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Pham LNG, Niimi T, Suzuki S, Nguyen MD, Nguyen LCH, Nguyen TD, Hoang KA, Nguyen DM, Sakuma C, Hayakawa T, Hiyori M, Natsume N, Furukawa H, Imura H, Akashi J, Ohta T, Natsume N. Association between IRF6, TP63, GREM1 Gene Polymorphisms and Non-Syndromic Orofacial Cleft Phenotypes in Vietnamese Population: A Case-Control and Family-Based Study. Genes (Basel) 2023; 14:1995. [PMID: 38002937 PMCID: PMC10671090 DOI: 10.3390/genes14111995] [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: 10/03/2023] [Revised: 10/18/2023] [Accepted: 10/24/2023] [Indexed: 11/26/2023] Open
Abstract
This study aims to identify potential variants in the TP63-IRF6 pathway and GREM1 for the etiology of non-syndromic orofacial cleft (NSOFC) among the Vietnamese population. By collecting 527 case-parent trios and 527 control samples, we conducted a stratified analysis based on different NSOFC phenotypes, using allelic, dominant, recessive and over-dominant models for case-control analyses, and family-based association tests for case-parent trios. Haplotype and linkage disequilibrium analyses were also conducted. IRF6 rs2235375 showed a significant association with an increased risk for non-syndromic cleft lip and palate (NSCLP) and cleft lip with or without cleft palate (NSCL/P) in the G allele, with pallele values of 0.0018 and 0.0003, respectively. Due to the recessive model (p = 0.0011) for the NSCL/P group, the reduced frequency of the GG genotype of rs2235375 was associated with a protective effect against NSCL/P. Additionally, offspring who inherited the G allele at rs2235375 had a 1.34-fold increased risk of NSCL/P compared to the C allele holders. IRF6 rs846810 and a G-G haplotype at rs2235375-rs846810 of IRF6 impacted NSCL/P, with p-values of 0.0015 and 0.0003, respectively. In conclusion, our study provided additional evidence for the association of IRF6 rs2235375 with NSCLP and NSCL/P. We also identified IRF6 rs846810 as a novel marker associated with NSCL/P, and haplotypes G-G and C-A at rs2235375-rs846810 of IRF6 associated with NSOFC.
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Affiliation(s)
- Loc Nguyen Gia Pham
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, Aichi Gakuin University, 2–11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (L.N.G.P.); (T.N.); (S.S.); (D.M.N.); (C.S.); (N.N.); (H.I.)
- Odonto-Maxillo Facial Hospital of Ho Chi Minh City, 263-265 Tran Hung Dao Street, District 1, Ho Chi Minh City 71000, Vietnam; (M.D.N.); (L.C.H.N.); (T.D.N.); (K.A.H.)
| | - Teruyuki Niimi
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, Aichi Gakuin University, 2–11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (L.N.G.P.); (T.N.); (S.S.); (D.M.N.); (C.S.); (N.N.); (H.I.)
- Cleft Lip and Palate Center, Aichi Gakuin Dental Hospital, 2-11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan;
- Division of Speech, Hearing, and Language, Aichi Gakuin Dental Hospital, 2-11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (T.H.); (M.H.)
| | - Satoshi Suzuki
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, Aichi Gakuin University, 2–11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (L.N.G.P.); (T.N.); (S.S.); (D.M.N.); (C.S.); (N.N.); (H.I.)
| | - Minh Duc Nguyen
- Odonto-Maxillo Facial Hospital of Ho Chi Minh City, 263-265 Tran Hung Dao Street, District 1, Ho Chi Minh City 71000, Vietnam; (M.D.N.); (L.C.H.N.); (T.D.N.); (K.A.H.)
| | - Linh Cao Hoai Nguyen
- Odonto-Maxillo Facial Hospital of Ho Chi Minh City, 263-265 Tran Hung Dao Street, District 1, Ho Chi Minh City 71000, Vietnam; (M.D.N.); (L.C.H.N.); (T.D.N.); (K.A.H.)
| | - Tuan Duc Nguyen
- Odonto-Maxillo Facial Hospital of Ho Chi Minh City, 263-265 Tran Hung Dao Street, District 1, Ho Chi Minh City 71000, Vietnam; (M.D.N.); (L.C.H.N.); (T.D.N.); (K.A.H.)
| | - Kien Ai Hoang
- Odonto-Maxillo Facial Hospital of Ho Chi Minh City, 263-265 Tran Hung Dao Street, District 1, Ho Chi Minh City 71000, Vietnam; (M.D.N.); (L.C.H.N.); (T.D.N.); (K.A.H.)
| | - Duc Minh Nguyen
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, Aichi Gakuin University, 2–11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (L.N.G.P.); (T.N.); (S.S.); (D.M.N.); (C.S.); (N.N.); (H.I.)
- School of Odonto-Stomatology, Hanoi Medical University, Hanoi 10000, Vietnam
| | - Chisato Sakuma
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, Aichi Gakuin University, 2–11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (L.N.G.P.); (T.N.); (S.S.); (D.M.N.); (C.S.); (N.N.); (H.I.)
- Cleft Lip and Palate Center, Aichi Gakuin Dental Hospital, 2-11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan;
- Division of Speech, Hearing, and Language, Aichi Gakuin Dental Hospital, 2-11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (T.H.); (M.H.)
| | - Toko Hayakawa
- Division of Speech, Hearing, and Language, Aichi Gakuin Dental Hospital, 2-11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (T.H.); (M.H.)
| | - Makino Hiyori
- Division of Speech, Hearing, and Language, Aichi Gakuin Dental Hospital, 2-11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (T.H.); (M.H.)
| | - Nagana Natsume
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, Aichi Gakuin University, 2–11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (L.N.G.P.); (T.N.); (S.S.); (D.M.N.); (C.S.); (N.N.); (H.I.)
- Cleft Lip and Palate Center, Aichi Gakuin Dental Hospital, 2-11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan;
- Division of Speech, Hearing, and Language, Aichi Gakuin Dental Hospital, 2-11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (T.H.); (M.H.)
| | - Hiroo Furukawa
- Cleft Lip and Palate Center, Aichi Gakuin Dental Hospital, 2-11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan;
- Division of Speech, Hearing, and Language, Aichi Gakuin Dental Hospital, 2-11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (T.H.); (M.H.)
| | - Hideto Imura
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, Aichi Gakuin University, 2–11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (L.N.G.P.); (T.N.); (S.S.); (D.M.N.); (C.S.); (N.N.); (H.I.)
- Cleft Lip and Palate Center, Aichi Gakuin Dental Hospital, 2-11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan;
- Division of Speech, Hearing, and Language, Aichi Gakuin Dental Hospital, 2-11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (T.H.); (M.H.)
| | - Junko Akashi
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, Aichi Gakuin University, 2–11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (L.N.G.P.); (T.N.); (S.S.); (D.M.N.); (C.S.); (N.N.); (H.I.)
| | - Tohru Ohta
- Advanced Research Promotion Center, Health Sciences University of Hokkaido, Ishikari-Tobetsu 061-0293, Japan;
| | - Nagato Natsume
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, Aichi Gakuin University, 2–11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (L.N.G.P.); (T.N.); (S.S.); (D.M.N.); (C.S.); (N.N.); (H.I.)
- Cleft Lip and Palate Center, Aichi Gakuin Dental Hospital, 2-11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan;
- Division of Speech, Hearing, and Language, Aichi Gakuin Dental Hospital, 2-11 Suemori-dori, Chikusa-ku, Nagoya 464-8651, Japan; (T.H.); (M.H.)
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Li MJ, Kumari P, Lin YS, Yao ML, Zhang BH, Yin B, Duan SJ, Cornell RA, Marazita ML, Shi B, Jia ZL. A Variant in the IRF6 Promoter Associated with the Risk for Orofacial Clefting. J Dent Res 2023:220345231165210. [PMID: 37161310 PMCID: PMC10399074 DOI: 10.1177/00220345231165210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
The single-nucleotide polymorphism (SNP) rs2235371 (IRF6 V274I) is associated with nonsyndromic cleft lip with or without cleft palate (NSCL/P) in Han Chinese and other populations but appears to be without a functional effect. To find the common etiologic variant or variants within the haplotype tagged by rs2235371, we carried out targeted sequencing of an interval containing IRF6 in 159 Han Chinese with NSCL/P. This study revealed that the SNP rs12403599, within the IRF6 promoter, is associated with all phenotypes of NSCL/P, especially nonsyndromic cleft lip (NSCLO) and a subphenotype of it, microform cleft lip (MCL). This association was replicated in 2 additional much larger cohorts of cases and controls from the Han Chinese. Conditional logistic analysis indicated that association of rs2235371 with NSCL/P was lost if rs12403599 was excluded. rs12403599 contributes the most risk to MCL: its G allele is responsible for 38.47% of the genetic contribution to MCL, and the odds ratios of G/C and G/G genotypes were 2.91 and 6.58, respectively, for MCL. To test if rs12403599 is functional, we carried out reporter assays in a fetal oral epithelium cells (GMSM-K). Unexpectedly, the risk allele G yielded higher promoter activity in GMSM-K. Consistent with the reporter studies, expression of IRF6 in lip tissues from NSCLO and MCL patients with the G/G phenotype was higher than in those from patients with the C/C phenotype. These results indicate that rs12403599 is tagging the risk haplotype for NSCL/P better than rs2235371 in Han Chinese and supports investigation of the mechanisms by which the allele of rs12403599 affects IRF6 expression and tests of this association in different populations.
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Affiliation(s)
- M-J Li
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - P Kumari
- Department of Oral Health Sciences, University of Washington, Seattle, WA, USA
| | - Y-S Lin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - M-L Yao
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - B-H Zhang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - B Yin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - S-J Duan
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - R A Cornell
- Department of Oral Health Sciences, University of Washington, Seattle, WA, USA
| | - M L Marazita
- Centre for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - B Shi
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Z-L Jia
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of Cleft Lip and Palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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Zawiślak A, Woźniak K, Kawala B, Gupta S, Znamirowska-Bajowska A, Janiszewska-Olszowska J, Lubiński J, Calvo-Guirado JL, Grocholewicz K, Jakubowska A. IRF6 and FGF1 polymorphisms in non-syndromic cleft lip with or without cleft palate in the Polish population. Open Med (Wars) 2023; 18:20230677. [PMID: 37020525 PMCID: PMC10068750 DOI: 10.1515/med-2023-0677] [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: 08/06/2022] [Revised: 12/26/2022] [Accepted: 02/06/2023] [Indexed: 04/05/2023] Open
Abstract
Non-syndromic cleft lip with or without cleft palate (NSCL/P) is the most common developmental defect that significantly affects the morphology and function of the stomatognathic system in children. The etiology of these birth defects is multifactorial, and single nucleotide polymorphisms (SNPs) in IRF6 and FGF1 have been associated with NSCL/P. This study aimed to evaluate whether SNPs in IRF6, namely rs2013162, rs642961, rs2235373, and rs34010 in FGF1, are associated with NSCL/P occurrence in the Polish population. The study included 627 participants: 209 children with NSCL/P and 418 healthy controls. DNA was isolated from saliva in the study group and from umbilical cord blood in controls. Genotyping of polymorphisms was performed using quantitative PCR. There was no statistically significant association of IRF6 gene variants with NSCL/P occurrence, although for rs2013162, AA genotype, odds ratio (OR) = 1.16 and for AC genotype, OR = 0.83; for rs642961, AA genotype, OR = 0.84 and for AG genotype, OR = 1.41; and for rs2235373, AA genotype, OR = 0.79 and for AG, OR = 0.85. In the instance of rs34010 polymorphism in FGF1, the presence of the AA genotype was statistically significant in reducing the risk of NSCL/P (OR = 0.31, p = 0.001). Genetic variation in FGF1 is an important risk marker of NSCL/P in the Polish population, which cannot be stated for the polymorphisms in the IRF6 gene.
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Affiliation(s)
- Alicja Zawiślak
- Department of Maxillofacial Orthopaedics and Orthodontics, Institute of Mother and Child, 01-211 Warsaw, Poland
- Department of Interdisciplinary Dentistry, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Krzysztof Woźniak
- Department of Orthodontics, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Beata Kawala
- Department of Dentofacial Orthopaedics and Orthodontics, Wrocław Medical University, 50-425 Wrocław, Poland
| | - Satish Gupta
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Anna Znamirowska-Bajowska
- Department of Dentofacial Orthopaedics and Orthodontics, Wrocław Medical University, 50-425 Wrocław, Poland
| | | | - Jan Lubiński
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - José Luis Calvo-Guirado
- Department of Oral Surgery and Implant Dentistry, Faculty of Health Sciences, Universidad Católica de Murcia, UCAM, 30107, Murcia, Spain
| | - Katarzyna Grocholewicz
- Department of Interdisciplinary Dentistry, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Anna Jakubowska
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
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Zhang S, Chen Q, Yang C, Shi J, Lin Y, Duan S, Shi B, Jia Z. Association between variants around IRF6 and non-syndromic orofacial cleft in Western Han Chinese. Oral Dis 2023; 29:1115-1127. [PMID: 34894020 DOI: 10.1111/odi.14100] [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: 08/20/2021] [Revised: 11/21/2021] [Accepted: 11/25/2021] [Indexed: 02/05/2023]
Abstract
OBJECTIVES Considering limitations of previous studies and differences across populations and subtypes, this study aimed to identify new potential SNPs around IRF6 associated with non-syndromic orofacial cleft (NSOC) in Western Han Chinese. MATERIALS AND METHODS We recruited 376 NSOC case-parent trios, including 125 non-syndromic cleft lip only (NSCLO) trios, 151 non-syndromic cleft lip and palate (NSCLP) trios, and 100 non-syndromic cleft palate only (NSCPO) trios. Twenty-two single-nucleotide polymorphisms (SNPs) were genotyped using MassARRAY method. Hardy-Weinberg equilibrium test, allelic transmission disequilibrium test (TDT) analysis, sliding-window haplotype TDT analysis, and tests for parent-of-origin effect were performed using the PLINK software. Pairwise linkage disequilibrium (LD) was computed using the Haploview program. RESULTS In TDT analysis, allele A at rs17015217 (p = 0.00011, OR = 0.61 and 95% CI: 0.47-0.78) and allele T at rs12080691 (p = 0.00011, OR = 0.61 and 95% CI: 0.47-0.78) were under-transmitted among NSCLO trios but over-transmitted among NSCPO trios. Haplotypes showing evidence of under-transmission in NSCLO trios were over-transmitted in NSCPO trios. In tests for parent-of-origin effects, T allele at rs12080691 presented paternal under-transmission among NSCLO trios but over-transmission among NSCPO trios. CONCLUSIONS Allele A at rs17015217 and allele T at rs12080691 are associated with NSCLO and NSCPO with potential to have opposite effects on two subtypes in this sample from Western Han Chinese.
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Affiliation(s)
- Sidi Zhang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, China
| | - Qianming Chen
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, China
| | - Chao Yang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, China
| | - Jiayu Shi
- Division of Growth and Development and Section of Orthodontics, School of Dentistry, University of California, Los Angeles, California, USA
| | - Yansong Lin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, China
| | - Shijun Duan
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, China
| | - Bing Shi
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, China
| | - Zhonglin Jia
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, China
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Phan HDB, Phuong LH, Dang TN, Tram DB, Vu HA. Association of single nucleotide polymorphisms in the IRF6 gene with nonsyndromic cleft lip with or without cleft palate in Kinh Vietnamese patients. Mol Biol Rep 2023; 50:1469-1476. [PMID: 36484949 DOI: 10.1007/s11033-022-08164-9] [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: 07/10/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND The interferon regulatory factor 6 (IRF6) gene, which causes Van der Woude syndrome, is associated with nonsyndromic cleft lip with or without cleft palate (NSCL/P). Single nucleotide polymorphisms (SNPs) in the IRF6 gene were identified as susceptibility indicators of this defect in several populations. To further evaluate its role in this birth defect, we conducted this study with the aim of identifying allele frequencies, genotype frequencies, and associations of 5 SNPs (rs2235373, rs2235371, rs2235375, rs2013162, and rs2236907) in the IRF6 gene with NSCL/P in Kinh Vietnamese patients. METHODS A total of 132 patients with NSCL/P and 132 healthy individuals were included in our study group. Direct sequencing was performed to genotype the tag SNPs. Genetic models were used to compare genotype and allele frequencies between the case and control groups. RESULTS In the recessive model, the genotypes C/C of rs2236907, C/C of rs2013162, G/G of rs2235375, and A/A of rs2235373 were associated with an increased risk of NSCL/P, whereas there was no clear association between rs2235371 and the malformation in any genetic model. When subgroup analysis was performed, we observed a similar risk trend in the cleft lip and palate, cleft palate only and cleft lip only phenotypes. In haplotype analysis, haplotype models of 5 tag SNPs were associated with increased risks of this defect in all phenotypic models (ORGCGCC/CCAA = 23.64, 95% CI 12.28-45.49, p < 0.0001). CONCLUSIONS These findings point to a considerable contribution of rs2236907, rs2013162, rs2235373, and rs2235375 to the NSCL/P defect in Kinh Vietnamese individuals.
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Affiliation(s)
- Hoanh Duy Ba Phan
- Faculty of Odonto-Stomatology, National University Ho Chi Minh City, Ho Chi Minh City, Vietnam.,Department of Oral and Maxillofacial Surgery, University Medical Center, Ho Chi Minh City, Vietnam
| | - Lam Hoai Phuong
- Faculty of Odonto-Stomatology, Hong Bang International University, Ho Chi Minh City, Vietnam
| | - Tran Ngoc Dang
- Faculty of Public Health, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Duong Bich Tram
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Hoang Anh Vu
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam.
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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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Goida J, Pilmane M. The Evaluation of FGFR1, FGFR2 and FOXO1 in Orofacial Cleft Tissue. CHILDREN 2022; 9:children9040516. [PMID: 35455561 PMCID: PMC9032315 DOI: 10.3390/children9040516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 11/21/2022]
Abstract
Although cleft lip with or without cleft palate (CL/P) is one of the most common congenital anomalies worldwide, the morphopathogenesis of non-syndromic orofacial clefts is still unclear. Many candidate genes have been proposed to play a causal role; however, only a few have been confirmed, leaving many still to be assessed. Taking into account the significance of FGFR1, FGFR2 and FOXO1 in embryogenesis, the aim of this work was to detect and compare the three candidate genes in cleft-affected lip and palatine tissue. Ten soft tissue samples were taken during cheiloplasty and veloplasty. The signals of the candidate genes were visualized using chromogenic in situ hybridization and analyzed using a semi-quantitative method. No statistically important difference in the distribution of FGFR1, FGFR2 and FOXO1 between neither the patients’ lip and vomer mucosa nor the control group was observed. Statistically significant very strong and strong correlations were found between genes in the lip and palatine tissue. The expression of FGFR1, FGFR2 and FOXO1 in cleft-affected lip and palatine tissue seems to be highly individual. Numerous intercorrelations between the genes do not exclude their role in the possible complex morphopathogenesis of orofacial clefts.
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Cobourne MT, Irving M, Seller A. Welcome to the new genomics: an introduction to the NHS Genomic Medicine Service for oral healthcare professionals. Br Dent J 2020; 229:682-686. [DOI: 10.1038/s41415-020-2348-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 06/22/2020] [Indexed: 11/09/2022]
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Sylvester B, Brindopke F, Suzuki A, Giron M, Auslander A, Maas RL, Tsai B, Gao H, Magee W, Cox TC, Sanchez-Lara PA. A Synonymous Exonic Splice Silencer Variant in IRF6 as a Novel and Cryptic Cause of Non-Syndromic Cleft Lip and Palate. Genes (Basel) 2020; 11:genes11080903. [PMID: 32784565 PMCID: PMC7465030 DOI: 10.3390/genes11080903] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/28/2020] [Accepted: 08/04/2020] [Indexed: 12/31/2022] Open
Abstract
Missense, nonsense, splice site and regulatory region variants in interferon regulatory factor 6 (IRF6) have been shown to contribute to both syndromic and non-syndromic forms of cleft lip and/or palate (CL/P). We report the diagnostic evaluation of a complex multigeneration family of Honduran ancestry with a pedigree structure consistent with autosomal-dominant inheritance with both incomplete penetrance and variable expressivity. The proband's grandmother bore children with two partners and CL/P segregates on both sides of each lineage. Through whole-exome sequencing of five members of the family, we identified a single shared synonymous variant, located in the middle of exon 7 of IRF6 (p.Ser307Ser; g.209963979 G>A; c.921C>T). The variant was shown to segregate in the seven affected individuals and through three unaffected obligate carriers, spanning both sides of this pedigree. This variant is very rare, only being found in three (all of Latino ancestry) of 251,352 alleles in the gnomAD database. While the variant did not create a splice acceptor/donor site, in silico analysis predicted it to impact an exonic splice silencer element and the binding of major splice regulatory factors. In vitro splice assays supported this by revealing multiple abnormal splicing events, estimated to impact >60% of allelic transcripts. Sequencing of the alternate splice products demonstrated the unmasking of a cryptic splice site six nucleotides 5' of the variant, as well as variable utilization of cryptic splice sites in intron 6. The ectopic expression of different splice regulatory proteins altered the proportion of abnormal splicing events seen in the splice assay, although the alteration was dependent on the splice factor. Importantly, each alternatively spliced mRNA is predicted to result in a frame shift and prematurely truncated IRF6 protein. This is the first study to identify a synonymous variant as a likely cause of NS-CL/P and highlights the care that should be taken by laboratories when considering and interpreting variants.
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Affiliation(s)
- Beau Sylvester
- Division of Plastic and Maxillofacial Surgery, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (B.S.); (A.A.); (W.M.III)
| | | | - Akiko Suzuki
- Department of Oral & Craniofacial Sciences, University of Missouri-Kansas City School of Dentistry, Kansas City, MO 64108, USA; (A.S.); (T.C.C.)
| | - Melissa Giron
- Operación Sonrisa Honduras, Tegucigalpa 11101, Honduras;
| | - Allyn Auslander
- Division of Plastic and Maxillofacial Surgery, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (B.S.); (A.A.); (W.M.III)
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Richard L. Maas
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
| | - Becky Tsai
- Fulgent Genetics, Temple City, CA 91780, USA; (B.T.); (H.G.)
| | - Hanlin Gao
- Fulgent Genetics, Temple City, CA 91780, USA; (B.T.); (H.G.)
| | - William Magee
- Division of Plastic and Maxillofacial Surgery, Children’s Hospital Los Angeles, Los Angeles, CA 90027, USA; (B.S.); (A.A.); (W.M.III)
| | - Timothy C. Cox
- Department of Oral & Craniofacial Sciences, University of Missouri-Kansas City School of Dentistry, Kansas City, MO 64108, USA; (A.S.); (T.C.C.)
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
| | - Pedro A. Sanchez-Lara
- Department of Pediatrics, Cedars-Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA
- Correspondence: ; Tel.: +1-(310)-423-4461
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10
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Yu Q, Deng Q, Fu F, Li R, Zhang W, Wan J, Yang X, Wang D, Li F, Wu S, Li J, Li D, Liao C. A novel splicing mutation of ARHGAP29 is associated with nonsyndromic cleft lip with or without cleft palate. J Matern Fetal Neonatal Med 2020; 35:2499-2506. [PMID: 32698641 DOI: 10.1080/14767058.2020.1786523] [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] [Indexed: 12/17/2022]
Abstract
BACKGROUND Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is one of the most common birth defects, and occurs in approximately 1/700 live births worldwide. The correlation between the ABCA4-ARHGAP29 region and NSCL/P was first identified by genome-wide association studies (GWAS), but few reports have examined NSCL/P caused by ARHGAP29 mutations in the Chinese population. METHODS We performed chromosome microarray analysis (CMA) for two consecutive abnormal fetuses and whole exome sequencing (WES) for the family, including 3 patients and 2 normal family members, Sanger sequencing and RT-PCR were used to confirm the mutation. RESULTS We identified a novel splice donor mutation (ARHGAP29 c.1920 + 1G > A) in two consecutive NSCL/P fetuses, and the variant was inherited from the mother and grandfather. The mutation caused abnormal skipping of exon 17, and the mRNA level of ARHGAP29 was significantly decreased compared to the wild type. CONCLUSIONS In this study, we successfully diagnosed the genetic cause of NSCL/P in a family and first report that the c.1920 + 1G > A mutation in ARHGAP29 is associated with NSCL/P. Our study enriches the genetic landscape of NSCL/P, extends the mutation spectrum of ARHGAP29, and provides a new direction for the diagnosis of NSCL/P in patients and its prenatal diagnosis in fetuses.
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Affiliation(s)
- Qiuxia Yu
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, P. R. China
| | - Qiong Deng
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, P. R. China
| | - Fang Fu
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, P. R. China
| | - Ru Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, P. R. China
| | - Wenwen Zhang
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, P. R. China
| | - Junhui Wan
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, P. R. China
| | - Xin Yang
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, P. R. China
| | - Dan Wang
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, P. R. China
| | - Fucheng Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, P. R. China
| | - Shaoqing Wu
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, P. R. China
| | - Jian Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, P. R. China
| | - Dongzhi Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, P. R. China
| | - Can Liao
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, P. R. China
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11
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Reynolds K, Zhang S, Sun B, Garland MA, Ji Y, Zhou CJ. Genetics and signaling mechanisms of orofacial clefts. Birth Defects Res 2020; 112:1588-1634. [PMID: 32666711 DOI: 10.1002/bdr2.1754] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/11/2020] [Accepted: 06/15/2020] [Indexed: 12/31/2022]
Abstract
Craniofacial development involves several complex tissue movements including several fusion processes to form the frontonasal and maxillary structures, including the upper lip and palate. Each of these movements are controlled by many different factors that are tightly regulated by several integral morphogenetic signaling pathways. Subject to both genetic and environmental influences, interruption at nearly any stage can disrupt lip, nasal, or palate fusion and result in a cleft. Here, we discuss many of the genetic risk factors that may contribute to the presentation of orofacial clefts in patients, and several of the key signaling pathways and underlying cellular mechanisms that control lip and palate formation, as identified primarily through investigating equivalent processes in animal models, are examined.
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Affiliation(s)
- Kurt Reynolds
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children-Northern California; University of California Davis, School of Medicine, Sacramento, California, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, California, USA
| | - Shuwen Zhang
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children-Northern California; University of California Davis, School of Medicine, Sacramento, California, USA
| | - Bo Sun
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children-Northern California; University of California Davis, School of Medicine, Sacramento, California, USA
| | - Michael A Garland
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children-Northern California; University of California Davis, School of Medicine, Sacramento, California, USA
| | - Yu Ji
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children-Northern California; University of California Davis, School of Medicine, Sacramento, California, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, California, USA
| | - Chengji J Zhou
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, California, USA.,Institute for Pediatric Regenerative Medicine, Shriners Hospitals for Children-Northern California; University of California Davis, School of Medicine, Sacramento, California, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, California, USA
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12
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Zhang M, Zhang J, Zhao H, Ievlev V, Zhong W, Huang W, Cornell RA, Lin J, Chen F. Functional Characterization of a Novel IRF6 Frameshift Mutation From a Van Der Woude Syndrome Family. Front Genet 2020; 11:562. [PMID: 32582293 PMCID: PMC7289175 DOI: 10.3389/fgene.2020.00562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 05/11/2020] [Indexed: 12/14/2022] Open
Abstract
Background Loss-of-function mutations in interferon regulatory factor-6 (IRF6) are responsible for about 70% of cases of Van Der Woude Syndrome (VWS), an autosomal dominant developmental disorder characterized by pits and/or sinuses of the lower lip and cleft lip, cleft palate, or both. Methods We collected a Chinese Han VWS pedigree, performed sequencing and screening for the causal gene mutant. Initially, species conservation analysis and homology protein modeling were used to predict the potential pathogenicity of mutations. To test whether a VWS family-derived mutant variant of IRF6 retained function, we carried out rescue assays in irf6 maternal-null mutant zebrafish embryos. To assess protein stability, we overexpressed reference and family-variants of IRF6 in vitro. Results We focused on a VWS family that includes a son with bilateral lip pits, uvula fissa and his father with bilateral cleft lip and palate. After sequencing and screening, a frameshift mutation of IRF6 was identified as the potential causal variant (NM.006147.3, c.1088-1091delTCTA; p.Ile363ArgfsTer33). The residues in this position are strongly conserved among species and homology modeling suggests the variant alters the protein structure. In irf6 maternal-null mutant zebrafish embryos the periderm differentiates abnormally and the embryos rupture and die during gastrulation. Injection of mRNA encoding the reference variant of human IRF6, but not of the frame-shift variant, rescued such embryos through gastrulation. Upon overexpression in HEK293FT cells, the IRF6 frame-shift mutant was relatively unstable and was preferentially targeted to the proteasome in comparison to the reference variant. Conclusion In this VWS pedigree, a novel frameshift of IRF6 was identified as the likely causative gene variant. It is a lost function mutation which could not rescue abnormal periderm phenotype in irf6 maternal-null zebrafish and which causes the protein be unstable through proteasome-dependent degradation.
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Affiliation(s)
- Mengqi Zhang
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, China
| | - Jieni Zhang
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, China
| | - Huaxiang Zhao
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, China
| | - Vitaly Ievlev
- Department of Anatomy and Cell Biology Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Wenjie Zhong
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, China
| | - Wenbin Huang
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, China
| | - Robert A Cornell
- Department of Anatomy and Cell Biology Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Jiuxiang Lin
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, China
| | - Feng Chen
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China
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13
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Vsevolozhskaya OA, Shi M, Hu F, Zaykin DV. DOT: Gene-set analysis by combining decorrelated association statistics. PLoS Comput Biol 2020; 16:e1007819. [PMID: 32287273 PMCID: PMC7182280 DOI: 10.1371/journal.pcbi.1007819] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 04/24/2020] [Accepted: 03/23/2020] [Indexed: 12/12/2022] Open
Abstract
Historically, the majority of statistical association methods have been designed assuming availability of SNP-level information. However, modern genetic and sequencing data present new challenges to access and sharing of genotype-phenotype datasets, including cost of management, difficulties in consolidation of records across research groups, etc. These issues make methods based on SNP-level summary statistics particularly appealing. The most common form of combining statistics is a sum of SNP-level squared scores, possibly weighted, as in burden tests for rare variants. The overall significance of the resulting statistic is evaluated using its distribution under the null hypothesis. Here, we demonstrate that this basic approach can be substantially improved by decorrelating scores prior to their addition, resulting in remarkable power gains in situations that are most commonly encountered in practice; namely, under heterogeneity of effect sizes and diversity between pairwise LD. In these situations, the power of the traditional test, based on the added squared scores, quickly reaches a ceiling, as the number of variants increases. Thus, the traditional approach does not benefit from information potentially contained in any additional SNPs, while our decorrelation by orthogonal transformation (DOT) method yields steady gain in power. We present theoretical and computational analyses of both approaches, and reveal causes behind sometimes dramatic difference in their respective powers. We showcase DOT by analyzing breast cancer and cleft lip data, in which our method strengthened levels of previously reported associations and implied the possibility of multiple new alleles that jointly confer disease risk.
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Affiliation(s)
- Olga A. Vsevolozhskaya
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, Kentucky, United States of America
| | - Min Shi
- Biostatistics and Computational Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Fengjiao Hu
- Biostatistics and Computational Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Dmitri V. Zaykin
- Biostatistics and Computational Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
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14
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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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15
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Azevedo CDMS, Machado RA, Martelli-Júnior H, Reis SRDA, Persuhn DC, Coletta RD, Rangel ALCA. Exploring GRHL3 polymorphisms and SNP-SNP interactions in the risk of non-syndromic oral clefts in the Brazilian population. Oral Dis 2019; 26:145-151. [PMID: 31564061 DOI: 10.1111/odi.13204] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/27/2019] [Accepted: 09/20/2019] [Indexed: 01/02/2023]
Abstract
OBJECTIVE To investigate the association of single-nucleotide polymorphisms (SNP) in grainyhead-like 3 (GRHL3) and to verify its possible interactions with others genes responsible for craniofacial development in the risk of non-syndromic oral cleft (NSOC). METHODS Applying TaqMan allelic discrimination assays, we evaluated GRHL3 SNPs (rs10903078, rs41268753, and rs4648975) in an ancestry-structured case-control sample composed of 1,127 Brazilian participants [272 non-syndromic cleft palate only (NSCPO), 242 non-syndromic cleft lip only (NSCLO), 319 non-syndromic cleft lip and palate (NSCLP), and 294 healthy controls]. Additionally, SNP-SNP interactions of GRHL3 and previously reported variants in FAM49A, FOXE1, NTN1, and VAX1 were verified in non-syndromic cleft lip with or without cleft palate (NSCL ± P). To eliminate false-positive associations, Bonferroni correction or 1,000 permutation method was applied. RESULTS The multiple logistic regression analysis showed that the CC genotype of rs10903078 (p = .03) and the haplotype C-C formed by the SNPs rs10903078 and rs41268753 (p = .04) were associated with NSCLO, but the p-values did not withstand Bonferroni correction. However, SNP-SNP test revealed significant interactions between GRHL3 SNPs and FAM49A (rs7552), FOXE1 (rs3758249), VAX1 (rs7078160 and rs751231), and NTN1 (rs9891446). CONCLUSIONS Our results confirm the importance of GRHL3 and its interactions with previously NSOC-associated genes, including FAM49A, FOXE1, NTN1, and VAX1, in the pathogenesis of NSOC in the Brazilian population.
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Affiliation(s)
| | - Renato Assis Machado
- Department of Oral Diagnosis, School of Dentistry, University of Campinas, Piracicaba, Brazil
| | - Hercílio Martelli-Júnior
- Dental School, Stomatology Clinic, State University of Montes Claros, Montes Claros, Brazil.,Center for Rehabilitation of Craniofacial Anomalies, Dental School, University of José Rosario Vellano, Alfenas, Brazil
| | | | | | - Ricardo D Coletta
- Department of Oral Diagnosis, School of Dentistry, University of Campinas, Piracicaba, Brazil
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16
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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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17
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Wang TJ, Hsieh KS, Lai JP, Tsai MH, Liang YC, Chang YH. Novel mutations of IRF6 gene in Taiwanese Van der Woude syndrome patients. Pediatr Neonatol 2019; 60:218-220. [PMID: 30982524 DOI: 10.1016/j.pedneo.2018.04.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 04/09/2018] [Accepted: 04/24/2018] [Indexed: 11/18/2022] Open
Affiliation(s)
- Tzu-Jou Wang
- Department of Pediatrics, Chang Gung Memorial Hospital, Kaohsiung, Taiwan.
| | - Kai-Shen Hsieh
- Department of Pediatrics, Chang Gung Memorial Hospital, Kaohsiung, Taiwan.
| | - Jui-Pin Lai
- Department of Plastic and Reconstructive Surgery, Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Meng-Han Tsai
- Department of Neurological, Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Yi-Chih Liang
- Department of Pediatrics, Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Yen-Hsun Chang
- Department of Pediatrics, Chang Gung Memorial Hospital, Kaohsiung, Taiwan
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18
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Wu D, Wang M, Wang X, Zhang YB, Song T, Yin N, Zhao Z. Interaction between interferon regulatory factor 6 and glycine receptor beta shows a protective effect on developing nonsyndromic cleft lip with or without cleft palate in the Han Chinese population. Eur J Oral Sci 2018; 127:27-32. [PMID: 30462859 DOI: 10.1111/eos.12587] [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] [Accepted: 10/04/2018] [Indexed: 12/16/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) in protein-coding regions of genes which were previously reported to be associated with nonsyndromic cleft lip, with or without palate involvement (NSCL/P), were investigated. Twelve candidate loci [platelet-derived growth factor C (PDGFC), platelet-derived growth factor subunit A (PDGFA), platelet-derived growth factor receptor alpha (PDGFRA), glycine receptor alpha 2 (GLRA2), glycine receptor beta (GLRB), ATP binding cassette subfamily A member 4 (ABCA4), MAF bZIP transcription factor B (MAFB), interferon regulatory factor 6 (IRF6), CCDC26 long non-coding RNA (CCDC26), paired box 7 (PAX7), ventral anterior homeobox 1 (VAX1), and netrin 1 (NTN1)] covering 1.5 Mbp were sequenced in 136 NSCL/P patients and 54 healthy controls. Twenty-five genomic variants identified were further validated in another 400 NSCL/P and 200 controls. Two SNPs in IRF6 showed a protective effect against the development of NSCL/P (rs12405750, OR = 0.54, 95% CI: 0.41-0.69; and rs2235371, OR = 0.55, 95% CI: 0.43-0.71). The missense variant, rs2235371, alters the conserved amino acid valine to isoleucine at codon 274 (V274I). We observed that SNPs at IRF6 (rs2235371 and rs12405750) and GLRB (rs73856838 and rs72685584) show consistent interaction effects. The association between the missense SNP rs2235371 in gene IRF6 and NSCL/P suggests that this SNP may play an important role as a risk factor for NSCL/P in the Han Chinese populations. The marginal signal near 4q31 detected in previous genome-wide association studies might be caused by an interaction between the IRF6 and GLRB genes. This interaction needs to be further validated by experimentation in follow-up studies.
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Affiliation(s)
- Di Wu
- Department of Cleft Lip and Palate, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing
| | - Mei Wang
- School of Life Science, Peking University, Beijing
| | - Xingang Wang
- Department of Oral and Maxillofacial Surgery, Beijing Children Hospital, Capital Medical University, Beijing
| | - Yong-Biao Zhang
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing, China
| | - Tao Song
- Department of Cleft Lip and Palate, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing
| | - Ningbei Yin
- Department of Cleft Lip and Palate, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing
| | - Zhenmin Zhao
- Department of Cleft Lip and Palate, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing
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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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Transcriptome profiling reveals candidate cleft palate-related genes in cultured Chinese sturgeons (Acipenser sinensis). Gene 2018; 666:1-8. [PMID: 29733966 DOI: 10.1016/j.gene.2018.05.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/26/2018] [Accepted: 05/03/2018] [Indexed: 11/20/2022]
Abstract
The Chinese sturgeon (Acipenser sinensis) is an anadromous fish distributed in the Yangtze River and the East China Sea. In this study, we report the novel finding of cleft palates in Chinese sturgeons derived from artificial fertilization. To explore the genetic basis of palate malformation in A. sinensis, Illumina RNA-seq technology was used to analyze the transcriptome data of farmed Chinese sturgeons with normal palates and cleft-palates. Raw reads were obtained and assembled into 808,612 unigenes, with an average length of 509.33 bp and an N50 of 574 bp. Sequence similarity analyses against four public databases (Nr, UniProt, KEGG, and COGs) found 158,642 unigenes that could be annotated. GABAergic synapses and TGF-β signal pathways were the two most enriched pathways with high Rich Factors in the analyses of differentially expressed genes. In these two signal pathways, six genes (GABRA4, GS, GNS, S6K, PITX2, and BMP8) were found as candidate cleft-palate genes in Chinese sturgeon. These findings contribute to our understanding of cleft palate genetics in sturgeon, while simultaneously adding to our knowledge about craniofacial development.
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21
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Genetic heterogeneity in Van der Woude syndrome: identification of NOL4 and IRF6 haplotype from the noncoding region as candidates in two families. J Genet 2018. [DOI: 10.1007/s12041-018-0903-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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22
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Kumari PK, Ali A, Singh SK, Chaurasia A, Raman R. Genetic heterogeneity in Van der Woude syndrome: identification of NOL4 and IRF6 haplotype from the noncoding region as candidates in two families. J Genet 2018; 97:275-285. [PMID: 29666346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Van der Woude syndrome (VWS) shows an autosomal dominant pattern of inheritance with two known candidate genes, IRF6 and GRHL3. In this study, by employing genome-wide linkage analyses on two VWS affected families, we report the cosegregation of an intronic rare variant in NOL4 in one family, and a haplotype consisting of three variants in the noncoding region of IRF6 (introns 1, 8 and 3'UTR) in the other family. Using mouse, as well as human embryos as a model, we demonstrate the expression of NOL4 in the lip and palate primordia during their development. Luciferase, as well as miRNA-transfection assays show decline in the expression of mutant NOL4 construct due to the creation of a binding site for hsa-miR-4796-5p. In family 2, the noncoding region IRF6 haplotype turns out to be the candidate possibly by diminishing its IRF6 expression to half of its normal activity. Thus, here we report a new candidate gene (NOL4) and a haplotype of IRF6 forVWS, and highlight the genetic heterogeneity of this disorder in the Indian population.
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Affiliation(s)
- Priyanka Kumari Kumari
- Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221 005, India. ,
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23
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Rafighdoost H, Hashemi M, Danesh H, Bizhani F, Bahari G, Taheri M. Association of single nucleotide polymorphisms in AXIN2, BMP4, and IRF6 with Non-Syndromic Cleft Lip with or without Cleft Palate in a sample of the southeast Iranian population. J Appl Oral Sci 2018; 25:650-656. [PMID: 29211286 PMCID: PMC5701535 DOI: 10.1590/1678-7757-2017-0191] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 06/30/2017] [Indexed: 01/25/2023] Open
Abstract
Non-syndromic cleft lip with or without palate (NSCL/P) is a common congenital malformation worldwide, with complex etiology. It has been proposed that interaction of genes and environmental factors play a role in the predisposition to this disease.
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Affiliation(s)
- Houshang Rafighdoost
- Zahedan University of Medical Sciences, Cellular and Molecular Research Center, Zahedan, Iran.,Zahedan University of Medical Sciences, School of Medicine, Department of Anatomy, Zahedan, Iran
| | - Mohammad Hashemi
- Zahedan University of Medical Sciences, School of Medicine, Department of Clinical Biochemistry, Zahedan, Iran
| | - Hiva Danesh
- Zahedan University of Medical Sciences, School of Medicine, Department of Clinical Biochemistry, Zahedan, Iran
| | - Fatemeh Bizhani
- Zahedan University of Medical Sciences, School of Medicine, Department of Clinical Biochemistry, Zahedan, Iran
| | - Gholamreza Bahari
- Zahedan University of Medical Sciences, School of Medicine, Department of Clinical Biochemistry, Zahedan, Iran
| | - Mohsen Taheri
- Genetic of Non-Communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
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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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25
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Starink E, Hokken-Koelega ACS, Visser TJ, Baan J, Peeters RP, de Graaff LCG. Genetic analysis of IRF6, a gene involved in craniofacial midline formation, in relation to pituitary and facial morphology of patients with idiopathic growth hormone deficiency. Pituitary 2017; 20:499-508. [PMID: 28593555 PMCID: PMC5606942 DOI: 10.1007/s11102-017-0808-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
INTRODUCTION Growth hormone is secreted by the pituitary gland, which forms part of the craniofacial midline. IRF6 encodes a transcription factor involved in the development of the craniofacial midline and mutations in IRF6 are known to disturb craniofacial development. Craniofacial and pituitary development are closely related. After whole exome sequencing revealed a new mutation in IRF6 in a family with Idiopathic Growth Hormone Deficiency (IGHD), we screened the remainder of our IGHD cohort for mutations in this gene and related their genotypes to pituitary and craniofacial morphology. MATERIALS AND METHODS We sequenced all coding exons and exon-intron boundaries of IRF6 in 81 patients with IGHD. We performed a multiplex ligation-dependent probe amplification (MLPA) in order to exclude copy number variations in IRF6. We analyzed facial measurements taken from standardized digital pictures of 48 patients. RESULTS We found two new variants and eleven polymorphisms. Apart from the new mutation found in the index family (p.Arg233Cys), we found one other new heterozygous missense mutation in IRF6 (Pro456Ser). p.Arg233Cys was reported as extremely rare in exome databases (1 allele out of 120.852 alleles sequenced), strictly conserved among species and was predicted deleterious by all variant predictor programs. Pro456Ser was predicted to be benign. MLPA did not reveal any exon deletions or duplications in any of the patients. CONCLUSION This is the first report of IRF6 analysis in an IGHD cohort. We found one new mutation which, based on in silico analysis, could be of functional relevance. However, we did not find any mutations in the other patients. Therefore, we conclude that IRF6 defects are rare in IGHD patients and further research should focus on new candidate genes.
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Affiliation(s)
- Eline Starink
- Dept. of Internal Medicine, Subdiv. Endocrinology, Erasmus MC, University Medical Center, 's Gravendijkwal 230, 3015 CE, Rotterdam, The Netherlands
| | - Anita C S Hokken-Koelega
- Pediatrics, Subdiv. Endocrinology, Erasmus MC, Rotterdam, The Netherlands
- Dutch Growth Research Foundation, Rotterdam, The Netherlands
| | - Theo J Visser
- Dept. of Internal Medicine, Subdiv. Endocrinology, Erasmus MC, University Medical Center, 's Gravendijkwal 230, 3015 CE, Rotterdam, The Netherlands
| | - Janneke Baan
- Dept. of Internal Medicine, Subdiv. Endocrinology, Erasmus MC, University Medical Center, 's Gravendijkwal 230, 3015 CE, Rotterdam, The Netherlands
| | - Robin P Peeters
- Dept. of Internal Medicine, Subdiv. Endocrinology, Erasmus MC, University Medical Center, 's Gravendijkwal 230, 3015 CE, Rotterdam, The Netherlands
| | - Laura C G de Graaff
- Dept. of Internal Medicine, Subdiv. Endocrinology, Erasmus MC, University Medical Center, 's Gravendijkwal 230, 3015 CE, Rotterdam, The Netherlands.
- Dutch Growth Research Foundation, Rotterdam, The Netherlands.
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26
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Salagovic J, Klimcakova L, Zabavnikova M, Behunova J, Hudakova T, Fedeles J, Molnarova A, Podracka L. Polymorphisms at 1q32, 8q24, and 17q22 loci are associated with nonsyndromic cleft lip with or without cleft palate risk in the Slovak population. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2017; 161:152-157. [PMID: 28422192 DOI: 10.5507/bp.2017.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 03/16/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Nonsyndromic cleft lip with or without cleft palate (nsCL/P) is the most common orofacial birth defect with an aetiology involving both genetic and environmental factors. Genome-wide association studies (GWAS) have identified several genomic susceptibility regions for nsCL/P. In the present study, the three well established single nucleotide polymorphisms (SNPs) identified by GWAS (rs987525 at 8q24, rs7078160 at 10q25, and rs227731 at 17q22 loci) and one SNP identified by candidate gene study (rs642961 in IRF6 gene at 1q32 locus) were analysed for an association with nsCL/P in Slovak population. METHODS Nucleotide variants were genotyped in 165 nsCL/P patients and 326 unaffected controls. All variants of interest were genotyped using high-resolution melting analysis after real-time PCR. RESULTS We found significant differences between patient and control groups with respect to the allele and genotype frequencies for the SNPs at the 1q32, 8q24, and 17q22 loci. SNP at the 10q25 locus showed a trend toward association with nsCL/P risk. CONCLUSIONS The results suggest that SNPs at the 1q32, 8q24 and 17q22 loci may contribute to the nsCL/P risk in Slovak population.
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Affiliation(s)
- Jan Salagovic
- Department of Medical Biology, Faculty of Medicine, PJ Safarik University in Kosice, Slovak Republic
| | - Lucia Klimcakova
- Department of Medical Biology, Faculty of Medicine, PJ Safarik University in Kosice, Slovak Republic
| | - Marianna Zabavnikova
- Department of Plastic, Reconstructive and Aesthetic Surgery, LP University Hospital, Kosice, Slovak Republic
| | - Jana Behunova
- Department of Paediatrics, Faculty of Medicine, PJ Safarik University in Kosice and Children's University Hospital, Kosice, Slovak Republic.,Institut fur Medizinische Genetik, Medizinische Universitat Wien, Austria
| | - Terezia Hudakova
- Department of Medical Biology, Faculty of Medicine, PJ Safarik University in Kosice, Slovak Republic
| | - Jozef Fedeles
- Department of Plastic, Reconstructive and Aesthetic Surgery, Faculty of Medicine, Commenius University and University Hospital, Bratislava, Slovak Republic
| | - Agata Molnarova
- Department of Plastic, Reconstructive and Aesthetic Surgery, Faculty of Medicine, Commenius University and University Hospital, Bratislava, Slovak Republic
| | - Ludmila Podracka
- Department of Paediatrics, Faculty of Medicine, PJ Safarik University in Kosice and Children's University Hospital, Kosice, Slovak Republic.,1st Department of Paediatrics, Faculty of Medicine, Comenius University and Children's University Hospital, Bratislava, Slovak Republic
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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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28
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Peng HH, Chang NC, Chen KT, Lu JJ, Chang PY, Chang SC, Wu-Chou YH, Chou YT, Phang W, Cheng PJ. Nonsynonymous variants in MYH9 and ABCA4 are the most frequent risk loci associated with nonsyndromic orofacial cleft in Taiwanese population. BMC MEDICAL GENETICS 2016; 17:59. [PMID: 27527345 PMCID: PMC4986225 DOI: 10.1186/s12881-016-0322-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 06/10/2016] [Indexed: 11/10/2022]
Abstract
BACKGROUND Nonsyndromic orofacial cleft is a common birth defect with a complex etiology, including multiple genetic and environmental risk factors. Recent whole genome analyses suggested associations between nonsyndromic orofacial cleft and up to 18 genetic risk loci (ABCA4, BMP4, CRISPLD2, GSTT1, FGF8, FGFR2, FOXE1, IRF6, MAFB, MSX1, MTHFR, MYH9, PDGFC, PVRL1, SUMO1, TGFA, TGFB3, and VAX1), each of which confers a different relative risk in different populations. We evaluate the nonsynonymous variants in these 18 genetic risk loci in nonsyndromic orofacial clefts and normal controls to clarify the specific variants in Taiwanese population. METHODS We evaluated these 18 genetic risk loci in 103 cases of nonsyndromic orofacial clefts and 100 normal controls using a next-generation sequencing (NGS) customized panel and manipulated a whole-exon targeted-sequencing study based on the NGS system of an Ion Torrent Personal Genome Machine (IT-PGM). IT-PGM data processing, including alignment with the human genome build 19 reference genome (hg19), base calling, trimming of barcoded adapter sequences, and filtering of poor signal reads, was performed using the IT platform-specific pipeline software Torrent Suite, version 4.2, with the plug-in "variant caller" program. Further advanced annotation was facilitated by uploading the exported VCF file from Variant Caller to the commercial software package Ion Reporter; the free online annotation software Vanno and Mutation Taster. Benign or tolerated amino acid changes were excluded after analysis using sorting intolerant from tolerant and polymorphism phenotyping. Sanger sequencing was used to validate the significant variants identified by NGS. Furthermore, each variant was confirmed in asymptomatic controls using the Sequenom MassARRAY (San Diego, CA, USA). RESULTS We identified totally 22 types of nonsynonymous variants specific in nonsyndromic orofacial clefts, including 19 single nucleotide variants, 2 deletions, and 1 duplication in 10 studied genes(ABCA4, MYH9, MTHFR, CRISPLD2, FGF8, PVRL1, FOXE1, VAX1, FGFR2, and IRF6). Nonsynonymous variants in MYH9 and ABCA4, which were detected in 6 and 5 individuals, respectively, were identified to be the most frequent risk loci in nonsyndromic orofacial clefts in the Taiwanese population. CONCLUSIONS Nonsynonymous variants in MYH9 and ABCA4 were identified to be the most frequent risk loci in nonsyndromic orofacial clefts in the Taiwanese population. These findings in our study have provided additional information regarding specific variants associated with nonsyndromic orofacial clefts in different population and demonstrate the power of our customized NGS panel, which is clinically useful for the simultaneous detection of multiple genes associated with nonsyndromic orofacial clefts.
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Affiliation(s)
- Hsiu-Huei Peng
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan.,Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Nai-Chung Chang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Kuo-Ting Chen
- Chang Gung University College of Medicine, Taoyuan, Taiwan.,Department of Plastic and Reconstructive surgery, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Jang-Jih Lu
- Chang Gung University College of Medicine, Taoyuan, Taiwan.,Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Pi-Yueh Chang
- Chang Gung University College of Medicine, Taoyuan, Taiwan.,Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Shih-Cheng Chang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Yah-Huei Wu-Chou
- Chang Gung University College of Medicine, Taoyuan, Taiwan.,Human Molecular Genetics Laboratory, Department of Medical Research, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Yi-Ting Chou
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Wanni Phang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Po-Jen Cheng
- Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan. .,Chang Gung University College of Medicine, Taoyuan, Taiwan.
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Jafary F, Nadeali Z, Salehi M, Hosseinzadeh M, Sedghi M, Gholamrezapour T, Nouri N. Significant association between nonsyndromic cleft lip with or without cleft palate and IRF6rs2235371 polymorphism in Iranian familiar population. Mol Biol 2015. [DOI: 10.1134/s0026893315060102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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30
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Liu YP, Xu LF, Wang Q, Zhou XL, Zhou JL, Pan C, Zhang JP, Wu QR, Li YQ, Xia YJ, Peng X, Zhang MR, Yu HM, Xu LC. Identification of susceptibility genes in non-syndromic cleft lip with or without cleft palate using whole-exome sequencing. Med Oral Patol Oral Cir Bucal 2015; 20:e763-70. [PMID: 26449438 PMCID: PMC4670259 DOI: 10.4317/medoral.20758] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 06/06/2015] [Indexed: 01/16/2023] Open
Abstract
Background Non-syndromic cleft lip with or without cleft palate (NSCL/P) is among the most common congenital malformations. The etiology of NSCL/P remains poorly characterized owing to its complex genetic heterogeneity. The objective of this study was to identify genetic variants that increase susceptibility to NSCL/P. Material and Methods Whole-exome sequencing (WES) was performed in 8 fetuses with NSCL/P in China. Bioinformatics analysis was performed using commercially available software. Variants detected by WES were validated by Sanger sequencing. Results By filtering out synonymous variants in exons, we identified average 8575 nonsynonymous single nucleotide variants (SNVs). We subsequently compared the SNVs against public databases including NCBI dbSNP build 135 and 1000 Genomes Project and obtained an average of 203 SNVs. Total 12 reported candidate genes were verified by Sanger sequencing. Sanger sequencing also confirmed 16 novel SNVs shared by two or more samples. Conclusions We have found and confirmed 16 susceptibility genes responsible for NSCL/P, which may play important role in the etiology of NSCL/P. The susceptibility genes identified in this study will not only be useful in revealing the etiology of NSCL/P but also in diagnosis and treatment of the patients with NSCL/P. Key words:Non-syndromic cleft lip with or without cleft palate, whole-exome sequencing, sanger sequencing, susceptibility gene, single nucleotide variants (SNVs).
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Affiliation(s)
- Ya-Peng Liu
- School of Public Health, Xuzhou Medical College, 209 Tongshan Road. Xuzhou, Jiangsu, 221004, China,
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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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do Rego Borges A, Sá J, Hoshi R, Viena CS, Mariano LC, de Castro Veiga P, Medrado AP, Machado RA, de Aquino SN, Messetti AC, Spritz RA, Coletta RD, Reis SRA. Genetic risk factors for nonsyndromic cleft lip with or without cleft palate in a Brazilian population with high African ancestry. Am J Med Genet A 2015. [DOI: 10.1002/ajmg.a.37181] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Andrea do Rego Borges
- Department of Basic Science; Bahiana School of Medicine and Public Health; Salvador Bahia Brazil
| | - Jamile Sá
- Department of Basic Science; Bahiana School of Medicine and Public Health; Salvador Bahia Brazil
| | - Ryuichi Hoshi
- Department of Basic Science; Bahiana School of Medicine and Public Health; Salvador Bahia Brazil
| | - Camila Sane Viena
- Department of Basic Science; Bahiana School of Medicine and Public Health; Salvador Bahia Brazil
| | - Lorena C. Mariano
- Department of Basic Science; Bahiana School of Medicine and Public Health; Salvador Bahia Brazil
| | - Patricia de Castro Veiga
- Department of Basic Science; Bahiana School of Medicine and Public Health; Salvador Bahia Brazil
| | - Alena Peixoto Medrado
- Department of Basic Science; Bahiana School of Medicine and Public Health; Salvador Bahia Brazil
| | - Renato Assis Machado
- Department of Oral Diagnosis; School of Dentistry; State University of Campinas; Piracicaba São Paulo Brazil
| | | | - Ana Camila Messetti
- Department of Oral Diagnosis; School of Dentistry; State University of Campinas; Piracicaba São Paulo Brazil
| | - Richard A. Spritz
- Human Medical Genetics and Genomics Program; University of Colorado School of Medicine; Aurora Colorado
| | - Ricardo D. Coletta
- Department of Oral Diagnosis; School of Dentistry; State University of Campinas; Piracicaba São Paulo Brazil
| | - Silvia R. A. Reis
- Department of Basic Science; Bahiana School of Medicine and Public Health; Salvador Bahia Brazil
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Liu K, Lu Y, Ai L, Jiao B, Yu J, Zhang B, Liu Q. Association between FOXE1 and non-syndromic orofacial clefts in a northeastern Chinese population. Br J Oral Maxillofac Surg 2015; 53:705-10. [PMID: 26100861 DOI: 10.1016/j.bjoms.2015.05.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 05/22/2015] [Indexed: 01/07/2023]
Abstract
Non-syndromic orofacial clefts are among the most common congenital defects, and several reports have shown that the FOXE1 gene has strong associations with them. To find out if the gene was a risk factor we used a case-control and family-based analysis, and recruited 230 patients with non-syndromic oral clefts including 179 with non-syndromic cleft lip with or without cleft palate, and 51 with non-syndromic cleft palate alone, their parents (166 mothers and 161 fathers, including 135 complete trios), and 180 healthy controls. Polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) were used to genotype the 2 most strongly associated markers (rs4460498 and rs3758249) in FOXE1, and case-control and family-based associations were analysed. In the case-control analyses we found a significant association with non-syndromic cleft lip and palate in rs4460498 (p=0.009) and rs3758249 (p=0.014), but no association in patients with cleft palate alone. For rs4460498 in FOXE1, the odds ratio (OR) for cases with CC homozygotes compared with TC+CC genotypes was 1.813 (95% CI 1.176 to 2.796), and for rs3758249 in FOXE1, the OR for cases with GG homozygotes compared with those with AG+AA genotypes was 0.561 (95%CI 0.371 to 0.848). The results of transmission-disequilibrium tests for rs4460698 and rs3758249 for non-syndromic orofacial clefts were p=0.003, OR=2.781 (95% CI 1.414 to 5.469) and p=0.001, OR=2.552 (95%CI 1.574 to 4.138), respectively. This suggests that FOXE1 (rs4460498 and rs3758249) is strongly associated with non-syndromic cleft lip and palate in populations in northeast China, and further study between FOXE1 and non-syndromic orofacial clefts is necessary.
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Affiliation(s)
- Kun Liu
- Department of Oral and Maxillofacial Surgery, School of Stomatology, China Medical University, Shenyang, Liaoning 110002, PR China.
| | - Yongping Lu
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, Liaoning 110002, PR China.
| | - Lisi Ai
- Department of Periodontics,School of Stomatology, China Medical University, Shenyang, Liaoning 110002, PR China.
| | - Boqiang Jiao
- Department of Oral and Maxillofacial Surgery, School of Stomatology, China Medical University, Shenyang, Liaoning 110002, PR China.
| | - Jiantao Yu
- Department of Oral and Maxillofacial Surgery, School of Stomatology, China Medical University, Shenyang, Liaoning 110002, PR China.
| | - Bin Zhang
- Department of Oral and Maxillofacial Surgery, School of Stomatology, China Medical University, Shenyang, Liaoning 110002, PR China.
| | - Qiang Liu
- Department of Oral and Maxillofacial Surgery, School of Stomatology, China Medical University, Shenyang, Liaoning 110002, PR China.
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Mehrotra D. Genomic expression in non syndromic cleft lip and palate patients: A review. J Oral Biol Craniofac Res 2015; 5:86-91. [PMID: 26258020 DOI: 10.1016/j.jobcr.2015.03.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 03/25/2015] [Indexed: 11/29/2022] Open
Abstract
Cleft lip and palate are common congenital anomalies with significant medical, psychological, social, and economic ramifications, affecting one in seven hundred live births. Genetic causes of non syndromic cleft lip and/or palate (NSCLP) include chromosomal rearrangements, genetic susceptibility to teratogenic exposures, and complex genetic contributions of multiple genes. Development of the orofacial clefts in an individual will depend on the interaction of several moderately effecting genes with environmental factors. Several candidate genes have been genotyped in different population types, using case parent trio or case control design; also genes have been sequenced and SNPs have been reported. Quantitative and molecular analysis have shown linkage and association studies to be more relevant. Recent literature search shows genome wide association studies using microarray. The aim of this paper was to review the approaches to identify genes associated with NSCLP and to analyze their differential expressions. Although no major gene has been confirmed, a lot of research is ongoing to provide an understanding of the pathophysiology of the orofacial clefts.
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Affiliation(s)
- D Mehrotra
- Professor, Department of Oral & Maxillofacial Surgery, King George Medical University, Lucknow, India
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Kerameddin S, Namipashaki A, Ebrahimi S, Ansari-Pour N. IRF6 Is a Marker of Severity in Nonsyndromic Cleft Lip/Palate. J Dent Res 2015; 94:226S-32S. [DOI: 10.1177/0022034515581013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Nonsyndromic cleft lip with or without palate (CL/P) is thought to be caused by the interplay of genetic and environmental factors, and this has thus hindered the process of identifying genetic causative factors. Numerous studies in the past decade have implicated IRF6 in CL/P, but this has not often been replicated in other populations. In specific, the only etiologic single-nucleotide polymorphism (SNP) identified in the IRF6 locus (rs642961) has recently been shown not to be associated with CL/P in diverse populations. We therefore used a genewide tagging SNP (tagSNP) haplotyping approach (including rs642961 as a tagSNP) to detect all potential risk-conferring haplotypes and combined this with detailed subphenotyping of CL/P cases ( N = 150) according to severity. We observed a significant overrepresentation of a tagSNP haplotype carrying the rs642961 risk allele in the most severe subphenotype of CL/P (complete bilateral CL/P; P = 0.008, odds ratio = 4.97, 95% confidence interval = 1.33 to 18.46). It was recently shown that >80% of IRF6 mutations in syndromic CL/P occur on the same haplotype background. We therefore suggest that IRF6 is a marker of CL/P severity.
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Affiliation(s)
- S. Kerameddin
- Department of Plastic and Reconstructive Surgery, Iran University of Medical Sciences, Tehran, Iran
| | - A. Namipashaki
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - S. Ebrahimi
- Faculty of New Sciences and Technology, University of Tehran, Tehran, Iran
| | - N. Ansari-Pour
- Faculty of New Sciences and Technology, University of Tehran, Tehran, Iran
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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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Mijiti A, Ling W, Guli, Moming A. Association of single-nucleotide polymorphisms in the IRF6 gene with non-syndromic cleft lip with or without cleft palate in the Xinjiang Uyghur population. Br J Oral Maxillofac Surg 2015; 53:268-74. [PMID: 25592222 DOI: 10.1016/j.bjoms.2014.12.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 12/12/2014] [Indexed: 12/30/2022]
Abstract
Our main aim was to investigate the association between the interferon regulatory factor (IRF6) gene and non-syndromic cleft lip and palate (nsCLP) in the Xinjiang Uyghur population. Twelve single nucleotide polymorphisms (SNP) were screened in a group of 100 patients with nsCLP and in a control group of 60 unaffected subjects by next generation sequencing using a MiSeq Benchtop Sequencer (Illumina). Our case-control association analysis showed that the SNP marker rs7545538 differed significantly in genotype (codominant model; CC compared with CG compared with GG; p=0.038) and allele frequencies (odds ratio (OR)=1.89, 95% CI 1.18-3.03, p=0.007) between patients with nsCLP and controls. Analysis of the recessive model of inheritance showed that distribution of the recessive model of rs7545538 (GG compared with CC+GC) was significantly higher in patients with nsCLP than in controls (OR=2.5, 95% CI 1.13-5.37, p=0.021) and had a borderline association with an increased risk of nsCLP (OR=2.5, 95% CI 1.13-5.37, p=0.021). Markers rs2235377 and rs2235371 also differed significantly in dominant and over-dominant models of inheritance (p=0.037) while increased G allele frequency was seen in SNP rs2235373 (p=0.03). A haplotype analysis showed four common haplotypes in Block 1: CCGGT>CCGAT>CACAT>TAGAC (in frequency). The 5-marker combination haplotype CCGAT was significantly more common in patients with nsCLP than in controls (p=0.032). In Block 2, the overall distribution of the haplotypes TAC and TAG predicted by the three SNP differed significantly between the patients with nsCLP and control subjects (p=0.009 and 0.003, respectively). Our results showed that genetic polymorphism of the IRF6 gene is associated with increased risk of nsCLP in a Xinjiang Uyghur population.
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Affiliation(s)
- Ainiwaer Mijiti
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, People's Republic of China; Stomatological Research Institute of Xinjiang Uyghur Autonomous Region, Urumqi, Xinjiang 830054, People's Republic of China
| | - Wang Ling
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, People's Republic of China; Stomatological Research Institute of Xinjiang Uyghur Autonomous Region, Urumqi, Xinjiang 830054, People's Republic of China
| | - Guli
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, People's Republic of China; Stomatological Research Institute of Xinjiang Uyghur Autonomous Region, Urumqi, Xinjiang 830054, People's Republic of China
| | - Adili Moming
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830054, People's Republic of China; Stomatological Research Institute of Xinjiang Uyghur Autonomous Region, Urumqi, Xinjiang 830054, People's Republic of China.
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Nouri N, Memarzadeh M, Carinci F, Cura F, Scapoli L, Nouri N, Jafary F, Sedghi M, Sadri L, Salehi M. Family-based association analysis between nonsyndromic cleft lip with or without cleft palate and IRF6 polymorphism in an Iranian population. Clin Oral Investig 2014; 19:891-4. [DOI: 10.1007/s00784-014-1305-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 08/15/2014] [Indexed: 11/24/2022]
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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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Sequencing of the interferon regulatory factor 6 (IRF6) gene and correlation to its phenotypes in familial non-syndromic cleft lip and palate in North Indian population. EUROPEAN JOURNAL OF PLASTIC SURGERY 2014. [DOI: 10.1007/s00238-014-0937-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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41
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Blanton SH, Burt A, Garcia E, Mulliken JB, Stal S, Hecht JT. Ethnic heterogeneity of IRF6 AP-2a binding site promoter SNP association with nonsyndromic cleft lip and palate. Cleft Palate Craniofac J 2014; 47:574-7. [PMID: 21039277 DOI: 10.1597/09-153] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVE The goal of this study was to confirm the reported association between a noncoding SNP (rs642961) in IRF6 and nonsyndromic cleft lip and palate. DESIGN, SETTING, AND PARTICIPANTS Two SNPs in IRF6 (rs2235371 and rs64296) were genotyped in Hispanic and non-Hispanic white multiplex (122) and simplex (308) nonsyndromic cleft lip and palate families. Linkage and family-based association analyses were performed on the individual SNPs as well as the 2-SNP haplotype. RESULTS Only modest evidence was found for an association with rs642961 and the 2-SNP haplotype. In contrast, strong evidence was found for the association with rs2235371; this was most evident in the non-Hispanic white simplex families. CONCLUSIONS Although it is confirmed that variation in IRF6 is associated with nonsyndromic cleft lip and palate, the results do not support the reported association with SNP rs64296. Importantly, the association varies between ethnic groups. This finding underscores the need for evaluating additional variations in IRF6 across multiple populations to better determine its role in nonsyndromic cleft lip and palate.
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Affiliation(s)
- Susan H Blanton
- University of Miami, Miller School of Medicine, Miami, Florida, USA
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42
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Chhabra N, Goswami M, Chhabra A. Genetic basis of dental agenesis--molecular genetics patterning clinical dentistry. Med Oral Patol Oral Cir Bucal 2014; 19:e112-9. [PMID: 24121910 PMCID: PMC4015040 DOI: 10.4317/medoral.19158] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 09/04/2013] [Indexed: 11/05/2022] Open
Abstract
Tooth agenesis is one of the most common congenital malformations in humans. Hypodontia can either occur as an isolated condition (non-syndromic hypodontia) or can be associated with a syndrome (syndromic hypodontia), highlighting the heterogeneity of the condition. Though much progress has been made to identify the developmental basis of tooth formation, knowledge of the etiological basis of inherited tooth loss is still lacking. To date, the mutation spectra of non-syndromic form of familial and sporadic tooth agenesis in humans have revealed defects in various such genes that encode transcription factors, MSX1 and PAX9 or genes that code for a protein involved in canonical Wnt signaling (AXIN2), and a transmembrane receptor of fibroblast growth factors (FGFR1). The aim of this paper is to review the current literature on the molecular mechanisms responsible for selective hypodontia in humans and to present a detailed overview of causative genes and syndromes associated with hypodontia.
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Affiliation(s)
- N Chhabra
- Maulana Azad Institute of Dental Sciences, Delhi, India-110002,
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43
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Peng S, Tan J, Hu S, Zhou H, Guo J, Jin L, Tang K. Detecting genetic association of common human facial morphological variation using high density 3D image registration. PLoS Comput Biol 2013; 9:e1003375. [PMID: 24339768 PMCID: PMC3854494 DOI: 10.1371/journal.pcbi.1003375] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 10/14/2013] [Indexed: 12/20/2022] Open
Abstract
Human facial morphology is a combination of many complex traits. Little is known about the genetic basis of common facial morphological variation. Existing association studies have largely used simple landmark-distances as surrogates for the complex morphological phenotypes of the face. However, this can result in decreased statistical power and unclear inference of shape changes. In this study, we applied a new image registration approach that automatically identified the salient landmarks and aligned the sample faces using high density pixel points. Based on this high density registration, three different phenotype data schemes were used to test the association between the common facial morphological variation and 10 candidate SNPs, and their performances were compared. The first scheme used traditional landmark-distances; the second relied on the geometric analysis of 15 landmarks and the third used geometric analysis of a dense registration of ∼30,000 3D points. We found that the two geometric approaches were highly consistent in their detection of morphological changes. The geometric method using dense registration further demonstrated superiority in the fine inference of shape changes and 3D face modeling. Several candidate SNPs showed potential associations with different facial features. In particular, one SNP, a known risk factor of non-syndromic cleft lips/palates, rs642961 in the IRF6 gene, was validated to strongly predict normal lip shape variation in female Han Chinese. This study further demonstrated that dense face registration may substantially improve the detection and characterization of genetic association in common facial variation. Heritability of human facial appearance is an intriguing question to the general public and researchers. Although it is known that some facial features are highly heritable, the exact genetic basis is unknown. Previous studies used simple linear measurements such as landmark distances, to evaluate the facial shape variation. Such approaches, although easy to carry out, may lack statistical power and miss complex morphological changes. In this study, we utilized a new 3D face registration method that enables subtle differences to be detected at high resolution 3D images. Based on this, we tried to test and characterize the associations of 10 candidate genetic variants to common facial morphological variations. Different types of phenotype data were extracted and compared in the association tests. Our results show that geometry based data performed better than simple distance based data. Furthermore, high density geometric data outstood the others in capturing small shape changes and modeling the 3D face visualization. Interestingly, a genetic variant from IRF6 gene, which is also a well-known risk factor of non-syndrome cleft lip, was found to strongly predispose the mouth shape in Han Chinese females.
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Affiliation(s)
- Shouneng Peng
- Human Functional Genetic Variation Group, CAS-MPG Partner Institute for Computational Biology, SIBS, Shanghai, China
| | - Jingze Tan
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Sile Hu
- Human Functional Genetic Variation Group, CAS-MPG Partner Institute for Computational Biology, SIBS, Shanghai, China
| | - Hang Zhou
- Human Functional Genetic Variation Group, CAS-MPG Partner Institute for Computational Biology, SIBS, Shanghai, China
| | - Jing Guo
- Human Functional Genetic Variation Group, CAS-MPG Partner Institute for Computational Biology, SIBS, Shanghai, China
| | - Li Jin
- Human Functional Genetic Variation Group, CAS-MPG Partner Institute for Computational Biology, SIBS, Shanghai, China
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Kun Tang
- Human Functional Genetic Variation Group, CAS-MPG Partner Institute for Computational Biology, SIBS, Shanghai, China
- * E-mail:
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44
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Leslie EJ, Marazita ML. Genetics of cleft lip and cleft palate. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2013; 163C:246-58. [PMID: 24124047 DOI: 10.1002/ajmg.c.31381] [Citation(s) in RCA: 269] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Orofacial clefts are common birth defects and can occur as isolated, nonsyndromic events or as part of Mendelian syndromes. There is substantial phenotypic diversity in individuals with these birth defects and their family members: from subclinical phenotypes to associated syndromic features that is mirrored by the many genes that contribute to the etiology of these disorders. Identification of these genes and loci has been the result of decades of research using multiple genetic approaches. Significant progress has been made recently due to advances in sequencing and genotyping technologies, primarily through the use of whole exome sequencing and genome-wide association studies. Future progress will hinge on identifying functional variants, investigation of pathway and other interactions, and inclusion of phenotypic and ethnic diversity in studies.
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Zhou Q, Li M, Zhu W, Guo J, Wang Y, Li Y, Li S. Association between Interferon Regulatory Factor 6 Gene Polymorphisms and Nonsyndromic Cleft Lip with or without Cleft Palate in a Chinese Population. Cleft Palate Craniofac J 2013; 50:570-6. [DOI: 10.1597/12-234] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Objective To further confirm the association between two IRF6 single nucleotide polymorphisms and nonsyndromic cleft lip with or without cleft palate in a Chinese population. Participants A total of 106 nonsyndromic cleft lip with or without cleft palate case trios and 129 control trios. Intervention Two IRF6 single nucleotide polymorphisms, rs2235371 and rs642961, were genotyped for all case and control families. Case-control analysis and family-based linkage analysis were both performed for the two single nucleotide polymorphisms. Results The genotype and allele frequencies of rs2235371 (odds ratioAG+AA vs. GG, 0.581; 95% confidence interval, 0.345 to 0.976; P = .039) and rs642961 (odds ratioAG+AA vs. GG, 5.389; 95% confidence interval, 2.936 to 9.893; P = 5e-08) were significantly higher in nonsyndromic cleft lip with or without cleft palate patients compared with controls. There was an obvious dosage effect of allele A at rs642961. The transmission of a major allele (G) of rs2235371 and a minor allele (A) of rs642961 was in disequilibrium ( P < .05) in complete case-parent trios. The association between the two single nucleotide polymorphisms and nonsyndromic cleft lip with or without cleft palate was confirmed by the Family-Based Association Test for rs642961 ( P = .008), but there was no significance for rs2235371 ( P = 0.057). Haplotype analysis found that rs2235371 G/rs642961 A haplotype increased the risk of nonsyndromic cleft lip with or without cleft palate ( P = 2.42e-07); whereas, rs2235371 A/rs642961 G haplotype reduced the risk of nonsyndromic cleft lip with or without cleft palate ( P = 4.37e-05). No evidence of linkage disequilibrium was found between the two single nucleotide polymorphisms (D′ = 0.303, r2 = 0.017). Conclusion Our results confirmed the involvement of the IRF6 variants rs642961 and rs2235371 in the etiology of nonsyndromic cleft lip with or without cleft palate in a Chinese population.
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Affiliation(s)
- Qian Zhou
- Department of Nutrition and Food Hygiene, School of Public Health, Laboratory of Molecular Toxicology and Development Molecular Biology, Peking University, Beijing, People's Republic of China
| | - Mengjie Li
- Department of Nutrition and Food Hygiene, School of Public Health, Laboratory of Molecular Toxicology and Development Molecular Biology, Peking University, Beijing, People's Republic of China
| | - Wenli Zhu
- Department of Nutrition and Food Hygiene, School of Public Health, Laboratory of Molecular Toxicology and Development Molecular Biology, Peking University, Beijing, People's Republic of China
| | - Jinzhen Guo
- Department of Nutrition and Food Hygiene, School of Public Health, Laboratory of Molecular Toxicology and Development Molecular Biology, Peking University, Beijing, People's Republic of China
| | - Yun Wang
- Department of Nutrition and Food Hygiene, School of Public Health, Laboratory of Molecular Toxicology and Development Molecular Biology, Peking University, Beijing, People's Republic of China
| | - Yong Li
- Department of Nutrition and Food Hygiene, School of Public Health, Laboratory of Molecular Toxicology and Development Molecular Biology, Peking University, Beijing, People's Republic of China
| | - Shuqin Li
- Sheng-Jing Hospital of China Medical University, Shenyang, People's Republic of China
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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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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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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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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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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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