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Brooks EC, Han SJY, Bonatto Paese CL, Lewis AA, Aarnio-Peterson M, Brugmann SA. The ciliary protein C2cd3 is required for mandibular musculoskeletal tissue patterning. Differentiation 2024; 138:100782. [PMID: 38810379 PMCID: PMC11227401 DOI: 10.1016/j.diff.2024.100782] [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: 02/22/2024] [Revised: 05/06/2024] [Accepted: 05/22/2024] [Indexed: 05/31/2024]
Abstract
The mandible is composed of several musculoskeletal tissues including bone, cartilage, and tendon that require precise patterning to ensure structural and functional integrity. Interestingly, most of these tissues are derived from one multipotent cell population called cranial neural crest cells (CNCCs). How CNCCs are properly instructed to differentiate into various tissue types remains nebulous. To better understand the mechanisms necessary for the patterning of mandibular musculoskeletal tissues we utilized the avian mutant talpid2 (ta2) which presents with several malformations of the facial skeleton including dysplastic tendons, mispatterned musculature, and bilateral ectopic cartilaginous processes extending off Meckel's cartilage. We found an ectopic epithelial BMP signaling domain in the ta2 mandibular prominence (MNP) that correlated with the subsequent expansion of SOX9+ cartilage precursors. These findings were validated with conditional murine models suggesting an evolutionarily conserved mechanism for CNCC-derived musculoskeletal patterning. Collectively, these data support a model in which cilia are required to define epithelial signal centers essential for proper musculoskeletal patterning of CNCC-derived mesenchyme.
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Affiliation(s)
- Evan C Brooks
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH, 45267, USA; Molecular and Developmental Biology Graduate Program, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Simon J Y Han
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH, 45267, USA; Molecular and Developmental Biology Graduate Program, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA; Medical Scientist Training Program, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH, 45267, USA
| | - Christian Louis Bonatto Paese
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH, 45267, USA
| | - Amya A Lewis
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH, 45267, USA
| | - Megan Aarnio-Peterson
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH, 45267, USA
| | - Samantha A Brugmann
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Avenue, Cincinnati, OH, 45267, USA; Division of Plastic Surgery, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH, 45229, USA.
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2
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Hannes L, Atzori M, Goldenberg A, Argente J, Attie-Bitach T, Amiel J, Attanasio C, Braslavsky DG, Bruel AL, Castanet M, Dubourg C, Jacobs A, Lyonnet S, Martinez-Mayer J, Pérez Millán MI, Pezzella N, Pelgrims E, Aerden M, Bauters M, Rochtus A, Scaglia P, Swillen A, Sifrim A, Tammaro R, Mau-Them FT, Odent S, Thauvin-Robinet C, Franco B, Breckpot J. Differential alternative splicing analysis links variation in ZRSR2 to a novel type of oral-facial-digital syndrome. Genet Med 2024; 26:101059. [PMID: 38158857 DOI: 10.1016/j.gim.2023.101059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024] Open
Abstract
PURPOSE Oral-facial-digital (OFD) syndromes are genetically heterogeneous developmental disorders, caused by pathogenic variants in genes involved in primary cilia formation and function. We identified a previously undescribed type of OFD with brain anomalies, ranging from alobar holoprosencephaly to pituitary anomalies, in 6 unrelated families. METHODS Exome sequencing of affected probands was supplemented with alternative splicing analysis in patient and control lymphoblastoid and fibroblast cell lines, and primary cilia structure analysis in patient fibroblasts. RESULTS In 1 family with 2 affected males, we identified a germline variant in the last exon of ZRSR2, NM_005089.4:c.1211_1212del NP_005080.1:p.(Gly404GlufsTer23), whereas 7 affected males from 5 unrelated families were hemizygous for the ZRSR2 variant NM_005089.4:c.1207_1208del NP_005080.1:p.(Arg403GlyfsTer24), either occurring de novo or inherited in an X-linked recessive pattern. ZRSR2, located on chromosome Xp22.2, encodes a splicing factor of the minor spliceosome complex, which recognizes minor introns, representing 0.35% of human introns. Patient samples showed significant enrichment of minor intron retention. Among differentially spliced targets are ciliopathy-related genes, such as TMEM107 and CIBAR1. Primary fibroblasts containing the NM_005089.4:c.1207_1208del ZRSR2 variant had abnormally elongated cilia, confirming an association between defective U12-type intron splicing, OFD and abnormal primary cilia formation. CONCLUSION We introduce a novel type of OFD associated with elongated cilia and differential splicing of minor intron-containing genes due to germline variation in ZRSR2.
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Affiliation(s)
- Laurens Hannes
- Department of Human Genetics, KU Leuven, Leuven, Belgium; Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Marta Atzori
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Alice Goldenberg
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, CHU Rouen, Rouen, France
| | - Jesús Argente
- Department of Pediatrics & Pediatric Endocrinology, Hospital Infantil Universitario Niño Jesús, Madrid, Spain; Department of Pediatrics, Universidad Autónoma de Madrid, Madrid, Spain; CIBEROBN de fisiopatología de la obesidad y nutrición, Instituto de Salud Carlos III, Madrid, Spain; IMDEA Food Institute, Madrid, Spain
| | - Tania Attie-Bitach
- Université Paris Cité, INSERM, IHU Imagine - Institut des maladies génétiques, Paris, France; Service de médecine génomique des maladies rares, Hôpital Universitaire Necker-Enfants Malades, AP-HP, Institut Imagine, Paris, France
| | - Jeanne Amiel
- Université Paris Cité, INSERM, IHU Imagine - Institut des maladies génétiques, Paris, France; Service de médecine génomique des maladies rares, Hôpital Universitaire Necker-Enfants Malades, AP-HP, Institut Imagine, Paris, France
| | | | - Débora G Braslavsky
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE) CONICET - FEI - División de Endocrinología, Hospital de Niños Ricardo Gutiérrez. Buenos Aires, Argentina
| | - Ange-Line Bruel
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France; UF Innovation diagnostique des maladies rares, FHU TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Mireille Castanet
- Normandie Univ, UNIROUEN, Inserm U1239, CHU Rouen, Department of Pediatrics, Rouen, France
| | - Christèle Dubourg
- Department of Molecular Genetics and Genomics, Rennes University Hospital, Rennes, France; Univ Rennes, CNRS, INSERM, IGDR, UMR 6290, ERL U1305, Rennes, France
| | - An Jacobs
- Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
| | - Stanislas Lyonnet
- Université Paris Cité, INSERM, IHU Imagine - Institut des maladies génétiques, Paris, France; Service de médecine génomique des maladies rares, Hôpital Universitaire Necker-Enfants Malades, AP-HP, Institut Imagine, Paris, France
| | - Julian Martinez-Mayer
- Instituto de Biociencias, Biotecnología y Biología Traslacional (IB3), Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - María Inés Pérez Millán
- Instituto de Biociencias, Biotecnología y Biología Traslacional (IB3), Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad de Buenos Aires, Argentina
| | - Nunziana Pezzella
- Telethon Institute of Genetics and Medicine-TIGEM, Naples, Italy; Scuola Superiore Meridionale, School for Advanced Studies, Genomics and Experimental Medicine program, Naples, Italy
| | - Elise Pelgrims
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Mio Aerden
- Department of Human Genetics, KU Leuven, Leuven, Belgium; Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Marijke Bauters
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Anne Rochtus
- Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
| | - Paula Scaglia
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE) CONICET - FEI - División de Endocrinología, Hospital de Niños Ricardo Gutiérrez. Buenos Aires, Argentina
| | - Ann Swillen
- Department of Human Genetics, KU Leuven, Leuven, Belgium; Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | | | - Roberta Tammaro
- Telethon Institute of Genetics and Medicine-TIGEM, Naples, Italy
| | - Frederic Tran Mau-Them
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France; UF Innovation diagnostique des maladies rares, FHU TRANSLAD, CHU Dijon Bourgogne, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic Génomique des maladies rares, CHU Dijon Bourgogne, Dijon, France
| | - Sylvie Odent
- Department of Molecular Genetics and Genomics, Rennes University Hospital, Rennes, France; Univ Rennes, CNRS, INSERM, IGDR, UMR 6290, ERL U1305, Rennes, France; Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Ouest, ERN ITHACA, FHU GenOmedS, Centre Hospitalier Universitaire Rennes, Rennes, France
| | - Christel Thauvin-Robinet
- INSERM, U1231, Génétique des Anomalies du Développement, Université de Bourgogne Franche-Comté, UMR Lipides, Nutrition, Dijon, France; UF Innovation diagnostique des maladies rares, FHU TRANSLAD, CHU Dijon Bourgogne, Dijon, France; Centre de Référence Anomalies du Développement de l'Est, Centre de Génétique, Centre Hospitalier Universitaire Dijon Bourgogne, Dijon, France
| | - Brunella Franco
- Telethon Institute of Genetics and Medicine-TIGEM, Naples, Italy; Scuola Superiore Meridionale, School for Advanced Studies, Genomics and Experimental Medicine program, Naples, Italy; Department of Translational Medicine, Medical Genetics Federico II University of Naples, Naples, Italy
| | - Jeroen Breckpot
- Department of Human Genetics, KU Leuven, Leuven, Belgium; Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium.
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She Y, Ren R, Jiang N. Mechanical stress can regulate temporomandibular joint cavitation via signalling pathways. Dev Biol 2024; 507:1-8. [PMID: 38114053 DOI: 10.1016/j.ydbio.2023.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 12/10/2023] [Accepted: 12/15/2023] [Indexed: 12/21/2023]
Abstract
The temporomandibular joint (TMJ), composed of temporal fossa, mandibular condyle and a fibrocartilage disc with upper and lower cavities, is the biggest synovial joint and biomechanical hinge of the craniomaxillofacial musculoskeletal system. The initial events that give rise to TMJ cavities across diverse species are not fully understood. Most studies focus on the pivotal role of molecules such as Indian hedgehog (Ihh) and hyaluronic acid (HA) in TMJ cavitation. Although biologists have observed that mechanical stress plays an irreplaceable role in the development of biological tissues and organs, few studies have been concerned with how mechanical stress regulates TMJ cavitation. Based on the evidence from human or other animal embryos today, it is implicated that mechanical stress plays an essential role in TMJ cavitation. In this review, we discuss the relationship between mechanical stress and TMJ cavitation from evo-devo perspectives and review the clinical features and potential pathogenesis of TMJ dysplasia.
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Affiliation(s)
- Yilin She
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Disease and West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Rong Ren
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Disease and West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Nan Jiang
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Disease and West China Hospital of Stomatology, Sichuan University, Chengdu, China.
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4
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Cross T, Øvstebø R, Brusletto BS, Trøseid AMS, Olstad OK, Aspelin T, Jackson CJ, Chen X, Utheim TP, Haug KBF. RNA Profiles of Tear Fluid Extracellular Vesicles in Patients with Dry Eye-Related Symptoms. Int J Mol Sci 2023; 24:15390. [PMID: 37895069 PMCID: PMC10607363 DOI: 10.3390/ijms242015390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
Currently, diagnosing and stratifying dry eye disease (DED) require multiple tests, motivating interest in a single definitive test. The purpose of this study was to investigate the potential for using tear fluid extracellular vesicle (EV)-RNA in DED diagnostics. With a role in intercellular communication, nanosized EVs facilitate the protected transport of diverse bioactive molecules in biofluids, including tears. Schirmer strips were used to collect tears from 10 patients presenting with dry eye-related symptoms at the Norwegian Dry Eye Clinic. The samples comprised two groups, five from patients with a tear film break-up time (TBUT) of 2 s and five from patients with a TBUT of 10 s. Tear fluid EV-RNA was isolated using a Qiagen exoRNeasy Midi Kit, and the RNA was characterized using Affymetrix ClariomTM D microarrays. The mean signal values of the two groups were compared using a one-way ANOVA. A total of 26,639 different RNA transcripts were identified, comprising both mRNA and ncRNA subtypes. Approximately 6% of transcripts showed statistically significant differential abundance between the two groups. The mRNA sodium channel modifier 1 (SCNM1) was detected at a level 3.8 times lower, and the immature microRNA-130b was detected at a level 1.5 times higher in the group with TBUT 2 s compared to the group with TBUT 10 s. This study demonstrates the potential for using tear fluid EV-RNA in DED diagnostics.
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Affiliation(s)
- Tanya Cross
- The Regenerative Medicine Unit, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway; (T.C.)
| | - Reidun Øvstebø
- Blood Cell Research Group, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway; (R.Ø.)
| | - Berit Sletbakk Brusletto
- Blood Cell Research Group, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway; (R.Ø.)
| | - Anne-Marie Siebke Trøseid
- Blood Cell Research Group, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway; (R.Ø.)
| | - Ole Kristoffer Olstad
- Blood Cell Research Group, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway; (R.Ø.)
| | - Trude Aspelin
- Blood Cell Research Group, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway; (R.Ø.)
| | - Catherine Joan Jackson
- The Regenerative Medicine Unit, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway; (T.C.)
| | - Xiangjun Chen
- The Regenerative Medicine Unit, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway; (T.C.)
- Department of Ophthalmology, Sørlandet Hospital Arendal, 4838 Arendal, Norway
| | - Tor Paaske Utheim
- The Regenerative Medicine Unit, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway; (T.C.)
- Department of Ophthalmology, Sørlandet Hospital Arendal, 4838 Arendal, Norway
- The Norwegian Dry Eye Clinic, 0369 Oslo, Norway
- Department of Ophthalmology, Oslo University Hospital, 0450 Oslo, Norway
- Department of Ophthalmology, Vestfold Hospital Trust, 3103 Tønsberg, Norway
| | - Kari Bente Foss Haug
- Blood Cell Research Group, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway; (R.Ø.)
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5
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Bruel AL, Ganga AK, Nosková L, Valenzuela I, Martinovic J, Duffourd Y, Zikánová M, Majer F, Kmoch S, Mohler M, Sun J, Sweeney LK, Martínez-Gil N, Thauvin-Robinet C, Breslow DK. Pathogenic RAB34 variants impair primary cilium assembly and cause a novel oral-facial-digital syndrome. Hum Mol Genet 2023; 32:2822-2831. [PMID: 37384395 PMCID: PMC10481091 DOI: 10.1093/hmg/ddad109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/12/2023] [Accepted: 06/17/2023] [Indexed: 07/01/2023] Open
Abstract
Oral-facial-digital syndromes (OFDS) are a group of clinically and genetically heterogeneous disorders characterized by defects in the development of the face and oral cavity along with digit anomalies. Pathogenic variants in over 20 genes encoding ciliary proteins have been found to cause OFDS through deleterious structural or functional impacts on primary cilia. We identified by exome sequencing bi-allelic missense variants in a novel disease-causing ciliary gene RAB34 in four individuals from three unrelated families. Affected individuals presented a novel form of OFDS (OFDS-RAB34) accompanied by cardiac, cerebral, skeletal and anorectal defects. RAB34 encodes a member of the Rab GTPase superfamily and was recently identified as a key mediator of ciliary membrane formation. Unlike many genes required for cilium assembly, RAB34 acts selectively in cell types that use the intracellular ciliogenesis pathway, in which nascent cilia begin to form in the cytoplasm. We find that the protein products of these pathogenic variants, which are clustered near the RAB34 C-terminus, exhibit a strong loss of function. Although some variants retain the ability to be recruited to the mother centriole, cells expressing mutant RAB34 exhibit a significant defect in cilium assembly. While many Rab proteins have been previously linked to ciliogenesis, our studies establish RAB34 as the first small GTPase involved in OFDS and reveal the distinct clinical manifestations caused by impairment of intracellular ciliogenesis.
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Affiliation(s)
- Ange-Line Bruel
- INSERM U1231 Génétique des Anomalies du Développement (GAD), University Bourgogne Franche-Comté, 21070 Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU-TRANSLAD), Centre Hospitalo-Universitaire (CHU) Dijon Bourgogne, 21079 Dijon, France
| | - Anil Kumar Ganga
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Lenka Nosková
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 128 08, Czech Republic
| | - Irene Valenzuela
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital, 08035 Barcelona, Spain
- Medical Genetics Group, Vall d'Hebron Research Institute,08035 Barcelona, Spain
| | - Jelena Martinovic
- Unit of Embryo-Fetal Pathology, AP-HP, Antoine Béclère Hospital, Paris Saclay University, 92141 Clamart, France
| | - Yannis Duffourd
- INSERM U1231 Génétique des Anomalies du Développement (GAD), University Bourgogne Franche-Comté, 21070 Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU-TRANSLAD), Centre Hospitalo-Universitaire (CHU) Dijon Bourgogne, 21079 Dijon, France
| | - Marie Zikánová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 128 08, Czech Republic
| | - Filip Majer
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 128 08, Czech Republic
| | - Stanislav Kmoch
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague 128 08, Czech Republic
| | - Markéta Mohler
- Institute of Molecular and Clinical Pathology and Medical Genetics, University Hospital Ostrava, Ostrava 708 52, Czech Republic
| | - Jingbo Sun
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Lauren K Sweeney
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Núria Martínez-Gil
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital, 08035 Barcelona, Spain
- Medical Genetics Group, Vall d'Hebron Research Institute,08035 Barcelona, Spain
| | - Christel Thauvin-Robinet
- INSERM U1231 Génétique des Anomalies du Développement (GAD), University Bourgogne Franche-Comté, 21070 Dijon, France
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU-TRANSLAD), Centre Hospitalo-Universitaire (CHU) Dijon Bourgogne, 21079 Dijon, France
- Centre de Génétique et Centre de référence maladies rares ‘Anomalies du Développement et Syndromes Malformatifs’, FHU-TRANSLAD, Hôpital d'Enfants, CHU Dijon Bourgogne, 21079 Dijon, France
| | - David K Breslow
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA
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6
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Nabavizadeh N, Bressin A, Shboul M, Moreno Traspas R, Chia PH, Bonnard C, Szenker‐Ravi E, Sarıbaş B, Beillard E, Altunoglu U, Hojati Z, Drutman S, Freier S, El‐Khateeb M, Fathallah R, Casanova J, Soror W, Arafat A, Escande‐Beillard N, Mayer A, Reversade B. A progeroid syndrome caused by a deep intronic variant in TAPT1 is revealed by RNA/SI-NET sequencing. EMBO Mol Med 2023; 15:e16478. [PMID: 36652330 PMCID: PMC9906387 DOI: 10.15252/emmm.202216478] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 01/19/2023] Open
Abstract
Exome sequencing has introduced a paradigm shift for the identification of germline variations responsible for Mendelian diseases. However, non-coding regions, which make up 98% of the genome, cannot be captured. The lack of functional annotation for intronic and intergenic variants makes RNA-seq a powerful companion diagnostic. Here, we illustrate this point by identifying six patients with a recessive Osteogenesis Imperfecta (OI) and neonatal progeria syndrome. By integrating homozygosity mapping and RNA-seq, we delineated a deep intronic TAPT1 mutation (c.1237-52 G>A) that segregated with the disease. Using SI-NET-seq, we document that TAPT1's nascent transcription was not affected in patients' fibroblasts, indicating instead that this variant leads to an alteration of pre-mRNA processing. Predicted to serve as an alternative splicing branchpoint, this mutation enhances TAPT1 exon 12 skipping, creating a protein-null allele. Additionally, our study reveals dysregulation of pathways involved in collagen and extracellular matrix biology in disease-relevant cells. Overall, our work highlights the power of transcriptomic approaches in deciphering the repercussions of non-coding variants, as well as in illuminating the molecular mechanisms of human diseases.
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Affiliation(s)
- Nasrinsadat Nabavizadeh
- Laboratory of Human Genetics & TherapeuticsGenome Institute of Singapore, A*STARSingapore CitySingapore
- Division of Genetics, Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and TechnologyUniversity of IsfahanIsfahanIran
- Medical Genetics DepartmentKoç University School of MedicineIstanbulTurkey
| | | | - Mohammad Shboul
- Department of Medical Laboratory SciencesJordan University of Science and TechnologyIrbidJordan
| | - Ricardo Moreno Traspas
- Laboratory of Human Genetics & TherapeuticsGenome Institute of Singapore, A*STARSingapore CitySingapore
| | - Poh Hui Chia
- Laboratory of Human Genetics & TherapeuticsGenome Institute of Singapore, A*STARSingapore CitySingapore
| | - Carine Bonnard
- Model Development, A*STAR Skin Research Labs (A*SRL)Singapore CitySingapore
| | - Emmanuelle Szenker‐Ravi
- Laboratory of Human Genetics & TherapeuticsGenome Institute of Singapore, A*STARSingapore CitySingapore
| | - Burak Sarıbaş
- Laboratory of Human Genetics & TherapeuticsGenome Institute of Singapore, A*STARSingapore CitySingapore
- Medical Genetics DepartmentKoç University School of MedicineIstanbulTurkey
| | | | - Umut Altunoglu
- Medical Genetics DepartmentKoç University School of MedicineIstanbulTurkey
| | - Zohreh Hojati
- Division of Genetics, Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and TechnologyUniversity of IsfahanIsfahanIran
| | - Scott Drutman
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller BranchRockefeller UniversityNew YorkNYUSA
| | - Susanne Freier
- Max Planck Institute for Molecular GeneticsBerlinGermany
| | | | - Rajaa Fathallah
- National Center for Diabetes, Endocrinology and GeneticsAmmanJordan
| | - Jean‐Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller BranchRockefeller UniversityNew YorkNYUSA
- Laboratory of Human Genetics of Infectious Diseases, Necker BranchINSERM U1163, Necker Hospital for Sick ChildrenParisFrance
- Imagine InstituteUniversity of ParisParisFrance
- Howard Hughes Medical InstituteNew YorkNYUSA
- Pediatric Hematology and Immunology UnitNecker Hospital for Sick ChildrenParisFrance
| | - Wesam Soror
- National Center for Diabetes, Endocrinology and GeneticsAmmanJordan
| | - Alaa Arafat
- National Center for Diabetes, Endocrinology and GeneticsAmmanJordan
| | - Nathalie Escande‐Beillard
- Medical Genetics DepartmentKoç University School of MedicineIstanbulTurkey
- Institute of Molecular and Cell Biology, A*STARSingapore CitySingapore
| | - Andreas Mayer
- Max Planck Institute for Molecular GeneticsBerlinGermany
| | - Bruno Reversade
- Laboratory of Human Genetics & TherapeuticsGenome Institute of Singapore, A*STARSingapore CitySingapore
- Medical Genetics DepartmentKoç University School of MedicineIstanbulTurkey
- Institute of Molecular and Cell Biology, A*STARSingapore CitySingapore
- Department of PaediatricsNational University of SingaporeSingapore CitySingapore
- Smart‐Health Initiative, BESE, KAUSTThuwalKingdom of Saudi Arabia
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