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Golshan-Tafti M, Dastgheib SA, Bahrami R, Aarafi H, Foroughi E, Mirjalili SR, Kheirandish N, Aghasipour M, Shiri A, Azizi S, Aghili K, Manzourolhojeh M, Neamatzadeh H. A comprehensive consolidation of data on the relationship between IRF6 polymorphisms and non-syndromic cleft lip/palate susceptibility: From 79 case-control studies. JOURNAL OF STOMATOLOGY, ORAL AND MAXILLOFACIAL SURGERY 2024:101809. [PMID: 38431084 DOI: 10.1016/j.jormas.2024.101809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/29/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a prevalent craniofacial birth defect on a global scale. A number of candidate genes have been identified as having an impact on NSCL/P. However, the association between interferon regulatory factor 6 (IRF6) polymorphisms and NSCL/P has yielded inconsistent results, prompting the need for a meta-analysis to obtain more accurate estimates. METHODS We conducted a thorough screening of all relevant articles published up until November 15, 2023, in online bibliographic databases. The statistical analysis of the collected data was performed using the Comprehensive Meta-Analysis (Version 4.0) software. RESULTS A total of 79 case-control studies, comprising 14,003 cases and 19,905 controls, were included in our analysis. The combined data indicated that the IRF6 rs642961 and rs2235371 polymorphisms were associated with an increased risk of NSCL/P in the overall population. However, no significant association was found between the rs2013162 and rs2235375 polymorphisms and the risk of NSCL/P in the overall population. Furthermore, subgroup analyses revealed significant correlations between the IRF6 rs642961, rs2235371, and rs2235375 polymorphisms and the risk of NSCL/P based on ethnic background and country of origin. Nevertheless, the rs2013162 polymorphism plays a protective role in Caucasians and mixed populations. CONCLUSIONS Our collective data indicates a significant association between the rs642961 and rs2235371 polymorphisms and the risk of NSCL/P in the overall population. The rs2235375 polymorphism could influence the susceptibility to NSCL/P based on ethnic background. Meanwhile, the rs2013162 polymorphism provides protective effects in Caucasian, mixed populations, and the Brazilian population.
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Affiliation(s)
| | - Seyed Alireza Dastgheib
- Department of Medical Genetics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Reza Bahrami
- Neonatal Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Hossein Aarafi
- Department of Pediatrics, Islamic Azad University of Yazd, Yazd, Iran.
| | - Elnaz Foroughi
- Department of Pediatric Dentistry, School of Dentistry, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Seyed Reza Mirjalili
- Mother and Newborn Health Research Center, Shahid Sadoughi Hospital, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Naeimeh Kheirandish
- Oral and Maxillofacial Pathology, School of Dentistry, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Maryam Aghasipour
- Department of Cancer Biology, College of Medicine, University of Cincinnati, Ohio, USA
| | - Amirmasoud Shiri
- Student Research Committee, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sepideh Azizi
- Shahid Akbarabadi Clinical Research Development Unit, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Kazem Aghili
- Department of Radiology, Shahid Rahnemoon Hospital, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mohammad Manzourolhojeh
- Mother and Newborn Health Research Center, Shahid Sadoughi Hospital, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Hossein Neamatzadeh
- Mother and Newborn Health Research Center, Shahid Sadoughi Hospital, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
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2
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Ghazali N, Rahman NA, Kannan TP, Ahmad A, Sulong S. Identification of copy neutral loss of heterozygosity on chromosomes 1p, 1q, and 6p among nonsyndromic cleft lip and/or without cleft palate with hypodontia. BMC Oral Health 2023; 23:945. [PMID: 38031027 PMCID: PMC10685534 DOI: 10.1186/s12903-023-03464-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 09/27/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND Nonsyndromic cleft lip and/or without cleft palate (NSCL/P) with or without hypodontia is a common developmental aberration in humans and animals. This study aimed to identify the loss of heterozygosity (LOH) involved in hypodontia and NSCL/P pathogenesis. METHODS This is a cross-sectional study that conducted genome-wide copy number analysis using CytoScan 750K array on salivary samples from Malay subjects with NSCL/P with or without hypodontia aged 7-13 years. To confirm the significant results, simple logistic regression was employed to conduct statistical data analysis using SPSS software. RESULTS The results indicated the most common recurrent copy neutral LOH (cnLOH) observed at 1p33-1p32.3, 1q32.2-1q42.13 and 6p12.1-6p11.1 loci in 8 (13%), 4 (7%), and 3 (5%) of the NSCL/P subjects, respectively. The cnLOHs at 1p33-1p32.3 (D1S197), 1q32.2-1q42.13 (D1S160), and 6p12.1-6p11.1 (D1S1661) were identified observed in NSCL/P and noncleft children using microsatellite analysis markers as a validation analysis. The regions affected by the cnLOHs at 1p33-1p32.3, 1q32.2-1q42.13, and 6p12.1-6p11.1 loci contained selected genes, namely FAF1, WNT3A and BMP5, respectively. There was a significant association between the D1S197 (1p33-32.3) markers containing the FAF1 gene among NSCL/P subjects with or without hypodontia compared with the noncleft subjects (p-value = 0.023). CONCLUSION The results supported the finding that the genetic aberration on 1p33-32.3 significantly contributed to the development of NSCL/P with or without hypodontia. These results have an exciting prospect in the promising field of individualized preventive oral health care.
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Affiliation(s)
- Norliana Ghazali
- School of Dental Sciences, Universiti Sains Malaysia (USM), Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Normastura Abd Rahman
- School of Dental Sciences, Universiti Sains Malaysia (USM), Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - Thirumulu Ponnuraj Kannan
- School of Dental Sciences, Universiti Sains Malaysia (USM), Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Azlina Ahmad
- School of Dental Sciences, Universiti Sains Malaysia (USM), Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Sarina Sulong
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia (USM), Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia
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3
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Babai A, Irving M. Orofacial Clefts: Genetics of Cleft Lip and Palate. Genes (Basel) 2023; 14:1603. [PMID: 37628654 PMCID: PMC10454293 DOI: 10.3390/genes14081603] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/24/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
Orofacial clefting is considered one of the commonest birth defects worldwide. It presents as cleft lip only, isolated cleft palate or cleft lip and palate. The condition has a diverse genetic background influenced by gene-gene and gene-environment interaction, resulting in two main types, syndromic and nonsyndromic orofacial clefts. Orofacial clefts lead to significant physiological difficulties that affect feeding, speech and language development and other developmental aspects, which results in an increased social and financial burden on the affected individuals and their families. The management of cleft lip and palate is solely based on following a multidisciplinary team approach. In this narrative review article, we briefly summarize the different genetic causes of orofacial clefts and discuss some of the common syndromes and the approach to the management of orofacial clefts.
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Affiliation(s)
- Arwa Babai
- Department of Clinical Genetics, Guy’s Hospital, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 9RT, UK;
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4
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Nasroen SL, Maskoen AM, Soedjana H, Hilmanto D, Gani BA. The IRF6 AP-2α binding site polymorphism relate to the severity of non-syndromic orofacial cleft of Indonesian patients. Minerva Dent Oral Sci 2023; 72:8-15. [PMID: 36847740 DOI: 10.23736/s2724-6329.21.04572-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
BACKGROUND IRF6 AP-2α binding site polymorphism is known as IRF6 rs642961. It has been associated with a nonsyndromic orofacial cleft (NS OFC). This study aimed to determine the IRF6 rs642961 as a risk factor associated with NS OFC and its phenotypes. METHODS The case-control design used for 264 subjects consists of 158 NS CLP subjects (42 CU CLP, 34 CB CLP, 33 CLO, 49 CPOs) and 106 healthy controls. The DNA is extracted from venous blood. The segment of IRF6 rs642961 amplified by polymerase chain reaction (PCR) followed by restriction fragment length of polymorphisms (RFLPs) used the MspI digestion enzyme. The qPCR method to identify the mRNA expression levels of the IRF6 gene rs642961 was analyzed by the Livak method. RESULTS The study results show that in NS CB CLP phenotype as the most severe phenotype of NS OFC, the Odds Ratio (OR) of A mutant allele was 5.094 (CI=1.456-17.820; P=0.011) and the OR of AA homozygous mutant genotype was 13.481 (CI=2.648-68.635; P=0.001). There are different levels of mRNA expression changes from NS OFC and its phenotypes. It is substantial among the 2-ΔΔCt and the group of AA, GA, and GG genotypes (P<0.05); in the NS CPO phenotype, it shows IRF6 mRNA under-expression in GA, AA genotypes while in other phenotypes it shows IRF6 mRNA overexpression. CONCLUSIONS The IRF6 AP-2α binding site polymorphism is strongly associated with the severity of NS OFC, and this polymorphism has a functional role in affecting IRF6 mRNA expression that is variable in each phenotype.
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Affiliation(s)
- Saskia L Nasroen
- Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, Universitas Jenderal Achmad Yani Cimahi, Bandung, Indonesia -
| | - Ani M Maskoen
- Department of Oral Biology, Faculty of Dentistry, Universitas Padjadjaran, Bandung, Indonesia
| | - Hardisiswo Soedjana
- Division of Plastic Surgery Reconstruction and Esthetic, Department of Surgery, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Dany Hilmanto
- Department of Pediatrics, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Basri A Gani
- Department of Oral Biology, Faculty of Dentistry, Universitas Syiah Kuala, Aceh, Indonesia
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5
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das Neves LT, de Carvalho IMM, Cobourne MT, Gomide MR. Dental anomalies in non-syndromic orofacial clefts: a clinical approach. Oral Dis 2022; 28:1351-1368. [PMID: 35485181 DOI: 10.1111/odi.14226] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 04/13/2022] [Accepted: 04/21/2022] [Indexed: 11/28/2022]
Abstract
Orofacial clefts (OC) represent some of the most common congenital malformations and affect multiple structures in the craniofacial region. There are a wide range of morphological OC types within the spectrum of both non-syndromic OC (NSOC) and syndromic OC, including cleft lip (CL); cleft lip and palate (CLP) and cleft palate (CP). Here, we describe the most frequent dental anomalies seen in the permanent dentition of individuals with NSOC, comparing them between the three main cleft types (CL, CLP, CP). We present these findings from the perspective of prevalence relating to each anomaly, as well as the clinical characteristics and potential impact in the rehabilitation process. The investigation of dental anomalies associated with NSOC is important, helping to expand the phenotypic characterization of NSOC, improve initial diagnostics and establish appropriate rehabilitation and counseling.
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Affiliation(s)
- Lucimara Teixeira das Neves
- Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, Brazil.,Bauru School of Dentistry, University of Sao Paulo, Department of Biological Science - FOB/USP), Bauru, Brazil
| | | | - Martyn T Cobourne
- Centre for Craniofacial & Regenerative Biology, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, Guy's Hospital, London, UK.,Department of Orthodontics, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Marcia Ribeiro Gomide
- Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, Brazil
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6
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Lace B, Pajusalu S, Livcane D, Grinfelde I, Akota I, Mauliņa I, Barkāne B, Stavusis J, Inashkina I. Monogenic Versus Multifactorial Inheritance in the Development of Isolated Cleft Palate: A Whole Genome Sequencing Study. Front Genet 2022; 13:828534. [PMID: 35281813 PMCID: PMC8907258 DOI: 10.3389/fgene.2022.828534] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/25/2022] [Indexed: 11/24/2022] Open
Abstract
Craniofacial morphogenesis is highly complex, as is the anatomical region involved. Errors during this process, resulting in orofacial clefts, occur in more than 400 genetic syndromes. Some cases of cleft lip and/or palate (CLP) are caused by mutations in single genes; however, complex interactions between genetic and environmental factors are considered to be responsible for the majority of non-syndromic CLP development. The aim of the current study was to identify genetic risk factors in patients with isolated cleft palate (CP) by whole genome sequencing. Patients with isolated CP (n = 30) recruited from the Riga Cleft Lip and Palate Centre, Institute of Stomatology, Riga, were analyzed by whole genome sequencing. Pathogenic or likely pathogenic variants were discovered in genes associated with CP (TBX22, COL2A1, FBN1, PCGF2, and KMT2D) in five patients; hence, rare disease variants were identified in 17% of patients with non-syndromic isolated CP. Our results were relevant to routine genetic counselling practice and genetic testing recommendations. Based on our data, we propose that all newborns with orofacial clefts should be offered genetic testing, at least for a panel of known CLP genes. Only if the results are negative and there is no suggestive family history or additional clinical symptoms (which would support additional exome or genome-wide investigation), should multifactorial empiric recurrence risk prediction tools be applied for families.
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Affiliation(s)
- Baiba Lace
- Latvian Biomedical Research and Study Centre, Riga, Latvia
- *Correspondence: Baiba Lace, , orcid.org/0000-0001-5371-6756
| | - Sander Pajusalu
- Latvian Biomedical Research and Study Centre, Riga, Latvia
- Department of Clinical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia
| | - Diana Livcane
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Ieva Grinfelde
- Cleft, Lip and Palate Center, Institute of Stomatology, Riga Stradins’University, Riga, Latvia
- Medical Genetics Clinic, Children’s Clinical University Hospital, Riga, Latvia
| | - Ilze Akota
- Cleft, Lip and Palate Center, Institute of Stomatology, Riga Stradins’University, Riga, Latvia
| | - Ieva Mauliņa
- Cleft, Lip and Palate Center, Institute of Stomatology, Riga Stradins’University, Riga, Latvia
| | - Biruta Barkāne
- Cleft, Lip and Palate Center, Institute of Stomatology, Riga Stradins’University, Riga, Latvia
| | - Janis Stavusis
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Inna Inashkina
- Latvian Biomedical Research and Study Centre, Riga, Latvia
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7
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Wu Q, Li Z, Zhang Y, Peng X, Zhou X. Dental caries and periodontitis risk factors in cleft lip and palate patients. Front Pediatr 2022; 10:1092809. [PMID: 36683789 PMCID: PMC9846248 DOI: 10.3389/fped.2022.1092809] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/09/2022] [Indexed: 01/06/2023] Open
Abstract
Cleft lip and palate (CLP) is the most common congenital facial malformation and has a significant developmental, physical, and psychological impact on those with the deformity and their families. Risk factors contributing to CLP may conclude as genetic factors and environmental factors. The anatomical and morphological abnormalities related to CLP are favorable for dental plaque accumulation on the tooth surface. Therefore, patients with CLP undergo poorer oral hygiene and higher susceptibility to dental caries and periodontitis. In this review, we aim to conclude and update probable causes underlying the association between CLP and poor oral health and provide novel ideas of targeted early prevention for such oral diseases.
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Affiliation(s)
- Qinrui Wu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhengyi Li
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yixin Zhang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xian Peng
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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8
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Ghazali N, Abd Rahman N, Ahmad A, Sulong S, Kannan TP. Identification of Copy Number Variation Among Nonsyndromic Cleft Lip and or Without Cleft Palate With Hypodontia: A Genome-Wide Association Study. Front Physiol 2021; 12:637306. [PMID: 33732167 PMCID: PMC7959817 DOI: 10.3389/fphys.2021.637306] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/18/2021] [Indexed: 12/27/2022] Open
Abstract
Nonsyndromic cleft lip and or without cleft palate (NSCL/P) with the hypodontia is a common developmental abnormality in humans and animals. This study identified the genetic aberration involved in both NSCL/P and hypodontia pathogenesis. A cross-sectional study using genome-wide study copy number variation-targeted CytoScan 750K array carried out on salivary samples from 61 NSCL/P and 20 noncleft with and without hypodontia Malay subjects aged 7-13 years old. Copy number variations (CNVs) of SKI and fragile histidine triad (FHIT) were identified in NSCL/P and noncleft children using quantitative polymerase chain reaction (qPCR) as a validation analysis. Copy number calculated (CNC) for each gene determined with Applied Biosystems CopyCaller Software v2.0. The six significant CNVs included gains (12q14.3, 15q26.3, 1p36.32, and 1p36.33) and losses (3p14.2 and 4q13.2) in NSCL/P with hypodontia patients compared with the NSCL/P only. The genes located in these regions encoded LEMD3, IGF1R, TP73, SKI, FHIT, and UGT2β15. There were a significant gain and loss of both SKI and FHIT copy number in NSCL/P with hypodontia compared with the noncleft group (p < 0.05). The results supported that CNVs significantly furnish to the development of NSCL/P with hypodontia.
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Affiliation(s)
- Norliana Ghazali
- School of Dental Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | | | - Azlina Ahmad
- School of Dental Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
| | - Sarina Sulong
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian, Malaysia
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9
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Rizell S, Küseler A, Heliövaara A, Skaare P, Brinck E, Bellardie H, Mooney J, Mølsted K, Karsten A, Sæle P, Chalien MN, Marcusson A, Eyres P, Shaw W, Semb G. Scandcleft randomized trials of primary surgery for unilateral cleft lip and palate: impact of maxillary dental agenesis on craniofacial growth and dental arch relationship in 8 year olds. Eur J Orthod 2021; 43:381-386. [PMID: 33693582 DOI: 10.1093/ejo/cjab007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND It is suggested that dental agenesis affects maxillary protrusion and dental arch relationship in children with unilateral cleft lip and palate (UCLP). In addition, an association between the need for orthognathic surgery and dental agenesis is reported. AIM The aim was to study the impact of maxillary dental agenesis on craniofacial growth and dental arch relationship in 8-year-old children with UCLP. SUBJECTS AND METHODS The sample consisted of individuals with UCLP from Scandcleft randomized trials. The participants had available data from diagnosis of maxillary dental agenesis as well as cephalometric measurements (n = 399) and GOSLON assessment (n = 408) at 8 years of age. RESULTS A statistically significant difference was found for ANB between individuals with agenesis of two or more maxillary teeth (mean 1.52°) in comparison with those with no or only one missing maxillary tooth (mean 3.30° and 2.70°, respectively). Mean NSL/NL was lower among individuals with agenesis of two or more maxillary teeth (mean 9.90°), in comparison with individuals with no or one missing maxillary tooth (mean 11.46° and 11.45°, respectively). The number of individuals with GOSLON score 4-5 was 47.2% in the group with two or more missing maxillary teeth and 26.1% respectively 26.3% in the groups with no or one missing maxillary tooth. No statistically significant difference was found in the comparison between individuals with no agenesis or with agenesis solely of the cleft-side lateral. CONCLUSION Maxillary dental agenesis impacts on craniofacial growth as well as dental arch relationship and should be considered in orthodontic treatment planning.
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Affiliation(s)
- Sara Rizell
- Clinic of Orthodontics, Gothenburg, Public Dental Service, Region Västra Götaland, Sweden
| | - Annelise Küseler
- Cleft Palate Centre and University Hospital Aarhus and University of Aarhus, Denmark
| | - Arja Heliövaara
- Cleft Palate and Craniofacial Center, Department of Plastic Surgery, Helsinki University Hospital, Finland
| | - Pål Skaare
- Department of Plastic and Reconstructive Surgery, Oslo University Hospital, Rikshospitalet, Norway
| | - Eli Brinck
- Department of Plastic and Reconstructive Surgery, Oslo University Hospital, Rikshospitalet, Norway
| | - Haydn Bellardie
- University of the Western Cape, South Africa.,Greater Manchester Cleft Lip and Palate Unit, Royal Manchester Children's Hospital, Manchester, UK
| | - Jeanette Mooney
- Greater Manchester Cleft Lip and Palate Unit, Royal Manchester Children's Hospital, Manchester, UK
| | - Kirsten Mølsted
- Copenhagen Cleft Palate Centre, University Hospital of Copenhagen, Denmark
| | - Agneta Karsten
- Section of Orthodontics, Division of Orthodontics and Pedodontics, Department of Dental Medicine, Karolinska Institutet, Stockholm Craniofacial Team, Stockholm, Sweden
| | - Paul Sæle
- Oral Health Centre of Expertise, Western Norway, Bergen, Norway
| | - Midia Najar Chalien
- Clinic of Orthodontics, Gothenburg, Public Dental Service, Region Västra Götaland, Sweden
| | - Agneta Marcusson
- Maxillofacial Unit, and Department of Clinical and Experimental Medicine, Linköping University, Sweden
| | - Philip Eyres
- Greater Manchester Cleft Lip and Palate Unit, Royal Manchester Children's Hospital, Manchester, UK
| | - William Shaw
- Greater Manchester Cleft Lip and Palate Unit, Royal Manchester Children's Hospital, Manchester, UK
| | - Gunvor Semb
- Department of Plastic and Reconstructive Surgery, Oslo University Hospital, Rikshospitalet, Norway.,Greater Manchester Cleft Lip and Palate Unit, Royal Manchester Children's Hospital, Manchester, UK
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10
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Bonczek O, Krejci P, Izakovicova-Holla L, Cernochova P, Kiss I, Vojtesek B. Tooth agenesis: What do we know and is there a connection to cancer? Clin Genet 2021; 99:493-502. [PMID: 33249565 DOI: 10.1111/cge.13892] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/17/2020] [Accepted: 11/26/2020] [Indexed: 12/22/2022]
Abstract
Like all developmental processes, odontogenesis is highly complex and dynamically regulated, with hundreds of genes co-expressed in reciprocal networks. Tooth agenesis (missing one or more/all teeth) is a common human craniofacial anomaly and may be caused by genetic variations and/or environmental factors. Variants in PAX9, MSX1, AXIN2, EDA, EDAR, and WNT10A genes are associated with tooth agenesis. Currently, variants in ATF1, DUSP10, CASC8, IRF6, KDF1, GREM2, LTBP3, and components and regulators of WNT signaling WNT10B, LRP6, DKK, and KREMEN1 are at the forefront of interest. Due to the interconnectedness of the signaling pathways of carcinogenesis and odontogenesis, tooth agenesis could be a suitable marker for early detection of cancer predisposition. Variants in genes associated with tooth agenesis could serve as prognostic or therapeutic targets in cancer. This review aims to summarize existing knowledge of development and clinical genetics of teeth. Concurrently, the review proposes possible approaches for future research in this area, with particular attention to roles in monitoring, early diagnosis and therapy of tumors associated with defective tooth development.
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Affiliation(s)
- Ondrej Bonczek
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Premysl Krejci
- Institute of Dentistry and Oral Sciences, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Lydie Izakovicova-Holla
- Department of Stomatology, Institution shared with St. Anne's University Hospital, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Pavlina Cernochova
- Department of Stomatology, Institution shared with St. Anne's University Hospital, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Igor Kiss
- Clinic of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Borivoj Vojtesek
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
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11
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Bezamat M, Souza JF, Silva FMF, Corrêa EG, Fatturi AL, Brancher JA, Carvalho FM, Cavallari T, Bertolazo L, Machado-Souza C, Koruyucu M, Bayram M, Racic A, Harrison BM, Sweat YY, Letra A, Studen-Pavlovich D, Seymen F, Amendt B, Werneck RI, Costa MC, Modesto A, Vieira AR. Gene-environment interaction in molar-incisor hypomineralization. PLoS One 2021; 16:e0241898. [PMID: 33406080 PMCID: PMC7787379 DOI: 10.1371/journal.pone.0241898] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 10/22/2020] [Indexed: 01/12/2023] Open
Abstract
Molar incisor hypomineralization (MIH) is an enamel condition characterized by lesions ranging in color from white to brown which present rapid caries progression, and mainly affects permanent first molars and incisors. These enamel defects usually occur when there are disturbances during the mineralization or maturation stage of amelogenesis. Both genetic and environmental factors have been suggested to play roles in MIH’s development, but no conclusive risk factors have shown the source of the disease. During head and neck development, the interferon regulatory factor 6 (IRF6) gene is involved in the structure formation of the oral and maxillofacial regions, and the transforming growth factor alpha (TGFA) is an essential cell regulator, acting during proliferation, differentiation, migration and apoptosis. In this present study, it was hypothesized that these genes interact and contribute to predisposition of MIH. Environmental factors affecting children that were 3 years of age or older were also hypothesized to play a role in the disease etiology. Those factors included respiratory issues, malnutrition, food intolerance, infection of any sort and medication intake. A total of 1,065 salivary samples from four different cohorts were obtained, and DNA was extracted from each sample and genotyped for nine different single nucleotide polymorphisms. Association tests and logistic regression implemented in PLINK were used for analyses. A potential interaction between TGFA rs930655 with all markers tested in the cohort from Turkey was identified. These interactions were not identified in the remaining cohorts. Associations (p<0.05) between the use of medication after three years of age and MIH were also found, suggesting that conditions acquired at the age children start to socialize might contribute to the development of MIH.
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Affiliation(s)
- Mariana Bezamat
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Juliana F. Souza
- Department of Stomatology, Federal University of Paraná, Curitiba, State of Paraná, Brazil
| | - Fernanda M. F. Silva
- Department of Pediatric Dentistry and Orthodontics, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Emilly G. Corrêa
- Graduate Program of Dentistry, Pontifical Catholic University of Paraná, Curitiba, State of Paraná, Brazil
| | - Aluhe L. Fatturi
- Department of Stomatology, Federal University of Paraná, Curitiba, State of Paraná, Brazil
| | - João A. Brancher
- Graduate Program of Dentistry, Positivo University, Curitiba, State of Pará, Brazil
| | - Flávia M. Carvalho
- Department of Genetics, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tayla Cavallari
- Graduate Program of Dentistry, Pontifical Catholic University of Paraná, Curitiba, State of Paraná, Brazil
| | - Laís Bertolazo
- Graduate Program of Dentistry, Pontifical Catholic University of Paraná, Curitiba, State of Paraná, Brazil
| | - Cleber Machado-Souza
- Graduate Program of Applied Biotechnology to Child and Adolescent Health, Pequeno Príncipe College, Curitiba, State of Pará, Brazil
| | - Mine Koruyucu
- Department of Pedodontics, Istanbul University, Istanbul, Turkey
| | - Merve Bayram
- Department of Pedodontics, Medipol Istanbul University, Istanbul, Turkey
| | - Andrea Racic
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Benjamin M. Harrison
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Yan Y. Sweat
- Craniofacial Anomalies Research Center and Department of Orthodontics, College of Dentistry, The University of Iowa, Iowa City, Iowa, United States of America
| | - Ariadne Letra
- Department of Diagnostic and Biomedical Sciences, and Center for Craniofacial Research, UTHealth School of Dentistry at Houston, Houston, Texas, United States of America
| | - Deborah Studen-Pavlovich
- Department of Pediatric Dentistry, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Figen Seymen
- Department of Pedodontics, Istanbul University, Istanbul, Turkey
| | - Brad Amendt
- Craniofacial Anomalies Research Center and Department of Orthodontics, College of Dentistry, The University of Iowa, Iowa City, Iowa, United States of America
| | - Renata I. Werneck
- Graduate Program of Dentistry, Pontifical Catholic University of Paraná, Curitiba, State of Paraná, Brazil
| | - Marcelo C. Costa
- Department of Pediatric Dentistry and Orthodontics, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Adriana Modesto
- Department of Pediatric Dentistry, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Alexandre R. Vieira
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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12
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Sufiawati I, Maskoen AM, Soemantri ESS. Genetic variation of IRF6 and TGFA genes in an HIV-exposed newborn with non-syndromic cleft lip palate. Oral Dis 2020; 26 Suppl 1:165-168. [PMID: 32862534 DOI: 10.1111/odi.13403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 01/08/2020] [Accepted: 01/30/2020] [Indexed: 12/16/2022]
Abstract
We present here the first reported case of a non-syndromic cleft lip and palate (NSCLP) in an HIV-exposed newborn of a mother on antiretroviral therapy (ART) in Indonesia. Genetic testing was performed to confirm a suspected genetic condition. Genomic DNA was extracted from the blood, and genetic variations of the interferon regulatory factor 6 (IRF6) rs642961 (Mspl) (G>A) and transforming growth factor alpha (TGFA) BamHI (rs11466297, A>C) and RsaI (rs3732248, C>T) were performed by PCR-RFLP and IRF6 gene analysis by PCR sequencing. Genotyping of DNA sequence variants in the IRF6 gene showed both parents had genotype GA, while the child had genotype GG (genotype wild type). There was no difference observed in the TGFA BamHI gene variant between the child and her mother and father that were wild-type polymorphisms (normal), while the Rsa1 polymorphisms of them were heterozygotes. A genetic variant of IRF6 might be a protective factor for NSCLP, while Rsa1 gene variant (A) allele can be considered to be the risk factor associated with NSCLP development. This case report also highlights the possible etiologic role of ART in NSCLP; therefore, early control of adverse effects of ART might be an important factor in decreasing the incidence of the congenital anomalies in HIV-infected children.
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Affiliation(s)
- Irna Sufiawati
- Department of Oral Medicine, Faculty of Dentistry, Universitas Padjadjaran, Bandung, Indonesia
| | - Ani Melani Maskoen
- Department of Oral Biology, Faculty of Dentistry, Universitas Padjadjaran, Bandung, Indonesia
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13
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Martinelli M, Palmieri A, Carinci F, Scapoli L. Non-syndromic Cleft Palate: An Overview on Human Genetic and Environmental Risk Factors. Front Cell Dev Biol 2020; 8:592271. [PMID: 33195260 PMCID: PMC7606870 DOI: 10.3389/fcell.2020.592271] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/28/2020] [Indexed: 12/27/2022] Open
Abstract
The epithelial and mesenchymal cells involved in early embryonic facial development are guided by complex regulatory mechanisms. Any factor perturbing the growth, approach and fusion of the frontonasal and maxillary processes could result in orofacial clefts that represent the most common craniofacial malformations in humans. The rarest and, probably for this reason, the least studied form of cleft involves only the secondary palate, which is posterior to the incisive foramen. The etiology of cleft palate only is multifactorial and involves both genetic and environmental risk factors. The intention of this review is to give the reader an overview of the efforts made by researchers to shed light on the underlying causes of this birth defect. Most of the scientific papers suggesting potential environmental and genetic causes of non-syndromic cleft palate are summarized in this review, including genome-wide association and gene–environment interaction studies.
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Affiliation(s)
- Marcella Martinelli
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Annalisa Palmieri
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Francesco Carinci
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Luca Scapoli
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum - University of Bologna, Bologna, Italy
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14
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王 梦, 李 文, 周 仁, 王 斯, 刘 冬, 郑 鸿, 李 静, 李 楠, 周 治, 朱 洪, 吴 涛, 胡 永. [Evaluating the effect of WNT pathway genes considering interactions on the risk of non-syndromic oral clefts among Chinese populations]. BEIJING DA XUE XUE BAO. YI XUE BAN = JOURNAL OF PEKING UNIVERSITY. HEALTH SCIENCES 2020; 52:815-820. [PMID: 33047713 PMCID: PMC7653429 DOI: 10.19723/j.issn.1671-167x.2020.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Indexed: 06/11/2023]
Abstract
OBJECTIVE In this study, we used genome-wide association study (GWAS) data to explore whether WNT pathway genes were associated with non-syndromic oral clefts (NSOC) considering gene-gene interaction and gene-environment interaction. METHODS We conducted the analysis using 806 non-syndromic cleft lip with or without cleft palate (NSCL/P) case-parent trios and 202 non-syndromic cleft palate (NSCP) case-parent trios among Chinese populations selected from an international consortium established for a GWAS of non-syndromic oral clefts. Genotype data and maternal environmental exposures were collected through DNA samples and questionnaires. Conditional Logistic regression models were adopted to explore gene-gene interaction and gene-environment in teraction using trio package in R software. The threshold of significance level was set as 3.47×10-4 using Bonferroni correction. RESULTS A total of 144 single nucleotide polymorphisms (SNPs) in seven genes passed the quality control process in NSCL/P trios and NSCP trios, respectively. Totally six pairs of SNPs interactions showed statistically significant SNP-SNP interaction (P < 3.47×10-4) after Bonferroni correction, which were rs7618735 (WNT5A) and rs10848543 (WNT5B), rs631948 (WNT11) and rs556874 (WNT5A), and rs631948 (WNT11) and rs472631 (WNT5A) among NSCL/P trios; rs589149 (WNT11) and rs4765834 (WNT5B), rs1402704 (WNT11) and rs358792 (WNT5A), and rs1402704 (WNT11) and rs358793 (WNT5A) among NSCP trios, respectively. In addition, no significant result was found for gene-environment interaction analysis in both of the NSCL/P trios and NSCP trios. CONCLUSION Though this study failed to detect significant association based on gene-environment interactions of seven WNT pathway genes and the risk of NSOC, WNT pathway genes may influence the risk of NSOC through potential gene-gene interaction.
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Affiliation(s)
- 梦莹 王
- 北京大学公共卫生学院流行病与卫生统计学系,北京 100191Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China
| | - 文咏 李
- 北京大学公共卫生学院流行病与卫生统计学系,北京 100191Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China
| | - 仁 周
- 北京大学公共卫生学院流行病与卫生统计学系,北京 100191Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China
| | - 斯悦 王
- 北京大学公共卫生学院流行病与卫生统计学系,北京 100191Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China
| | - 冬静 刘
- 北京大学公共卫生学院流行病与卫生统计学系,北京 100191Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China
| | - 鸿尘 郑
- 北京大学公共卫生学院流行病与卫生统计学系,北京 100191Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China
| | - 静 李
- 北京大学口腔医学院·口腔医院,儿童口腔科 国家口腔疾病临床医学研究中心 口腔数字化医疗技术和材料国家工程实验室 口腔数字医学北京市重点实验室,北京 100081Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology, Beijing 100081, China
| | - 楠 李
- 北京大学口腔医学院·口腔医院颌面外科,北京 100081Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing 100081, China
| | - 治波 周
- 北京大学口腔医学院·口腔医院颌面外科,北京 100081Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing 100081, China
| | - 洪平 朱
- 北京大学口腔医学院·口腔医院颌面外科,北京 100081Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing 100081, China
| | - 涛 吴
- 北京大学公共卫生学院流行病与卫生统计学系,北京 100191Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China
| | - 永华 胡
- 北京大学公共卫生学院流行病与卫生统计学系,北京 100191Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China
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15
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Cunha AS, Dos Santos LV, Marañón-Vásquez GA, Kirschneck C, Gerber JT, Stuani MB, Matsumoto MAN, Vieira AR, Scariot R, Küchler EC. Genetic variants in tooth agenesis-related genes might be also involved in tooth size variations. Clin Oral Investig 2020; 25:1307-1318. [PMID: 32648061 DOI: 10.1007/s00784-020-03437-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 06/26/2020] [Indexed: 02/06/2023]
Abstract
OBJECTIVE The present study aimed to evaluate if genetic variants in PAX9, MSX1, TGFα, FGF3, FGF10, FGF13, GLI2 and GLI3 are involved in TS of permanent teeth. MATERIALS AND METHODS Pretreatment dental records from orthodontic patients were assessed prior to recruitment. Patients with tooth agenesis and congenital anomalies (including oral cleft) and/or syndromes were excluded. Dental casts were used to measure the maximum crown dimensions of all fully erupted permanent teeth except second and third molars in mesiodistal direction. Teeth with caries, occlusal wear, mesiodistal restorations, and obvious deformities were not evaluated. Genomic DNA samples were used for genotyping. The allelic discrimination of 13 genetic variants was performed. The associations between TS and genotype were analyzed by linear regression, adjusted by gender at a significance level of p ≤ 0.05. RESULTS Genetic polymorphisms in the tooth agenesis-related genes studied here were associated with increased and decreased TS, in both maxilla and mandible (p < 0.05). CONCLUSION This study reported associations of novel tooth agenesis-related gene variants with permanent tooth size variations. CLINICAL RELEVANCE The presence of some genetic variants could allow the prediction of permanent tooth size.
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Affiliation(s)
- Arthur S Cunha
- Department of Pediatric Dentistry, School of Dentistry of Ribeirão Preto, University of São Paulo, Avenida do Café s/n - Campus da USP, Sao Paulo, 4040-904, Brazil.
| | - Luiza Vertuan Dos Santos
- Department of Pediatric Dentistry, School of Dentistry of Ribeirão Preto, University of São Paulo, Avenida do Café s/n - Campus da USP, Sao Paulo, 4040-904, Brazil
| | - Guido Artemio Marañón-Vásquez
- Department of Pediatric Dentistry, School of Dentistry of Ribeirão Preto, University of São Paulo, Avenida do Café s/n - Campus da USP, Sao Paulo, 4040-904, Brazil
| | - Christian Kirschneck
- Department of Orthodontics, University Medical Centre of Regensburg, Franz-Josef-Strauss-Allee 11, 93053, Regensburg, Germany
| | | | - Maria Bernadete Stuani
- Department of Pediatric Dentistry, School of Dentistry of Ribeirão Preto, University of São Paulo, Avenida do Café s/n - Campus da USP, Sao Paulo, 4040-904, Brazil
| | - Mírian Aiko Nakane Matsumoto
- Department of Pediatric Dentistry, School of Dentistry of Ribeirão Preto, University of São Paulo, Avenida do Café s/n - Campus da USP, Sao Paulo, 4040-904, Brazil
| | - Alexandre Rezende Vieira
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, 412 Salk Pavilion, 335 Sutherland Street, Pittsburgh, PA, 15261, USA
| | - Rafaela Scariot
- Department of Stomatology, Federal University of Parana, Curitiba, Paraná, Brazil
| | - Erika Calvano Küchler
- Department of Pediatric Dentistry, School of Dentistry of Ribeirão Preto, University of São Paulo, Avenida do Café s/n - Campus da USP, Sao Paulo, 4040-904, Brazil.
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16
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Morris VE, Hashmi SS, Zhu L, Maili L, Urbina C, Blackwell S, Greives MR, Buchanan EP, Mulliken JB, Blanton SH, Zheng WJ, Hecht JT, Letra A. Evidence for craniofacial enhancer variation underlying nonsyndromic cleft lip and palate. Hum Genet 2020; 139:1261-1272. [PMID: 32318854 DOI: 10.1007/s00439-020-02169-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/13/2020] [Indexed: 12/14/2022]
Abstract
Nonsyndromic cleft lip with or without cleft palate (NSCLP) is a common birth defect for which only ~ 20% of the underlying genetic variation has been identified. Variants in noncoding regions have been increasingly suggested to contribute to the missing heritability. In this study, we investigated whether variation in craniofacial enhancers contributes to NSCLP. Candidate enhancers were identified using VISTA Enhancer Browser and previous publications. Prioritization was based on patterning defects in knockout mice, deletion/duplication of craniofacial genes in animal models and results of whole exome/whole genome sequencing studies. This resulted in 20 craniofacial enhancers to be investigated. Custom amplicon-based sequencing probes were designed and used for sequencing 380 NSCLP probands (from multiplex and simplex families of non-Hispanic white (NHW) and Hispanic ethnicities) using Illumina MiSeq. The frequencies of identified variants were compared to ethnically matched European (CEU) and Los Angeles Mexican (MXL) control genomes and used for association analyses. Variants in mm427/MSX1 and hs1582/SPRY1 showed genome-wide significant association with NSCLP (p ≤ 6.4 × 10-11). In silico analysis showed that these enhancer variants may disrupt important transcription factor binding sites. Haplotypes involving these enhancers and also mm435/ABCA4 were significantly associated with NSCLP, especially in NHW (p ≤ 6.3 × 10-7). Importantly, groupwise burden analysis showed several enhancer combinations significantly over-represented in NSCLP individuals, revealing novel NSCLP pathways and supporting a polygenic inheritance model. Our findings support the role of craniofacial enhancer sequence variation in the etiology of NSCLP.
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Affiliation(s)
- Vershanna E Morris
- Department of Pediatrics, UTHealth McGovern Medical School, Houston, TX, 77030, USA.,Pediatric Research Center, UTHealth McGovern Medical School, Houston, TX, 77030, USA
| | - S Shahrukh Hashmi
- Department of Pediatrics, UTHealth McGovern Medical School, Houston, TX, 77030, USA.,Pediatric Research Center, UTHealth McGovern Medical School, Houston, TX, 77030, USA
| | - Lisha Zhu
- UTHealth School of Biomedical Informatics, Houston, TX, 77054, USA
| | - Lorena Maili
- Department of Pediatrics, UTHealth McGovern Medical School, Houston, TX, 77030, USA.,Pediatric Research Center, UTHealth McGovern Medical School, Houston, TX, 77030, USA
| | - Christian Urbina
- Department of Pediatrics, UTHealth McGovern Medical School, Houston, TX, 77030, USA.,Pediatric Research Center, UTHealth McGovern Medical School, Houston, TX, 77030, USA
| | | | - Matthew R Greives
- Department of Pediatric Surgery, University of Texas Health Science Center McGovern Medical School, Houston, TX, 77030, USA
| | - Edward P Buchanan
- Department of Plastic Surgery, Texas Children's Hospital, Houston, TX, 77030, USA
| | - John B Mulliken
- Department of Plastic Surgery, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Susan H Blanton
- Dr. John T. Macdonald Foundation Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - W Jim Zheng
- UTHealth School of Biomedical Informatics, Houston, TX, 77054, USA
| | - Jacqueline T Hecht
- Department of Pediatrics, UTHealth McGovern Medical School, Houston, TX, 77030, USA.,Pediatric Research Center, UTHealth McGovern Medical School, Houston, TX, 77030, USA.,Shriners' Hospital for Children, Houston, TX, 77030, USA.,Center for Craniofacial Research, UTHealth School of Dentistry, Houston, TX, 77054, USA
| | - Ariadne Letra
- School of Dentistry, Department of Diagnostic and Biomedical Sciences, University of Texas Health Science Center At Houston, 1941 East Road, BBSB 4210, Houston, TX, 77054, USA. .,Center for Craniofacial Research, UTHealth School of Dentistry, Houston, TX, 77054, USA.
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17
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Rizell S, Bellardie H, Karsten A, Sæle P, Mooney J, Heliövaara A, Küseler A, Brinck E, Skaare P, Mølsted K, Chalien MN, Marcusson A, Eyres P, Shaw W, Semb G. Scandcleft randomized trials of primary surgery for unilateral cleft lip and palate: dental anomalies in 8-year olds. Eur J Orthod 2020; 42:8-14. [PMID: 31579919 DOI: 10.1093/ejo/cjz070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Children born with unilateral cleft lip and palate (UCLP) are reported to display several dental anomalies including agenesis, supernumeraries, as well as variations in dental size, shape, and path of eruption. The extensive sample of individuals with UCLP included in the Scandcleft randomized control trials offers the opportunity to study more rare conditions, which is seldom possible with limited samples. OBJECTIVES The aim was to study dental anomalies at 8 years of age in children born with UCLP included in the Scandcleft randomized control trials. METHODS Panoramic and intraoral radiographs from 425 individuals (279 males and 146 females) with a mean age of 8.1 years were assessed by four orthodontists regarding dental anomalies. RESULTS Agenesis was found in 52.5 per cent and supernumerary teeth in 16.9 per cent of the participants. The cleft lateral was missing in 43.8 per cent and was found peg shaped in 44.7 per cent. The distribution of ectopic eruption was 14.6 per cent, mainly affecting maxillary first molars, while transposition was found in 3.4 per cent of the individuals. In addition, infraocclusion of one or several primary molars was registered in 7.2 per cent of the participants. CONCLUSION We conclude that 8-year-old children born with UCLP display multiple dental anomalies. The Scandcleft sample allowed rarely studied conditions such as infraocclusion of primary molars and transposition to be studied in children born with UCLP. TRIAL REGISTRATION ISRCTN29932826.
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Affiliation(s)
- Sara Rizell
- Department of Orthodontics, Institute of Odontology, Sahlgrenska Academy, University of Gothenburg, Sweden
| | - Haydn Bellardie
- Greater Manchester Cleft Lip and Palate Unit, Royal Manchester Childrens' Hospital, UK.,Department of Orthodontics and Paediatric Dentistry, The University of the Western Cape, Cape Town, South Africa
| | - Agneta Karsten
- Stockholm Craniofacial Team, Section for Orthodontics, Division of Orthodontics and Pedodontics, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Paul Sæle
- Oral Health Center of Expertise, Western Norway, Bergen, Norway
| | - Jeanette Mooney
- Greater Manchester Cleft Lip and Palate Unit, Royal Manchester Childrens' Hospital, UK
| | - Arja Heliövaara
- Cleft Palate and Craniofacial Center, Department of Plastic Surgery, Helsinki University Hospital, Finland
| | - Annelise Küseler
- Cleft Palate Center and University Hospital Aarhus and University of Aarhus, Denmark
| | - Eli Brinck
- Department of Plastic and Reconstructive Surgery, Oslo University Hospital, Rikshospitalet, Norway
| | - Pål Skaare
- Department of Plastic and Reconstructive Surgery, Oslo University Hospital, Rikshospitalet, Norway
| | - Kirsten Mølsted
- Copenhagen Cleft Palate Center, University Hospital of Copenhagen, Denmark
| | - Midia Najar Chalien
- Department of Orthodontics, Institute of Odontology, Sahlgrenska Academy, University of Gothenburg, Sweden
| | - Agneta Marcusson
- Department of Dentofacial Orthopedics, Maxillofacial Unit, University Hospital, Linköping, Sweden
| | - Phil Eyres
- Greater Manchester Cleft Lip and Palate Unit, Royal Manchester Childrens' Hospital, UK
| | - W Shaw
- Greater Manchester Cleft Lip and Palate Unit, Royal Manchester Childrens' Hospital, UK
| | - Gunvor Semb
- Greater Manchester Cleft Lip and Palate Unit, Royal Manchester Childrens' Hospital, UK.,Department of Plastic and Reconstructive Surgery, Oslo University Hospital, Rikshospitalet, Norway
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18
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Maili L, Letra A, Silva R, Buchanan EP, Mulliken JB, Greives MR, Teichgraeber JF, Blackwell SJ, Ummer R, Weber R, Chiquet B, Blanton SH, Hecht JT. PBX-WNT-P63-IRF6 pathway in nonsyndromic cleft lip and palate. Birth Defects Res 2019; 112:234-244. [PMID: 31825181 DOI: 10.1002/bdr2.1630] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/18/2019] [Accepted: 11/21/2019] [Indexed: 01/01/2023]
Abstract
Nonsyndromic cleft lip and palate (NSCLP) is one of the most common craniofacial anomalies in humans, affecting more than 135,000 newborns worldwide. NSCLP has a multifactorial etiology with more than 50 genes postulated to play an etiologic role. The genetic pathway comprised of Pbx-Wnt-p63-Irf6 genes was shown to control facial morphogenesis in mice and proposed as a regulatory pathway for NSCLP. Based on these findings, we investigated whether variation in PBX1, PBX2, and TP63, and their proposed interactions were associated with NSCLP. Fourteen single nucleotide variants (SNVs) in/nearby PBX1, PBX2, and TP63 were genotyped in 780 NSCLP families of nonHispanic white (NHW) and Hispanic ethnicities. Family-based association tests were performed for individual SNVs stratified by ethnicity and family history of NSCLP. Gene-gene interactions were also tested. A significant association was found for PBX2 rs3131300 and NSCLP in combined Hispanic families (p = .003) while nominal association was found for TP63 rs9332461 in multiplex Hispanic families (p = .005). Significant haplotype associations were observed for PBX2 in NHW (p = .0002) and Hispanic families (p = .003), and for TP63 in multiplex Hispanic families (.003). An independent case-control group was used to validate findings, and significant associations were found with PBX1 rs6426870 (p = .007) and TP63 rs9332461 (p = .03). Gene-gene interactions were detected between PBX1/PBX2/TP63 with IRF6 in NHW families, and between PBX1 with WNT9B in both NHW and Hispanic families (p < .0018). This study provides the first evidence for a role of PBX1 and PBX2, additional evidence for the role of TP63, and support for the proposed PBX-WNT-TP63-IRF6 regulatory pathway in the etiology of NSCLP.
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Affiliation(s)
- Lorena Maili
- Department of Pediatrics, University of Texas Health Science Center McGovern Medical School at Houston, Houston, Texas
| | - Ariadne Letra
- Department of Diagnostic and Biomedical Sciences, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas.,Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas
| | - Renato Silva
- Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas.,Department of Endodontics, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas
| | - Edward P Buchanan
- Department of Plastic Surgery, Texas Children's Hospital, Houston, Texas
| | | | - Matthew R Greives
- Department of Pediatric Surgery, University of Texas Health Science Center McGovern Medical School at Houston, Houston, Texas
| | - John F Teichgraeber
- Department of Pediatric Surgery, University of Texas Health Science Center McGovern Medical School at Houston, Houston, Texas
| | | | - Rohit Ummer
- Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas
| | - Ryan Weber
- Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas
| | - Brett Chiquet
- Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas.,Department of Pediatric Dentistry, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas
| | - Susan H Blanton
- Dr. John T. MacDonald Foundation Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Jacqueline T Hecht
- Department of Pediatrics, University of Texas Health Science Center McGovern Medical School at Houston, Houston, Texas.,Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas
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Bezerra JF, Silva HPVD, Bortolin RH, Luchessi AD, Ururahy MAG, Loureiro MB, Gil-da-Silva-Lopes VL, Almeida MDG, Amaral VSD, Rezende AAD. IRF6 polymorphisms in Brazilian patients with non-syndromic cleft lip with or without palate. Braz J Otorhinolaryngol 2019; 86:696-702. [PMID: 31495697 PMCID: PMC9422540 DOI: 10.1016/j.bjorl.2019.04.011] [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: 07/29/2018] [Revised: 02/04/2019] [Accepted: 04/17/2019] [Indexed: 12/19/2022] Open
Abstract
INTRODUCTION Non-syndromic orofacial clefts have a complex etiology due to the contribution from both genetic and environmental risk factors, as well as the interaction between them. Among the more than 15 susceptibility loci for non-syndromic orofacial clefts with considerable statistical and biological support, the IRF6 is the most validated gene by the majority of studies. Nonetheless, in genetically heterogeneous populations such as Brazilian, the confirmation of association between non-syndromic orofacial clefts and IRF6 common variants is not a consolidated fact and unrecognized IRF6 variants are poorly investigated. OBJECTIVE The aim of this study was to investigate the association of IRF6 polymorphisms with non-syndromic orofacial clefts development in a population from northeast Brazil. METHODS Blood samples of 186 non-syndromic orofacial clefts patients and 182 controls from Rio Grande do Norte, Brazil, were obtained to analyze IRF6 polymorphisms (rs2235371, rs642961, rs2236907, rs861019, and rs1044516) by real-time polymerase chain reaction. Non-syndromic orofacial clefts patients were classified in cleft lip and palate, cleft palate only and cleft lip only groups. RESULTS The genotype and allele frequencies of single nucleotide polymorphism rs2235371 in IRF6 showed significant differences in patients with cleft palate when compared to the controls, whereas no association was shown between rs642961, rs2236907, rs861019, and rs1044516 and non-syndromic orofacial clefts. CONCLUSION The association found between rs2235371 and isolated cleft palate should be interpreted with caution due to the low number of individuals investigated, and more studies with larger sample size are needed to confirm these association. In addition, there is a lack of association of the rs642961, rs2236907 and rs861019 polymorphisms with non-syndromic orofacial clefts susceptibility.
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Affiliation(s)
- João Felipe Bezerra
- Universidade Federal do Rio Grande do Norte, Departamento de Análises Clínicas e Toxicológicas, Natal, RN, Brazil
| | | | - Raul Hernandes Bortolin
- Universidade Federal do Rio Grande do Norte, Departamento de Análises Clínicas e Toxicológicas, Natal, RN, Brazil; Universidade de São Paulo (USP), Departamento de Análises Clínicas e Toxicológicas, São Paulo, SP, Brazil
| | - André Ducati Luchessi
- Universidade Federal do Rio Grande do Norte, Departamento de Análises Clínicas e Toxicológicas, Natal, RN, Brazil
| | | | - Melina Bezerra Loureiro
- Universidade Federal do Rio Grande do Norte, Departamento de Análises Clínicas e Toxicológicas, Natal, RN, Brazil
| | - Vera Lúcia Gil-da-Silva-Lopes
- Universidade Estadual de Campinas, Escola de Ciências Médicas, Departamento de Genética Médica, Campinas, Campinas, SP, Brazil
| | - Maria das Graças Almeida
- Universidade Federal do Rio Grande do Norte, Departamento de Análises Clínicas e Toxicológicas, Natal, RN, Brazil
| | - Viviane Souza do Amaral
- Universidade Federal do Rio Grande do Norte, Departamento de Biologia Celular e Genética, Natal, RN, Brazil
| | - Adriana Augusto de Rezende
- Universidade Federal do Rio Grande do Norte, Departamento de Análises Clínicas e Toxicológicas, Natal, RN, Brazil.
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20
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Xing Y, Zhang W, Wan X, Hong Z, Zhao H, Liang W, Shi L, Chen J, Zhong X, Zhou J, Tang S. Association Between an Interferon Regulatory Factor 6 Gene Polymorphism and Nonsyndromic Cleft Palate Risk. Genet Test Mol Biomarkers 2019; 23:652-663. [PMID: 31448957 DOI: 10.1089/gtmb.2018.0315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Background: Involvement of interferon regulatory factor 6 (IRF6) gene polymorphisms in nonsyndromic cleft palate (NSCP) risk remains controversial. This investigation was performed to evaluate the relationship between IRF6 gene polymorphisms and NSCP risk. Materials and Methods: Two hundred forty-one patients with NSCP (including 103 complete trio families) were recruited, and 242 unaffected individuals were included as controls. Polymorphisms for the IRF6 rs2235371, rs801619, rs642961, rs44844880, and rs8049367 loci were characterized in both groups. Furthermore, eligible studies were identified from the databases through June 1, 2017, and were included in a meta-analysis to enhance the robustness of our conclusions. Results: The IRF6 rs2235371 A allele and AA genotype in the case group were found at higher frequencies than in the control group (A allele: p < 0.0016; AA genotype: p < 0.0049). The IRF6 rs801619 AA genotype and G allele were associated with NSCP risk (G allele: p < 0.0061; AA genotype: p < 0.0195). At the IRF6 rs642961, rs44844880, and rs8049367 loci genotype and allele frequencies were not statistically different between the NSCP group and normal controls. In the meta-analysis, the IRF6 A/G gene polymorphism (rs2235371) and IRF6 A/G gene polymorphism (rs642961) were associated with NSCP risk in the general population, whereas the IRF6 A/C gene polymorphism (rs2013162) was not. Conclusion: The IRF6 A/G gene polymorphisms at rs2235371 and rs642961, but not the IRF6 A/C gene polymorphism rs2013162, were associated with NSCP risk.
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Affiliation(s)
- Yue Xing
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, the Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, Guangdong, China
| | - Wancong Zhang
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, the Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Xinhong Wan
- Central Laboratory, Shenzhen Longgang District Maternity and Child Healthcare Hospital, Shenzhen, Guangdong, China
| | - Zhiqian Hong
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, the Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Hanxing Zhao
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, the Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, Guangdong, China
| | - Weijie Liang
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, the Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, Guangdong, China
| | - Lungang Shi
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, the Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, Guangdong, China
| | - Jiasheng Chen
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, the Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, Guangdong, China
| | - Xiaoping Zhong
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, the Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, Guangdong, China
| | - Jianda Zhou
- Department of Plastic and Reconstructive Surgery, Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shijie Tang
- Department of Burns and Plastic Surgery, Cleft Lip and Palate Treatment Center, the Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
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21
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Li W, Wang M, Zhou R, Wang S, Zheng H, Liu D, Zhou Z, Zhu H, Wu T, Beaty TH. Exploring the interaction between FGF Genes and T-box genes among chinese nonsyndromic cleft lip with or without cleft palate case-parent trios. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2019; 60:602-606. [PMID: 30848863 DOI: 10.1002/em.22286] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 02/17/2019] [Accepted: 03/05/2019] [Indexed: 06/09/2023]
Abstract
Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect. Genetic variants causing syndromic orofacial clefts can also contribute to the etiology of NSCL/P. The purpose of the present study was to explore gene-gene (G × G) interaction using common single nucleotide polymorphic (SNP) markers in fibroblast growth factor (FGF) family and its receptors and T-box genes, which were associated with syndromic orofacial clefts. Our study was conducted in 806 Chinese NSCL/P case-parent trios drawn from an international consortium. A total of 252 SNPs in FGF8, FGF10, FGFR1, FGFR2, and TBX5 passed the quality control criteria and were included in the analysis. The interactions between SNPs in different genes were assessed using Cordell's method, which fitted a conditional logistic regression model. The analysis was performed using the R-package trio (Version 3.8.0). Bonferroni correction was used to adjust for multiple comparisons, and the overall significance threshold was set as P = 1.98 × 10-4 (0.05/252). Conditional logistic regression revealed the most significant interaction between rs2330542 in FGF10 and rs1946295 in TBX5, which remained significant (P = 9.63 × 10-6 ) after Bonferroni correction. The relative risk of allele C in rs2330542 (FGF10) was 1.02 (95%CI 0.81-1.28), while the relative risk was 1.42 (95%CI 1.03-1.97) when the exposure was a combination of allele C in rs2330542 and allele A in rs1946295 (TBX5). Our findings confirmed the importance of considering G × G interaction when exploring the genetic risk factors of NSCL/P. Further investigations are warranted to validate the potential interaction and reveal the biological function of FGF10/FGFR2/TBX5. Environ. Mol. Mutagen. 2019. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Wenyong Li
- School of Public Health, Peking University, Beijing, China
| | - Mengying Wang
- School of Public Health, Peking University, Beijing, China
| | - Ren Zhou
- School of Public Health, Peking University, Beijing, China
| | - Siyue Wang
- School of Public Health, Peking University, Beijing, China
| | - Hongchen Zheng
- School of Public Health, Peking University, Beijing, China
| | - Dongjing Liu
- School of Public Health, Peking University, Beijing, China
| | - Zhibo Zhou
- School of Stomatology, Peking University, Beijing, China
| | - Hongping Zhu
- School of Stomatology, Peking University, Beijing, China
| | - Tao Wu
- School of Public Health, Peking University, Beijing, China
- Key Laboratory of Reproductive Health, Ministry of Health, Beijing, China
| | - Terri H Beaty
- School of Public Health, Johns Hopkins University, Baltimore, Maryland
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22
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Thompson J, Mendoza F, Tan E, Bertol JW, Gaggar AS, Jun G, Biguetti C, Fakhouri WD. A cleft lip and palate gene, Irf6, is involved in osteoblast differentiation of craniofacial bone. Dev Dyn 2019; 248:221-232. [PMID: 30684382 DOI: 10.1002/dvdy.13] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 01/14/2019] [Accepted: 01/15/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Interferon regulatory factor 6 (IRF6) plays a critical role in embryonic tissue development, including differentiation of epithelial cells. Besides orofacial clefting due to haploinsufficiency of IRF6, recent human genetic studies indicated that mutations in IRF6 are linked to small mandible and digit abnormalities. The function of IRF6 has been well studied in oral epithelium; however, its role in craniofacial skeletal formation remains unknown. In this study, we investigated the role of Irf6 in craniofacial bone development using comparative analyses between wild-type (WT) and Irf6-null littermate mice. RESULTS Immunostaining revealed the expression of IRF6 in hypertrophic chondrocytes, osteocytes, and bone matrix of craniofacial tissues. Histological analysis of Irf6-null mice showed a remarkable reduction in the number of lacunae, embedded osteocytes in matrices, and a reduction in mineralization during bone formation. These abnormalities may explain the decreased craniofacial bone density detected by micro-CT, loss of incisors, and mandibular bone abnormality of Irf6-null mice. To validate the autonomous role of IRF6 in bone, extracted primary osteoblasts from calvarial bone of WT and Irf6-null pups showed no effect on osteoblastic viability and proliferation. However, a reduction in mineralization was detected in Irf6-null cells. CONCLUSIONS Altogether, these findings suggest an autonomous role of Irf6 in regulating bone differentiation and mineralization. Developmental Dynamics 248:221-232, 2019. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Jake Thompson
- Center for Craniofacial Research, Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston, Texas
| | - Fabian Mendoza
- Center for Craniofacial Research, Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston, Texas
| | - Ethan Tan
- Center for Craniofacial Research, Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston, Texas
| | - Jessica Wildgrube Bertol
- Center for Craniofacial Research, Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston, Texas
| | - Arju S Gaggar
- School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas
| | - Goo Jun
- School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas
| | - Claudia Biguetti
- Department of Basic Sciences, São Paulo State University (Unesp), School of Dentistry, Araçatuba, São Paulo
| | - Walid D Fakhouri
- Center for Craniofacial Research, Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston, Texas.,Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center, Houston, Texas.,Graduate School of Biomedical Sciences, University of Texas Health Science Center and MD Anderson Cancer Center at Houston, Houston, Texas
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23
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Wang M, Liu D, Schwender H, Wang H, Wang P, Zhou Z, Li J, Wu T, Zhu H, Beaty TH. Evaluating the effect of nicotinic cholinergic receptor genes on the risk of nonsyndromic cleft lip with or without cleft palate. Oral Dis 2018; 24:1068-1072. [PMID: 29688589 DOI: 10.1111/odi.12879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/31/2018] [Accepted: 04/16/2018] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Multiple studies have suggested nonsyndromic cleft lip with or without cleft palate (NSCL/P), and lung cancer may have common genetic etiology. Previous studies have showed genetic variants in nicotinic cholinergic receptor genes (CHRNs) may influence risk of lung cancer. We aimed to explore the effect of CHRNs on risk of NSCL/P considering gene-gene (GxG) interaction for these genes. SUBJECTS AND METHODS We selected 120 markers in 14 CHRNs to test for GxG interaction using 806 Chinese case-parent trios recruited from an international consortium established for a GWAS of oral clefts. RESULTS Totally, two pairs of SNPs yielded significant GxG interactions after Bonferroni correction (rs935865 and rs2337980 with p = 4.04 × 10-5 , rs2741335 and rs3743077 with p = 4.80 × 10-4 ), and these pairwise interactions were confirmed in permutation tests. In addition, the relative risk (RR) of the putative interaction between rs935865 and rs2337980 was 1.10 (95% CI: 0.92~1.31). CONCLUSIONS While the single SNP association and the gene-environment interaction analysis of 14 CHRN genes yielded no signal, this study did demonstrate the importance of considering potential GxG interaction for exploring etiology of NSCL/P. This study suggests an important role for particular combinations of SNPs in CHRN genes in influencing risk to NSCL/P, which needs further study.
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Affiliation(s)
- Mengying Wang
- School of Public Health, Peking University, Beijing, China
| | - Dongjing Liu
- School of Public Health, Peking University, Beijing, China
| | - Holger Schwender
- Mathematical Institute, Heinrich Heine University Duesseldorf, Duesseldorf, Germany
| | - Hong Wang
- School of Public Health, Peking University, Beijing, China
| | - Ping Wang
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Zhibo Zhou
- School of Stomatology, Peking University, Beijing, China
| | - Jing Li
- School of Stomatology, Peking University, Beijing, China
| | - Tao Wu
- School of Public Health, Peking University, Beijing, China.,Key Laboratory of Reproductive Health, Ministry of Health, Beijing, China
| | - Hongping Zhu
- School of Stomatology, Peking University, Beijing, China
| | - Terri H Beaty
- School of Public Health, Johns Hopkins University, Baltimore, Maryland
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24
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Wang P, Wu T, Schwender H, Wang H, Shi B, Wang ZQ, Yuan Y, Liu DJ, Wang MY, Li J, Zhou ZB, Zhu HP, Beaty TH. Evidence of interaction between genes in the folate/homocysteine metabolic pathway in controlling risk of non-syndromic oral cleft. Oral Dis 2018; 24:820-828. [PMID: 29356306 DOI: 10.1111/odi.12831] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/20/2017] [Accepted: 01/09/2018] [Indexed: 01/09/2023]
Abstract
OBJECTIVE Little consistent evidence is available for the association between the risk of non-syndromic cleft lip with or without cleft palate (NSCL/P) and any of the individual genes in the folate/homocysteine metabolic pathway. We investigated the genes in the folate pathway to further clarify its potential influence on the risk of NSCL/P considering gene-gene (G×G) interaction. SUBJECTS AND METHODS We selected markers in 18 genes from the pathway and applied Cordell's method to test for G×G interaction using 1,908 NSCL/P case-parent trios ascertained in an international consortium where a genomewide association study (GWAS) of oral clefts was conducted. RESULTS We found intriguing signals among Asian and European ancestry groups for G×G interaction between markers in betaine-homocysteine methyltransferase gene (BHMT/BHMT2) and dimethylglycine dehydrogenase gene (DMGDH) attaining genomewide significance. In the pooled data, the top significant interaction was found between rs13158309 (BHMT) and rs10514154 (DMGDH, p = 1.45 × 10-12 ). CONCLUSIONS Our study illustrated the importance of taking into account potential G×G interaction for genetic association analysis in NSCL/P, and this study suggested both BHMT/BHMT2 and DMGDH should be considered as candidate genes for NSCL/P in future studies.
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Affiliation(s)
- P Wang
- School of Public Health, Peking University, Beijing, China.,Department of Statistics and Information, Beijing Center for Disease Prevention and Control & Beijing Research Center for Preventive Medicine, Beijing, China
| | - T Wu
- School of Public Health, Peking University, Beijing, China.,Key Laboratory of Reproductive Health, Ministry of Health, Beijing, China
| | - H Schwender
- Mathematical Institute, Heinrich Heine University Duesseldorf, Duesseldorf, Germany
| | - H Wang
- School of Public Health, Peking University, Beijing, China
| | - B Shi
- State Key Laboratory of Oral Disease, West China School of Stomatology, Sichuan University, Chengdu, China
| | - Z Q Wang
- School of Public Health, Peking University, Beijing, China
| | - Y Yuan
- School of Public Health, Peking University, Beijing, China
| | - D J Liu
- School of Public Health, Peking University, Beijing, China
| | - M Y Wang
- School of Public Health, Peking University, Beijing, China
| | - J Li
- Pediatric Dentistry, Peking University School of Stomatology, Beijing, China
| | - Z B Zhou
- Oral and Maxillofacial Surgery, Peking University School of Stomatology, Beijing, China
| | - H P Zhu
- Oral and Maxillofacial Surgery, Peking University School of Stomatology, Beijing, China
| | - T H Beaty
- School of Public Health, Johns Hopkins University, Baltimore, MD, USA
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25
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26
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Assis Machado R, de Toledo IP, Martelli-Júnior H, Reis SR, Neves Silva Guerra E, Coletta RD. Potential genetic markers for nonsyndromic oral clefts in the Brazilian population: A systematic review and meta-analysis. Birth Defects Res 2018; 110:827-839. [DOI: 10.1002/bdr2.1208] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/10/2018] [Accepted: 01/22/2018] [Indexed: 12/29/2022]
Affiliation(s)
- Renato Assis Machado
- Department of Oral Diagnosis, School of Dentistry; University of Campinas; Piracicaba SP Brazil
| | - Isabela Porto de Toledo
- Laboratory of Oral Histopathology, Health Sciences Faculty; University of Brasília; Brasília DF Brazil
| | | | | | - Eliete Neves Silva Guerra
- Laboratory of Oral Histopathology, Health Sciences Faculty; University of Brasília; Brasília DF Brazil
| | - Ricardo D. Coletta
- Department of Oral Diagnosis, School of Dentistry; University of Campinas; Piracicaba SP Brazil
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27
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Liu D, Schwender H, Wang M, Wang H, Wang P, Zhu H, Zhou Z, Li J, Wu T, Beaty TH. Gene-gene interaction between MSX1 and TP63 in Asian case-parent trios with nonsyndromic cleft lip with or without cleft palate. Birth Defects Res 2018; 110:317-324. [PMID: 29341488 DOI: 10.1002/bdr2.1139] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 08/27/2017] [Accepted: 09/06/2017] [Indexed: 01/10/2023]
Abstract
BACKGROUND Small ubiquitin-like modification, also known as sumoylation, is a crucial post-translational regulatory mechanisms involved in development of the lip and palate. Recent studies reported two sumoylation target genes, MSX1 and TP63, to have achieved genome-wide level significance in tests of association with nonsyndromic clefts. Here, we performed a candidate gene analysis considering gene-gene and gene-environment interaction for SUMO1, MSX1, and TP63 to further explore the etiology of nonsyndromic cleft lip with or without cleft palate (NSCL/P). METHODS A total of 130 single-nucleotide polymorphisms (SNPs) in or near SUMO1, MSX1, and TP63 was analyzed among 1,038 Asian NSCL/P trios ascertained through an international consortium. Conditional logistic regression models were used to explore gene-gene (G × G) and gene-environment (G × E) interaction involving maternal environmental tobacco smoke and multivitamin supplementation. Bonferroni correction was used for G × E analysis and permutation tests were used for G × G analysis. RESULTS While transmission disequilibrium tests and gene-environment interaction analysis showed no significant results, we did find signals of gene-gene interaction between SNPs near MSX1 and TP63. Three pairwise interactions yielded significant p values in permutation tests (rs884690 and rs9290890 with p = 9.34 × 10-5 and empirical p = 1.00 × 10-4 , rs1022136 and rs4687098 with p = 2.41 × 10-4 and empirical p = 2.95 × 10-4 , rs6819546 and rs9681004 with p = 5.15 × 10-4 and empirical p = 3.02 × 10-4 ). CONCLUSION Gene-gene interaction between MSX1 and TP63 may influence the risk of NSCL/P in Asian populations. Our study provided additional understanding of the genetic etiology of NSCL/P and underlined the importance of considering gene-gene interaction in the etiology of this common craniofacial malformation.
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Affiliation(s)
- Dongjing Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Holger Schwender
- Mathematical Institute, Heinrich Heine University Duesseldorf, Duesseldorf, Germany
| | - Mengying Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Hong Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Ping Wang
- Department of Statistics and Information, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Hongping Zhu
- School of Stomatology, Peking University, Beijing, China
| | - Zhibo Zhou
- School of Stomatology, Peking University, Beijing, China
| | - Jing Li
- School of Stomatology, Peking University, Beijing, China
| | - Tao Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China.,Key Laboratory of Reproductive Health, Ministry of Health, Beijing, China
| | - Terri H Beaty
- Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, Maryland
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Metwalli KA, Do MA, Nguyen K, Mallick S, Kin K, Farokhnia N, Jun G, Fakhouri WD. Interferon Regulatory Factor 6 Is Necessary for Salivary Glands and Pancreas Development. J Dent Res 2017; 97:226-236. [PMID: 28898113 DOI: 10.1177/0022034517729803] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Interferon regulatory factor 6 ( IRF6) acts as a tumor suppressor and controls cell differentiation in ectodermal and craniofacial tissues by regulating expression of target genes. Haploinsufficiency of IRF6 causes Van der Woude and popliteal pterygium syndrome, 2 syndromic forms of cleft lip and palate. Around 85% of patients with Van der Woude express pits on the lower lip that continuously or intermittently drain saliva, and patients with the common cleft lip and palate have a higher prevalence of dental caries and gingivitis. This study aims to identify the role of IRF6 in development of exocrine glands, specifically the major salivary glands. Our transgenic mouse model that expresses LacZ reporter under the control of the human IRF6 enhancer element showed high expression of IRF6 in major and minor salivary glands and ducts. Immunostaining data also confirmed the endogenous expression of IRF6 in the developing ductal, serous, and mucous acinar cells of salivary glands. As such, we hypothesized that Irf6 is important for proper development of salivary glands and potentially other exocrine glands. Loss of Irf6 in mice causes an increase in the proliferation level of salivary cells, disorganized branching morphogenesis, and a lack of differentiated mucous acinar cells in submandibular and sublingual glands. Expression and localization of the acinar differentiation marker MIST1 were altered in Irf6-null salivary gland and pancreas. The RNA-Seq analysis demonstrated that 168 genes are differentially expressed and confer functions associated with transmembrane transporter activity, spliceosome, and transcriptional regulation. Furthermore, expression of genes involved in the EGF pathway-that is, Ereg, Ltbp4, Matn1, Matn3, and Tpo-was decreased at embryonic day 14.5, while levels of apoptotic proteins were elevated at postnatal day 0. In conclusion, our data report a novel role of Irf6 in exocrine gland development and support a rationale for performing exocrine functional tests for patients with IRF6-damaging mutations.
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Affiliation(s)
- K A Metwalli
- 1 Center for Craniofacial Research, Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - M A Do
- 1 Center for Craniofacial Research, Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - K Nguyen
- 1 Center for Craniofacial Research, Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - S Mallick
- 1 Center for Craniofacial Research, Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - K Kin
- 1 Center for Craniofacial Research, Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - N Farokhnia
- 1 Center for Craniofacial Research, Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - G Jun
- 2 Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - W D Fakhouri
- 1 Center for Craniofacial Research, Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, USA.,3 Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA
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29
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Liu D, Wang H, Schwender H, Marazita ML, Wang Z, Yuan Y, Wang P, Liang KY, Wu-Chou YH, Wang M, Shi B, Zhu H, Wu T, Beaty TH. Gene-gene interaction of single nucleotide polymorphisms in 16p13.3 may contribute to the risk of non-syndromic cleft lip with or without cleft palate in Chinese case-parent trios. Am J Med Genet A 2017; 173:1489-1494. [PMID: 28402597 DOI: 10.1002/ajmg.a.38190] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 12/13/2016] [Accepted: 02/01/2017] [Indexed: 11/07/2022]
Abstract
Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect with a complex and heterogeneous etiology. A recent genome-wide association study (GWAS) among Chinese populations has identified a new region at 16p13.3 as being associated with NSCL/P, which requires further replication. Here, we attempted to replicate and further clarify the genetic association between this region and NSCL/P, as well as testing for potential gene-gene (G × G) and gene-environment (G × E) interactions. We conducted transmission disequilibrium tests on 69 single nucleotide polymorphisms (SNPs) mapping to 16p13.3 among 806 Chinese case-parent trios ascertained through an international consortium where a GWAS of oral clefts was conducted. G × G, as well as G × E interactions involving maternal environmental tobacco smoke (ETS) and multivitamin supplementation, were explored using conditional logistic regression model. We applied Cordell's method as implemented in the R package TRIO to test for possible interactions. While no SNPs showed evidence of linkage and association with NSCL/P after Bonferroni correction, we found signals of G × G interactions between SNPs in 16p13.3. Nine pairs of SNP-SNP interactions attained significance after Bonferroni correction, among which the most significant interaction was found between rs2072346 (ADCY9) and rs11646137 (intergenic region, P = 7.2 × 10-5 ). Linkage disequilibrium (LD) analysis revealed only low level of LD between these SNPs. This study failed to confirm the significant association between SNPs within 16p13.3 and the risk of NSCL/P, but underlined the importance of taking into account potential G × G interactions for the genetic association analysis of NSCL/P.
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Affiliation(s)
- Dongjing Liu
- School of Public Health, Peking University, Beijing, China
| | - Hong Wang
- School of Public Health, Peking University, Beijing, China
| | - Holger Schwender
- Mathematical Institute, Heinrich Heine University Duesseldorf, Duesseldorf, Germany
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Zhuqing Wang
- School of Public Health, Peking University, Beijing, China
| | - Yuan Yuan
- School of Public Health, Peking University, Beijing, China
| | - Ping Wang
- Beijing Center for Disease Prevention and Control, Beijing, China
| | | | | | - Mengying Wang
- School of Public Health, Peking University, Beijing, China
| | - Bing Shi
- State Key Laboratory of Oral Disease, West China College of Stomatology, Sichuan University, Chengdu, China
| | - Hongping Zhu
- School of Stomatology, Peking University, Beijing, China
| | - Tao Wu
- School of Public Health, Peking University, Beijing, China.,Key Laboratory of Reproductive Health, Ministry of Health, Beijing, China
| | - Terri H Beaty
- School of Public Health, Johns Hopkins University, Baltimore, Maryland
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Tooth agenesis and orofacial clefting: genetic brothers in arms? Hum Genet 2016; 135:1299-1327. [PMID: 27699475 PMCID: PMC5065589 DOI: 10.1007/s00439-016-1733-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 09/21/2016] [Indexed: 12/16/2022]
Abstract
Tooth agenesis and orofacial clefts represent the most common developmental anomalies and their co-occurrence is often reported in patients as well in animal models. The aim of the present systematic review is to thoroughly investigate the current literature (PubMed, EMBASE) to identify the genes and genomic loci contributing to syndromic or non-syndromic co-occurrence of tooth agenesis and orofacial clefts, to gain insight into the molecular mechanisms underlying their dual involvement in the development of teeth and facial primordia. Altogether, 84 articles including phenotype and genotype description provided 9 genomic loci and 26 gene candidates underlying the co-occurrence of the two congenital defects: MSX1, PAX9, IRF6, TP63, KMT2D, KDM6A, SATB2, TBX22, TGFα, TGFβ3, TGFβR1, TGFβR2, FGF8, FGFR1, KISS1R, WNT3, WNT5A, CDH1, CHD7, AXIN2, TWIST1, BCOR, OFD1, PTCH1, PITX2, and PVRL1. The molecular pathways, cellular functions, tissue-specific expression and disease association were investigated using publicly accessible databases (EntrezGene, UniProt, OMIM). The Gene Ontology terms of the biological processes mediated by the candidate genes were used to cluster them using the GOTermMapper (Lewis-Sigler Institute, Princeton University), speculating on six super-clusters: (a) anatomical development, (b) cell division, growth and motility, (c) cell metabolism and catabolism, (d) cell transport, (e) cell structure organization and (f) organ/system-specific processes. This review aims to increase the knowledge on the mechanisms underlying the co-occurrence of tooth agenesis and orofacial clefts, to pave the way for improving targeted (prenatal) molecular diagnosis and finally to reflect on therapeutic or ultimately preventive strategies for these disabling conditions in the future.
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31
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Wattanawong K, Rattanasiri S, McEvoy M, Attia J, Thakkinstian A. Association between IRF6 and 8q24 polymorphisms and nonsyndromic cleft lip with or without cleft palate: Systematic review and meta-analysis. ACTA ACUST UNITED AC 2016; 106:773-88. [PMID: 27511269 PMCID: PMC5095821 DOI: 10.1002/bdra.23540] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 05/07/2016] [Accepted: 05/24/2016] [Indexed: 12/12/2022]
Abstract
BACKGROUND We conducted a systematic review and meta-analysis of interferon regulatory factor 6 and 8q24 polymorphisms with nonsyndromic cleft lip with/without cleft palate (NSCL/P). METHODS Data extraction was independently performed by two reviewers. Genotypic effects of four polymorphisms from 31 studies were pooled separately by ethnicity using a mixed-effect logit model with accounting for heterogeneity. RESULTS For rs2235371, AA and GA carried, respectively, 51% (95% confidence interval [CI], 37%-61%) and 42% (95% CI, 32%-50%) lower risks of NSCL/P than GG genotypes in Asians, but these genotypes were not significant in Caucasians. For rs2013162, only AA was significant, that is, carried 0.65 (95% CI, 0.52-0.82) times lower odds than CC in Caucasians but not for Asians. For rs642961, AA and GA genotypes, respectively, carried 2.47 (95% CI, 1.41-4.35) and 1.40 (95% CI, 1.12-1.75) times higher odds in Asian, and 2.03 (95% CI, 1.52-2.71) and 1.58 (95% CI, 1.37-1.82) times higher odds in Caucasians compare with GG genotypes. For rs987525, AA and CA genotypes carried 2.27 (95% CI, 1.43-3.60) and 1.34 (95% CI, 1.02-1.77) times higher odds in Asian, and 5.25 (95% CI, 3.98-6.91) and 2.13 (95% CI-1.82, 2.49) times higher odds in Caucasians, and 1.42 (95% CI, 1.10-1.82) and 1.28 (95% CI, 1.09-1.50) times higher odds in mixed ethnicities compared with CC genotypes. These variant effects remained significant based on applying Bonferroni corrected-thresholds, except in the mixed ethnicity. CONCLUSION We show robust variant effects in NSCL/P. Considering them with other genes and risk factors might be useful to improve prediction of NSCL/P occurrence. Birth Defects Research (Part A) 106:773-788, 2016. © 2016 The Authors Birth Defects Research Part A: Clinical and Molecular Teratology Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Kachin Wattanawong
- Section for Clinical Epidemiology and Biostatistics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.,Department of Surgery, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Sasivimol Rattanasiri
- Section for Clinical Epidemiology and Biostatistics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
| | - Mark McEvoy
- Centre for Clincial Epidemiology and Biostatistics, School of Medicine and Public Health, Faculty of Health and Medicine, University of Newcastle, and Hunter Medical Research Institute, NSW, Australia
| | - John Attia
- Centre for Clincial Epidemiology and Biostatistics, School of Medicine and Public Health, Faculty of Health and Medicine, University of Newcastle, and Hunter Medical Research Institute, NSW, Australia
| | - Ammarin Thakkinstian
- Section for Clinical Epidemiology and Biostatistics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
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Messetti AC, Machado RA, de Oliveira CE, Martelli-Júnior H, de Almeida Reis SR, Moreira HSB, Persuhn DC, Wu T, Coletta RD. Brazilian multicenter study of association between polymorphisms in CRISPLD2 and JARID2 and non-syndromic oral clefts. J Oral Pathol Med 2016; 46:232-239. [PMID: 27328068 DOI: 10.1111/jop.12470] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND Variants in the cysteine-rich secretory protein LCCL domain containing 2 gene (CRISPLD2) and in the jumonji, AT-rich interaction domain 2 gene (JARID2) were previously shown to influence non-syndromic oral cleft susceptibility. Herein, we performed a case-control study to examine the potential association of single-nucleotide polymorphisms (SNPs) in CRISPLD2 and JARID2 with non-syndromic cleft lip and/or palate (NSCL/P) in the Brazilian population. Given the ethnicity-dependent genetic predisposition to NSCL/P, we performed a structured analysis taking into account the genomic ancestry variation of each individual. METHODS Four SNPs in CRISPLD2 (rs1546124, rs8061351, rs2326398, and rs4783099) and four in JARID2 (rs915344, rs2299043, rs2237138, and rs2076056), that were previously reported to be associated with NSCL/P, were genotyped in 785 Brazilian patients with NSCL/P (549 with cleft lip with or without cleft palate-NSCL ± P, and 236 with cleft palate only-NSCPO) and 693 unaffected Brazilian controls. Genomic ancestry was assessed with a set of 40 biallelic short insertion/deletion variants previously validated as ancestry informative markers of the Brazilian population. RESULTS After adjustment of ancestry variations, allelic analysis revealed marginal associations between the CRISPLD2 rs4783099 T allele and increased risk for NSCPO (OR: 1.31, 95% CI: 1.05-1.62, P = 0.01) and between JARID2 rs2237138 and decreased NSCL ± P risk (OR: 0.80, 95% CI: 0.67-0.97, P = 0.02). Haplotype analysis indicated a lack of association between JARID2 haplotypes and non-syndromic oral cleft risk. CONCLUSIONS Our results suggest that CRISPLD2 rs4783099 may represent a risk factor for NSCPO while JARID2 rs2237138 shows a protective effect against NSCL ± P in the Brazilian population.
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Affiliation(s)
- Ana Camila Messetti
- Department of Oral Diagnosis, School of Dentistry, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Renato Assis Machado
- Department of Oral Diagnosis, School of Dentistry, University of Campinas, Piracicaba, São Paulo, Brazil
| | | | - Hercílio Martelli-Júnior
- Stomatology Clinic, Dental School, State University of Montes Claros, Montes Claros, Minas Gerais, Brazil.,Center for Rehabilitation of Craniofacial Anomalies, Dental School, University of José Rosario Vellano, Alfenas, Minas Gerais, Brazil
| | | | | | - Darlene Camati Persuhn
- Department of Molecular Biology, Federal University of Paraíba, João Pessoa, Paraíba, Brazil
| | - Tao Wu
- Peking University School of Public Health, Beijing, China
| | - Ricardo D Coletta
- Department of Oral Diagnosis, School of Dentistry, University of Campinas, Piracicaba, São Paulo, Brazil
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33
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Velázquez-Aragón JA, Alcántara-Ortigoza MA, Estandia-Ortega B, Reyna-Fabián ME, Méndez-Adame CD, González-Del Angel A. Gene Interactions Provide Evidence for Signaling Pathways Involved in Cleft Lip/Palate in Humans. J Dent Res 2016; 95:1257-64. [PMID: 27154735 DOI: 10.1177/0022034516647034] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a common craniofacial birth defect that has a complex etiology. Genome-wide association studies have recently identified new loci associated with NSCL/P, but these loci have not been analyzed in a Mexican Mestizo population. A complex etiology implies the presence of genetic interactions, but there is little available information regarding this in NSCL/P, and no signaling pathway has been clearly implicated in humans. Here, we analyzed the associations of 24 single nucleotide polymorphisms (SNPs) with NSCL/P in a Mexican Mestizo population (133 cases, 263 controls). The multifactorial dimensionality reduction method was used to examine gene-gene and gene-folic acid consumption interactions for the 24 SNPs analyzed in this study and for 2 additional SNPs that had previously been genotyped in the same study population. Six SNPs located in paired box 7, ventral anterior homeobox 1, sprouty RTK signaling antagonist 2, bone morphogenetic protein 4, and tropomyosin 1 genes were associated with higher risks of NSCL/P (P = 0.0001 to 0.04); 2 SNPs, 1 each in netrin 1 and V-maf avian musculoaponeurotic fibrosarcoma oncogene homolog B, were associated with a lower risk of NSCL/P (P = 0.013 to 0.03); and 2 SNPs, 1 each in ATP binding cassette subfamily A member 4 (ABCA4) and noggin, showed associations with NSCL/P that approached the threshold of significance (P = 0.056 to 0.07). In addition, 6 gene-gene interactions (P = 0.0001 to 0.001) and an ABCA4-folic acid consumption interaction (P < 0.0001) were identified. On the basis of these results, combined with those of previous association studies in the literature and biological characterizations of murine models, we propose an interaction network in which interferon regulatory factor 6 plays a central role in the etiology of NSCL/P.
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Affiliation(s)
- J A Velázquez-Aragón
- Laboratorio de Biología Molecular, Departamento de Genética Humana, Instituto Nacional de Pediatría, Secretaría de Salud, Coyoacán, Distrito Federal, México
| | - M A Alcántara-Ortigoza
- Laboratorio de Biología Molecular, Departamento de Genética Humana, Instituto Nacional de Pediatría, Secretaría de Salud, Coyoacán, Distrito Federal, México
| | - B Estandia-Ortega
- Laboratorio de Biología Molecular, Departamento de Genética Humana, Instituto Nacional de Pediatría, Secretaría de Salud, Coyoacán, Distrito Federal, México
| | - M E Reyna-Fabián
- Laboratorio de Biología Molecular, Departamento de Genética Humana, Instituto Nacional de Pediatría, Secretaría de Salud, Coyoacán, Distrito Federal, México
| | - C D Méndez-Adame
- Instituto Nacional de Pediatría, Secretaría de Salud, Coyoacán, Distrito Federal, México
| | - A González-Del Angel
- Laboratorio de Biología Molecular, Departamento de Genética Humana, Instituto Nacional de Pediatría, Secretaría de Salud, Coyoacán, Distrito Federal, México
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34
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Howe BJ, Cooper ME, Vieira AR, Weinberg SM, Resick JM, Nidey NL, Wehby GL, Marazita ML, Moreno Uribe LM. Spectrum of Dental Phenotypes in Nonsyndromic Orofacial Clefting. J Dent Res 2015; 94:905-12. [PMID: 26082386 DOI: 10.1177/0022034515588281] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Children with oral clefts show a wide range of dental anomalies, adding complexity to understanding the phenotypic spectrum of orofacial clefting. The evidence is mixed, however, on whether the prevalence of dental anomalies is elevated in unaffected relatives and is mostly based on small samples. In the largest international cohort to date of children with nonsyndromic clefts, their relatives, and controls, this study characterizes the spectrum of cleft-related dental anomalies and evaluates whether families with clefting have a significantly higher risk for such anomalies compared with the general population. A total of 3,811 individuals were included: 660 cases with clefts, 1,922 unaffected relatives, and 1,229 controls. Dental anomalies were identified from in-person dental exams or intraoral photographs, and case-control differences were tested using χ(2) statistics. Cases had higher rates of dental anomalies in the maxillary arch than did controls for primary (21% vs. 4%, P = 3 × 10(-8)) and permanent dentitions (51% vs. 8%, P = 4 × 10(-62)) but not in the mandible. Dental anomalies were more prevalent in cleft lip with cleft palate than other cleft types. More anomalies were seen in the ipsilateral side of the cleft. Agenesis and tooth displacements were the most common dental anomalies found in case probands for primary and permanent dentitions. Compared with controls, unaffected siblings (10% vs. 2%, P = 0.003) and parents (13% vs. 7%, P = 0.001) showed a trend for increased anomalies of the maxillary permanent dentition. Yet, these differences were nonsignificant after multiple-testing correction, suggesting genetic heterogeneity in some families carrying susceptibility to both overt clefts and dental anomalies. Collectively, the findings suggest that most affected families do not have higher genetic risk for dental anomalies than the general population and that the higher prevalence of anomalies in cases is primarily a physical consequence of the cleft and surgical interventions.
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Affiliation(s)
- B J Howe
- Department of Family Dentistry, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - M E Cooper
- Center for Craniofacial and Dental Genetics School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - A R Vieira
- Center for Craniofacial and Dental Genetics School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - S M Weinberg
- Center for Craniofacial and Dental Genetics School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - J M Resick
- Center for Craniofacial and Dental Genetics School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - N L Nidey
- Department of Pediatrics, College of Medicine, University of Iowa, Iowa City, IA, USA
| | - G L Wehby
- Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, IA, USA
| | - M L Marazita
- Center for Craniofacial and Dental Genetics School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - L M Moreno Uribe
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA, USA Dows Institute for Dental Research, College of Dentistry, University of Iowa, Iowa City, IA, USA
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35
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Figueiredo JC, Ly S, Magee KS, Ihenacho U, Baurley JW, Sanchez-Lara PA, Brindopke F, Nguyen THD, Nguyen V, Tangco MI, Giron M, Abrahams T, Jang G, Vu A, Zolfaghari E, Yao CA, Foong A, DeClerk YA, Samet JM, Magee W. Parental risk factors for oral clefts among Central Africans, Southeast Asians, and Central Americans. ACTA ACUST UNITED AC 2015; 103:863-79. [PMID: 26466527 PMCID: PMC5049483 DOI: 10.1002/bdra.23417] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Revised: 07/11/2015] [Accepted: 07/15/2015] [Indexed: 12/20/2022]
Abstract
Background Several lifestyle and environmental exposures have been suspected as risk factors for oral clefts, although few have been convincingly demonstrated. Studies across global diverse populations could offer additional insight given varying types and levels of exposures. Methods We performed an international case–control study in the Democratic Republic of the Congo (133 cases, 301 controls), Vietnam (75 cases, 158 controls), the Philippines (102 cases, 152 controls), and Honduras (120 cases, 143 controls). Mothers were recruited from hospitals and their exposures were collected from interviewer‐administered questionnaires. We used logistic regression modeling to estimate odds ratios (OR) and 95% confidence intervals (CI). Results Family history of clefts was strongly associated with increased risk (maternal: OR = 4.7; 95% CI, 3.0–7.2; paternal: OR = 10.5; 95% CI, 5.9–18.8; siblings: OR = 5.3; 95% CI, 1.4–19.9). Advanced maternal age (5 year OR = 1.2; 95% CI, 1.0–1.3), pregestational hypertension (OR = 2.6; 95% CI, 1.3–5.1), and gestational seizures (OR = 2.9; 95% CI, 1.1–7.4) were statistically significant risk factors. Lower maternal (secondary school OR = 1.6; 95% CI, 1.2–2.2; primary school OR = 2.4, 95% CI, 1.6–2.8) and paternal education (OR = 1.9; 95% CI, 1.4–2.5; and OR = 1.8; 95% CI, 1.1–2.9, respectively) and paternal tobacco smoking (OR = 1.5, 95% CI, 1.1–1.9) were associated with an increased risk. No other significant associations between maternal and paternal factors were found; some environmental factors including rural residency, indoor cooking with wood, chemicals and water source appeared to be associated with an increased risk in adjusted models. Conclusion Our study represents one of the first international studies investigating risk factors for clefts among multiethnic underserved populations. Our findings suggest a multifactorial etiology including both maternal and paternal factors. Birth Defects Research (Part A) 103:863–879, 2015. © 2015 The Authors Birth Defects Research Part A: Clinical and Molecular Teratology Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Jane C Figueiredo
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Stephanie Ly
- Division of Plastic & Maxillofacial Surgery, Children's Hospital Los Angeles, Los Angeles, California.,Department of Community Health Sciences and California Center for Population Research, UCLA Fielding School of Public Health, Los Angeles, California
| | | | - Ugonna Ihenacho
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - James W Baurley
- BioRealm LLC, Los Angeles, California.,Bioinformatics and Data Science Research Center, Bina Nusantara University, Jakarta, Indonesia
| | - Pedro A Sanchez-Lara
- Departments of Pediatrics and Pathology & Laboratory Medicine, Keck School of Medicine, University of Southern California, Children's Hospital Los Angeles, Los Angeles, California
| | - Frederick Brindopke
- Division of Plastic & Maxillofacial Surgery, Children's Hospital Los Angeles, Los Angeles, California
| | | | | | - Maria Irene Tangco
- Operation Smile Philippines, Manila, Philippines.,Department of Surgery, Faculty of Medicine and Surgery, University of Santo Tomas, Manila, Philippines
| | | | | | - Grace Jang
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Annie Vu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Emily Zolfaghari
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Caroline A Yao
- Division of Plastic & Maxillofacial Surgery, Children's Hospital Los Angeles, Los Angeles, California
| | - Athena Foong
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Yves A DeClerk
- Departments of Pediatrics and Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California and Children's Hospital Los Angeles, Los Angeles, California
| | - Jonathan M Samet
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - William Magee
- Division of Plastic & Maxillofacial Surgery, Children's Hospital Los Angeles, Los Angeles, California
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Cuddapah SR, Kominek S, Grant JH, Robin NH. IRF6 Sequencing in Interrupted Clefting. Cleft Palate Craniofac J 2015; 53:373-6. [PMID: 26090788 DOI: 10.1597/14-204] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In a retrospective review of patients seen at the University of Alabama at Birmingham Cleft and Craniofacial Center, four patients with rare interrupted clefting were identified who had undergone genetic testing. Each of these patients had a typical cleft lip, with intact hard palate and cleft of the soft palate. Given this picture of mixed clefting, IRF6 sequencing was done and was negative for mutations in all four patients. As genetic testing for single-gene mutations and exome sequencing become clinically available, it may be possible to identify novel mutations responsible for this previously unreported type of interrupted clefting.
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Beyeler J, Schnyder I, Katsaros C, Chiquet M. Accelerated wound closure in vitro by fibroblasts from a subgroup of cleft lip/palate patients: role of transforming growth factor-α. PLoS One 2014; 9:e111752. [PMID: 25360592 PMCID: PMC4216129 DOI: 10.1371/journal.pone.0111752] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 10/02/2014] [Indexed: 01/11/2023] Open
Abstract
In a fraction of patients surgically treated for cleft lip/palate, excessive scarring disturbs maxillary growth and dento-alveolar development. Since certain genes are involved in craniofacial morphogenesis as well as tissue repair, a primary defect causing cleft lip/palate could lead to altered wound healing. We performed in vitro wound healing assays with primary lip fibroblasts from 16 cleft lip/palate patients. Nine foreskin fibroblast strains were included for comparison. Cells were grown to confluency and scratch wounds were applied; wound closure was monitored morphometrically over time. Wound closure rate showed highly significant differences between fibroblast strains. Statistically, fibroblast strains from the 25 individuals could be divided into three migratory groups, namely “fast”, “intermediate”, and “slow”. Most cleft lip/palate fibroblasts were distributed between the “fast” (5 strains) and the “intermediate” group (10 strains). These phenotypes were stable over different cell passages from the same individual. Expression of genes involved in cleft lip/palate and wound repair was determined by quantitative PCR. Transforming growth factor-α mRNA was significantly up-regulated in the “fast” group. 5 ng/ml transforming growth factor-α added to the culture medium increased the wound closure rate of cleft lip/palate strains from the “intermediate” migratory group to the level of the “fast”, but had no effect on the latter group. Conversely, antibody to transforming growth factor-α or a specific inhibitor of its receptor most effectively reduced the wound closure rate of “fast” cleft lip/palate strains. Thus, fibroblasts from a distinct subgroup of cleft lip/palate patients exhibit an increased migration rate into wounds in vitro, which is linked to higher transforming growth factor-α expression and attenuated by interfering with its signaling.
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Affiliation(s)
- Joël Beyeler
- Department of Orthodontics and Dentofacial Orthopedics, School of Dental Medicine, University of Bern, Bern, Switzerland
| | - Isabelle Schnyder
- University Clinic for Childrens' Surgery, Bern University Hospital, Bern, Switzerland
| | - Christos Katsaros
- Department of Orthodontics and Dentofacial Orthopedics, School of Dental Medicine, University of Bern, Bern, Switzerland
| | - Matthias Chiquet
- Department of Orthodontics and Dentofacial Orthopedics, School of Dental Medicine, University of Bern, Bern, Switzerland
- * E-mail:
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Desai AL, Dinesh MR, Amarnath BC, Dharma RM, Akshai KR, Prashanth CS. Association of Transforming Growth Factor Alpha and Methylenetetrahydrofolate reductase gene variants with nonsyndromic cleft lip and palate in the Indian population. Contemp Clin Dent 2014; 5:329-33. [PMID: 25191068 PMCID: PMC4147808 DOI: 10.4103/0976-237x.137932] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Objectives: The aim was to evaluate the relationship of the K-primer variant of the transforming growth factor-alpha (TGF-α) gene and C677T variant of the methylenetetrahydrofolate reductase (MTHFR) gene with nonsyndromic cleft lip and palate (CL/P) in the Indian population. Setting and Sample Population: The study group consisted of DNA samples of 25 subjects with nonsyndromic CL with or without cleft palate and 25 unrelated controls, already existing in the Department of Orthodontics, D.A.P.M.R.V. Dental College, Bengaluru, Karnataka, India. Materials and Methods: The DNA samples were divided into two categories: Group A which included the 25 subjects with nonsyndromic CL/P; and Group B, which consisted of the 25 unrelated controls. The polymerase chain reaction (PCR) test was done for amplification of the region of interest from the DNA samples. Restriction digestion was then performed on the amplified product using the restriction enzyme HinfI, separately for each of the variants. The digested PCR products were separated into channels on a 1.5% agarose gel containing ethidium bromide in an electrophoretic chamber. A U.V. transilluminator was used to see the specific bands of base pairs of the digested PCR products. Results: In Group A, the TGF-α gene variant was present in 16 subjects (P = 0.001) and MTHFR gene variant was present in 8 subjects (P = 0.185). A combination of both gene variants were present in seven subjects, which was an interesting finding. In Group B, four subjects tested positive for the TGF-α and MTHFR gene variants. Conclusions: The TGF-α gene variant and a combination of TGF-α + MTHFR gene variants significantly contribute to the development of nonsyndromic CL/P and can be considered as genetic markers for Indian population. The MTHFR gene variant, though a minor risk factor, cannot be considered as a genetic marker.
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Affiliation(s)
- Asavari L Desai
- Department of Orthodontics, Manipal College of Dental Sciences, Mangalore, Karnataka, India
| | - M R Dinesh
- Department of Orthodontics, D.A.P.M.R.V. Dental College, Bengaluru, Karnataka, India
| | - B C Amarnath
- Department of Orthodontics, D.A.P.M.R.V. Dental College, Bengaluru, Karnataka, India
| | - R M Dharma
- Department of Orthodontics, D.A.P.M.R.V. Dental College, Bengaluru, Karnataka, India
| | - K R Akshai
- Department of Orthodontics, D.A.P.M.R.V. Dental College, Bengaluru, Karnataka, India
| | - C S Prashanth
- Department of Orthodontics, D.A.P.M.R.V. Dental College, Bengaluru, Karnataka, India
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Kenney MC, Chwa M, Atilano SR, Falatoonzadeh P, Ramirez C, Malik D, Tarek M, Del Carpio JC, Nesburn AB, Boyer DS, Kuppermann BD, Vawter MP, Jazwinski SM, Miceli MV, Wallace DC, Udar N. Molecular and bioenergetic differences between cells with African versus European inherited mitochondrial DNA haplogroups: implications for population susceptibility to diseases. BIOCHIMICA ET BIOPHYSICA ACTA 2014; 1842:208-19. [PMID: 24200652 PMCID: PMC4326177 DOI: 10.1016/j.bbadis.2013.10.016] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 10/18/2013] [Accepted: 10/29/2013] [Indexed: 02/08/2023]
Abstract
The geographic origins of populations can be identified by their maternally inherited mitochondrial DNA (mtDNA) haplogroups. This study compared human cybrids (cytoplasmic hybrids), which are cell lines with identical nuclei but mitochondria from different individuals with mtDNA from either the H haplogroup or L haplogroup backgrounds. The most common European haplogroup is H while individuals of maternal African origin are of the L haplogroup. Despite lower mtDNA copy numbers, L cybrids had higher expression levels for nine mtDNA-encoded respiratory complex genes, decreased ATP (adenosine triphosphate) turnover rates and lower levels of reactive oxygen species production, parameters which are consistent with more efficient oxidative phosphorylation. Surprisingly, GeneChip arrays showed that the L and H cybrids had major differences in expression of genes of the canonical complement system (5 genes), dermatan/chondroitin sulfate biosynthesis (5 genes) and CCR3 (chemokine, CC motif, receptor 3) signaling (9 genes). Quantitative nuclear gene expression studies confirmed that L cybrids had (a) lower expression levels of complement pathway and innate immunity genes and (b) increased levels of inflammation-related signaling genes, which are critical in human diseases. Our data support the hypothesis that mtDNA haplogroups representing populations from different geographic origins may play a role in differential susceptibilities to diseases.
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Affiliation(s)
- M Cristina Kenney
- Gavin Herbert Eye Institute, Univ. of California Irvine, Irvine, CA, USA; Department of Pathology and Laboratory Medicine, Univ. of California Irvine, Irvine, CA, USA.
| | - Marilyn Chwa
- Gavin Herbert Eye Institute, Univ. of California Irvine, Irvine, CA, USA
| | - Shari R Atilano
- Gavin Herbert Eye Institute, Univ. of California Irvine, Irvine, CA, USA
| | | | - Claudio Ramirez
- Gavin Herbert Eye Institute, Univ. of California Irvine, Irvine, CA, USA
| | - Deepika Malik
- Gavin Herbert Eye Institute, Univ. of California Irvine, Irvine, CA, USA
| | - Mohamed Tarek
- Gavin Herbert Eye Institute, Univ. of California Irvine, Irvine, CA, USA
| | | | - Anthony B Nesburn
- Gavin Herbert Eye Institute, Univ. of California Irvine, Irvine, CA, USA; Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - David S Boyer
- Retina-Vitreous Associates Medical Group, Beverly Hills, CA, USA
| | | | - Marquis P Vawter
- Functional Genomics Laboratory, Department of Psychiatry and Human Behavior, Univ. of California Irvine, Irvine, CA, USA
| | | | - Michael V Miceli
- Tulane Center for Aging, Tulane University, New Orleans, LA, USA
| | | | - Nitin Udar
- Gavin Herbert Eye Institute, Univ. of California Irvine, Irvine, CA, USA
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Lu XC, Yu W, Tao Y, Zhao PL, Li K, Tang LJ, Zheng JY, Li LX. Contribution of transforming growth factor α polymorphisms to nonsyndromic orofacial clefts: a HuGE review and meta-analysis. Am J Epidemiol 2014; 179:267-81. [PMID: 24243742 DOI: 10.1093/aje/kwt262] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We performed a meta-analysis of the association of transforming growth factor α gene (TGFA) polymorphisms with the risk of cleft lip with or without cleft palate (CL/P) or cleft palate (CP). In total, data from 29 studies were pooled for the following 3 polymorphisms: TGFA/TaqI, TGFA/BamHI, and TGFA/RasI in the TGFA gene. A fixed-effects or random-effects model was used to calculate the pooled odds ratios based on the results from the heterogeneity tests. A significantly increased CL/P or CP risk was observed in persons carrying a C2 allele at the TaqI polymorphism (odds ratio (OR) = 1.70, 95% confidence interval (CI): 1.41, 2.05) compared with those with a C1 allele (OR = 1.57, 95% CI: 1.23, 2.01). For the TGFA/BamHI polymorphism, carriers of the minor A1 allele had an estimated relative decrease in CL/P risk (OR = 0.44, 95% CI: 0.30, 0.64). These associations remained significant when only high-quality studies were included. However, no significant association was observed between the TGFA/RasI variant and CL/P risk. In summary, this meta-analysis provided a robust estimate of the positive association of the TGFA/TaqI polymorphism with both CL/P and CP and suggests that persons with an A1 allele may have a markedly decreased risk of CL/P.
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Leslie EJ, Mancuso JL, Schutte BC, Cooper ME, Durda KM, L'Heureux J, Zucchero TM, Marazita ML, Murray JC. Search for genetic modifiers of IRF6 and genotype-phenotype correlations in Van der Woude and popliteal pterygium syndromes. Am J Med Genet A 2013; 161A:2535-2544. [PMID: 23949966 DOI: 10.1002/ajmg.a.36133] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 06/14/2013] [Indexed: 01/03/2023]
Abstract
Van der Woude syndrome is the most common form of syndromic orofacial clefting, accounting for 1-2% of all patients with cleft lip and/or cleft palate. Van der Woude and popliteal pterygium syndromes are caused by mutations in IRF6, but phenotypic variability within and among families with either syndrome suggests that other genetic factors contribute to the phenotypes. The aim of this study was to identify common variants acting as genetic modifiers of IRF6 as well as genotype-phenotype correlations based on mutation type and location. We identified an association between mutations in the DNA-binding domain of IRF6 and limb defects (including pterygia). Although we did not detect formally significant associations with the genes tested, borderline associations suggest several genes that could modify the VWS phenotype, including FOXE1, TGFB3, and TFAP2A. Some of these genes are hypothesized to be part of the IRF6 gene regulatory network and may suggest additional genes for future study when larger sample sizes are also available. We also show that families with the Van de Woude phenotype but in whom no mutations have been identified have a lower frequency of cleft lip, suggesting there may be locus and/or mutation class differences in Van de Woude syndrome.
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Affiliation(s)
| | | | - Brian C Schutte
- Departments of Microbiology and Molecular Genetics, Pediatrics and Human Development, Michigan State University, East Lansing, MI
| | - Margaret E Cooper
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Kate M Durda
- Department of Pediatrics, University of Iowa, Iowa City, IA
| | | | | | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
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42
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Lu Y, Liu Q, Xu W, Li Z, Jiang M, Li X, Zhao N, Liu W, Sui Y, Ma C, Feng W, Han W, Li J. TGFA and IRF6 contribute to the risk of nonsyndromic cleft lip with or without cleft palate in northeast China. PLoS One 2013; 8:e70754. [PMID: 23940636 PMCID: PMC3735505 DOI: 10.1371/journal.pone.0070754] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 06/23/2013] [Indexed: 11/19/2022] Open
Abstract
Nonsyndromic cleft lip with or without cleft palate (NSCL/P) are common birth defects with a complex etiology. Multiple interacting loci and possible environmental factors influence the risk of NSCL/P. 12 single nucleotide polymorphisms (SNPs) in 7 candidate genes were tested using an allele-specific primer extension for case-control and case-parent analyses in northeast China in 236 unrelated patients, 185 mothers and 154 fathers, including 128 complete trios, and 400 control individuals. TGFA and IRF6 genes showed a significant association with NSCL/P. In IRF6, statistical evidence of an association between rs2235371 (p = 0.003), rs2013162 (p<0.0001) and NSCL/P was observed in case-control analyses. Family based association tests (FBATs) showed over-transmission of the C allele at the rs2235371 polymorphism (p = 0.007). In TGFA, associations between rs3771494, rs3771523 (G3822A), rs11466285 (T3851C) and NSCL/P were observed in case-control and FBAT analyses. Associations between other genes (BCL3, TGFB3, MTHFR, PVRL1 and SUMO1) and NSCL/P were not detected.
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Affiliation(s)
- Yongping Lu
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
| | - Qiang Liu
- Department of Oral-Maxillofacial Surgery and Plastic Surgery, School of Stomatology, China Medical University, Shenyang, China
| | - Wei Xu
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
| | - Zengjian Li
- Department of Oral-Maxillofacial Surgery and Plastic Surgery, School of Stomatology, China Medical University, Shenyang, China
| | - Miao Jiang
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
| | - Xuefu Li
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
| | - Ning Zhao
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
| | - Wei Liu
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
| | - Yu Sui
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
| | - Chao Ma
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
| | - Wenhua Feng
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
| | - Weitian Han
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
- * E-mail: (JL); (WH)
| | - Jianxin Li
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, China
- * E-mail: (JL); (WH)
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Iwata JI, Suzuki A, Pelikan RC, Ho TV, Sanchez-Lara PA, Urata M, Dixon MJ, Chai Y. Smad4-Irf6 genetic interaction and TGFβ-mediated IRF6 signaling cascade are crucial for palatal fusion in mice. Development 2013; 140:1220-30. [PMID: 23406900 DOI: 10.1242/dev.089615] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Cleft palate is one of the most common human birth defects and is associated with multiple genetic and environmental risk factors. Although mutations in the genes encoding transforming growth factor beta (TGFβ) signaling molecules and interferon regulatory factor 6 (Irf6) have been identified as genetic risk factors for cleft palate, little is known about the relationship between TGFβ signaling and IRF6 activity during palate formation. Here, we show that TGFβ signaling regulates expression of Irf6 and the fate of the medial edge epithelium (MEE) during palatal fusion in mice. Haploinsufficiency of Irf6 in mice with basal epithelial-specific deletion of the TGFβ signaling mediator Smad4 (Smad4(fl/fl);K14-Cre;Irf6(+/R84C)) results in compromised p21 expression and MEE persistence, similar to observations in Tgfbr2(fl/fl);K14-Cre mice, although the secondary palate of Irf6(+/R84C) and Smad4(fl/fl);K14-Cre mice form normally. Furthermore, Smad4(fl/fl);K14-Cre;Irf6(+/R84C) mice show extra digits that are consistent with abnormal toe and nail phenotypes in individuals with Van der Woude and popliteal pterygium syndromes, suggesting that the TGFβ/SMAD4/IRF6 signaling cascade might be a well-conserved mechanism in regulating multiple organogenesis. Strikingly, overexpression of Irf6 rescued p21 expression and MEE degeneration in Tgfbr2(fl/fl);K14-Cre mice. Thus, IRF6 and SMAD4 synergistically regulate the fate of the MEE, and TGFβ-mediated Irf6 activity is responsible for MEE degeneration during palatal fusion in mice.
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Affiliation(s)
- Jun-ichi Iwata
- Center for Craniofacial Molecular Biology, Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
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