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de Andrade RS, Oliveira FESD, Martelli DRB, de Barros LM, Martelli Júnior H. Maternal consumption of caffeine and second-hand tobacco smoke as risk factors for the development of oral clefts. Clinics (Sao Paulo) 2023; 78:100266. [PMID: 37567043 PMCID: PMC10432903 DOI: 10.1016/j.clinsp.2023.100266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 07/18/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
OBJECTIVE The aim of this case-control study was to investigate environmental factors, such as caffeine, folic acid, nutritional iron supplementation, multivitamin complexes, alcohol, and tobacco (second-hand smoking), which have been described as risk factors for the development of oral clefts. METHODS This case-control study employed convenience sampling and included 409 mothers: 132 with children with oral clefts (cases) and 277 with children without oral clefts (controls). The age range of the children in both groups was 0 to 2 years. A questionnaire was administered to each mother to inquire about their habits and food consumption during the first trimester of pregnancy. RESULTS Folic acid supplementation was observed in 116 (87.8%) of the case group (p < 0.001) and 271 (97.8%) of the control group. Regarding the use of ferrous sulfate, 114 (86.3%) of the case group and 271 (97.8%) of the control group reported using it. In the case group, 84 (63.6%) mothers reported being exposed to second-hand smoke, and 5 (3.7%) reported alcohol consumption (p = 0.797). In terms of caffeine consumption, 127 mothers (95.4%) in the case group consumed it (p = 0.13), while 247 (88.8%) reported consumption in the control group. CONCLUSIONS The results suggest a direct relationship between secondhand smoke, alcohol consumption, and the lack of maternal supplementation with oral clefts.
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Affiliation(s)
| | - Fabrício Emanuel Soares de Oliveira
- Postgraduate Program in Primary Health Care, Unimontes, Montes Claros, Minas Gerais, Brazil; Postgraduate Program in Health Sciences, Unimontes, Montes Claros, Minas Gerais, Brazil.
| | | | - Letízia Monteiro de Barros
- José do Rosário Vellano University, Institute of Dentistry and Health Sciences, Periodontics, Alfenas, Minas Gerais, Brazil
| | - Hercílio Martelli Júnior
- Postgraduate Program in Primary Health Care, Unimontes, Montes Claros, Minas Gerais, Brazil; Postgraduate Program in Health Sciences, Unimontes, Montes Claros, Minas Gerais, Brazil
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2
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Wang S, Shi J, Liu C, Wang P, Wang M, Li W, Zhou R, Zheng H, Jiang J, Li N, Li J, Zhou Z, Zhu H, Wu Y, Jia Z, Wu T, Hu Y, Beaty TH. Evidence of the folate-mediated one-carbon metabolism pathway genes in controlling the non-syndromic oral clefts risks. Oral Dis 2023; 29:1080-1088. [PMID: 34739175 DOI: 10.1111/odi.14068] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/21/2021] [Accepted: 10/26/2021] [Indexed: 02/05/2023]
Abstract
The folate-mediated one-carbon metabolism pathway is thought to play an important role in the etiology of non-syndromic oral clefts (NSOFC), although none of the genes in this pathway has shown significant signals in genome-wide association studies (GWAS). Recent evidence indicated that enhanced understanding could be gained by aggregating multiple SNPs effect simultaneously into polygenic risk score (PRS) to assess its association with disease risks. This study is aimed to assess the association between the genetic effect of folate-mediated one-carbon metabolism pathway and NSOFC risks using PRS based on a case-parent trio design. A total of 297 SNPs mapped from 18 genes in the folate-mediated one-carbon metabolism pathway were aggregated from a GWAS of 2458 case-parent trios recruited from an international consortium. We found a PRS based on the folate-mediated one-carbon metabolism pathway was significant among all NSOFC trios (OR = 1.95, 95% CI: 1.66-2.28, p = 2.39 × 10-16 ), as well as two major subtypes, non-syndromic cleft lip with or without cleft palate (NSCL/P) trios (OR = 1.71, 95% CI: 1.50-1.96, p = 7.66 × 10-15 ) and non-syndromic cleft palate only (NSCPO) trios (OR = 1.51, 95% CI: 1.36-1.68, p = 2.1 × 10-14 ). Similar results were also observed in further subgroup analyses stratified into Asian and European trios. The averaged PRS of the folate-mediated one-carbon metabolism pathway varied between the NSOFC case group and its comparison group (p < 0.05) with higher average PRS in the cases. Moreover, the top 5% pathway PRS group had 2.25 (95% CI: 1.85-2.73) times increased NSOFC risk, also 3.09 (95% CI: 2.50-3.81) and 2.06 (95% CI: 1.39-3.02) times increased risk of NSCL/P and NSCPO compared to the remainder of the distribution. The results of our study confirmed the folate-mediated one-carbon metabolism pathway was important in controlling risk to NSOFC and this study enhanced evidence towards understanding the genetic risks of NSOFC.
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Affiliation(s)
- Siyue Wang
- Peking University Health Science Center, Beijing, China
| | - Jiayu Shi
- Division of Growth and Development and Section of Orthodontics, School of Dentistry, University of California, Los Angeles, USA
| | | | - Ping Wang
- Peking University Health Science Center, Beijing, China
| | - Mengying Wang
- Peking University Health Science Center, Beijing, China
| | - Wenyong Li
- Peking University Health Science Center, Beijing, China
| | - Ren Zhou
- Peking University Health Science Center, Beijing, China
| | | | - Jin Jiang
- Peking University Health Science Center, Beijing, China
| | - Nan Li
- Peking University School of Stomatology, Beijing, China
| | - Jing Li
- Peking University School of Stomatology, Beijing, China
| | - Zhibo Zhou
- Peking University School of Stomatology, Beijing, China
| | - Hongping Zhu
- Peking University School of Stomatology, Beijing, China
| | - Yiqun Wu
- Peking University Health Science Center, Beijing, China
| | - Zhonglin Jia
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Tao Wu
- Peking University Health Science Center, Beijing, China
- Institute of Reproductive and Child Health/Key Laboratory of Reproductive Health, National Health Commission of the People's Republic of China, Beijing, China
| | - Yonghua Hu
- Peking University Health Science Center, Beijing, China
| | - Terri H Beaty
- School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
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3
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Genetic variants in S-adenosyl-methionine synthesis pathway and nonsyndromic cleft lip with or without cleft palate in Chile. Pediatr Res 2021; 89:1020-1025. [PMID: 32492698 DOI: 10.1038/s41390-020-0994-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 05/25/2020] [Indexed: 02/03/2023]
Abstract
BACKGROUND The S-adenosyl-methionine (SAM) availability is crucial for DNA methylation, an epigenetic mechanism involved in nonsyndromic cleft lip with or without cleft palate (NSCL/P) expression. The aim of this study was to assess the association between single-nucleotide polymorphisms (SNPs) of genes involved in SAM synthesis and NSCL/P in a Chilean population. METHODS In 234 cases and 309 controls, 18 SNPs in AHCY, MTR, MTRR, and MAT2A were genotyped, and the association between them and the phenotype was evaluated based on additive (allele), dominant, recessive and haplotype models, by odds ratio (OR) computing. RESULTS Three deep intronic SNPs of MTR showed a protective effect on NSCL/P expression: rs10925239 (OR 0.68; p = 0.0032; q = 0.0192), rs10925254 (OR 0.66; p = 0.0018; q = 0.0162), and rs3768142 (OR 0.66; p = 0.0015; q = 0.0162). Annotations in expression database demonstrate that the protective allele of the three SNPs is associated with a reduction of MTR expression summed to the prediction by bioinformatic tools of its potentiality to modify splicing sites. CONCLUSIONS The protective effect against NSCL/P of these intronic MTR SNPs seems to be related to a decrease in MTR enzyme expression, modulating the SAM availability for proper substrate methylation. However, functional analyses are necessary to confirm our findings. IMPACT SAM synthesis pathway genetic variants are factors associated to NSCL/P. This article adds new evidence for folate related genes in NSCL/P in Chile. Its impact is to contribute with potential new markers for genetic counseling.
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Cáceres-Rojas G, Salamanca C, Krause BJ, Recabarren AS, Recabarren PA, Pantoja R, Leiva N, Pardo R, Santos JL, Suazo J. Nonsyndromic orofacial clefts in Chile: LINE-1 methylation and MTHFR variants. Epigenomics 2020; 12:1783-1791. [PMID: 33147056 DOI: 10.2217/epi-2020-0021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To evaluate the risk of nonsyndromic orofacial clefts (NSOFCs) associated with LINE-1 methylation, as a marker of global DNA methylation, and the effect of MTHFR functional variants on this variable. Patients & methods: LINE-1 methylation was evaluated by bisulfite modification coupled to DNA pyrosequencing in 95 NSOFC cases and 95 controls. In these subjects, MTHFR genotypes for variants c.C677T (rs1801133) and c.A1298C (rs1801131) were obtained. Results: Middle levels (second tertile) of LINE-1 methylation increase the risk of NSOFCs. In addition, LINE-1 methylation depends on c.A1298C genotypes in controls but not in cases. Conclusion: A nonlinear association between global DNA methylation and NSOFCs was detected in this Chilean population, which appears to be influenced by MTHFR functional variants.
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Affiliation(s)
- Gabriela Cáceres-Rojas
- Institute for Research in Dental Sciences, School of Dentistry, Universidad de Chile, Santiago, Chile
| | - Carlos Salamanca
- Institute for Research in Dental Sciences, School of Dentistry, Universidad de Chile, Santiago, Chile.,Research Centre in Dental Sciences (CICO), Dental School, Universidad de La Frontera, Chile.,Universidad Adventista de Chile, Chillán, Chile
| | - Bernardo J Krause
- Instituto de Ciencias de la Salud, Universidad de O'Higgins, Rancagua, Chile
| | - Andrea S Recabarren
- Institute for Research in Dental Sciences, School of Dentistry, Universidad de Chile, Santiago, Chile
| | - Pamela A Recabarren
- Institute for Research in Dental Sciences, School of Dentistry, Universidad de Chile, Santiago, Chile
| | - Roberto Pantoja
- Maxillofacial Surgery Service, Cleft Lip & Palate Unit, Hospital Clínico San Borja-Arriaran. Santiago de Chile, Chile.,Department of Oral & Maxillofacial Surgery, School of Dentistry, Universidad de Chile, Santiago, Chile
| | - Noemi Leiva
- Unit of Maxillofacial Malformations, School of Dentistry, Universidad de Chile, Santiago, Chile
| | - Rosa Pardo
- Section of Genetics, Hospital Clínico Universidad de Chile, Santiago, Chile.,Unit of Neonatology, Hospital Clínico Universidad de Chile, Santiago, Chile.,Unit of Genetics, Hospital Dr Sótero del Río, Santiago, Chile
| | - José Luis Santos
- Department of Nutrition, Diabetes & Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - José Suazo
- Institute for Research in Dental Sciences, School of Dentistry, Universidad de Chile, Santiago, Chile
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5
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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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6
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Machado RA, de Oliveira Silva C, Martelli-Junior H, das Neves LT, Coletta RD. Machine learning in prediction of genetic risk of nonsyndromic oral clefts in the Brazilian population. Clin Oral Investig 2020; 25:1273-1280. [PMID: 32617779 DOI: 10.1007/s00784-020-03433-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 06/24/2020] [Indexed: 01/07/2023]
Abstract
OBJECTIVES Genetic variants in multiple genes and loci have been associated with the risk of nonsyndromic cleft lip with or without cleft palate (NSCL ± P). However, the estimation of risk remains challenge, because most of these variants are population-specific rendering the identification of the underlying genetic risk difficult. Herein we examined the use of machine learning network in previously reported single nucleotide polymorphisms (SNPs) to predict risk of NSCL ± P in the Brazilian population. MATERIALS AND METHODS Random forest and neural network methods were applied in 72 SNPs in a case-control sample composed by 722 NSCL ± P and 866 controls for discrimination of NSCL ± P risk. SNP-SNP interactions and functional annotation biological processes associated with the identified NSCL ± P risk genes were verified. RESULTS Supervised random forest decision trees revealed high scores of importance for the SNPs rs11717284 and rs1875735 in FGF12, rs41268753 in GRHL3, rs2236225 in MTHFD1, rs2274976 in MTHFR, rs2235371 and rs642961 in IRF6, rs17085106 in RHPN2, rs28372960 in TCOF1, rs7078160 in VAX1, rs10762573 and rs2131960 in VCL, and rs227731 in 17q22, with an accuracy of 99% and an error rate of approximately 3% to predict the risk of NSCL ± P. Those same 13 SNPs were considered the most important for the neural network to effectively predict NSCL ± P risk, with an overall accuracy of 94%. Multivariate regression model revealed significant interactions among all SNPs, with an exception of those in FGF12 and MTHFD1. The most significantly biological processes for selected genes were those involved in tissue and epithelium development; neural tube closure; and metabolism of methionine, folate, and homocysteine. CONCLUSIONS Our results provide novel clues for genetic mechanism studies of NSCL ± P and point out for a machine learning model composed by 13 SNPs that is capable of predicting NSCL ± P risk. CLINICAL RELEVANCE Although validation is necessary, this genetic panel can be useful in the near future to assist in NSCL ± P genetic counseling.
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Affiliation(s)
- Renato Assis Machado
- Department of Oral Diagnosis, School of Dentistry, University of Campinas, Piracicaba, São Paulo, CEP 13414-018, Brazil
- Post-Graduation Program in Rehabilitation Sciences, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
| | - Carolina de Oliveira Silva
- Department of Oral Diagnosis, School of Dentistry, University of Campinas, Piracicaba, São Paulo, CEP 13414-018, Brazil
| | - Hercílio Martelli-Junior
- Stomatology Clinic, Dental School, State University of Montes Claros, Montes Claros, Minas Gerais, Brazil
- Center for Rehabilitation of Craniofacial Anomalies, Dental School, University of José Rosario Vellano, Alfenas, Minas Gerais, Brazil
| | - Lucimara Teixeira das Neves
- Post-Graduation Program in Rehabilitation Sciences, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Bauru, São Paulo, Brazil
| | - Ricardo D Coletta
- Department of Oral Diagnosis, School of Dentistry, University of Campinas, Piracicaba, São Paulo, CEP 13414-018, Brazil.
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Badr DA, Sanchez TC, Kang X, Olivier C, Jani JC. The impact of family history of non-syndromic oral clefts on their incidence in pregnancy. J Matern Fetal Neonatal Med 2020; 35:1523-1526. [PMID: 32367753 DOI: 10.1080/14767058.2020.1759539] [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: 10/24/2022]
Abstract
Background and objective: Orofacial clefts are the most commonly diagnosed birth defects of the face during pregnancy. They can be either syndromic or non-syndromic. The objective of this study was to calculate the incidence of non-syndromic cleft lip with or without cleft palate (CL/CP) and isolated cleft palate (CP) in patients with a positive family history of non-syndromic oral clefts, and to identify the familial risk factors of oral cleft development in these patients.Methods: This was a retrospective study that included all patients with a positive family history of non-syndromic oral clefts, followed up in the department of fetal medicine in Brugmann University Hospital, Brussels, Belgium, between 1 January 2009 and 31 December 2019.Results: Over the study period, the incidence of non-syndromic oral clefts was 10.81/10,000 pregnancies. Seventy-three (0.15%) women had a positive family history of oral clefts, and had 86 pregnancies during this period. The incidence of oral clefts in this group was 9.3% (86-fold increase). This incidence varied depending on many factors, including the type of oral clefts in the family, the degree of relation of the fetus or baby to the family member who has the cleft, and the number of siblings with oral clefts.Conclusion: The offspring of pregnant patients with a positive family history of oral clefts are at risk for recurrence. The incidence is very high when there are 3 or more siblings with oral clefts, when the father or mother has the anomaly, or when there is bilateral CL/CP in the family history.
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Affiliation(s)
- Dominique A Badr
- Department of Obstetrics and Gynecology, University Hospital Brugmann, Université Libre de Bruxelles, Vrije Universiteit Brussel, Brussels, Belgium
| | - Teresa Cos Sanchez
- Department of Obstetrics and Gynecology, University Hospital Brugmann, Université Libre de Bruxelles, Vrije Universiteit Brussel, Brussels, Belgium
| | - Xin Kang
- Department of Obstetrics and Gynecology, University Hospital Brugmann, Université Libre de Bruxelles, Vrije Universiteit Brussel, Brussels, Belgium
| | - Camille Olivier
- Department of Obstetrics and Gynecology, University Hospital Brugmann, Université Libre de Bruxelles, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jacques C Jani
- Department of Obstetrics and Gynecology, University Hospital Brugmann, Université Libre de Bruxelles, Vrije Universiteit Brussel, Brussels, Belgium
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8
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Salamanca C, González-Hormazábal P, Recabarren AS, Recabarren PA, Pantoja R, Leiva N, Pardo R, Suazo J. A SHMT1 variant decreases the risk of nonsyndromic cleft lip with or without cleft palate in Chile. Oral Dis 2019; 26:159-165. [PMID: 31713293 DOI: 10.1111/odi.13229] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To assess the association between polymorphic variants from SHMT1 and MTHFS genes, involved in the cytoplasmic futile folate cycle, and the risk of nonsyndromic cleft lip with or without cleft palate (NSCL/P) in the Chilean population. SUBJECTS AND METHODS In a sample of 139 Chilean NSCL/P cases and 278 controls, we obtained the genotypes for nine variants of SHMT1 and MTHFS and the association between them and the phenotype was evaluated using odds ratios (OR) in additive (allele), dominant, and recessive models. RESULTS After correction for multiple comparisons, only the variant rs1979277 (G > A; p.Leu474Phe) from SHMT1 showed a significant and protective effect for additive (OR 0.60; 95% CI 0.42-0.86; p = .0054, q = 0.0488) and dominant models (OR 0.48; 95% CI 0.29-0.75; p = .0009; q = 0.0081). Our bioinformatic prediction plus functional evidence from previous reports demonstrate that the A allele for this missense variant decreases the enzymatic activity. CONCLUSIONS Owing to the rs1979277 A allele, which reduces the cytoplasmic SHMT activity and has a higher frequency in controls than in NSCL/P cases, we hypothesized that a low enzyme activity may increase the cytoplasmic concentration of folates and, therefore, explain the protective role against OFCs.
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Affiliation(s)
- Carlos Salamanca
- Institute for Research in Dental Sciences, School of Dentistry, Universidad de Chile, Santiago, Chile.,Research Centre in Dental Sciences (CICO), Dental School, Universidad de La Frontera, Temuco, Chile.,Universidad Adventista de Chile, Chillán, Chile
| | - Patricio González-Hormazábal
- Human Genetics Program, Institute of Biomedical Sciences, School of Medicine, Universidad de Chile, Santiago, Chile
| | - Andrea S Recabarren
- Institute for Research in Dental Sciences, School of Dentistry, Universidad de Chile, Santiago, Chile
| | - Pamela A Recabarren
- Institute for Research in Dental Sciences, School of Dentistry, Universidad de Chile, Santiago, Chile
| | - Roberto Pantoja
- Unit of Oral and Maxillofacial Surgery, Hospital Clínico San Borja-Arriaran, Santiago de Chile, Chile.,Department of Oral and Maxillofacial Surgery, School of Dentistry, Universidad de Chile, Santiago, Chile
| | - Noemi Leiva
- Unit of Maxillofacial Malformations, School of Dentistry, Universidad de Chile, Santiago, Chile
| | - Rosa Pardo
- Section of Genetics, Hospital Clínico Universidad de Chile, Santiago, Chile.,Unit of Neonatology, Hospital Clínico Universidad de Chile, Santiago, Chile.,Unit of Genetics, Hospital Dr. Sótero del Río, Santiago, Chile
| | - José Suazo
- Institute for Research in Dental Sciences, School of Dentistry, Universidad de Chile, Santiago, Chile
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9
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Imani MM, Lopez-Jornet P, López EPF, Ghanbari F, Sadeghi M. Association of Betaine-Homocysteine S-Methyl Transferase (rs3797546 and rs3733890) polymorphisms with non-syndromic cleft lip/palate: A meta-analysis. Int Orthod 2019; 17:643-651. [PMID: 31451344 DOI: 10.1016/j.ortho.2019.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE Non-syndromic cleft lip/palate (NSCL/P) has a multifactorial and polygenic aetiology. The role of genetics in its occurrence has not been fully clarified. The present meta-analysis aimed to evaluate the association of betaine-homocysteine S-methyltransferase (BHMT) polymorphisms (rs3797546 and rs3733890) with the risk of NSCL/P. MATERIALS AND METHODS PubMed/Medline, Scopus, Cochrane Library, and Web of Science databases were systematically searched for articles published up until December 2018 with no language restriction. Quality evaluation of each study was performed by the Newcastle-Ottawa Scale (NOS). The crude odds ratio (OR) and 95% confidence interval (CI) were calculated for each study by RevMan 5.3 software, and a funnel plot analysis was performed by the CMA 2.0 software using the Egger's and Begg's tests. RESULTS Review of the four selected studies revealed that the CC genotype of rs3797546 polymorphism significantly increased the risk of NSCL/P. No association was noted between NSCL/P risk and rs3733890 polymorphism except in Chinese (elevated risk of NSCL/P) and Polish (decreased risk of NSCL/P) populations. CONCLUSIONS According to the present meta-analysis, rs3733890 polymorphism does not play a role in susceptibility to NSCL/P; whereas, rs3797546 polymorphism may play a role in susceptibility to NSCL/P. Future studies are required to examine the association between BHMT polymorphisms and the NSCL/P risk in different ethnicities with a larger sample size.
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Affiliation(s)
- Mohammad Moslem Imani
- Department of Orthodontics, School of Dentistry, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Pia Lopez-Jornet
- Facultad de Medicina y Odontologia Universidad de Murcia, Hospital Morales Meseguer, Clinica Odontologic Adv Marques Velez s/n, 30008 Murcia, Spain
| | - Eduardo Pons-Fuster López
- Insitituto Murciano de Investigación Biomédica, Murcia, Campus de Ciencias de la Salud, Carretera Buenavista s/n, 30120 El Palmar, Murcia, Spain
| | - Fatemeh Ghanbari
- Department of Orthodontics, Dental Branch, Islamic Azad University, Tehran, Iran
| | - Masoud Sadeghi
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran; Students Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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10
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Liu D, Wang M, Yuan Y, Schwender H, Wang H, Wang P, Zhou Z, Li J, Wu T, Zhu H, Beaty TH. Gene-gene interaction among cell adhesion genes and risk of nonsyndromic cleft lip with or without cleft palate in Chinese case-parent trios. Mol Genet Genomic Med 2019; 7:e00872. [PMID: 31419083 PMCID: PMC6785639 DOI: 10.1002/mgg3.872] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/27/2019] [Accepted: 07/08/2019] [Indexed: 01/07/2023] Open
Abstract
Background Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect with complex etiology. One strategy for studying the genetic risk factors of NSCL/P is to consider gene–gene interaction (G × G) among gene pathways having a role in craniofacial development. The present study aimed to investigate the G × G among cell adhesion gene pathway. Methods We carried out an interaction analysis of eight genes involved in cell adherens junctions among 806 NSCL/P Chinese case‐parent trios originally recruited for a genome‐wide association study (GWAS). Regression‐based approach was used to test for two‐way G × G interaction, while machine learning algorithm was run for exploring both two‐way and multi‐way interaction that may affect the risk of NSCL/P. Results A two‐way ACTN1 × CTNNB1 interaction reached the adjusted significance level. The single nucleotide polymorphisms pair composed of rs17252114 (CTNNB1) and rs1274944 (ACTN1) yielded a p value of .0002, and this interaction was also supported by the logic regression algorithm. Higher order interactions involving ACTN1, CTNNB1, and CDH1 were picked out by logic regression, suggesting a potential role in NSCL/P risk. Conclusion This study suggests for the first time evidence of both two‐way and multi‐way G × G interactions among cell adhesion genes contributing to the NSCL/P risk.
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Affiliation(s)
- Dongjing Liu
- School of Public Health, Peking University, Beijing, China
| | - Mengying Wang
- School of Public Health, Peking University, Beijing, China
| | - Yuan Yuan
- School of Public Health, Peking University, Beijing, China
| | - Holger Schwender
- Mathematical Institute, Heinrich Heine University Duesseldorf, Duesseldorf, Germany
| | - Hong Wang
- School of Public Health, Peking University, Beijing, China
| | - Ping Wang
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Zhibo Zhou
- School of Stomatology, Peking University, Beijing, China
| | - Jing Li
- School of Stomatology, Peking University, Beijing, China
| | - Tao Wu
- School of Public Health, Peking University, Beijing, China.,Key Laboratory of Reproductive Health, Ministry of Health, Beijing, China
| | - Hongping Zhu
- School of Stomatology, Peking University, Beijing, China
| | - Terri H Beaty
- School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
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11
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Seelan RS, Pisano M, Greene RM. Nucleic acid methylation and orofacial morphogenesis. Birth Defects Res 2019; 111:1593-1610. [PMID: 31385455 DOI: 10.1002/bdr2.1564] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/17/2019] [Accepted: 07/19/2019] [Indexed: 12/19/2022]
Abstract
In this review, we highlight the current state of knowledge of the diverse roles nucleic acid methylation plays in the embryonic development of the orofacial region and how aberrant methylation may contribute to orofacial clefts. We also consider the role of methylation in the regulation of neural crest cell function as it pertains to orofacial ontogeny. Changes in DNA methylation, as a consequence of environmental effects, have been observed in the regulatory regions of several genes, potentially identifying new candidate genes for orofacial clefting and opening promising new avenues for further research. While the focus of this review is primarily on the nonsyndromic forms of orofacial clefting, syndromic forms are briefly discussed in the context of aberrant nucleic acid methylation.
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Affiliation(s)
- Ratnam S Seelan
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, Kentucky
| | - Michele Pisano
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, Kentucky
| | - Robert M Greene
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, Kentucky
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12
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Machado RA, de Oliveira Silva C, Persuhn DC, de Melo Cavalcanti Dantas V, de Almeida Reis SR, Wu T, Line SR, Martelli-Junior H, Graner E, Coletta RD. Interactions between superoxide dismutase and paraoxonase polymorphic variants in nonsyndromic cleft lip with or without cleft palate in the Brazilian population. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2019; 60:185-196. [PMID: 30240501 DOI: 10.1002/em.22239] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/19/2018] [Accepted: 08/09/2018] [Indexed: 06/08/2023]
Abstract
During development, oxidative stress is hypothesized to mediate embryotoxicity, which may be intensified by exposition to environmental factors and by genetic variations in the enzymes involved in protecting cells from these damaging effects, including superoxide dismutase (SOD) and paraoxonase (PON). The aim of this study was to evaluate the influence of single-nucleotide polymorphisms (SNP) in genes associated with the neutralization of oxidative stress (SOD and PON family members) in the risk of nonsyndromic oral cleft in the Brazilian population. Initially, we tested for association between 28 SNP in SOD1, SOD2, SOD3, PON1, PON2, and PON3 among 325 nonsyndromic cleft lip with or without cleft palate (NSCL±P) case-parent trios. Multiple logistic regression analyses were used to explore gene, GxG and GxE, involving factors that induce oxidative stress accumulation during pregnancy. Signals still significant after both Bonferroni correction and in permutation test were subsequently confirmed in an ancestry-structured case-control analysis with 722 NSCL±P and 866 controls from the same population. In the trio sample, transmission disequilibrium test (TDT) (allele and haplotype) and GxE analysis showed no significant associations, but multiple pairwise GxG interactions involving 10 SNP in PON1, PON2, and PON3 were detected and further examined in the case-control sample. The PON1 rs2237583 and PON2 rs17166879 yielded significant evidence of SNP-SNP interactions after adjustment for multiple tests (both Bonferroni correction and 10,000 permutation test). The C allele and the CT genotype of PON1 rs2237583 were associated with significant protective effects against NSCL±P, while rs3917490 showed a significant association only in the sample composed of patients displaying high African ancestry. Our results reveal associations between rs2237583 and rs3917490 in PON1 and GxG interactions containing rs2237583 and rs17166879 with the susceptibility of NSCL±P in the Brazilian population. Furthermore, this study underlines the recent tendency of taking into account potential GxG interactions to clarify the underlying mechanisms associated with the etiology of this common malformation. Environ. Mol. Mutagen. 60: 185-196, 2019. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Renato Assis Machado
- Department of Oral Diagnosis, School of Dentistry, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Carolina de Oliveira Silva
- Department of Oral Diagnosis, School of Dentistry, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Darlene Camati Persuhn
- Molecular Biology Department, Federal University of Paraiba, João Pessoa, Paraiba, Brazil
| | | | | | - Tao Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, People's Republic of China
| | - Sergio Roberto Line
- Department of Morphology, School of Dentistry, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Hercilio Martelli-Junior
- Stomatology Clinic, Dental School, State University of Montes Claros, Montes Claros, Minas Gerais, Brazil and Center for Rehabilitation of Craniofacial Anomalies, University of José Rosario Vellano, Alfenas, Minas Gerais, Brazil
| | - Edgard Graner
- Department of Oral Diagnosis, School of Dentistry, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Ricardo D Coletta
- Department of Oral Diagnosis, School of Dentistry, University of Campinas, Piracicaba, São Paulo, Brazil
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13
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Machine Learning Models for Genetic Risk Assessment of Infants with Non-syndromic Orofacial Cleft. GENOMICS PROTEOMICS & BIOINFORMATICS 2018; 16:354-364. [PMID: 30578914 PMCID: PMC6364041 DOI: 10.1016/j.gpb.2018.07.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 06/19/2018] [Accepted: 07/17/2018] [Indexed: 11/30/2022]
Abstract
The isolated type of orofacial cleft, termed non-syndromic cleft lip with or without cleft palate (NSCL/P), is the second most common birth defect in China, with Asians having the highest incidence in the world. NSCL/P involves multiple genes and complex interactions between genetic and environmental factors, imposing difficulty for the genetic assessment of the unborn fetus carrying multiple NSCL/P-susceptible variants. Although genome-wide association studies (GWAS) have uncovered dozens of single nucleotide polymorphism (SNP) loci in different ethnic populations, the genetic diagnostic effectiveness of these SNPs requires further experimental validation in Chinese populations before a diagnostic panel or a predictive model covering multiple SNPs can be built. In this study, we collected blood samples from control and NSCL/P infants in Han and Uyghur Chinese populations to validate the diagnostic effectiveness of 43 candidate SNPs previously detected using GWAS. We then built predictive models with the validated SNPs using different machine learning algorithms and evaluated their prediction performance. Our results showed that logistic regression had the best performance for risk assessment according to the area under curve. Notably, defective variants in MTHFR and RBP4, two genes involved in folic acid and vitamin A biosynthesis, were found to have high contributions to NSCL/P incidence based on feature importance evaluation with logistic regression. This is consistent with the notion that folic acid and vitamin A are both essential nutritional supplements for pregnant women to reduce the risk of conceiving an NSCL/P baby. Moreover, we observed a lower predictive power in Uyghur than in Han cases, likely due to differences in genetic background between these two ethnic populations. Thus, our study highlights the urgency to generate the HapMap for Uyghur population and perform resequencing-based screening of Uyghur-specific NSCL/P markers.
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