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Hennocq Q, Paternoster G, Collet C, Amiel J, Bongibault T, Bouygues T, Cormier-Daire V, Douillet M, Dunaway DJ, Jeelani NO, van de Lande LS, Lyonnet S, Ong J, Picard A, Rickart AJ, Rio M, Schievano S, Arnaud E, Garcelon N, Khonsari RH. AI-based diagnosis and phenotype - Genotype correlations in syndromic craniosynostoses. J Craniomaxillofac Surg 2024:S1010-5182(24)00055-6. [PMID: 39187417 DOI: 10.1016/j.jcms.2024.02.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 02/02/2024] [Indexed: 08/28/2024] Open
Abstract
Apert (AS), Crouzon (CS), Muenke (MS), Pfeiffer (PS), and Saethre Chotzen (SCS) are among the most frequently diagnosed syndromic craniosynostoses. The aims of this study were (1) to train an innovative model using artificial intelligence (AI)-based methods on two-dimensional facial frontal, lateral, and external ear photographs to assist diagnosis for syndromic craniosynostoses vs controls, and (2) to screen for genotype/phenotype correlations in AS, CS, and PS. We included retrospectively and prospectively, from 1979 to 2023, all frontal and lateral pictures of patients genetically diagnosed with AS, CS, MS, PS and SCS syndromes. After a deep learning-based preprocessing, we extracted geometric and textural features and used XGboost (eXtreme Gradient Boosting) to classify patients. The model was tested on an independent international validation set of genetically confirmed patients and non-syndromic controls. Between 1979 and 2023, we included 2228 frontal and lateral facial photographs corresponding to 541 patients. In all, 70.2% [0.593-0.797] (p < 0.001) of patients in the validation set were correctly diagnosed. Genotypes linked to a splice donor site of FGFR2 in Crouzon-Pfeiffer syndrome (CPS) caused a milder phenotype in CPS. Here we report a new method for the automatic detection of syndromic craniosynostoses using AI.
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Affiliation(s)
- Quentin Hennocq
- Imagine Institute, INSERM UMR1163, 75015, Paris, France; Département de chirurgie maxillo-faciale et chirurgie plastique, Hôpital Necker - Enfants Malades, Assistance Publique - Hôpitaux de Paris, Centre de Référence des Malformations Rares de la Face et de la Cavité Buccale MAFACE, Filière Maladies Rares TeteCou, Faculté de Médecine, Université de Paris Cité, 75015, Paris, France; Laboratoire 'Forme et Croissance du Crâne', Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Faculté de Médecine, Université Paris Cité, Paris, France.
| | - Giovanna Paternoster
- Imagine Institute, INSERM UMR1163, 75015, Paris, France; Département de neurochirurgie, Hôpital Necker - Enfants Malades, Assistance Publique - Hôpitaux de Paris, Centre de Référence des Malformations Rares de la Face et de la Cavité Buccale MAFACE, Filière Maladies Rares TeteCou, Faculté de Médecine, Université de Paris Cité, 75015, Paris, France
| | - Corinne Collet
- Département de génétique moléculaire, Hôpital Robert Debré, Université de Paris Cité, Paris, France
| | - Jeanne Amiel
- Imagine Institute, INSERM UMR1163, 75015, Paris, France; Service de médecine génomique des maladies rares, Hôpital Necker - Enfants Malades, Assistance Publique - Hôpitaux de Paris, Faculté de Médecine, Université de Paris Cité, 75015, Paris, France
| | - Thomas Bongibault
- Imagine Institute, INSERM UMR1163, 75015, Paris, France; Laboratoire 'Forme et Croissance du Crâne', Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Faculté de Médecine, Université Paris Cité, Paris, France
| | - Thomas Bouygues
- Imagine Institute, INSERM UMR1163, 75015, Paris, France; Laboratoire 'Forme et Croissance du Crâne', Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Faculté de Médecine, Université Paris Cité, Paris, France
| | - Valérie Cormier-Daire
- Imagine Institute, INSERM UMR1163, 75015, Paris, France; Service de médecine génomique des maladies rares, Hôpital Necker - Enfants Malades, Assistance Publique - Hôpitaux de Paris, Faculté de Médecine, Université de Paris Cité, 75015, Paris, France
| | | | - David J Dunaway
- UCL Great Ormond Street Institute of Child Health and Craniofacial Unit, Great Ormond Street Hospital for Children, London, UK
| | - Nu Owase Jeelani
- UCL Great Ormond Street Institute of Child Health and Craniofacial Unit, Great Ormond Street Hospital for Children, London, UK
| | - Lara S van de Lande
- UCL Great Ormond Street Institute of Child Health and Craniofacial Unit, Great Ormond Street Hospital for Children, London, UK; Department of Oral and Maxillofacial Surgery, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Stanislas Lyonnet
- Imagine Institute, INSERM UMR1163, 75015, Paris, France; Service de médecine génomique des maladies rares, Hôpital Necker - Enfants Malades, Assistance Publique - Hôpitaux de Paris, Faculté de Médecine, Université de Paris Cité, 75015, Paris, France
| | - Juling Ong
- UCL Great Ormond Street Institute of Child Health and Craniofacial Unit, Great Ormond Street Hospital for Children, London, UK
| | - Arnaud Picard
- Département de chirurgie maxillo-faciale et chirurgie plastique, Hôpital Necker - Enfants Malades, Assistance Publique - Hôpitaux de Paris, Centre de Référence des Malformations Rares de la Face et de la Cavité Buccale MAFACE, Filière Maladies Rares TeteCou, Faculté de Médecine, Université de Paris Cité, 75015, Paris, France
| | - Alexander J Rickart
- UCL Great Ormond Street Institute of Child Health and Craniofacial Unit, Great Ormond Street Hospital for Children, London, UK
| | - Marlène Rio
- Imagine Institute, INSERM UMR1163, 75015, Paris, France; Service de médecine génomique des maladies rares, Hôpital Necker - Enfants Malades, Assistance Publique - Hôpitaux de Paris, Faculté de Médecine, Université de Paris Cité, 75015, Paris, France
| | - Silvia Schievano
- UCL Great Ormond Street Institute of Child Health and Craniofacial Unit, Great Ormond Street Hospital for Children, London, UK
| | - Eric Arnaud
- Département de neurochirurgie, Hôpital Necker - Enfants Malades, Assistance Publique - Hôpitaux de Paris, Centre de Référence des Malformations Rares de la Face et de la Cavité Buccale MAFACE, Filière Maladies Rares TeteCou, Faculté de Médecine, Université de Paris Cité, 75015, Paris, France; Clinique Marcel Sembat (Ramsay), Boulogne, France
| | | | - Roman H Khonsari
- Imagine Institute, INSERM UMR1163, 75015, Paris, France; Département de chirurgie maxillo-faciale et chirurgie plastique, Hôpital Necker - Enfants Malades, Assistance Publique - Hôpitaux de Paris, Centre de Référence des Malformations Rares de la Face et de la Cavité Buccale MAFACE, Filière Maladies Rares TeteCou, Faculté de Médecine, Université de Paris Cité, 75015, Paris, France; Laboratoire 'Forme et Croissance du Crâne', Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Faculté de Médecine, Université Paris Cité, Paris, France; Département de neurochirurgie, Hôpital Necker - Enfants Malades, Assistance Publique - Hôpitaux de Paris, Centre de Référence des Malformations Rares de la Face et de la Cavité Buccale MAFACE, Filière Maladies Rares TeteCou, Faculté de Médecine, Université de Paris Cité, 75015, Paris, France
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Smith C, Kitzman JO. Benchmarking splice variant prediction algorithms using massively parallel splicing assays. Genome Biol 2023; 24:294. [PMID: 38129864 PMCID: PMC10734170 DOI: 10.1186/s13059-023-03144-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Variants that disrupt mRNA splicing account for a sizable fraction of the pathogenic burden in many genetic disorders, but identifying splice-disruptive variants (SDVs) beyond the essential splice site dinucleotides remains difficult. Computational predictors are often discordant, compounding the challenge of variant interpretation. Because they are primarily validated using clinical variant sets heavily biased to known canonical splice site mutations, it remains unclear how well their performance generalizes. RESULTS We benchmark eight widely used splicing effect prediction algorithms, leveraging massively parallel splicing assays (MPSAs) as a source of experimentally determined ground-truth. MPSAs simultaneously assay many variants to nominate candidate SDVs. We compare experimentally measured splicing outcomes with bioinformatic predictions for 3,616 variants in five genes. Algorithms' concordance with MPSA measurements, and with each other, is lower for exonic than intronic variants, underscoring the difficulty of identifying missense or synonymous SDVs. Deep learning-based predictors trained on gene model annotations achieve the best overall performance at distinguishing disruptive and neutral variants, and controlling for overall call rate genome-wide, SpliceAI and Pangolin have superior sensitivity. Finally, our results highlight two practical considerations when scoring variants genome-wide: finding an optimal score cutoff, and the substantial variability introduced by differences in gene model annotation, and we suggest strategies for optimal splice effect prediction in the face of these issues. CONCLUSION SpliceAI and Pangolin show the best overall performance among predictors tested, however, improvements in splice effect prediction are still needed especially within exons.
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Affiliation(s)
- Cathy Smith
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Jacob O Kitzman
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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3
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Na B, Wang AC, Watterson CT, Martinez-Agosto J, Saitta S, Dutra-Clarke M, Bhansali F, Pineles SL, Chang VY, Shah VS, de Blank P. An unusual presentation of bilateral optic pathway glioma in Crouzon Syndrome. Pediatr Hematol Oncol 2023; 40:800-806. [PMID: 37334681 DOI: 10.1080/08880018.2023.2201264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 02/13/2023] [Accepted: 03/02/2023] [Indexed: 06/20/2023]
Abstract
Crouzon Syndrome is a genetic craniosynostosis disorder associated with a high risk of ophthalmologic sequelae secondary to structural causes. However, ophthalmologic disorders due to intrinsic nerve aberrations in Crouzon Syndrome have not been described. Optic pathway gliomas (OPGs) are low grade gliomas that are intrinsic to the visual pathway, frequently associated with Neurofibromatosis type 1 (NF-1). OPGs involving both optic nerves without affecting the optic chiasm are rarely seen outside of NF-1. We report an unusual case of bilateral optic nerve glioma without chiasmatic involvement in a 17-month-old male patient with Crouzon Syndrome without any clinical or genetic findings of NF-1. This case suggests that close ophthalmologic follow up and orbital MRIs may benefit patients with Crouzon Syndrome.
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Affiliation(s)
- Brian Na
- UCLA Neuro-Oncology Program, Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, California, USA
- Department of Molecular and Medical Pharmacology, UCLA David Geffen School of Medicine, Los Angeles, California, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California, USA
| | - Anthony C Wang
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California, USA
- Division of Pediatric Neurosurgery, Department of Neurosurgery, UCLA David Geffen School of Medicine, Los Angeles, California, USA
| | | | - Julian Martinez-Agosto
- Department of Human Genetics, UCLA David Geffen School of Medicine, Los Angeles, California, USA
- Division of Genetics, Department of Pediatrics, UCLA David Geffen School of Medicine, Los Angeles, California, USA
- Department of Psychiatry, UCLA David Geffen School of Medicine, Los Angeles, California, USA
| | - Sulagna Saitta
- Department of Human Genetics, UCLA David Geffen School of Medicine, Los Angeles, California, USA
- Division of Genetics, Department of Pediatrics, UCLA David Geffen School of Medicine, Los Angeles, California, USA
| | - Marina Dutra-Clarke
- Division of Genetics, Department of Pediatrics, UCLA David Geffen School of Medicine, Los Angeles, California, USA
| | - Franceska Bhansali
- Division of Genetics, Department of Pediatrics, UCLA David Geffen School of Medicine, Los Angeles, California, USA
| | - Stacy L Pineles
- Department of Ophthalmology, UCLA David Geffen School of Medicine, Los Angeles, California, USA
| | - Vivian Y Chang
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California, USA
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, UCLA David Geffen School of Medicine, Los Angeles, California, USA
- Children's Discovery and Innovation Institute, UCLA David Geffen School of Medicine, Los Angeles, California, USA
| | - Veeral S Shah
- Division of Pediatric Neurology and Department of Ophthalmology, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Peter de Blank
- Division of Oncology, The Cure Starts Now Brain Tumor Center, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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4
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Smith C, Kitzman JO. Benchmarking splice variant prediction algorithms using massively parallel splicing assays. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.04.539398. [PMID: 37205456 PMCID: PMC10187268 DOI: 10.1101/2023.05.04.539398] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Background Variants that disrupt mRNA splicing account for a sizable fraction of the pathogenic burden in many genetic disorders, but identifying splice-disruptive variants (SDVs) beyond the essential splice site dinucleotides remains difficult. Computational predictors are often discordant, compounding the challenge of variant interpretation. Because they are primarily validated using clinical variant sets heavily biased to known canonical splice site mutations, it remains unclear how well their performance generalizes. Results We benchmarked eight widely used splicing effect prediction algorithms, leveraging massively parallel splicing assays (MPSAs) as a source of experimentally determined ground-truth. MPSAs simultaneously assay many variants to nominate candidate SDVs. We compared experimentally measured splicing outcomes with bioinformatic predictions for 3,616 variants in five genes. Algorithms' concordance with MPSA measurements, and with each other, was lower for exonic than intronic variants, underscoring the difficulty of identifying missense or synonymous SDVs. Deep learning-based predictors trained on gene model annotations achieved the best overall performance at distinguishing disruptive and neutral variants. Controlling for overall call rate genome-wide, SpliceAI and Pangolin also showed superior overall sensitivity for identifying SDVs. Finally, our results highlight two practical considerations when scoring variants genome-wide: finding an optimal score cutoff, and the substantial variability introduced by differences in gene model annotation, and we suggest strategies for optimal splice effect prediction in the face of these issues. Conclusion SpliceAI and Pangolin showed the best overall performance among predictors tested, however, improvements in splice effect prediction are still needed especially within exons.
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Affiliation(s)
- Cathy Smith
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jacob O. Kitzman
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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5
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Hoshino Y, Takechi M, Moazen M, Steacy M, Koyabu D, Furutera T, Ninomiya Y, Nuri T, Pauws E, Iseki S. Synchondrosis fusion contributes to the progression of postnatal craniofacial dysmorphology in syndromic craniosynostosis. J Anat 2023; 242:387-401. [PMID: 36394990 PMCID: PMC9919486 DOI: 10.1111/joa.13790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/16/2022] [Accepted: 10/28/2022] [Indexed: 11/18/2022] Open
Abstract
Syndromic craniosynostosis (CS) patients exhibit early, bony fusion of calvarial sutures and cranial synchondroses, resulting in craniofacial dysmorphology. In this study, we chronologically evaluated skull morphology change after abnormal fusion of the sutures and synchondroses in mouse models of syndromic CS for further understanding of the disease. We found fusion of the inter-sphenoid synchondrosis (ISS) in Apert syndrome model mice (Fgfr2S252W/+ ) around 3 weeks old as seen in Crouzon syndrome model mice (Fgfr2cC342Y/+ ). We then examined ontogenic trajectories of CS mouse models after 3 weeks of age using geometric morphometrics analyses. Antero-ventral growth of the face was affected in Fgfr2S252W/+ and Fgfr2cC342Y/+ mice, while Saethre-Chotzen syndrome model mice (Twist1+/- ) did not show the ISS fusion and exhibited a similar growth pattern to that of control littermates. Further analysis revealed that the coronal suture synostosis in the CS mouse models induces only the brachycephalic phenotype as a shared morphological feature. Although previous studies suggest that the fusion of the facial sutures during neonatal period is associated with midface hypoplasia, the present study suggests that the progressive postnatal fusion of the cranial synchondrosis also contributes to craniofacial dysmorphology in mouse models of syndromic CS. These morphological trajectories increase our understanding of the progression of syndromic CS skull growth.
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Affiliation(s)
- Yukiko Hoshino
- Department of Molecular Craniofacial Embryology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.,Office of New Drug V, Pharmaceuticals and Medical Devices Agency (PMDA), Tokyo, Japan
| | - Masaki Takechi
- Department of Molecular Craniofacial Embryology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.,Department of Anatomy and Life Structure, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Mehran Moazen
- Department of UCL Mechanical Engineering, University College London, London, UK
| | - Miranda Steacy
- Institute of Child Health, Great Ormond Street, University College London, London, UK
| | - Daisuke Koyabu
- Department of Molecular Craniofacial Embryology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.,Research and Development Center for Precision Medicine, Tsukuba University, Tsukuba, Japan
| | - Toshiko Furutera
- Department of Molecular Craniofacial Embryology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.,Department of Anatomy and Life Structure, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Youichirou Ninomiya
- Research Organization of Information and Systems, National Institute of Informatics, Tokyo, Japan
| | - Takashi Nuri
- Department of Plastic and Reconstructive Surgery, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Erwin Pauws
- Institute of Child Health, Great Ormond Street, University College London, London, UK
| | - Sachiko Iseki
- Department of Molecular Craniofacial Embryology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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Sarkar A, Panati K, Narala VR. Code inside the codon: The role of synonymous mutations in regulating splicing machinery and its impact on disease. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108444. [PMID: 36307006 DOI: 10.1016/j.mrrev.2022.108444] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 10/10/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
Abstract
In eukaryotes, precise pre-mRNA processing, including alternative splicing, is essential to carry out the intricate protein translation process. Both point mutations (that alter the translated protein sequence) and synonymous mutations (that do not alter the translated protein sequence) are capable of affecting the splicing process. Synonymous mutations are known to affect gene expression via altering mRNA stability, mRNA secondary structure, splicing processes, and translational kinetics. In higher eukaryotes, precise splicing is regulated by three weakly conserved cis-elements, 5' and 3' splice sites and the branch site. Many other cis-acting elements (exonic/intronic splicing enhancers and silencers) and trans-acting splicing factors (serine and arginine-rich proteins and heterogeneous nuclear ribonucleoproteins) have also been found to enhance or suppress the splicing process. The appearance of synonymous mutations in cis-acting elements can alter the splicing process by changing the binding pattern of splicing factors to exonic splicing enhancers or silencer motifs. This results in exon skipping, intron retention, and various other forms of alternative splicing, eventually leading to the emergence of a wide range of diseases. The focus of this review is to elucidate the role of synonymous mutations and their impact on abnormal splicing mechanisms. Further, this study highlights the function of synonymous mutation in mediating abnormal splicing in cancer and development of X-linked, and autosomal inherited diseases.
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Affiliation(s)
- Avik Sarkar
- Department of Zoology, Vidyasagar University, Midnapore, West Bengal 721102, India
| | - Kalpana Panati
- Department of Biotechnology, Government College for Men, Kadapa 516004, India
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Lo Vecchio F, Tabolacci E, Nobile V, Pomponi MG, Pietrobono R, Neri G, Amenta S, Candida E, Grippaudo C, Lo Cascio E, Vita A, Tiberio F, Arcovito A, Lattanzi W, Genuardi M, Chiurazzi P. Mother and Daughter Carrying of the Same Pathogenic Variant in FGFR2 with Discordant Phenotype. Genes (Basel) 2022; 13:genes13071161. [PMID: 35885943 PMCID: PMC9319849 DOI: 10.3390/genes13071161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 11/16/2022] Open
Abstract
Craniosynostosis are a heterogeneous group of genetic conditions characterized by the premature fusion of the skull bones. The most common forms of craniosynostosis are Crouzon, Apert and Pfeiffer syndromes. They differ from each other in various additional clinical manifestations, e.g., syndactyly is typical of Apert and rare in Pfeiffer syndrome. Their inheritance is autosomal dominant with incomplete penetrance and one of the main genes responsible for these syndromes is FGFR2, mapped on chromosome 10, encoding fibroblast growth factor receptor 2. We report an FGFR2 gene variant in a mother and daughter who present with different clinical features of Crouzon syndrome. The daughter is more severely affected than her mother, as also verified by a careful study of the face and oral cavity. The c.1032G>A transition in exon 8, already reported as a synonymous p.Ala344 = variant in Crouzon patients, also activates a new donor splice site leading to the loss of 51 nucleotides and the in-frame removal of 17 amino acids. We observed lower FGFR2 transcriptional and translational levels in the daughter compared to the mother and healthy controls. A preliminary functional assay and a molecular modeling added further details to explain the discordant phenotype of the two patients.
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Affiliation(s)
- Filomena Lo Vecchio
- UOC Genetica Medica, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Roma, Italy; (F.L.V.); (M.G.P.); (S.A.); (M.G.)
| | - Elisabetta Tabolacci
- Dipartimento Universitario Scienze Della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (E.T.); (V.N.); (R.P.); (G.N.)
- Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Roma, Italy;
| | - Veronica Nobile
- Dipartimento Universitario Scienze Della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (E.T.); (V.N.); (R.P.); (G.N.)
- Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Roma, Italy;
| | - Maria Grazia Pomponi
- UOC Genetica Medica, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Roma, Italy; (F.L.V.); (M.G.P.); (S.A.); (M.G.)
| | - Roberta Pietrobono
- Dipartimento Universitario Scienze Della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (E.T.); (V.N.); (R.P.); (G.N.)
- Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Roma, Italy;
| | - Giovanni Neri
- Dipartimento Universitario Scienze Della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (E.T.); (V.N.); (R.P.); (G.N.)
| | - Simona Amenta
- UOC Genetica Medica, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Roma, Italy; (F.L.V.); (M.G.P.); (S.A.); (M.G.)
| | | | - Cristina Grippaudo
- Dipartimento Testa Collo, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, Università Cattolica del Sacro Cuore, 00168 Roma, Italy;
| | - Ettore Lo Cascio
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (A.A.); (E.L.C.)
| | - Alessia Vita
- Dipartimento Universitario Scienze della Vita e Sanità Pubblica, Sezione di Biologia Applicata, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168 Roma, Italy; (A.V.); (F.T.)
| | - Federica Tiberio
- Dipartimento Universitario Scienze della Vita e Sanità Pubblica, Sezione di Biologia Applicata, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168 Roma, Italy; (A.V.); (F.T.)
| | - Alessandro Arcovito
- Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Roma, Italy;
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (A.A.); (E.L.C.)
| | - Wanda Lattanzi
- Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Roma, Italy;
- Dipartimento Universitario Scienze della Vita e Sanità Pubblica, Sezione di Biologia Applicata, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168 Roma, Italy; (A.V.); (F.T.)
| | - Maurizio Genuardi
- UOC Genetica Medica, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Roma, Italy; (F.L.V.); (M.G.P.); (S.A.); (M.G.)
- Dipartimento Universitario Scienze Della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (E.T.); (V.N.); (R.P.); (G.N.)
| | - Pietro Chiurazzi
- UOC Genetica Medica, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Roma, Italy; (F.L.V.); (M.G.P.); (S.A.); (M.G.)
- Dipartimento Universitario Scienze Della Vita e Sanità Pubblica, Sezione di Medicina Genomica, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (E.T.); (V.N.); (R.P.); (G.N.)
- Correspondence: ; Tel.: +39-06-3015-4606
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Improving genetic diagnosis of Mendelian disease with RNA sequencing: a narrative review. JOURNAL OF BIO-X RESEARCH 2022. [DOI: 10.1097/jbr.0000000000000100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Mapping RNA splicing variations in clinically accessible and nonaccessible tissues to facilitate Mendelian disease diagnosis using RNA-seq. Genet Med 2020; 22:1181-1190. [PMID: 32225167 DOI: 10.1038/s41436-020-0780-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 03/03/2020] [Accepted: 03/05/2020] [Indexed: 01/14/2023] Open
Abstract
PURPOSE RNA-seq is a promising approach to improve diagnoses by detecting pathogenic aberrations in RNA splicing that are missed by DNA sequencing. RNA-seq is typically performed on clinically accessible tissues (CATs) from blood and skin. RNA tissue specificity makes it difficult to identify aberrations in relevant but nonaccessible tissues (non-CATs). We determined how RNA-seq from CATs represent splicing in and across genes and non-CATs. METHODS We quantified RNA splicing in 801 RNA-seq samples from 56 different adult and fetal tissues from Genotype-Tissue Expression Project (GTEx) and ArrayExpress. We identified genes and splicing events in each non-CAT and determined when RNA-seq in each CAT would inadequately represent them. We developed an online resource, MAJIQ-CAT, for exploring our analysis for specific genes and tissues. RESULTS In non-CATs, 40.2% of genes have splicing that is inadequately represented by at least one CAT; 6.3% of genes have splicing inadequately represented by all CATs. A majority (52.1%) of inadequately represented genes are lowly expressed in CATs (transcripts per million (TPM) < 1), but 5.8% are inadequately represented despite being well expressed (TPM > 10). CONCLUSION Many splicing events in non-CATs are inadequately evaluated using RNA-seq from CATs. MAJIQ-CAT allows users to explore which accessible tissues, if any, best represent splicing in genes and tissues of interest.
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Hines EA, Jones MKN, Harvey JF, Perlyn C, Ornitz DM, Sun X, Verheyden JM. Crouzon syndrome mouse model exhibits cartilage hyperproliferation and defective segmentation in the developing trachea. SCIENCE CHINA-LIFE SCIENCES 2019; 62:1375-1380. [PMID: 31463736 DOI: 10.1007/s11427-019-9568-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/16/2019] [Indexed: 12/30/2022]
Abstract
Crouzon syndrome is the result of a gain-of-function point mutation in FGFR2. Mimicking the human mutation, a mouse model of Crouzon syndrome (Fgfr2342Y) recapitulates patient deformities, including failed tracheal cartilage segmentation, resulting in a cartilaginous sleeve in the homozygous mutants. We found that the Fgfr2C342Y/C342Y mutants exhibited an increase in chondrocytes prior to segmentation. This increase is due at least in part to over proliferation. Genetic ablation of chondrocytes in the mutant led to restoration of segmentation in the lateral but not central portion of the trachea. These results suggest that in the Fgfr2C342Y/C342Y mutants, increased cartilage cell proliferation precedes and contributes to the disruption of cartilage segmentation in the developing trachea.
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Affiliation(s)
- Elizabeth A Hines
- Laboratory of Genetics, University of Wisconsin, Madison, WI, 53706, USA
| | - Mary-Kayt N Jones
- Laboratory of Genetics, University of Wisconsin, Madison, WI, 53706, USA
| | - Julie F Harvey
- Laboratory of Genetics, University of Wisconsin, Madison, WI, 53706, USA
| | - Chad Perlyn
- Department of Surgery, Florida International University College of Medicine, Miami, FL, 33199, USA
| | - David M Ornitz
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Xin Sun
- Laboratory of Genetics, University of Wisconsin, Madison, WI, 53706, USA. .,Department of Pediatrics, University of California-San Diego, La Jolla, CA, 92093, USA.
| | - Jamie M Verheyden
- Laboratory of Genetics, University of Wisconsin, Madison, WI, 53706, USA. .,Department of Pediatrics, University of California-San Diego, La Jolla, CA, 92093, USA.
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Abstract
Craniosynostosis refers to a condition during early development in which one or more of the fibrous sutures of the skull prematurely fuse by turning into bone, which produces recognizable patterns of cranial shape malformations depending on which suture(s) are affected. In addition to cases with isolated cranial dysmorphologies, craniosynostosis appears in syndromes that include skeletal features of the eyes, nose, palate, hands, and feet as well as impairment of vision, hearing, and intellectual development. Approximately 85% of the cases are nonsyndromic sporadic and emerge after de novo structural genome rearrangements or single nucleotide variation, while the remainders consist of syndromic cases following mendelian inheritance. By karyotyping, genome wide linkage, and CNV analyses as well as by whole exome and whole genome sequencing, numerous candidate genes for craniosynostosis belonging to the FGF, Wnt, BMP, Ras/ERK, ephrin, hedgehog, STAT, and retinoic acid signaling pathways have been identified. Many of the craniosynostosis-related candidate genes form a functional network based upon protein-protein or protein-DNA interactions. Depending on which node of this craniosynostosis-related network is affected by a gene mutation or a change in gene expression pattern, a distinct craniosynostosis syndrome or set of phenotypes ensues. Structural variations may alter the dosage of one or several genes or disrupt the genomic architecture of genes and their regulatory elements within topologically associated chromatin domains. These may exert dominant effects by either haploinsufficiency, dominant negative partial loss of function, gain of function, epistatic interaction, or alteration of levels and patterns of gene expression during development. Molecular mechanisms of dominant modes of action of these mutations may include loss of one or several binding sites for cognate protein partners or transcription factor binding sequences. Such losses affect interactions within functional networks governing development and consequently result in phenotypes such as craniosynostosis. Many of the novel variants identified by genome wide CNV analyses, whole exome and whole genome sequencing are incorporated in recently developed diagnostic algorithms for craniosynostosis.
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Affiliation(s)
- Martin Poot
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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12
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One-Stage Treatment for Adult Patients With Crouzonoid Appearance by Orthognathic and Face Contouring Surgery. J Craniofac Surg 2017; 28:e441-e444. [PMID: 28538070 DOI: 10.1097/scs.0000000000003633] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Crouzon syndrome is a rare genetic disorder with autosomal-dominant inheritance that shows a triad of hallmark characteristics: craniosynostosis, exophthalmos, and midface retrusion. General treatment protocol for patients with Crouzon syndrome has already been established, but there is no standard treatment strategy for adult patients with Crouzonoid appearance. The authors present clinical patients of 1-stage orthognathic and face contouring surgery to achieve functional and aesthetic improvement.One-stage surgery was performed in adult patients with Crouzonoid appearance without a history of facial surgery. Orthognathic 2-jaw surgery was first performed to treat class III malocclusion. Face contouring surgery was conducted next to improve the aesthetic appearance using midface augmentation with onlay rib bone graft, advancement genioplasty, augmentation rhinoplasty, and ancillary procedures such as neck lift, fat graft, or fillers.Five patients (2 men, 3 women) were enrolled in this study. The mean age at the time of surgery was 19.0 years. No specific surgery-related complications such as infection, nerve injury, or recurred malocclusion were observed during the 3.5 years of follow-up. Normal class I occlusion was reached in all patients. The frontonasal angle, nasolabial angle, and labiomental angle improved from 125.1° to 135.1° (P > 0.05), 60.9° to 86.3° (P = 0.018), and 146.3° to 125.0° (P = 0.018), respectively. The Global Aesthetic Improvement Scale score was 4.75 and 5.00 in frontal and profile views, respectively.One-stage orthognathic and face contouring surgery may be an effective surgical option with good postoperative functional and aesthetic improvement in adult patients with Crouzonoid appearance.
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Palagano E, Susani L, Menale C, Ramenghi U, Berger M, Uva P, Oppo M, Vezzoni P, Villa A, Sobacchi C. Synonymous Mutations Add a Layer of Complexity in the Diagnosis of Human Osteopetrosis. J Bone Miner Res 2017; 32:99-105. [PMID: 27468155 DOI: 10.1002/jbmr.2929] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/25/2016] [Accepted: 07/27/2016] [Indexed: 11/08/2022]
Abstract
Autosomal recessive osteopetroses (AROs) are rare, genetically heterogeneous skeletal diseases with increased bone density that are often lethal if left untreated. A precise molecular classification is relevant for the patient's management, because in some subgroups hematopoietic stem cell transplantation (HSCT), which is the only curative therapy, is contraindicated. In two unrelated ARO patients, the molecular analysis revealed the presence of a synonymous variant in known ARO genes, namely in the TCIRG1 gene in one patient and in the CLCN7 in the other patient, predicted to impact on the splicing process. In the latter case, sequencing of the transcript confirmed the splicing defect, whereas in the former, for whom an RNA sample was not available, the defect was reconstructed in vitro by the minigene technology. These results strongly suggest that these synonymous changes were responsible for the disease in our patients. Our findings are novel with respect to ARO and add to the few reports in literature dealing with different diseases, underlining the importance of cDNA analysis for the correct assessment of exonic changes, even when exome sequencing is performed. In particular, we highlight the possibility that at least in some cases ARO is due to synonymous changes, erroneously considered clinically silent, in the genes already described in literature, and suggest carefully reevaluating the sequencing results of these genes when mutations are not found at a first analysis. In addition, with respect to the CLCN7 gene, we suggest that synonymous variants might also contribute to the large spectrum of severity typical of CLCN7-dependent osteopetrosis through more subtle, but not negligible, effects on protein availability and functionality. © 2016 American Society for Bone and Mineral Research.
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Affiliation(s)
- Eleonora Palagano
- Humanitas Clinical and Research Institute, Rozzano, Italy.,Department of Medical Biotechnologies and Translational Medicine, University of Milan, Milan, Italy
| | - Lucia Susani
- Humanitas Clinical and Research Institute, Rozzano, Italy.,National Research Council-Institute of Genetics and Biomedical Research (CNR-IRGB), Milan Unit, Milan, Italy
| | - Ciro Menale
- Humanitas Clinical and Research Institute, Rozzano, Italy.,National Research Council-Institute of Genetics and Biomedical Research (CNR-IRGB), Milan Unit, Milan, Italy
| | - Ugo Ramenghi
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Massimo Berger
- Pediatric Onco-Hematology and Stem Cell Transplant Division, Regina Margherita Children Hospital, City of Health and Science, Turin, Italy
| | - Paolo Uva
- CRS4, Science and Technology Park Polaris, Pula, Italy
| | - Manuela Oppo
- CRS4, Science and Technology Park Polaris, Pula, Italy.,Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Paolo Vezzoni
- Humanitas Clinical and Research Institute, Rozzano, Italy.,National Research Council-Institute of Genetics and Biomedical Research (CNR-IRGB), Milan Unit, Milan, Italy
| | - Anna Villa
- Humanitas Clinical and Research Institute, Rozzano, Italy.,National Research Council-Institute of Genetics and Biomedical Research (CNR-IRGB), Milan Unit, Milan, Italy
| | - Cristina Sobacchi
- Humanitas Clinical and Research Institute, Rozzano, Italy.,National Research Council-Institute of Genetics and Biomedical Research (CNR-IRGB), Milan Unit, Milan, Italy
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