, fundus autofluorescence (FAF) imaging, spectral-domain optical coherence tomography (SD-OCT), and electroretinography (ERG). Six patients had follow-up eye exams. All patients also underwent comprehensive examination for features of extra-retinal Roifman syndrome. RESULTS All patients had biallelic RNU4ATAC variants. Nyctalopia was common (7/10). Visual acuity at presentation ranged from 20/20 to 20/200 (Age Range: 5-41 years). Retinal exam revealed features of generalized retinopathy with mid-peripheral pigment epithelial changes. A para or peri-foveal ring of hyper-autofluorescence was the commonest FAF abnormality noted (6/8). The SD-OCT demonstrated relative preservation of the foveal ellipsoid zone in six cases; associated features included cystoid changes (5/10) and posterior staphyloma (3/10). The ERG was abnormal in all patients; nine showed generalized rod-cone dystrophy, whilst one patient with sectoral retinal involvement only had isolated rod dystrophy (20 years old). On follow-up examination (Mean duration: 8.16 years), progressive loss of visual acuity (2/6), mid-peripheral retinal atrophy (3/6) or shortening of ellipsoid zone width (1/6) were observed. CONCLUSION This study has characterized the retinal phenotype in RNU4ATAC-associated Roifman syndrome. Retinal involvement is universal, early-onset, and overall, the retinal and FAF features are consistent with rod-cone degeneration that is slowly progressive over time. The sub-foveal retinal ultrastructure is relatively preserved in majority of patients. Phenotypic variability independent of age exists, and more study of allelic- and sex-based determinants of disease severity are necessary.
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Affiliation(s)
- Brian G Ballios
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON, Canada
| | - Amarilla Mandola
- Division of Immunology and Allergy, The Hospital for Sick Children and the University of Toronto, Toronto, ON, Canada
| | - Alaa Tayyib
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON, Canada
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, ON, Canada
| | - Anupreet Tumber
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jenny Garkaby
- Division of Immunology and Allergy, The Hospital for Sick Children and the University of Toronto, Toronto, ON, Canada
| | - Linda Vong
- The Canadian Centre for Primary Immunodeficiency and The Jeffrey Modell Research Laboratory for the Diagnosis of Primary Immunodeficiency, The Hospital for Sick Children, Toronto, ON, Canada
| | - Elise Heon
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON, Canada
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, ON, Canada
| | - Chaim M Roifman
- Division of Immunology and Allergy, The Hospital for Sick Children and the University of Toronto, Toronto, ON, Canada
- The Canadian Centre for Primary Immunodeficiency and The Jeffrey Modell Research Laboratory for the Diagnosis of Primary Immunodeficiency, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ajoy Vincent
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON, Canada.
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, ON, Canada.
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2
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Khatri D, Putoux A, Cologne A, Kaltenbach S, Besson A, Bertiaux E, Guguin J, Fendler A, Dupont MA, Benoit-Pilven C, Qebibo L, Ahmed-Elie S, Audebert-Bellanger S, Blanc P, Rambaud T, Castelle M, Cornen G, Grotto S, Guët A, Guibaud L, Michot C, Odent S, Ruaud L, Sacaze E, Hamel V, Bordonné R, Leutenegger AL, Edery P, Burglen L, Attié-Bitach T, Mazoyer S, Delous M. Deficiency of the minor spliceosome component U4atac snRNA secondarily results in ciliary defects in human and zebrafish. Proc Natl Acad Sci U S A 2023; 120:e2102569120. [PMID: 36802443 PMCID: PMC9992838 DOI: 10.1073/pnas.2102569120] [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: 02/12/2021] [Accepted: 12/12/2022] [Indexed: 02/23/2023] Open
Abstract
In the human genome, about 750 genes contain one intron excised by the minor spliceosome. This spliceosome comprises its own set of snRNAs, among which U4atac. Its noncoding gene, RNU4ATAC, has been found mutated in Taybi-Linder (TALS/microcephalic osteodysplastic primordial dwarfism type 1), Roifman (RFMN), and Lowry-Wood (LWS) syndromes. These rare developmental disorders, whose physiopathological mechanisms remain unsolved, associate ante- and post-natal growth retardation, microcephaly, skeletal dysplasia, intellectual disability, retinal dystrophy, and immunodeficiency. Here, we report bi-allelic RNU4ATAC mutations in five patients presenting with traits suggestive of the Joubert syndrome (JBTS), a well-characterized ciliopathy. These patients also present with traits typical of TALS/RFMN/LWS, thus widening the clinical spectrum of RNU4ATAC-associated disorders and indicating ciliary dysfunction as a mechanism downstream of minor splicing defects. Intriguingly, all five patients carry the n.16G>A mutation, in the Stem II domain, either at the homozygous or compound heterozygous state. A gene ontology term enrichment analysis on minor intron-containing genes reveals that the cilium assembly process is over-represented, with no less than 86 cilium-related genes containing at least one minor intron, among which there are 23 ciliopathy-related genes. The link between RNU4ATAC mutations and ciliopathy traits is supported by alterations of primary cilium function in TALS and JBTS-like patient fibroblasts, as well as by u4atac zebrafish model, which exhibits ciliopathy-related phenotypes and ciliary defects. These phenotypes could be rescued by WT but not by pathogenic variants-carrying human U4atac. Altogether, our data indicate that alteration of cilium biogenesis is part of the physiopathological mechanisms of TALS/RFMN/LWS, secondarily to defects of minor intron splicing.
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Affiliation(s)
- Deepak Khatri
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
| | - Audrey Putoux
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
- Department of Genetics, Clinical Genetics Unit, Centre de Référence Maladies Rares des Anomalies du Développement, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69500Bron, France
| | - Audric Cologne
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
- Institut national de recherche en sciences et technologies du numérique Erable, Laboratoire de Biométrie et Biologie Evolutive, UMR5558 CNRS, Université Claude Bernard Lyon 1, 69622Villeurbanne, France
| | - Sophie Kaltenbach
- Department of Histology Embryology and Cytogenetics, Assistance Publique - Hôpitaux de Paris, Necker-Enfants Malades Hospital, University of Paris, 75015Paris, France
| | - Alicia Besson
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
| | - Eloïse Bertiaux
- Department of Cell Biology, Sciences III, University of Geneva, 1211-Geneva, Switzerland
| | - Justine Guguin
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
| | - Adèle Fendler
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
| | - Marie A. Dupont
- Laboratory of hereditary kidney diseases, Imagine Institute, U1163 INSERM, University of Paris, 75015Paris, France
| | - Clara Benoit-Pilven
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
- Institut national de recherche en sciences et technologies du numérique Erable, Laboratoire de Biométrie et Biologie Evolutive, UMR5558 CNRS, Université Claude Bernard Lyon 1, 69622Villeurbanne, France
| | - Leila Qebibo
- Département de Génétique, Centre de Référence des Malformations et Maladies Congénitales du Cervelet, Assistance Publique - Hôpitaux de Paris, Sorbonne University, Trousseau Hospital, 75012Paris, France
| | - Samira Ahmed-Elie
- Département de Génétique, Centre de Référence des Malformations et Maladies Congénitales du Cervelet, Assistance Publique - Hôpitaux de Paris, Sorbonne University, Trousseau Hospital, 75012Paris, France
| | - Séverine Audebert-Bellanger
- Department of Genetics, Clinical Genetics Unit, Centre de Compétence Anomalies du Développement et Syndromes Polymalformatifs, Centre Hospitalier Universitaire Morvan, 29200Brest, France
| | | | | | - Martin Castelle
- Hematology-Immunology Unit, Assistance Publique - Hôpitaux de Paris, Necker-Enfants Malades Hospital, 75015Paris, France
| | - Gaëlle Cornen
- Pediatric service, Centre Hospitalier Morlaix, 29600Morlaix, France
| | - Sarah Grotto
- Clinical Genetics Unit, Maternité Port-Royal, Assistance Publique - Hôpitaux de Paris, Cochin Broca Hôtel-Dieu Hospitals75014Paris, France
| | - Agnès Guët
- Neonatal and Pediatric Units, Louis-Mourier Hospital, 92700Colombes, France
| | - Laurent Guibaud
- Pediatric and Fetal Imaging, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69500Bron, France
| | - Caroline Michot
- Clinical Genetics Department, Centre de Référence Maladies Rares–Maladies Osseuses Constitutionnelles, Assistance Publique - Hôpitaux de Paris, Necker-Enfants Malades Hospital, 75015Paris, France
- Developmental Brain Disorders Laboratory, Imagine Institute, U1163 INSERM, University of Paris, 75015Paris, France
| | - Sylvie Odent
- Service de Génétique Clinique, Centre Hospitalier Universitaire Rennes, Centre de référence Anomalies du développement et syndromes malformatifs, Univ Rennes, CNRS, INSERM, Institut de Génétique et Développement de Rennes UMR 6290/ Equipe de Recherche Labellisée 1305, 35000Rennes, France
| | - Lyse Ruaud
- NeuroDiderot, UMR1141, University of Paris, 75019Paris, France
- Departement of Genetics, Assistance Publique - Hôpitaux de Paris, Robert Debré Hospital, 75019Paris, France
| | - Elise Sacaze
- Pediatric Service, Centre Hospitalier Régional Universitaire Brest, 29200Brest, France
| | - Virginie Hamel
- Department of Cell Biology, Sciences III, University of Geneva, 1211-Geneva, Switzerland
| | - Rémy Bordonné
- Institute of Molecular Genetics of Montpellier, UMR5535 CNRS, University of Montpellier, 34000Montpellier, France
| | | | - Patrick Edery
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
- Department of Genetics, Clinical Genetics Unit, Centre de Référence Maladies Rares des Anomalies du Développement, Hospices Civils de Lyon, Université Claude Bernard Lyon 1, 69500Bron, France
| | - Lydie Burglen
- Département de Génétique, Centre de Référence des Malformations et Maladies Congénitales du Cervelet, Assistance Publique - Hôpitaux de Paris, Sorbonne University, Trousseau Hospital, 75012Paris, France
- Developmental Brain Disorders Laboratory, Imagine Institute, U1163 INSERM, University of Paris, 75015Paris, France
| | - Tania Attié-Bitach
- Department of Histology Embryology and Cytogenetics, Assistance Publique - Hôpitaux de Paris, Necker-Enfants Malades Hospital, University of Paris, 75015Paris, France
- Developmental Brain Disorders Laboratory, Imagine Institute, U1163 INSERM, University of Paris, 75015Paris, France
| | - Sylvie Mazoyer
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
| | - Marion Delous
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon CRNL U1028 UMR5292,Genetics of Neurodevelopment Team, 69500Bron, France
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Almentina Ramos Shidi F, Cologne A, Delous M, Besson A, Putoux A, Leutenegger AL, Lacroix V, Edery P, Mazoyer S, Bordonné R. Mutations in the non-coding RNU4ATAC gene affect the homeostasis and function of the Integrator complex. Nucleic Acids Res 2022; 51:712-727. [PMID: 36537210 PMCID: PMC9881141 DOI: 10.1093/nar/gkac1182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 11/17/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Various genetic diseases associated with microcephaly and developmental defects are due to pathogenic variants in the U4atac small nuclear RNA (snRNA), a component of the minor spliceosome essential for the removal of U12-type introns from eukaryotic mRNAs. While it has been shown that a few RNU4ATAC mutations result in impaired binding of essential protein components, the molecular defects of the vast majority of variants are still unknown. Here, we used lymphoblastoid cells derived from RNU4ATAC compound heterozygous (g.108_126del;g.111G>A) twin patients with MOPD1 phenotypes to analyze the molecular consequences of the mutations on small nuclear ribonucleoproteins (snRNPs) formation and on splicing. We found that the U4atac108_126del mutant is unstable and that the U4atac111G>A mutant as well as the minor di- and tri-snRNPs are present at reduced levels. Our results also reveal the existence of 3'-extended snRNA transcripts in patients' cells. Moreover, we show that the mutant cells have alterations in splicing of INTS7 and INTS10 minor introns, contain lower levels of the INTS7 and INTS10 proteins and display changes in the assembly of Integrator subunits. Altogether, our results show that compound heterozygous g.108_126del;g.111G>A mutations induce splicing defects and affect the homeostasis and function of the Integrator complex.
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Affiliation(s)
- Fatimat Almentina Ramos Shidi
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS UMR5535, 34293 Montpellier, France
| | - Audric Cologne
- INRIA Erable, CNRS LBBE UMR 5558, University Lyon 1, University of Lyon, 69622 Villeurbanne, France
| | - Marion Delous
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon U1028 UMR5292, GENDEV, 69500 Bron, France
| | - Alicia Besson
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon U1028 UMR5292, GENDEV, 69500 Bron, France
| | - Audrey Putoux
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon U1028 UMR5292, GENDEV, 69500 Bron, France,Clinical Genetics Unit, Department of Genetics, Centre de Référence Anomalies du Développement et Syndromes Polymalformatifs, Hospices Civils de Lyon, University Lyon 1, Bron, France
| | | | - Vincent Lacroix
- INRIA Erable, CNRS LBBE UMR 5558, University Lyon 1, University of Lyon, 69622 Villeurbanne, France
| | - Patrick Edery
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon U1028 UMR5292, GENDEV, 69500 Bron, France,Clinical Genetics Unit, Department of Genetics, Centre de Référence Anomalies du Développement et Syndromes Polymalformatifs, Hospices Civils de Lyon, University Lyon 1, Bron, France
| | - Sylvie Mazoyer
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon U1028 UMR5292, GENDEV, 69500 Bron, France
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Clifford D, Moloney F, Leahy TR, Murray DM. Roifman syndrome: a description of further immunological and radiological features. BMJ Case Rep 2022; 15:e249109. [PMID: 35450878 PMCID: PMC9024203 DOI: 10.1136/bcr-2022-249109] [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] [Accepted: 04/02/2022] [Indexed: 11/03/2022] Open
Abstract
Roifman syndrome is a rare autosomal recessive inherited syndromic immunodeficiency. We wish to add to the available literature by reporting two brothers with clinical, radiological and immunological features of Roifman syndrome, confirmed on whole exome sequencing. We report an excellent response to subcutaneous immunoglobulin therapy in both brothers, reducing infection burden and hospital admissions. New radiological features are also described here which may assist in the diagnosis of other patients.
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Affiliation(s)
- Danielle Clifford
- Department of Paediatrics and Child Health, Cork University Hospital, Cork, Ireland
| | - Fiachra Moloney
- Department of Paediatric Radiology, Cork University Hospital, Cork, Ireland
| | - Timothy Ronan Leahy
- Department of Paediatric Immunology, Children's Health Ireland at Crumlin, Dublin, Ireland
- Department of Paediatrics, Trinity College Dublin, Dublin, Ireland
| | - Deirdre M Murray
- Department of Paediatrics and Child Health, Cork University Hospital, Cork, Ireland
- Department of Paediatrics and Child Health, University College Cork, Cork, Ireland
- Principal Investigator, INFANT Centre, University College Cork, Cork, Ireland
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Eddens T, Van Meerbeke S, Zhang M, Petrov A, Fajt ML. A 33-year-old man with a history of recurrent pneumonia presenting with hypoxemic respiratory failure. Allergy Asthma Proc 2021; 42:439-442. [PMID: 34256898 DOI: 10.2500/aap.2021.42.210032] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The patient was a 33-year-old man with a history of recurrent pneumonia, autism, bipolar disorder, hypothyroidism, intermittent asthma, and nonischemic cardiomyopathy attributed to cocaine use who was admitted with hypoxemic respiratory distress with bilateral infiltrates seen on a chest radiograph. He was treated for community-acquired pneumonia but progressed to respiratory failure that required intubation and broad-spectrum antibiotic therapy. His medical history was notable for short stature, abnormal facial features, and, since childhood, at least two pneumonias per year that required antibiotics. The initial evaluation for an underlying primary immunodeficiency found that the patient had normal quantitative immunoglobulin levels, with absent CD19+ B cells. This case highlighted the evaluation of the humoral immune system for hospitalized adult patients with recurrent infections as well as the use of genetic testing to diagnose rare immunodeficiency syndromes.
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Hagiwara H, Matsumoto H, Uematsu K, Zaha K, Sekinaka Y, Miyake N, Matsumoto N, Nonoyama S. Immunodeficiency in a patient with microcephalic osteodysplastic primordial dwarfism type I as compared to Roifman syndrome. Brain Dev 2021; 43:337-342. [PMID: 33059947 DOI: 10.1016/j.braindev.2020.09.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 09/08/2020] [Accepted: 09/13/2020] [Indexed: 12/26/2022]
Abstract
BACKGROUND Microcephalic osteodysplastic primordial dwarfism type I (MOPD I, also known as Taybi-Linder syndrome) is a rare genetic disorder associated with severe intrauterine growth retardation, short stature, microcephaly, brain anomalies, stunted limbs, and early mortality. RNU4ATAC, the gene responsible for this disorder, does not encode a protein but instead the U4atac small nuclear RNA (snRNA), a crucial component of the minor spliceosome. Roifman syndrome is an allelic disorder of MOPD I that is characterized by immunodeficiency complications. CASE REPORT The patient described herein is an 18-year-old woman exhibiting congenital dwarfism and microcephaly with structural brain anomaly. She suffered human herpesvirus 6 (HHV-6)-associated acute necrotizing encephalopathy at the age of one, thereafter resulting in severe psychomotor disabilities. Genetic analysis using gene microarray and whole-exome sequencing could not identify the cause of her congenital anomalies. However, Sanger sequencing revealed a compound heterozygous mutation within RNU4ATAC (NR_023343.1:n.[50G > A];[55G > A]). Immunological findings showed decreases in total lymphocytes, CD4+ T cells, and T cell regenerative activity. Furthermore, antibodies against varicella-zoster, rubella, measles, mumps, and influenza were very low or negative despite having received vaccinations for these viruses. HHV-6 IgG antibodies were also undetected. DISCUSSION The patient here exhibited a marked MOPD I phenotype complicated by various immunodeficiencies. Previous studies have not demonstrated immunodeficiency comorbidities within MOPD I subjects, but this report suggests an evident immunodeficiency in MOPD I. Patients with MOPD I should be treated with one of the immunodeficiency syndromes.
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Affiliation(s)
- Hidetoshi Hagiwara
- Department of Pediatrics, National Defense Medical College Hospital, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan
| | - Hiroshi Matsumoto
- Department of Pediatrics, National Defense Medical College Hospital, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan.
| | - Kenji Uematsu
- Department of Pediatrics, National Defense Medical College Hospital, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan
| | - Kiyotaka Zaha
- Department of Pediatrics, National Defense Medical College Hospital, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan
| | - Yujin Sekinaka
- Department of Pediatrics, National Defense Medical College Hospital, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Shigeaki Nonoyama
- Department of Pediatrics, National Defense Medical College Hospital, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan
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Clinical interpretation of variants identified in RNU4ATAC, a non-coding spliceosomal gene. PLoS One 2020; 15:e0235655. [PMID: 32628740 PMCID: PMC7337319 DOI: 10.1371/journal.pone.0235655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/19/2020] [Indexed: 12/16/2022] Open
Abstract
Biallelic variants in RNU4ATAC, a non-coding gene transcribed into the minor spliceosome component U4atac snRNA, are responsible for three rare recessive developmental diseases, namely Taybi-Linder/MOPD1, Roifman and Lowry-Wood syndromes. Next-generation sequencing of clinically heterogeneous cohorts (children with either a suspected genetic disorder or a congenital microcephaly) recently identified mutations in this gene, illustrating how profoundly these technologies are modifying genetic testing and assessment. As RNU4ATAC has a single non-coding exon, the bioinformatic prediction algorithms assessing the effect of sequence variants on splicing or protein function are irrelevant, which makes variant interpretation challenging to molecular diagnostic laboratories. In order to facilitate and improve clinical diagnostic assessment and genetic counseling, we present i) an update of the previously reported RNU4ATAC mutations and an analysis of the genetic variations affecting this gene using the Genome Aggregation Database (gnomAD) resource; ii) the pathogenicity prediction performances of scores computed based on an RNA structure prediction tool and of those produced by the Combined Annotation Dependent Depletion tool for the 285 RNU4ATAC variants identified in patients or in large-scale sequencing projects; iii) a method, based on a cellular assay, that allows to measure the effect of RNU4ATAC variants on splicing efficiency of a minor (U12-type) reporter intron. Lastly, the concordance of bioinformatic predictions and cellular assay results was investigated.
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8
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Cologne A, Benoit-Pilven C, Besson A, Putoux A, Campan-Fournier A, Bober MB, De Die-Smulders CEM, Paulussen ADC, Pinson L, Toutain A, Roifman CM, Leutenegger AL, Mazoyer S, Edery P, Lacroix V. New insights into minor splicing-a transcriptomic analysis of cells derived from TALS patients. RNA (NEW YORK, N.Y.) 2019; 25:1130-1149. [PMID: 31175170 PMCID: PMC6800510 DOI: 10.1261/rna.071423.119] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 05/28/2019] [Indexed: 06/09/2023]
Abstract
Minor intron splicing plays a central role in human embryonic development and survival. Indeed, biallelic mutations in RNU4ATAC, transcribed into the minor spliceosomal U4atac snRNA, are responsible for three rare autosomal recessive multimalformation disorders named Taybi-Linder (TALS/MOPD1), Roifman (RFMN), and Lowry-Wood (LWS) syndromes, which associate numerous overlapping signs of varying severity. Although RNA-seq experiments have been conducted on a few RFMN patient cells, none have been performed in TALS, and more generally no in-depth transcriptomic analysis of the ∼700 human genes containing a minor (U12-type) intron had been published as yet. We thus sequenced RNA from cells derived from five skin, three amniotic fluid, and one blood biosamples obtained from seven unrelated TALS cases and from age- and sex-matched controls. This allowed us to describe for the first time the mRNA expression and splicing profile of genes containing U12-type introns, in the context of a functional minor spliceosome. Concerning RNU4ATAC-mutated patients, we show that as expected, they display distinct U12-type intron splicing profiles compared to controls, but that rather unexpectedly mRNA expression levels are mostly unchanged. Furthermore, although U12-type intron missplicing concerns most of the expressed U12 genes, the level of U12-type intron retention is surprisingly low in fibroblasts and amniocytes, and much more pronounced in blood cells. Interestingly, we found several occurrences of introns that can be spliced using either U2, U12, or a combination of both types of splice site consensus sequences, with a shift towards splicing using preferentially U2 sites in TALS patients' cells compared to controls.
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Affiliation(s)
- Audric Cologne
- INRIA Erable, CNRS LBBE UMR 5558, University Lyon 1, University of Lyon, F-69622 Villeurbanne, France
- "Genetics of Neurodevelopment" Team, Lyon Neuroscience Research Centre, UMR5292 CNRS U1028 Inserm, University of Lyon, F-69500 Bron, France
| | - Clara Benoit-Pilven
- INRIA Erable, CNRS LBBE UMR 5558, University Lyon 1, University of Lyon, F-69622 Villeurbanne, France
- "Genetics of Neurodevelopment" Team, Lyon Neuroscience Research Centre, UMR5292 CNRS U1028 Inserm, University of Lyon, F-69500 Bron, France
| | - Alicia Besson
- "Genetics of Neurodevelopment" Team, Lyon Neuroscience Research Centre, UMR5292 CNRS U1028 Inserm, University of Lyon, F-69500 Bron, France
| | - Audrey Putoux
- "Genetics of Neurodevelopment" Team, Lyon Neuroscience Research Centre, UMR5292 CNRS U1028 Inserm, University of Lyon, F-69500 Bron, France
- Clinical Genetics Unit, Department of Genetics, Hospices Civils de Lyon, F-69500 Bron, France
| | - Amandine Campan-Fournier
- INRIA Erable, CNRS LBBE UMR 5558, University Lyon 1, University of Lyon, F-69622 Villeurbanne, France
- "Genetics of Neurodevelopment" Team, Lyon Neuroscience Research Centre, UMR5292 CNRS U1028 Inserm, University of Lyon, F-69500 Bron, France
| | - Michael B Bober
- Division of Medical Genetics, Nemours/Alfred I. du Pont Hospital for Children, Wilmington, Delaware 19803, USA
| | - Christine E M De Die-Smulders
- Department of Clinical Genetics, Maastricht University Medical Center, 6202 AZ Maastricht, The Netherlands
- School for Oncology and Developmental Biology, GROW, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Aimee D C Paulussen
- Department of Clinical Genetics, Maastricht University Medical Center, 6202 AZ Maastricht, The Netherlands
- School for Oncology and Developmental Biology, GROW, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Lucile Pinson
- Genetic Department for Rare Diseases and Personalized Medicine, Clinical Division, CHU Montpellier, F-34000 Montpellier, France
| | - Annick Toutain
- Department of Genetics, Tours University Hospital, F-37000 Tours, France
- UMR 1253, iBrain, Tours University, Inserm, F-37000 Tours, France
| | - Chaim M Roifman
- Department of Paediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
- Division for Immunology and Allergy, Canadian Center for Primary Immunodeficiency, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | | | - Sylvie Mazoyer
- "Genetics of Neurodevelopment" Team, Lyon Neuroscience Research Centre, UMR5292 CNRS U1028 Inserm, University of Lyon, F-69500 Bron, France
| | - Patrick Edery
- "Genetics of Neurodevelopment" Team, Lyon Neuroscience Research Centre, UMR5292 CNRS U1028 Inserm, University of Lyon, F-69500 Bron, France
- Clinical Genetics Unit, Department of Genetics, Hospices Civils de Lyon, F-69500 Bron, France
| | - Vincent Lacroix
- INRIA Erable, CNRS LBBE UMR 5558, University Lyon 1, University of Lyon, F-69622 Villeurbanne, France
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Hallermayr A, Graf J, Koehler U, Laner A, Schönfeld B, Benet‐Pagès A, Holinski‐Feder E. Extending the critical regions for mutations in the non-coding gene RNU4ATAC in another patient with Roifman Syndrome. Clin Case Rep 2018; 6:2224-2228. [PMID: 30455926 PMCID: PMC6230649 DOI: 10.1002/ccr3.1830] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 08/10/2018] [Accepted: 08/25/2018] [Indexed: 12/13/2022] Open
Abstract
Compound heterozygosity of a previously described pathogenic variant and a second novel nucleotide substitution (NR_023343.1:n.116A>C) affecting a highly conserved nucleotide in the noncoding RNU4ATAC gene could be identified in a patient with overlapping features of Roifman Syndrome. These data extend the spectrum of pathogenic variants in RNU4ATAC.
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10
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Heremans J, Garcia-Perez JE, Turro E, Schlenner SM, Casteels I, Collin R, de Zegher F, Greene D, Humblet-Baron S, Lesage S, Matthys P, Penkett CJ, Put K, Stirrups K, Thys C, Van Geet C, Van Nieuwenhove E, Wouters C, Meyts I, Freson K, Liston A. Abnormal differentiation of B cells and megakaryocytes in patients with Roifman syndrome. J Allergy Clin Immunol 2018; 142:630-646. [DOI: 10.1016/j.jaci.2017.11.061] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/28/2017] [Accepted: 11/06/2017] [Indexed: 12/12/2022]
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