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Naicker T, Alade A, Adeleke C, Mossey PA, Awotoye WA, Busch T, Li M, Olotu J, Aldous C, Butali A. Novel IRF6 variant in orofacial cleft patients from Durban, South Africa. Mol Genet Genomic Med 2023; 11:e2138. [PMID: 36811272 PMCID: PMC10178789 DOI: 10.1002/mgg3.2138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 12/22/2022] [Accepted: 01/10/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND To date, there are over 320 variants identified in the IRF6 gene that cause Van der Woude syndrome or popliteal pterygium syndrome. We sequenced this gene in a South African orofacial cleft cohort to identify the causal IRF6 variants in our population. METHOD Saliva samples from 100 patients with syndromic and non-syndromic CL ± P were collected. Patients were recruited from the cleft clinics at two public, tertiary hospitals in Durban, South Africa (SA), namely Inkosi Albert Luthuli Central Hospital (IALCH) and KwaZulu-Natal Children's Hospital (KZNCH). We prospectively sequenced the exons of IRF6 in 100 orofacial cleft cases, and where possible, we also sequenced the parents of the individuals to determine the segregation pattern. RESULTS Two variants were identified; one novel (p.Cys114Tyr) and one known (p.Arg84His) missense variant in IRF6 gene were identified. The patient with the p.Cys114Tyr variant was non-syndromic with no clinical VWS phenotype expected of individuals with IRF6 coding variants, and the patient with the p.Arg84His had phenotypic features of popliteal pterygium syndrome. The p.Arg84His variant segregated in the family, with the father also being affected. CONCLUSIONS This study provides evidence that IRF6 variants are found in the South African population. Genetic counselling is essential for affected families, particularly in the absence of a known clinical phenotype since it helps with the plans for future pregnancies.
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Affiliation(s)
- Thirona Naicker
- Genetics, Department of PaediatricsUniversity of KwaZulu‐NatalDurbanSouth Africa
- Smile Train PartnerNew YorkNew YorkUSA
| | - Azeez Alade
- Department of Oral Pathology, Radiology and Medicine, College of DentistryUniversity of IowaIowa CityIowaUSA
| | - Chinyere Adeleke
- Department of Oral Pathology, Radiology and Medicine, College of DentistryUniversity of IowaIowa CityIowaUSA
| | - Peter A. Mossey
- Department of OrthodonticsUniversity of DundeeDundeeUK
- Smile Train Global Medical Advisory BoardUSA
| | - Waheed A. Awotoye
- Department of Oral Pathology, Radiology and Medicine, College of DentistryUniversity of IowaIowa CityIowaUSA
| | - Tamara Busch
- Department of Oral Pathology, Radiology and Medicine, College of DentistryUniversity of IowaIowa CityIowaUSA
| | - Mary Li
- Department of Oral Pathology, Radiology and Medicine, College of DentistryUniversity of IowaIowa CityIowaUSA
| | - Joy Olotu
- Department of AnatomyUniversity of Port HarcourtPort HarcourtNigeria
| | - Colleen Aldous
- School of Clinical MedicineUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Azeez Butali
- Department of Oral Pathology, Radiology and Medicine, College of DentistryUniversity of IowaIowa CityIowaUSA
- Smile Train Research and Innovation Advisory CouncilUSA
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Slavec L, Geršak K, Eberlinc A, Hovnik T, Lovrečić L, Mlinarič-Raščan I, Karas Kuželički N. A Comprehensive Genetic Analysis of Slovenian Families with Multiple Cases of Orofacial Clefts Reveals Novel Variants in the Genes IRF6, GRHL3, and TBX22. Int J Mol Sci 2023; 24:ijms24054262. [PMID: 36901693 PMCID: PMC10002089 DOI: 10.3390/ijms24054262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/13/2023] [Accepted: 02/15/2023] [Indexed: 02/23/2023] Open
Abstract
Although the aetiology of non-syndromic orofacial clefts (nsOFCs) is usually multifactorial, syndromic OFCs (syOFCs) are often caused by single mutations in known genes. Some syndromes, e.g., Van der Woude syndrome (VWS1; VWS2) and X-linked cleft palate with or without ankyloglossia (CPX), show only minor clinical signs in addition to OFC and are sometimes difficult to differentiate from nsOFCs. We recruited 34 Slovenian multi-case families with apparent nsOFCs (isolated OFCs or OFCs with minor additional facial signs). First, we examined IRF6, GRHL3, and TBX22 by Sanger or whole exome sequencing to identify VWS and CPX families. Next, we examined 72 additional nsOFC genes in the remaining families. Variant validation and co-segregation analysis were performed for each identified variant using Sanger sequencing, real-time quantitative PCR and microarray-based comparative genomic hybridization. We identified six disease-causing variants (three novel) in IRF6, GRHL3, and TBX22 in 21% of families with apparent nsOFCs, suggesting that our sequencing approach is useful for distinguishing syOFCs from nsOFCs. The novel variants, a frameshift variant in exon 7 of IRF6, a splice-altering variant in GRHL3, and a deletion of the coding exons of TBX22, indicate VWS1, VWS2, and CPX, respectively. We also identified five rare variants in nsOFC genes in families without VWS or CPX, but they could not be conclusively linked to nsOFC.
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Affiliation(s)
- Lara Slavec
- Research Unit, Division of Gynaecology and Obstetrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Ksenija Geršak
- Research Unit, Division of Gynaecology and Obstetrics, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Department of Gynaecology and Obstetrics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Andreja Eberlinc
- Department of Maxillofacial and Oral Surgery, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Tinka Hovnik
- Clinical Institute for Special Laboratory Diagnostics, University Children’s Hospital, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Luca Lovrečić
- Department of Gynaecology and Obstetrics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
| | - Irena Mlinarič-Raščan
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Nataša Karas Kuželički
- Department of Clinical Biochemistry, Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
- Correspondence:
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Li K, Fan L, Tian Y, Lou S, Li D, Ma L, Wang L, Pan Y. Application of zebrafish in the study of craniomaxillofacial developmental anomalies. Birth Defects Res 2022; 114:583-595. [PMID: 35437950 DOI: 10.1002/bdr2.2014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/18/2022] [Accepted: 04/03/2022] [Indexed: 12/13/2022]
Abstract
Craniomaxillofacial developmental anomalies are one of the most prevalent congenital defects worldwide and could result from any disruption of normal development processes, which is generally influenced by interactions between genes and the environment. Currently, with the advances in genetic screening strategies, an increasing number of novel variants and their roles in orofacial diseases have been explored. Zebrafish is recognized as a powerful animal model, and its homologous genes and similar oral structure and development process provide an ideal platform for studying the contributions of genetic and environmental factors to human craniofacial malformations. Here, we reviewed zebrafish models for the study of craniomaxillofacial developmental anomalies, such as human nonsyndromic cleft lip with or without an affected palate and jaw and tooth developmental anomalies. Due to its potential for gene expression and regulation research, zebrafish may provide new perspectives for understanding craniomaxillofacial diseaseand its treatment.
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Affiliation(s)
- Kang Li
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Liwen Fan
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Yu Tian
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Shu Lou
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Dandan Li
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Lan Ma
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Lin Wang
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Yongchu Pan
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
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Estévez-Arroyo B, Gómez-Mendo I, Romero-Maroto M, Solano-Reina E, Iglesias-Linares A. Craniofacial characteristics in Van der Woude syndrome. Oral Dis 2022; 29:1680-1691. [PMID: 35286743 DOI: 10.1111/odi.14187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 02/22/2022] [Accepted: 03/03/2022] [Indexed: 11/28/2022]
Abstract
AIM To describe the particular craniofacial characteristics of Van der Woude syndrome(VWS) patients compared to patients with a non-syndromic cleft(CG1) and to a malocclusive healthy population(CG2). MATERIAL AND METHODS Retrospective case-control study. A sample of 110matched-patients was recruited(VWS(n=7),CG1(n=49),CG2(n=49)).Subsequently, 37 radiometric-variables were analysed and the dental-skeletal ages were determined. The intra/inter-observer method errors were quantified.Descriptive statistics were computed, and different inferential analysis tests were used depending on the normality of the data(Chi-square-test,Fisher-exact-test,paired-Student'sT-test,Mann-Whitney´s-test)(p-value<0.05).Pairwise comparisons were corrected by Bonferroni´s criteria. RESULTS VW-patients presented specific craniofacial characteristics and morphology. A marked tendency to the vertical growth pattern was found in VW-patients compared to CG1-CG2(p<0.001); at the sagittal level, skeletal class II caused by mandibular retrognathism, with a greatly increased ANB angle compared to CG1(p=0.042). Dental analysis showed that the lower incisor was more retruded and retroclined(p<0.05 in all cases)and the interincisal angulation was increased(p<0.001(CG2)).At the profile level, an open nasolabial angle(p=0.040;CG1) and a more protruding lower lip with respect to the Sn-Pg plane(p=0.040(CG1);p=0.044(CG2))were observed. CONCLUSIONS VW-patients present particular characteristics in the facial skeletal structures. There is a critical necessity to increase the evidence regarding specific clinical features and orofacial pathology of rare diseases such as VWS, which will help to these minorities to gain access in the future to a better quality of care with precise treatment and diagnostic necessities.
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Affiliation(s)
- Blanca Estévez-Arroyo
- Department of Orthodontics, College of Dentistry, University of Seville, Seville, Spain
| | - Ignacio Gómez-Mendo
- Maxillofacial and Stomatology Department, Virgen Macarena University Hospital of Seville, Seville, Spain
| | | | | | - Alejandro Iglesias-Linares
- Orthodontics, Vice Dean for Research, Complutense University of Madrid, Plaza Ramón y Cajal s-n, 28001, Madrid, Spain
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Huang W, He Q, Li M, Ding Y, Liang W, Li W, Lin J, Zhao H, Chen F. Two rare variants reveal the significance of Grainyhead‐like 3 Arginine 391 underlying non‐syndromic cleft palate only. Oral Dis 2022; 29:1632-1643. [PMID: 35189007 DOI: 10.1111/odi.14164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/07/2022] [Accepted: 02/12/2022] [Indexed: 11/27/2022]
Abstract
OBJECTIVES Non-syndromic cleft palate only (NSCPO) is one of the most common craniofacial birth defects with largely undetermined genetic etiology. It has been established that Grainyhead-like 3 (GRHL3) plays an essential role in the pathogenesis of NSCPO. This study aimed to identify and verify the first-reported GRHL3 variant underlying NSCPO among the Chinese cohort. METHODS We performed whole-exome sequencing (WES) on a Chinese NSCPO patient and identified a rare variant of GRHL3 (p.Arg391His). A validated deleterious variant p.Arg391Cys was introduced as a positive control. Zebrafish embryos injection, reporter assays, live-cell imaging, and RNA sequencing were conducted to test the pathogenicity of the variants. RESULTS Zebrafish embryos microinjection demonstrated that overexpression of the variants could disrupt the normal development of zebrafish embryos. Reporter assays showed that Arg391His disturbed transcriptional activity of GRHL3 and exerted a dominant-negative effect. Interestingly, Arg391His and Arg391Cys displayed distinct nuclear localization patterns from that of wild-type GRHL3 in live-cell imaging. Bulk RNA sequencing suggested that the two variants changed the pattern of gene expression. CONCLUSIONS In aggregate, this study identified and characterized a rare GRHL3 variant in NSCPO, revealing the critical role of Arginine 391 in GRHL3. Our findings will help facilitate understanding and genetic counseling of NSCPO.
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Affiliation(s)
- Wenbin Huang
- Department of Orthodontics Peking University School and Hospital of Stomatology 100081 Beijing China
- National Center of Stomatology National Clinical Research Center for Oral Diseases National Engineering Laboratory for Digital and Material Technology of Stomatology Beijing Key Laboratory for Digital Stomatology, Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health, NMPA Key Laboratory for Dental Materials 100081 Beijing China
| | - Qing He
- Department of Physiology and Pathophysiology School of Basic Medical Sciences Xi’an Jiaotong University Health Science Center 710061 Xi’an, Shaanxi China
| | - Mingzhao Li
- Department of Orthodontics Peking University School and Hospital of Stomatology 100081 Beijing China
- National Center of Stomatology National Clinical Research Center for Oral Diseases National Engineering Laboratory for Digital and Material Technology of Stomatology Beijing Key Laboratory for Digital Stomatology, Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health, NMPA Key Laboratory for Dental Materials 100081 Beijing China
| | - Yi Ding
- Department of Physiology and Pathophysiology School of Basic Medical Sciences Xi’an Jiaotong University Health Science Center 710061 Xi’an, Shaanxi China
| | - Wei Liang
- Department of Orthodontics Peking University School and Hospital of Stomatology 100081 Beijing China
- National Center of Stomatology National Clinical Research Center for Oral Diseases National Engineering Laboratory for Digital and Material Technology of Stomatology Beijing Key Laboratory for Digital Stomatology, Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health, NMPA Key Laboratory for Dental Materials 100081 Beijing China
| | - Weiran Li
- Department of Orthodontics Peking University School and Hospital of Stomatology 100081 Beijing China
- National Center of Stomatology National Clinical Research Center for Oral Diseases National Engineering Laboratory for Digital and Material Technology of Stomatology Beijing Key Laboratory for Digital Stomatology, Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health, NMPA Key Laboratory for Dental Materials 100081 Beijing China
| | - Jiuxiang Lin
- Department of Orthodontics Peking University School and Hospital of Stomatology 100081 Beijing China
- National Center of Stomatology National Clinical Research Center for Oral Diseases National Engineering Laboratory for Digital and Material Technology of Stomatology Beijing Key Laboratory for Digital Stomatology, Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health, NMPA Key Laboratory for Dental Materials 100081 Beijing China
| | - Huaxiang Zhao
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research College of Stomatology Xi’an Jiaotong University 710004 Xi'an, Shaanxi China
- Department of Orthodontics College of Stomatology Xi’an Jiaotong University 710004 Xi’an, Shaanxi China
| | - Feng Chen
- Central laboratory Peking University School and Hospital of Stomatology 100081 Beijing China
- National Center of Stomatology National Clinical Research Center for Oral Diseases National Engineering Laboratory for Digital and Material Technology of Stomatology Beijing Key Laboratory for Digital Stomatology, Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health, NMPA Key Laboratory for Dental Materials 100081 Beijing China
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Ghassibe-Sabbagh M, El Hajj J, Al Saneh M, El Baba N, Abou Issa J, Al Haddad M, El Atat O, Sabbagh J, Abou Chebel N, El-Sibai M. Altered regulation of cell migration in IRF6-mutated orofacial cleft patients-derived primary cells reveals a novel role of Rho GTPases in cleft/lip palate development. Cells Dev 2021; 166:203674. [PMID: 33994351 DOI: 10.1016/j.cdev.2021.203674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/22/2021] [Accepted: 03/10/2021] [Indexed: 11/30/2022]
Abstract
Orofacial clefts are the most common congenital craniofacial birth defects. They occur from a failure in cell proliferation and fusion of neural crest cells of the lip buds and/or palatal shelves. In this study, we investigate the genetic basis and molecular mechanisms in primary cells derived from a cleft and lip palate patient presenting van der Woude syndrome (VWS). Since mutations in the integrin genes are widely correlated with VWS, Interferon Regulatory Factor 6 (IRF6) screening was conducted in a cohort of 200 participants presenting with orofacial anomalies. Primary fibroblastic cells derived from the upper right gingiva and palatal regions were isolated and two cellular populations from two participants were obtained: a control with no cleft phenotype and a patient with a cleft phenotype typical of van der Woude syndrome (VWS). IRF6 targeted sequencing revealed mutations in two distinct families. Our results showed no alteration in the viability of the CLP/VWS patient cells, suggesting the phenotype associate with the disease is not secondary to a defect in cell proliferation. We did however detect a significant decrease in the migratory ability of the CLP with Van der Woude syndrome (CLP/VWS) patient cells, which could account for the phenotype. When compared to normal cells, patient cells showed a lack of polarization, which would account for their lack of mobility. Patient cells showed protrusions all around the cells and a lack of defined leading edge. This was reflected with actin staining, WAVE2 and Arp2 around the cell, and correlated with an increase in Rac1 activation. Consistently with the increase in Rac1 activation, patient cells showed a loss in the maturation of focal adhesions needed for contractility, which also accounts for the lack in cell migration. Our findings give increased understanding of the molecular mechanisms of VWS and expands the knowledge of van der Woude syndrome (VWS) occurrence by providing a strong molecular evidence that CLP with Van der Woude syndrome (CLP/VWS) phenotype is caused by a defect in normal physiological processes of cells.
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Affiliation(s)
- Michella Ghassibe-Sabbagh
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut, Lebanon.
| | - Joelle El Hajj
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut, Lebanon.
| | - Mounir Al Saneh
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut, Lebanon.
| | - Nada El Baba
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut, Lebanon.
| | - Jamil Abou Issa
- School of Medicine, Lebanese American University, Beirut, Lebanon.
| | - Maria Al Haddad
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut, Lebanon.
| | - Oula El Atat
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut, Lebanon.
| | - Joseph Sabbagh
- Department of Restorative Dentistry and Endodontics, Faculty of Dental Medicine, Lebanese University, Beirut, Lebanon
| | - Naji Abou Chebel
- Department of Otolaryngology - Head and Neck Surgery, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.
| | - Mirvat El-Sibai
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut, Lebanon.
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Velázquez-Aragón JA, González-Del Angel A, Alcántara-Ortigoza MA, Reyna-Fabián ME, Estandia-Ortega B. Screening of IRF6 Variants in Patients Subjected to Genetic Association Studies for Nonsyndromic Cleft Lip/Palate. Cleft Palate Craniofac J 2020; 58:1128-1134. [PMID: 33334172 DOI: 10.1177/1055665620980238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To screen for interferon regulatory factor 6 (IRF6) pathogenic variants in patients clinically diagnosed with nonsyndromic cleft lip palate (NSCL/P) and establish the proportion of misdiagnosed Van der Woude syndrome (VWS) cases, which could have biased previous NSCL/P case-control association studies. DESIGN Retrospective case series. SETTING Tertiary care children's hospital. PARTICIPANTS One hundred seventy-two unrelated Mexican patients with NSCL/P, 128 of whom had previously been included in a NSCL/P case-control association study. MAIN OUTCOMES MEASUREMENTS Sanger sequencing of the 9 IRF6 exons were performed, all variants respect with sequence reference were reported and classified for their pathogenic significance according to the American College of Medical Genetics and Genomics guidelines. RESULTS Seven percent of cases were familial. No pathogenic variant was identified in IRF6. We identified 12 previously reported benign variants; their frequencies did not significantly differ from those reported for individuals of Mexican ancestry. Three of them were uncommon intronic variants not reported in ClinVar. The rs2235371 and rs2235375 variants, which were previously analyzed in a NSCL/P case-control association study (containing 132 patients, 128 of whom were analyzed herein) did not show discordant association results comparing to the 370 controls from the previous study. CONCLUSIONS The misdiagnosis of IRF6-related VWS as NSCL/P appears to be infrequent in our sample, suggesting that mutational screening of IRF6 would have a low diagnostic yield in patients with NSCL/P. The absence of IRF6 pathogenic alleles could be related to the application of an exhaustive clinical evaluation that discarded the syndromic forms and/or the low proportion of familial cases included.
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8
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Yu Y, Wan Y, Qin C, Yue H, Bian Z, He M. Novel IRF6 mutations in Chinese Han families with Van der Woude syndrome. Mol Genet Genomic Med 2020; 8:e1196. [PMID: 32108996 PMCID: PMC7216816 DOI: 10.1002/mgg3.1196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/02/2020] [Accepted: 02/14/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Interferon Regulatory Factor 6 (IRF6) gene encodes a member of the IRF family of transcription factors. Mutations in IRF6 cause Van der Woude Syndrome (VWS), which is the most common malformation of syndromic orofacial clefts in humans. METHODS Here, we performed sequencing studies of six families with VWS in the Chinese Han population. The entire IRF6-coding region and the exon-intron boundaries including exons 3-8 and part of exon 9 were screened among all the collected family members by Sanger sequencing. RESULTS We found a novel splice site variant c.175-6T>A, two novel missense variants (p.Lys66Arg and p.Pro107Thr), in addition with a previously reported missense variant (p.Leu87Phe), which were all located in and nearby exon 4 of IRF6. Meanwhile, a novel frameshift variant p.G257Vfs*46 in exon 7 of IRF6 was also detected. All the mutations presented to be co-segregated in each family. CONCLUSION Our study has advanced the understanding of the genetic architecture of VWS and provides the basis for genetic counseling, antenatal diagnosis, and gene therapy of high risk groups.
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Affiliation(s)
- Yanqin Yu
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Yatao Wan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, China
| | - Chuanqi Qin
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Haitang Yue
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Zhuan Bian
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Miao He
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Demeer B, Revencu N, Helaers R, Devauchelle B, François G, Bayet B, Vikkula M. Unmasking familial CPX by WES and identification of novel clinical signs. Am J Med Genet A 2018; 176:2661-2667. [PMID: 30462376 DOI: 10.1002/ajmg.a.40630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 08/15/2018] [Accepted: 08/17/2018] [Indexed: 12/17/2022]
Abstract
Mutations in the T-Box transcription factor gene TBX22 are found in X-linked Cleft Palate with or without Ankyloglossia syndrome (CPX syndrome). In addition to X-linked inheritance, ankyloglossia, present in the majority of CPX patients, is an important diagnostic marker, but it is frequently missed or unreported, as it is a "minor" feature. Other described anomalies include cleft lip, micro and/or hypodontia, and features of CHARGE syndrome. We conducted whole exome sequencing (WES) on 22 individuals from 17 "a priori" non-syndromic cleft lip and/or cleft palate (CL/P) families. We filtered the data for heterozygous pathogenic variants within a set of predefined candidate genes. Two canonical splice-site mutations were found in TBX22. Detailed re-phenotyping of the two probands and their families unravelled orofacial features previously not associated with the CPX phenotypic spectrum: choanal atresia, Pierre-Robin sequence, and overgrowths on the posterior edge of the hard palate, on each side of the palatal midline. This study emphasizes the importance of WES analysis in familial CLP cases, combined with deep (reverse) phenotyping in "a priori" non-syndromic clefts.
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Affiliation(s)
- Bénédicte Demeer
- Human Molecular Genetics, de Duve Institute, University of Louvain, Brussels, Belgium.,Center for Human Genetics, CLAD nord de France, CHU Amiens-Picardie, Amiens, France.,EA CHIMERE, Université Picardie Jules Verne, Amiens, France
| | - Nicole Revencu
- Human Molecular Genetics, de Duve Institute, University of Louvain, Brussels, Belgium.,Center for Human Genetics, Cliniques universitaires Saint-Luc, University of Louvain, Brussels, Belgium
| | - Raphael Helaers
- Human Molecular Genetics, de Duve Institute, University of Louvain, Brussels, Belgium
| | - Bernard Devauchelle
- EA CHIMERE, Université Picardie Jules Verne, Amiens, France.,Department of Maxillofacial Surgery and Stomatology, centre de compétence fentes et malformations faciales MAFACE, CHU Amiens-Picardie, Amiens, France
| | - Geneviève François
- Department of Pediatrics, Cliniques universitaires Saint-Luc, University of Louvain, Brussels, Belgium
| | - Bénédicte Bayet
- Centre Labiopalatin, Division of Plastic Surgery, Cliniques universitaires Saint-Luc, University of Louvain, Brussels, Belgium
| | - Miikka Vikkula
- Human Molecular Genetics, de Duve Institute, University of Louvain, Brussels, Belgium
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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12
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Basha M, Demeer B, Revencu N, Helaers R, Theys S, Bou Saba S, Boute O, Devauchelle B, Francois G, Bayet B, Vikkula M. Whole exome sequencing identifies mutations in 10% of patients with familial non-syndromic cleft lip and/or palate in genes mutated in well-known syndromes. J Med Genet 2018; 55:449-458. [DOI: 10.1136/jmedgenet-2017-105110] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 02/02/2018] [Accepted: 02/12/2018] [Indexed: 01/08/2023]
Abstract
BackgroundOral clefts, that is, clefts of the lip and/or cleft palate (CL/P), are the most common craniofacial birth defects with an approximate incidence of ~1/700. To date, physicians stratify patients with oral clefts into either syndromic CL/P (syCL/P) or non-syndromic CL/P (nsCL/P) depending on whether the CL/P is associated with another anomaly or not. In general, patients with syCL/P follow Mendelian inheritance, while those with nsCL/P have a complex aetiology and, as such, do not adhere to Mendelian inheritance. Genome-wide association studies have identified approximately 30 risk loci for nsCL/P, which could explain a small fraction of heritability.MethodsTo identify variants causing nsCL/P, we conducted whole exome sequencing on 84 individuals with nsCL/P, drawn from multiplex families (n=46).ResultsWe identified rare damaging variants in four genes known to be mutated in syCL/P: TP63 (one family), TBX1 (one family), LRP6 (one family) and GRHL3 (two families), and clinical reassessment confirmed the isolated nature of their CL/P.ConclusionThese data demonstrate that patients with CL/P without cardinal signs of a syndrome may still carry a mutation in a gene linked to syCL/P. Rare coding and non-coding variants in syCL/P genes could in part explain the controversial question of ‘missing heritability’ for nsCL/P. Therefore, gene panels designed for diagnostic testing of syCL/P should be used for patients with nsCL/P, especially when there is at least third-degree family history. This would allow a more precise management, follow-up and genetic counselling. Moreover, stratified cohorts would allow hunting for genetic modifiers.
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Gowans LJJ, Busch TD, Mossey PA, Eshete MA, Adeyemo WL, Aregbesola B, Donkor P, Arthur FKN, Agbenorku P, Olutayo J, Twumasi P, Braimah R, Oti AA, Plange-Rhule G, Obiri-Yeboah S, Abate F, Hoyte-Williams PE, Hailu T, Murray JC, Butali A. The prevalence, penetrance, and expressivity of etiologic IRF6 variants in orofacial clefts patients from sub-Saharan Africa. Mol Genet Genomic Med 2017; 5:164-171. [PMID: 28361103 PMCID: PMC5370218 DOI: 10.1002/mgg3.273] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/16/2016] [Accepted: 12/08/2016] [Indexed: 01/08/2023] Open
Abstract
Background Orofacial clefts are congenital malformations of the orofacial region, with a global incidence of one per 700 live births. Interferon Regulatory Factor 6 (IRF6) (OMIM:607199) gene has been associated with the etiology of both syndromic and nonsyndromic orofacial clefts. The aim of this study was to show evidence of potentially pathogenic variants in IRF6 in orofacial clefts cohorts from Africa. Methods We carried out Sanger Sequencing on DNA from 184 patients with nonsyndromic orofacial clefts and 80 individuals with multiple congenital anomalies that presented with orofacial clefts. We sequenced all the nine exons of IRF6 as well as the 5′ and 3′ untranslated regions. In our analyses pipeline, we used various bioinformatics tools to detect and describe the potentially etiologic variants. Results We observed that potentially etiologic exonic and splice site variants were nonrandomly distributed among the nine exons of IRF6, with 92% of these variants occurring in exons 4 and 7. Novel variants were also observed in both nonsyndromic orofacial clefts (p.Glu69Lys, p.Asn185Thr, c.175‐2A>C and c.1060+26C>T) and multiple congenital anomalies (p.Gly65Val, p.Lys320Asn and c.379+1G>T) patients. Our data also show evidence of compound heterozygotes that may modify phenotypes that emanate from IRF6 variants. Conclusions This study demonstrates that exons 4 and 7 of IRF6 are mutational ‘hotspots’ in our cohort and that IRF6 mutants‐induced orofacial clefts may be prevalent in the Africa population, however, with variable penetrance and expressivity. These observations are relevant for detection of high‐risk families as well as genetic counseling. In conclusion, we have shown that there may be a need to combine both molecular and clinical evidence in the grouping of orofacial clefts into syndromic and nonsyndromic forms.
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Affiliation(s)
- Lord Jephthah Joojo Gowans
- Department of Biochemistry and BiotechnologyKwame Nkrumah University of Science and Technology (KNUST)KumasiGhana; Cleft ClinicKomfo Anokye Teaching HospitalKumasiGhana; Department of PaediatricsUniversity of IowaIowa CityIowa; Department of Oral PathologyRadiology and MedicineUniversity of IowaIowa CityIowa
| | - Tamara D Busch
- Department of Oral Pathology Radiology and Medicine University of Iowa Iowa City Iowa
| | - Peter A Mossey
- Department of Orthodontics University of Dundee Dundee Scotland
| | | | | | | | - Peter Donkor
- Cleft ClinicKomfo Anokye Teaching HospitalKumasiGhana; Department of SurgerySchool of Medical SciencesKNUSTKumasiGhana
| | - Fareed K N Arthur
- Department of Biochemistry and Biotechnology Kwame Nkrumah University of Science and Technology (KNUST) Kumasi Ghana
| | - Pius Agbenorku
- Cleft ClinicKomfo Anokye Teaching HospitalKumasiGhana; Department of SurgerySchool of Medical SciencesKNUSTKumasiGhana
| | - James Olutayo
- College of Medicine University of Lagos Lagos Nigeria
| | - Peter Twumasi
- Department of Biochemistry and Biotechnology Kwame Nkrumah University of Science and Technology (KNUST) Kumasi Ghana
| | - Rahman Braimah
- Obafemi Awolowo University Teaching Hospital Ile-Ife Nigeria
| | - Alexander A Oti
- Cleft ClinicKomfo Anokye Teaching HospitalKumasiGhana; Department of SurgerySchool of Medical SciencesKNUSTKumasiGhana
| | | | - Solomon Obiri-Yeboah
- Cleft ClinicKomfo Anokye Teaching HospitalKumasiGhana; Department of SurgerySchool of Medical SciencesKNUSTKumasiGhana
| | | | | | - Taye Hailu
- Addis Ababa University Addis Ababa Ethiopia
| | | | - Azeez Butali
- Department of Oral Pathology Radiology and Medicine University of Iowa Iowa City Iowa
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14
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Tan EC, Lim HW, Lim ECP, Lee ST. A Novel Interferon Regulatory Factor 6 Mutation in an Asian Family With Van der Woude Syndrome. Cleft Palate Craniofac J 2016; 54:442-445. [PMID: 27243668 DOI: 10.1597/15-327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Van der Woude syndrome (VWS) is a rare autosomal dominant genetic disorder characterized by orofacial clefting and lip pits. Mutations in the transcription factor interferon regulatory factor 6 gene (IRF6) have been identified in individuals with VWS. We performed direct sequencing of the gene for molecular investigation of a proband with Bangladeshi-Malay ancestry. A novel transition mutation (c.113T>C), which resulted in an amino acid substitution (p.Ile38Thr) in the deoxyribonucleic acid-binding domain was detected. Testing of family members showed that the mutation segregated with the VWS phenotype for members of her immediate family. Although there is some phenotypic variability, all of the affected members are of the female gender.
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15
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Rafighdoost F, Rafighdoost A, Rafighdoost H, Rigi-Ladez MA, Hashemi M, Eskandari-Nasab E. The 19-bp deletion polymorphism of dihydrofolate reductase (DHFR) and nonsyndromic cleft lip with or without cleft palate: evidence for a protective role. J Appl Oral Sci 2015. [PMID: 26221921 PMCID: PMC4510661 DOI: 10.1590/1678-775720140473] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
OBJECTIVE Nonsyndromic cleft lip with or without cleft palate (NS-CL/P) are among the most common congenital birth defects worldwide. Several lines of evidence point to the involvement of folate, as well as folate metabolizing enzymes in risk reduction of orofacial clefts. Dihydrofolate reductase (DHFR) enzyme participates in the metabolic cycle of folate and has a crucial role in DNA synthesis, a fundamental feature of gestation and development. A functional polymorphic 19-bp deletion within intron-1 of DHFR has been associated with the risk of common congenital malformations. The present study aimed to evaluate the possible association between DHFR 19-bp deletion polymorphism and susceptibility to NS-CL/P in an Iranian population. MATERIAL AND METHODS The current study recruited 100 NS-CL/P patients and 100 healthy controls. DHFR 19-bp deletion was determined using an allele specific-PCR method. RESULTS We observed the DHFR 19-bp homozygous deletion genotype (D/D) vs. homozygous wild genotype (WW) was more frequent in controls than in NS-CL/P patients (25% vs. 13%), being associated with a reduced risk of NS-CL/P in both codominant (OR=0.33, P=0.027) and recessive (OR=0.45, P=0.046) tested inheritance models. We also stratified the cleft patients and reanalyzed the data. The association trend for CL+CL/P group compared to the controls revealed that the DD genotype in both codominant (OR=0.30, P=0.032) and recessive models (OR=0.35, P=0.031) was associated with a reduced risk of CL+CL/P. CONCLUSIONS Our results for the first time suggested the DHFR 19-bp D/D genotype may confer a reduced risk of NS-CL/P and might act as a protective factor against NS-CL/P in the Iranian subjects.
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Affiliation(s)
| | - Amir Rafighdoost
- School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Houshang Rafighdoost
- Department of Anatomy, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | | | - Mohammad Hashemi
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Ebrahim Eskandari-Nasab
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Butali A, Mossey PA, Adeyemo WL, Eshete MA, Gaines LA, Even D, Braimah RO, Aregbesola BS, Rigdon JV, Emeka CI, James O, Ogunlewe MO, Ladeinde AL, Abate F, Hailu T, Mohammed I, Gravem PE, Deribew M, Gesses M, Adeyemo AA, Murray JC. Novel IRF6 mutations in families with Van Der Woude syndrome and popliteal pterygium syndrome from sub-Saharan Africa. Mol Genet Genomic Med 2014; 2:254-60. [PMID: 24936515 PMCID: PMC4049366 DOI: 10.1002/mgg3.66] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 12/18/2013] [Accepted: 12/19/2013] [Indexed: 12/23/2022] Open
Abstract
Orofacial clefts (OFC) are complex genetic traits that are often classified as syndromic or nonsyndromic clefts. Currently, there are over 500 types of syndromic clefts in the Online Mendelian Inheritance in Man (OMIM) database, of which Van der Woude syndrome (VWS) is one of the most common (accounting for 2% of all OFC). Popliteal pterygium syndrome (PPS) is considered to be a more severe form of VWS. Mutations in the IRF6 gene have been reported worldwide to cause VWS and PPS. Here, we report studies of families with VWS and PPS in sub-Saharan Africa. We screened the DNA of eight families with VWS and one family with PPS from Nigeria and Ethiopia by Sanger sequencing of the most commonly affected exons in IRF6 (exons 3, 4, 7, and 9). For the VWS families, we found a novel nonsense variant in exon 4 (p.Lys66X), a novel splice-site variant in exon 4 (p.Pro126Pro), a novel missense variant in exon 4 (p.Phe230Leu), a previously reported splice-site variant in exon 7 that changes the acceptor splice site, and a known missense variant in exon 7 (p.Leu251Pro). A previously known missense variant was found in exon 4 (p.Arg84His) in the PPS family. All the mutations segregate in the families. Our data confirm the presence of IRF6-related VWS and PPS in sub-Saharan Africa and highlights the importance of screening for novel mutations in known genes when studying diverse global populations. This is important for counseling and prenatal diagnosis for high-risk families.
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Affiliation(s)
- Azeez Butali
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa Iowa City, Iowa
| | - Peter A Mossey
- Department of Orthodontics, University of Dundee Dundee, Scotland
| | | | | | - LauRen A Gaines
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa Iowa City, Iowa
| | - Dee Even
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa Iowa City, Iowa
| | | | | | - Jennifer V Rigdon
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa Iowa City, Iowa
| | | | - Olutayo James
- College of Medicine, University of Lagos Lagos, Nigeria
| | | | | | - Fikre Abate
- Addis Ababa University Addis Ababa, Ethiopia
| | - Taye Hailu
- Addis Ababa University Addis Ababa, Ethiopia
| | | | | | | | | | - Adebowale A Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health Bethesda, Maryland
| | - Jeffrey C Murray
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa Iowa City, Iowa
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18
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Malik S, Wilcox ER, Naz S. Novel lip pit phenotypes and mutations of IRF6 in Van der Woude syndrome patients from Pakistan. Clin Genet 2013; 85:487-91. [PMID: 23713753 DOI: 10.1111/cge.12207] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Revised: 05/23/2013] [Indexed: 11/29/2022]
Abstract
The role of interferon regulatory factor 6 (IRF6) gene mutations in causing Van der Woude syndrome (VWS) and poplyteal pterygium syndrome has been described in different populations worldwide. The former is one of the major syndromes of cleft lip and/or cleft palate (CL/P) with the distinct phenotype of presence of pits with or without sinuses on the lower lip. We identified seven probands with VWS from Punjab province of Pakistan and recognized two previously unreported lip pit phenotypes. The mutational analysis of IRF6 in this cohort revealed four novel and two previously reported mutations. The newly identified mutations include three frameshifts (c.635delG; c.21_33del13; c.627delC) and one transition mutation (c.2T>C) affecting the first codon of IRF6. Together with a past epidemiological study on VWS in Pakistan, the frequency of this syndrome among CL/P individuals from Punjab was calculated to be 1.17%.
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Affiliation(s)
- S Malik
- School of Biological Sciences; Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
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Wu-Chou YH, Lo LJ, Chen KTP, Chang CSF, Chen YR. A combined targeted mutation analysis of IRF6 gene would be useful in the first screening of oral facial clefts. BMC Med Genet 2013; 14:37. [PMID: 23510002 PMCID: PMC3606492 DOI: 10.1186/1471-2350-14-37] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 03/13/2013] [Indexed: 01/30/2023]
Abstract
Background Interferon Regulatory Factor 6 (IRF6) is a member of the IRF family of transcription factors. It has been suggested to be an important contributor to orofacial development since mutations of the IRF6 gene has been found in Van der Woude (VWS) and popliteal pterygium syndromes (PPS), two disorders that can present with isolated cleft lip and palate. The association between IRF6 gene and cleft lip and palate has also been independently replicated in many populations. Methods We screened a total of 155 Taiwanese patients with cleft lip with or without cleft palate (CL/P); 31 syndromic (including 19 VWS families), 44 non-syndromic families with at least two affected members, and 80 non-syndromic patients through a combined targeted, polymerase chain reaction (PCR)-based mutation analysis for the entire coding regions of IRF6 gene. Results We found 11 mutations in 57.89% (11/19) of the VWS patients and no IRF6 mutation in 44 of the non-syndromic multiplex families and 80 non-syndromic oral cleft patients. In this IRF6 gene screening, five of these mutations (c.290 A>G, p.Tyr97Cys; c.360-375 16 bp deletion, p.Gln120HisfsX24; c.411_412 insA, p.Glu136fsX3; c.871 A>C, p.Thr291Pro; c.969 G>A, and p.Trp323X) have not been reported in the literature previously. Exon deletion was not detected in this series of IRF6 gene screening. Conclusions Our results confirm the crucial role of IRF6 in the VWS patients and further work is needed to explore for its function in the non-syndromic oral cleft with vary clinical features.
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Affiliation(s)
- Yah-Huei Wu-Chou
- Department of Medical Research, Chang Gung Memorial Hospital, No. 5, Fushing Street, Kweishan, Taoyuan, Taiwan.
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Leslie EJ, Standley J, Compton J, Bale S, Schutte BC, Murray JC. Comparative analysis of IRF6 variants in families with Van der Woude syndrome and popliteal pterygium syndrome using public whole-exome databases. Genet Med 2013; 15:338-44. [PMID: 23154523 DOI: 10.1038/gim.2012.141] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Purpose: Mutations in the transcription factor IRF6 cause allelic autosomal dominant clefting syndromes, Van der Woude syndrome, and popliteal pterygium syndrome. We compared the distribution of IRF6 coding and splice-site mutations from 549 families with Van der Woude syndrome or popliteal pterygium syndrome with that of variants from the 1000 Genomes and National Heart, Lung, and Blood Institute Exome Sequencing Projects. Methods: We compiled all published pathogenic IRF6 mutations and performed direct sequencing of IRF6 in families with Van der Woude syndrome or popliteal pterygium syndrome. Results: Although mutations causing Van der Woude syndrome or popliteal pterygium syndrome were nonrandomly distributed with significantly increased frequencies in the DNA-binding domain (P = 0.0001), variants found in controls were rare and evenly distributed in IRF6. Of 194 different missense or nonsense variants described as potentially pathogenic, we identified only two in more than 6,000 controls. PolyPhen and SIFT (sorting intolerant from tolerant) reported 5.9% of missense mutations in patients as benign, suggesting that use of current in silico prediction models to determine function can have significant false negatives. Conclusion: Mutation of IRF6 occurs infrequently in controls, suggesting that for IRF6 there is a high probability that disruption of the coding sequence, particularly the DNA-binding domain, will result in syndromic features. Prior associations of coding sequence variants in IRF6 with clefting syndromes have had few false positives.
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Laugel-Haushalter V, Langer A, Marrie J, Fraulob V, Schuhbaur B, Koch-Phillips M, Dollé P, Bloch-Zupan A. From the transcription of genes involved in ectodermal dysplasias to the understanding of associated dental anomalies. Mol Syndromol 2012; 3:158-68. [PMID: 23239958 DOI: 10.1159/000342833] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2012] [Indexed: 01/17/2023] Open
Abstract
Orodental anomalies are one aspect of rare diseases and are increasingly identified as diagnostic and predictive traits. To understand the rationale behind gene expression during tooth or other ectodermal derivative development and the disruption of odontogenesis or hair and salivary gland formation in human syndromes we analyzed the expression patterns of a set of genes (Irf6, Nfkbia, Ercc3, Evc2, Map2k1) involved in human ectodermal dysplasias in mouse by in situ hybridization. The expression patterns of Nfkbia, Ercc3 and Evc2 during odontogenesis had never been reported previously. All genes were indeed transcribed in different tissues/organs of ectodermal origin. However, for Nfkbia, Ercc3, Evc2, and Map2k1, signals were also present in the ectomesenchymal components of the tooth germs. These expression patterns were consistent in timing and localization with the known dental anomalies (tooth agenesis, microdontia, conical shape, enamel hypoplasia) encountered in syndromes resulting from mutations in those genes. They could also explain the similar orodental anomalies encountered in some of the corresponding mutant mouse models. Translational approaches in development and medicine are relevant to gain understanding of the molecular events underlying clinical manifestations.
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Affiliation(s)
- V Laugel-Haushalter
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (UMR 7104), Institut National de la Santé et de la Recherche Médicale (U 964), Université de Strasbourg, Illkirch, Strasbourg, France
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de la Garza G, Schleiffarth JR, Dunnwald M, Mankad A, Weirather JL, Bonde G, Butcher S, Mansour TA, Kousa YA, Fukazawa CF, Houston DW, Manak JR, Schutte BC, Wagner DS, Cornell RA. Interferon regulatory factor 6 promotes differentiation of the periderm by activating expression of Grainyhead-like 3. J Invest Dermatol 2012; 133:68-77. [PMID: 22931925 PMCID: PMC3541433 DOI: 10.1038/jid.2012.269] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Interferon Regulatory Factor 6 (IRF6) is a transcription factor that, in mammals, is required for the differentiation of skin, breast epithelium, and oral epithelium. However, the transcriptional targets that mediate these effects are currently unknown. In zebrafish and frog embryos Irf6 is necessary for differentiation of the embryonic superficial epithelium, or periderm. Here we use microarrays to identify genes that are expressed in the zebrafish periderm and whose expression is inhibited by a dominant-negative variant of Irf6 (dnIrf6). These methods identify Grhl3, an ancient regulator of the epidermal permeability barrier, as acting downstream of Irf6. In human keratinocytes, IRF6 binds conserved elements near the GHRL3 promoter. We show that one of these elements has enhancer activity in human keratinocytes and zebrafish periderm, suggesting that Irf6 directly stimulates Grhl3 expression in these tissues. Simultaneous inhibition of grhl1 and grhl3 disrupts periderm differentiation in zebrafish, and, intriguingly, forced grhl3 expression restores periderm markers in both zebrafish injected with dnIrf6 and frog embryos depleted of Irf6. Finally, in Irf6 deficient mouse embryos, Grhl3 expression in the periderm and oral epithelium is virtually absent. These results indicate that Grhl3 is a key effector of Irf6 in periderm differentiation.
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Affiliation(s)
- Gabriel de la Garza
- Department of Otolaryngology-Head and Neck Surgery, University of Iowa, Iowa City, IA, USA
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Salahshourifar I, Wan Sulaiman WA, Halim AS, Zilfalil BA. Mutation screening of IRF6 among families with non-syndromic oral clefts and identification of two novel variants: Review of the literature. Eur J Med Genet 2012; 55:389-93. [PMID: 22440537 DOI: 10.1016/j.ejmg.2012.02.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2011] [Accepted: 02/13/2012] [Indexed: 12/17/2022]
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Kosaki R, Kaneko T, Torii C, Kosaki K. EEC syndrome-like phenotype in a patient with an IRF6 mutation. Am J Med Genet A 2012; 158A:1219-20. [PMID: 22488974 DOI: 10.1002/ajmg.a.35273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Accepted: 12/27/2011] [Indexed: 11/10/2022]
Affiliation(s)
- Rika Kosaki
- Division of Medical Genetics, National Center for Child Health and Development, Tokyo, Japan.
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Ghassibe-Sabbagh M, Desmyter L, Langenberg T, Claes F, Boute O, Bayet B, Pellerin P, Hermans K, Backx L, Mansilla MA, Imoehl S, Nowak S, Ludwig KU, Baluardo C, Ferrian M, Mossey PA, Noethen M, Dewerchin M, François G, Revencu N, Vanwijck R, Hecht J, Mangold E, Murray J, Rubini M, Vermeesch JR, Poirel HA, Carmeliet P, Vikkula M. FAF1, a gene that is disrupted in cleft palate and has conserved function in zebrafish. Am J Hum Genet 2011; 88:150-61. [PMID: 21295280 DOI: 10.1016/j.ajhg.2011.01.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 11/24/2010] [Accepted: 01/06/2011] [Indexed: 10/18/2022] Open
Abstract
Cranial neural crest (CNC) is a multipotent migratory cell population that gives rise to most of the craniofacial bones. An intricate network mediates CNC formation, epithelial-mesenchymal transition, migration along distinct paths, and differentiation. Errors in these processes lead to craniofacial abnormalities, including cleft lip and palate. Clefts are the most common congenital craniofacial defects. Patients have complications with feeding, speech, hearing, and dental and psychological development. Affected by both genetic predisposition and environmental factors, the complex etiology of clefts remains largely unknown. Here we show that Fas-associated factor-1 (FAF1) is disrupted and that its expression is decreased in a Pierre Robin family with an inherited translocation. Furthermore, the locus is strongly associated with cleft palate and shows an increased relative risk. Expression studies show that faf1 is highly expressed in zebrafish cartilages during embryogenesis. Knockdown of zebrafish faf1 leads to pharyngeal cartilage defects and jaw abnormality as a result of a failure of CNC to differentiate into and express cartilage-specific markers, such as sox9a and col2a1. Administration of faf1 mRNA rescues this phenotype. Our findings therefore identify FAF1 as a regulator of CNC differentiation and show that it predisposes humans to cleft palate and is necessary for lower jaw development in zebrafish.
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