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Chen X, Zhou Z, Li Y, Wang S, Xue E, Wang X, Peng H, Fan M, Wang M, Qin X, Wu Y, Li J, Zhu H, Chen D, Hu Y, Beaty TH, Wu T. Detecting Gene-Gene Interaction among DNA Repair Genes in Chinese non-Syndromic Cleft lip with or Without Palate Trios. Cleft Palate Craniofac J 2024:10556656241228124. [PMID: 38303570 DOI: 10.1177/10556656241228124] [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: 02/03/2024] Open
Abstract
OBJECTIVE The objective of this study is to investigate the gene-gene interactions associated with NSCL/P among DNA repair genes. DESIGN This study included 806 NSCL/P case-parent trios from China. Quality control process was conducted for genotyped single nucleotide polymorphisms (SNPs) located in six DNA repair genes (ATR, ERCC4, RFC1, TYMS, XRCC1 and XRCC3). We tested gene-gene interactions with Cordell's method using statistical package TRIO in R software. Bonferroni corrected significance level was set as P = 4.24 × 10-4. We also test the robustness of the interactions by permutation tests. SETTING Not applicable. PATIENTS/PARTICIPANTS A total of 806 NSCL/P case-parent trios (complete trios: 682, incomplete trios: 124) with Chinese ancestry. INTERVENTIONS Not applicable. MAIN OUTCOME MEASURE(S) Not applicable. RESULTS A total of 118 SNPs were extracted for the interaction tests. Fourteen pairs of significant interactions were identified after Bonferroni correction, which were confirmed in permutation tests. Twelve pairs were between ATR and ERCC4 or XRCC3. The most significant interaction occurred between rs2244500 in TYMS and rs3213403 in XRCC1(P = 8.16 × 10-15). CONCLUSIONS The current study identified gene-gene interactions among DNA repair genes in 806 Chinese NSCL/P trios, providing additional evidence for the complicated genetic structure underlying NSCL/P. ATR, ERCC4, XRCC3, TYMS and RFC1 were suggested to be possible candidate genes for NSCL/P.
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Affiliation(s)
- Xi Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Zhibo Zhou
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, China
| | - Yixin Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Siyue Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Enci Xue
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Xueheng Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Hexiang Peng
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Meng Fan
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Mengying Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Xueying Qin
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Yiqun Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Jing Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Hongping Zhu
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, China
| | - Dafang Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Yonghua Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Terri H Beaty
- School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Tao Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Key Laboratory of Reproductive Health, Ministry of Health, Beijing, China
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Cheng X, Du F, Long X, Huang J. Genetic Inheritance Models of Non-Syndromic Cleft Lip with or without Palate: From Monogenic to Polygenic. Genes (Basel) 2023; 14:1859. [PMID: 37895208 PMCID: PMC10606748 DOI: 10.3390/genes14101859] [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: 08/14/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
Non-syndromic cleft lip with or without palate (NSCL/P) is a prevalent birth defect that affects 1/500-1/1400 live births globally. The genetic basis of NSCL/P is intricate and involves both genetic and environmental factors. In the past few years, various genetic inheritance models have been proposed to elucidate the underlying mechanisms of NSCL/P. These models range from simple monogenic inheritance to more complex polygenic inheritance. Here, we present a comprehensive overview of the genetic inheritance model of NSCL/P exemplified by representative genes and regions from both monogenic and polygenic perspectives. We also summarize existing association studies and corresponding loci of NSCL/P within the Chinese population and highlight the potential of utilizing polygenic risk scores for risk stratification of NSCL/P. The potential application of polygenic models offers promising avenues for improved risk assessment and personalized approaches in the prevention and management of NSCL/P individuals.
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Affiliation(s)
- Xi Cheng
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China; (X.C.); (F.D.); (X.L.)
| | - Fengzhou Du
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China; (X.C.); (F.D.); (X.L.)
- Department of Plastic Surgery, Peking Union Medical College Hospital, Beijing 100730, China
| | - Xiao Long
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China; (X.C.); (F.D.); (X.L.)
- Department of Plastic Surgery, Peking Union Medical College Hospital, Beijing 100730, China
| | - Jiuzuo Huang
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China; (X.C.); (F.D.); (X.L.)
- Department of Plastic Surgery, Peking Union Medical College Hospital, Beijing 100730, China
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Babai A, Irving M. Orofacial Clefts: Genetics of Cleft Lip and Palate. Genes (Basel) 2023; 14:1603. [PMID: 37628654 PMCID: PMC10454293 DOI: 10.3390/genes14081603] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/24/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
Orofacial clefting is considered one of the commonest birth defects worldwide. It presents as cleft lip only, isolated cleft palate or cleft lip and palate. The condition has a diverse genetic background influenced by gene-gene and gene-environment interaction, resulting in two main types, syndromic and nonsyndromic orofacial clefts. Orofacial clefts lead to significant physiological difficulties that affect feeding, speech and language development and other developmental aspects, which results in an increased social and financial burden on the affected individuals and their families. The management of cleft lip and palate is solely based on following a multidisciplinary team approach. In this narrative review article, we briefly summarize the different genetic causes of orofacial clefts and discuss some of the common syndromes and the approach to the management of orofacial clefts.
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Affiliation(s)
- Arwa Babai
- Department of Clinical Genetics, Guy’s Hospital, Guy’s and St Thomas’ NHS Foundation Trust, London SE1 9RT, UK;
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Daltveit DS, Klungsøyr K, Engeland A, Ekbom A, Gissler M, Glimelius I, Grotmol T, Madanat-Harjuoja L, Ording AG, Sørensen HT, Troisi R, Bjørge T. Sex differences in childhood cancer risk among children with major birth defects: a Nordic population-based nested case-control study. Int J Epidemiol 2022; 52:450-465. [PMID: 36179253 PMCID: PMC10114053 DOI: 10.1093/ije/dyac192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 09/19/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Childhood cancer is more common among children with birth defects, suggesting a common aetiology. Whether this association differs by sex is unclear. METHODS We performed a population-based nested case-control study using nationwide health registries in four Nordic countries. We included 21 898 cancer cases (0-19 years) and 218 980 matched population controls, born 1967-2014. Associations between childhood cancer and major birth defects were calculated as odds ratios (ORs) with 95% confidence intervals (CIs) using logistic regression models. Effect modification was evaluated using a counterfactual framework to estimate confidence intervals and P-values for the natural indirect effects. RESULTS Birth defects were present for 5.1% (1117/21 898) of childhood cancer cases and 2.2% (4873/218 980) of controls; OR of cancer was higher for chromosomal (OR = 10, 95% CI = 8.6-12) than for non-chromosomal defects (OR = 1.9, 95% CI = 1.8-2.1), strongest between genetic syndromes/microdeletion and renal tumours, Down syndrome and leukaemia, and nervous system defects and central nervous system tumours. The association between birth defects and cancer was stronger among females (OR = 2.8, 95% CI = 2.6-3.1) than males (OR = 2.1, 95% CI = 1.9-2.2, Pinteraction <0.001). Male sex was an independent risk factor for childhood cancer, but very little of the overall association between sex and childhood cancer was mediated through birth defects (4.8%, PNIE <0.001), although more at younger ages (10% below years and 28% below 1 year). CONCLUSIONS The birth defect-cancer associations were generally stronger among females than males. Birth defects did not act as a strong mediator for the modest differences in childhood cancer risk by sex, suggesting that other biological pathways are involved.
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Affiliation(s)
- Dagrun Slettebø Daltveit
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Norwegian Quality Registry of Cleft Lip and Palate, Surgical Clinic, Haukeland University Hospital, Bergen, Norway
| | - Kari Klungsøyr
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Division of Mental and Physical Health, Norwegian Institute of Public Health, Bergen, Norway
| | - Anders Engeland
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Division of Mental and Physical Health, Norwegian Institute of Public Health, Bergen, Norway
| | - Anders Ekbom
- Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Mika Gissler
- Department of Knowledge Brokers, Finnish Institute for Health and Welfare, Helsinki, Finland.,Region Stockholm, Academic Primary Health Care Centre, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Ingrid Glimelius
- Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden.,Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | | | - Laura Madanat-Harjuoja
- Cancer Society of Finland, Finnish Cancer Registry, Helsinki, Finland.,Dana Farber Cancer Institute, Boston Children's Cancer and Blood Disorders Centre, Boston, MA, USA
| | - Anne Gulbech Ording
- Department of Clinical Epidemiology, Aarhus University Hospital and Aarhus University, Aarhus, Denmark
| | - Henrik Toft Sørensen
- Department of Clinical Epidemiology, Aarhus University Hospital and Aarhus University, Aarhus, Denmark
| | - Rebecca Troisi
- Trans-divisional Research Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Tone Bjørge
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Cancer Registry of Norway, Oslo, Norway
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Fashina A, Busch T, Young M, Adamson O, Awotoye W, Alade A, Adeleke C, Hassan M, Oladayo AM, Gowans LJJ, Eshete M, Naicker T, Olotu J, Adeyemo WL, Butali A. Investigating the relationship between cancer and orofacial clefts using GWAS significant loci for cancers: A case-control and case-triad study. FRONTIERS IN ORAL HEALTH 2022; 3:915361. [PMID: 35990505 PMCID: PMC9388935 DOI: 10.3389/froh.2022.915361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundSeveral population-based case-control studies have reported concurrent presentation of cancer and congenital malformations. Many associations have been made between oral clefting and cancers, though some of these results are conflicting. Some studies have reported an increased risk of cancer among 1st-degree relatives of cleft cases and vice versa, and also an excess risk of cancers of the breast, lung, and brain among those with oral clefts. This study aimed to determine if the genetic polymorphisms found in some cancers are also associated with orofacial cleft in an African cohort.MethodsThe study was a case-control and case-triad study in which cases were 400 individuals clinically diagnosed with non-syndromic cleft lip and/or palate (CL/P), while controls were 450 individuals without CL/P. Samples were obtained from three African countries while DNA extraction, PCR, and genotyping were carried out at the University of Iowa, US. Eleven SNPs in genes coding for SWI/SNF subunits and 13 GWAS significant SNPs for cancers associated with orofacial cleft were selected. Case-control analysis, transmission disequilibrium test (TDT), and DFAM to combine the parent-offspring trio data and unrelated case/control data in a single analysis were carried out using PLINK.ResultsFor the case-control analyses that included all the clefts and for the CLP subtype, none of the SNPs were statistically significant. Statistically increased risk for the following SNPs rs34775372 (p = 0.02; OR = 1.54, CI:1.07–2.22), rs55658222 (p = 0.009; OR = 2.64, CI:1.28–5.45) and rs72728755 (p = 0.02; OR=2.27, CI:1.17–4.45) was observed with the CL only sub-group. None of these were significant after Bonferoni correction. In the TDT analyses, a significantly reduced risk with rs10941679 (p = 0.003; OR = 0.43, CI:0.24–0.75) was observed and this was significant after Bonferroni correction. The rs10941679 was also significant (p = 0.003) in the DFAM analyses as well even after Bonferroni correction.ConclusionThe results from this study represent an important starting point for understanding the concurrent presentation of some cancers in orofacial clefts, and cancer risks in cleft patients. The associations observed warrant further investigation in a larger cohort and will set the stage for a more mechanistic approach toward understanding the risk for cancers in families with clefts.
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Affiliation(s)
- Azeez Fashina
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos, Nigeria
- *Correspondence: Azeez Fashina
| | - Tamara Busch
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, United States
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, United States
| | - Mary Young
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, United States
| | - Olawale Adamson
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos, Nigeria
| | - Waheed Awotoye
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, United States
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, United States
| | - Azeez Alade
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, United States
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, United States
| | - Chinyere Adeleke
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, United States
| | - Mohaned Hassan
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, United States
| | - Abimbola M. Oladayo
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, United States
| | - Lord J. J. Gowans
- Komfo Anokye Teaching Hospital, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Mekonen Eshete
- Department of Surgery, School of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - Thirona Naicker
- School of Clinical Medicine, KwaZulu-Natal University, Durban, South Africa
| | - Joy Olotu
- Department of Anatomy, University of Port Harcourt, Port Harcourt, Nigeria
| | - Wasiu L. Adeyemo
- Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos, Nigeria
| | - Azeez Butali
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA, United States
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, United States
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6
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Fonseca CDAD, Martelli DRB, Almeida ILF, Mesquita LGM, Dias VO, Martelli-Júnior H. Are dental agenesis and oral clefts clinical markers of ovarian or uterine cancer? Oral Dis 2020; 28:243-244. [PMID: 33188718 DOI: 10.1111/odi.13720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 11/27/2022]
Affiliation(s)
- Cláudia de Alvarenga Diniz Fonseca
- Health Science Program, State University of Montes Claros, Unimontes, Montes Claros, Brazil.,Medicine School, State University of Montes Claros, Unimontes, Montes Claros, Brazil
| | | | | | | | - Verônica Oliveira Dias
- Oral Diagnosis, Dental School, State University of Montes Claros, Unimontes, Montes Claros, Brazil
| | - Hercílio Martelli-Júnior
- Health Science Program, State University of Montes Claros, Unimontes, Montes Claros, Brazil.,Oral Diagnosis, Dental School, State University of Montes Claros, Unimontes, Montes Claros, Brazil.,Center for Rehabilitation of Craniofacial Anomalies, University of José Rosario Vellano, Alfenas, Brazil
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Howe LJ, Hemani G, Lesseur C, Gaborieau V, Ludwig KU, Mangold E, Brennan P, Ness AR, St Pourcain B, Davey Smith G, Lewis SJ. Evaluating shared genetic influences on nonsyndromic cleft lip/palate and oropharyngeal neoplasms. Genet Epidemiol 2020; 44:924-933. [PMID: 32710482 PMCID: PMC8240308 DOI: 10.1002/gepi.22343] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 06/12/2020] [Accepted: 07/15/2020] [Indexed: 12/23/2022]
Abstract
It has been hypothesised that nonsyndromic cleft lip/palate (nsCL/P) and cancer may share aetiological risk factors. Population studies have found inconsistent evidence for increased incidence of cancer in nsCL/P cases, but several genes (e.g., CDH1, AXIN2) have been implicated in the aetiologies of both phenotypes. We aimed to evaluate shared genetic aetiology between nsCL/P and oral cavity/oropharyngeal cancers (OC/OPC), which affect similar anatomical regions. Using a primary sample of 5,048 OC/OPC cases and 5,450 controls of European ancestry and a replication sample of 750 cases and 336,319 controls from UK Biobank, we estimate genetic overlap using nsCL/P polygenic risk scores (PRS) with Mendelian randomization analyses performed to evaluate potential causal mechanisms. In the primary sample, we found strong evidence for an association between a nsCL/P PRS and increased odds of OC/OPC (per standard deviation increase in score, odds ratio [OR]: 1.09; 95% confidence interval [CI]: 1.04, 1.13; p = .000053). Although confidence intervals overlapped with the primary estimate, we did not find confirmatory evidence of an association between the PRS and OC/OPC in UK Biobank (OR 1.02; 95% CI: 0.95, 1.10; p = .55). Mendelian randomization analyses provided evidence that major nsCL/P risk variants are unlikely to influence OC/OPC. Our findings suggest possible shared genetic influences on nsCL/P and OC/OPC.
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Affiliation(s)
- Laurence J. Howe
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUK
- Institute of Cardiovascular ScienceUniversity College LondonLondonUK
- Max Planck Institute for PsycholinguisticsNijmegenThe Netherlands
| | - Gibran Hemani
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUK
| | - Corina Lesseur
- Section of GeneticsInternational Agency for Research on CancerLyonFrance
| | - Valérie Gaborieau
- Section of GeneticsInternational Agency for Research on CancerLyonFrance
| | | | | | - Paul Brennan
- Section of GeneticsInternational Agency for Research on CancerLyonFrance
| | - Andy R. Ness
- NIHR Bristol Biomedical Research CentreUniversity Hospitals BristolBristolUK
- Weston NHS Foundation TrustUniversity of BristolBristolUK
| | - Beate St Pourcain
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUK
- Max Planck Institute for PsycholinguisticsNijmegenThe Netherlands
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUK
| | - Sarah J. Lewis
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUK
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Linnenkamp BDW, Raskin S, Esposito SE, Herai RH. A comprehensive analysis of AHRR gene as a candidate for cleft lip with or without cleft palate. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 785:108319. [PMID: 32800270 DOI: 10.1016/j.mrrev.2020.108319] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 02/06/2023]
Abstract
Cleft lip and palate (CL/P) is among the most common congenital malformations and affects 1 in 700 newborns. CL/P is caused by genetic and environmental factors (maternal smoking, alcohol or drug use and others). Many genes and loci were associated with cleft lip/palate but the amount of heterogeneity justifies identifying new causal genes and variants. AHRR (Aryl-Hydrocarbon Receptor Repressor) gene has recently been related to CL/P however, few functional studies analyze the genotypephenotype interaction of AHRR with CL/P. Several studies associate the molecular pathway of AHRR to CL/P which indicates this gene as a functional candidate in CL/P etiology. METHODS Systematic Literature Review was performed using PUBMED database with the keywords cleft lip, cleft palate, orofacial cleft, AHRR and synonyms. SLR resulted in 37 included articles. RESULTS AHRR is a positional and functional candidate gene for CL/P. In silico analysis detected interactions with other genes previously associated to CL/P like ARNT and CYP1A1. AHRR protein regulates cellular toxicity through TCDD mediated AHR pathway. Exposure to TCDD in animal embryos is AHR mediated and lead to cleft palate due to palate fusion failure and post fusion rupture. AHRR regulates cellular growth and differentiation, fundamental to lip and palatogenesis. AHRR decreases carcinogenesis and recently a higher tumor risk has been described in CL/P patients and families. AHRR is also a smoking biomarker due to changed methylation sites found in smokers DNA although folate intake may partially revert these methylation alterations. This corroborates the role of maternal smoking and lack of folate supplementation as risk factors for CL/P. CONCLUSION This research identified the importance of AHRR in dioxin response and demonstrated an example of genetic and environmental interaction, indispensable in the development of many complex diseases.
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Affiliation(s)
- Bianca Domit Werner Linnenkamp
- Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Paraná, Brazil
| | - Salmo Raskin
- School of Medicine, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Paraná, Brazil
| | - Selene Elifio Esposito
- Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Paraná, Brazil; School of Life Sciences, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Paraná, Brazil
| | - Roberto Hirochi Herai
- Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Paraná, Brazil; Research Department, Lico Kaesemodel Institute (ILK), Curitiba, Paraná, Brazil.
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Phenome-Wide Scan Finds Potential Orofacial Risk Markers for Cancer. Sci Rep 2020; 10:4869. [PMID: 32184411 PMCID: PMC7078198 DOI: 10.1038/s41598-020-61654-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/21/2020] [Indexed: 11/15/2022] Open
Abstract
Cancer is a disease caused by a process that drives the transformation of normal cells into malignant cells. The late diagnosis of cancer has a negative impact on the health care system due to high treatment cost and decreased chances of favorable prognosis. Here, we aimed to identify orofacial conditions that can serve as potential risk markers for cancers by performing a phenome-wide scan (PheWAS). From a pool of 6,100 individuals, both genetic and epidemiological data of 1,671 individuals were selected: 350 because they were previously diagnosed with cancer and 1,321 to match to those individuals that had cancer, based on age, sex, and ethnicity serving as a comparison group. Results of this study showed that when analyzing the individuals affected by cancer separately, tooth loss/edentulism is associated with SNPs in AXIN2 (rs11867417 p = 0.02 and rs2240308 p = 0.02), and leukoplakia of oral mucosa is associated with both AXIN2 (rs2240308 p = 0.03) and RHEB (rs2374261 p = 0.03). These phenotypes did not show the same trends in patients that were not diagnosed with cancer, allowing for the conclusion that these phenotypes are unique to cases with higher cancer risk.
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10
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Artificial Intelligence and the detection of pediatric concussion using epigenomic analysis. Brain Res 2019; 1726:146510. [PMID: 31628932 DOI: 10.1016/j.brainres.2019.146510] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 12/12/2022]
Abstract
Concussion, also referred to as mild traumatic brain injury (mTBI) is the most common type of traumatic brain injury. Currently concussion is an area ofintensescientific interest to better understand the biological mechanisms and for biomarker development. We evaluated whole genome-wide blood DNA cytosine ('CpG') methylation in 17 pediatric concussion isolated cases and 18 unaffected controls using Illumina Infinium MethylationEPIC assay. Pathway analysis was performed using Ingenuity Pathway Analysis to help elucidate the epigenetic and molecular mechanisms of the disorder. Area under the receiver operating characteristics (AUC) curves and FDR p-values were calculated for mTBI detection based on CpG methylation levels. Multiple Artificial Intelligence (AI) platforms including Deep Learning (DL), the newest form of AI, were used to predict concussion based on i) CpG methylation markers alone, and ii) combined epigenetic, clinical and demographic predictors. We found 449 CpG sites (473 genes), those were statistically significantly methylated in mTBI compared to controls. There were four CpGs with excellent individual accuracy (AUC ≥ 0.90-1.00) while 119 displayed good accuracy (AUC ≥ 0.80-0.89) for the prediction of mTBI. The CpG methylation changes ≥10% were observed in many CpG loci after concussion suggesting biological significance. Pathway analysis identified several biologically important neurological pathways that were perturbed including those associated with: impaired brain function, cognition, memory, neurotransmission, intellectual disability and behavioral change and associated disorders. The combination of epigenomic and clinical predictors were highly accurate for the detection of concusion using AI techniques. Using DL/AI, a combination of epigenomic and clinical markers had sensitivity and specificity ≧95% for prediction of mTBI. In this novel study, we identified significant methylation changes in multiple genes in response to mTBI. Gene pathways that were epigenetically dysregulated included several known to be involved in neurological function, thus giving biological plausibility to our findings.
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Li W, Wang M, Zhou R, Wang S, Zheng H, Liu D, Zhou Z, Zhu H, Wu T, Beaty TH. Exploring the interaction between FGF Genes and T-box genes among chinese nonsyndromic cleft lip with or without cleft palate case-parent trios. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2019; 60:602-606. [PMID: 30848863 DOI: 10.1002/em.22286] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 02/17/2019] [Accepted: 03/05/2019] [Indexed: 06/09/2023]
Abstract
Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect. Genetic variants causing syndromic orofacial clefts can also contribute to the etiology of NSCL/P. The purpose of the present study was to explore gene-gene (G × G) interaction using common single nucleotide polymorphic (SNP) markers in fibroblast growth factor (FGF) family and its receptors and T-box genes, which were associated with syndromic orofacial clefts. Our study was conducted in 806 Chinese NSCL/P case-parent trios drawn from an international consortium. A total of 252 SNPs in FGF8, FGF10, FGFR1, FGFR2, and TBX5 passed the quality control criteria and were included in the analysis. The interactions between SNPs in different genes were assessed using Cordell's method, which fitted a conditional logistic regression model. The analysis was performed using the R-package trio (Version 3.8.0). Bonferroni correction was used to adjust for multiple comparisons, and the overall significance threshold was set as P = 1.98 × 10-4 (0.05/252). Conditional logistic regression revealed the most significant interaction between rs2330542 in FGF10 and rs1946295 in TBX5, which remained significant (P = 9.63 × 10-6 ) after Bonferroni correction. The relative risk of allele C in rs2330542 (FGF10) was 1.02 (95%CI 0.81-1.28), while the relative risk was 1.42 (95%CI 1.03-1.97) when the exposure was a combination of allele C in rs2330542 and allele A in rs1946295 (TBX5). Our findings confirmed the importance of considering G × G interaction when exploring the genetic risk factors of NSCL/P. Further investigations are warranted to validate the potential interaction and reveal the biological function of FGF10/FGFR2/TBX5. Environ. Mol. Mutagen. 2019. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Wenyong Li
- School of Public Health, Peking University, Beijing, China
| | - Mengying Wang
- School of Public Health, Peking University, Beijing, China
| | - Ren Zhou
- School of Public Health, Peking University, Beijing, China
| | - Siyue Wang
- School of Public Health, Peking University, Beijing, China
| | - Hongchen Zheng
- School of Public Health, Peking University, Beijing, China
| | - Dongjing Liu
- School of Public Health, Peking University, Beijing, China
| | - Zhibo Zhou
- School of Stomatology, Peking University, Beijing, China
| | - Hongping Zhu
- School of Stomatology, Peking University, Beijing, China
| | - Tao Wu
- School of Public Health, Peking University, Beijing, China
- Key Laboratory of Reproductive Health, Ministry of Health, Beijing, China
| | - Terri H Beaty
- School of Public Health, Johns Hopkins University, Baltimore, Maryland
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12
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Gajera M, Desai N, Suzuki A, Li A, Zhang M, Jun G, Jia P, Zhao Z, Iwata J. MicroRNA-655-3p and microRNA-497-5p inhibit cell proliferation in cultured human lip cells through the regulation of genes related to human cleft lip. BMC Med Genomics 2019; 12:70. [PMID: 31122291 PMCID: PMC6533741 DOI: 10.1186/s12920-019-0535-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 05/16/2019] [Indexed: 12/12/2022] Open
Abstract
Background The etiology of cleft lip with or without cleft palate (CL/P), a common congenital birth defect, is complex and involves the contribution of genetic and environmental factors. Although many candidate genes have been identified, the regulation and interaction of these genes in CL/P remain unclear. In addition, the contribution of microRNAs (miRNAs), non-coding RNAs that regulate the expression of multiple genes, to the etiology of CL/P is largely unknown. Methods To identify the signatures of causative biological pathways for human CL/P, we conducted a systematic literature review for human CL/P candidate genes and subsequent bioinformatics analyses. Functional enrichment analyses of the candidate CL/P genes were conducted using the pathway databases GO and KEGG. The miRNA-mediated post-transcriptional regulation of the CL/P candidate genes was analyzed with miRanda, PITA, and TargetScan, and miRTarbase. Genotype-phenotype association analysis was conducted using GWAS. The functional significance of the candidate miRNAs was evaluated experimentally in cell proliferation and target gene regulation assays in human lip fibroblasts. Results Through an extensive search of the main biomedical databases, we mined 177 genes with mutations or association/linkage reported in individuals with CL/P, and considered them as candidate genes for human CL/P. The genotype-phenotype association study revealed that mutations in 12 genes (ABCA4, ADAM3A, FOXE1, IRF6, MSX2, MTHFR, NTN1, PAX7, TP63, TPM1, VAX1, and WNT9B) were significantly associated with CL/P. In addition, our bioinformatics analysis predicted 16 microRNAs (miRNAs) to be post-transcriptional regulators of CL/P genes. To validate the bioinformatics results, the top six candidate miRNAs (miR-124-3p, miR-369-3p, miR-374a-5p, miR-374b-5p, miR-497-5p, and miR-655-3p) were evaluated by cell proliferation/survival assays and miRNA-gene regulation assays in cultured human lip fibroblasts. We found that miR-497-5p and miR-655-3p significantly suppressed cell proliferation in these cells. Furthermore, the expression of the predicted miRNA-target genes was significantly downregulated by either miR-497-5p or miR-655-3p mimic. Conclusion Expression of miR-497-5p and miR-655-3p suppresses cell proliferation through the regulation of human CL/P-candidate genes. This study provides insights into the role of miRNAs in the etiology of CL/P and suggests possible strategies for the diagnosis of CL/P. Electronic supplementary material The online version of this article (10.1186/s12920-019-0535-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mona Gajera
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Neha Desai
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Akiko Suzuki
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Aimin Li
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Musi Zhang
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Goo Jun
- Department of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA.,Department of Epidemiology, Human Genetics & Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA.,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Junichi Iwata
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX, USA. .,Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX, USA. .,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA.
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13
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Razaghi-Moghadam Z, Namipashaki A, Farahmand S, Ansari-Pour N. Systems genetics of nonsyndromic orofacial clefting provides insights into its complex aetiology. Eur J Hum Genet 2018; 27:226-234. [PMID: 30254216 DOI: 10.1038/s41431-018-0263-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 07/22/2018] [Accepted: 08/09/2018] [Indexed: 12/14/2022] Open
Abstract
Nonsyndromic oral clefting (NSOC) is although one of the most common congenital disorders worldwide, its underlying molecular basis remains elusive. This process has been hindered by the overwhelmingly high level of heterogeneity observed. Given that hitherto multiple loci and genes have been associated with NSOC, and that complex diseases are usually polygenic and show a considerable level of missing heritability, we used a systems genetics approach to reconstruct the NSOC network by integrating human-based physical and regulatory interactome with whole-transcriptome microarray data. We show that the network component contains 53% (23/43) of the curated NSOC-implicated gene set and displays a highly significant propinquity (P < 0.0001) between genes implicated at the genomic level and those differentially expressed at the transcriptome level. In addition, we identified bona fide candidate genes based on topological features and dysregulation (e.g. ANGPTL4), and similarly prioritised genes at GWA loci (e.g. MYC and CREBBP), thus providing further insight into the underlying heterogeneity of NSOC. Gene ontology analysis results were consistent with the NSOC network being associated with embryonic organ morphogenesis and also hinted at an aetiological overlap between NSOC and cancer. We therefore recommend this approach to be applied to other heterogeneous complex diseases to not only provide a molecular framework to unify genes which may seem as disparate entities linked to the same disease, but to also predict and prioritise candidate genes for further validation, thus addressing the missing heritability.
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Affiliation(s)
- Zahra Razaghi-Moghadam
- Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran.,Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Atefeh Namipashaki
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Saman Farahmand
- College of Science and Mathematics, University of Massachusetts Boston, Boston, Massachusetts, USA
| | - Naser Ansari-Pour
- Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran. .,Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LF, UK.
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14
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Chiquet BT, Yuan Q, Swindell EC, Maili L, Plant R, Dyke J, Boyer R, Teichgraeber JF, Greives MR, Mulliken JB, Letra A, Blanton SH, Hecht JT. Knockdown of Crispld2 in zebrafish identifies a novel network for nonsyndromic cleft lip with or without cleft palate candidate genes. Eur J Hum Genet 2018; 26:1441-1450. [PMID: 29899370 DOI: 10.1038/s41431-018-0192-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 04/10/2018] [Accepted: 05/08/2018] [Indexed: 11/09/2022] Open
Abstract
Orofacial development is a multifaceted process involving tightly regulated genetic signaling networks, that when perturbed, lead to orofacial abnormalities including cleft lip and/or cleft palate. We and others have shown an association between the cysteine-rich secretory protein LCCL domain containing 2 (CRISPLD2) gene and nonsyndromic cleft lip with or without cleft palate (NSCLP). Further, we demonstrated that knockdown of Crispld2 in zebrafish alters neural crest cell migration patterns resulting in abnormal jaw and palate development. In this study, we performed RNA profiling in zebrafish embryos and identified 249 differentially expressed genes following knockdown of Crispld2. In silico pathway analysis identified a network of seven genes previously implicated in orofacial development for which differential expression was validated in three of the seven genes (CASP8, FOS, and MMP2). Single nucleotide variant (SNV) genotyping of these three genes revealed significant associations between NSCLP and FOS/rs1046117 (GRCh38 chr14:g.75746690 T > C, p = 0.0005) in our nonHispanic white (NHW) families and MMP2/rs243836 (GRCh38 chr16:g.55534236 G > A; p = 0.002) in our Hispanic families. Nominal association was found between NSCLP and CASP8/rs3769825 (GRCh38 chr2:g.202111380 C > A; p < 0.007). Overtransmission of MMP2 haplotypes were identified in the Hispanic families (p < 0.002). Significant gene-gene interactions were identified for FOS-MMP2 in the NHW families and for CASP8-FOS in the NHW simplex family subgroup (p < 0.004). Additional in silico analysis revealed a novel gene regulatory network including five of these newly identified and 23 previously reported NSCLP genes. Our results demonstrate that animal models of orofacial clefting can be powerful tools to identify novel candidate genes and gene regulatory networks underlying NSCLP.
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Affiliation(s)
- Brett T Chiquet
- Center for Craniofacial Research, University of Texas Health Science Center at Houston (UTHealth) School of Dentistry, Houston, TX, 77054, USA. .,Pediatric Research Center, Department of Pediatrics, UTHealth McGovern Medical School, Houston, TX, 77030, USA.
| | - Qiuping Yuan
- Pediatric Research Center, Department of Pediatrics, UTHealth McGovern Medical School, Houston, TX, 77030, USA
| | - Eric C Swindell
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.,Department of Biochemistry and Molecular Biology, UTHealth McGovern Medical School, Houston, Texas, 77030, USA
| | - Lorena Maili
- Pediatric Research Center, Department of Pediatrics, UTHealth McGovern Medical School, Houston, TX, 77030, USA.,The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - Robert Plant
- Pediatric Research Center, Department of Pediatrics, UTHealth McGovern Medical School, Houston, TX, 77030, USA
| | - Jeffrey Dyke
- Center for Craniofacial Research, University of Texas Health Science Center at Houston (UTHealth) School of Dentistry, Houston, TX, 77054, USA
| | - Ryan Boyer
- Center for Craniofacial Research, University of Texas Health Science Center at Houston (UTHealth) School of Dentistry, Houston, TX, 77054, USA
| | - John F Teichgraeber
- Divison of Pediatric Plastic Surgery, Department of Pediatric Surgery, UTHealth McGovern Medical School, Houston, TX, 77030, USA
| | - Matthew R Greives
- Divison of Pediatric Plastic Surgery, Department of Pediatric Surgery, UTHealth McGovern Medical School, Houston, TX, 77030, USA
| | | | - Ariadne Letra
- Center for Craniofacial Research, University of Texas Health Science Center at Houston (UTHealth) School of Dentistry, Houston, TX, 77054, USA.,Pediatric Research Center, Department of Pediatrics, UTHealth McGovern Medical School, Houston, TX, 77030, USA
| | - Susan H Blanton
- Dr. John T. Macdonald Foundation Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Jacqueline T Hecht
- Center for Craniofacial Research, University of Texas Health Science Center at Houston (UTHealth) School of Dentistry, Houston, TX, 77054, USA.,Pediatric Research Center, Department of Pediatrics, UTHealth McGovern Medical School, Houston, TX, 77030, USA.,The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
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15
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Wang M, Liu D, Schwender H, Wang H, Wang P, Zhou Z, Li J, Wu T, Zhu H, Beaty TH. Evaluating the effect of nicotinic cholinergic receptor genes on the risk of nonsyndromic cleft lip with or without cleft palate. Oral Dis 2018; 24:1068-1072. [PMID: 29688589 DOI: 10.1111/odi.12879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/31/2018] [Accepted: 04/16/2018] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Multiple studies have suggested nonsyndromic cleft lip with or without cleft palate (NSCL/P), and lung cancer may have common genetic etiology. Previous studies have showed genetic variants in nicotinic cholinergic receptor genes (CHRNs) may influence risk of lung cancer. We aimed to explore the effect of CHRNs on risk of NSCL/P considering gene-gene (GxG) interaction for these genes. SUBJECTS AND METHODS We selected 120 markers in 14 CHRNs to test for GxG interaction using 806 Chinese case-parent trios recruited from an international consortium established for a GWAS of oral clefts. RESULTS Totally, two pairs of SNPs yielded significant GxG interactions after Bonferroni correction (rs935865 and rs2337980 with p = 4.04 × 10-5 , rs2741335 and rs3743077 with p = 4.80 × 10-4 ), and these pairwise interactions were confirmed in permutation tests. In addition, the relative risk (RR) of the putative interaction between rs935865 and rs2337980 was 1.10 (95% CI: 0.92~1.31). CONCLUSIONS While the single SNP association and the gene-environment interaction analysis of 14 CHRN genes yielded no signal, this study did demonstrate the importance of considering potential GxG interaction for exploring etiology of NSCL/P. This study suggests an important role for particular combinations of SNPs in CHRN genes in influencing risk to NSCL/P, which needs further study.
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Affiliation(s)
- Mengying Wang
- School of Public Health, Peking University, Beijing, China
| | - Dongjing Liu
- School of Public Health, Peking University, Beijing, China
| | - Holger Schwender
- Mathematical Institute, Heinrich Heine University Duesseldorf, Duesseldorf, Germany
| | - Hong Wang
- School of Public Health, Peking University, Beijing, China
| | - Ping Wang
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Zhibo Zhou
- School of Stomatology, Peking University, Beijing, China
| | - Jing Li
- School of Stomatology, Peking University, Beijing, China
| | - Tao Wu
- School of Public Health, Peking University, Beijing, China.,Key Laboratory of Reproductive Health, Ministry of Health, Beijing, China
| | - Hongping Zhu
- School of Stomatology, Peking University, Beijing, China
| | - Terri H Beaty
- School of Public Health, Johns Hopkins University, Baltimore, Maryland
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16
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Zhang W, Zhou S, Gao Y, Song H, Jiao X, Wang X, Li Y. Alterations in DNA methyltransferases and methyl-CpG binding domain proteins during cleft palate formation as induced by 2,3,7,8-tetrachlorodibenzo-p-dioxin in mice. Mol Med Rep 2018; 17:5396-5401. [PMID: 29393476 DOI: 10.3892/mmr.2018.8521] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 01/23/2018] [Indexed: 11/06/2022] Open
Abstract
Maternal exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) induces cleft palate formation in mice. This TCDD treatment, which may be considered an environmental factor in cleft palate formation, is associated with alterations in DNA methylation. However, the underlying molecular mechanisms of DNA methylation produced by TCDD in mouse embryos are poorly understood. DNA methyltransferases (DNMTs) and methyl‑CpG binding domain proteins (MBDs) are thought to be closely associated with the actions of DNA methylation. Therefore, the present study tested the hypothesis that this cleft palate inducing effect of TCDD will alter the expression levels of DNMTs and various MBDs in palate tissue of fetal mice. Pregnant C57BL/6J mice were treated with either TCDD (64 µg/kg) or corn oil (control) at embryonic day 10.5 (E10.5) and fetal palates were harvested for structural and molecular analyses at E13.5, E14.5, E15.5 and E17.5. Expression levels of DNMTs and MBDs were assayed using reverse transcription‑quantitative polymerase chain reaction and western blotting. The incidence of cleft palates in the TCDD group was 98.24%, whereas no cases of cleft palate were observed in the control group. Expression levels of DNMTs and MBDs were significantly increased in the TCDD group compared with the control. The results demonstrate clear alterations in DNMTs and MBDs, as induced by TCDD, and suggest that such alterations are important in cleft palate formation in fetal mice.
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Affiliation(s)
- Wei Zhang
- Department of Stomatology, The Fourth Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Shanshan Zhou
- Department of Neurology, The First Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Yuwei Gao
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Hongquan Song
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Xiaohui Jiao
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Xiaotong Wang
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Yong Li
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital, Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
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17
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Živicová V, Lacina L, Mateu R, Smetana K, Kavková R, Krejčí ED, Grim M, Kvasilová A, Borský J, Strnad H, Hradilová M, Šáchová J, Kolář M, Dvořánková B. Analysis of dermal fibroblasts isolated from neonatal and child cleft lip and adult skin: Developmental implications on reconstructive surgery. Int J Mol Med 2017; 40:1323-1334. [PMID: 28901389 PMCID: PMC5627884 DOI: 10.3892/ijmm.2017.3128] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 08/21/2017] [Indexed: 01/12/2023] Open
Abstract
The nonsyndromic cleft is one of the most frequent congenital defects in humans. Clinical data demonstrated improved and almost scarless neonatal healing of reparative surgery. Based on our previous results on crosstalk between neonatal fibroblasts and adult keratinocytes, the present study focused on characterization of fibroblasts prepared from cleft lip tissue samples of neonates and older children, and compared them with samples isolated from normal adult skin (face and breast) and scars. Although subtle variances in expression profiles of children and neonates were observed, the two groups differed significantly from adult cells. Compared with adult cells, differences were observed in nestin and smooth muscle actin (SMA) expression at the protein and transcript level. Furthermore, fibroblast to myofibroblast differentiation drives effective wound healing and is largely regulated by the cytokine, transforming growth factor-β1 (TGF-β1). Dysregulation of the TGF-β signalling pathway, including low expression of the TGF-β receptor II, may contribute to reducing scarring in neonates. Fibroblasts of facial origin also exhibited age independent differences from the cells prepared from the breast, reflecting the origin of the facial cells from neural crest-based ectomesenchyme.
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Affiliation(s)
- Veronika Živicová
- Institute of Anatomy
- Department of Otorhinolaryngology, Head and Neck Surgery
| | - Lukáš Lacina
- Institute of Anatomy
- BIOCEV and
- Department of Dermatovenerology, The First Faculty of Medicine, Charles University, 121 08 Prague
| | | | | | | | | | | | | | - Jiří Borský
- Department of Otorhinolaryngology, The Second Faculty of Medicine, Charles University, 150 06 Prague
| | - Hynek Strnad
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic v.v.i., 142 20 Prague, Czech Republic
| | - Miluše Hradilová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic v.v.i., 142 20 Prague, Czech Republic
| | - Jana Šáchová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic v.v.i., 142 20 Prague, Czech Republic
| | - Michal Kolář
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic v.v.i., 142 20 Prague, Czech Republic
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18
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Xu M, Ma L, Lou S, Du Y, Yin X, Zhang C, Fan L, Wang H, Wang Z, Zhang W, Wang L, Pan Y. Genetic variants of microRNA processing genes and risk of non-syndromic orofacial clefts. Oral Dis 2017; 24:422-428. [PMID: 28833944 DOI: 10.1111/odi.12741] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 07/31/2017] [Accepted: 08/01/2017] [Indexed: 12/21/2022]
Abstract
OBJECTIVE MicroRNA (miRNA) processing genes play important roles in the craniofacial development. The aim of this study was to explore the associations between single nucleotide polymorphisms (SNPs) of miRNA processing genes with the risk of non-syndromic orofacial clefts (NSOC). METHODS We genotyped 12 potentially functional SNPs from seven miRNA processing genes (GEMIN3, DROSHA, DGCR8, GEMIN4, PIWIL1, XPO5, and DICER) in a case-control study of 602 NSOC cases and 605 controls. RESULTS Two SNPs were associated with the susceptibility of CL/P: rs10719 in DROSHA led to an increased risk of cleft lip with or without palate (CL/P) (GA/AA: p = .024, OR = 1.33, 95% CI = [1.04, 1.70]; GG + GA/AA: p = .037, OR = 1.29, 95% CI = [1.02, 1.63]), while rs493760 in DROSHA (CC/TT: p = .049, OR = 0.58, 95% CI = [0.34, 0.99]) could reduce the risk of CL/P. In addition, rs10719 (A)-rs493760 (C) haplotype contributed to a decreased risk of CL/P (OR = 0.77, 95% CI = [0.63, 0.94]), whereas the rs10719 (G)-rs493760 (C) haplotype contributed to the increased risk of cleft palate only (CPO) (OR = 2.70, 95% CI = [1.15, 6.35]). However, there was no difference observed in these SNPs after the Bonferroni correction. CONCLUSION Taken together, our results provided the potential evidence that rs10719 and rs493760 might contribute to the risk of CL/P and suggested potential genetic basis and mechanisms of CL/P. The lack of association between these SNPs and CPO might be due to the limited sample size of CPO subgroup.
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Affiliation(s)
- M Xu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - L Ma
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - S Lou
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Y Du
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - X Yin
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - C Zhang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - L Fan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - H Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Z Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - W Zhang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - L Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Y Pan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
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