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Zawiślak A, Woźniak K, Tartaglia G, Kawala B, Gupta S, Znamirowska-Bajowska A, Grocholewicz K, Lubiński J, Jakubowska A. Testing Reported Associations of Gene Variants with Non-Syndromic Orofacial Clefts in the Polish Population. Biomedicines 2024; 12:1700. [PMID: 39200165 PMCID: PMC11351639 DOI: 10.3390/biomedicines12081700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 07/27/2024] [Accepted: 07/30/2024] [Indexed: 09/02/2024] Open
Abstract
Orofacial clefts (OFCs) are the second most common birth defect worldwide. The etiology of OFCs involves complex interactions between genetics and environment. Advances in genomic technologies have identified gene variants associated with OFCs. This study aimed to investigate whether selected SNPs in the MYH9, MTHFR, MAFB, and SUMO1 genes influence the occurrence of non-syndromic OFCs in the Polish population. The study included 209 individuals with non-syndromic OFCs and 418 healthy controls. Saliva and umbilical cord blood samples were collected for DNA extraction. Four SNPs in the MYH9, MTHFR, MAFB, and SUMO1 genes were genotyped using real-time PCR-based TaqMan assays. Statistical analysis was performed using logistic regression to assess the association between SNPs and OFCs. A significant association was found between the rs7078 CC polymorphism and OFCs (OR = 3.22, CI 1.68-6.17, p < 0.001). No significant associations were identified for the rs1081131, rs13041247, and rs3769817 polymorphisms. The research indicates that the rs7078 polymorphism significantly influences the occurrence of orofacial cleft palate in the Polish population, whereas the rs3769817, rs1801131, and rs13041247 SNPs do not show such a correlation.
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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;
| | - Gianluca Tartaglia
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20100 Milan, Italy;
| | - Beata Kawala
- Department of Dentofacial Orthopaedics and Orthodontics, Wrocław Medical University, 50-425 Wroclaw, Poland; (B.K.); (A.Z.-B.)
| | - Satish Gupta
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland; (S.G.); (J.L.); (A.J.)
| | - Anna Znamirowska-Bajowska
- Department of Dentofacial Orthopaedics and Orthodontics, Wrocław Medical University, 50-425 Wroclaw, Poland; (B.K.); (A.Z.-B.)
| | - Katarzyna Grocholewicz
- Department of Interdisciplinary Dentistry, Pomeranian Medical University, 70-111 Szczecin, Poland;
| | - Jan Lubiński
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland; (S.G.); (J.L.); (A.J.)
| | - Anna Jakubowska
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland; (S.G.); (J.L.); (A.J.)
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, 70-111 Szczecin, Poland
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Zawiślak A, Woźniak K, Tartaglia G, Agirre X, Gupta S, Kawala B, Znamirowska-Bajowska A, Grocholewicz K, Prosper F, Lubiński J, Jakubowska A. Single-Nucleotide Polymorphisms in WNT Genes in Patients with Non-Syndromic Orofacial Clefts in a Polish Population. Diagnostics (Basel) 2024; 14:1537. [PMID: 39061674 PMCID: PMC11275573 DOI: 10.3390/diagnostics14141537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 07/04/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Non-syndromic orofacial cleft (OFC) is the most common facial developmental defect in the global population. The etiology of these birth defects is complex and multifactorial, involving both genetic and environmental factors. This study aimed to determine if SNPs in the WNT gene family (rs1533767, rs708111, rs3809857, rs7207916, rs12452064) are associated with OFCs in a Polish population. The study included 627 individuals: 209 children with OFCs and 418 healthy controls. DNA was extracted from saliva for the study group and from umbilical cord blood for the control group. Polymorphism genotyping was conducted using quantitative PCR. No statistically significant association was found between four variants and clefts, with odds ratios for rs708111 being 1.13 (CC genotype) and 0.99 (CT genotype), for rs3809857 being 1.05 (GT genotype) and 0.95 (TT genotype), for rs7207916 being 0.86 (AA genotype) and 1.29 (AG genotype) and for rs12452064 being 0.97 (AA genotype) and 1.24 (AG genotype). However, the rs1533767 polymorphism in WNT showed a statistically significant increase in OFC risk for the GG genotype (OR = 1.76, p < 0.001). This research shows that the rs1533767 polymorphism in the WNT gene is an important risk marker for OFC in the Polish population.
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Affiliation(s)
- Alicja Zawiślak
- Department of Interdisciplinary Dentistry, Pomeranian Medical University, 70-111 Szczecin, Poland;
- Department of Maxillofacial Orthopaedics and Orthodontics, Institute of Mother and Child, 01-211 Warsaw, Poland
| | - Krzysztof Woźniak
- Department of Orthodontics, Pomeranian Medical University, 70-111 Szczecin, Poland;
| | - Gianluca Tartaglia
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, 20122 Milan, Italy;
| | - Xabier Agirre
- Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Avenida Pío XII-55, 31008 Pamplona, Spain; (X.A.); (F.P.)
| | - Satish Gupta
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland; (S.G.); (J.L.)
| | - Beata Kawala
- Department of Dentofacial Orthopaedics and Orthodontics, Wrocław Medical University, 50-425 Wrocław, Poland; (B.K.); (A.Z.-B.)
| | - Anna Znamirowska-Bajowska
- Department of Dentofacial Orthopaedics and Orthodontics, Wrocław Medical University, 50-425 Wrocław, Poland; (B.K.); (A.Z.-B.)
| | - Katarzyna Grocholewicz
- Department of Interdisciplinary Dentistry, Pomeranian Medical University, 70-111 Szczecin, Poland;
| | - Felipe Prosper
- Centro de Investigación Médica Aplicada, IDISNA, Universidad de Navarra, Avenida Pío XII-55, 31008 Pamplona, Spain; (X.A.); (F.P.)
| | - Jan Lubiński
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland; (S.G.); (J.L.)
| | - Anna Jakubowska
- Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, 70-111 Szczecin, Poland;
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Bezamat M, Carver CE, Vieira AR. Family-based GWAS for dental class I malocclusion and clefts. BMC Oral Health 2024; 24:665. [PMID: 38849772 PMCID: PMC11162011 DOI: 10.1186/s12903-024-04444-x] [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: 03/25/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Individuals born with cleft lip and/or palate who receive corrective surgery regularly have abnormal growth in the midface region such that they exhibit premaxillary hypoplasia. However, there are also genetic contributions to craniofacial morphology in the midface region, so although these individuals appear to have Class III skeletal discrepancy, their molar relationship may be Class I. Past genome-wide association studies (GWASs) on skeletal Class II and III malocclusion suggested that multiple genetic markers contribute to these phenotypes via a multifactorial inheritance model, but research has yet to examine the genetic markers associated with dental Class I malocclusion. Thus, our goal was to conduct a family based GWAS to identify genes across the genome that are associated with Class I malocclusion, as defined by molar relations, in humans with and without clefts. METHODS Our cohort consisted of 739 individuals from 47 Filipino families originally recruited in 2006 to investigate the genetic basis of orofacial clefts. All individuals supplied blood samples for DNA extraction and genotyping, and a 5,766 single nucleotide polymorphism (SNP) custom panel was used for the analyses. We performed a transmission disequilibrium test for participants with and without clefts to identify genetic contributors potentially involved with Class I malocclusion. RESULTS In the total cohort, 13 SNPs had associations that reached the genomic control threshold (p < 0.005), while five SNPs were associated with Class I in the cohort of participants without clefts, including four associations that were identified in the total cohort. The associations for the SNPs ABCA4 rs952499, SOX1-OT rs726455, and RORA rs877228 are of particular interest, as past research found associations between these genes and various craniofacial phenotypes, including cleft lip and/or palate. CONCLUSIONS These findings support the multifactorial inheritance model for dental Class I malocclusion and suggest a common genetic basis for different aspects of craniofacial development.
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Affiliation(s)
- Mariana Bezamat
- Department of Oral and Craniofacial Sciences, University of Pittsburgh School of Dental Medicine, Pittsburgh, PA, USA
| | - Chelsea E Carver
- Department of Oral and Craniofacial Sciences, University of Pittsburgh School of Dental Medicine, Pittsburgh, PA, USA
| | - Alexandre R Vieira
- School of Dental Medicine, East Carolina University, Greenville, NC, 27834-4354, USA.
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Mougeot JLC, Beckman MF, Hovan AJ, Hasséus B, Legert KG, Johansson JE, von Bültzingslöwen I, Brennan MT, Bahrani Mougeot F. Identification of single nucleotide polymorphisms (SNPs) associated with chronic graft-versus-host disease in patients undergoing allogeneic hematopoietic cell transplantation. Support Care Cancer 2023; 31:587. [PMID: 37731134 PMCID: PMC10511391 DOI: 10.1007/s00520-023-08044-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 09/06/2023] [Indexed: 09/22/2023]
Abstract
INTRODUCTION Chronic graft-versus-host disease (cGVHD) is a debilitating side effect of allogeneic hematopoietic cell transplantation (HCT), affecting the quality of life of patients. We used whole exome sequencing to identify candidate SNPs and complete a multi-marker gene-level analysis using a cohort of cGVHD( +) (N = 16) and cGVHD( -) (N = 66) HCT patients. METHODS Saliva samples were collected from HCT patients (N = 82) pre-conditioning in a multi-center study from March 2011 to May 2018. Exome sequencing was performed and FASTQ files were processed for sequence alignments. Significant SNPs were identified by logistic regression using PLINK2v3.7 and Fisher's exact test. One cGVHD( -) patient sample was excluded from further analysis since no SNP was present in at least 10% of the sample population. The FUMA platform's SNP2GENE was utilized to annotate SNPs and generate a MAGMA output. Chromatin state visualization of lead SNPs was completed using Epilogos tool. FUMA's GENE2FUNC was used to obtain gene function and tissue expression from lead genomic loci. RESULTS Logistic regression classified 986 SNPs associated with cGVHD( +). SNP2GENE returned three genomic risk loci, four lead SNPs, 48 candidate SNPs, seven candidate GWAS tagged SNPs, and four mapped genes. Fisher's exact test identified significant homozygous genotypes of four lead SNPs (p < 0.05). GENE2FUNC analysis of multi-marker SNP sets identified one positional gene set including lead SNPs for KANK1 and KDM4C and two curated gene sets including lead SNPs for PTPRD, KDM4C, and/or KANK1. CONCLUSIONS Our data suggest that SNPs in three genes located on chromosome 9 confer genetic susceptibility to cGVHD in HCT patients. These genes modulate STAT3 expression and phosphorylation in cancer pathogenesis. The findings may have implications in the modulation of pathways currently targeted by JAK inhibitors in cGVHD clinical trials.
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Affiliation(s)
- Jean-Luc C Mougeot
- Translational Research Laboratories, Department of Oral Medicine/Oral & Maxillofacial Surgery, Atrium Health - Carolinas Medical Center, Charlotte, NC, USA.
| | - Micaela F Beckman
- Translational Research Laboratories, Department of Oral Medicine/Oral & Maxillofacial Surgery, Atrium Health - Carolinas Medical Center, Charlotte, NC, USA
| | - Allan J Hovan
- BC Cancer, Oral Oncology and Dentistry, Vancouver, BC, Canada
| | - Bengt Hasséus
- Department of Oral Medicine and Pathology, University of Gothenburg, Gothenburg, Sweden
| | | | - Jan-Erik Johansson
- Department of Hematology and Coagulation, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | - Michael T Brennan
- Translational Research Laboratories, Department of Oral Medicine/Oral & Maxillofacial Surgery, Atrium Health - Carolinas Medical Center, Charlotte, NC, USA
- Department of Otolaryngology/Head & Neck Surgery, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Farah Bahrani Mougeot
- Translational Research Laboratories, Department of Oral Medicine/Oral & Maxillofacial Surgery, Atrium Health - Carolinas Medical Center, Charlotte, NC, USA.
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Imani MM, Shalchi M, Ahmadabadi G, Sadeghi M. Evaluation of matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs) in human cases with orofacial clefts: A systematic review. Int Orthod 2023; 21:100781. [PMID: 37301105 DOI: 10.1016/j.ortho.2023.100781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 06/12/2023]
Abstract
INTRODUCTION The interaction between several cell populations or many genes and the coordination of multiple signal transmission pathways can lead to defects such as orofacial clefts (OFCs). Herein, a systematic review was designed to evaluate a group of important biomarkers (matrix metalloproteinases [MMPs] and tissue inhibitors of metalloproteinases [TIMPs]) in human cases with OFCs. MATERIAL AND METHODS Four databases including PubMed, Scopus, Web of Science, and Cochrane Library databases were searched until March 10, 2023, without any restriction. STRING, the protein-protein interaction (PPI) network software, was applied to investigate the functional interactions among the examined genes. The effect sizes including odds ratio (OR) dealing with a 95% confidence interval (CI), were extracted by the Comprehensive Meta-Analysis version 2.0 (CMA 2.0) software. RESULTS Thirty-one articles were entered into the systematic review that four articles were analyzed in the meta-analysis. Single studies reported that several polymorphisms of MMPs (rs243865, rs9923304, rs17576, rs6094237, rs7119194, and rs7188573); and TIMPs (rs8179096, rs7502916, rs4789936, rs6501266, rs7211674, rs7212662, and rs242082) had an association with OFC risk. There was no significant difference for MMP-3 rs3025058 polymorphism in allelic (OR: 0.832; P=0.490), dominant (OR: 1.177; P=0.873), and recessive (OR: 0.363; P=0.433) models and MMP-9 rs17576 polymorphism in an allelic model (OR: 0.885; P=0.107) between the OFC cases and the controls. Based on immunohistochemistry reports, three MMPs (MMP-2, MMP-8, and MMP-9) and TIMP-2 had significant correlations with several other biomarkers in OFC cases. CONCLUSIONS MMPs and TIMPs can impact the tissue and cells affected by OFCs and the process of apoptosis. The interaction between some biomarkers with MMPs and TIMPs (e.g., TGFb1) in OFCs can be interesting for future research.
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Affiliation(s)
- Mohammad Moslem Imani
- Department of Orthodontics, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Majid Shalchi
- Department of Orthodontics, School of Dentistry, Guilan University of Medical Sciences, Rasht, Iran
| | | | - Masoud Sadeghi
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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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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Mungmunpuntipantip R, Wiwanitkit V. Vax1 rs7078160 polymorphisms and non-syndromic cleft lip: correspondence. Braz J Otorhinolaryngol 2022; 88:487. [PMID: 35168926 PMCID: PMC9422612 DOI: 10.1016/j.bjorl.2022.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 11/28/2022] Open
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