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Walton IS, McCann E, Weber A, Morton JEV, Noons P, Wilson LC, Ching RC, Cilliers D, Johnson D, Phipps JM, Shears DJ, Thomas GPL, Wall SA, Twigg SRF, Wilkie AOM. Reassessing the association: Evaluation of a polyalanine deletion variant of RUNX2 in non-syndromic sagittal and metopic craniosynostosis. J Anat 2024. [PMID: 38760592 DOI: 10.1111/joa.14052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/09/2024] [Accepted: 04/12/2024] [Indexed: 05/19/2024] Open
Abstract
The RUNT-related transcription factor RUNX2 plays a critical role in osteoblast differentiation, and alterations to gene dosage cause distinct craniofacial anomalies. Uniquely amongst the RUNT-related family, vertebrate RUNX2 encodes a polyglutamine/polyalanine repeat (Gln23-Glu-Ala17 in humans), with the length of the polyalanine component completely conserved in great apes. Surprisingly, a frequent 6-amino acid deletion polymorphism, p.(Ala84_Ala89)del, occurs in humans (termed 11A allele), and a previous association study (Cuellar et al. Bone 137:115395;2020) reported that the 11A variant was significantly more frequent in non-syndromic sagittal craniosynostosis (nsSag; allele frequency [AF] = 0.156; 95% confidence interval [CI] 0.126-0.189) compared to non-syndromic metopic craniosynostosis (nsMet; AF = 0.068; 95% CI 0.045-0.098). However, the gnomAD v.2.1.1 control population used by Cuellar et al. did not display Hardy-Weinberg equilibrium, hampering interpretation. To re-examine this association, we genotyped the RUNX2 11A polymorphism in 225 individuals with sporadic nsSag as parent-child trios and 164 singletons with sporadic nsMet, restricting our analysis to individuals of European ancestry. We compared observed allele frequencies to the non-transmitted alleles in the parent-child trios, and to the genome sequencing data from gnomAD v.4, which display Hardy-Weinberg equilibrium. Observed AFs (and 95% CI) were 0.076 (0.053-0.104) in nsSag and 0.082 (0.055-0.118) in nsMet, compared with 0.062 (0.042-0.089) in non-transmitted parental alleles and 0.065 (0.063-0.067) in gnomAD v.4.0.0 non-Finnish European control genomes. In summary, we observed a non-significant excess, compared to gnomAD data, of 11A alleles in both nsSag (relative risk 1.18, 95% CI 0.83-1.67) and nsMet (relative risk 1.29, 95% CI 0.87-1.92), but we did not replicate the much higher excess of RUNX2 11A alleles in nsSag previously reported (p = 0.0001).
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Affiliation(s)
- Isaac S Walton
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Emma McCann
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, England, UK
| | - Astrid Weber
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, England, UK
| | - Jenny E V Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
- Birmingham Craniofacial Unit, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | - Peter Noons
- Birmingham Craniofacial Unit, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | - Louise C Wilson
- Clinical Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Rosanna C Ching
- Oxford Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Deirdre Cilliers
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - David Johnson
- Oxford Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Julie M Phipps
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Deborah J Shears
- Oxford Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Gregory P L Thomas
- Oxford Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Steven A Wall
- Oxford Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Stephen R F Twigg
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Andrew O M Wilkie
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Oxford Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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Cronin BJ, Lee JC. Discussion: Comparison of Morphometric Outcomes following Open Posterior Expansion versus Endoscopic Strip Craniectomy for Sagittal Synostosis. Plast Reconstr Surg 2024; 153:1107-1108. [PMID: 38657010 DOI: 10.1097/prs.0000000000010780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Affiliation(s)
- Brendan J Cronin
- From the Division of Plastic and Reconstructive Surgery, University of California, Los Angeles
| | - Justine C Lee
- From the Division of Plastic and Reconstructive Surgery, University of California, Los Angeles
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Luyckx I, Walton IS, Boeckx N, Van Schil K, Pang C, De Praeter M, Lord H, Watson CM, Bonthron DT, Van Laer L, Wilkie AOM, Loeys B. Homozygous SMAD6 variants in two unrelated patients with craniosynostosis and radioulnar synostosis. J Med Genet 2024; 61:363-368. [PMID: 38290823 PMCID: PMC10982635 DOI: 10.1136/jmg-2023-109151] [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: 01/17/2023] [Accepted: 11/29/2023] [Indexed: 02/01/2024]
Abstract
BACKGROUND SMAD6 encodes an intracellular inhibitor of the bone morphogenetic protein (BMP) signalling pathway. Until now, rare heterozygous loss-of-function variants in SMAD6 were demonstrated to increase the risk of disparate clinical disorders including cardiovascular disease, craniosynostosis and radioulnar synostosis. Only two unrelated patients harbouring biallelic SMAD6 variants presenting a complex cardiovascular phenotype and facial dysmorphism have been described. CASES Here, we present the first two patients with craniosynostosis harbouring homozygous SMAD6 variants. The male probands, both born to healthy consanguineous parents, were diagnosed with metopic synostosis and bilateral or unilateral radioulnar synostosis. Additionally, one proband had global developmental delay. Echocardiographic evaluation did not reveal cardiac or outflow tract abnormalities. MOLECULAR ANALYSES The novel missense (c.[584T>G];[584T>G], p.[(Val195Gly)];[(Val195Gly)]) and missense/splice-site variant (c.[817G>A];[817G>A], r.[(817g>a,817delins[a;817+2_817+228])];[(817g>a,817delins[a;817+2_817+228])], p.[(Glu273Lys,Glu273Serfs*72)];[(Glu273Lys,Glu273Serfs*72)]) both locate in the functional MH1 domain of the protein and have not been reported in gnomAD database. Functional analyses of the variants showed reduced inhibition of BMP signalling or abnormal splicing, respectively, consistent with a hypomorphic mechanism of action. CONCLUSION Our data expand the spectrum of variants and phenotypic spectrum associated with homozygous variants of SMAD6 to include craniosynostosis.
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Affiliation(s)
- Ilse Luyckx
- Center of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
- Department of Clinical Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Isaac Scott Walton
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Nele Boeckx
- Center of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Kristof Van Schil
- Center of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Chingyiu Pang
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Mania De Praeter
- Department of Paediatric Neurosurgery, University Hospital Antwerp, Antwerp, Belgium
| | - Helen Lord
- Oxford Medical Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
| | - Christopher Mark Watson
- Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Leeds, UK
| | - David T Bonthron
- Leeds Institute of Medical Research, University of Leeds, St. James's University Hospital, Leeds, UK
| | - Lut Van Laer
- Center of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - Andrew O M Wilkie
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Bart Loeys
- Center of Medical Genetics, Faculty of Medicine and Health Sciences, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
- Department of Clinical Genetics, Radboud University Medical Center, Nijmegen, Netherlands
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Hong Z, He X, Duan J, Yu F, Liu H, Lu D, Wang M, Zhang Y. Prenatal diagnostic approaches diagnosed craniosynostosis and identified a novel nonsense variant in SMAD6 in a Chinese fetus. Gene 2024; 896:147994. [PMID: 37977316 DOI: 10.1016/j.gene.2023.147994] [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: 04/14/2023] [Revised: 10/06/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Craniosynostosis is one of the most common congenital craniofacial birth defects. The genetic etiology is complex, involving syndromic developmental diseases, chromosomal abnormalities, and monogenic non-syndromic diseases. Herein, we presented a proband of craniosynostosis, who firstly displayed structural abnormalities. This research conducted dynamic ultrasound monitoring a fetus with gradually developing intrauterine growth retardation (IUGR). A novel de novo variant c.41G > A: p.W14* in SMAD6 was identified by pedigree analysis and genetic examination approaches. Recombinant plasmid carrying wild-type sequence and mutant that carries c.41G > A in SMAD6 were constructed and transfected into HEK293T cells. mRNA and protein expression of SMAD6 were reduced in SMAD6 mutants compared to the wild type. Cycloheximide (CHX) treatment and si-UPF1 transfection rescued the SMAD6 mRNA expression in the mutant construct, indicating that c.41G > A: p.W14* in SMAD6 triggered nonsense-mediated mRNA degradation (NMD) process and thus led to haploinsufficiency of the protein product. Our study demonstrated that whole-exome sequencing (WES) was a powerful tool for further diagnosis and etiological identification once fetal malformation was detected by ultrasound. Novel de novo c.41G > A: p.W14* in SMAD6 is pathogenic and potentially leads to craniosynostosis via NMD process.
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Affiliation(s)
- Zhidan Hong
- Center for Reproductive Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China; Clinical Medicine Research Center of Prenatal Diagnosis and Birth Health in Hubei Province, Wuhan, Hubei, PR China; Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan, Hubei, PR China
| | - Xuanyi He
- Center for Reproductive Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China; Clinical Medicine Research Center of Prenatal Diagnosis and Birth Health in Hubei Province, Wuhan, Hubei, PR China; Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan, Hubei, PR China
| | - Jie Duan
- Clinical Medicine Research Center of Prenatal Diagnosis and Birth Health in Hubei Province, Wuhan, Hubei, PR China; Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan, Hubei, PR China; Department of Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
| | - Fang Yu
- Clinical Medicine Research Center of Prenatal Diagnosis and Birth Health in Hubei Province, Wuhan, Hubei, PR China; Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan, Hubei, PR China; Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
| | - Huanyu Liu
- Center for Reproductive Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China; Clinical Medicine Research Center of Prenatal Diagnosis and Birth Health in Hubei Province, Wuhan, Hubei, PR China; Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan, Hubei, PR China
| | - Dan Lu
- Clinical Medicine Research Center of Prenatal Diagnosis and Birth Health in Hubei Province, Wuhan, Hubei, PR China; Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan, Hubei, PR China; Department of Ultrasound, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
| | - Mei Wang
- Center for Reproductive Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China; Clinical Medicine Research Center of Prenatal Diagnosis and Birth Health in Hubei Province, Wuhan, Hubei, PR China; Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan, Hubei, PR China
| | - Yuanzhen Zhang
- Center for Reproductive Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China; Clinical Medicine Research Center of Prenatal Diagnosis and Birth Health in Hubei Province, Wuhan, Hubei, PR China; Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan, Hubei, PR China.
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Fox SC, Waskiewicz AJ. Transforming growth factor beta signaling and craniofacial development: modeling human diseases in zebrafish. Front Cell Dev Biol 2024; 12:1338070. [PMID: 38385025 PMCID: PMC10879340 DOI: 10.3389/fcell.2024.1338070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/18/2024] [Indexed: 02/23/2024] Open
Abstract
Humans and other jawed vertebrates rely heavily on their craniofacial skeleton for eating, breathing, and communicating. As such, it is vital that the elements of the craniofacial skeleton develop properly during embryogenesis to ensure a high quality of life and evolutionary fitness. Indeed, craniofacial abnormalities, including cleft palate and craniosynostosis, represent some of the most common congenital abnormalities in newborns. Like many other organ systems, the development of the craniofacial skeleton is complex, relying on specification and migration of the neural crest, patterning of the pharyngeal arches, and morphogenesis of each skeletal element into its final form. These processes must be carefully coordinated and integrated. One way this is achieved is through the spatial and temporal deployment of cell signaling pathways. Recent studies conducted using the zebrafish model underscore the importance of the Transforming Growth Factor Beta (TGF-β) and Bone Morphogenetic Protein (BMP) pathways in craniofacial development. Although both pathways contain similar components, each pathway results in unique outcomes on a cellular level. In this review, we will cover studies conducted using zebrafish that show the necessity of these pathways in each stage of craniofacial development, starting with the induction of the neural crest, and ending with the morphogenesis of craniofacial elements. We will also cover human skeletal and craniofacial diseases and malformations caused by mutations in the components of these pathways (e.g., cleft palate, craniosynostosis, etc.) and the potential utility of zebrafish in studying the etiology of these diseases. We will also briefly cover the utility of the zebrafish model in joint development and biology and discuss the role of TGF-β/BMP signaling in these processes and the diseases that result from aberrancies in these pathways, including osteoarthritis and multiple synostoses syndrome. Overall, this review will demonstrate the critical roles of TGF-β/BMP signaling in craniofacial development and show the utility of the zebrafish model in development and disease.
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Albaugh SL, Diaz A, Wang E, Shen TC, Williams L, He TC, Reid RR. Systematic Review of Nonsyndromic Craniosynostosis: Genomic Alterations and Impacted Signaling Pathways. Plast Reconstr Surg 2024; 153:383e-396e. [PMID: 37070824 DOI: 10.1097/prs.0000000000010522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
BACKGROUND Genetic research in nonsyndromic craniosynostosis remains limited compared with syndromic craniosynostosis. This systematic review aimed to comprehensively summarize the genetic literature of nonsyndromic craniosynostosis and highlight key signaling pathways. METHODS The authors performed a systematic literature search of PubMed, Ovid, and Google Scholar databases from inception until December of 2021 using search terms related to nonsyndromic craniosynostosis and genetics. Two reviewers screened titles and abstract for relevance, and three reviewers independently extracted study characteristics and genetic data. Gene networks were constructed using Search Tool for Retrieval of Interacting Genes/Proteins (version 11) analysis. RESULTS Thirty-three articles published between 2001 and 2020 met inclusion criteria. Studies were further classified into candidate gene screening and variant identification studies ( n = 16), genetic expression studies ( n = 13), and common and rare variant association studies ( n = 4). Most studies were good quality. Using our curated list of 116 genes extracted from the studies, two main networks were constructed. CONCLUSIONS This systematic review concerns the genetics of nonsyndromic craniosynostosis, with network construction revealing TGF-β/BMP, Wnt, and NF-κB/RANKL as important signaling pathways. Future studies should focus on rare rather than common variants to examine the missing heritability in this defect and, going forward, adopt a standard definition.
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Affiliation(s)
| | - Ashley Diaz
- From the Pritzker School of Medicine, University of Chicago
| | - Esther Wang
- From the Pritzker School of Medicine, University of Chicago
| | - Timothy C Shen
- From the Pritzker School of Medicine, University of Chicago
| | - Lydia Williams
- Laboratory of Craniofacial Biology and Development, Department of Surgery, Section of Plastic and Reconstructive Surgery
| | - Tong-Chuan He
- Molecular Oncology Laboratory, Department of Surgery, Department of Orthopaedic Surgery and Rehabilitation Medicine, University of Chicago Medical Center
| | - Russell R Reid
- Laboratory of Craniofacial Biology and Development, Department of Surgery, Section of Plastic and Reconstructive Surgery
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Watson AL, Winters R. Nonsyndromic Craniofacial Disorders. Facial Plast Surg Clin North Am 2024; 32:127-139. [PMID: 37981408 DOI: 10.1016/j.fsc.2023.06.004] [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] [Indexed: 11/21/2023]
Abstract
We describe the investigation and management of select pediatric craniofacial disorders their recent advances. Positional plagiocephaly: The incidence of positional plagiocephaly has increased since the institution of the "safe to sleep" campaign to reduce sudden infant death syndrome. Positional plagiocephaly may be associated with underlying developmental delay. Nonsyndromic craniosynostosis: Treatment of nonsyndromic craniosynostosis depends on the age of the patient and the suture involved. Pediatric skull lesions: Management of skull lesions depends on histologic diagnosis. Some benign skull lesions are managed conservatively, whereas erosive and malignant lesions may require surgical excision, radiotherapy, chemotherapy, or multimodality treatment.
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Affiliation(s)
- Antonia L Watson
- Department of Otolaryngology - Head & Neck Surgery, John Hunter Hospital, Lookout Road, New Lambton Heights, New South Wales 2035, Australia
| | - Ryan Winters
- Department of Otolaryngology - Head & Neck Surgery, John Hunter Hospital, Lookout Road, New Lambton Heights, New South Wales 2035, Australia; Department of Otolaryngology-Head & Neck Surgery, Tulane University, New Orleans, LA, USA; Division of Plastic & Reconstructive Surgery, Tulane University, New Orleans, LA, USA.
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Kiziltug E, Duy PQ, Allington G, Timberlake AT, Kawaguchi R, Long AS, Almeida MN, DiLuna ML, Alper SL, Alperovich M, Geschwind DH, Kahle KT. Concurrent impact of de novo mutations on cranial and cortical development in nonsyndromic craniosynostosis. J Neurosurg Pediatr 2024; 33:59-72. [PMID: 37890181 PMCID: PMC10783441 DOI: 10.3171/2023.8.peds23155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 08/17/2023] [Indexed: 10/29/2023]
Abstract
OBJECTIVE Nonsyndromic craniosynostosis (nsCS), characterized by premature cranial suture fusion, is considered a primary skull disorder in which impact on neurodevelopment, if present, results from the mechanical hindrance of brain growth. Despite surgical repair of the cranial defect, neurocognitive deficits persist in nearly half of affected children. Therefore, the authors performed a functional genomics analysis of nsCS to determine when, where, and in what cell types nsCS-associated genes converge during development. METHODS The authors integrated whole-exome sequencing data from 291 nsCS proband-parent trios with 29,803 single-cell transcriptomes of the prenatal and postnatal neurocranial complex to inform when, where, and in what cell types nsCS-mutated genes might exert their pathophysiological effects. RESULTS The authors found that nsCS-mutated genes converged in cranial osteoprogenitors and pial fibroblasts and their transcriptional networks that regulate both skull ossification and cerebral neurogenesis. Nonsyndromic CS-mutated genes also converged in inhibitory neurons and gene coexpression modules that overlapped with autism and other developmental disorders. Ligand-receptor cell-cell communication analysis uncovered crosstalk between suture osteoblasts and neurons via the nsCS-associated BMP, FGF, and noncanonical WNT signaling pathways. CONCLUSIONS These data implicate a concurrent impact of nsCS-associated de novo mutations on cranial morphogenesis and cortical development via cell- and non-cell-autonomous mechanisms in a developmental nexus of fetal osteoblasts, pial fibroblasts, and neurons. These results suggest that neurodevelopmental outcomes in nsCS patients may be driven more by mutational status than surgical technique.
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Affiliation(s)
- Emre Kiziltug
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut
| | - Phan Q. Duy
- Department of Neurosurgery, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Garrett Allington
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut
| | - Andrew T. Timberlake
- Hansjörg Wyss Department of Plastic Surgery, New York University Langone Medical Center, New York, New York
| | - Riki Kawaguchi
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Aaron S. Long
- Department of Surgery, Division of Plastic Surgery, Yale University School of Medicine, New Haven, Connecticut
| | - Mariana N. Almeida
- Department of Surgery, Division of Plastic Surgery, Yale University School of Medicine, New Haven, Connecticut
| | - Michael L. DiLuna
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut
| | - Seth L. Alper
- Department of Medicine, Division of Nephrology and Vascular Biology Research Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts
| | - Michael Alperovich
- Department of Surgery, Division of Plastic Surgery, Yale University School of Medicine, New Haven, Connecticut
| | - Daniel H. Geschwind
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Kristopher T. Kahle
- Department of Neurosurgery, Massachusetts General Hospital, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts; and
- Harvard Center for Developmental Brain Disorders, Massachusetts General Hospital, Boston, Massachusetts
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Tooze RS, Miller KA, Swagemakers SMA, Calpena E, McGowan SJ, Boute O, Collet C, Johnson D, Laffargue F, de Leeuw N, Morton JV, Noons P, Ockeloen CW, Phipps JM, Tan TY, Timberlake AT, Vanlerberghe C, Wall SA, Weber A, Wilson LC, Zackai EH, Mathijssen IMJ, Twigg SRF, Wilkie AOM. Pathogenic variants in the paired-related homeobox 1 gene (PRRX1) cause craniosynostosis with incomplete penetrance. Genet Med 2023; 25:100883. [PMID: 37154149 DOI: 10.1016/j.gim.2023.100883] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/30/2023] [Accepted: 04/30/2023] [Indexed: 05/10/2023] Open
Abstract
PURPOSE Studies have previously implicated PRRX1 in craniofacial development, including demonstration of murine Prrx1 expression in the preosteogenic cells of the cranial sutures. We investigated the role of heterozygous missense and loss-of-function (LoF) variants in PRRX1 associated with craniosynostosis. METHODS Trio-based genome, exome, or targeted sequencing were used to screen PRRX1 in patients with craniosynostosis; immunofluorescence analyses were used to assess nuclear localization of wild-type and mutant proteins. RESULTS Genome sequencing identified 2 of 9 sporadically affected individuals with syndromic/multisuture craniosynostosis, who were heterozygous for rare/undescribed variants in PRRX1. Exome or targeted sequencing of PRRX1 revealed a further 9 of 1449 patients with craniosynostosis harboring deletions or rare heterozygous variants within the homeodomain. By collaboration, 7 additional individuals (4 families) were identified with putatively pathogenic PRRX1 variants. Immunofluorescence analyses showed that missense variants within the PRRX1 homeodomain cause abnormal nuclear localization. Of patients with variants considered likely pathogenic, bicoronal or other multisuture synostosis was present in 11 of 17 cases (65%). Pathogenic variants were inherited from unaffected relatives in many instances, yielding a 12.5% penetrance estimate for craniosynostosis. CONCLUSION This work supports a key role for PRRX1 in cranial suture development and shows that haploinsufficiency of PRRX1 is a relatively frequent cause of craniosynostosis.
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Affiliation(s)
- Rebecca S Tooze
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Kerry A Miller
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Sigrid M A Swagemakers
- Department of Pathology & Clinical Bioinformatics, Erasmus University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Eduardo Calpena
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Simon J McGowan
- Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Odile Boute
- Univ. Lille, CHU Lille, ULR 7364 - RADEME - Maladies Rares du Développement Embryonnaire et du Métabolisme, Clinique de Génétique, Lille, France
| | - Corinne Collet
- Genetics Department, Robert Debré University Hospital, APHP, Paris, France
| | - David Johnson
- Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Fanny Laffargue
- Clinical Genetics Service and Reference Centre for Rare Developmental Abnormalities and Intellectual Disabilities, University Hospital of Clermont-Ferrand, Clermont-Ferrand, France
| | - Nicole de Leeuw
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jenny V Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, United Kingdom
| | - Peter Noons
- Department of Craniofacial Surgery, Birmingham Children's Hospital NHS Foundation Trust, Birmingham, United Kingdom
| | - Charlotte W Ockeloen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Julie M Phipps
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Tiong Yang Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| | - Andrew T Timberlake
- Hansjörg Wyss Department of Plastic Surgery, NYU Langone Medical Center, New York, NY
| | - Clemence Vanlerberghe
- Univ. Lille, CHU Lille, ULR 7364 - RADEME - Maladies Rares du Développement Embryonnaire et du Métabolisme, Clinique de Génétique, Lille, France
| | - Steven A Wall
- Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Astrid Weber
- Liverpool Centre for Genomic Medicine, Liverpool Women's NHS Foundation Trust, Liverpool, United Kingdom
| | - Louise C Wilson
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Elaine H Zackai
- Clinical Genetics Center, Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Irene M J Mathijssen
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus Medical Centre, University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Stephen R F Twigg
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom.
| | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
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10
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Fu Z, Chen X, Xu C, Li G, Wu Y, Liu Q, Weng Z, Yan Q, Wang G, Gu A. Association of gut microbiota composition and craniosynostosis. Transl Pediatr 2023; 12:1464-1475. [PMID: 37692543 PMCID: PMC10485648 DOI: 10.21037/tp-23-76] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 07/28/2023] [Indexed: 09/12/2023] Open
Abstract
Background Gut microbiota has been reported to be associated with a series of metabolic diseases including metabolic bone disease. However, study about gut microbiota and craniosynostosis (CS) is very rare. We aim to investigate the gut microbiota composition in CS patients and assess the possible relationship. Methods A total of 30 infants with CS and 30 infants with non-CS treated in Children's Hospital of Nanjing Medical University of Jiangsu Province from June 2021 to March 2022 were finally included in this study. All processing and analysis are carried out using 16S ribosomal RNA (rRNA) high-throughput gene sequencing. Results The CS group have significantly lower levels of family, genus, and species than non-CS group (all P<0.05). Furthermore, Staphylococcales and Lactobacillales at the order level, Enterococcaceae and Staphylococcaceae at the family level, and Enterococcus and Staphylococcus at the genus level were significantly enriched in the CS group (all P<0.05). Additionally, functional prediction showed that six metabolic pathways significantly differed between the two groups (all P<0.05). Of those, pathways involving polycyclic aromatic hydrocarbon degradation (P=0.030) and penicillin and cephalosporin biosynthesis (P=0.027) were more abundant in CS group than in non-CS group. Conclusions Gut microbiota was statistically associated with the development of CS, and several taxa and specific functional pathways with significantly altered abundance have been identified in CS patients. These findings can provide clues for the study on the mechanism and early diagnosis of CS.
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Affiliation(s)
- Zuqiang Fu
- State Key Laboratory of Reproductive Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Nanjing Medical University, Nanjing, China
- School of Public Health, Southeast University, Nanjing, China
| | - Xiu Chen
- State Key Laboratory of Reproductive Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Cheng Xu
- State Key Laboratory of Reproductive Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Guang Li
- Department of Neurosurgery, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Yuying Wu
- Department of Neurosurgery, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Qian Liu
- State Key Laboratory of Reproductive Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Zhenkun Weng
- State Key Laboratory of Reproductive Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Nanjing Medical University, Nanjing, China
| | - Qing Yan
- Department of Neurosurgery, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Gang Wang
- Department of Neurosurgery, Children’s Hospital of Nanjing Medical University, Nanjing, China
| | - Aihua Gu
- State Key Laboratory of Reproductive Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
- Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Nanjing Medical University, Nanjing, China
- School of Public Health, Southeast University, Nanjing, China
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11
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Tooze RS, Calpena E, Twigg SRF, D'Arco F, Wakeling EL, Wilkie AOM. Craniosynostosis, inner ear, and renal anomalies in a child with complete loss of SPRY1 (sprouty homolog 1) function. J Med Genet 2023; 60:712-716. [PMID: 36543535 PMCID: PMC10359576 DOI: 10.1136/jmg-2022-108946] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/11/2022] [Indexed: 12/24/2022]
Abstract
INTRODUCTION SPRY1 encodes protein sprouty homolog 1 (Spry-1), a negative regulator of receptor tyrosine kinase signalling. Null mutant mice display kidney/urinary tract abnormalities and altered size of the skull; complete loss-of-function of Spry-1 in humans has not been reported. METHODS Analysis of whole-genome sequencing data from individuals with craniosynostosis enrolled in the 100,000 Genomes Project identified a likely pathogenic variant within SPRY1. Reverse-transcriptase PCR and western blot analysis were used to investigate the effect of the variant on SPRY1 mRNA and protein, in lymphoblastoid cell lines from the patient and both parents. RESULTS A nonsense variant in SPRY1, encoding p.(Leu27*), was confirmed to be heterozygous in the unaffected parents and homozygous in the child. The child's phenotype, which included sagittal craniosynostosis, subcutaneous cystic lesions overlying the lambdoid sutures, hearing loss associated with bilateral cochlear and vestibular dysplasia and a unilateral renal cyst, overlapped the features reported in Spry1-/- null mice. Functional studies supported escape from nonsense-mediated decay, but western blot analysis demonstrated complete absence of full-length protein in the affected child and a marked reduction in both parents. CONCLUSION This is the first report of complete loss of Spry-1 function in humans, associated with abnormalities of the cranial sutures, inner ear, and kidneys.
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Affiliation(s)
- Rebecca S Tooze
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Eduardo Calpena
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Stephen R F Twigg
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Felice D'Arco
- Department of Radiology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Emma L Wakeling
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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12
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Timberlake AT. SMAD6 variants in nonsyndromic craniosynostosis. Eur J Hum Genet 2023; 31:611-612. [PMID: 36797468 PMCID: PMC10250304 DOI: 10.1038/s41431-023-01317-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 02/06/2023] [Indexed: 02/18/2023] Open
Affiliation(s)
- Andrew T Timberlake
- Hansjörg Wyss Department of Plastic Surgery, NYU Langone Medical Center, New York, NY, USA.
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13
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Timberlake AT, McGee S, Allington G, Kiziltug E, Wolfe EM, Stiegler AL, Boggon TJ, Sanyoura M, Morrow M, Wenger TL, Fernandes EM, Caluseriu O, Persing JA, Jin SC, Lifton RP, Kahle KT, Kruszka P. De novo variants implicate chromatin modification, transcriptional regulation, and retinoic acid signaling in syndromic craniosynostosis. Am J Hum Genet 2023; 110:846-862. [PMID: 37086723 PMCID: PMC10183468 DOI: 10.1016/j.ajhg.2023.03.017] [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: 10/03/2022] [Accepted: 03/24/2023] [Indexed: 04/24/2023] Open
Abstract
Craniosynostosis (CS) is the most common congenital cranial anomaly. Several Mendelian forms of syndromic CS are well described, but a genetic etiology remains elusive in a substantial fraction of probands. Analysis of exome sequence data from 526 proband-parent trios with syndromic CS identified a marked excess (observed 98, expected 33, p = 4.83 × 10-20) of damaging de novo variants (DNVs) in genes highly intolerant to loss-of-function variation (probability of LoF intolerance > 0.9). 30 probands harbored damaging DNVs in 21 genes that were not previously implicated in CS but are involved in chromatin modification and remodeling (4.7-fold enrichment, p = 1.1 × 10-11). 17 genes had multiple damaging DNVs, and 13 genes (CDK13, NFIX, ADNP, KMT5B, SON, ARID1B, CASK, CHD7, MED13L, PSMD12, POLR2A, CHD3, and SETBP1) surpassed thresholds for genome-wide significance. A recurrent gain-of-function DNV in the retinoic acid receptor alpha (RARA; c.865G>A [p.Gly289Arg]) was identified in two probands with similar CS phenotypes. CS risk genes overlap with those identified for autism and other neurodevelopmental disorders, are highly expressed in cranial neural crest cells, and converge in networks that regulate chromatin modification, gene transcription, and osteoblast differentiation. Our results identify several CS loci and have major implications for genetic testing and counseling.
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Affiliation(s)
- Andrew T Timberlake
- Hansjörg Wyss Department of Plastic Surgery, NYU Langone Medical Center, New York, NY, USA
| | | | - Garrett Allington
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Emre Kiziltug
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Erin M Wolfe
- Division of Plastic and Reconstructive Surgery, University of Miami Hospital, Miami, FL, USA
| | - Amy L Stiegler
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Titus J Boggon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | | | | | - Tara L Wenger
- Division of Genetic Medicine, University of Washington, Seattle, WA, USA
| | | | - Oana Caluseriu
- Department of Medical Genetics, University of Alberta, AB, Canada
| | - John A Persing
- Section of Plastic and Reconstructive Surgery, Yale University School of Medicine, New Haven, CT, USA
| | - Sheng Chih Jin
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Richard P Lifton
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA.
| | - Kristopher T Kahle
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, Boston, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
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14
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Duy PQ, Timberlake AT, Lifton RP, Kahle KT. Molecular genetics of human developmental neurocranial anomalies: towards "precision surgery". Cereb Cortex 2023; 33:2912-2918. [PMID: 35739418 PMCID: PMC10016031 DOI: 10.1093/cercor/bhac249] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/30/2022] [Accepted: 05/30/2022] [Indexed: 11/14/2022] Open
Abstract
Recent trio-based whole-exome sequencing studies of congenital hydrocephalus and nonsyndromic craniosynostosis have identified multiple novel disease genes that have illuminated the pathogenesis of these disorders and shed new insight into the genetic regulation of human brain and skull development. Continued study of these and other historically understudied developmental anomalies has the potential to replace the current antiquated, anatomically based disease classification systems with a molecular nomenclature that may increase precision for genetic counseling, prognostication, and surgical treatment stratification-including when not to operate. Data will also inform future clinical trials, catalyze the development of targeted therapies, and generate infrastructure and publicly available data sets relevant for other related nonsurgical neurodevelopmental and neuropsychiatric diseases.
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Affiliation(s)
| | | | - Richard P Lifton
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Kristopher T Kahle
- Corresponding author: Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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15
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Tooze RS, Calpena E, Weber A, Wilson LC, Twigg SRF, Wilkie AOM. Review of Recurrently Mutated Genes in Craniosynostosis Supports Expansion of Diagnostic Gene Panels. Genes (Basel) 2023; 14:615. [PMID: 36980886 PMCID: PMC10048212 DOI: 10.3390/genes14030615] [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: 01/29/2023] [Revised: 02/17/2023] [Accepted: 02/23/2023] [Indexed: 03/05/2023] Open
Abstract
Craniosynostosis, the premature fusion of the cranial sutures, affects ~1 in 2000 children. Although many patients with a genetically determined cause harbor a variant in one of just seven genes or have a chromosomal abnormality, over 60 genes are known to be recurrently mutated, thus comprising a long tail of rarer diagnoses. Genome sequencing for the diagnosis of rare diseases is increasingly used in clinical settings, but analysis of the data is labor intensive and involves a trade-off between achieving high sensitivity or high precision. PanelApp, a crowd-sourced disease-focused set of gene panels, was designed to enable prioritization of variants in known disease genes for a given pathology, allowing enhanced identification of true-positives. For heterogeneous disorders like craniosynostosis, these panels must be regularly updated to ensure that diagnoses are not being missed. We provide a systematic review of genetic literature on craniosynostosis over the last 5 years, including additional results from resequencing a 42-gene panel in 617 affected individuals. We identify 16 genes (representing a 25% uplift) that should be added to the list of bona fide craniosynostosis disease genes and discuss the insights that these new genes provide into pathophysiological mechanisms of craniosynostosis.
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Affiliation(s)
- Rebecca S. Tooze
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Eduardo Calpena
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Astrid Weber
- Liverpool Centre for Genomic Medicine, Liverpool Women’s NHS Foundation Trust, Liverpool L8 7SS, UK
| | - Louise C. Wilson
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Stephen R. F. Twigg
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Andrew O. M. Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
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16
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Timberlake AT, Kiziltug E, Jin SC, Nelson-Williams C, Loring E, Allocco A, Marlier A, Banka S, Stuart H, Passos-Buenos MR, Rosa R, Rogatto SR, Tonne E, Stiegler AL, Boggon TJ, Alperovich M, Steinbacher D, Staffenberg DA, Flores RL, Persing JA, Kahle KT, Lifton RP. De novo mutations in the BMP signaling pathway in lambdoid craniosynostosis. Hum Genet 2023; 142:21-32. [PMID: 35997807 DOI: 10.1007/s00439-022-02477-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/08/2022] [Indexed: 01/18/2023]
Abstract
Lambdoid craniosynostosis (CS) is a congenital anomaly resulting from premature fusion of the cranial suture between the parietal and occipital bones. Predominantly sporadic, it is the rarest form of CS and its genetic etiology is largely unexplored. Exome sequencing of 25 kindreds, including 18 parent-offspring trios with sporadic lambdoid CS, revealed a marked excess of damaging (predominantly missense) de novo mutations that account for ~ 40% of sporadic cases. These mutations clustered in the BMP signaling cascade (P = 1.6 × 10-7), including mutations in genes encoding BMP receptors (ACVRL1 and ACVR2A), transcription factors (SOX11, FOXO1) and a transcriptional co-repressor (IFRD1), none of which have been implicated in other forms of CS. These missense mutations are at residues critical for substrate or target sequence recognition and many are inferred to cause genetic gain-of-function. Additionally, mutations in transcription factor NFIX were implicated in syndromic craniosynostosis affecting diverse sutures. Single cell RNA sequencing analysis of the mouse lambdoid suture identified enrichment of mutations in osteoblast precursors (P = 1.6 × 10-6), implicating perturbations in the balance between proliferation and differentiation of osteoprogenitor cells in lambdoid CS. The results contribute to the growing knowledge of the genetics of CS, have implications for genetic counseling, and further elucidate the molecular etiology of premature suture fusion.
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Affiliation(s)
- Andrew T Timberlake
- Hansjörg Wyss Department of Plastic Surgery, New York University Langone Medical Center, New York, NY, USA.
| | - Emre Kiziltug
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Sheng Chih Jin
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.,Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | | | - Erin Loring
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | | | - August Allocco
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Arnaud Marlier
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Siddharth Banka
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9WL, UK.,Manchester Centre for Genomic Medicine, Health Innovation Manchester, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Helen Stuart
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9WL, UK.,Manchester Centre for Genomic Medicine, Health Innovation Manchester, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL, UK
| | | | - Rafael Rosa
- Clinical Genetics, UFCSPA and Irmandade da Santa Casa de Misericórdia de Porto Alegre (ISCMPA), Porto Alegre, RS, Brazil
| | - Silvia R Rogatto
- Neogene Laboratory, Research Center (CIPE), AC Camargo Cancer Center, São Paulo, SP, Brazil
| | - Elin Tonne
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.,University of Oslo, Oslo, Norway
| | - Amy L Stiegler
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Titus J Boggon
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Michael Alperovich
- Section of Plastic and Reconstructive Surgery, Yale University School of Medicine, New Haven, CT, USA
| | - Derek Steinbacher
- Section of Plastic and Reconstructive Surgery, Yale University School of Medicine, New Haven, CT, USA
| | - David A Staffenberg
- Hansjörg Wyss Department of Plastic Surgery, New York University Langone Medical Center, New York, NY, USA
| | - Roberto L Flores
- Hansjörg Wyss Department of Plastic Surgery, New York University Langone Medical Center, New York, NY, USA
| | - John A Persing
- Section of Plastic and Reconstructive Surgery, Yale University School of Medicine, New Haven, CT, USA
| | - Kristopher T Kahle
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Boston, MA, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA. .,Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA.
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17
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Luyckx I, Verstraeten A, Goumans MJ, Loeys B. SMAD6-deficiency in human genetic disorders. NPJ Genom Med 2022; 7:68. [DOI: 10.1038/s41525-022-00338-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022] Open
Abstract
AbstractSMAD6 encodes an intracellular inhibitor of the bone morphogenetic protein (BMP) signalling pathway. Until now, SMAD6-deficiency has been associated with three distinctive human congenital conditions, i.e., congenital heart diseases, including left ventricular obstruction and conotruncal defects, craniosynostosis and radioulnar synostosis. Intriguingly, a similar spectrum of heterozygous loss-of-function variants has been reported to cause these clinically distinct disorders without a genotype–phenotype correlation. Even identical nucleotide changes have been described in patients with either a cardiovascular phenotype, craniosynostosis or radioulnar synostosis. These findings suggest that the primary pathogenic variant alone cannot explain the resultant patient phenotype. In this review, we summarise clinical and (patho)genetic (dis)similarities between these three SMAD6-related conditions, compare published Madh6 mouse models, in which the importance and impact of the genetic background with respect to the observed phenotype is highlighted, and elaborate on the cellular key mechanisms orchestrated by SMAD6 in the development of these three discrete inherited disorders. In addition, we discuss future research needed to elucidate the pathogenetic mechanisms underlying these diseases in order to improve their molecular diagnosis, advance therapeutic strategies and facilitate counselling of patients and their families.
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18
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Caengprasath N, Buasong A, Ittiwut C, Khongphatthanayothin A, Porntaveetus T, Shotelersuk V. Severe coarctation of the aorta, developmental delay, and multiple dysmorphic features in a child with SMAD6 and SMARCA4 variants. Eur J Med Genet 2022; 65:104601. [PMID: 36049609 DOI: 10.1016/j.ejmg.2022.104601] [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: 04/12/2022] [Revised: 06/18/2022] [Accepted: 08/25/2022] [Indexed: 01/28/2023]
Abstract
Pathogenic variants in SMARCA4 cause Coffin-Siris syndrome (CSS) while those in SMAD6 lead to aortic valve disease and other dysmorphisms. We identified a 6-year-old Thai boy with features of CSS alongside unusual manifestations including, very severe coarctation of the aorta (CoA) requiring coarctectomy in the neonatal period and bilateral radioulnar synostoses. Trio exome sequencing revealed that the patient harbored two de novo variants, a missense c.2475G > T, p.(Trp825Cys) in SMARCA4 and a nonsense c.652C > T, p.(Gln218Ter) in SMAD6. Both of which have never been previously reported. The clinical presentations in our patient are a result of the combinational features of each genetic variant: the SMARCA4 p.(Trp825Cys) variant leads to facial features of Coffin Siris syndrome and Dandy-Walker malformation, while the SMAD6 p.(Gln218Ter) variant underlies radioulnar synostosis. Interestingly, the severity of CoA in the proband is beyond the phenotypic spectra of each genetic variant and may be a result of the synergistic effects of both variants. Here, we report a child with variants in SMARCA4 or SMAD6 with combined features of each plus a severe CoA, possibly due to an additive effect of each variant.
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Affiliation(s)
- Natarin Caengprasath
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Aayalida Buasong
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Chupong Ittiwut
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
| | - Apichai Khongphatthanayothin
- Center of Excellence in Arrhythmia Research, Department of Medicine, Chulalongkorn University and Bangkok General Hospital, Bangkok, Thailand
| | - Thantrira Porntaveetus
- Center of Excellence in Genomics and Precision Dentistry, Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand.
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, The Thai Red Cross Society, Bangkok, Thailand
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19
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Martins TF, Braga Magalhães AF, Verardo LL, Santos GC, Silva Fernandes AA, Gomes Vieira JI, Irano N, dos Santos DB. Functional analysis of litter size and number of teats in pigs: From GWAS to post-GWAS. Theriogenology 2022; 193:157-166. [DOI: 10.1016/j.theriogenology.2022.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/03/2022] [Accepted: 09/05/2022] [Indexed: 10/31/2022]
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20
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Song C, Broadie K. Dysregulation of BMP, Wnt, and Insulin Signaling in Fragile X Syndrome. Front Cell Dev Biol 2022; 10:934662. [PMID: 35880195 PMCID: PMC9307498 DOI: 10.3389/fcell.2022.934662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/06/2022] [Indexed: 01/21/2023] Open
Abstract
Drosophila models of neurological disease contribute tremendously to research progress due to the high conservation of human disease genes, the powerful and sophisticated genetic toolkit, and the rapid generation time. Fragile X syndrome (FXS) is the most prevalent heritable cause of intellectual disability and autism spectrum disorders, and the Drosophila FXS disease model has been critical for the genetic screening discovery of new intercellular secretion mechanisms. Here, we focus on the roles of three major signaling pathways: BMP, Wnt, and insulin-like peptides. We present Drosophila FXS model defects compared to mouse models in stem cells/embryos, the glutamatergic neuromuscular junction (NMJ) synapse model, and the developing adult brain. All three of these secreted signaling pathways are strikingly altered in FXS disease models, giving new mechanistic insights into impaired cellular outcomes and neurological phenotypes. Drosophila provides a powerful genetic screening platform to expand understanding of these secretory mechanisms and to test cellular roles in both peripheral and central nervous systems. The studies demonstrate the importance of exploring broad genetic interactions and unexpected regulatory mechanisms. We discuss a number of research avenues to pursue BMP, Wnt, and insulin signaling in future FXS investigations and the development of potential therapeutics.
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Affiliation(s)
- Chunzhu Song
- Department of Biological Sciences, College of Arts and Science, Vanderbilt University, Nashville, TN, United States
| | - Kendal Broadie
- Department of Biological Sciences, College of Arts and Science, Vanderbilt University, Nashville, TN, United States,Department of Cell and Developmental Biology, School of Medicine, Vanderbilt University, Nashville, TN, United States,Kennedy Center for Research on Human Development, Nashville, TN, United States,Vanderbilt Brain Institute, School of Medicine, Vanderbilt University and Medical Center, Nashville, TN, United States,*Correspondence: Kendal Broadie,
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21
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ASSAMADI M, EL HADWE S, BARRIT S, GILIS N, DE WITTE O. Concordant non-syndromic sagittal craniosynostoses in dizygotic twins discordant for sex. Chirurgia (Bucur) 2022. [DOI: 10.23736/s0394-9508.21.05272-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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22
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Justice CM, Musolf AM, Cuellar A, Lattanzi W, Simeonov E, Kaneva R, Paschall J, Cunningham M, Wilkie AOM, Wilson AF, Romitti PA, Boyadjiev SA. Targeted Sequencing of Candidate Regions Associated with Sagittal and Metopic Nonsyndromic Craniosynostosis. Genes (Basel) 2022; 13:816. [PMID: 35627201 PMCID: PMC9141801 DOI: 10.3390/genes13050816] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/07/2022] [Accepted: 04/12/2022] [Indexed: 02/04/2023] Open
Abstract
Craniosynostosis (CS) is a major birth defect in which one or more skull sutures fuse prematurely. We previously performed a genome-wide association study (GWAS) for sagittal non-syndromic CS (sNCS), identifying associations downstream from BMP2 on 20p12.3 and intronic to BBS9 on 7p14.3; analyses of imputed variants in DLG1 on 3q29 were also genome-wide significant. We followed this work with a GWAS for metopic non-syndromic NCS (mNCS), discovering a significant association intronic to BMP7 on 20q13.31. In the current study, we sequenced the associated regions on 3q29, 7p14.3, and 20p12.3, including two candidate genes (BMP2 and BMPER) near some of these regions in 83 sNCS child-parent trios, and sequenced regions on 7p14.3 and 20q13.2-q13.32 in 80 mNCS child-parent trios. These child-parent trios were selected from the original GWAS cohorts if the probands carried at least one copy of the top associated GWAS variant (rs1884302 C allele for sNCS; rs6127972 T allele for mNCS). Many of the variants sequenced in these targeted regions are strongly predicted to be within binding sites for transcription factors involved in craniofacial development or bone morphogenesis. Variants enriched in more than one trio and predicted to be damaging to gene function are prioritized for functional studies.
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Affiliation(s)
- Cristina M. Justice
- Genometrics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institute of Health (NIH), Baltimore, MD 21224, USA; (C.M.J.); (A.F.W.)
| | - Anthony M. Musolf
- Statistical Genetics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institute of Health (NIH), Baltimore, MD 21224, USA;
| | - Araceli Cuellar
- Department of Pediatrics, University of California Davis, Sacramento, CA 95616, USA;
| | - Wanda Lattanzi
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy;
- Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Emil Simeonov
- Pediatric Clinic, Alexandrovska University Hospital, Medical University of Sofia, 1431 Sofia, Bulgaria;
| | - Radka Kaneva
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University of Sofia, 1431 Sofia, Bulgaria;
| | - Justin Paschall
- Bioinformatics Core, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institute of Health (NIH), Bethesda, MD 20892, USA;
| | - Michael Cunningham
- Seattle Children’s Craniofacial Center, Center of Developmental Biology and Regenerative Medicine and Division of Craniofacial Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98105, USA;
| | - Andrew O. M. Wilkie
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK;
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DS, UK
- Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DS, UK
| | - Alexander F. Wilson
- Genometrics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institute of Health (NIH), Baltimore, MD 21224, USA; (C.M.J.); (A.F.W.)
| | - Paul A. Romitti
- Department of Epidemiology, College of Public Health, The University of Iowa, Iowa City, IA 52242, USA
| | - Simeon A. Boyadjiev
- Department of Pediatrics, University of California Davis, Sacramento, CA 95616, USA;
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23
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Abstract
BACKGROUND Nonsyndromic craniosynostosis is one of the most common anomalies treated by craniofacial surgeons. Despite optimal surgical management, nearly half of affected children have subtle neurocognitive deficits. Whereas timing and type of surgical intervention have been studied, the possibility of genetic influence on neurodevelopment in nonsyndromic craniosynostosis patients remains unexplored. METHODS The authors performed whole-exome sequencing for 404 case-parent trios with sporadic nonsyndromic craniosynostosis. Statistical analyses were performed to assess the burden of de novo mutations in cases compared to both expectation and 1789 healthy control trios. Individuals with and without each mutation class were analyzed, and the presence or absence of various types of neurodevelopmental delay were recorded alongside demographic information. RESULTS The authors identified a highly significant burden of damaging de novo mutations in mutation-intolerant [probability of loss of function intolerance (pLI) >0.9] genes in nonsyndromic craniosynostosis probands (p = 5.9 × 10-6). Children with these mutations had a two-fold higher incidence of neurodevelopmental delay (p = 0.001) and a more than 20-fold greater incidence of intellectual disability (p = 7.2 × 10-7), and were 3.6-fold more likely to have delays that persisted past 5 years of age (p = 4.4 × 10-4) in comparison with children with nonsyndromic craniosynostosis without these mutations. Transmitted loss of function mutations in high-pLI genes also conferred a 1.9-fold greater risk of neurodevelopmental delay (p = 4.5 ×10-4). CONCLUSIONS These findings implicate genetic lesions concurrently impacting neurodevelopment and cranial morphogenesis in the pathoetiology of nonsyndromic craniosynostosis and identify a strong genetic influence on neurodevelopmental outcomes in affected children. These findings may eventually prove useful in determining which children with nonsyndromic craniosynostosis are most likely to benefit from surgical intervention. CLINICAL QUESTION/LEVEL OF EVIDENCE Risk, III.
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24
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Calpena E, Wurmser M, McGowan SJ, Atique R, Bertola DR, Cunningham ML, Gustafson JA, Johnson D, Morton JEV, Passos-Bueno MR, Timberlake AT, Lifton RP, Wall SA, Twigg SRF, Maire P, Wilkie AOM. Unexpected role of SIX1 variants in craniosynostosis: expanding the phenotype of SIX1-related disorders. J Med Genet 2022; 59:165-169. [PMID: 33436522 PMCID: PMC8273188 DOI: 10.1136/jmedgenet-2020-107459] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 01/19/2023]
Abstract
BACKGROUND Pathogenic heterozygous SIX1 variants (predominantly missense) occur in branchio-otic syndrome (BOS), but an association with craniosynostosis has not been reported. METHODS We investigated probands with craniosynostosis of unknown cause using whole exome/genome (n=628) or RNA (n=386) sequencing, and performed targeted resequencing of SIX1 in 615 additional patients. Expression of SIX1 protein in embryonic cranial sutures was examined in the Six1nLacZ/+ reporter mouse. RESULTS From 1629 unrelated cases with craniosynostosis we identified seven different SIX1 variants (three missense, including two de novo mutations, and four nonsense, one of which was also present in an affected twin). Compared with population data, enrichment of SIX1 loss-of-function variants was highly significant (p=0.00003). All individuals with craniosynostosis had sagittal suture fusion; additionally four had bilambdoid synostosis. Associated BOS features were often attenuated; some carrier relatives appeared non-penetrant. SIX1 is expressed in a layer basal to the calvaria, likely corresponding to the dura mater, and in the mid-sagittal mesenchyme. CONCLUSION Craniosynostosis is associated with heterozygous SIX1 variants, with possible enrichment of loss-of-function variants compared with classical BOS. We recommend screening of SIX1 in craniosynostosis, particularly when sagittal±lambdoid synostosis and/or any BOS phenotypes are present. These findings highlight the role of SIX1 in cranial suture homeostasis.
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Affiliation(s)
- Eduardo Calpena
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Maud Wurmser
- Institut Cochin, INSERM, CNRS, Université de Paris, Paris, France
| | - Simon J McGowan
- Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Rodrigo Atique
- Centro de Estudos do Genoma Humano, Universidade de São Paulo, São Paulo, Brazil
| | - Débora R Bertola
- Unidade de Genética Clínica, Instituto da Criança do Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Michael L Cunningham
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, Washington, USA
- Seattle Children's Craniofacial Center, Seattle Children's Hospital, and Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, Washington, USA
| | - Jonas A Gustafson
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, Washington, USA
| | - David Johnson
- Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jenny E V Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | | | - Andrew T Timberlake
- Hansjörg Wyss Department of Plastic Surgery, New York University Langone Medical Center, New York, New York, USA
| | | | - Steven A Wall
- Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Stephen R F Twigg
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Pascal Maire
- Institut Cochin, INSERM, CNRS, Université de Paris, Paris, France
| | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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25
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Tønne E, Due-Tønnessen BJ, Vigeland MD, Amundsen SS, Ribarska T, Åsten PM, Sheng Y, Helseth E, Gilfillan GD, Mero IL, Heimdal KR. Whole-exome sequencing in syndromic craniosynostosis increases diagnostic yield and identifies candidate genes in osteogenic signaling pathways. Am J Med Genet A 2022; 188:1464-1475. [PMID: 35080095 DOI: 10.1002/ajmg.a.62663] [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: 09/29/2021] [Revised: 11/26/2021] [Accepted: 12/26/2021] [Indexed: 11/07/2022]
Abstract
Craniosynostosis (CS) is a common congenital anomaly defined by premature fusion of one or more cranial sutures. Syndromic CS involves additional organ anomalies or neurocognitive deficits and accounts for 25%-30% of the cases. In a recent population-based study by our group, 84% of the syndromic CS cases had a genetically verified diagnosis after targeted analyses. A number of different genetic causes were detected, confirming that syndromic CS is highly heterogeneous. In this study, we performed whole-exome sequencing of 10 children and parents from the same cohort where previous genetic results were negative. We detected pathogenic, or likely pathogenic, variants in four additional genes (NFIA, EXTL3, POLR2A, and FOXP2) associated with rare conditions. In two of these (POLR2A and FOXP2), CS has not previously been reported. We further detected a rare predicted damaging variant in SH3BP4, which has not previously been related to human disease. All findings were clustered in genes involved in the pathways of osteogenesis and suture patency. We conclude that whole-exome sequencing expands the list of genes associated with syndromic CS, and provides new candidate genes in osteogenic signaling pathways.
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Affiliation(s)
- Elin Tønne
- Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.,Norwegian National Unit for Craniofacial Surgery, Oslo University Hospital, Oslo, Norway
| | - Bernt Johan Due-Tønnessen
- Norwegian National Unit for Craniofacial Surgery, Oslo University Hospital, Oslo, Norway.,Department of Neurosurgery, Oslo University Hospital, Oslo, Norway
| | - Magnus Dehli Vigeland
- Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | | | - Teodora Ribarska
- Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | | | - Ying Sheng
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Eirik Helseth
- Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Neurosurgery, Oslo University Hospital, Oslo, Norway
| | - Gregor Duncan Gilfillan
- Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Inger-Lise Mero
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Ketil Riddervold Heimdal
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.,Norwegian National Unit for Craniofacial Surgery, Oslo University Hospital, Oslo, Norway
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26
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Kague E, Medina-Gomez C, Boyadjiev SA, Rivadeneira F. The genetic overlap between osteoporosis and craniosynostosis. Front Endocrinol (Lausanne) 2022; 13:1020821. [PMID: 36225206 PMCID: PMC9548872 DOI: 10.3389/fendo.2022.1020821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/08/2022] [Indexed: 11/29/2022] Open
Abstract
Osteoporosis is the most prevalent bone condition in the ageing population. This systemic disease is characterized by microarchitectural deterioration of bone, leading to increased fracture risk. In the past 15 years, genome-wide association studies (GWAS), have pinpointed hundreds of loci associated with bone mineral density (BMD), helping elucidate the underlying molecular mechanisms and genetic architecture of fracture risk. However, the challenge remains in pinpointing causative genes driving GWAS signals as a pivotal step to drawing the translational therapeutic roadmap. Recently, a skull BMD-GWAS uncovered an intriguing intersection with craniosynostosis, a congenital anomaly due to premature suture fusion in the skull. Here, we recapitulate the genetic contribution to both osteoporosis and craniosynostosis, describing the biological underpinnings of this overlap and using zebrafish models to leverage the functional investigation of genes associated with skull development and systemic skeletal homeostasis.
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Affiliation(s)
- Erika Kague
- School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences, University of Bristol, Bristol, United Kingdom
- *Correspondence: Erika Kague,
| | - Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus Medical Center (MC), University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Simeon A. Boyadjiev
- Department of Pediatrics, University of California, Davis, Sacramento, CA, United States
| | - Fernando Rivadeneira
- Department of Oral and Maxillofacial Surgery, Erasmus Medical Center (MC), University Medical Center Rotterdam, Rotterdam, Netherlands
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27
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Twins with Craniosynostosis: An Unidentified Variant/Twin Research: Kangaroo Care for Premature Twins; Developmental Delay in MZ Twins; Osteosarcoma in One Identical Twin; Controversies in Twin Pregnancy Management/Media Reports: Twin and Triplet Olympians; Twin's Rescue from a Crocodile; Twin Pandas in Japan; Twin Surrogacy; Identical Twins in Pennsylvania. Twin Res Hum Genet 2021; 24:352-357. [PMID: 34879893 DOI: 10.1017/thg.2021.39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Craniosynostosis involves the early closure of one or more joints connecting the bones of an infant's skull. A case of young monozygotic (MZ) male twins with an unidentified variant of this condition is described, followed by a summary of relevant published reports. This overview is followed by descriptions of a kangaroo care program for premature twins, developmental delay in an MZ twin pair, osteosarcoma in one MZ twin and controversial issues in the management of multiple pregnancies. Media reports of twin and triplet Olympic athletes, a twin's rescue from a crocodile, the birth of twin pandas in Japan, a case of twin surrogacy and the birth of identical triplets are also presented.
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28
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Yamada M, Funato M, Kondo G, Suzuki H, Uehara T, Takenouchi T, Sakamoto Y, Kosaki K. Noonan syndrome-like phenotype in a patient with heterozygous ERF truncating variant. Congenit Anom (Kyoto) 2021; 61:226-230. [PMID: 34184330 DOI: 10.1111/cga.12435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/01/2021] [Accepted: 06/15/2021] [Indexed: 12/27/2022]
Abstract
Craniosynostosis is caused by abnormalities of multiple signaling pathways, including excessive RAS signaling. Recently, a truncating variant in ETS2 repressor factor (ERF), a negative transcriptional regulator of the RAS pathway, was shown to be associated with craniosynostosis. Here, we report a 10-year-old male patient with a heterozygous nonsense mutation, p.Arg183*, in ERF who exhibited craniosynostosis with Noonan syndrome-like phenotypes. In consideration that loss-of-function variants in ERF would result in excessive RAS signaling and RASopathy phenotypes, we propose that ERF may represent a causative gene for Noonan syndrome. Since preceding studies on ERF mutations dealt with patients who were ascertained because of craniosynostosis, further studies are needed to evaluate whether patients with variants in ERF can present with Noonan syndrome-like features without craniosynostosis.
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Affiliation(s)
- Mamiko Yamada
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Michinori Funato
- Department of Pediatrics, National Hospital Organization Nagara Medical Center, Gifu, Japan
| | - Goro Kondo
- Department of Neurosurgery, National Hospital Organization Nagara Medical Center, Gifu, Japan
| | - Hisato Suzuki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Tomoko Uehara
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan.,Department of Pediatrics, Central Hospital, Aichi Developmental Disability Center, Aichi, Japan
| | - Toshiki Takenouchi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Yoshiaki Sakamoto
- Department of Plastic and Reconstructive Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
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29
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Proteomic Analysis of Exosomes during Cardiogenic Differentiation of Human Pluripotent Stem Cells. Cells 2021; 10:cells10102622. [PMID: 34685602 PMCID: PMC8533815 DOI: 10.3390/cells10102622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 09/23/2021] [Accepted: 09/28/2021] [Indexed: 11/26/2022] Open
Abstract
Efforts to direct the specification of human pluripotent stem cells (hPSCs) to therapeutically important somatic cell types have focused on identifying proper combinations of soluble cues. Yet, whether exosomes, which mediate intercellular communication, play a role in the differentiation remains unexplored. We took a first step toward addressing this question by subjecting hPSCs to stage-wise specification toward cardiomyocytes (CMs) in scalable stirred-suspension cultures and collecting exosomes. Samples underwent liquid chromatography (LC)/mass spectrometry (MS) and subsequent proteomic analysis revealed over 300 unique proteins from four differentiation stages including proteins such as PPP2CA, AFM, MYH9, MYH10, TRA2B, CTNNA1, EHD1, ACTC1, LDHB, and GPC4, which are linked to cardiogenic commitment. There was a significant correlation of the protein composition of exosomes with the hPSC line and stage of commitment. Differentiating hPSCs treated with exosomes from hPSC-derived CMs displayed improved efficiency of CM formation compared to cells without exogenously added vesicles. Collectively, these results demonstrate that exosomes from hPSCs induced along the CM lineage contain proteins linked to the specification process with modulating effects and open avenues for enhancing the biomanufacturing of stem cell products for cardiac diseases.
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30
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Fonteles CS, Finnell RH, Lei Y, Zurita-Jimenez ME, Monteiro AJ, George TM, Harshbarger RJ. De novo ALX4 variant detected in child with non-syndromic craniosynostosis. Braz J Med Biol Res 2021; 54:e11396. [PMID: 34586326 DOI: 10.1590/1414-431x2021e11396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 08/11/2021] [Indexed: 02/03/2023] Open
Abstract
Current understanding of the genetic factors contributing to the etiology of non-syndromic craniosynostosis (NSC) remains scarce. The present work investigated the presence of variants in ALX4, EFNA4, and TWIST1 genes in children with NSC to verify if variants within these genes may contribute to the occurrence of these abnormal phenotypes. A total of 101 children (aged 45.07±40.94 months) with NSC participated in this cross-sectional study. Parents and siblings of the probands were invited to participate. Medical and family history of craniosynostosis were documented. Biological samples were collected to obtain genomic DNA. Coding exons of human TWIST1, ALX4, and EFNA4 genes were amplified by polymerase chain reaction and Sanger sequenced. Five missense variants were identified in ALX4 in children with bilateral coronal, sagittal, and metopic synostosis. A de novo ALX4 variant, c.799G>A: p.Ala267Thr, was identified in a proband with sagittal synostosis. Three missense variants were identified in the EFNA4 gene in children with metopic and sagittal synostosis. A TWIST1 variant occurred in a child with unilateral coronal synostosis. Variants were predicted to be among the 0.1% (TWIST1, c.380C>A: p. Ala127Glu) and 1% (ALX4, c.769C>T: p.Arg257Cys, c.799G>A: p.Ala267Thr, c.929G>A: p.Gly310Asp; EFNA4, c.178C>T: p.His60Tyr, C.283A>G: p.Lys95Glu, c.349C>A: Pro117Thr) most deleterious variants in the human genome. With the exception of ALX4, c.799G>A: p.Ala267Thr, all other variants were present in at least one non-affected family member, suggesting incomplete penetrance. Thus, these variants may contribute to the development of craniosynostosis, and should not be discarded as potential candidate genes in the diagnosis of this condition.
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Affiliation(s)
- C S Fonteles
- Programa de Pós-graduação em Odontologia, Faculdade de Farmácia, Odontologia e Enfermagem, Universidade Federal do Ceará, Fortaleza, CE, Brasil
| | - R H Finnell
- Center for Precision Environmental Health, Departments of Molecular and Cellular Biology, Molecular and Human Genetics and Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Y Lei
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - M E Zurita-Jimenez
- Dell Pediatric Research Institute, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - A J Monteiro
- Departamento de Estatística e Matemática Aplicada, Universidade Federal do Ceará, Fortaleza, CE, Brasil
| | - T M George
- Plastic Surgery, Craniofacial Team at the Dell Children's Medical Center of Central Texas, Department of Neurosurgery, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - R J Harshbarger
- Plastic Surgery, Craniofacial Team at the Dell Children's Medical Center of Central Texas, Department of Pediatrics, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
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Haploinsufficiency of SF3B2 causes craniofacial microsomia. Nat Commun 2021; 12:4680. [PMID: 34344887 PMCID: PMC8333351 DOI: 10.1038/s41467-021-24852-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 07/12/2021] [Indexed: 02/02/2023] Open
Abstract
Craniofacial microsomia (CFM) is the second most common congenital facial anomaly, yet its genetic etiology remains unknown. We perform whole-exome or genome sequencing of 146 kindreds with sporadic (n = 138) or familial (n = 8) CFM, identifying a highly significant burden of loss of function variants in SF3B2 (P = 3.8 × 10-10), a component of the U2 small nuclear ribonucleoprotein complex, in probands. We describe twenty individuals from seven kindreds harboring de novo or transmitted haploinsufficient variants in SF3B2. Probands display mandibular hypoplasia, microtia, facial and preauricular tags, epibulbar dermoids, lateral oral clefts in addition to skeletal and cardiac abnormalities. Targeted morpholino knockdown of SF3B2 in Xenopus results in disruption of cranial neural crest precursor formation and subsequent craniofacial cartilage defects, supporting a link between spliceosome mutations and impaired neural crest development in congenital craniofacial disease. The results establish haploinsufficient variants in SF3B2 as the most prevalent genetic cause of CFM, explaining ~3% of sporadic and ~25% of familial cases.
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32
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Functional Network Development in Sagittal Craniosynostosis Treated With Whole Vault Cranioplasty. J Craniofac Surg 2021; 32:1721-1726. [PMID: 33534301 DOI: 10.1097/scs.0000000000007505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
INTRODUCTION In this study, the authors seek to clarify the neurological changes before and after whole vault cranioplasty (WVC) in patients born with sagittal craniosynostosis. METHODS A case control study design was performed that included thirty functional MRI scans, from 25 individual patients. Functional MRI and diffusion tension imaging data were analyzed with BioImageSuite (Yale University, USA). 9 functional brain networks were analyzed, with appropriate correlated functional regions of the brain and utilized for analysis. RESULTS Comparing functional MRI the infants after WVC versus infants before WVC group, the after WVC group demonstrated an increased connectivity in the left frontoparietal, secondary (V2), and third (V3) visual networks (P < 0.001). The right frontoparietal (RFPN) had decreased connectivity (P < 0.001). There is also a decrease and increase in anisotropy in the cingulum and precuneus despite surgery, respectively (P < 0.05). Adolescents treated with WVC compared to controls, demonstrated an increased connectivity in the salience and decreased connectivity in the RFPN relative to adolescent controls. CONCLUSIONS Patients born with sagittal craniosynostosis have different connections in infancy in most of the defined cerebral networks compared to controls. After surgery, there are specific connectivity changes that occur in the RFPN, left frontoparietal, V2, and V3 networks, which are areas associated with executive function and emotional control. Changes identified in white matter tract microstructure connections could be influential in changes in functional connectivity. Although, as a child with sagittal craniosynostosis develops, much of the abnormal network connections, seen in infancy preoperatively, corrects to some degree after surgery. However, some aberrancies in the salience and RFPN networks remain potentially affecting executive functioning.
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33
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Calpena E, McGowan SJ, Blanco Kelly F, Boudry-Labis E, Dieux-Coeslier A, Harrison R, Johnson D, Lachlan K, Morton JEV, Stewart H, Vasudevan P, Twigg SRF, Wilkie AOM. Dissection of contiguous gene effects for deletions around ERF on chromosome 19. Hum Mutat 2021; 42:811-817. [PMID: 33993607 DOI: 10.1002/humu.24213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/07/2021] [Accepted: 04/18/2021] [Indexed: 11/10/2022]
Abstract
Heterozygous intragenic loss-of-function mutations of ERF, encoding an ETS transcription factor, were previously reported to cause a novel craniosynostosis syndrome, suggesting that ERF is haploinsufficient. We describe six families harboring heterozygous deletions including, or near to, ERF, of which four were characterized by whole-genome sequencing and two by chromosomal microarray. Based on the severity of associated intellectual disability (ID), we identify three categories of ERF-associated deletions. The smallest (32 kb) and only inherited deletion included two additional centromeric genes and was not associated with ID. Three larger deletions (264-314 kb) that included at least five further centromeric genes were associated with moderate ID, suggesting that deletion of one or more of these five genes causes ID. The individual with the most severe ID had a more telomerically extending deletion, including CIC, a known ID gene. Children found to harbor ERF deletions should be referred for craniofacial assessment, to exclude occult raised intracranial pressure.
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Affiliation(s)
- Eduardo Calpena
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Simon J McGowan
- Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Fiona Blanco Kelly
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Elise Boudry-Labis
- UF Cytogénomique des Déficiences Intellectuelles et Anomalies du Développement, Institut de Génétique Médicale, Hôpital Jeanne de Flandre, CHRU Lille, France
| | | | - Rachel Harrison
- Nottingham Regional Genetics Service, City Hospital Campus, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Diana Johnson
- Sheffield Regional Genetics Services, Sheffield Children's NHS Trust, Sheffield, UK
| | - Katherine Lachlan
- Wessex Clinical Genetics Service, University Hospital Southampton, Princess Anne Hospital, Southampton, UK
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Jenny E V Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | - Helen Stewart
- Oxford Centre for Genomic Medicine, Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Pradeep Vasudevan
- Leicestershire Genetics Centre, University Hospitals of Leicester NHS Trust, Leicester Royal Infirmary NHS Trust, Leicester, UK
| | - Stephen R F Twigg
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Craniofacial Unit, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, UK
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Xu J, Yan Q, Song C, Liang J, Zhao L, Zhang X, Weng Z, Xu C, Liu Q, Xu S, Pang L, Zhang L, Sun Y, Wang G, Gu A. An Axin2 mutation and perinatal risk factors contribute to sagittal craniosynostosis: evidence from a Chinese female monochorionic diamniotic twin family. Hereditas 2021; 158:20. [PMID: 34134783 PMCID: PMC8210395 DOI: 10.1186/s41065-021-00182-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/27/2021] [Indexed: 11/10/2022] Open
Abstract
Background Craniosynostosis, defined as premature fusion of one or more cranial sutures, affects approximately 1 in every 2000–2500 live births. Sagittal craniosynostosis (CS), the most prevalent form of isolated craniosynostosis, is caused by interplay between genetic and perinatal environmental insults. However, the underlying details remain largely unknown. Methods The proband (a female monochorionic twin diagnosed with CS), her healthy co-twin sister and parents were enrolled. Obstetric history was extracted from medical records. Genetic screening was performed by whole exome sequencing (WES) and confirmed by Sanger sequencing. Functional annotation, conservation and structural analysis were predicted in public database. Phenotype data of Axin2 knockout mice was downloaded from The International Mouse Phenotyping Consortium (IMPC, http://www.mousephenotype.org). Results Obstetric medical records showed that, except for the shared perinatal risk factors by the twins, the proband suffered additional persistent breech presentation and intrauterine growth restriction. We identified a heterozygous mutation of Axin2 (c.1181G > A, p.R394H, rs200899695) in monochorionic twins and their father, but not in the mother. This mutation is not reported in Asian population and results in replacement of Arg at residue 394 by His (p.R394H). Arg 394 is located at the GSK3β binding domain of Axin2 protein, which is highly conserved across species. The mutation was predicted to be potentially deleterious by in silico analysis. Incomplete penetrance of Axin2 haploinsufficiency was found in female mice. Conclusions Axin2 (c.1181G > A, p.R394H, rs200899695) mutation confers susceptibility and perinatal risk factors trigger the occurrence of sagittal craniosynostosis. Our findings provide a new evidence for the gene-environment interplay in understanding pathogenesis of craniosynostosis in Chinese population. Supplementary Information The online version contains supplementary material available at 10.1186/s41065-021-00182-0.
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Affiliation(s)
- Jin Xu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, 211166, China.,Key Laboratory of Modern Toxicology, Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Department of Maternal, Child and Adolescent Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Qing Yan
- Department of Neurosurgery, Children's Hospital of Nanjing Medical University, Nanjing, 210017, China
| | - Chengcheng Song
- Obstetrics and Gynecology Hospital, NHC Key Laboratory of Reproduction Regulation (Shanghai Institute of Planned Parenthood Research), School of Life Sciences, Shanghai, 200011, China
| | - Jingjia Liang
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, 211166, China.,Key Laboratory of Modern Toxicology, Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Liang Zhao
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Xin Zhang
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, 211166, China.,Key Laboratory of Modern Toxicology, Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Zhenkun Weng
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, 211166, China.,Key Laboratory of Modern Toxicology, Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Cheng Xu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, 211166, China.,Key Laboratory of Modern Toxicology, Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Qian Liu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, 211166, China.,Key Laboratory of Modern Toxicology, Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Shuqin Xu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, 211166, China.,Key Laboratory of Modern Toxicology, Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Lu Pang
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, 211166, China.,Key Laboratory of Modern Toxicology, Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Liye Zhang
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, 211166, China.,Key Laboratory of Modern Toxicology, Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Yuan Sun
- Key Laboratory of Modern Toxicology, Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Gang Wang
- Department of Neurosurgery, Children's Hospital of Nanjing Medical University, Nanjing, 210017, China.
| | - Aihua Gu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing, 211166, China. .,Key Laboratory of Modern Toxicology, Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
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Singh R, Cohen ASA, Poulton C, Hjortshøj TD, Akahira-Azuma M, Mendiratta G, Khan WA, Azmanov DN, Woodward KJ, Kirchhoff M, Shi L, Edelmann L, Baynam G, Scott SA, Jabs EW. Deletion of ERF and CIC causes abnormal skull morphology and global developmental delay. Cold Spring Harb Mol Case Stud 2021; 7:mcs.a005991. [PMID: 34117072 PMCID: PMC8208047 DOI: 10.1101/mcs.a005991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/26/2021] [Indexed: 11/24/2022] Open
Abstract
The ETS2 repressor factor (ERF) is a transcription factor in the RAS-MEK-ERK signal transduction cascade that regulates cell proliferation and differentiation, and pathogenic sequence variants in the ERF gene cause variable craniosynostosis inherited in an autosomal dominant pattern. The reported ERF variants are largely loss-of-function, implying haploinsufficiency as a primary disease mechanism; however, ERF gene deletions have not been reported previously. Here we describe three probands with macrocephaly, craniofacial dysmorphology, and global developmental delay. Clinical genetic testing for fragile X and other relevant sequencing panels were negative; however, chromosomal microarray identified heterozygous deletions (63.7–583.2 kb) on Chromosome 19q13.2 in each proband that together included five genes associated with Mendelian diseases (ATP1A3, ERF, CIC, MEGF8, and LIPE). Parental testing indicated that the aberrations were apparently de novo in two of the probands and were inherited in the one proband with the smallest deletion. Deletion of ERF is consistent with the reported loss-of-function ERF variants, prompting clinical copy-number-variant classifications of likely pathogenic. Moreover, the recent characterization of heterozygous loss-of-function CIC sequence variants as a cause of intellectual disability and neurodevelopmental disorders inherited in an autosomal dominant pattern is also consistent with the developmental delays and intellectual disabilities identified among the two probands with CIC deletions. Taken together, this case series adds to the previously reported patients with ERF and/or CIC sequence variants and supports haploinsufficiency of both genes as a mechanism for a variable syndromic cranial phenotype with developmental delays and intellectual disability inherited in an autosomal dominant pattern.
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Affiliation(s)
- Ram Singh
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Sema4, Stamford, Connecticut 06902, USA
| | - Ana S A Cohen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Sema4, Stamford, Connecticut 06902, USA
| | - Cathryn Poulton
- Genetic Service of Western Australia, King Edward Memorial Hospital, Perth, Western Australia 6008, Australia
| | - Tina Duelund Hjortshøj
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Moe Akahira-Azuma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Geetu Mendiratta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Sema4, Stamford, Connecticut 06902, USA
| | - Wahab A Khan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Sema4, Stamford, Connecticut 06902, USA
| | - Dimitar N Azmanov
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia 6009, Australia.,Pathology and Laboratory Medicine, Medical School, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Karen J Woodward
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia 6009, Australia.,Pathology and Laboratory Medicine, Medical School, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Maria Kirchhoff
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Lisong Shi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Sema4, Stamford, Connecticut 06902, USA
| | - Lisa Edelmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Sema4, Stamford, Connecticut 06902, USA
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, Western Australia 6008, Australia.,Faculty of Health and Medical Sciences, Division of Paediatrics and Telethon Kids Institute, University of Western Australia, Perth, Western Australia 6008, Australia.,Faculty of Medicine, University of Notre Dame, Australia, Perth, Western Australia 6160, Australia
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.,Sema4, Stamford, Connecticut 06902, USA
| | - Ethylin Wang Jabs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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36
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A Pilot Study of Identification Genetic Background of Craniosynostosis Cases. J Craniofac Surg 2021; 32:1059-1062. [PMID: 33252532 DOI: 10.1097/scs.0000000000007285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
ABSTRACT The early fusion of the cranial sutures was described as a craniosynostosis. The early diagnosis and management of craniosynostosis is very important. Environmental factors and genetic abnormalities plays a key role during the development of craniosynostosis. Syndromic craniosynostosis cases are related with autosomal dominant disorders but nearly half of the affected cases carry a new mutation. In this study, in order to identify the genetic etiology of craniosynostosis the authors analyzed 20 craniosynostosis patients by using conventional karyotype, aCGH, sanger sequencing, next generation sequencing (NGS) and Multiplex ligation-dependent probe amplification (MLPA) techniques. The authors identified mutations on FGFR2 and FGFR3 genes which were associated with Muenke syndrome, Crouzon syndrome and skeletal dysplasia syndromes. NGS applied all of the cases and 7 clinical variations in 5 different gene were detected in %20 of cases. In addition to these abnormalities; del(11)(q14.1q22.2), del(17)(q21.31), dup(22)(q13.31) and t(2;16)(q37;p13) have been identified in our cohort which are not previously detected in craniosynostosis cases. Our study demonstrates the importance of detailed genetic analysis for the diagnosis, progression and management of the craniosynostosis.
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37
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Wu J, Chen X, Sehgal P, Zhang T, Jackson-Weaver O, Gou Y, Bautch V, Frenkel B, Sun H, Xu J. Arginine methylation of R81 in Smad6 confines BMP-induced Smad1 signaling. J Biol Chem 2021; 296:100496. [PMID: 33667543 PMCID: PMC8050389 DOI: 10.1016/j.jbc.2021.100496] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/05/2021] [Accepted: 03/01/2021] [Indexed: 12/13/2022] Open
Abstract
Bone morphogenetic proteins (BMPs) secreted by a variety of cell types are known to play essential roles in cell differentiation and matrix formation in the bone, cartilage, muscle, blood vessel, and neuronal tissue. BMPs activate intracellular effectors via C-terminal phosphorylation of Smad1, Smad5, and Smad9, which relay the signaling by forming a complex with Smad4 and translocate to the nucleus for transcriptional activation. Smad6 inhibits BMP signaling through diverse mechanisms operative at the membrane, cytosolic, and nuclear levels. However, the mechanistic underpinnings of Smad6 functional diversity remain unclear. Here, using a biochemical approach and cell differentiation systems, we report a cytosolic mechanism of action for Smad6 that requires arginine methylation at arginine 81 (R81) and functions through association with Smad1 and interference with the formation of Smad1–Smad4 complexes. By mutating the methylated arginine residue, R81, and by silencing the expression of protein arginine methyltransferase 1, we show that protein arginine methyltransferase 1 catalyzes R81 methylation of Smad6 upon BMP treatment, R81 methylation subsequently facilitates Smad6 interaction with the phosphorylated active Smad1, and R81 methylation facilitates Smad6-mediated interruption of Smad1–Smad4 complex formation and nuclear translocation. Furthermore, Smad6 WT but not the methylation-deficient R81A mutant inhibited BMP-responsive transcription, attenuated BMP-mediated osteogenic differentiation, and antagonized BMP-mediated inhibition of cell invasion. Taken together, our results suggest that R81 methylation plays an essential role in Smad6-mediated inhibition of BMP responses.
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Affiliation(s)
- Jian Wu
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California, USA
| | - Xi Chen
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California, USA; College of Stomatology, China Medical University, Shenyang, China
| | - Prerna Sehgal
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California, USA
| | - Tingwei Zhang
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California, USA; Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, College of Stomatology, Chongqing Medical University, Chongqing, China
| | - Olan Jackson-Weaver
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California, USA
| | - Yongchao Gou
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California, USA; Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, College of Stomatology, Chongqing Medical University, Chongqing, China
| | - Victoria Bautch
- Department of Biology and McAllister Heart Institute, University of Northern Carolina, Chapel Hill, North Carolina, USA
| | - Baruch Frenkel
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Hongchen Sun
- College of Stomatology, China Medical University, Shenyang, China.
| | - Jian Xu
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California, USA; Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, USA; Norris Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, USA.
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38
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Sadler B, Wilborn J, Antunes L, Kuensting T, Hale AT, Gannon SR, McCall K, Cruchaga C, Harms M, Voisin N, Reymond A, Cappuccio G, Brunetti-Pierri N, Tartaglia M, Niceta M, Leoni C, Zampino G, Ashley-Koch A, Urbizu A, Garrett ME, Soldano K, Macaya A, Conrad D, Strahle J, Dobbs MB, Turner TN, Shannon CN, Brockmeyer D, Limbrick DD, Gurnett CA, Haller G. Rare and de novo coding variants in chromodomain genes in Chiari I malformation. Am J Hum Genet 2021; 108:100-114. [PMID: 33352116 DOI: 10.1016/j.ajhg.2020.12.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/24/2020] [Indexed: 12/16/2022] Open
Abstract
Chiari I malformation (CM1), the displacement of the cerebellum through the foramen magnum into the spinal canal, is one of the most common pediatric neurological conditions. Individuals with CM1 can present with neurological symptoms, including severe headaches and sensory or motor deficits, often as a consequence of brainstem compression or syringomyelia (SM). We conducted whole-exome sequencing (WES) on 668 CM1 probands and 232 family members and performed gene-burden and de novo enrichment analyses. A significant enrichment of rare and de novo non-synonymous variants in chromodomain (CHD) genes was observed among individuals with CM1 (combined p = 2.4 × 10-10), including 3 de novo loss-of-function variants in CHD8 (LOF enrichment p = 1.9 × 10-10) and a significant burden of rare transmitted variants in CHD3 (p = 1.8 × 10-6). Overall, individuals with CM1 were found to have significantly increased head circumference (p = 2.6 × 10-9), with many harboring CHD rare variants having macrocephaly. Finally, haploinsufficiency for chd8 in zebrafish led to macrocephaly and posterior hindbrain displacement reminiscent of CM1. These results implicate chromodomain genes and excessive brain growth in CM1 pathogenesis.
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Yoon JG, Hahn HM, Choi S, Kim SJ, Aum S, Yu JW, Park EK, Shim KW, Lee MG, Kim YO. Molecular Diagnosis of Craniosynostosis Using Targeted Next-Generation Sequencing. Neurosurgery 2020; 87:294-302. [PMID: 31754721 DOI: 10.1093/neuros/nyz470] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 08/18/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Genetic factors play an important role in the pathogenesis of craniosynostosis (CRS). However, the molecular diagnosis of CRS in clinical practice is limited because of its heterogeneous etiology. OBJECTIVE To investigate the genomic landscape of CRS in a Korean cohort and also to establish a practical diagnostic workflow by applying targeted panel sequencing. METHODS We designed a customized panel covering 34 CRS-related genes using in-solution hybrid capture method. We enrolled 110 unrelated Korean patients with CRS, including 40 syndromic and 70 nonsyndromic cases. A diagnostic pipeline was established by combining in-depth clinical reviews and multiple bioinformatics tools for analyzing single-nucleotide variants (SNV)s and copy number variants (CNV)s. RESULTS The diagnostic yield of the targeted panel was 30.0% (33/110). Twenty-five patients (22.7%) had causal genetic variations resulting from SNVs or indels in 9 target genes (TWIST1, FGFR3, TCF12, ERF, FGFR2, ALPL, EFNB1, FBN1, and SKI, in order of frequency). CNV analysis identified 8 (7.3%) additional patients with chromosomal abnormalities involving 1p32.3p31.3, 7p21.1, 10q26, 15q21.3, 16p11.2, and 17p13.3 regions; these cases mostly presented with syndromic clinical features. CONCLUSION The present study shows the wide genomic landscape of CRS, revealing various genetic factors for CRS pathogenesis. In addition, the results demonstrate that an efficient diagnostic workup using target panel sequencing provides great clinical utility in the molecular diagnosis of CRS.
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Affiliation(s)
- Jihoon G Yoon
- Department of Pharmacology, Research Center for Human Genetics, College of Medicine, Yonsei University, Seoul, Republic of Korea
| | - Hyung Min Hahn
- Department of Plastic and Reconstructive Surgery, Institute for Human Tissue Restoration, College of Medicine, Yonsei University, Seoul, Republic of Korea
| | - Sungkyoung Choi
- Department of Pharmacology, Research Center for Human Genetics, College of Medicine, Yonsei University, Seoul, Republic of Korea
| | - Soo Jung Kim
- Department of Plastic and Reconstructive Surgery, Institute for Human Tissue Restoration, College of Medicine, Yonsei University, Seoul, Republic of Korea
| | - Sowon Aum
- Department of Pharmacology, Research Center for Human Genetics, College of Medicine, Yonsei University, Seoul, Republic of Korea
| | - Jung Woo Yu
- Department of Pharmacology, Research Center for Human Genetics, College of Medicine, Yonsei University, Seoul, Republic of Korea.,Department of Pediatric Neurosurgery, Craniofacial Reforming and Reconstruction Clinic, College of Medicine, Yonsei University, Seoul, Republic of Korea
| | - Eun Kyung Park
- Department of Pediatric Neurosurgery, Craniofacial Reforming and Reconstruction Clinic, College of Medicine, Yonsei University, Seoul, Republic of Korea
| | - Kyu Won Shim
- Department of Pediatric Neurosurgery, Craniofacial Reforming and Reconstruction Clinic, College of Medicine, Yonsei University, Seoul, Republic of Korea
| | - Min Goo Lee
- Department of Pharmacology, Research Center for Human Genetics, College of Medicine, Yonsei University, Seoul, Republic of Korea
| | - Yong Oock Kim
- Department of Plastic and Reconstructive Surgery, Institute for Human Tissue Restoration, College of Medicine, Yonsei University, Seoul, Republic of Korea
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40
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Calpena E, Cuellar A, Bala K, Swagemakers SMA, Koelling N, McGowan SJ, Phipps JM, Balasubramanian M, Cunningham ML, Douzgou S, Lattanzi W, Morton JEV, Shears D, Weber A, Wilson LC, Lord H, Lester T, Johnson D, Wall SA, Twigg SRF, Mathijssen IMJ, Boardman-Pretty F, Boyadjiev SA, Wilkie AOM. SMAD6 variants in craniosynostosis: genotype and phenotype evaluation. Genet Med 2020; 22:1498-1506. [PMID: 32499606 PMCID: PMC7462747 DOI: 10.1038/s41436-020-0817-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 12/16/2022] Open
Abstract
PURPOSE Enrichment of heterozygous missense and truncating SMAD6 variants was previously reported in nonsyndromic sagittal and metopic synostosis, and interaction of SMAD6 variants with a common polymorphism nearBMP2 (rs1884302) was proposed to contribute to inconsistent penetrance. We determined the occurrence of SMAD6 variants in all types of craniosynostosis, evaluated the impact of different missense variants on SMAD6 function, and tested independently whether rs1884302 genotype significantly modifies the phenotype. METHODS We performed resequencing of SMAD6 in 795 unsolved patients with any type of craniosynostosis and genotyped rs1884302 in SMAD6-positive individuals and relatives. We examined the inhibitory activity and stability of SMAD6 missense variants. RESULTS We found 18 (2.3%) different rare damaging SMAD6 variants, with the highest prevalence in metopic synostosis (5.8%) and an 18.3-fold enrichment of loss-of-function variants comparedwith gnomAD data (P < 10-7). Combined with eight additional variants, ≥20/26 were transmitted from an unaffected parent but rs1884302 genotype did not predict phenotype. CONCLUSION Pathogenic SMAD6 variants substantially increase the risk of both nonsyndromic and syndromic presentations of craniosynostosis, especially metopic synostosis. Functional analysis is important to evaluate missense variants. Genotyping of rs1884302 is not clinically useful. Mechanisms to explain the remarkable diversity of phenotypes associated with SMAD6 variants remain obscure.
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Affiliation(s)
- Eduardo Calpena
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Araceli Cuellar
- Department of Pediatrics, University of California-Davis, Sacramento, CA, USA
| | - Krithi Bala
- Department of Pediatrics, University of California-Davis, Sacramento, CA, USA
| | - Sigrid M A Swagemakers
- Departments of Pathology and Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Nils Koelling
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Simon J McGowan
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Julie M Phipps
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Michael L Cunningham
- Division of Craniofacial Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Sofia Douzgou
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Saint Mary's Hospital, Manchester, UK
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK
| | - Wanda Lattanzi
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Department of Life Science and Public Health, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Jenny E V Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | - Deborah Shears
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Craniofacial Unit, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, UK
| | - Astrid Weber
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - Louise C Wilson
- Clinical Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Helen Lord
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, The Churchill Hospital, Oxford, UK
| | - Tracy Lester
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, The Churchill Hospital, Oxford, UK
| | - David Johnson
- Craniofacial Unit, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, UK
| | - Steven A Wall
- Craniofacial Unit, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, UK
| | - Stephen R F Twigg
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Irene M J Mathijssen
- Department of Plastic and Reconstructive Surgery and Hand Surgery, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Freya Boardman-Pretty
- Genomics England, London, UK
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Simeon A Boyadjiev
- Department of Pediatrics, University of California-Davis, Sacramento, CA, USA
| | - Andrew O M Wilkie
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
- Craniofacial Unit, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, UK.
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41
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Min Swe NM, Kobayashi Y, Kamimoto H, Moriyama K. Aberrantly activated Wnt/β-catenin pathway co-receptors LRP5 and LRP6 regulate osteoblast differentiation in the developing coronal sutures of an Apert syndrome (Fgfr2 S252W /+ ) mouse model. Dev Dyn 2020; 250:465-476. [PMID: 32822074 DOI: 10.1002/dvdy.239] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/13/2020] [Accepted: 08/13/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Apert syndrome is an autosomal, dominant inherited disorder characterized by craniosynostosis and syndactyly caused by gain-of-function mutations in the fibroblast growth factor receptor 2 (FGFR2) gene. Wnt/β-catenin signaling plays critical roles in regulating the skeletal development. Here, we analyzed the role of this pathway in the developing coronal sutures (CS) of a murine Apert syndrome model (Fgfr2S252W/+ ). RESULTS We observed aberrantly increased mRNA expression of Lrp5 and Lrp6 in CS of Fgfr2S252W/+ mice, whereas both wild type (WT) and Fgfr2S252W/+ mice showed similar expression of other Wnt/β-catenin-related genes, such as Wnt3, Wnt3a, Fzd4, Fzd6, Axin2, and Dkk1 as evidenced by in situ hybridization. Significantly increased Lrp5 and Lrp6 mRNA expression was observed by quantitative PCR analysis of cultured cells isolated from CS of Fgfr2S252W/+ mice. Phospho-LRP5, phospho-LRP6, and non-phospho-β-catenin were upregulated in Fgfr2S252W/+ CS compared with that in WT CS. Short-interfering RNA targeting Lrp5 and Lrp6 significantly reduced runt-related transcription factor 2, collagen type 1 alpha 1, and osteocalcin mRNA expression, and alkaline phosphatase activity in cultured cells. CONCLUSIONS The Wnt/β-catenin pathway was activated in the CS of Fgfr2S252W/+ mice during craniofacial development, suggesting the involvement of the Wnt/β-catenin pathway in the pathogenesis of CS synostosis in Fgfr2S252W/+ mice.
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Affiliation(s)
- Nay Myo Min Swe
- Department of Maxillofacial Orthognathics, Division of Maxillofacial and Neck Reconstruction, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Yukiho Kobayashi
- Department of Maxillofacial Orthognathics, Division of Maxillofacial and Neck Reconstruction, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Hiroyuki Kamimoto
- Department of Maxillofacial Orthognathics, Division of Maxillofacial and Neck Reconstruction, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Keiji Moriyama
- Department of Maxillofacial Orthognathics, Division of Maxillofacial and Neck Reconstruction, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
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42
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Justice CM, Cuellar A, Bala K, Sabourin JA, Cunningham ML, Crawford K, Phipps JM, Zhou Y, Cilliers D, Byren JC, Johnson D, Wall SA, Morton JEV, Noons P, Sweeney E, Weber A, Rees KEM, Wilson LC, Simeonov E, Kaneva R, Yaneva N, Georgiev K, Bussarsky A, Senders C, Zwienenberg M, Boggan J, Roscioli T, Tamburrini G, Barba M, Conway K, Sheffield VC, Brody L, Mills JL, Kay D, Sicko RJ, Langlois PH, Tittle RK, Botto LD, Jenkins MM, LaSalle JM, Lattanzi W, Wilkie AOM, Wilson AF, Romitti PA, Boyadjiev SA. A genome-wide association study implicates the BMP7 locus as a risk factor for nonsyndromic metopic craniosynostosis. Hum Genet 2020; 139:1077-1090. [PMID: 32266521 PMCID: PMC7415527 DOI: 10.1007/s00439-020-02157-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 03/25/2020] [Indexed: 12/31/2022]
Abstract
Our previous genome-wide association study (GWAS) for sagittal nonsyndromic craniosynostosis (sNCS) provided important insights into the genetics of midline CS. In this study, we performed a GWAS for a second midline NCS, metopic NCS (mNCS), using 215 non-Hispanic white case-parent triads. We identified six variants with genome-wide significance (P ≤ 5 × 10-8): rs781716 (P = 4.71 × 10-9; odds ratio [OR] = 2.44) intronic to SPRY3; rs6127972 (P = 4.41 × 10-8; OR = 2.17) intronic to BMP7; rs62590971 (P = 6.22 × 10-9; OR = 0.34), located ~ 155 kb upstream from TGIF2LX; and rs2522623, rs2573826, and rs2754857, all intronic to PCDH11X (P = 1.76 × 10-8, OR = 0.45; P = 3.31 × 10-8, OR = 0.45; P = 1.09 × 10-8, OR = 0.44, respectively). We performed a replication study of these variants using an independent non-Hispanic white sample of 194 unrelated mNCS cases and 333 unaffected controls; only the association for rs6127972 (P = 0.004, OR = 1.45; meta-analysis P = 1.27 × 10-8, OR = 1.74) was replicated. Our meta-analysis examining single nucleotide polymorphisms common to both our mNCS and sNCS studies showed the strongest association for rs6127972 (P = 1.16 × 10-6). Our imputation analysis identified a linkage disequilibrium block encompassing rs6127972, which contained an enhancer overlapping a CTCF transcription factor binding site (chr20:55,798,821-55,798,917) that was significantly hypomethylated in mesenchymal stem cells derived from fused metopic compared to open sutures from the same probands. This study provides additional insights into genetic factors in midline CS.
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Affiliation(s)
- Cristina M Justice
- Genometrics Section, Computational and Statistical Genomics Branch, Division of Intramural Research, NHGRI, NIH, Baltimore, MD, USA
| | - Araceli Cuellar
- Department of Pediatrics, University of California Davis, 4625 2nd Avenue, Research Building II, Sacramento, CA, 95817, USA
| | - Krithi Bala
- Department of Pediatrics, University of California Davis, 4625 2nd Avenue, Research Building II, Sacramento, CA, 95817, USA
| | - Jeremy A Sabourin
- Genometrics Section, Computational and Statistical Genomics Branch, Division of Intramural Research, NHGRI, NIH, Baltimore, MD, USA
| | - Michael L Cunningham
- Department of Pediatrics, Division of Craniofacial Medicine, Seattle Children's Craniofacial Center, Seattle Children's Research Institute, University of Washington, Seattle, WA, USA
| | - Karen Crawford
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Julie M Phipps
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Yan Zhou
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Deirdre Cilliers
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jo C Byren
- Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - David Johnson
- Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Steven A Wall
- Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jenny E V Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
- Birmingham Craniofacial Unit, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | - Peter Noons
- Birmingham Craniofacial Unit, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham, UK
| | - Elizabeth Sweeney
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, England, UK
| | - Astrid Weber
- Department of Clinical Genetics, Liverpool Women's NHS Foundation Trust, Liverpool, England, UK
| | - Katie E M Rees
- Clinical Genetics Service, Great Ormond Street Hospital for Children, NHS Foundation Trust, London, UK
| | - Louise C Wilson
- Clinical Genetics Service, Great Ormond Street Hospital for Children, NHS Foundation Trust, London, UK
| | - Emil Simeonov
- National Institute of Pediatrics, Sofia Medical University, Sofia, Bulgaria
| | - Radka Kaneva
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University of Sofia, Sofia, Bulgaria
| | - Nadezhda Yaneva
- National Genetic Laboratory, University Hospital of Obstetrics and Gynecology "Maichin Dom", Medical University of Sofia, Sofia, Bulgaria
| | - Kiril Georgiev
- Department of Neurosurgery, University Hospital 'St. Ivan Rilski', Medical University of Sofia, Sofia, Bulgaria
| | - Assen Bussarsky
- Department of Neurosurgery, University Hospital 'St. Ivan Rilski', Medical University of Sofia, Sofia, Bulgaria
| | - Craig Senders
- Department of Otolaryngology, Head and Neck Surgery, University of California Davis, Sacramento, CA, USA
| | - Marike Zwienenberg
- Department of Neurosurgery, University of California Davis, Sacramento, CA, USA
| | - James Boggan
- Department of Neurosurgery, University of California Davis, Sacramento, CA, USA
| | - Tony Roscioli
- Neuroscience Research Australia, University of New South Wales, Sydney, Australia
| | - Gianpiero Tamburrini
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Section of Neurosurgery, Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Marta Barba
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Section of Experimental Biology, Department of Life Science and Public Health, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Kristin Conway
- Department of Epidemiology, College of Public Health, The University of Iowa, 145 N Riverside Dr, S416 CPHB, Iowa City, IA, 52242, USA
| | - Val C Sheffield
- Department of Pediatrics, Division of Medical Genetics, Carver College of Medicine, The University of Iowa, Iowa City, IA, USA
| | - Lawrence Brody
- Gene and Environment Interaction Section, NHGRI, Bethesda, NIHMD, USA
| | - James L Mills
- Epidemiology Branch, Eunice Kennedy Shriver NICHD, NIH, Bethesda, MD, USA
| | - Denise Kay
- Division of Genetics, NYS Department of Health, Wadsworth CenterAlbany, NY, USA
| | - Robert J Sicko
- Division of Genetics, NYS Department of Health, Wadsworth CenterAlbany, NY, USA
| | - Peter H Langlois
- Birth Defects Epidemiology and Surveillance Branch, Texas Department of State Health Services, Austin, TX, USA
| | - Rachel K Tittle
- Department of Nutritional Sciences, University of Texas at Austin, Austin, TX, USA
| | - Lorenzo D Botto
- Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Mary M Jenkins
- National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, Genome Center, and MIND Institute, University of California Davis, Davis, CA, USA
| | - Wanda Lattanzi
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Section of Experimental Biology, Department of Life Science and Public Health, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Andrew O M Wilkie
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Craniofacial Unit, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Alexander F Wilson
- Genometrics Section, Computational and Statistical Genomics Branch, Division of Intramural Research, NHGRI, NIH, Baltimore, MD, USA
| | - Paul A Romitti
- Department of Epidemiology, College of Public Health, The University of Iowa, 145 N Riverside Dr, S416 CPHB, Iowa City, IA, 52242, USA.
| | - Simeon A Boyadjiev
- Department of Pediatrics, University of California Davis, 4625 2nd Avenue, Research Building II, Sacramento, CA, 95817, USA.
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Hasan MR, Takatalo M, Ma H, Rice R, Mustonen T, Rice DP. RAB23 coordinates early osteogenesis by repressing FGF10-pERK1/2 and GLI1. eLife 2020; 9:55829. [PMID: 32662771 PMCID: PMC7423339 DOI: 10.7554/elife.55829] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 07/13/2020] [Indexed: 12/20/2022] Open
Abstract
Mutations in the gene encoding Ras-associated binding protein 23 (RAB23) cause Carpenter Syndrome, which is characterized by multiple developmental abnormalities including polysyndactyly and defects in skull morphogenesis. To understand how RAB23 regulates skull development, we generated Rab23-deficient mice that survive to an age where skeletal development can be studied. Along with polysyndactyly, these mice exhibit premature fusion of multiple sutures resultant from aberrant osteoprogenitor proliferation and elevated osteogenesis in the suture. FGF10-driven FGFR1 signaling is elevated in Rab23-/-sutures with a consequent imbalance in MAPK, Hedgehog signaling and RUNX2 expression. Inhibition of elevated pERK1/2 signaling results in the normalization of osteoprogenitor proliferation with a concomitant reduction of osteogenic gene expression, and prevention of craniosynostosis. Our results suggest a novel role for RAB23 as an upstream negative regulator of both FGFR and canonical Hh-GLI1 signaling, and additionally in the non-canonical regulation of GLI1 through pERK1/2.
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Affiliation(s)
- Md Rakibul Hasan
- Craniofacial Development and Malformations research group, Orthodontics, Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland
| | - Maarit Takatalo
- Craniofacial Development and Malformations research group, Orthodontics, Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland
| | - Hongqiang Ma
- Craniofacial Development and Malformations research group, Orthodontics, Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland
| | - Ritva Rice
- Craniofacial Development and Malformations research group, Orthodontics, Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland
| | - Tuija Mustonen
- Craniofacial Development and Malformations research group, Orthodontics, Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland
| | - David Pc Rice
- Craniofacial Development and Malformations research group, Orthodontics, Oral and Maxillofacial Diseases, University of Helsinki, Helsinki, Finland.,Oral and Maxillofacial Diseases, Helsinki University Hospital, Helsinki, Finland
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44
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Bishop MR, Diaz Perez KK, Sun M, Ho S, Chopra P, Mukhopadhyay N, Hetmanski JB, Taub MA, Moreno-Uribe LM, Valencia-Ramirez LC, Restrepo Muñeton CP, Wehby G, Hecht JT, Deleyiannis F, Weinberg SM, Wu-Chou YH, Chen PK, Brand H, Epstein MP, Ruczinski I, Murray JC, Beaty TH, Feingold E, Lipinski RJ, Cutler DJ, Marazita ML, Leslie EJ. Genome-wide Enrichment of De Novo Coding Mutations in Orofacial Cleft Trios. Am J Hum Genet 2020; 107:124-136. [PMID: 32574564 PMCID: PMC7332647 DOI: 10.1016/j.ajhg.2020.05.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/26/2020] [Indexed: 01/05/2023] Open
Abstract
Although de novo mutations (DNMs) are known to increase an individual's risk of congenital defects, DNMs have not been fully explored regarding orofacial clefts (OFCs), one of the most common human birth defects. Therefore, whole-genome sequencing of 756 child-parent trios of European, Colombian, and Taiwanese ancestry was performed to determine the contributions of coding DNMs to an individual's OFC risk. Overall, we identified a significant excess of loss-of-function DNMs in genes highly expressed in craniofacial tissues, as well as genes associated with known autosomal dominant OFC syndromes. This analysis also revealed roles for zinc-finger homeobox domain and SOX2-interacting genes in OFC etiology.
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Affiliation(s)
- Madison R. Bishop
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kimberly K. Diaz Perez
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Miranda Sun
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - Samantha Ho
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Pankaj Chopra
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nandita Mukhopadhyay
- Department of Oral Biology, University of Pittsburgh School of Dental Medicine, Pittsburgh, PA 15219, USA
| | - Jacqueline B. Hetmanski
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Margaret A. Taub
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Lina M. Moreno-Uribe
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA 52242, USA
| | | | | | - George Wehby
- Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, IA 52242, USA
| | - Jacqueline T. Hecht
- Department of Pediatrics, McGovern Medical School and School of Dentistry, UT Health at Houston, Houston, TX 77030, USA
| | | | - Seth M. Weinberg
- Department of Oral Biology, University of Pittsburgh School of Dental Medicine, Pittsburgh, PA 15219, USA,Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15219, USA
| | - Yah Huei Wu-Chou
- Department of Medical Research, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Philip K. Chen
- Craniofacial Centre, Taipei Medical University Hospital and Taipei Medical University, Taipei, Taiwan
| | - Harrison Brand
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Michael P. Epstein
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jeffrey C. Murray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Terri H. Beaty
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Eleanor Feingold
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15219, USA
| | - Robert J. Lipinski
- Department of Comparative Biosciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI 53706, USA
| | - David J. Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Mary L. Marazita
- Department of Oral Biology, University of Pittsburgh School of Dental Medicine, Pittsburgh, PA 15219, USA,Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15219, USA
| | - Elizabeth J. Leslie
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA,Corresponding author
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45
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Zhao G, Li K, Li B, Wang Z, Fang Z, Wang X, Zhang Y, Luo T, Zhou Q, Wang L, Xie Y, Wang Y, Chen Q, Xia L, Tang Y, Tang B, Xia K, Li J. Gene4Denovo: an integrated database and analytic platform for de novo mutations in humans. Nucleic Acids Res 2020; 48:D913-D926. [PMID: 31642496 PMCID: PMC7145562 DOI: 10.1093/nar/gkz923] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/19/2019] [Accepted: 10/08/2019] [Indexed: 12/14/2022] Open
Abstract
De novo mutations (DNMs) significantly contribute to sporadic diseases, particularly in neuropsychiatric disorders. Whole-exome sequencing (WES) and whole-genome sequencing (WGS) provide effective methods for detecting DNMs and prioritizing candidate genes. However, it remains a challenge for scientists, clinicians, and biologists to conveniently access and analyse data regarding DNMs and candidate genes from scattered publications. To fill the unmet need, we integrated 580 799 DNMs, including 30 060 coding DNMs detected by WES/WGS from 23 951 individuals across 24 phenotypes and prioritized a list of candidate genes with different degrees of statistical evidence, including 346 genes with false discovery rates <0.05. We then developed a database called Gene4Denovo (http://www.genemed.tech/gene4denovo/), which allowed these genetic data to be conveniently catalogued, searched, browsed, and analysed. In addition, Gene4Denovo integrated data from >60 genomic sources to provide comprehensive variant-level and gene-level annotation and information regarding the DNMs and candidate genes. Furthermore, Gene4Denovo provides end-users with limited bioinformatics skills to analyse their own genetic data, perform comprehensive annotation, and prioritize candidate genes using custom parameters. In conclusion, Gene4Denovo conveniently allows for the accelerated interpretation of DNM pathogenicity and the clinical implication of DNMs in humans.
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Affiliation(s)
- Guihu Zhao
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Kuokuo Li
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Bin Li
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zheng Wang
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhenghuan Fang
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Xiaomeng Wang
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yi Zhang
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Tengfei Luo
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Qiao Zhou
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lin Wang
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yali Xie
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yijing Wang
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Qian Chen
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lu Xia
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yu Tang
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Beisha Tang
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Kun Xia
- Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jinchen Li
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.,Centre for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
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46
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Adapting SureSelect enrichment protocol to the Ion Torrent S5 platform in molecular diagnostics of craniosynostosis. Sci Rep 2020; 10:4159. [PMID: 32139749 PMCID: PMC7058001 DOI: 10.1038/s41598-020-61048-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 02/18/2020] [Indexed: 12/12/2022] Open
Abstract
Obtaining reliable and high fidelity next-generation sequencing (NGS) data requires to choose a suitable sequencing platform and a library preparation approach, which both have their inherent assay-specific limitations. Here, we present the results of successful adaptation of SureSelect hybridisation-based target enrichment protocol for the sequencing on the Ion Torrent S5 platform, which is designed to work preferably with amplicon-based panels. In our study, we applied a custom NGS panel to screen a cohort of 16 unrelated patients affected by premature fusion of the cranial sutures, i.e. craniosynostosis (CS). CS occurs either as an isolated malformation or in a syndromic form, representing a genetically heterogeneous and clinically variable group of disorders. The approach presented here allowed us to achieve high quality NGS data and confirmed molecular diagnosis in 19% of cases, reaching the diagnostic yield similar to some of the published research reports. In conclusion, we demonstrated that an alternative enrichment strategy for library preparations can be successfully applied prior to sequencing on the Ion Torrent S5 platform. Also, we proved that the custom NGS panel designed by us represents a useful and effective tool in the molecular diagnostics of patients with CS.
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Kang L, Liu Y, Jin Y, Li M, Song J, Zhang Y, Zhang Y, Yang Y. Mutations of MACF1, Encoding Microtubule-Actin Crosslinking-Factor 1, Cause Spectraplakinopathy. Front Neurol 2020; 10:1335. [PMID: 32010038 PMCID: PMC6974614 DOI: 10.3389/fneur.2019.01335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 12/02/2019] [Indexed: 02/01/2023] Open
Abstract
As a member of spectraplakin family of cytoskeletal crosslinking proteins, microtubule-actin crosslinking factor 1 (MACF1) controls cytoskeleton network dynamics. Knockout of Macf1 in mice resulted in the developmental retardation and embryonic lethality. Spectraplakinopathy type I, a novel neuromuscular condition characterized by periodic hypotonia, lax muscles, joint contracture, and diminished motor skill, was reported to be associated with heterozygous genomic duplication involving the MACF1 loci, with incomplete penetrance and highly variable clinical presentation in a single pedigree. In this study, parental-derived compound heterozygous novel missense mutations of MACF1, c.1517C>T (p.Thr506Ile) and c.11654T>C (p.Ile3885Thr), were found to co-segregate with disease status in two affected brothers presenting with progressive spastic tetraplegia, dystonia, joint contracture, feeding difficulty and developmental delay. We speculated that MACF1 mutations cause spectraplakinopathy inherited in an autosomal recessive manner. Our clinical findings expanded the phenotype of this neuromuscular disorder and provided new insights into the function of MACF1.
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Affiliation(s)
- Lulu Kang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yi Liu
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Ying Jin
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Mengqiu Li
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Jinqing Song
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | | | - Yao Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yanling Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
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Mutations in TFAP2B and previously unimplicated genes of the BMP, Wnt, and Hedgehog pathways in syndromic craniosynostosis. Proc Natl Acad Sci U S A 2019; 116:15116-15121. [PMID: 31292255 PMCID: PMC6660739 DOI: 10.1073/pnas.1902041116] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Craniosynostosis (CS) is a frequent congenital malformation featuring premature fusion of cranial sutures; 15% of these children have syndromic disease, often due to rare mutations with large effect. While many genes causing Mendelian forms of syndromic CS have been identified, clinical sequencing often fails to identify a likely causative mutation. We performed whole-exome sequencing of 12 case-parent trios with previously negative genetic evaluations. The results identified likely pathogenic mutations in TFAP2B, KAT6A, GLI2, SOX11, CTNNA1, and GPC4 in these families, adding several loci to those known to cause syndromic CS. The findings have implications for determining risk of disease in subsequent offspring and demonstrate that unexplained syndromic CS cases are a particularly rich vein for discovery of CS loci. Craniosynostosis (CS) is a frequent congenital anomaly featuring the premature fusion of 1 or more sutures of the cranial vault. Syndromic cases, featuring additional congenital anomalies, make up 15% of CS. While many genes underlying syndromic CS have been identified, the cause of many syndromic cases remains unknown. We performed exome sequencing of 12 syndromic CS cases and their parents, in whom previous genetic evaluations were unrevealing. Damaging de novo or transmitted loss of function (LOF) mutations were found in 8 genes that are highly intolerant to LOF mutation (P = 4.0 × 10−8); additionally, a rare damaging mutation in SOX11, which has a lower level of intolerance, was identified. Four probands had rare damaging mutations (2 de novo) in TFAP2B, a transcription factor that orchestrates neural crest cell migration and differentiation; this mutation burden is highly significant (P = 8.2 × 10−12). Three probands had rare damaging mutations in GLI2, SOX11, or GPC4, which function in the Hedgehog, BMP, and Wnt signaling pathways; other genes in these pathways have previously been implicated in syndromic CS. Similarly, damaging de novo mutations were identified in genes encoding the chromatin modifier KAT6A, and CTNNA1, encoding catenin α-1. These findings establish TFAP2B as a CS gene, have implications for assessing risk to subsequent children in these families, and provide evidence implicating other genes in syndromic CS. This high yield indicates the value of performing exome sequencing of syndromic CS patients when sequencing of known disease loci is unrevealing.
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What is the Functional Difference Between Sagittal With Metopic and Isolated Sagittal Craniosynotosis? J Craniofac Surg 2019; 30:968-973. [DOI: 10.1097/scs.0000000000005288] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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SMAD6 is frequently mutated
in nonsyndromic radioulnar synostosis. Genet Med 2019; 21:2577-2585. [DOI: 10.1038/s41436-019-0552-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 05/14/2019] [Indexed: 01/10/2023] Open
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