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Vieira AR, Koruyucu M, Bekele EK, Seymen F, Modesto A. IRF6 Genetic Variation and Maternal Smoking During Pregnancy in Cleft Lip/Palate. FRONTIERS IN DENTAL MEDICINE 2021. [DOI: 10.3389/fdmed.2021.632055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The goal of the present work was to revisit published data to test if genetic variation in interferon regulatory factor 6 (IRF6) is associated with children born with cleft lip with or without cleft palate (CL/P) for cases with positive history of maternal smoking. From the 573 individuals originally studied, this reanalysis focused on 57 who had a positive history of maternal smoking during pregnancy (39 born with CL/P and 18 born without CL/P). Seven IRF6 markers (rs4844880, rs2235371, rs2013162, ra861019, rs2073487, rs642961, and rs658860) were tested for over-transmission of alleles and an alpha of 0.05 was considered statistically significant. All individuals born with CL/P were homozygous for the wild type allele of rs2235371 in comparison to just two individuals born without clefts (p = 0.0000001). For rs861019, individuals born with CL/P were more likely to have the variant allele (p = 0.006). A similar trend was seen for rs642961 (p = 0.09). The results suggest that statistical evidence of over-representation of IRF6 alleles in individuals born with CL/P may be unveiled only when maternal smoking during pregnancy is used as the inclusion criterion in the analysis.
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Dash S, Trainor PA. The development, patterning and evolution of neural crest cell differentiation into cartilage and bone. Bone 2020; 137:115409. [PMID: 32417535 DOI: 10.1016/j.bone.2020.115409] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 05/04/2020] [Indexed: 12/12/2022]
Abstract
Neural crest cells are a vertebrate-specific migratory, multipotent cell population that give rise to a diverse array of cells and tissues during development. Cranial neural crest cells, in particular, generate cartilage, bone, tendons and connective tissue in the head and face as well as neurons, glia and melanocytes. In this review, we focus on the chondrogenic and osteogenic potential of cranial neural crest cells and discuss the roles of Sox9, Runx2 and Msx1/2 transcription factors and WNT, FGF and TGFβ signaling pathways in regulating neural crest cell differentiation into cartilage and bone. We also describe cranioskeletal defects and disorders arising from gain or loss-of-function of genes that are required for patterning and differentiation of cranial neural crest cells. Finally, we discuss the evolution of skeletogenic potential in neural crest cells and their function as a conduit for intraspecies and interspecies variation, and the evolution of craniofacial novelties.
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Affiliation(s)
- Soma Dash
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Paul A Trainor
- Stowers Institute for Medical Research, Kansas City, MO, USA; Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS, USA.
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Wu-Chou YH, Lu YC, Chen KTP, Chang HF, Lin YT, Lo LJ. Association Studies Between Regulatory Regions of IRF6/ TP63 Genes and Nonsyndromic Oral Clefts. Cleft Palate Craniofac J 2018; 56:778-785. [PMID: 30419764 DOI: 10.1177/1055665618809244] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
OBJECTIVE To evaluate genetic variants within the regulatory regions of interferon regulatory factor 6 (IRF6) and TP63 for the etiology of nonsyndromic oral clefts risk factors. DESIGN We performed allelic transmission disequilibrium test analysis on 5 eligible single-nucleotide polymorphisms (SNPs) and SNP haplotypes using the Family-Based Association Test. PARTICIPANTS The study sample consisted of 334 case-parent trios of nonsyndromic oral clefts from Taiwanese population, separated into nonsyndromic cleft lip/palate (NSCL/P) and nonsyndromic cleft palate only (NSCPO) groups. RESULTS We found all 3 selected SNPs of the IRF6 gene show significant association with nonsyndromic oral clefts (rs2235371, P = 5.10E-07; rs642961, P = .00194; and rs77542756, P = 9.08E-07). Haplotype analyses identified 3 possible SNP combination haplotypes in the IRF6 gene and found that C-G-G showed significant undertransmission (P = .058), whereas 2 other haplotypes, T-G-A and C-A-G (P = 2.71E-06 and P = 5.00E-04, respectively), were significantly overtransmitted to the NSCL/P children but not to the NSCPO children. For the TP63 gene, we failed to detect evidence of nonsyndromic oral cleft association in the 2 SNPs within the TP63 large intron 1 region. CONCLUSIONS We used a family-based analysis in 334 Taiwanese case-parent trios to evaluate selected SNPs of IRF6 genes and TP63 genes for a risk of orofacial clefting. This study provides additional evidence for an association between IRF6 and NSCL/P, including the genetic variants within the 5'-noncoding region of the gene. We also confirmed that NSCL/P and NSCPO individuals belong to different groups. For the TP63, our data did not favor the direct involvement of TAp63 isoforms during orofacial development.
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Affiliation(s)
- Yah-Huei Wu-Chou
- 1 Department of Medical Research, Chang Gung University, Taoyuan.,2 Craniofacial Research Center, Chang Gung Memorial Hospital, Taoyuan
| | - Yi-Chieh Lu
- 1 Department of Medical Research, Chang Gung University, Taoyuan.,2 Craniofacial Research Center, Chang Gung Memorial Hospital, Taoyuan
| | - Kuo-Ting Philip Chen
- 2 Craniofacial Research Center, Chang Gung Memorial Hospital, Taoyuan.,3 Department of Plastic and Reconstructive Surgery, Chang Gung Memorial Hospital, Taoyuan
| | - Hsien-Fang Chang
- 4 Center of Genomic Medicine, National Taiwan University, Taipei
| | - Yin-Ting Lin
- 1 Department of Medical Research, Chang Gung University, Taoyuan.,2 Craniofacial Research Center, Chang Gung Memorial Hospital, Taoyuan
| | - Lun-Jou Lo
- 2 Craniofacial Research Center, Chang Gung Memorial Hospital, Taoyuan.,3 Department of Plastic and Reconstructive Surgery, Chang Gung Memorial Hospital, Taoyuan.,5 Graduate Institute of Dental and Craniofacial Science, Chang Gung University, Taoyuan
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de Souza LT, Kowalski TW, Ferrari J, Monlléo IL, Ribeiro EM, de Souza J, Fett-Conte AC, de Araujo TK, Gil-da-Silva-Lopes VL, Ribeiro-dos-Santos ÂKC, dos Santos SEB, Félix TM. Study ofIRF6and 8q24 region in non-syndromic oral clefts in the Brazilian population. Oral Dis 2016; 22:241-5. [DOI: 10.1111/odi.12432] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/24/2015] [Accepted: 12/17/2015] [Indexed: 02/03/2023]
Affiliation(s)
- LT de Souza
- Laboratório de Medicina Genômica - Hospital de Clínicas de Porto Alegre; Porto Alegre Brazil
- Programa de Pós-Graduação em Saúde da Criança e do Adolescente; Universidade Federal do Rio Grande do Sul; Porto Alegre Brazil
| | - TW Kowalski
- Programa de Pós-Graduação em Genética e Biologia Molecular; Universidade Federal do Rio Grande do Sul; Porto Alegre Brazil
| | - J Ferrari
- Laboratório de Medicina Genômica - Hospital de Clínicas de Porto Alegre; Porto Alegre Brazil
| | - IL Monlléo
- Serviço de Genética Clínica; Faculdade de Medicina; Hospital Universitário Professor Alberto Antunes; Universidade Federal de Alagoas; Maceió Brazil
| | - EM Ribeiro
- Hospital Infantil Albert Sabin; Fortaleza Brazil
| | - J de Souza
- Centro de Atendimento Integral ao Fissurado Lábio-palatal; Curitiba Brazil
| | - AC Fett-Conte
- Serviço de Genética; Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto Brazil
| | - TK de Araujo
- Departamento de Genética Médica; Faculdade de Ciências Médicas; Universidade de Campinas; Campinas Brazil
| | - VL Gil-da-Silva-Lopes
- Departamento de Genética Médica; Faculdade de Ciências Médicas; Universidade de Campinas; Campinas Brazil
| | - ÂKC Ribeiro-dos-Santos
- Laboratório de Genética Humana e Médica; Instituto de Ciências Biológicas; Universidade Federal do Pará; Belém Brazil
| | - SEB dos Santos
- Laboratório de Genética Humana e Médica; Instituto de Ciências Biológicas; Universidade Federal do Pará; Belém Brazil
| | - TM Félix
- Laboratório de Medicina Genômica - Hospital de Clínicas de Porto Alegre; Porto Alegre Brazil
- Programa de Pós-Graduação em Saúde da Criança e do Adolescente; Universidade Federal do Rio Grande do Sul; Porto Alegre Brazil
- Serviço de Genética Médica; Hospital de Clínicas de Porto Alegre; Porto Alegre Brazil
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Wen Y, Lu Q. Risk prediction models for oral clefts allowing for phenotypic heterogeneity. Front Genet 2015; 6:264. [PMID: 26322076 PMCID: PMC4534829 DOI: 10.3389/fgene.2015.00264] [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] [Received: 05/05/2015] [Accepted: 07/28/2015] [Indexed: 11/17/2022] Open
Abstract
Oral clefts are common birth defects that have a major impact on the affected individual, their family and society. World-wide, the incidence of oral clefts is 1/700 live births, making them the most common craniofacial birth defects. The successful prediction of oral clefts may help identify sub-population at high risk, and promote new diagnostic and therapeutic strategies. Nevertheless, developing a clinically useful oral clefts risk prediction model remains a great challenge. Compelling evidences suggest the etiologies of oral clefts are highly heterogeneous, and the development of a risk prediction model with consideration of phenotypic heterogeneity may potentially improve the accuracy of a risk prediction model. In this study, we applied a previously developed statistical method to investigate the risk prediction on sub-phenotypes of oral clefts. Our results suggested subtypes of cleft lip (CL) and palate have similar genetic etiologies (AUC = 0.572) with subtypes of CL only (AUC = 0.589), while the subtypes of cleft palate only (CPO) have heterogeneous underlying mechanisms (AUCs for soft CPO and hard CPO are 0.617 and 0.623, respectively). This highlighted the potential that the hard and soft forms of CPO have their own mechanisms despite sharing some of the genetic risk factors. Comparing with conventional methods for risk prediction modeling, our method considers phenotypic heterogeneity of a disease, which potentially improves the accuracy for predicting each sub-phenotype of oral clefts.
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Affiliation(s)
- Yalu Wen
- Department of Statistics, University of Auckland, Auckland New Zealand
| | - Qing Lu
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI USA
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Ibarra-Arce A, García-Álvarez M, Cortés-González D, Ortiz de Zarate-Alarcón G, Flores-Peña L, Sánchez-Camacho S, Arenas-Díaz S, Romero-Valdovinos M, Olivo-Díaz A. IRF6 polymorphisms in Mexican patients with non-syndromic cleft lip. Meta Gene 2015; 4:8-16. [PMID: 25853057 PMCID: PMC4354917 DOI: 10.1016/j.mgene.2015.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 02/20/2015] [Indexed: 12/24/2022] Open
Abstract
Cleft lip with or without cleft palate (CL/P) is one of the most common birth defects; it is a multifactorial disease affecting > 1/1,000 live births in Europe, and its etiology is largely unknown, although it is very likely genetic and environmental factors contribute to this malformation. Orofacial development is a complex process involving many genes and signaling pathways. Mutations in the gene for the interferon regulatory factor 6 (IRF6) cause a hereditary dominant malformation syndrome including CL/P, and polymorphisms are associated with non-syndromic CL/P (MIM 119530). Five SNPs at the locus with high heterozygosity in Caucasian populations were chosen for the present research due to their very strong association with CL/P. A case–parent trio study was performed using 292 samples from Mexico. Association with the rs1319435-C/C genotype (P = 0.02) was found in patients (73) as compared to pseudocontrols (219), while the genotype rs1319435-T/C was related with protection (P = 0.041) in the triad design. Significant over-transmission of the G allele for marker rs2235375 (P = 0.049) was found. Only the TACGT haplotype was diminished in the affected child, either in single (P = 0.0208) or double (P = 0.0208) dose. The pairwise analysis showed rs2235543 and rs2235371 were in strong linkage disequilibrium. These results point to a substantial contribution of IRF6 in the etiology of non-syndromic CL/P in a sample of the Mexican population. Cleft lip with or without cleft palate (CL/P) is one of the most common birth defects. Association with the rs1319435-C/C genotype was found in patients as compared to pseudocontrols. In the triad design, the genotype rs1319435-T/C was related with protection. The IRF6 contributes to the etiology of non-syndromic CL/P in a sample of the Mexican population.
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Affiliation(s)
- Aurora Ibarra-Arce
- División de Genética, Hospital General Doctor Manuel Gea González, Mexico DF, Mexico
| | - Martín García-Álvarez
- División de Genética, Hospital General Doctor Manuel Gea González, Mexico DF, Mexico
| | - Daniel Cortés-González
- Departamento de Biología Molecular e Histocompatibilidad, Hospital General Doctor Manuel Gea González, Mexico DF, Mexico
| | | | - Laura Flores-Peña
- División de Genética, Hospital General Doctor Manuel Gea González, Mexico DF, Mexico
| | | | | | - Mirza Romero-Valdovinos
- Departamento de Biología Molecular e Histocompatibilidad, Hospital General Doctor Manuel Gea González, Mexico DF, Mexico
| | - Angélica Olivo-Díaz
- Departamento de Biología Molecular e Histocompatibilidad, Hospital General Doctor Manuel Gea González, Mexico DF, Mexico
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Chandrasekharan D, Ramanathan A. Identification of a novel heterozygous truncation mutation in exon 1 of ARHGAP29 in an Indian subject with nonsyndromic cleft lip with cleft palate. Eur J Dent 2014; 8:528-532. [PMID: 25512736 PMCID: PMC4253111 DOI: 10.4103/1305-7456.143637] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Objective: Mutations in exon 1 of ARHGAP29, a RhoA specific GTPase have been identified in North American and Filipino subjects with nonsyndromic cleft palate and cleft lip with or without cleft palate. Since the genetic status of ARHGAP29 in Indian subjects with nonsyndromic oral clefts is not known, we designed the present study to investigate the occurrence of the above mutations in them. Materials and Methods: Total genomic DNA extracted from peripheral blood of 60 subjects with nonsyndromic cleft palate and cleft lip with or without cleft palate, and equal number of control healthy subjects were amplified with primers flanking exon 1 of ARHGAP29 gene and subjected to direct sequencing. Results: Sequencing analysis identified a nonsense mutation in exon 1 of ARHGAP29 that caused substitution of lysine to stop codon at codon position 32 in a subject with nonsyndromic cleft lip with cleft palate. The mutation, however, occurred in heterozygous condition. None of the other subjects carried mutation in this region. Conclusion: The study has thus identified a rare but novel truncation mutation in ARHGAP29 gene for the first time in nonsyndromic oral clefts.
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Affiliation(s)
- Deepak Chandrasekharan
- Research Scholar, Human Genetics Laboratory, Central Research Facility, Sree Balaji Medical and Dental College and Hospital, Bharath University, Chennai, Tamil Nadu, India
| | - Arvind Ramanathan
- Research Scholar, Human Genetics Laboratory, Central Research Facility, Sree Balaji Medical and Dental College and Hospital, Bharath University, Chennai, Tamil Nadu, India
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Figueiredo JC, Ly S, Raimondi H, Magee K, Baurley JW, Sanchez-Lara PA, Ihenacho U, Yao C, Edlund CK, van den Berg D, Casey G, DeClerk YA, Samet JM, Magee W. Genetic risk factors for orofacial clefts in Central Africans and Southeast Asians. Am J Med Genet A 2014; 164A:2572-80. [DOI: 10.1002/ajmg.a.36693] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 06/27/2014] [Indexed: 12/18/2022]
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
| | | | | | - James W. Baurley
- BioRealm LLC; Los Angeles California
- Bioinformatics Research Group; 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
| | - Ugonna Ihenacho
- Department of Preventive Medicine; Keck School of Medicine; University of Southern California; Los Angeles California
| | - Caroline Yao
- Division of Plastic & Maxillofacial Surgery; Children's Hospital Los Angeles; Los Angeles California
| | - Christopher K. Edlund
- Department of Preventive Medicine; Keck School of Medicine; University of Southern California; Los Angeles California
- BioRealm LLC; Los Angeles California
| | - David van den Berg
- Department of Preventive Medicine; Keck School of Medicine; University of Southern California; Los Angeles California
| | - Graham Casey
- 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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Song T, Wu D, Wang Y, Li H, Yin N, Zhao Z. SNPs and interaction analyses of IRF6, MSX1 and PAX9 genes in patients with non‑syndromic cleft lip with or without palate. Mol Med Rep 2013; 8:1228-34. [PMID: 23921572 DOI: 10.3892/mmr.2013.1617] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Accepted: 07/23/2013] [Indexed: 11/06/2022] Open
Abstract
Non‑syndromic cleft lip with or without cleft palate (NSCL/P) is a common congenital deformity, often associated with missing or deformed teeth. The genes interferon regulatory factor 6 (IRF6), muscle segment homeobox 1 (MSX1) and paired box gene 9 (PAX9) are important for the development of the maxillofacial region and dentition. The aim of this study was to explore how genetic variations in IRF6, MSX1 and PAX9, as well as gene‑gene interactions, are associated with NSCL/P. We investigated 9 IRF6 tag single nucleotide polymorphisms (SNPs), 2 MSX1 tag SNPs and 8 PAX9 tag SNPs selected from HapMap data from the Chinese population. The SNPs were examined for associations with NSCL/P in 204 patients and 226 controls. The results demonstrated a significant association between NSCL/P and rs2073485, rs2235371, rs2236909 and rs861020 in the IRF6 gene, and haplotype analysis supported these findings. A marginally significant difference was observed in the NSCL/P group for rs17176643 in the PAX9 gene compared to the control group. The results of gene‑gene interaction analyses also indicated that the combination of rs2073485, rs2235371 or rs2236909 in IRF6 and rs17176643 in PAX9, increased the risk of NSCL/P. Thus, our study provided additional understanding of IRF6 variations in patients with NSCL/P and suggested that interactions between the IRF6 and PAX9 genes are potentially important for susceptibility to NSCL/P.
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Affiliation(s)
- Tao Song
- Center of Cleft Lip and Palate, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shijingshan, Beijing 100144, P.R. China
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Paranaiba LMR, Coletta RD, Swerts MSO, Quintino RP, De Barros LM, Martelli-Júnior H. Prevalence of Dental Anomalies in Patients with Nonsyndromic Cleft Lip and/or Palate in a Brazilian Population. Cleft Palate Craniofac J 2013; 50:400-5. [DOI: 10.1597/11-029] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Objective Many studies have demonstrated a high frequency of dental anomalies in patients with cleft lip and/or palate. Because dental anomalies may complicate dental treatment, we investigated the prevalence of dental anomalies in a group of Brazilian patients with nonsyndromic cleft lip and/or palate. Design, Participants, Setting Retrospective analysis was performed using clinical records of 296 patients aged between 12 and 30 years with repaired nonsyndromic cleft lip and/or palate without history of tooth extraction and orthodontic treatment. Associations between oral clefts and presence of dental anomalies outside the cleft area were investigated. Results Dental anomalies were identified in 39.9% of the nonsyndromic cleft lip and/or palate patients, and tooth agenesis (47.5%), impacted tooth (13.1%), and microdontia (12.7%) were the most common anomalies. Cleft lip patients were less affected by dental anomalies compared with cleft palate or cleft lip and palate patients ( p = .057). Specifically, patients with unilateral cleft lip and palate were significantly more affected by dental anomalies than those with bilateral cleft lip and palate ( p = .00002), and individuals with unilateral complete cleft lip and palate ( p = .002) and complete cleft palate ( p = .01) were significantly more affected by tooth agenesis than other cleft types. Agenesis of the premolars ( p = .043) and maxillary lateral incisors ( p = .03) were significantly more frequent in patients with unilateral complete cleft lip and palate. Conclusions The present study revealed a high frequency of dental anomalies in nonsyndromic cleft lip and/or palate patients and further demonstrated that patients with unilateral cleft lip and palate were frequently more affected by dental anomalies than those with bilateral cleft lip and palate. Moreover, our results demonstrate that dental anomalies should be considered during dental treatment planning for individuals affected by nonsyndromic cleft lip and/or palate.
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Affiliation(s)
| | - Ricardo D. Coletta
- Department of Oral Diagnosis, School of Dentistry, State University of Campinas, Piracicaba, São Paulo, Brazil
| | | | | | | | - Hercílio Martelli-Júnior
- Stomatology Clinic, School of Dentistry, State University of Montes Claros, Montes Claros, Minas Gerais, Brazil
- School of Dentistry, José do Rosário Vellano University, Alfenas, Minas Gerais, Brazil
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Wu-Chou YH, Lo LJ, Chen KTP, Chang CSF, Chen YR. A combined targeted mutation analysis of IRF6 gene would be useful in the first screening of oral facial clefts. BMC MEDICAL GENETICS 2013; 14:37. [PMID: 23510002 PMCID: PMC3606492 DOI: 10.1186/1471-2350-14-37] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Accepted: 03/13/2013] [Indexed: 01/30/2023]
Abstract
Background Interferon Regulatory Factor 6 (IRF6) is a member of the IRF family of transcription factors. It has been suggested to be an important contributor to orofacial development since mutations of the IRF6 gene has been found in Van der Woude (VWS) and popliteal pterygium syndromes (PPS), two disorders that can present with isolated cleft lip and palate. The association between IRF6 gene and cleft lip and palate has also been independently replicated in many populations. Methods We screened a total of 155 Taiwanese patients with cleft lip with or without cleft palate (CL/P); 31 syndromic (including 19 VWS families), 44 non-syndromic families with at least two affected members, and 80 non-syndromic patients through a combined targeted, polymerase chain reaction (PCR)-based mutation analysis for the entire coding regions of IRF6 gene. Results We found 11 mutations in 57.89% (11/19) of the VWS patients and no IRF6 mutation in 44 of the non-syndromic multiplex families and 80 non-syndromic oral cleft patients. In this IRF6 gene screening, five of these mutations (c.290 A>G, p.Tyr97Cys; c.360-375 16 bp deletion, p.Gln120HisfsX24; c.411_412 insA, p.Glu136fsX3; c.871 A>C, p.Thr291Pro; c.969 G>A, and p.Trp323X) have not been reported in the literature previously. Exon deletion was not detected in this series of IRF6 gene screening. Conclusions Our results confirm the crucial role of IRF6 in the VWS patients and further work is needed to explore for its function in the non-syndromic oral cleft with vary clinical features.
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Affiliation(s)
- Yah-Huei Wu-Chou
- Department of Medical Research, Chang Gung Memorial Hospital, No. 5, Fushing Street, Kweishan, Taoyuan, Taiwan.
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12
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Letra A, Fakhouri W, Fonseca RF, Menezes R, Kempa I, Prasad JL, McHenry TG, Lidral AC, Moreno L, Murray JC, Daack-Hirsch S, Marazita ML, Castilla EE, Lace B, Orioli IM, Granjeiro JM, Schutte BC, Vieira AR. Interaction between IRF6 and TGFA genes contribute to the risk of nonsyndromic cleft lip/palate. PLoS One 2012; 7:e45441. [PMID: 23029012 PMCID: PMC3447924 DOI: 10.1371/journal.pone.0045441] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 08/22/2012] [Indexed: 01/08/2023] Open
Abstract
Previous evidence from tooth agenesis studies suggested IRF6 and TGFA interact. Since tooth agenesis is commonly found in individuals with cleft lip/palate (CL/P), we used four large cohorts to evaluate if IRF6 and TGFA interaction contributes to CL/P. Markers within and flanking IRF6 and TGFA genes were tested using Taqman or SYBR green chemistries for case-control analyses in 1,000 Brazilian individuals. We looked for evidence of gene-gene interaction between IRF6 and TGFA by testing if markers associated with CL/P were overtransmitted together in the case-control Brazilian dataset and in the additional family datasets. Genotypes for an additional 142 case-parent trios from South America drawn from the Latin American Collaborative Study of Congenital Malformations (ECLAMC), 154 cases from Latvia, and 8,717 individuals from several cohorts were available for replication of tests for interaction. Tgfa and Irf6 expression at critical stages during palatogenesis was analyzed in wild type and Irf6 knockout mice. Markers in and near IRF6 and TGFA were associated with CL/P in the Brazilian cohort (p<10−6). IRF6 was also associated with cleft palate (CP) with impaction of permanent teeth (p<10−6). Statistical evidence of interaction between IRF6 and TGFA was found in all data sets (p = 0.013 for Brazilians; p = 0.046 for ECLAMC; p = 10−6 for Latvians, and p = 0.003 for the 8,717 individuals). Tgfa was not expressed in the palatal tissues of Irf6 knockout mice. IRF6 and TGFA contribute to subsets of CL/P with specific dental anomalies. Moreover, this potential IRF6-TGFA interaction may account for as much as 1% to 10% of CL/P cases. The Irf6-knockout model further supports the evidence of IRF6-TGFA interaction found in humans.
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Affiliation(s)
- Ariadne Letra
- Department of Oral Biology, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
| | - Walid Fakhouri
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Renata F. Fonseca
- Department of Genetics, Institute of Biology, Center of Health Sciences; Federal University of Rio de Janeiro; Rio de Janeiro, RJ, Brazil
| | - Renato Menezes
- Department of Oral Biology, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
| | - Inga Kempa
- Latvian Biomedical Research and Study Centre, Riga, Latvia
- Department of Biology and Microbiology, Riga Stradins University, Riga, Latvia
| | - Joanne L. Prasad
- Department of Diagnostic Sciences, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
| | - Toby G. McHenry
- Department of Oral Biology, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
| | - Andrew C. Lidral
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Lina Moreno
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Jeffrey C. Murray
- Department of Pediatrics, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Sandra Daack-Hirsch
- Department of Pediatrics, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Mary L. Marazita
- Department of Oral Biology, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Eduardo E. Castilla
- ECLAMC (Latin American Collaborative Study of Congenital Malformations) at CEMIC (Center of Medical Education and Clinical Research “Norberto Quirno”), Buenos Aires, Argentina
- CONICET (National Research Council of Argentina), Buenos Aires, Argentina
- iNaGeMP-CNPq (National Institute of Population Medical Genetics), Porto Alegre, RS, Brazil
| | - Baiba Lace
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Ieda M. Orioli
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
- iNaGeMP-CNPq (National Institute of Population Medical Genetics), Porto Alegre, RS, Brazil
| | - Jose M. Granjeiro
- Department of Cell and Molecular Biology, Fluminense Federal University, Niterói, RJ, Brazil and INMETRO, Duque de Caxias, RJ, Brazil
| | - Brian C. Schutte
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Alexandre R. Vieira
- Department of Oral Biology, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
- Department of Pediatric Dentistry, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, PA, USA
- * E-mail:
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Freitas JADS, das Neves LT, de Almeida ALPF, Garib DG, Trindade-Suedam IK, Yaedú RYF, Lauris RDCMC, Soares S, Oliveira TM, Pinto JHN. Rehabilitative treatment of cleft lip and palate: experience of the Hospital for Rehabilitation of Craniofacial Anomalies/USP (HRAC/USP)--Part 1: overall aspects. J Appl Oral Sci 2012; 20:9-15. [PMID: 22437671 PMCID: PMC3928765 DOI: 10.1590/s1678-77572012000100003] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 10/08/2011] [Indexed: 11/22/2022] Open
Abstract
Cleft lip and palate is the most common among craniofacial malformations and causes
several esthetic and functional implications that require rehabilitation. This paper
aims to generally describe the several aspects related to this complex pathology and
the treatment protocol used by the Hospital for Rehabilitation of Craniofacial
Anomalies, University of São Paulo (HRAC-USP) along 40 years of experience in the
treatment of individuals with cleft lip and palate.
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Affiliation(s)
- José Alberto de Souza Freitas
- Hospital for Rehabilitation of Craniofacial Anomalies, Department of Stomatology, Bauru School of Dentistry, University of São Paulo, Bauru, SP, Brazil
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14
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Yuan Q, Chiquet BT, Devault L, Warman ML, Nakamura Y, Swindell EC, Hecht JT. Craniofacial abnormalities result from knock down of nonsyndromic clefting gene, crispld2, in zebrafish. Genesis 2012; 50:871-81. [PMID: 22887593 DOI: 10.1002/dvg.22051] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 07/24/2012] [Accepted: 07/29/2012] [Indexed: 11/10/2022]
Abstract
Nonsyndromic cleft lip and palate (NSCLP), a common birth defect, affects 4,000 newborns in the US each year. Previously, we described an association between CRISPLD2 and NSCLP and showed Crispld2 expression in the murine palate. These results suggested that a perturbation in CRISPLD2 activity affects craniofacial development. Here, we describe crispld2 expression and the phenotypic consequence of its loss of function in zebrafish. crispld2 was expressed at all stages of zebrafish morphogenesis examined and localized to the rostral end by 1-day postfertilization. Morpholino knockdown of crispld2 resulted in significant jaw and palatal abnormalities in a dose-dependent manner. Loss of crispld2 caused aberrant patterning of neural crest cells (NCC) suggesting that crispld2 is necessary for normal NCC formation. Altogether, we show that crispld2 plays a significant role in the development of the zebrafish craniofacies and alteration of normal protein levels disturbs palate and jaw formation. These data provide support for a role of CRISPLD2 in NSCLP.
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Affiliation(s)
- Qiuping Yuan
- Department of Pediatrics, University of Texas Medical School at Houston, Houston, Texas, USA
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15
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Lace B, Kempa I, Piekuse L, Grinfelde I, Klovins J, Pliss L, Krumina A, Vieira AR. Association studies of candidate genes and cleft lip and palate taking into consideration geographical origin. Eur J Oral Sci 2011; 119:413-7. [DOI: 10.1111/j.1600-0722.2011.00877.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Mossey P, Little J. Addressing the challenges of cleft lip and palate research in India. Indian J Plast Surg 2011; 42 Suppl:S9-S18. [PMID: 19884687 PMCID: PMC2825065 DOI: 10.4103/0970-0358.57182] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The Indian sub-continent remains one of the most populous areas of the world with an estimated population of 1.1 billion in India alone. This yields an estimated 24.5 million births per year and the birth prevalence of clefts is somewhere between 27,000 and 33,000 clefts per year. Inequalities exist, both in access to and quality of cleft care with distinct differences in urban versus rural access and over the years the accumulation of unrepaired clefts of the lip and palate make this a significant health care problem in India. In recent years the situation has been significantly improved through the intervention of Non Governmental Organisations such as SmileTrain and Transforming Faces Worldwide participating in primary surgical repair programmes. The cause of clefts is multi factorial with both genetic and environmental input and intensive research efforts have yielded significant advances in recent years facilitated by molecular technologies in the genetic field. India has tremendous potential to contribute by virtue of improving research expertise and a population that has genetic, cultural and socio-economic diversity. In 2008, the World Health Organisation (WHO) has recognised that non-communicable diseases, including birth defects cause significant infant mortality and childhood morbidity and have included cleft lip and palate in their Global Burden of Disease (GBD) initiative. This will fuel the interest of India in birth defects registration and international efforts aimed at improving quality of care and ultimately prevention of non-syndromic clefts of the lip and palate.
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Affiliation(s)
- Peter Mossey
- Unit of Orthodontics, Dundee University Dental School, 1 Park Place, Dundee, DD1 4HR, Scotland, United Kingdom
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17
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Abstract
Cleft palate, a malformation of the secondary palate development, is one of the most common human congenital birth defects. Palate formation is a complex process resulting in the separation of the oral and nasal cavities that involves multiple events, including palatal growth, elevation, and fusion. Recent findings show that transforming growth factor beta (TGF-β) signaling plays crucial roles in regulating palate development in both the palatal epithelium and mesenchyme. Here, we highlight recent advances in our understanding of TGF-β signaling during palate development.
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Affiliation(s)
- J Iwata
- Center for Craniofacial Molecular Biology, Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA
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18
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Vieira AR, Pliss L, Pelnena I, Krumina A, Baumanis V, Lace B. Mitochondrial DNA origins of the Latvian clefting population. Mitochondrion 2011; 11:357-9. [DOI: 10.1016/j.mito.2010.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 09/20/2010] [Accepted: 10/01/2010] [Indexed: 11/29/2022]
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19
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Wang Y, Li X, Zhu WL, Guo JZ, Song XM, Li SQ, Li Y. Genome-wide and interaction linkage scan for nonsyndromic cleft lip with or without cleft palate in two multiplex families in Shenyang, China. BIOMEDICAL AND ENVIRONMENTAL SCIENCES : BES 2010; 23:363-370. [PMID: 21112484 DOI: 10.1016/s0895-3988(10)60077-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Accepted: 07/12/2010] [Indexed: 05/30/2023]
Abstract
OBJECTIVES To identify the loci involved in nonsyndromic cleft lip with or without cleft palate (NSCL/P) in Northern Chinese people in Shenyang by using genomewide and interaction linkage scan. METHODS Two multiplex families in Shenyang from North China were ascertained through probands with NSCL/P. Blood of every member was drawn for DNA extraction and analysis. Genotypes were available for 382 autosomal short tandem repeat (STR) markers from the ABI Prism Linkage Mapping Set version 2.5. Linkage between markers and NSCL/P was assessed by 2-point parametric LOD scores, multipoint-heterogeneity parametric LOD scores (HLODs), and multipoint nonparametric linkage score (NPL). RESULTS The initial scan suggested linkage on Chromosomes 1, 2, and 15. In subsequent fine mapping, 1q32-q42 showed a maximum multipoint LOD score of 1.9(empirical P=0.013) and an NPL score of 2.35 (empirical P=0.053). For 2p24-p25, the multipoint NPL increased to 2.94 (empirical P=0.007). 2-locus interaction analysis obtained a maximum NPL score of 3.73 (P=0.00078) and a maximum LOD score of 3 for Chromosome 1 (at 221 cM) and Chromosome 2 (at 29 cM). CONCLUSION Both parametric and nonparametric linkage scores greatly increased over the initial linkage scores on 1q32-q42, suggesting a susceptibility locus in this region. Nonparametric linkage gave a strong evidence for a candidate region on chromosome 2p24-p25. The superiority of 2-locus linkage scores compared to single-locus scores gave additional evidence for linkage on 1q32-q42 and 2p24-p25, and suggested that certain genes in the two regions may contribute to NCSL/P risks with interaction.
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Affiliation(s)
- Yun Wang
- Department of Nutrition and Food Hygiene, School of Public Health, Peking University Health Science Centre, Beijing 100191, China
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20
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Evidence of gene-environment interaction for the IRF6 gene and maternal multivitamin supplementation in controlling the risk of cleft lip with/without cleft palate. Hum Genet 2010; 128:401-10. [PMID: 20652317 DOI: 10.1007/s00439-010-0863-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Accepted: 07/11/2010] [Indexed: 10/19/2022]
Abstract
Although multiple genes have been identified as genetic risk factors for isolated, non-syndromic cleft lip with/without cleft palate (CL/P), a complex and heterogeneous birth defect, interferon regulatory factor 6 gene (IRF6) is one of the best documented genetic risk factors. In this study, we tested for association between markers in IRF6 and CL/P in 326 Chinese case-parent trios, considering gene-environment interaction for two common maternal exposures, and parent-of-origin effects. CL/P case-parent trios from three sites in mainland China and Taiwan were genotyped for 22 single nucleotide polymorphisms (SNPs) in IRF6. The transmission disequilibrium test was used to test for marginal effects of individual SNPs. We used PBAT to screen the SNPs and haplotypes for gene-environment (G×E) interaction and conditional logistic regression models to quantify effect sizes for SNP-environment interaction. After Bonferroni correction, 14 SNPs showed statistically significant association with CL/P. Evidence of G×E interaction was found for both maternal exposures, multivitamin supplementation and environmental tobacco smoke (ETS). Two SNPs showed evidence of interaction with multivitamin supplementation in conditional logistic regression models (rs2076153 nominal P=0.019, rs17015218 nominal P=0.012). In addition, rs1044516 yielded evidence for interaction with maternal ETS (nominal P=0.041). Haplotype analysis using PBAT also suggested interaction between SNPs in IRF6 and both multivitamin supplementation and ETS. However, no evidence for maternal genotypic effects or significant parent-of-origin effects was seen in these data. These results suggest IRF6 gene may influence risk of CL/P through interaction with multivitamin supplementation and ETS in the Chinese population.
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21
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Marinucci L, Balloni S, Carinci F, Locci P, Pezzetti F, Bodo M. Diazepam effects on non-syndromic cleft lip with or without palate: epidemiological studies, clinical findings, genes and extracellular matrix. Expert Opin Drug Saf 2010; 10:23-33. [PMID: 20645675 DOI: 10.1517/14740338.2010.506478] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
IMPORTANCE OF THE FIELD This review analyses international studies investigating the combined genetic and environmental causes of cleft lip with or without cleft palate (CL/P) and describes successes and limitations in identifying underlying genetic and environmental factors. CL/P, the most common congenital facial malformation, is a major public health burden in terms of medical costs and emotional stress to patients and families. Because genetic and environmental factors determine risk of occurrence, CL/P has a complex, multifactor aetiology. AREAS COVERED IN THIS REVIEW English language reports from 1980 to 2010 were searched for in Medline, PubMed, Science Citation Index, textbooks and review articles on drugs and pregnancy. Key words were diazepam or benzodiazepine(s) combined with cleft lip, cleft palate, oral malformations, prenatal exposure, GABA, gene expression and extracellular matrix. WHAT THE READER WILL GAIN This review presents an updated assessment of the mutagenic and genotoxic effects of diazepam (DZ), one of the most commonly used benzodiazepines, on CL/P occurrence. TAKE HOME MESSAGE Data are divergent; more studies are needed for an in-depth picture of the effects of DZ during gestation on the child's development, particularly on orofacial clefts.
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Affiliation(s)
- Lorella Marinucci
- Department of Experimental Medicine and Biochemical Sciences, Section of Histology and Embryology, Faculty of Medicine, University of Perugia, via del Giochetto, Perugia, Italy.
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22
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Mostowska A, Hozyasz KK, Wojcicki P, Biedziak B, Paradowska P, Jagodzinski PP. Association between genetic variants of reported candidate genes or regions and risk of cleft lip with or without cleft palate in the polish population. ACTA ACUST UNITED AC 2010; 88:538-45. [DOI: 10.1002/bdra.20687] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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23
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Desmyter L, Ghassibe M, Revencu N, Boute O, Lees M, François G, Verellen-Dumoulin C, Sznajer Y, Moncla A, Benateau H, Claes K, Devriendt K, Mathieu M, Van Maldergem L, Addor MC, Drouin-Garraud V, Mortier G, Bouma M, Dieux-Coeslier A, Genevieve D, Goldenberg A, Gozu A, Makrythanasis P, McEntagart U, Sanchez A, Vilain C, Vermeer S, Connell F, Verheij J, Manouvrier S, Pierquin G, Odent S, Holder-Espinasse M, Vincent-Delorme C, Gillerot Y, Vanwijck R, Bayet B, Vikkula M. IRF6 Screening of Syndromic and a priori Non-Syndromic Cleft Lip and Palate Patients: Identification of a New Type of Minor VWS Sign. Mol Syndromol 2010; 1:67-74. [PMID: 21045959 DOI: 10.1159/000313786] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Van der Woude syndrome (VWS), caused by dominant IRF6 mutation, is the most common cleft syndrome. In 15% of the patients, lip pits are absent and the phenotype mimics isolated clefts. Therefore, we hypothesized that some of the families classified as having non-syndromic inherited cleft lip and palate could have an IRF6 mutation. We screened in total 170 patients with cleft lip with or without cleft palate (CL/P): 75 were syndromic and 95 were a priori part of multiplex non-syndromic families. A mutation was identified in 62.7 and 3.3% of the patients, respectively. In one of the 95 a priori non-syndromic families with an autosomal dominant inheritance (family B), new insights into the family history revealed the presence, at birth, of lower lip pits in two members and the diagnosis was revised as VWS. A novel lower lip sign was observed in one individual in this family. Interestingly, a similar lower lip sign was also observed in one individual from a 2nd family (family A). This consists of 2 nodules below the lower lip on the external side. In a 3rd multiplex family (family C), a de novo mutation was identified in an a priori non-syndromic CL/P patient. Re-examination after mutation screening revealed the presence of a tiny pit-looking lesion on the inner side of the lower lip leading to a revised diagnosis of VWS. On the basis of this data, we conclude that IRF6 should be screened when any doubt rises about the normality of the lower lip and also if a non-syndromic cleft lip patient (with or without cleft palate) has a family history suggestive of autosomal dominant inheritance.
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Affiliation(s)
- L Desmyter
- Laboratory of Human Molecular Genetics, de Duve Institute, Belgium, France
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A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4. Nat Genet 2010; 42:525-9. [PMID: 20436469 DOI: 10.1038/ng.580] [Citation(s) in RCA: 452] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 04/06/2010] [Indexed: 01/10/2023]
Abstract
Case-parent trios were used in a genome-wide association study of cleft lip with and without cleft palate. SNPs near two genes not previously associated with cleft lip with and without cleft palate (MAFB, most significant SNP rs13041247, with odds ratio (OR) per minor allele = 0.704, 95% CI 0.635-0.778, P = 1.44 x 10(-11); and ABCA4, most significant SNP rs560426, with OR = 1.432, 95% CI 1.292-1.587, P = 5.01 x 10(-12)) and two previously identified regions (at chromosome 8q24 and IRF6) attained genome-wide significance. Stratifying trios into European and Asian ancestry groups revealed differences in statistical significance, although estimated effect sizes remained similar. Replication studies from several populations showed confirming evidence, with families of European ancestry giving stronger evidence for markers in 8q24, whereas Asian families showed stronger evidence for association with MAFB and ABCA4. Expression studies support a role for MAFB in palatal development.
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25
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Paranaíba LMR, Bufalino A, Martelli-Júnior H, de Barros LM, Graner E, Coletta RD. Lack of association betweenIRF6polymorphisms (rs2235371 and rs642961) and non-syndromic cleft lip and/or palate in a Brazilian population. Oral Dis 2010; 16:193-7. [DOI: 10.1111/j.1601-0825.2009.01627.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Neiswanger K, Walker K, Chirigos KW, Klotz CM, Cooper ME, Bardi KM, Brandon CA, Weinberg SM, Vieira AR, Martin RA, Czeizel AE, Castilla EE, Poletta FA, Marazita ML. Whorl patterns on the lower lip are associated with nonsyndromic cleft lip with or without cleft palate. Am J Med Genet A 2010; 149A:2673-9. [PMID: 19921634 DOI: 10.1002/ajmg.a.33089] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Nonsyndromic cleft lip with or without cleft palate (CL/P) is a common birth defect due to both genetic and environmental factors. Whorl lip print patterns are circular grooves on the central upper lip and/or the left and right lower lip. To determine if whorls are more common in families with CL/P than in controls, the Pittsburgh Orofacial Cleft Study collected lip prints from over 450 subjects, that is, individuals with CL/P, their relatives, and unrelated controls-from the U.S., Argentina, and Hungary. Using a narrow definition of lower-lip whorl, the frequency of whorls in the U.S. sample was significantly elevated in cleft individuals and their family members, compared to unrelated controls (14.8% and 13.2% vs. 2.3%; P = 0.003 and 0.001, respectively). Whorls were more frequent in CL/P families from Argentina than in CL/P families from the U.S. or Hungary. If these results are confirmed, whorl lip print patterns could be part of an expanded phenotypic spectrum of nonsyndromic CL/P. As such, they may eventually be useful in a clinical setting, allowing recurrence risk calculations to incorporate individual phenotypic information in addition to family history data.
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Affiliation(s)
- Katherine Neiswanger
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA 14219, USA.
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27
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Abstract
Clefts of the lip and palate are generally divided into two groups, isolated cleft palate and cleft lip with or without cleft palate, representing a heterogeneous group of disorders affecting the lips and oral cavity. These defects arise in about 1.7 per 1000 liveborn babies, with ethnic and geographic variation. Effects on speech, hearing, appearance, and psychology can lead to longlasting adverse outcomes for health and social integration. Typically, children with these disorders need multidisciplinary care from birth to adulthood and have higher morbidity and mortality throughout life than do unaffected individuals. This Seminar describes embryological developmental processes, epidemiology, known environmental and genetic risk factors, and their interaction. Although access to care has increased in recent years, especially in developing countries, quality of care still varies substantially. Prevention is the ultimate objective for clefts of the lip and palate, and a prerequisite of this aim is to elucidate causes of the disorders. Technological advances and international collaborations have yielded some successes.
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Affiliation(s)
- Peter A Mossey
- Department of Dental and Oral Health, University of Dundee, Dental Hospital and School, Dundee, UK.
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28
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Birnbaum S, Ludwig KU, Reutter H, Herms S, De Assis NA, Diaz-Lacava A, Barth S, Lauster C, Schmidt G, Scheer M, Saffar M, Martini M, Reich RH, Schiefke F, Hemprich A, Pötzsch S, Pötzsch B, Wienker TF, Hoffmann P, Knapp M, Kramer FJ, Nöthen MM, Mangold E. IRF6gene variants in Central European patients with non-syndromic cleft lip with or without cleft palate. Eur J Oral Sci 2009; 117:766-9. [DOI: 10.1111/j.1600-0722.2009.00680.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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29
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Marazita ML, Lidral AC, Murray JC, Field LL, Maher BS, Goldstein McHenry T, Cooper ME, Govil M, Daack-Hirsch S, Riley B, Jugessur A, Felix T, Morene L, Mansilla MA, Vieira AR, Doheny K, Pugh E, Valencia-Ramirez C, Arcos-Burgos M. Genome scan, fine-mapping, and candidate gene analysis of non-syndromic cleft lip with or without cleft palate reveals phenotype-specific differences in linkage and association results. Hum Hered 2009; 68:151-70. [PMID: 19521098 DOI: 10.1159/000224636] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Accepted: 02/12/2009] [Indexed: 01/11/2023] Open
Abstract
OBJECTIVES Non-syndromic orofacial clefts, i.e. cleft lip (CL) and cleft palate (CP), are among the most common birth defects. The goal of this study was to identify genomic regions and genes for CL with or without CP (CL/P). METHODS We performed linkage analyses of a 10 cM genome scan in 820 multiplex CL/P families (6,565 individuals). Significant linkage results were followed by association analyses of 1,476 SNPs in candidate genes and regions, utilizing a weighted false discovery rate (wFDR) approach to control for multiple testing and incorporate the genome scan results. RESULTS Significant (multipoint HLOD >or=3.2) or genome-wide-significant (HLOD >or=4.02) linkage results were found for regions 1q32, 2p13, 3q27-28, 9q21, 12p11, 14q21-24 and 16q24. SNPs in IRF6 (1q32) and in or near FOXE1 (9q21) reached formal genome-wide wFDR-adjusted significance. Further, results were phenotype dependent in that the IRF6 region results were most significant for families in which affected individuals have CL alone, and the FOXE1 region results were most significant in families in which some or all of the affected individuals have CL with CP. CONCLUSIONS These results highlight the importance of careful phenotypic delineation in large samples of families for genetic analyses of complex, heterogeneous traits such as CL/P.
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Affiliation(s)
- Mary L Marazita
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA.
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30
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Candidate gene/loci studies in cleft lip/palate and dental anomalies finds novel susceptibility genes for clefts. Genet Med 2009; 10:668-74. [PMID: 18978678 DOI: 10.1097/gim.0b013e3181833793] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
PURPOSE We revisited 42 families with two or more cleft-affected siblings who participated in previous studies. Complete dental information was collected to test the hypothesis that dental anomalies are part of the cleft phenotype spectrum, and can provide new opportunities for identification of cleft susceptibility genes. METHODS Genotypes from 1489 single nucleotide polymorphism markers located in 150 candidate genes/loci were reanalyzed. Two sets of association analyses were carried out. First, we ran the analysis solely on the cleft status. Second, we assigned affection to any cleft or dental anomaly (tooth agenesis, supernumerary teeth, and microdontia) and repeated the analysis. RESULTS Significant over-transmission was seen for a single nucleotide polymorphism in ankyrin repeat and sterile alpha motif domain containing 6 (rs4742741, 9q22.33; P = 0.0004) when a dental anomaly phenotype was included in the analysis. Significant over-transmission was also seen for a single nucleotide polymorphism in ERBB2 (rs1810132, 17q21.1; P = 0.0006). In the clefts only data, the most significant result was also for ERBB2 (P = 0.0006). Other markers with suggestive P values included interferon regulatory factor 6 and 6q21-q23 loci. In contrast to the above results, suggestive over-transmission of markers in GART, DPF3, and neurexin 3 were seen only when the dental anomaly phenotype was included in the analysis. CONCLUSIONS These findings support the hypothesis that some loci may contribute to both clefts and congenital dental anomalies. Thus, including dental anomalies information in the genetics analysis of cleft lip and palate will provide new opportunities to map susceptibility loci for clefts.
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Tang W, Du X, Feng F, Long J, Lin Y, Li P, Liu L, Tian W. Association analysis between the IRF6 G820A polymorphism and nonsyndromic cleft lip and/or cleft palate in a Chinese population. Cleft Palate Craniofac J 2009; 46:89-92. [PMID: 19115793 DOI: 10.1597/07-131.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVE To investigate whether an association occurred between the IRF6 G820A polymorphism and nonsyndromic cleft lip with or without cleft palate (CL+/-P) or cleft palate only (CPO) in Chinese patients. DESIGN AND SETTING Case-controlled study at the West China Hospital of Stomatology, Sichuan University, China. SUBJECTS A total of 91 patients with cleft lip and/or palate (CL/P) and 96 unrelated, healthy individuals with no family history of CL/P were genotyped. METHODS The IRF6 G820A polymorphism was genotyped by restriction digestion of polymerase chain reaction products with BseLI. Chi-square statistics were used to make case-controlled comparisons. RESULTS The frequency of the A allele was significantly increased and the frequency of the G allele was reduced in CPO patients in comparison with control subjects. The 820GG genotype had a significantly lower frequency in patients with CPO than in controls, with an odds ratio of 0.25 (95% confidence interval, -0.061 to 0.57). No difference in the distribution of genotypes was noted between CL+/-P patients and the total group of CL/P patients compared with controls. CONCLUSIONS The present findings indicate that the 820A allele is more frequent in the Chinese CPO population and may confer an increased risk for CPO in these individuals. The G820A variant may be in linkage disequilibrium with other disorder-causing mutations. CL+/-P or CPO results should be analyzed separately and stratified in future studies.
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Affiliation(s)
- Wei Tang
- State Key Laboratory of Oral Diseases, Sichuan University, Chengdu, China
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Suazo J, Santos JL, Jara L, Blanco R. Linkage disequilibrium betweenIRF6variants and nonsyndromic cleft lip/palate in the Chilean population. Am J Med Genet A 2008; 146A:2706-8. [DOI: 10.1002/ajmg.a.32494] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Vieira AR, McHenry TG, Daack-Hirsch S, Murray JC, Marazita ML. A genome wide linkage scan for cleft lip and palate and dental anomalies. Am J Med Genet A 2008; 146A:1406-13. [PMID: 18442096 DOI: 10.1002/ajmg.a.32295] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We revisited 46 families with two or more siblings affected with an orofacial cleft that participated in previous genome wide studies and collected complete dental information. Genotypes from 392 microsatellite markers at 10 cM intervals were reanalyzed. We carried out four sets of genome wide analyses. First, we ran the analysis solely on the cleft status. Second, we assigned to any dental anomaly (tooth agenesis, supernumerary teeth, and microdontia) an affection status, and repeated the analysis. Third, we ran only the 19 families where the proband had a cleft with no dental anomalies. Finally, we ran only the 27 families that had a proband with cleft and additional dental anomalies outside the cleft area. Chromosomes (1, 2, 6, 8, 16, and 19) presented regions with LOD scores >2.0. Chromosome 19 has the most compelling results in our study. The LOD scores increased from 3.11 (in the scan of all 46 families with clefts as the only assigned affection status) to 3.91 when the 19 families whose probands present with no additional dental anomalies were studied, suggesting the interval 19p13.12-19q12 may contain a gene that contributes to clefts but not to dental anomalies. On the other hand, we found a LOD score of 3.00 in the 2q22.3 region when dental anomalies data were added to the analysis to define affection status. Our preliminary results support the hypothesis that some loci may contribute to both clefts and congenital dental anomalies. Also, adding dental anomalies information will provide new opportunities to map susceptibility loci for clefts.
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Affiliation(s)
- Alexandre R Vieira
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA.
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Abstract
The focus of this work is to highlight the most recent advances in the understanding of cleft lip and palate occurrence. Information regarding research on long-term outcomes, genes and their interactions with other genes, and gene-environment interactions is compiled to provide the reader with a critical and up-to-date overview on the current knowledge of the etiology of cleft lip and palate. Recent epidemiological evidence strongly suggests that individuals born with clefts have a shorter lifespan and may have a higher incidence of cancer and psychological disorders. IRF6 has been shown to be an important contributor to cleft lip and palate, but the functional variant leading to the defect has not yet been defined. Inactivation of MSX1 and genes in the FGF family has also been shown to lead to cleft lip and palate. In addition, missense mutations in several candidate genes may cause cleft lip and palate, but definitive evidence regarding the biological consequences of these mutations is yet to be unraveled. Maternal cigarette smoking increases the risk of a baby born with clefts, in particular when the mother carries the GSTT1-null variants. The latest approaches in cleft research include the analysis of several additional phenotypical features of the population, with the goal of increasing the statistical power of genetics studies.
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Affiliation(s)
- A R Vieira
- Departments of Oral Biology and Pediatric Dentistry, School of Dental Medicine, University of Pittsburgh, PA 15261, USA.
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