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Li M, Wang H. Pathway analysis identified a significant association between cell-cell adherens junctions-related genes and non-syndromic cleft lip/palate in 895 Asian case-parent trios. Arch Oral Biol 2022; 136:105384. [DOI: 10.1016/j.archoralbio.2022.105384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 01/14/2022] [Accepted: 02/15/2022] [Indexed: 12/31/2022]
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2
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Adachi Y, Higuchi A, Wakai E, Shiromizu T, Koiwa J, Nishimura Y. Involvement of homeobox transcription factor Mohawk in palatogenesis. Congenit Anom (Kyoto) 2022; 62:27-37. [PMID: 34816492 DOI: 10.1111/cga.12451] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 10/05/2021] [Accepted: 11/06/2021] [Indexed: 12/17/2022]
Abstract
Palatogenesis is affected by many factors, including gene polymorphisms and exposure to toxic chemicals during sensitive developmental periods. Cleft palate is one of the most common congenital anomalies, and ongoing efforts to elucidate the molecular mechanisms underlying palatogenesis are providing useful insights to reduce the risk of this disorder. To identify novel potential regulators of palatogenesis, we analyzed public transcriptome datasets from a mouse model of cleft palate caused by selective deletion of transforming growth factor-β (TGFβ) receptor type 2 in cranial neural crest cells. We identified the homeobox transcription factor Mohawk (Mkx) as a gene downregulated in the maxilla of TGFβ knockout mice compared with wild-type mice. To examine the role of mkx in palatogenesis, we used CRISPR/Cas9 editing to generate zebrafish with impaired expression of mkxa and mkxb, the zebrafish homologs of Mkx. We found that mkx crispants expressed reduced levels of gli1, a critical transcription factor in the Sonic hedgehog (SHH) signaling pathway that plays an important role in the regulation of palatogenesis. Furthermore, we found that mkxa-/- zebrafish were more susceptible than mkxa+/+ zebrafish to the deleterious effects of cyclopamine, an inhibitor of SHH signaling, on upper jaw development. These results suggest that Mkx may be involved in palatogenesis regulated by TGFβ and SHH signaling, and that impairment in Mkx function may be related to the etiology of cleft palate.
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Affiliation(s)
- Yuka Adachi
- Department of Integrative Pharmacology, Mie University Graduate School of Medicine, Tsu, Mie, Japan
| | - Aina Higuchi
- Department of Integrative Pharmacology, Mie University Graduate School of Medicine, Tsu, Mie, Japan
| | - Eri Wakai
- Department of Integrative Pharmacology, Mie University Graduate School of Medicine, Tsu, Mie, Japan
| | - Takashi Shiromizu
- Department of Integrative Pharmacology, Mie University Graduate School of Medicine, Tsu, Mie, Japan
| | - Junko Koiwa
- Department of Integrative Pharmacology, Mie University Graduate School of Medicine, Tsu, Mie, Japan
| | - Yuhei Nishimura
- Department of Integrative Pharmacology, Mie University Graduate School of Medicine, Tsu, Mie, Japan
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Wang X, Wang H, You J, Zheng R, Xu Y, Fan F. Craniofacial development in patients of Tessier No.0 cleft with a bifid nose using 3D computed tomography. Front Pediatr 2022; 10:979345. [PMID: 36090555 PMCID: PMC9449123 DOI: 10.3389/fped.2022.979345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/02/2022] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVE Considerable studies have focused mainly on the facial deformity of Tessier No.0 cleft with a bifid nose, but the deformity of the skull is not well understood. Therefore, our study aimed to explore the evolution of cranial dysmorphology and the chronology of Tessier No.0 cleft with a bifid nose, by three-dimensional measurements. METHODS Ninety-six non-surgical patients and computed tomographic scans were included (Tessier No.0 cleft with a bifid nose, n = 48; controls, n = 48) and divided into five age subgroups. Craniofacial cephalometric measurements were analyzed by Mimics software. RESULTS The widening of nasal bone was the most remarkable and persistent from 2 years old appropriately. The overall cranial base length in patients compared with controls increased 11.8% (p < 0.01) on average. The middle and posterior cranial fossa increasing accounted for most of this change. The cranial base angles also showed increased obviously. By analyzing the linear of the nasopharynx and respiratory tract, it was found that its development did not affect respiration. CONCLUSIONS The cranial base deformity of Tessier No.0 cleft with a bifid nose consists of the whole skull base and particularly the middle and posterior cranial base length increase. At the same time, there may be late closure of the spheno-occipital synchondrosis and sella displacement. We believe this study is unique in providing valuable data for elucidating the pathological and morphological abnormalities of skull base development in Tessier No.0 cleft with a bifid nose.
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Affiliation(s)
- Xin Wang
- Department of Rhinoplasty, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Huan Wang
- Department of Rhinoplasty, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianjun You
- Department of Rhinoplasty, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ruobing Zheng
- Department of Rhinoplasty, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yihao Xu
- Department of Rhinoplasty, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fei Fan
- Department of Rhinoplasty, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Sood A, Arora A, Batra P, Sood S, Raghavan S. Comparison of dentofacial morphology between parents of children with and without craniofacial anomalies using cephalogram Imaging. Indian J Dent Res 2021; 32:472-479. [DOI: 10.4103/ijdr.ijdr_623_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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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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Demeer B, Revencu N, Helaers R, Gbaguidi C, Dakpe S, François G, Devauchelle B, Bayet B, Vikkula M. Likely Pathogenic Variants in One Third of Non-Syndromic Discontinuous Cleft Lip and Palate Patients. Genes (Basel) 2019; 10:genes10100833. [PMID: 31652620 PMCID: PMC6826364 DOI: 10.3390/genes10100833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 10/14/2019] [Accepted: 10/19/2019] [Indexed: 12/19/2022] Open
Abstract
Oral clefts are composed of cleft of the lip, cleft of the lip and palate, or cleft of the palate, and they are associated with a wide range of expression and severity. When cleft of the palate is associated with cleft of the lip with preservation of the primary palate, it defines an atypical phenotype called discontinuous cleft. Although this phenotype may represent 5% of clefts of the lip and/or palate (CLP), it is rarely specifically referred to and its pathophysiology is unknown. We conducted whole exome sequencing (WES) and apply a candidate gene approach to non-syndromic discontinuous CLP individuals in order to identify genes and deleterious variants that could underlie this phenotype. We discovered loss-of-function variants in two out of the seven individuals, implicating FGFR1 and DLG1 genes, which represents almost one third of this cohort. Whole exome sequencing of clinically well-defined subgroups of CLP, such as discontinuous cleft, is a relevant approach to study CLP etiopathogenesis. It could facilitate more accurate clinical, epidemiological and fundamental research, ultimately resulting in better diagnosis and care of CLP patients. Non-syndromic discontinuous cleft lip and palate seems to have a strong genetic basis.
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Affiliation(s)
- Bénédicte Demeer
- Human Molecular Genetics, de Duve Institute, University of Louvain, 1200 Brussels, Belgium.
- Center for Human Genetics, CLAD Nord de France, CHU Amiens-Picardie, 80054 Amiens, France.
- Université Picardie Jules Verne, EA CHIMERE, EA 7516, 80054 Amiens, France.
- Facing Faces Institute, 80054 Amiens, France.
| | - Nicole Revencu
- Human Molecular Genetics, de Duve Institute, University of Louvain, 1200 Brussels, Belgium.
- Center for Human Genetics, Cliniques universitaires Saint-Luc, University of Louvain, 1200 Brussels, Belgium.
| | - Raphael Helaers
- Human Molecular Genetics, de Duve Institute, University of Louvain, 1200 Brussels, Belgium.
| | - Cica Gbaguidi
- Department of Maxillofacial Surgery and Stomatology, Centre de Compétence Fentes et Malformations Faciales (MAFACE), CHU Amiens-Picardie, 80054 Amiens, France.
| | - Stéphanie Dakpe
- Université Picardie Jules Verne, EA CHIMERE, EA 7516, 80054 Amiens, France.
- Facing Faces Institute, 80054 Amiens, France.
- Department of Maxillofacial Surgery and Stomatology, Centre de Compétence Fentes et Malformations Faciales (MAFACE), CHU Amiens-Picardie, 80054 Amiens, France.
| | - Geneviève François
- Department of Pediatrics, Cliniques Universitaires Saint-Luc, University of Louvain, 1200 Brussels, Belgium.
| | - Bernard Devauchelle
- Université Picardie Jules Verne, EA CHIMERE, EA 7516, 80054 Amiens, France.
- Facing Faces Institute, 80054 Amiens, France.
- Department of Maxillofacial Surgery and Stomatology, Centre de Compétence Fentes et Malformations Faciales (MAFACE), CHU Amiens-Picardie, 80054 Amiens, France.
| | - Bénédicte Bayet
- Centre Labiopalatin, Division of Plastic Surgery, Cliniques Universitaires Saint-Luc, University of Louvain, 1200 Brussels, Belgium.
| | - Miikka Vikkula
- Human Molecular Genetics, de Duve Institute, University of Louvain, 1200 Brussels, Belgium.
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Lancia M, Machado RA, Dionísio TJ, Garib DG, Santos CFD, Coletta RD, Neves LTD. Association between MSX1 rs12532 polymorphism with nonsyndromic unilateral complete cleft lip and palate and tooth agenesis. Arch Oral Biol 2019; 109:104556. [PMID: 31568994 DOI: 10.1016/j.archoralbio.2019.104556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/15/2019] [Accepted: 09/15/2019] [Indexed: 10/26/2022]
Abstract
OBJECTIVES To investigate the association of MSX1 rs12532 polymorphism with the risk of nonsyndromic unilateral complete cleft lip and palate (NSCLP) and tooth agenesis. MATERIALS AND METHODS The study is comprised of 384 individuals divided into 4 groups: group 1, patients with unilateral complete NSCLP and premolar agenesis (n = 57); group 2, patients with unilateral NSCLP without tooth agenesis (n = 117); group 3, patients with premolar agenesis without oral cleft (n = 53) and group 4 (n = 157), a control group with individuals without tooth agenesis and oral cleft. Genotyping of rs12532 was carried out with Taqman chemistry, and associations were investigated using logistic regression analyses. RESULTS Overall rs12532 allele and genotype distributions revealed no significant differences between the groups of NSCLP or tooth agenesis. CONCLUSION Although our results are consistent with a lack of association of MSX1 rs12532 and the risk of unilateral NSCLP and tooth agenesis, further studies with additional SNPs and a more diverse ethnic cohort are warranted.
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Affiliation(s)
- Melissa Lancia
- Department of Orthodontics, Bauru Dental School, University of São Paulo, Bauru, São Paulo, Brazil
| | - Renato Assis Machado
- Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo (HRAC/USP), Bauru, São Paulo, Brazil
| | - Thiago José Dionísio
- Laboratory Specialist, Department of Biological Sciences, Bauru Dental School, University of São Paulo, Bauru, São Paulo, Brazil
| | - Daniela Gamba Garib
- Department of Orthodontics, Bauru Dental School, University of São Paulo, Post-Graduation Program in Rehabilitation Sciences, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo (HRAC/USP), Bauru, São Paulo, Brazil
| | - Carlos Ferreira Dos Santos
- Department of Biological Sciences, Bauru Dental School, University of São Paulo, Bauru, São Paulo, Brazil
| | - Ricardo D Coletta
- Department of Oral Diagnosis, School of Dentistry, University of Campinas, Piracicaba, São Paulo, Brazil
| | - Lucimara Teixeira das Neves
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Post-Graduation Program in Rehabilitation Sciences, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo (HRAC/USP), Bauru, São Paulo, Brazil.
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Mohamad Shah NS, Sulong S, Wan Sulaiman WA, Halim AS. Two novel genes TOX3 and COL21A1 in large extended Malay families with nonsyndromic cleft lip and/or palate. Mol Genet Genomic Med 2019; 7:e635. [PMID: 30924295 PMCID: PMC6503016 DOI: 10.1002/mgg3.635] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 01/09/2019] [Accepted: 02/11/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Nonsyndromic cleft lip and/or palate is one of the most common human birth defects worldwide that affects the lip and/or palate. The incidence of clefts varies among populations through ethnic, race, or geographical differences. The focus on Malay nonsyndromic cleft lip and/or palate (NSCL/P) is because of a scarce report on genetic study in relation to this deformity in Malaysia. We are interested to discuss about the genes that are susceptible to cause orofacial cleft formation in the family. METHODS Genome-wide linkage analysis was carried out on eight large extended families of NSCL/P with the total of 91 individuals among Malay population using microarray platform. Based on linkage analyses findings, copy number variation (CNV) of LPHN2, SATB2, PVRL3, COL21A1, and TOX3 were identified in four large extended families that showed linkage evidence using quantitative polymerase chain reaction (qPCR) as for a validation purpose. Copy number calculated (CNC) for each genes were determined with Applied Biosystems CopyCallerTM Software v2.0. Normal CNC of the target sequence expected was set at two. RESULTS Genome-wide linkage analysis had discovered several genes including TOX3 and COL21A1 in four different loci 4p15.2-p16.1, 6p11.2-p12.3, 14q13-q21, and 16q12.1. There was significant decreased, p < 0.05 of SATB2, COL21A1, and TOX3 copy number in extended families compared to the normal controls. CONCLUSION Novel linkage evidence and significant low copy number of COL21A1 and TOX3 in NSCLP family was confirmed. These genes increased the risks toward NSCLP formation in that family traits.
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Affiliation(s)
- Nurul Syazana Mohamad Shah
- Reconstructive Science Unit, School of Medical SciencesUniversiti Sains MalaysiaKubang KerianKelantanMalaysia
| | - Sarina Sulong
- Human Genome Centre, School of Medical SciencesUniversiti Sains MalaysiaKubang KerianKelantanMalaysia
| | - Wan Azman Wan Sulaiman
- Reconstructive Science Unit, School of Medical SciencesUniversiti Sains MalaysiaKubang KerianKelantanMalaysia
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Wu N, Lu Y, Liu K, Li Z, Liu Q, Lu L. Associations of ABCA4 and MAFB with Nonsyndromic Cleft Lip with or without Cleft Palate in a Northeastern Chinese Population. J HARD TISSUE BIOL 2018. [DOI: 10.2485/jhtb.27.181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Nan Wu
- Department of Oral and Maxillofacial Surgery, China Medical University School of Stomatology
| | - Yongping Lu
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning
| | - Kun Liu
- Department of Oral and Maxillofacial Surgery, Jinan Stomatological Hospital
| | - Zengjian Li
- Department of Oral and Maxillofacial Surgery, China Medical University School of Stomatology
| | - Qiang Liu
- Department of Oral and Maxillofacial Surgery, China Medical University School of Stomatology
| | - Li Lu
- Department of Oral and Maxillofacial Surgery, China Medical University School of Stomatology
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Basha M, Demeer B, Revencu N, Helaers R, Theys S, Bou Saba S, Boute O, Devauchelle B, Francois G, Bayet B, Vikkula M. Whole exome sequencing identifies mutations in 10% of patients with familial non-syndromic cleft lip and/or palate in genes mutated in well-known syndromes. J Med Genet 2018; 55:449-458. [DOI: 10.1136/jmedgenet-2017-105110] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 02/02/2018] [Accepted: 02/12/2018] [Indexed: 01/08/2023]
Abstract
BackgroundOral clefts, that is, clefts of the lip and/or cleft palate (CL/P), are the most common craniofacial birth defects with an approximate incidence of ~1/700. To date, physicians stratify patients with oral clefts into either syndromic CL/P (syCL/P) or non-syndromic CL/P (nsCL/P) depending on whether the CL/P is associated with another anomaly or not. In general, patients with syCL/P follow Mendelian inheritance, while those with nsCL/P have a complex aetiology and, as such, do not adhere to Mendelian inheritance. Genome-wide association studies have identified approximately 30 risk loci for nsCL/P, which could explain a small fraction of heritability.MethodsTo identify variants causing nsCL/P, we conducted whole exome sequencing on 84 individuals with nsCL/P, drawn from multiplex families (n=46).ResultsWe identified rare damaging variants in four genes known to be mutated in syCL/P: TP63 (one family), TBX1 (one family), LRP6 (one family) and GRHL3 (two families), and clinical reassessment confirmed the isolated nature of their CL/P.ConclusionThese data demonstrate that patients with CL/P without cardinal signs of a syndrome may still carry a mutation in a gene linked to syCL/P. Rare coding and non-coding variants in syCL/P genes could in part explain the controversial question of ‘missing heritability’ for nsCL/P. Therefore, gene panels designed for diagnostic testing of syCL/P should be used for patients with nsCL/P, especially when there is at least third-degree family history. This would allow a more precise management, follow-up and genetic counselling. Moreover, stratified cohorts would allow hunting for genetic modifiers.
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Haaland ØA, Lie RT, Romanowska J, Gjerdevik M, Gjessing HK, Jugessur A. A Genome-Wide Search for Gene-Environment Effects in Isolated Cleft Lip with or without Cleft Palate Triads Points to an Interaction between Maternal Periconceptional Vitamin Use and Variants in ESRRG. Front Genet 2018. [PMID: 29535761 PMCID: PMC5834486 DOI: 10.3389/fgene.2018.00060] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background: It is widely accepted that cleft lip with or without cleft palate (CL/P) results from the complex interplay between multiple genetic and environmental factors. However, a robust investigation of these gene-environment (GxE) interactions at a genome-wide level is still lacking for isolated CL/P. Materials and Methods: We used our R-package Haplin to perform a genome-wide search for GxE effects in isolated CL/P. From a previously published GWAS, genotypes and information on maternal periconceptional cigarette smoking, alcohol intake, and vitamin use were available on 1908 isolated CL/P triads of predominantly European or Asian ancestry. A GxE effect is present if the relative risk estimates for gene-effects in the offspring are different across exposure strata. We tested this using the relative risk ratio (RRR). Besides analyzing all ethnicities combined ("pooled analysis"), separate analyses were conducted on Europeans and Asians to investigate ethnicity-specific effects. To control for multiple testing, q-values were calculated from the p-values. Results: We identified significant GxVitamin interactions with three SNPs in "Estrogen-related receptor gamma" (ESRRG) in the pooled analysis. The RRRs (95% confidence intervals) were 0.56 (0.45-0.69) with rs1339221 (q = 0.011), 0.57 (0.46-0.70) with rs11117745 (q = 0.011), and 0.62 (0.50-0.76) with rs2099557 (q = 0.037). The associations were stronger when these SNPs were analyzed as haplotypes composed of two-SNP and three-SNP combinations. The strongest effect was with the "t-t-t" haplotype of the rs1339221-rs11117745-rs2099557 combination [RRR = 0.50 (0.40-0.64)], suggesting that the effects observed with the other SNP combinations, including those in the single-SNP analyses, were mainly driven by this haplotype. Although there were potential GxVitamin effects with rs17734557 and rs1316471 and GxAlcohol effects with rs9653456 and rs921876 in the European sample, respectively, none of the SNPs was located in or near genes with strong links to orofacial clefts. GxAlcohol and GxSmoke effects were not assessed in the Asian sample because of a lack of observations for these exposures. Discussion/Conclusion: We identified significant interactions between vitamin use and variants in ESRRG in the pooled analysis. These GxE effects are novel and warrant further investigations to elucidate their roles in orofacial clefting. If validated, they could provide prospects for exploring the impact of estrogens and vitamins on clefting, with potential translational applications.
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Affiliation(s)
- Øystein A Haaland
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Miriam Gjerdevik
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
| | - Håkon K Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
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12
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Skare Ø, Lie RT, Haaland ØA, Gjerdevik M, Romanowska J, Gjessing HK, Jugessur A. Analysis of Parent-of-Origin Effects on the X Chromosome in Asian and European Orofacial Cleft Triads Identifies Associations with DMD, FGF13, EGFL6, and Additional Loci at Xp22.2. Front Genet 2018. [PMID: 29520293 PMCID: PMC5827165 DOI: 10.3389/fgene.2018.00025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background: Although both the mother's and father's alleles are present in the offspring, they may not operate at the same level. These parent-of-origin (PoO) effects have not yet been explored on the X chromosome, which motivated us to develop new methods for detecting such effects. Orofacial clefts (OFCs) exhibit sex-specific differences in prevalence and are examples of traits where a search for various types of effects on the X chromosome might be relevant. Materials and Methods: We upgraded our R-package Haplin to enable genome-wide analyses of PoO effects, as well as power simulations for different statistical models. 14,486 X-chromosome SNPs in 1,291 Asian and 1,118 European case-parent triads of isolated OFCs were available from a previous GWAS. For each ethnicity, cleft lip with or without cleft palate (CL/P) and cleft palate only (CPO) were analyzed separately using two X-inactivation models and a sliding-window approach to haplotype analysis. In addition, we performed analyses restricted to female offspring. Results: Associations were identified in "Dystrophin" (DMD, Xp21.2-p21.1), "Fibroblast growth factor 13" (FGF13, Xq26.3-q27.1) and "EGF-like domain multiple 6" (EGFL6, Xp22.2), with biologically plausible links to OFCs. Unlike EGFL6, the other associations on chromosomal region Xp22.2 had no apparent connections to OFCs. However, the Xp22.2 region itself is of potential interest because it contains genes for clefting syndromes [for example, "Oral-facial-digital syndrome 1" (OFD1) and "Midline 1" (MID1)]. Overall, the identified associations were highly specific for ethnicity, cleft subtype and X-inactivation model, except for DMD in which associations were identified in both CPO and CL/P, in the model with X-inactivation and in Europeans only. Discussion/Conclusion: The specificity of the associations for ethnicity, cleft subtype and X-inactivation model underscores the utility of conducting subanalyses, despite the ensuing need to adjust for additional multiple testing. Further investigations are needed to confirm the associations with DMD, EGF16, and FGF13. Furthermore, chromosomal region Xp22.2 appears to be a hotspot for genes implicated in clefting syndromes and thus constitutes an exciting direction to pursue in future OFCs research. More generally, the new methods presented here are readily adaptable to the study of X-linked PoO effects in other outcomes that use a family-based design.
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Affiliation(s)
- Øivind Skare
- Department of Occupational Medicine and Epidemiology, National Institute of Occupational Health, Oslo, Norway
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway
| | - Øystein A Haaland
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Miriam Gjerdevik
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
| | - Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Håkon K Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway.,Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
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13
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Kreile M, Rots D, Zarina A, Rautiainen L, Visnevska-Preciniece Z, Kovalova Z, Gailite L. Association of ARID5B Genetic Variants with Risk of Childhood B Cell Precursor Acute Lymphoblastic Leukaemia in Latvia. Asian Pac J Cancer Prev 2018; 19:91-95. [PMID: 29373897 PMCID: PMC5844642 DOI: 10.22034/apjcp.2018.19.1.91] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Background: Acute lymphoblastic leukaemia (ALL) is the most common malignancy in childhood. Despite
numerous investigations very little is still known about its aetiology. However, in one genome wide association study
conducted to identify the possible genetic risk factors, two allelic variations rs10821936 and rs10994982 in the 3rd
intron of the ARID5B gene were identified as possible ALL risk alleles. Association between ARID5B gene variants and
ALL risk was also been confirmed for different ethnic groups. Materials and Methods: Eight genetic variants in the
gene ARID5B were genotyped - rs10994982, rs7908445, rs7923074, rs10821936, rs10821937, rs7896246, rs10821938
and rs7089424 in 77 ALL patients in remission and in 122 age and gender matched controls; parental samples were
also genotyped in 50 cases. Results: Six out of the eight (rs7908445, rs7923074, rs10821936, rs10821937, rs7896246
and rs7089424) analysed allelic variations were identified in the case-control analysis as statistically significant risk
alleles for ALL development. In the family study and using hybrid analysis, all allelic variations were significantly
associated with ALL. During the study, risk haplotype was identified rs10994982/rs7908445/rs7923074/ rs10821936/
rs10821937/rs7896246/rs10821938/rs7089424 – ATACCAAG – with a frequency in cases of 0.17 and in the control
group at 0.29 (chi square = 6.69, p value = 0.009). In the family association study the same haplotype showed statistical
significance (chi squared = 10.3, p value = 0.001). Conclusions: Results of the study replicate and extend previously
published findings for ARID5B localized allelic variants, but do not explain the mechanism of action related to the
pathogenesis of ALL.
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Affiliation(s)
- Madara Kreile
- Riga Stradiņš University, University Scientific Laboratory of Molecular Genetics, Riga Stradiņš University, Institute of Oncology, Children’s Clinical University Hospital, Latvia.
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14
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Masotti C, Brito L, Nica A, Ludwig K, Nunes K, Savastano C, Malcher C, Ferreira S, Kobayashi G, Bueno D, Alonso N, Franco D, Rojas-Martinez A, dos Santos S, Galante P, Meyer D, Hünemeier T, Mangold E, Dermitzakis E, Passos-Bueno M. MRPL53, a New Candidate Gene for Orofacial Clefting, Identified Using an eQTL Approach. J Dent Res 2017; 97:33-40. [DOI: 10.1177/0022034517735805] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
A valuable approach to understand how individual and population genetic differences can predispose to disease is to assess the impact of genetic variants on cellular functions (e.g., gene expression) of cell and tissue types related to pathological states. To understand the genetic basis of nonsyndromic cleft lip with or without cleft palate (NSCL/P) susceptibility, a complex and highly prevalent congenital malformation, we searched for genetic variants with a regulatory role in a disease-related tissue, the lip muscle (orbicularis oris muscle [OOM]), of affected individuals. From 46 OOM samples, which are frequently discarded during routine corrective surgeries on patients with orofacial clefts, we derived mesenchymal stem cells and correlated the individual genetic variants with gene expression from these cultured cells. Through this strategy, we detected significant cis-eQTLs (i.e., DNA variants affecting gene expression) and selected a few candidates to conduct an association study in a large Brazilian cohort (624 patients and 668 controls). This resulted in the discovery of a novel susceptibility locus for NSCL/P, rs1063588, the best eQTL for the MRPL53 gene, where evidence for association was mostly driven by the Native American ancestry component of our Brazilian sample. MRPL53 (2p13.1) encodes a 39S protein subunit of mitochondrial ribosomes and interacts with MYC, a transcription factor required for normal facial morphogenesis. Our study illustrates not only the importance of sampling admixed populations but also the relevance of measuring the functional effects of genetic variants over gene expression to dissect the complexity of disease phenotypes.
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Affiliation(s)
- C. Masotti
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
- Molecular Oncology Center, Hospital Sírio Libanês, São Paulo, SP, Brazil
| | - L.A. Brito
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
| | - A.C. Nica
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - K.U. Ludwig
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life&Brain Center, University of Bonn, Bonn, Germany
| | - K. Nunes
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
| | - C.P. Savastano
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
| | - C. Malcher
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
| | - S.G. Ferreira
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
| | - G.S. Kobayashi
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
| | - D.F. Bueno
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
| | - N. Alonso
- Department of Plastic Surgery, University of São Paulo Medical School, São Paulo, SP, Brazil
| | - D. Franco
- Department of Plastic Surgery, Hospital Clementino Braga Filho, Federal University of Rio de Janeiro Medical School, Rio de Janeiro, RJ, Brazil
| | - A. Rojas-Martinez
- Department of Biochemistry and Molecular Medicine, School of Medicine, and Centro de Investigación y Desarrollo en Ciencias de la Salud, Universidad Autonoma de Nuevo Leon, Monterrey, Mexico
| | - S.E. dos Santos
- Institute of Biological Sciences, Federal University of Pará, Belém, PA, Brazil
| | - P.A. Galante
- Molecular Oncology Center, Hospital Sírio Libanês, São Paulo, SP, Brazil
| | - D. Meyer
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
| | - T. Hünemeier
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
| | - E. Mangold
- Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - E.T. Dermitzakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
- Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - M.R. Passos-Bueno
- Department of Genetics and Evolutionary Biology, University of São Paulo, São Paulo, SP, Brazil
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15
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de Aquino SN, Machado RA, Paranaíba LMR, Martelli DRB, Popoff DAV, Swerts MSO, Martelli-Júnior H. A review of seasonality of cleft births - The Brazil experience. J Oral Biol Craniofac Res 2017; 7:2-6. [PMID: 28316913 DOI: 10.1016/j.jobcr.2016.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 03/15/2016] [Indexed: 11/17/2022] Open
Abstract
AIMS Evaluate the seasonal influence in nonsyndromic cleft lip and/or palate (NSCL/P) in Brazilian patients. METHODS A case-control study, with 361 unrelated patients with NSCL/P and 481 healthy individuals, was done on a reference service for craniofacial deformities in Minas Gerais State, Brazil. Information was collected from clinical records considering gender, month of birth, as well as with the seasons. RESULTS Nonparametric tests did not show a seasonal variation in month of birth and in seasons of year of NSCL/P compared to a control group (p = 0.902 and p = 0.679, respectively). A difference in births between the groups was identified only in January, however, was not significant. Moreover, among the control group there were more births in the months of February and August, and for the cleft group, more in July and August. The males were more affected by cleft lip with or without palate (CLP) and the females by isolated cleft palate (CP) manifestation. The ratio of CL:CLP:CP indicated that CLP was predominant when compared with CL and CP, CLP was more frequent in male patients, and CP predominance was seen in females. CONCLUSION This study did not show seasonal differences in births on NSCL/P in a Brazilian group, emphasizing that environmental factors may be related to oral clefts. These results provide a basis for further epidemiological studies of orofacial clefts in Brazil.
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Affiliation(s)
| | - Renato Assis Machado
- Department of Oral Diagnostic, Piracicaba Dental School - State University of Campinas, Piracicaba, São Paulo, Brazil
| | - Lívia Máris R Paranaíba
- Health Science Program, State University of Montes Claros, Montes Claros, Minas Gerais, Brazil
| | | | | | - Mário Sérgio O Swerts
- Center for Rehabilitation of Craniofacial Anomalies, Dental School, University Jose Rosário Vellano, Alfenas, Minas Gerais, Brazil
| | - Hercílio Martelli-Júnior
- Health Science Program, State University of Montes Claros, Montes Claros, Minas Gerais, Brazil; Center for Rehabilitation of Craniofacial Anomalies, Dental School, University Jose Rosário Vellano, Alfenas, Minas Gerais, Brazil
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16
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Validation of a genome-wide association study implied that SHTIN1 may involve in the pathogenesis of NSCL/P in Chinese population. Sci Rep 2016; 6:38872. [PMID: 28008912 PMCID: PMC5180092 DOI: 10.1038/srep38872] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 11/16/2016] [Indexed: 11/08/2022] Open
Abstract
Orofacial clefts are among the most common birth defects in humans worldwide. A large-scale, genome-wide association study (GWAS) in the Chinese population recently identified several genetic risk variants for nonsyndromic cleft lip with or without cleft palate (NSCL/P). We selected 16 significant SNPs from the GWAS I stage (P < 1.00E-5) that had not been replicated to validate their association with NSCL/P in 1931 NSCL/P cases and 2258 controls. Ultimately, we identified a NSCL/P susceptibility loci (rs17095681 at 10q25.3, intron of SHTN1 and 27.2 kb downstream of VAX1, Pmeta = 3.80E-9, OR = 0.64) in Chinese Han and Hui populations. This locus was not high LD with the reported loci in 10q25.3. It was a newly identified independent locus in 10q25.3 associated with NSCL/P. These results imply that SHTIN1 may involve in the pathogenesis of NSCL/P advance our understanding of the genetic susceptibility to NSCL/P.
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17
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Lewandowski SA, Fredriksson L, Lawrence DA, Eriksson U. Pharmacological targeting of the PDGF-CC signaling pathway for blood-brain barrier restoration in neurological disorders. Pharmacol Ther 2016; 167:108-119. [PMID: 27524729 PMCID: PMC5341142 DOI: 10.1016/j.pharmthera.2016.07.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 07/25/2016] [Indexed: 12/12/2022]
Abstract
Neurological disorders account for a majority of non-malignant disability in humans and are often associated with dysfunction of the blood-brain barrier (BBB). Recent evidence shows that despite apparent variation in the origin of neural damage, the central nervous system has a common injury response mechanism involving platelet-derived growth factor (PDGF)-CC activation in the neurovascular unit and subsequent dysfunction of BBB integrity. Inhibition of PDGF-CC signaling with imatinib in mice has been shown to prevent BBB dysfunction and have neuroprotective effects in acute damage conditions, including traumatic brain injury, seizures or stroke, as well as in neurodegenerative diseases that develop over time, including multiple sclerosis and amyotrophic lateral sclerosis. Stroke and traumatic injuries are major risk factors for age-associated neurodegenerative disorders and we speculate that restoring BBB properties through PDGF-CC inhibition might provide a common therapeutic opportunity for treatment of both acute and progressive neuropathology in humans. In this review we will summarize what is known about the role of PDGF-CC in neurovascular signaling events and the variety of seemingly different neuropathologies it is involved in. We will also discuss the pharmacological means of therapeutic interventions for anti-PDGF-CC therapy and ongoing clinical trials. In summary: inhibition of PDGF-CC signaling can be protective for immediate injury and decrease the long-term neurodegenerative consequences.
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Affiliation(s)
- Sebastian A Lewandowski
- Tissue Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Scheeles v. 2, 17177, Stockholm, Sweden.
| | - Linda Fredriksson
- Vascular Biology Groups, Division of Vascular Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Scheeles v. 2, 17177, Stockholm, Sweden; Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan Medical School, 7301 Medical Science Research Building III, 1150 West Medical Center Drive, Ann Arbor, MI 48109-0644, USA
| | - Daniel A Lawrence
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan Medical School, 7301 Medical Science Research Building III, 1150 West Medical Center Drive, Ann Arbor, MI 48109-0644, USA
| | - Ulf Eriksson
- Tissue Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Scheeles v. 2, 17177, Stockholm, Sweden.
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18
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Chiquet M, Blumer S, Angelini M, Mitsiadis TA, Katsaros C. Mesenchymal Remodeling during Palatal Shelf Elevation Revealed by Extracellular Matrix and F-Actin Expression Patterns. Front Physiol 2016; 7:392. [PMID: 27656150 PMCID: PMC5013070 DOI: 10.3389/fphys.2016.00392] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 08/23/2016] [Indexed: 12/17/2022] Open
Abstract
During formation of the secondary palate in mammalian embryos, two vertically oriented palatal shelves rapidly elevate into a horizontal position above the tongue, meet at the midline, and fuse to form a single entity. Previous observations suggested that elevation occurs by a simple 90° rotation of the palatal shelves. More recent findings showed that the presumptive midline epithelial cells are not located at the tips of palatal shelves before elevation, but mostly toward their medial/lingual part. This implied extensive tissue remodeling during shelf elevation. Nevertheless, it is still not known how the shelf mesenchyme reorganizes during this process, and what mechanism drives it. To address this question, we mapped the distinct and restricted expression domains of certain extracellular matrix components within the developing palatal shelves. This procedure allowed to monitor movements of entire mesenchymal regions relative to each other during shelf elevation. Consistent with previous notions, our results confirm a flipping movement of the palatal shelves anteriorly, whereas extensive mesenchymal reorganization is observed more posteriorly. There, the entire lingual portion of the vertical shelves moves close to the midline after elevation, whereas the mesenchyme at the original tip of the shelves ends up ventrolaterally. Moreover, we observed that the mesenchymal cells of elevating palatal shelves substantially align their actin cytoskeleton, their extracellular matrix, and their nuclei in a ventral to medial direction. This indicates that, like in other morphogenetic processes, actin-dependent cell contractility is a major driving force for mesenchymal tissue remodeling during palatogenesis.
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Affiliation(s)
- Matthias Chiquet
- Department of Orthodontics and Dentofacial Orthopedics, Medical Faculty, School of Dental Medicine, University of Bern Bern, Switzerland
| | - Susan Blumer
- Department of Orthodontics and Dentofacial Orthopedics, Medical Faculty, School of Dental Medicine, University of Bern Bern, Switzerland
| | - Manuela Angelini
- Department of Orthodontics and Dentofacial Orthopedics, Medical Faculty, School of Dental Medicine, University of Bern Bern, Switzerland
| | - Thimios A Mitsiadis
- Orofacial Development and Regeneration, Center for Dental Medicine, Institute for Oral Biology, University of Zurich Zurich, Switzerland
| | - Christos Katsaros
- Department of Orthodontics and Dentofacial Orthopedics, Medical Faculty, School of Dental Medicine, University of Bern Bern, Switzerland
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19
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Mcbride W, Mcintyre G, Carroll K, Mossey P. Subphenotyping and Classification of Orofacial Clefts: Need for Orofacial Cleft Subphenotyping Calls for Revised Classification. Cleft Palate Craniofac J 2016; 53:539-49. [DOI: 10.1597/15-029] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Nonsyndromic orofacial clefting (OFC) describes a range of phenotypes that represent the most common craniofacial birth defects in humans, with an overall birth prevalence of 1:700 live births. Because of the lifelong negative implications on health and well-being associated with OFC and the numbers of people affected, quality research into its etiology, diagnosis, treatment outcomes, and preventative strategies is essential. A range of different methods is used for recording and classifying OFC subphenotypes, one of which is the International Classification of Diseases (ICD) system. However, there is a general perception that research is being hampered by a lack of sensitivity and specificity in grouping those with OFC into subphenotypes, with potential heterogeneity and confounding in epidemiologic, genetic, and genotype-phenotype correlation studies. This article provides a background to the necessity of OFC research, discusses current controversies within cleft subphenotyping, and provides a brief overview of current OFC classifications as well as their limitations. The LAHSHAL classification is described in the context of a potentially useful tool for OFC that could complement the ICD-10/ICD-11 Beta coding systems to become a simply understood, universally accepted, clinically friendly, and research-sensitive instrument. Empowering registries, clinicians, and researchers to use a common classification system would have significant implications for OFC research across the world at a time when accurate subphenotyping is crucial and health care research is becoming increasingly tailored toward the individual.
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Affiliation(s)
- W.A. Mcbride
- Queen's University Dental School, Belfast, Northern Ireland
| | - G.T. Mcintyre
- Consultant of Orthodontics, Dundee Dental Hospital and School, Dundee, Scotland
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20
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Aylward A, Cai Y, Lee A, Blue E, Rabinowitz D, Haddad J. Using Whole Exome Sequencing to Identify Candidate Genes With Rare Variants In Nonsyndromic Cleft Lip and Palate. Genet Epidemiol 2016; 40:432-41. [PMID: 27229527 PMCID: PMC4985012 DOI: 10.1002/gepi.21972] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 02/28/2016] [Accepted: 03/07/2016] [Indexed: 11/06/2022]
Abstract
Studies suggest that nonsyndromic cleft lip and palate (NSCLP) is polygenic with variable penetrance, presenting a challenge in identifying all causal genetic variants. Despite relatively high prevalence of NSCLP among Amerindian populations, no large whole exome sequencing (WES) studies have been completed in this population. Our goal was to identify candidate genes with rare genetic variants for NSCLP in a Honduran population using WES. WES was performed on two to four members of 27 multiplex Honduran families. Genetic variants with a minor allele frequency > 1% in reference databases were removed. Heterozygous variants consistent with dominant disease with incomplete penetrance were ascertained, and variants with predicted functional consequence were prioritized for analysis. Pedigree-specific P-values were calculated as the probability of all affected members in the pedigree being carriers, given that at least one is a carrier. Preliminary results identified 3,727 heterozygous rare variants; 1,282 were predicted to be functionally consequential. Twenty-three genes had variants of interest in ≥3 families, where some genes had different variants in each family, giving a total of 50 variants. Variant validation via Sanger sequencing of the families and unrelated unaffected controls excluded variants that were sequencing errors or common variants not in databases, leaving four genes with candidate variants in ≥3 families. Of these, candidate variants in two genes consistently segregate with NSCLP as a dominant variant with incomplete penetrance: ACSS2 and PHYH. Rare variants found at the same gene in all affected individuals in several families are likely to be directly related to NSCLP.
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Affiliation(s)
- Alana Aylward
- Columbia University College of Physicians and Surgeons Otolaryngology Department, New York, NY
| | - Yi Cai
- Columbia University College of Physicians and Surgeons Otolaryngology Department, New York, NY
| | - Andrew Lee
- Columbia University College of Physicians and Surgeons Otolaryngology Department, New York, NY
| | - Elizabeth Blue
- University of Washington Department of Medicine, Division of Medical Genetics, Seattle, WA
| | | | | | - Joseph Haddad
- Columbia University College of Physicians and Surgeons Otolaryngology Department, New York, NY
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21
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Kreile M, Piekuse L, Rots D, Dobele Z, Kovalova Z, Lace B. Analysis of possible genetic risk factors contributing to development of childhood acute lymphoblastic leukaemia in the Latvian population. Arch Med Sci 2016; 12:479-85. [PMID: 27279837 PMCID: PMC4889682 DOI: 10.5114/aoms.2016.59920] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 11/10/2014] [Indexed: 01/25/2023] Open
Abstract
INTRODUCTION Childhood acute lymphoblastic leukaemia (ALL) is a complex disease caused by a combination of genetic susceptibility and environmental exposure. Previous genome-wide association studies have reported several single nucleotide polymorphisms (SNPs) associated with the incidence of ALL. Several variations in genes encoding enzymes involved in carcinogenesis are suggested as being associated with an increased risk of ALL development. MATERIAL AND METHODS We enrolled 77 paediatric ALL patients and 122 healthy controls, and in addition parental DNA was also available for 45 probands. SNPs rs10821936 (ARID5B), rs4132601 (IKZF1), rs2239633 (CEBPE), rs3731217 (CDKN2A) and rs1800566 (NQO1) and the presence of GSTT1 and GSTM1 null variants were detected. For statistical analysis the hybrid method of two designs 'Haplin' was used as well as linkage disequilibrium for family-based association studies. RESULTS We identified the SNP rs10821936 in the ARID5B gene as being statistically significantly associated with childhood ALL, especially if the C allele is in a homozygous state, relative risk (RR) 4.65, 95% CI: 2.03-10.6, p = 0.0006. Statistically significant differences were not found in other SNPs. We found risk combinations including all five variations, the strongest association being found in a combination where all five genetic variants are in a homozygous state, CCTTTTTTCC, p = 0.032. CONCLUSIONS The identified SNP rs10821936 could serve as a potential risk marker for childhood ALL development. Further studies in an independent population are needed for verification.
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Affiliation(s)
- Madara Kreile
- Scientific Laboratory of Molecular Genetics, Riga Stradiņš University, Riga, Latvia
- Institute of Oncology, Riga Stradiņš University, Riga, Latvia
| | - Linda Piekuse
- Scientific Laboratory of Molecular Genetics, Riga Stradiņš University, Riga, Latvia
| | - Dmitrijs Rots
- Scientific Laboratory of Molecular Genetics, Riga Stradiņš University, Riga, Latvia
| | - Zane Dobele
- Scientific Laboratory of Molecular Genetics, Riga Stradiņš University, Riga, Latvia
| | - Zhanna Kovalova
- Department of Hematology and Oncology, Children's Clinical University Hospital, Riga, Latvia
| | - Baiba Lace
- Latvian Biomedical Research and Study Centre, Riga, Latvia
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22
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Mohamad Shah NS, Salahshourifar I, Sulong S, Wan Sulaiman WA, Halim AS. Discovery of candidate genes for nonsyndromic cleft lip palate through genome-wide linkage analysis of large extended families in the Malay population. BMC Genet 2016; 17:39. [PMID: 26868259 PMCID: PMC4751652 DOI: 10.1186/s12863-016-0345-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 02/02/2016] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Nonsyndromic orofacial clefts are one of the most common birth defects worldwide. It occurs as a result of genetic or environmental factors. This study investigates the genetic contribution to nonsyndromic cleft lip and/or palate through the analysis of family pedigrees. Candidate genes associated with the condition were identified from large extended families from the Malay population. RESULTS A significant nonparametric linkage (NPL) score was detected in family 100. Other suggestive NPL and logarithm of the odds (LOD) scores were attained from families 50, 58, 99 and 100 under autosomal recessive mode. Heterogeneity LOD (HLOD) score ≥ 1 was determined for all families, confirming genetic heterogeneity of the population and indicating that a proportion of families might be linked to each other. Several candidate genes in linkage intervals were determined; LPHN2 at 1p31, SATB2 at 2q33.1-q35, PVRL3 at 3q13.3, COL21A1 at 6p12.1, FOXP2 at 7q22.3-q33, FOXG1 and HECTD1 at 14q12 and TOX3 at 16q12.1. CONCLUSIONS We have identified several novel and known candidate genes for nonsyndromic cleft lip and/or palate through genome-wide linkage analysis. Further analysis of the involvement of these genes in the condition will shed light on the disease mechanism. Comprehensive genetic testing of the candidate genes is warranted.
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Affiliation(s)
| | - Iman Salahshourifar
- Department of Biology, School of Basic Sciences, Science and Research Branch, Islamic Azad University, Isfahan, Iran.
| | - Sarina Sulong
- Human Genome Center, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia.
| | - Wan Azman Wan Sulaiman
- Reconstructive Science Unit, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia.
| | - Ahmad Sukari Halim
- School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kelantan, Malaysia.
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23
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Tello J, Torres-Pérez R, Grimplet J, Ibáñez J. Association analysis of grapevine bunch traits using a comprehensive approach. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:227-42. [PMID: 26536891 DOI: 10.1007/s00122-015-2623-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/17/2015] [Indexed: 05/09/2023]
Abstract
KEY MESSAGE A set of SNP markers associated to bunch compactness and related traits were identified in grapevine. ABSTRACT Bunch compactness plays an important role in the sanitary status and perceived quality of table and wine grapes, being influenced by cultural practices and by environmental and genetic factors, which are mostly unknown. In this work, we took advantage of genetic, genomic and bioinformatic advances to analyze part of its molecular basis through a combination of transcriptomic and association analyses. Results from different transcriptomic comparisons between loose and compact grapevine clones were analyzed to select a set of candidate genes likely involved in the observed variation for bunch compactness. Up to 183 genes were sequenced in a grapevine collection, and 7032 single nucleotide polymorphisms (SNPs) were detected in more than 100 varieties with a frequency of the minor allele over 5%. They were used to test their association in three consecutive seasons with bunch compactness and two of its most influencing factors: total berry number and length of the first ramification of the rachis. Only one SNP was associated with berry number in two seasons, suggesting the high sensitiveness of this trait to seasonal environmental changes. On the other hand, we found a set of SNPs associated with both the first ramification length and bunch compactness in various seasons, in several genes which had not previously related to bunch compactness or bunch compactness-related traits. They are proposed as interesting candidates for further functional analyses aimed to verify the results obtained in this work, as a previous step to their inclusion in marker-assisted selection strategies.
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Affiliation(s)
- Javier Tello
- Departamento de Viticultura, Instituto de Ciencias de la Vid y del Vino (ICVV, CSIC-Universidad de La Rioja-Gobierno de La Rioja), Carretera de Burgos km 6. Finca La Grajera, 26007, Logroño, Spain
| | - Rafael Torres-Pérez
- Departamento de Viticultura, Instituto de Ciencias de la Vid y del Vino (ICVV, CSIC-Universidad de La Rioja-Gobierno de La Rioja), Carretera de Burgos km 6. Finca La Grajera, 26007, Logroño, Spain
| | - Jérôme Grimplet
- Departamento de Viticultura, Instituto de Ciencias de la Vid y del Vino (ICVV, CSIC-Universidad de La Rioja-Gobierno de La Rioja), Carretera de Burgos km 6. Finca La Grajera, 26007, Logroño, Spain
| | - Javier Ibáñez
- Departamento de Viticultura, Instituto de Ciencias de la Vid y del Vino (ICVV, CSIC-Universidad de La Rioja-Gobierno de La Rioja), Carretera de Burgos km 6. Finca La Grajera, 26007, Logroño, Spain.
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Yin X, Zhang H, Zhu Z, Wang H, Du Y, Li S, Zhang Z, Fan W, Pan Y. FOXE1 polymorphisms and non-syndromic orofacial cleft susceptibility in a Chinese Han population. Oral Dis 2016; 22:274-9. [PMID: 26728781 DOI: 10.1111/odi.12435] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 10/22/2015] [Accepted: 10/23/2015] [Indexed: 11/30/2022]
Abstract
OBJECTIVE FOXE1 plays an important role in craniofacial development. The aim of this study was to investigate associations between genetic variants of FOXE1 and risk of non-syndromic orofacial clefts in a Chinese population. MATERIALS AND METHODS Three potentially functional SNPs of FOXE1 (rs3758250 and rs907577 in the 5' upstream and rs7043516 in the 3'-UTR) were selected and their associations with non-syndromic orofacial cleft susceptibility were investigated in a case-control study from a Chinese population (602 cases and 605 controls). Genotyping was performed with double ligation and multiplex fluorescence PCR. Associations between the SNPs and risk of non-syndromic orofacial clefts and its subgroups were estimated from unconditional logistic regression analysis. Luciferase reporter assay was conducted to assess SNP function. RESULTS Overall, we did not find any of the individual SNP or haplotype was associated with NSOC susceptibility. Nevertheless, in stratified analysis, we found rs7043516, locating in the 3'-UTR of FOXE1, was associated with risk of cleft lip only. Further in vitro luciferase assay indicated that this SNP could contribute to differential binding ability with miRNA. CONCLUSIONS Taken together, this study showed that rs7043516 may be considered as a potentially susceptible marker of cleft lip only among Chinese Han populations.
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Affiliation(s)
- X Yin
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - H Zhang
- Xuzhou First People's Hospital, Xuzhou, China
| | - Z Zhu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - H Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Y Du
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - S Li
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Z Zhang
- Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - W Fan
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Y Pan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
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Xie Y. Is Chromosome 15q13.3 Duplication Involving CHRNA7 Associated With Oral Clefts? Child Neurol Open 2015; 2:2329048X15618918. [PMID: 28503599 PMCID: PMC5417031 DOI: 10.1177/2329048x15618918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Revised: 10/17/2015] [Accepted: 10/27/2015] [Indexed: 11/15/2022] Open
Abstract
Copy number variants have been associated with intellectual disability, multiple congenital anomalies and craniofacial disorders. It has been reported that microduplication of 15q13.3 is associated with autism, cognitive impairment, seizures, and attention-deficit hyperactivity disorder. Here, the author identified microduplications in the 15q13.3 region in 4 cases from 3 Chinese families using chromosomal microarray analysis-single nucleotide polymorphism array (CMA-SNP). These 4 cases include 2 fetuses from 2 unrelated families and a father and a daughter from a third family. The identified microduplications of 15q13.3 are approximately 400 kb in size, encompassing just 1 gene, cholinergic receptor, neuronal nicotinic, alpha polypeptide 7 (CHRNA7). Three-fourths of the probands exhibit oral clefts, which has not been previously reported in cases with this duplication genotype. Therefore, in this study, the author describes for the first time the common feature of oral clefts in patients carrying a microduplication of 15q13.3 encompassing the CHRNA7 gene, which sheds light on the correlation between CHRNA7 and cleft palate.
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Affiliation(s)
- Yingjun Xie
- Department of Prenatal Diagnosis, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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Bu L, Chen Q, Wang H, Zhang T, Hetmanski JB, Schwender H, Parker M, Chou YHW, Yeow V, Chong SS, Zhang B, Jabs EW, Scott AF, Beaty TH. Novel evidence of association with nonsyndromic cleft lip with or without cleft palate was shown for single nucleotide polymorphisms in FOXF2 gene in an Asian population. BIRTH DEFECTS RESEARCH. PART A, CLINICAL AND MOLECULAR TERATOLOGY 2015; 103:857-62. [PMID: 26278207 PMCID: PMC5180447 DOI: 10.1002/bdra.23413] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 06/15/2015] [Accepted: 06/28/2015] [Indexed: 11/07/2022]
Abstract
BACKGROUND The forkhead box F2 gene (FOXF2) located in chromosome 6p25.3 has been shown to play a crucial role in palatal development in mouse and rat models. To date, no evidence of linkage or association has been reported for this gene in humans with oral clefts. METHODS Allelic transmission disequilibrium tests were used to robustly assess evidence of linkage and association with nonsyndromic cleft lip with or without cleft palate for nine single nucleotide polymorphisms (SNPs) in and around FOXF2 in both Asian and European trios using PLINK. RESULTS Statistically significant evidence of linkage and association was shown for two SNPs (rs1711968 and rs732835) in 216 Asian trios where the empiric P values with permutation tests were 0.0016 and 0.005, respectively. The corresponding estimated odds ratios for carrying the minor allele at these SNPs were 2.05 (95% confidence interval = 1.41, 2.98) and 1.77 (95% confidence interval = 1.26, 2.49), respectively. CONCLUSION Our results provided statistical evidence of linkage and association between FOXF2 and nonsyndromic cleft lip with or without cleft palate.
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Affiliation(s)
- Lingxue Bu
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Qianqian Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- National Center for Public Health Surveillance and Information Services, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hong Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- Ministry of Health KeyLaboratory of Reproductive Health, Beijing, China
| | - Tianxiao Zhang
- Division of Biology and Biomedical Sciences, Washington University, St. Louis, Missouri
| | - Jacqueline B Hetmanski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Holger Schwender
- Mathematical Institute, Heinrich Heine University Duesseldorf, Duesseldorf, Germany
| | - Margaret Parker
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Yah-Huei Wu Chou
- Department of Medical Research, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Vincent Yeow
- Department of Plastic Surgery, K K Women's and Children's Hospital, Singapore
| | - Samuel S Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore
| | - Bo Zhang
- Department of Biomedical Engineering, Xi'an JiaoTong University, Xi'an, China
| | - Ethylin Wang Jabs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA. Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alan F Scott
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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Liu K, Lu Y, Ai L, Jiao B, Yu J, Zhang B, Liu Q. Association between FOXE1 and non-syndromic orofacial clefts in a northeastern Chinese population. Br J Oral Maxillofac Surg 2015; 53:705-10. [PMID: 26100861 DOI: 10.1016/j.bjoms.2015.05.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 05/22/2015] [Indexed: 01/07/2023]
Abstract
Non-syndromic orofacial clefts are among the most common congenital defects, and several reports have shown that the FOXE1 gene has strong associations with them. To find out if the gene was a risk factor we used a case-control and family-based analysis, and recruited 230 patients with non-syndromic oral clefts including 179 with non-syndromic cleft lip with or without cleft palate, and 51 with non-syndromic cleft palate alone, their parents (166 mothers and 161 fathers, including 135 complete trios), and 180 healthy controls. Polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) were used to genotype the 2 most strongly associated markers (rs4460498 and rs3758249) in FOXE1, and case-control and family-based associations were analysed. In the case-control analyses we found a significant association with non-syndromic cleft lip and palate in rs4460498 (p=0.009) and rs3758249 (p=0.014), but no association in patients with cleft palate alone. For rs4460498 in FOXE1, the odds ratio (OR) for cases with CC homozygotes compared with TC+CC genotypes was 1.813 (95% CI 1.176 to 2.796), and for rs3758249 in FOXE1, the OR for cases with GG homozygotes compared with those with AG+AA genotypes was 0.561 (95%CI 0.371 to 0.848). The results of transmission-disequilibrium tests for rs4460698 and rs3758249 for non-syndromic orofacial clefts were p=0.003, OR=2.781 (95% CI 1.414 to 5.469) and p=0.001, OR=2.552 (95%CI 1.574 to 4.138), respectively. This suggests that FOXE1 (rs4460498 and rs3758249) is strongly associated with non-syndromic cleft lip and palate in populations in northeast China, and further study between FOXE1 and non-syndromic orofacial clefts is necessary.
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Affiliation(s)
- Kun Liu
- Department of Oral and Maxillofacial Surgery, School of Stomatology, China Medical University, Shenyang, Liaoning 110002, PR China.
| | - Yongping Lu
- Key Laboratory of Reproductive Health, Liaoning Province Research Institute of Family Planning, Shenyang, Liaoning 110002, PR China.
| | - Lisi Ai
- Department of Periodontics,School of Stomatology, China Medical University, Shenyang, Liaoning 110002, PR China.
| | - Boqiang Jiao
- Department of Oral and Maxillofacial Surgery, School of Stomatology, China Medical University, Shenyang, Liaoning 110002, PR China.
| | - Jiantao Yu
- Department of Oral and Maxillofacial Surgery, School of Stomatology, China Medical University, Shenyang, Liaoning 110002, PR China.
| | - Bin Zhang
- Department of Oral and Maxillofacial Surgery, School of Stomatology, China Medical University, Shenyang, Liaoning 110002, PR China.
| | - Qiang Liu
- Department of Oral and Maxillofacial Surgery, School of Stomatology, China Medical University, Shenyang, Liaoning 110002, PR China.
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Mehrotra D. Genomic expression in non syndromic cleft lip and palate patients: A review. J Oral Biol Craniofac Res 2015; 5:86-91. [PMID: 26258020 DOI: 10.1016/j.jobcr.2015.03.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 03/25/2015] [Indexed: 11/29/2022] Open
Abstract
Cleft lip and palate are common congenital anomalies with significant medical, psychological, social, and economic ramifications, affecting one in seven hundred live births. Genetic causes of non syndromic cleft lip and/or palate (NSCLP) include chromosomal rearrangements, genetic susceptibility to teratogenic exposures, and complex genetic contributions of multiple genes. Development of the orofacial clefts in an individual will depend on the interaction of several moderately effecting genes with environmental factors. Several candidate genes have been genotyped in different population types, using case parent trio or case control design; also genes have been sequenced and SNPs have been reported. Quantitative and molecular analysis have shown linkage and association studies to be more relevant. Recent literature search shows genome wide association studies using microarray. The aim of this paper was to review the approaches to identify genes associated with NSCLP and to analyze their differential expressions. Although no major gene has been confirmed, a lot of research is ongoing to provide an understanding of the pathophysiology of the orofacial clefts.
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Affiliation(s)
- D Mehrotra
- Professor, Department of Oral & Maxillofacial Surgery, King George Medical University, Lucknow, India
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29
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Nilsson S, Merlo J, Lyberg-Åhlander V, Psouni E. Psychotropic drug use in adolescents born with an orofacial cleft: a population-based study. BMJ Open 2015; 5:e005306. [PMID: 25838502 PMCID: PMC4390737 DOI: 10.1136/bmjopen-2014-005306] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES Being born with an orofacial cleft (OFC) can, due to an incomplete closure of the lip and/or palate, convey a deviant speech and/or deviant facial aesthetics, which may in turn increase the risk for poor psychological health later in life. Previous investigations have been based on small samples and self-reports, not distinguishing between the three different types of OFC: cleft lip (CL), CL and palate (CLP) and cleft palate only (CPO). We present a large population-based study, considering psychotropic drug use as a proxy for poor psychological health and distinguishing between three different types of OFC. DESIGN AND METHODS Using the Swedish Medical Birth Register, and linking to it the Swedish Prescribed Drug Register, the National Mortality Register, the Emigration Register and the National Inpatient Register, we identified all singletons born to native mothers in Sweden between 1987 and 1993, alive and residing in Sweden at the end of an 18-year follow-up period (N=626 109). We compared psychotropic drug use among individuals with and without OFC during the individuals' adolescence (2005-2008) by multiple logistic regressions, using ORs with 95% CIs. RESULTS When adjusted for potential confounders, having a CL (OR=1.63, 95% CI 1.08 to 2.46) or a CPO (OR=1.54, 95% CI 1.18 to 2.01) increased the risk of psychotropic drug use. Results were not significant regarding adolescents who had a CLP (OR=1.21, 95% CI 0.81 to 1.80). CONCLUSIONS Being born with a CL or a CPO increases the risk for psychotropic drug use in adolescence, but not for adolescents born with a CLP. Our findings suggest that, since the three OFC types are associated with different long-term risks of poor psychological health, the three groups should be studied separately concerning long-term psychosocial consequences.
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Affiliation(s)
- Sofia Nilsson
- Unit for Social Epidemiology, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Juan Merlo
- Unit for Social Epidemiology, Faculty of Medicine, Lund University, Malmö, Sweden
| | - Viveka Lyberg-Åhlander
- Department of Logopedics, Phoniatrics and Audiology, Faculty of Medicine, Lund University, Lund, Sweden
| | - Elia Psouni
- Department of Psychology, Faculty of Social Sciences, Lund University, Lund, Sweden
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Reiter R, Brosch S, Goebel I, Ludwig KU, Pickhard A, Högel J, Schlömer G, Mangold E, Kubisch C, Borck G. A post GWAS association study of SNPs associated with cleft lip with or without cleft palate in submucous cleft palate. Am J Med Genet A 2015; 167A:670-3. [DOI: 10.1002/ajmg.a.36891] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 10/30/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Rudolf Reiter
- Section of Phoniatrics and Pedaudiology; Department of Otolaryngology - Head and Neck Surgery; University of Ulm; Ulm Germany
| | - Sibylle Brosch
- Section of Phoniatrics and Pedaudiology; Department of Otolaryngology - Head and Neck Surgery; University of Ulm; Ulm Germany
| | - Ingrid Goebel
- Institute of Human Genetics; University of Ulm; Ulm Germany
- Institute of Human Genetics; University Medical Center Hamburg-Eppendorf; Hamburg Germany
| | - Kerstin U. Ludwig
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Department of Genomics; Life and Brain Center; University of Bonn; Bonn Germany
| | - Anja Pickhard
- Department of Otolaryngology - Head and Neck Surgery; Technical University Munich; Munich Germany
| | - Josef Högel
- Institute of Human Genetics; University of Ulm; Ulm Germany
| | - Guido Schlömer
- Department of Cranio-Maxillo-Facial Surgery; University of Ulm; Ulm Germany
| | | | - Christian Kubisch
- Institute of Human Genetics; University of Ulm; Ulm Germany
- Institute of Human Genetics; University Medical Center Hamburg-Eppendorf; Hamburg Germany
| | - Guntram Borck
- Institute of Human Genetics; University of Ulm; Ulm Germany
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Mijiti A, Ling W, Maimaiti A, Tuerdi M, Tuerxun J, Moming A. Preliminary evidence of an interaction between the CRISPLD2 gene and non-syndromic cleft lip with or without cleft palate (nsCL/P) in Xinjiang Uyghur population, China. Int J Pediatr Otorhinolaryngol 2015; 79:94-100. [PMID: 25496823 DOI: 10.1016/j.ijporl.2014.10.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 10/29/2014] [Accepted: 10/31/2014] [Indexed: 12/30/2022]
Abstract
BACKGROUND Non-syndromic cleft lip with or without cleft palate (nsCL/P) is a common birth defect results from the genetic factors alone or interactions with environmental changes. Single nucleotide polymorphisms (SNPs) of CRISPLD2 gene have been found to be an etiologic factor in the development of nsCL/P. However, few studies to date focused on the association of genetic variation of CRISPLD2 gene with nsCL/P, and the results are conflicting based on the different study population. The main purpose of the present study was to investigate the association between the CRISPLD2 gene and nsCL/P in Xinjiang Uyghur population. METHODS Eighteen SNPs were screened in a group of 200 patients with nsCL/P and in a control group consisting of 180 unaffected individuals by next generation sequencing using MiSeq Benchtop Sequencer (Illumina). RESULTS Our case-control association analysis showed that the SNP marker rs1546124 showed statistically significant differences in genotype (CC vs. CG vs. GG P=0.004) and allele frequencies (49% vs. 37.8% OR=1.58; 95% CI=1.19-2.1, P=0.002) between nsCL/P and controls. Under the recessive model of inheritance, the GG homozygotes had an OR of 2.4 (95% CI=1.37-4.18; P=0.002), and the result of significance was maintained even after multiple testing correction. Haplotype combinations of CACC were significantly more frequent in the nsCL/P patients than in controls (P=0.037). Finally, the MDR analysis identified the two-SNP model including rs1546124 and rs4782675 as best combination of possibly interactive polymorphisms (P<0.001). CONCLUSION Our results demonstrate that genetic polymorphism of CRISPLD2 gene is associated with an increased risk of nsCL/P in a Xinjiang Uyghur population.
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Affiliation(s)
- Ainiwaer Mijiti
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Xinjiang Medical University, No.137 South Li YU-shan Road, New City District 830054 Urumqi, Xinjiang, PR China; Stomatological Research Institute of Xinjiang Uyghur Autonomous Region, Urumqi, Xinjiang 830054, PR China.
| | - Wang Ling
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Xinjiang Medical University, No.137 South Li YU-shan Road, New City District 830054 Urumqi, Xinjiang, PR China; Stomatological Research Institute of Xinjiang Uyghur Autonomous Region, Urumqi, Xinjiang 830054, PR China.
| | - Abudukelimujiang Maimaiti
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Xinjiang Medical University, No.137 South Li YU-shan Road, New City District 830054 Urumqi, Xinjiang, PR China; Stomatological Research Institute of Xinjiang Uyghur Autonomous Region, Urumqi, Xinjiang 830054, PR China.
| | - Maimaitituxun Tuerdi
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Xinjiang Medical University, No.137 South Li YU-shan Road, New City District 830054 Urumqi, Xinjiang, PR China; Stomatological Research Institute of Xinjiang Uyghur Autonomous Region, Urumqi, Xinjiang 830054, PR China.
| | - Julaiti Tuerxun
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Xinjiang Medical University, No.137 South Li YU-shan Road, New City District 830054 Urumqi, Xinjiang, PR China; Stomatological Research Institute of Xinjiang Uyghur Autonomous Region, Urumqi, Xinjiang 830054, PR China.
| | - Adili Moming
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Xinjiang Medical University, No.137 South Li YU-shan Road, New City District 830054 Urumqi, Xinjiang, PR China; Stomatological Research Institute of Xinjiang Uyghur Autonomous Region, Urumqi, Xinjiang 830054, PR China.
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Reiter R, Brosch S, Lüdeke M, Fischbein E, Rinckleb A, Haase S, Schwandt A, Pickhard A, Maier C, Högel J, Vogel W. Do Orofacial Clefts Represent Different Genetic Entities? Cleft Palate Craniofac J 2015; 52:115-20. [DOI: 10.1597/13-016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Objective To contribute to the understanding of potential genetic differences between different cleft types. Method Analysis of family history concerning cleft type and search for cleft-type–specific associations in candidate genes performed in 98 individuals from 98 families. Results In a given family, the cleft type of a second case was more often identical to the index case than expected by chance. Each type of cleft (cleft lip [CL], cleft lip and palate [CLP], cleft palate only [CP], and submucous cleft palate only [SMCP]) was associated with different genes. Conclusion Family history indicates some specificity of cleft types. The observed phenotype-genotype associations were compatible with this interpretation in that significant associations occurred with disjoint sets of genes in each cleft type. These observations indicate that CL, CLP, CP, and SMCP might represent genetically different entities.
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Affiliation(s)
- Rudolf Reiter
- Section of Phoniatrics and Pedaudiology, University of Ulm, Ulm, Germany
| | - Sibylle Brosch
- Section of Phoniatrics and Pedaudiology, University of Ulm, Ulm, Germany
| | - Manuel Lüdeke
- Institute of Human Genetics, University of Ulm, Ulm, Germany
| | - Elena Fischbein
- Institute of Human Genetics, University of Ulm, Ulm, Germany
| | - Antje Rinckleb
- Institute of Human Genetics, University of Ulm, Ulm, Germany
| | - Stephan Haase
- Department of Cranio-Maxillo-Facial Surgery, University of Ulm, Ulm, Germany
| | - Anke Schwandt
- Institute of Human Genetics, University of Ulm, Ulm, Germany
| | - Anja Pickhard
- Department of Otolaryngology Head and Neck Surgery, Technical University Munich, Munich, Germany
| | | | - Josef Högel
- Institute of Human Genetics, University of Ulm, Ulm, Germany
| | - Walther Vogel
- Institute of Human Genetics, University of Ulm, Ulm, Germany
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Biggs LC, Goudy SL, Dunnwald M. Palatogenesis and cutaneous repair: A two-headed coin. Dev Dyn 2014; 244:289-310. [PMID: 25370680 DOI: 10.1002/dvdy.24224] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 10/14/2014] [Accepted: 10/27/2014] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The reparative mechanism that operates following post-natal cutaneous injury is a fundamental survival function that requires a well-orchestrated series of molecular and cellular events. At the end, the body will have closed the hole using processes like cellular proliferation, migration, differentiation and fusion. RESULTS These processes are similar to those occurring during embryogenesis and tissue morphogenesis. Palatogenesis, the formation of the palate from two independent palatal shelves growing towards each other and fusing, intuitively, shares many similarities with the closure of a cutaneous wound from the two migrating epithelial fronts. CONCLUSIONS In this review, we summarize the current information on cutaneous development, wound healing, palatogenesis and orofacial clefting and propose that orofacial clefting and wound healing are conserved processes that share common pathways and gene regulatory networks.
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Affiliation(s)
- Leah C Biggs
- Department of Pediatrics, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
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Watkins SE, Meyer RE, Strauss RP, Aylsworth AS. Classification, epidemiology, and genetics of orofacial clefts. Clin Plast Surg 2014; 41:149-63. [PMID: 24607185 DOI: 10.1016/j.cps.2013.12.003] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Orofacial clefts (OFCs) include a broad range of facial conditions that differ in cause and disease burden. In the published literature, there is substantial ambiguity in both terminology and classification of OFCs. This article discusses the terminology and classification of OFCs and the epidemiology of OFCs. Demographic, environmental, and genetic risk factors for OFCs are described, including suggestions for family counseling. This article enables clinicians to counsel families regarding the occurrence and recurrence of OFCs. Although much of the information is detailed, it is intended to be accessible to all health professionals for use in their clinical practices.
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Affiliation(s)
- Stephanie E Watkins
- Center for Health Promotion and Disease Prevention, University of North Carolina at Chapel Hill, 1700 Martin Luther King Jr Boulevard, Chapel Hill, NC, USA.
| | - Robert E Meyer
- Birth Defects Monitoring Program, Division of Public Health, North Carolina Department of Health and Human Services, State Center for Health Statistics, 222 North Dawson Street, Cotton Building, Raleigh, NC 27603, USA
| | - Ronald P Strauss
- UNC Center for AIDS Research, UNC School of Dentistry, UNC School of Medicine, University of North Carolina at Chapel Hill, 104 South Building, CB# 3000, Chapel Hill, NC 27599-3000, USA
| | - Arthur S Aylsworth
- Departments of Pediatrics and Genetics, University of North Carolina at Chapel Hill, CB# 7487, UNC Campus, Chapel Hill, NC 27599-7487, USA
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Joint testing of genotypic and gene-environment interaction identified novel association for BMP4 with non-syndromic CL/P in an Asian population using data from an International Cleft Consortium. PLoS One 2014; 9:e109038. [PMID: 25303326 PMCID: PMC4193821 DOI: 10.1371/journal.pone.0109038] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 08/28/2014] [Indexed: 11/23/2022] Open
Abstract
Background Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common disorder with complex etiology. The Bone Morphogenetic Protein 4 gene (BMP4) has been considered a prime candidate gene with evidence accumulated from animal experimental studies, human linkage studies, as well as candidate gene association studies. The aim of the current study is to test for linkage and association between BMP4 and NSCL/P that could be missed in genome-wide association studies (GWAS) when genotypic (G) main effects alone were considered. Methodology/Principal Findings We performed the analysis considering G and interactions with multiple maternal environmental exposures using additive conditional logistic regression models in 895 Asian and 681 European complete NSCL/P trios. Single nucleotide polymorphisms (SNPs) that passed the quality control criteria among 122 genotyped and 25 imputed single nucleotide variants in and around the gene were used in analysis. Selected maternal environmental exposures during 3 months prior to and through the first trimester of pregnancy included any personal tobacco smoking, any environmental tobacco smoke in home, work place or any nearby places, any alcohol consumption and any use of multivitamin supplements. A novel significant association held for rs7156227 among Asian NSCL/P and non-syndromic cleft lip and palate (NSCLP) trios after Bonferroni correction which was not seen when G main effects alone were considered in either allelic or genotypic transmission disequilibrium tests. Odds ratios for carrying one copy of the minor allele without maternal exposure to any of the four environmental exposures were 0.58 (95%CI = 0.44, 0.75) and 0.54 (95%CI = 0.40, 0.73) for Asian NSCL/P and NSCLP trios, respectively. The Bonferroni P values corrected for the total number of 117 tested SNPs were 0.0051 (asymptotic P = 4.39*10−5) and 0.0065 (asymptotic P = 5.54*10−5), accordingly. In European trios, no significant association was seen for any SNPs after Bonferroni corrections for the total number of 120 tested SNPs. Conclusions/Significance Our findings add evidence from GWAS to support the role of BMP4 in susceptibility to NSCL/P originally identified in linkage and candidate gene association studies.
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Bureau A, Parker MM, Ruczinski I, Taub MA, Marazita ML, Murray JC, Mangold E, Noethen MM, Ludwig KU, Hetmanski JB, Bailey-Wilson JE, Cropp CD, Li Q, Szymczak S, Albacha-Hejazi H, Alqosayer K, Field LL, Wu-Chou YH, Doheny KF, Ling H, Scott AF, Beaty TH. Whole exome sequencing of distant relatives in multiplex families implicates rare variants in candidate genes for oral clefts. Genetics 2014; 197:1039-44. [PMID: 24793288 PMCID: PMC4096358 DOI: 10.1534/genetics.114.165225] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 04/22/2014] [Indexed: 02/04/2023] Open
Abstract
A dozen genes/regions have been confirmed as genetic risk factors for oral clefts in human association and linkage studies, and animal models argue even more genes may be involved. Genomic sequencing studies should identify specific causal variants and may reveal additional genes as influencing risk to oral clefts, which have a complex and heterogeneous etiology. We conducted a whole exome sequencing (WES) study to search for potentially causal variants using affected relatives drawn from multiplex cleft families. Two or three affected second, third, and higher degree relatives from 55 multiplex families were sequenced. We examined rare single nucleotide variants (SNVs) shared by affected relatives in 348 recognized candidate genes. Exact probabilities that affected relatives would share these rare variants were calculated, given pedigree structures, and corrected for the number of variants tested. Five novel and potentially damaging SNVs shared by affected distant relatives were found and confirmed by Sanger sequencing. One damaging SNV in CDH1, shared by three affected second cousins from a single family, attained statistical significance (P = 0.02 after correcting for multiple tests). Family-based designs such as the one used in this WES study offer important advantages for identifying genes likely to be causing complex and heterogeneous disorders.
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Affiliation(s)
- Alexandre Bureau
- Centre de Recherche de l'Institut Universitaire en Santé Mentale de Québec and Département de Médecine Sociale et Préventive, Université Laval, Québec, QC G1V 0A6, Canada
| | - Margaret M Parker
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205
| | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205
| | - Margaret A Taub
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205
| | - Mary L Marazita
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15219
| | - Jeffrey C Murray
- Department of Pediatrics, School of Medicine, University of Iowa, Iowa City, Iowa 52242
| | - Elisabeth Mangold
- Institute of Human Genetics, University of Bonn, Bonn, Germany D-53111
| | - Markus M Noethen
- Institute of Human Genetics, University of Bonn, Bonn, Germany D-53111
| | - Kirsten U Ludwig
- Institute of Human Genetics, University of Bonn, Bonn, Germany D-53111
| | - Jacqueline B Hetmanski
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205
| | - Joan E Bailey-Wilson
- Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore Maryland 21121
| | - Cheryl D Cropp
- Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore Maryland 21121
| | - Qing Li
- Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore Maryland 21121
| | - Silke Szymczak
- Inherited Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore Maryland 21121
| | | | | | - L Leigh Field
- Department of Human Genetics, University of British Columbia, Vancouver, Canada V6T1Z3
| | - Yah-Huei Wu-Chou
- Laboratory of Human Molecular Genetics, Chang Gung Memorial Hospital, Taipei, Taiwan 333
| | - Kimberly F Doheny
- Center for Inherited Disease Research, Johns Hopkins School of Medicine, Baltimore Maryland 21224
| | - Hua Ling
- Center for Inherited Disease Research, Johns Hopkins School of Medicine, Baltimore Maryland 21224
| | - Alan F Scott
- Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland 21224
| | - Terri H Beaty
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205
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Younkin SG, Scharpf RB, Schwender H, Parker MM, Scott AF, Marazita ML, Beaty TH, Ruczinski I. A genome-wide study of de novo deletions identifies a candidate locus for non-syndromic isolated cleft lip/palate risk. BMC Genet 2014; 15:24. [PMID: 24528994 PMCID: PMC3929298 DOI: 10.1186/1471-2156-15-24] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 01/31/2014] [Indexed: 01/25/2023] Open
Abstract
Background Copy number variants (CNVs) may play an important part in the development of common birth defects such as oral clefts, and individual patients with multiple birth defects (including clefts) have been shown to carry small and large chromosomal deletions. In this paper we investigate de novo deletions defined as DNA segments missing in an oral cleft proband but present in both unaffected parents. We compare de novo deletion frequencies in children of European ancestry with an isolated, non-syndromic oral cleft to frequencies in children of European ancestry from randomly sampled trios. Results We identified a genome-wide significant 62 kilo base (kb) non-coding region on chromosome 7p14.1 where de novo deletions occur more frequently among oral cleft cases than controls. We also observed wider de novo deletions among cleft lip and palate (CLP) cases than seen among cleft palate (CP) and cleft lip (CL) cases. Conclusions This study presents a region where de novo deletions appear to be involved in the etiology of oral clefts, although the underlying biological mechanisms are still unknown. Larger de novo deletions are more likely to interfere with normal craniofacial development and may result in more severe clefts. Study protocol and sample DNA source can severely affect estimates of de novo deletion frequencies. Follow-up studies are needed to further validate these findings and to potentially identify additional structural variants underlying oral clefts.
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Affiliation(s)
- Samuel G Younkin
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore MD, USA.
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Wu T, Schwender H, Ruczinski I, Murray JC, Marazita ML, Munger RG, Hetmanski JB, Parker MM, Wang P, Murray T, Taub M, Li S, Redett RJ, Fallin MD, Liang KY, Wu-Chou YH, Chong SS, Yeow V, Ye X, Wang H, Huang S, Jabs EW, Shi B, Wilcox AJ, Jee SH, Scott AF, Beaty TH. Evidence of gene-environment interaction for two genes on chromosome 4 and environmental tobacco smoke in controlling the risk of nonsyndromic cleft palate. PLoS One 2014; 9:e88088. [PMID: 24516586 PMCID: PMC3916361 DOI: 10.1371/journal.pone.0088088] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 01/06/2014] [Indexed: 11/18/2022] Open
Abstract
Nonsyndromic cleft palate (CP) is one of the most common human birth defects and both genetic and environmental risk factors contribute to its etiology. We conducted a genome-wide association study (GWAS) using 550 CP case-parent trios ascertained in an international consortium. Stratified analysis among trios with different ancestries was performed to test for GxE interactions with common maternal exposures using conditional logistic regression models. While no single nucleotide polymorphism (SNP) achieved genome-wide significance when considered alone, markers in SLC2A9 and the neighboring WDR1 on chromosome 4p16.1 gave suggestive evidence of gene-environment interaction with environmental tobacco smoke (ETS) among 259 Asian trios when the models included a term for GxE interaction. Multiple SNPs in these two genes were associated with increased risk of nonsyndromic CP if the mother was exposed to ETS during the peri-conceptual period (3 months prior to conception through the first trimester). When maternal ETS was considered, fifteen of 135 SNPs mapping to SLC2A9 and 9 of 59 SNPs in WDR1 gave P values approaching genome-wide significance (10(-6)<P<10(-4)) in a test for GxETS interaction. SNPs rs3733585 and rs12508991 in SLC2A9 yielded P = 2.26×10(-7) in a test for GxETS interaction. SNPs rs6820756 and rs7699512 in WDR1 also yielded P = 1.79×10(-7) and P = 1.98×10(-7) in a 1 df test for GxE interaction. Although further replication studies are critical to confirming these findings, these results illustrate how genetic associations for nonsyndromic CP can be missed if potential GxE interaction is not taken into account, and this study suggest SLC2A9 and WDR1 should be considered as candidate genes for CP.
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Affiliation(s)
- Tao Wu
- Peking University Health Science Center, Beijing, China
- Johns Hopkins University, School of Public Health, Baltimore, Maryland, United States of America
- * E-mail:
| | - Holger Schwender
- Mathematical Institute, Heinrich Heine University Duesseldorf, Duesseldorf, Germany
| | - Ingo Ruczinski
- Johns Hopkins University, School of Public Health, Baltimore, Maryland, United States of America
| | - Jeffrey C. Murray
- University of Iowa, Children’s Hospital, Iowa City, Iowa, United States of America
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | | | - Jacqueline B. Hetmanski
- Johns Hopkins University, School of Public Health, Baltimore, Maryland, United States of America
| | - Margaret M. Parker
- Johns Hopkins University, School of Public Health, Baltimore, Maryland, United States of America
| | - Ping Wang
- Peking University Health Science Center, Beijing, China
| | - Tanda Murray
- Johns Hopkins University, School of Public Health, Baltimore, Maryland, United States of America
| | - Margaret Taub
- Johns Hopkins University, School of Public Health, Baltimore, Maryland, United States of America
| | - Shuai Li
- Peking University Health Science Center, Beijing, China
| | - Richard J. Redett
- Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States of America
| | - M. Daniele Fallin
- Johns Hopkins University, School of Public Health, Baltimore, Maryland, United States of America
| | - Kung Yee Liang
- Johns Hopkins University, School of Public Health, Baltimore, Maryland, United States of America
- National Yang-Ming University, Taipei, Taiwan
| | | | | | - Vincent Yeow
- KK Women’s & Children’s Hospital, Singapore, Singapore
| | - Xiaoqian Ye
- Wuhan University, School of Stomatology, Wuhan, China
- Mount Sinai Medical Center, New York, New York, United States of America
| | - Hong Wang
- Peking University Health Science Center, Beijing, China
| | | | - Ethylin W. Jabs
- Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States of America
- Mount Sinai Medical Center, New York, New York, United States of America
| | - Bing Shi
- State Key Laboratory of Oral Disease, West China College of Stomatology, Sichuan University, Chengdu, China
| | - Allen J. Wilcox
- NIEHS/NIH, Epidemiology Branch, Durham, North Carolina, United States of America
| | - Sun Ha Jee
- Yonsei University, School of Public Health, Seoul, Korea
| | - Alan F. Scott
- Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States of America
| | - Terri H. Beaty
- Johns Hopkins University, School of Public Health, Baltimore, Maryland, United States of America
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Kappen C. Modeling anterior development in mice: diet as modulator of risk for neural tube defects. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2013; 163C:333-56. [PMID: 24124024 PMCID: PMC4149464 DOI: 10.1002/ajmg.c.31380] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Head morphogenesis is a complex process that is controlled by multiple signaling centers. The most common defects of cranial development are craniofacial defects, such as cleft lip and cleft palate, and neural tube defects, such as anencephaly and encephalocoele in humans. More than 400 genes that contribute to proper neural tube closure have been identified in experimental animals, but only very few causative gene mutations have been identified in humans, supporting the notion that environmental influences are critical. The intrauterine environment is influenced by maternal nutrition, and hence, maternal diet can modulate the risk for cranial and neural tube defects. This article reviews recent progress toward a better understanding of nutrients during pregnancy, with particular focus on mouse models for defective neural tube closure. At least four major patterns of nutrient responses are apparent, suggesting that multiple pathways are involved in the response, and likely in the underlying pathogenesis of the defects. Folic acid has been the most widely studied nutrient, and the diverse responses of the mouse models to folic acid supplementation indicate that folic acid is not universally beneficial, but that the effect is dependent on genetic configuration. If this is the case for other nutrients as well, efforts to prevent neural tube defects with nutritional supplementation may need to become more specifically targeted than previously appreciated. Mouse models are indispensable for a better understanding of nutrient-gene interactions in normal pregnancies, as well as in those affected by metabolic diseases, such as diabetes and obesity.
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Chen CP, Chen M, Su YN, Huang JP, Chern SR, Wu PS, Su JW, Chang SP, Chen YT, Lee CC, Chen LF, Pan CW, Wang W. Mosaic small supernumerary marker chromosome 1 at amniocentesis: prenatal diagnosis, molecular genetic analysis and literature review. Gene 2013; 529:169-75. [PMID: 23933412 DOI: 10.1016/j.gene.2013.07.048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 07/01/2013] [Accepted: 07/10/2013] [Indexed: 11/28/2022]
Abstract
We present prenatal diagnosis and molecular cytogenetic analysis of mosaic small supernumerary marker chromosome 1 [sSMC(1)]. We review the literature of sSMC(1) at amniocentesis and chromosome 1p21.1-p12 duplication syndrome. We discuss the genotype-phenotype correlation of the involved genes of ALX3, RBM15, NTNG1, SLC25A24, GPSM2, TBX15 and NOTCH2 in this case.
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, Mackay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan; Department of Biotechnology, Asia University, Taichung, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang-Ming University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei, Taiwan.
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Leslie EJ, Marazita ML. Genetics of cleft lip and cleft palate. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2013; 163C:246-58. [PMID: 24124047 DOI: 10.1002/ajmg.c.31381] [Citation(s) in RCA: 269] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Orofacial clefts are common birth defects and can occur as isolated, nonsyndromic events or as part of Mendelian syndromes. There is substantial phenotypic diversity in individuals with these birth defects and their family members: from subclinical phenotypes to associated syndromic features that is mirrored by the many genes that contribute to the etiology of these disorders. Identification of these genes and loci has been the result of decades of research using multiple genetic approaches. Significant progress has been made recently due to advances in sequencing and genotyping technologies, primarily through the use of whole exome sequencing and genome-wide association studies. Future progress will hinge on identifying functional variants, investigation of pathway and other interactions, and inclusion of phenotypic and ethnic diversity in studies.
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Pelikan RC, Iwata J, Suzuki A, Chai Y, Hacia JG. Identification of candidate downstream targets of TGFβ signaling during palate development by genome-wide transcript profiling. J Cell Biochem 2013; 114:796-807. [PMID: 23060211 DOI: 10.1002/jcb.24417] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 10/01/2012] [Indexed: 02/01/2023]
Abstract
Nonsyndromic orofacial clefts are common birth defects whose etiology is influenced by complex genetic and environmental factors and gene-environment interactions. Although these risk factors are not yet fully elucidated, it is known that alterations in transforming growth factor-beta (TGFβ) signaling can cause craniofacial abnormalities, including cleft palate, in mammals. To elucidate the downstream targets of TGFβ signaling in palatogenesis, we analyzed the gene expression profiles of Tgfbr2(fl/fl) ;Wnt1-Cre mouse embryos with cleft palate and other craniofacial deformities resulting from the targeted inactivation of the Tgfbr2 gene in their cranial neural crest (CNC) cells. Relative to controls, palatal tissues obtained from Tgfbr2(fl/fl) ;Wnt1-Cre mouse embryos at embryonic day 14.5 (E14.5) of gestation have a robust gene expression signature reflective of known defects in CNC-derived mesenchymal cell proliferation. Groups of differentially expressed genes (DEGs) were involved in diverse cellular processes and components associated with orofacial clefting, including the extracellular matrix, cholesterol metabolism, ciliogenesis, and multiple signaling pathways. A subset of the DEGs are known or suspected to be associated with an increased risk of orofacial clefting in humans and/or genetically engineered mice. Based on bioinformatics analyses, we highlight the functional relationships among differentially expressed transcriptional regulators of palatogenesis as well as transcriptional factors not previously associated with this process. We suggest that gene expression profiling studies of mice with TGFβ signaling defects provide a valuable approach for identifying candidate mechanisms by which this pathway controls cell fate during palatogenesis and its role in the etiology of human craniofacial abnormalities.
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Affiliation(s)
- Richard C Pelikan
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California
| | - Junichi Iwata
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California
| | - Akiko Suzuki
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California
| | - Yang Chai
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, California
| | - Joseph G Hacia
- Department of Biochemistry and Molecular Biology, Broad Center for Regenerative Medicine and Stem Cell Research, University of Southern California, Los Angeles, California
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Nousome D, Lupo PJ, Okcu MF, Scheurer ME. Maternal and offspring xenobiotic metabolism haplotypes and the risk of childhood acute lymphoblastic leukemia. Leuk Res 2013; 37:531-5. [PMID: 23433810 DOI: 10.1016/j.leukres.2013.01.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 01/16/2013] [Accepted: 01/29/2013] [Indexed: 01/20/2023]
Abstract
Discovering genetic predictors of childhood acute lymphoblastic leukemia (ALL) necessitates the evaluation of novel factors including maternal genetic effects, which are a proxy for the intrauterine environment, and robust epidemiologic study designs. Therefore, we evaluated five maternal and offspring xenobiotic metabolism haplotypes and the risk of childhood ALL among 120 case-parent triads. Two of the five haplotypes were significantly associated with risk: GSTM3/GSTM4 (P=0.01) and GSTP1 (P=0.02). The EPHX1 haplotype was marginally associated with risk (P=0.05), whereas haplotypes in CYP1B1 and GSTA4 were not. Our results suggest genetic variation in xenobiotic metabolism is important in childhood ALL etiology.
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Affiliation(s)
- Darryl Nousome
- Human Genetics Center, Division of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Houston, TX, USA
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Shi M, Umbach DM, Weinberg CR. Case-sibling studies that acknowledge unstudied parents and permit the inclusion of unmatched individuals. Int J Epidemiol 2012; 42:298-307. [PMID: 23248214 DOI: 10.1093/ije/dys212] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Family-based designs enable assessment of genetic associations without bias from population stratification. When parents are not readily available - especially for diseases with onset later in life - the case-sibling design, where each case is matched with one or more unaffected siblings, is useful. Analysis typically accounts for within-family dependencies by using conditional logistic regression (CLR). METHODS We consider an alternative to CLR that treats each case-sibling set as a nuclear family with both parents missing by design. One can carry out maximum likelihood analysis by using the Expectation-Maximization (EM) algorithm to account for missing parental genotypes. We compare conditional logistic regression and the missing-parents approach under several risk scenarios. RESULTS We show that the missing-parents approach improves power when some families have more than one unaffected sibling and that under weak assumptions the approach permits the incorporation of supplemental cases who have no sibling available and supplemental controls whose case sibling is unavailable (e.g., due to disability or death). CONCLUSION The missing-parents approach offers both improved statistical efficiency and asymptotically unbiased estimation for genotype relative risks and genotype-by-exposure interaction parameters.
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Affiliation(s)
- Min Shi
- Biostatistics Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
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Lace B, Kempa I, Klovins J, Stavusis J, Krumina A, Akota I, Barkane B, Vieira AR, Nagle E, Grinfelde I, Maulina I. BCL3 gene role in facial morphology. ACTA ACUST UNITED AC 2012; 94:918-24. [PMID: 23115114 DOI: 10.1002/bdra.23085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 08/23/2012] [Accepted: 08/28/2012] [Indexed: 11/12/2022]
Abstract
BACKGROUND Cleft lip (CL) with or without palate (CLP) and isolated cleft palate (CP) are etiologically complex diseases with interactions among various environmental and genetic factors. The aim of the current study was to identify association with genetic markers and phenotypic craniofacial data in patients with CL/CLP/CP parents. METHODS Posteroanterior and lateral digital radiographs of the cranium were obtained from 74 parents of patients with CL/CLP/CP. One hundred seventy-three patients with CL/CLP/CP and 190 controls were enrolled in the study for the association test. Five genetic markers of the IRF6 gene and 14 markers of the 19q13 locus were genotyped. Linear regression analysis was performed for the relationship of cephalometric measurements with genotype data adjusted for age, gender, and cleft type. Chi-square and transmission disequilibrium tests were performed to evaluate differences in alleles of the BCL3 gene. Positive findings were replicated in an independent sample (n = 95) of patients with CL/CLP/CP parents. RESULTS Genetic markers of the BCL3 gene at 19q13, rs7257231, and rs1979377 in the familial association test and rs10401176 in the case-control association test, were associated with craniofacial phenotype. Carriers of BCL3 allele rs7257231T had longer posterior cranial bases than noncarriers (p(adjusted) = 0.0028), and in the familial-based association test showed the statistically strongest relationship (p(adjusted) = 0.05) to phenotype. Relation of rs7257231 to facial formation was confirmed in the replication group (p = 0.0024). CONCLUSIONS The results indicate that BCL3, which has functions related to cell adhesion and whose downregulation can cause disruption of ectodermal development, is likely to be important in facial formation. Birth Defects Research (Part A), 2012.
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Affiliation(s)
- Baiba Lace
- Latvian Biomedical Study and Research Centre, Riga, Latvia.
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Wu C, Endo M, Yang BH, Radecki MA, Davis PF, Zoltick PW, Spivak RM, Flake AW, Kirschner RE, Nah HD. Intra-amniotic transient transduction of the periderm with a viral vector encoding TGFβ3 prevents cleft palate in Tgfβ3(-/-) mouse embryos. Mol Ther 2012; 21:8-17. [PMID: 23089732 DOI: 10.1038/mt.2012.135] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Cleft palate is a developmental defect resulting from the failure of embryonic palatal shelves to fuse with each other at a critical time. Immediately before and during palatal fusion (E13-E15 in mice), transforming growth factor β3 (TGFβ3) is expressed in the palatal shelf medial edge epithelium (MEE) and plays a pivotal role in palatal fusion. Using Tgfβ3(-/-) mice, which display complete penetrance of the cleft palate phenotype, we tested the hypothesis that intra-amniotic gene transfer could be used to prevent cleft palate formation by restoring palatal midline epithelial function. An adenoviral vector encoding Tgfβ3 was microinjected into the amniotic sacs of mouse embryos at successive developmental stages. Transduced Tgfβ3(-/-) fetuses showed efficient recovery of palatal fusion with mesenchymal confluence following injection at E12.5 (100%), E13.5 (100%), E14.5 (82%), and E15.5 (75%). Viral vectors injected into the amniotic sac transduced the most superficial and transient peridermal cell layer but not underlying basal epithelial cells. TGFβ3 transduction of the peridermdal cell layer was sufficient to induce adhesion, fusion, and disappearance of the palatal shelf MEE in a cell nonautonomous manner. We propose that intra-amniotic gene transfer approaches have therapeutic potential to prevent cleft palate in utero, especially those resulting from palatal midline epithelial dysfunction.
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Affiliation(s)
- Chadwick Wu
- Division of Plastic and Reconstructive Surgery, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
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Site-specific expression of gelatinolytic activity during morphogenesis of the secondary palate in the mouse embryo. PLoS One 2012; 7:e47762. [PMID: 23091646 PMCID: PMC3472992 DOI: 10.1371/journal.pone.0047762] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 09/20/2012] [Indexed: 12/18/2022] Open
Abstract
Morphogenesis of the secondary palate in mammalian embryos involves two major events: first, reorientation of the two vertically oriented palatal shelves into a horizontal position above the tongue, and second, fusion of the two shelves at the midline. Genetic evidence in humans and mice indicates the involvement of matrix metalloproteinases (MMPs). As MMP expression patterns might differ from sites of activity, we used a recently developed highly sensitive in situ zymography technique to map gelatinolytic MMP activity in the developing mouse palate. At embryonic day 14.5 (E14.5), we detected strong gelatinolytic activity around the lateral epithelial folds of the nasopharyngeal cavity, which is generated as a consequence of palatal shelf elevation. Activity was concentrated in the basement membrane of the epithelial fold but extended into the adjacent mesenchyme, and increased in intensity with lateral outgrowth of the cavity at E15.5. Gelatinolytic activity at this site was not the consequence of epithelial fold formation, as it was also observed in Bmp7-deficient embryos where shelf elevation is delayed. In this case, gelatinolytic activity appeared in vertical shelves at the exact position where the epithelial fold will form during elevation. Mmp2 and Mmp14 (MT1-MMP), but not Mmp9 and Mmp13, mRNAs were expressed in the mesenchyme around the epithelial folds of the elevated palatal shelves; this was confirmed by immunostaining for MMP-2 and MT1-MMP. Weak gelatinolytic activity was also found at the midline of E14.5 palatal shelves, which increased during fusion at E15.5. Whereas MMPs have been implicated in palatal fusion before, this is the first report showing that gelatinases might contribute to tissue remodeling during early stages of palatal shelf elevation and formation of the nasopharynx.
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Letra A, Fakhouri W, Fonseca RF, Menezes R, Kempa I, Prasad JL, McHenry TG, Lidral AC, Moreno L, Murray JC, Daack-Hirsch S, Marazita ML, Castilla EE, Lace B, Orioli IM, Granjeiro JM, Schutte BC, Vieira AR. Interaction between IRF6 and TGFA genes contribute to the risk of nonsyndromic cleft lip/palate. PLoS One 2012; 7:e45441. [PMID: 23029012 PMCID: PMC3447924 DOI: 10.1371/journal.pone.0045441] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 08/22/2012] [Indexed: 01/08/2023] Open
Abstract
Previous evidence from tooth agenesis studies suggested IRF6 and TGFA interact. Since tooth agenesis is commonly found in individuals with cleft lip/palate (CL/P), we used four large cohorts to evaluate if IRF6 and TGFA interaction contributes to CL/P. Markers within and flanking IRF6 and TGFA genes were tested using Taqman or SYBR green chemistries for case-control analyses in 1,000 Brazilian individuals. We looked for evidence of gene-gene interaction between IRF6 and TGFA by testing if markers associated with CL/P were overtransmitted together in the case-control Brazilian dataset and in the additional family datasets. Genotypes for an additional 142 case-parent trios from South America drawn from the Latin American Collaborative Study of Congenital Malformations (ECLAMC), 154 cases from Latvia, and 8,717 individuals from several cohorts were available for replication of tests for interaction. Tgfa and Irf6 expression at critical stages during palatogenesis was analyzed in wild type and Irf6 knockout mice. Markers in and near IRF6 and TGFA were associated with CL/P in the Brazilian cohort (p<10−6). IRF6 was also associated with cleft palate (CP) with impaction of permanent teeth (p<10−6). Statistical evidence of interaction between IRF6 and TGFA was found in all data sets (p = 0.013 for Brazilians; p = 0.046 for ECLAMC; p = 10−6 for Latvians, and p = 0.003 for the 8,717 individuals). Tgfa was not expressed in the palatal tissues of Irf6 knockout mice. IRF6 and TGFA contribute to subsets of CL/P with specific dental anomalies. Moreover, this potential IRF6-TGFA interaction may account for as much as 1% to 10% of CL/P cases. The Irf6-knockout model further supports the evidence of IRF6-TGFA interaction found in humans.
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Affiliation(s)
- Ariadne Letra
- Department of Oral Biology, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
| | - Walid Fakhouri
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Renata F. Fonseca
- Department of Genetics, Institute of Biology, Center of Health Sciences; Federal University of Rio de Janeiro; Rio de Janeiro, RJ, Brazil
| | - Renato Menezes
- Department of Oral Biology, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
| | - Inga Kempa
- Latvian Biomedical Research and Study Centre, Riga, Latvia
- Department of Biology and Microbiology, Riga Stradins University, Riga, Latvia
| | - Joanne L. Prasad
- Department of Diagnostic Sciences, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
| | - Toby G. McHenry
- Department of Oral Biology, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
| | - Andrew C. Lidral
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Lina Moreno
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Jeffrey C. Murray
- Department of Pediatrics, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Sandra Daack-Hirsch
- Department of Pediatrics, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Mary L. Marazita
- Department of Oral Biology, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Eduardo E. Castilla
- ECLAMC (Latin American Collaborative Study of Congenital Malformations) at CEMIC (Center of Medical Education and Clinical Research “Norberto Quirno”), Buenos Aires, Argentina
- CONICET (National Research Council of Argentina), Buenos Aires, Argentina
- iNaGeMP-CNPq (National Institute of Population Medical Genetics), Porto Alegre, RS, Brazil
| | - Baiba Lace
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Ieda M. Orioli
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
- iNaGeMP-CNPq (National Institute of Population Medical Genetics), Porto Alegre, RS, Brazil
| | - Jose M. Granjeiro
- Department of Cell and Molecular Biology, Fluminense Federal University, Niterói, RJ, Brazil and INMETRO, Duque de Caxias, RJ, Brazil
| | - Brian C. Schutte
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Alexandre R. Vieira
- Department of Oral Biology, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
- Department of Pediatric Dentistry, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, School of Dental Medicine, Pittsburgh, PA, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, PA, USA
- * E-mail:
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Barbosa Martelli DR, Machado RA, Oliveira Swerts MS, Mendes Rodrigues LA, de Aquino SN, Júnior HM. Non sindromic cleft lip and palate: relationship between sex and clinical extension. Braz J Otorhinolaryngol 2012; 78:116-20. [PMID: 23108830 PMCID: PMC9450739 DOI: 10.5935/1808-8694.20120018] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 07/23/2012] [Indexed: 12/01/2022] Open
Abstract
Cleft lip and/or palate represent the most common congenital anomalies of the face. Aim Describe the relation between non sindromic cleft lip and/or palate and sex and severity of the clef in Brazilian population. Methods Conducted cross-sectional study, between the years 2009 and 2011, with a population of 366 patients. Data were analyzed with descriptive statistics and using the multinomial logistic regression with an interval of 95% estimated the chances of the types of cleft lip and/or palate between sex. Results Among the 366 cases of non sindromic cleft lip and/or palate, the more frequent clefts were cleft lip and palate, followed respectively by cleft lip and cleft palate. It is noted that cleft palate were more frequent in females, while the cleft lip and palate and cleft labial predominated in males. The risk of occurrence of cleft lip in relation the cleft palate was 2.19 times in males compared to females. While the risk of cleft lip and palate in relation cleft palate was 2.78 times in males compared to females. Conclusion This study showed that there were differences in the distribution of the non sindromic cleft lip and/or palate between male and female.
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Affiliation(s)
- Daniella Reis Barbosa Martelli
- MSc. Professor of Semiology - State University of Montes Claros. PhD student - State University of Montes Claros - Unimontes
| | | | | | | | | | - Hercílio Martelli Júnior
- PhD. Full Professor. Graduate Program in Health Sciences - Center of Biological and Health Sciences - Unimontes
- Send correspodence to: Hercílio Martelli Júnior. Rua Olegário da Silveira, n° 125/201, Centro. Montes Claros - MG. Brazil. CEP: 39400-020
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Freitas JADS, das Neves LT, de Almeida ALPF, Garib DG, Trindade-Suedam IK, Yaedú RYF, Lauris RDCMC, Soares S, Oliveira TM, Pinto JHN. Rehabilitative treatment of cleft lip and palate: experience of the Hospital for Rehabilitation of Craniofacial Anomalies/USP (HRAC/USP)--Part 1: overall aspects. J Appl Oral Sci 2012; 20:9-15. [PMID: 22437671 PMCID: PMC3928765 DOI: 10.1590/s1678-77572012000100003] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 10/08/2011] [Indexed: 11/22/2022] Open
Abstract
Cleft lip and palate is the most common among craniofacial malformations and causes
several esthetic and functional implications that require rehabilitation. This paper
aims to generally describe the several aspects related to this complex pathology and
the treatment protocol used by the Hospital for Rehabilitation of Craniofacial
Anomalies, University of São Paulo (HRAC-USP) along 40 years of experience in the
treatment of individuals with cleft lip and palate.
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Affiliation(s)
- José Alberto de Souza Freitas
- Hospital for Rehabilitation of Craniofacial Anomalies, Department of Stomatology, Bauru School of Dentistry, University of São Paulo, Bauru, SP, Brazil
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