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A Novel IRF6 Variant Detected in a Family With Nonsyndromic Cleft Lip and Palate by Whole Exome Sequencing. J Craniofac Surg 2020; 32:265-269. [PMID: 33136784 DOI: 10.1097/scs.0000000000007000] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
ABSTRACT Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is the most common congenital craniofacial malformation, and its harmful effects on affected individuals and families are apparent. The causative genes and their mechanisms are not completely clear, although several studies have been conducted. Accordingly, in the present study, we recruited a Han Chinese family with hereditary NSCL/P to explore the possible causative variants of this disease using whole exome sequencing. Bioinformatics screening and analysis, mutation function prediction, species conservation analysis, and homology protein modeling were used to identify the variants and evaluate their influence. A mutation in the interferon regulatory factor 6 (IRF6) gene (c.961C>T; p.Val321Met) was detected as a candidate causative variant and predicted to be deleterious. The codon was found to be conserved in many species, and the residue change caused by this mutation changed the structure of IRF6 to a certain degree. The findings suggest that this IRF6 variant is probably the pathogenic cause of NSCL/P in this family. Our results further provide evidence that IRF6 variants play a role in the etiology of NSCL/P.
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Demeer B, Revencu N, Helaers R, Gbaguidi C, Dakpe S, François G, Devauchelle B, Bayet B, Vikkula M. Likely Pathogenic Variants in One Third of Non-Syndromic Discontinuous Cleft Lip and Palate Patients. Genes (Basel) 2019; 10:genes10100833. [PMID: 31652620 PMCID: PMC6826364 DOI: 10.3390/genes10100833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/14/2019] [Accepted: 10/19/2019] [Indexed: 12/19/2022] Open
Abstract
Oral clefts are composed of cleft of the lip, cleft of the lip and palate, or cleft of the palate, and they are associated with a wide range of expression and severity. When cleft of the palate is associated with cleft of the lip with preservation of the primary palate, it defines an atypical phenotype called discontinuous cleft. Although this phenotype may represent 5% of clefts of the lip and/or palate (CLP), it is rarely specifically referred to and its pathophysiology is unknown. We conducted whole exome sequencing (WES) and apply a candidate gene approach to non-syndromic discontinuous CLP individuals in order to identify genes and deleterious variants that could underlie this phenotype. We discovered loss-of-function variants in two out of the seven individuals, implicating FGFR1 and DLG1 genes, which represents almost one third of this cohort. Whole exome sequencing of clinically well-defined subgroups of CLP, such as discontinuous cleft, is a relevant approach to study CLP etiopathogenesis. It could facilitate more accurate clinical, epidemiological and fundamental research, ultimately resulting in better diagnosis and care of CLP patients. Non-syndromic discontinuous cleft lip and palate seems to have a strong genetic basis.
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Affiliation(s)
- Bénédicte Demeer
- Human Molecular Genetics, de Duve Institute, University of Louvain, 1200 Brussels, Belgium.
- Center for Human Genetics, CLAD Nord de France, CHU Amiens-Picardie, 80054 Amiens, France.
- Université Picardie Jules Verne, EA CHIMERE, EA 7516, 80054 Amiens, France.
- Facing Faces Institute, 80054 Amiens, France.
| | - Nicole Revencu
- Human Molecular Genetics, de Duve Institute, University of Louvain, 1200 Brussels, Belgium.
- Center for Human Genetics, Cliniques universitaires Saint-Luc, University of Louvain, 1200 Brussels, Belgium.
| | - Raphael Helaers
- Human Molecular Genetics, de Duve Institute, University of Louvain, 1200 Brussels, Belgium.
| | - Cica Gbaguidi
- Department of Maxillofacial Surgery and Stomatology, Centre de Compétence Fentes et Malformations Faciales (MAFACE), CHU Amiens-Picardie, 80054 Amiens, France.
| | - Stéphanie Dakpe
- Université Picardie Jules Verne, EA CHIMERE, EA 7516, 80054 Amiens, France.
- Facing Faces Institute, 80054 Amiens, France.
- Department of Maxillofacial Surgery and Stomatology, Centre de Compétence Fentes et Malformations Faciales (MAFACE), CHU Amiens-Picardie, 80054 Amiens, France.
| | - Geneviève François
- Department of Pediatrics, Cliniques Universitaires Saint-Luc, University of Louvain, 1200 Brussels, Belgium.
| | - Bernard Devauchelle
- Université Picardie Jules Verne, EA CHIMERE, EA 7516, 80054 Amiens, France.
- Facing Faces Institute, 80054 Amiens, France.
- Department of Maxillofacial Surgery and Stomatology, Centre de Compétence Fentes et Malformations Faciales (MAFACE), CHU Amiens-Picardie, 80054 Amiens, France.
| | - Bénédicte Bayet
- Centre Labiopalatin, Division of Plastic Surgery, Cliniques Universitaires Saint-Luc, University of Louvain, 1200 Brussels, Belgium.
| | - Miikka Vikkula
- Human Molecular Genetics, de Duve Institute, University of Louvain, 1200 Brussels, Belgium.
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Iskandar RPD, Proboningrat A, Fadholly A, Narmada IB, Nidom CA, Sudjarwo SA. The Densitometric Analysis of Protein Pattern in Cleft Lip and Palate Patients. J Int Soc Prev Community Dent 2019; 9:240-244. [PMID: 31198695 PMCID: PMC6559042 DOI: 10.4103/jispcd.jispcd_388_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 03/05/2019] [Indexed: 01/15/2023] Open
Abstract
Objectives Cleft lip and palate (CLP) belongs to the congenital anomaly that is clinically seen as cleft in lip, alveolar bone, palate, and nasal septum. The patients suffer from esthetic and various functional defects. CLP is resulted from impaired palatogenesis during the embryonic phase. The etiology of CLP is influenced by genetic, environmental, and combination of both. According to the literature, CLP is highly associated with defect in interferon regulatory factor 6 (IRF6) and poliovirus receptor-like (PVRL1) genes. The present study aimed to investigate the total protein profile and to identify protein IRF6 and PVRL1 in plasma of CLP patients. Materials and Methods Dot-Blot analysis was performed to identify protein target of IRF6 and PVRL1. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis was performed in gel concentration 12% using plasma of CLP patients, their parents, and control population. The gels were stained by Coomassie blue afterward. Gels were analyzed through ImageLab 5.2.1 software. Results The intensity of major bands in CLP patients was darker than control group, but remains similar to the parents group. The target protein IRF6 and PVRL1 were positively identified through Dot-Blot. Retardation factor value was significantly different in major bands of CLP patients compared to control group. Conclusion There pattern of protein profile in CLP patients was different compared to non-CLP.
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Affiliation(s)
- Regina Purnama Dewi Iskandar
- Doctoral Student, Faculty of Medicine, Airlangga University, Surabaya, Indonesia.,Department of Orthodontics, Faculty of Dentistry, Airlangga University, Surabaya, Indonesia
| | - Annise Proboningrat
- Doctoral Student, Faculty of Veterinary Medicine, Airlangga University, Surabaya, Indonesia
| | - Amaq Fadholly
- Doctoral Student, Faculty of Veterinary Medicine, Airlangga University, Surabaya, Indonesia
| | - Ida Bagus Narmada
- Department of Orthodontics, Faculty of Dentistry, Airlangga University, Surabaya, Indonesia
| | - Chairul Anwar Nidom
- Department of Veterinary Basic Medicine, Faculty of Veterinary Medicine, Airlangga University, Surabaya, Indonesia
| | - Sri Agus Sudjarwo
- Department of Veterinary Basic Medicine, Faculty of Veterinary Medicine, Airlangga University, Surabaya, Indonesia
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Neves LT, Dionísio TJ, Garbieri TF, Parisi VA, Oliveira FV, Oliveira TM, Santos CF. Novel rare variations in
IRF6
in subjects with non‐syndromic cleft lip and palate and dental agenesis. Oral Dis 2018; 25:223-233. [DOI: 10.1111/odi.12975] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 08/30/2018] [Accepted: 09/03/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Lucimara T. Neves
- Department of Biological Sciences, Bauru School of Dentistry University of São Paulo Bauru Brazil
- Post‐Graduation Program in Rehabilitation Sciences, Hospital for Rehabilitation of Craniofacial Anomalies University of São Paulo Bauru Brazil
| | - Thiago J. Dionísio
- Department of Biological Sciences, Bauru School of Dentistry University of São Paulo Bauru Brazil
| | - Thais F. Garbieri
- Department of Biological Sciences, Bauru School of Dentistry University of São Paulo Bauru Brazil
| | - Viviane A. Parisi
- Department of Biological Sciences, Bauru School of Dentistry University of São Paulo Bauru Brazil
| | - Fernanda V. Oliveira
- Department of Pediatric Dentistry, Orthodontics and Community Health, Bauru School of Dentistry University of São Paulo Bauru Brazil
| | - Thais M. Oliveira
- Post‐Graduation Program in Rehabilitation Sciences, Hospital for Rehabilitation of Craniofacial Anomalies University of São Paulo Bauru Brazil
- Department of Pediatric Dentistry, Orthodontics and Community Health, Bauru School of Dentistry University of São Paulo Bauru Brazil
| | - Carlos F. Santos
- Department of Biological Sciences, Bauru School of Dentistry University of São Paulo Bauru Brazil
- Post‐Graduation Program in Rehabilitation Sciences, Hospital for Rehabilitation of Craniofacial Anomalies University of São Paulo Bauru Brazil
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Alvarez CW, Guion-Almeida ML, Richieri-Costa A. About Cuddapah et al. Paper Entitled “IRF6 Sequencing in Interrupted Clefting”. Cleft Palate Craniofac J 2017; 54:494. [DOI: 10.1597/16-161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
| | | | - Antonio Richieri-Costa
- Hospital for Rehabilitation of Craniofacial Anomalies University of São Paulo, Bauru, Brazil
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Ludwig KU, Ahmed ST, Böhmer AC, Sangani NB, Varghese S, Klamt J, Schuenke H, Gültepe P, Hofmann A, Rubini M, Aldhorae KA, Steegers-Theunissen RP, Rojas-Martinez A, Reiter R, Borck G, Knapp M, Nakatomi M, Graf D, Mangold E, Peters H. Meta-analysis Reveals Genome-Wide Significance at 15q13 for Nonsyndromic Clefting of Both the Lip and the Palate, and Functional Analyses Implicate GREM1 As a Plausible Causative Gene. PLoS Genet 2016; 12:e1005914. [PMID: 26968009 PMCID: PMC4788144 DOI: 10.1371/journal.pgen.1005914] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 02/15/2016] [Indexed: 12/22/2022] Open
Abstract
Nonsyndromic orofacial clefts are common birth defects with multifactorial etiology. The most common type is cleft lip, which occurs with or without cleft palate (nsCLP and nsCLO, respectively). Although genetic components play an important role in nsCLP, the genetic factors that predispose to palate involvement are largely unknown. In this study, we carried out a meta-analysis on genetic and clinical data from three large cohorts and identified strong association between a region on chromosome 15q13 and nsCLP (P = 8.13×10−14 for rs1258763; relative risk (RR): 1.46, 95% confidence interval (CI): 1.32–1.61)) but not nsCLO (P = 0.27; RR: 1.09 (0.94–1.27)). The 5 kb region of strongest association maps downstream of Gremlin-1 (GREM1), which encodes a secreted antagonist of the BMP4 pathway. We show during mouse embryogenesis, Grem1 is expressed in the developing lip and soft palate but not in the hard palate. This is consistent with genotype-phenotype correlations between rs1258763 and a specific nsCLP subphenotype, since a more than two-fold increase in risk was observed in patients displaying clefts of both the lip and soft palate but who had an intact hard palate (RR: 3.76, CI: 1.47–9.61, Pdiff<0.05). While we did not find lip or palate defects in Grem1-deficient mice, wild type embryonic palatal shelves developed divergent shapes when cultured in the presence of ectopic Grem1 protein (P = 0.0014). The present study identified a non-coding region at 15q13 as the second, genome-wide significant locus specific for nsCLP, after 13q31. Moreover, our data suggest that the closely located GREM1 gene contributes to a rare clinical nsCLP entity. This entity specifically involves abnormalities of the lip and soft palate, which develop at different time-points and in separate anatomical regions. Clefts of the lip and palate are common birth defects, and require long-term multidisciplinary management. Their etiology involves genetic factors and environmental influences and/or a combination of both, however, these interactions are poorly defined. Moreover, although clefts of the lip may or may not involve the palate, the determinants predisposing to specific subphenotypes are largely unknown. Here we demonstrate that variations in the non-coding region near the GREM1 gene show a highly significant association with a particular phenotype in which cleft lip and cleft palate co-occur (nsCLP; P = 8.13×10−14). Our data suggest that the risk is even higher for patients who have a cleft lip and a cleft of the soft palate, but not of the hard palate. Interestingly, this subphenotype corresponds to the expression of the mouse Grem1 gene, which is found in the developing lip and soft palate but not in the hard palate. While Grem1-deficient mice display no lip or palate defects, we demonstrate that ectopic Grem1 protein alters palatal shelve morphogenesis. Together, our results identify a region near GREM1 as the second, genome-wide significant risk locus for nsCLP, and suggest that deregulated GREM1 expression during craniofacial development may contribute to this common birth defect.
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Affiliation(s)
- Kerstin U. Ludwig
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life&Brain Center, University of Bonn, Bonn, Germany
- * E-mail: (KUL); (HP)
| | - Syeda Tasnim Ahmed
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle upon Tyne, United Kingdom
| | - Anne C. Böhmer
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life&Brain Center, University of Bonn, Bonn, Germany
| | - Nasim Bahram Sangani
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle upon Tyne, United Kingdom
| | - Sheryil Varghese
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle upon Tyne, United Kingdom
| | - Johanna Klamt
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life&Brain Center, University of Bonn, Bonn, Germany
| | - Hannah Schuenke
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life&Brain Center, University of Bonn, Bonn, Germany
| | - Pinar Gültepe
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life&Brain Center, University of Bonn, Bonn, Germany
| | - Andrea Hofmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life&Brain Center, University of Bonn, Bonn, Germany
| | - Michele Rubini
- Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, Italy
| | | | - Regine P. Steegers-Theunissen
- Department of Obstetrics and Gynaecology, ErasmusMC, Rotterdam, Netherlands
- Department of Epidemiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Augusto Rojas-Martinez
- Department of Biochemistry and Molecular Medicine, School of Medicine, and Centro de Investigación y Desarrollo en Ciencias de la Salud, Universidad Autonoma de Nuevo Leon, Monterrey, Mexico
| | - Rudolf Reiter
- Department of Otolaryngology—Head and Neck Surgery, Section of Phoniatrics and Pedaudiology, University of Ulm, Ulm, Germany
| | - Guntram Borck
- Institute of Human Genetics, University of Ulm, Ulm, Germany
| | - Michael Knapp
- Institute of Medical Biometry, Informatics and Epidemiology, University of Bonn, Bonn, Germany
| | | | - Daniel Graf
- Orofacial Development and Regeneration, Institute of Oral Biology, Center for Dental Medicine, University of Zurich, Zurich, Switzerland
- Departments of Dentistry and Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
| | | | - Heiko Peters
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle upon Tyne, United Kingdom
- * E-mail: (KUL); (HP)
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Leslie EJ, Koboldt DC, Kang CJ, Ma L, Hecht JT, Wehby GL, Christensen K, Czeizel AE, Deleyiannis FWB, Fulton RS, Wilson RK, Beaty TH, Schutte BC, Murray JC, Marazita ML. IRF6 mutation screening in non-syndromic orofacial clefting: analysis of 1521 families. Clin Genet 2015; 90:28-34. [PMID: 26346622 DOI: 10.1111/cge.12675] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 09/03/2015] [Accepted: 09/04/2015] [Indexed: 01/12/2023]
Abstract
Van der Woude syndrome (VWS) is an autosomal dominant malformation syndrome characterized by orofacial clefting (OFC) and lower lip pits. The clinical presentation of VWS is variable and can present as an isolated OFC, making it difficult to distinguish VWS cases from individuals with non-syndromic OFCs. About 70% of causal VWS mutations occur in IRF6, a gene that is also associated with non-syndromic OFCs. Screening for IRF6 mutations in apparently non-syndromic cases has been performed in several modestly sized cohorts with mixed results. In this study, we screened 1521 trios with presumed non-syndromic OFCs to determine the frequency of causal IRF6 mutations. We identified seven likely causal IRF6 mutations, although a posteriori review identified two misdiagnosed VWS families based on the presence of lip pits. We found no evidence for association between rare IRF6 polymorphisms and non-syndromic OFCs. We combined our results with other similar studies (totaling 2472 families) and conclude that causal IRF6 mutations are found in 0.24-0.44% of apparently non-syndromic OFC families. We suggest that clinical mutation screening for IRF6 be considered for certain family patterns such as families with mixed types of OFCs and/or autosomal dominant transmission.
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Affiliation(s)
- E J Leslie
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - D C Koboldt
- The Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - C J Kang
- The Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - L Ma
- Department of Oral Maxillofacial Surgery, Peking University School of Stomatology, Beijing, China
| | - J T Hecht
- Department of Pediatrics, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - G L Wehby
- Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, IA, USA
| | - K Christensen
- Department of Epidemiology, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - A E Czeizel
- Foundation for the Community Control of Hereditary Diseases, Budapest, Hungary
| | - F W-B Deleyiannis
- Department of Surgery, Plastic and Reconstructive Surgery, University of Colorado School of Medicine, Denver, CO, USA
| | - R S Fulton
- The Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - R K Wilson
- The Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - T H Beaty
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - B C Schutte
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - J C Murray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - M L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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