1
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Mendes J, Guimarães AR, Ribeiro JM, Oliveiros B, Mesquita LA, Fernandes MH, do Vale FJF, Silva HC. Role of MTHFR, IRF6, PAX7 and TP63 SNPs in susceptibility to non-syndromic orofacial cleft, a candidate gene study in a Portuguese population. Orthod Craniofac Res 2024. [PMID: 39049717 DOI: 10.1111/ocr.12838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 06/04/2024] [Accepted: 07/13/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND Non-syndromic orofacial cleft (NSOC) is a complex phenotype, involving multiple genetic and environmental factors. Association studies exploring the genetic susceptibility to this prevalent oral malformation show variability of results in different populations. Using a candidate gene approach, we aimed to verify the role of four single-nucleotide polymorphisms (SNPs) in the susceptibility to NSOC in Portuguese patients. METHODS A total of 254 non-consanguineous individuals of Portuguese were recruited, including 120 patients with NSOC and 134 controls. About 92% of these patients had non-syndromic cleft lip with or without cleft palate (NSCL/P) and 8% had only non-syndromic cleft palate (NSCP). SNPs in the MTHFR (rs1801133), IRF6 (rs642961), PAX7 (rs742071) and TP63 (rs9332461) genes were studied, using a real-time approach with TaqMan probes. Allelic, genotypic, dominant, recessive and over-dominant models were explored using a chi-squared test. Adjusted p-value was calculated for multiple comparisons using the Benjamini-Hochberg false discovery rate (FDR). RESULTS All SNPs were in Hardy-Weinberg equilibrium. For MTHFR, IRF6, and PAX7 SNPs, no statistically significant difference was highlighted for any of the evaluated models. For TP63 SNP, data fitted an over-dominant model, with a protective effect for heterozygotes (OR 1.897; CI 95% [1.144-3.147]; p < .016, when comparing controls vs. cases), but significance was lost when applying adjusted p-value for multiple comparisons (4 × 5 tests). CONCLUSION In this Portuguese population, there was no evidence of an association between the evaluated SNPs and NSOC. For TP63 SNP, the possibility of a protective effect of heterozygotes should be further investigated.
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Affiliation(s)
- João Mendes
- Institute of Medical Genetics/UCGenomics, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Coimbra, Portugal
- Center of Investigation in Environment, Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | | | - Joana Martins Ribeiro
- Institute of Medical Genetics/UCGenomics, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Bárbara Oliveiros
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Coimbra, Portugal
- Center of Investigation in Environment, Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Luís Alcides Mesquita
- Institute of Medical Genetics/UCGenomics, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | | | | | - Henriqueta Coimbra Silva
- Institute of Medical Genetics/UCGenomics, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Coimbra, Portugal
- Center of Investigation in Environment, Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, Coimbra, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), Faculty of Medicine, University of Coimbra, Coimbra, Portugal
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2
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Mohammed J, Arora N, Matthews HS, Hansen K, Bader M, Walsh S, Shaffer JR, Weinberg SM, Swigut T, Claes P, Selleri L, Wysocka J. A common cis-regulatory variant impacts normal-range and disease-associated human facial shape through regulation of PKDCC during chondrogenesis. eLife 2024; 13:e82564. [PMID: 38483448 PMCID: PMC10939500 DOI: 10.7554/elife.82564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 02/18/2024] [Indexed: 03/17/2024] Open
Abstract
Genome-wide association studies (GWAS) identified thousands of genetic variants linked to phenotypic traits and disease risk. However, mechanistic understanding of how GWAS variants influence complex morphological traits and can, in certain cases, simultaneously confer normal-range phenotypic variation and disease predisposition, is still largely lacking. Here, we focus on rs6740960, a single nucleotide polymorphism (SNP) at the 2p21 locus, which in GWAS studies has been associated both with normal-range variation in jaw shape and with an increased risk of non-syndromic orofacial clefting. Using in vitro derived embryonic cell types relevant for human facial morphogenesis, we show that this SNP resides in an enhancer that regulates chondrocytic expression of PKDCC - a gene encoding a tyrosine kinase involved in chondrogenesis and skeletal development. In agreement, we demonstrate that the rs6740960 SNP is sufficient to confer chondrocyte-specific differences in PKDCC expression. By deploying dense landmark morphometric analysis of skull elements in mice, we show that changes in Pkdcc dosage are associated with quantitative changes in the maxilla, mandible, and palatine bone shape that are concordant with the facial phenotypes and disease predisposition seen in humans. We further demonstrate that the frequency of the rs6740960 variant strongly deviated among different human populations, and that the activity of its cognate enhancer diverged in hominids. Our study provides a mechanistic explanation of how a common SNP can mediate normal-range and disease-associated morphological variation, with implications for the evolution of human facial features.
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Affiliation(s)
- Jaaved Mohammed
- Department of Chemical and Systems Biology, Stanford University School of MedicineStanfordUnited States
| | - Neha Arora
- Department of Chemical and Systems Biology, Stanford University School of MedicineStanfordUnited States
| | - Harold S Matthews
- Department of Human Genetics, KU LeuvenLeuvenBelgium
- Medical Imaging Research Center, University Hospitals LeuvenLeuvenBelgium
| | - Karissa Hansen
- Program in Craniofacial Biology, Department of Orofacial Sciences and Department of Anatomy, Institute of Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San FranciscoSan FranciscoUnited States
| | - Maram Bader
- Department of Chemical and Systems Biology, Stanford University School of MedicineStanfordUnited States
| | - Susan Walsh
- Department of Biology, Indiana University IndianapolisIndianapolisUnited States
| | - John R Shaffer
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of PittsburghPittsburghUnited States
- Department of Human Genetics, University of PittsburghPittsburghUnited States
| | - Seth M Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of PittsburghPittsburghUnited States
- Department of Human Genetics, University of PittsburghPittsburghUnited States
- Department of Anthropology, University of PittsburghPittsburghUnited States
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of MedicineStanfordUnited States
| | - Peter Claes
- Department of Human Genetics, KU LeuvenLeuvenBelgium
- Medical Imaging Research Center, University Hospitals LeuvenLeuvenBelgium
- Department of Electrical Engineering, ESAT/PSI, KU LeuvenLeuvenBelgium
- Murdoch Children’s Research InstituteMelbourneAustralia
| | - Licia Selleri
- Program in Craniofacial Biology, Department of Orofacial Sciences and Department of Anatomy, Institute of Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San FranciscoSan FranciscoUnited States
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of MedicineStanfordUnited States
- Department of Developmental Biology, Stanford University School of MedicineStanfordUnited States
- Howard Hughes Medical Institute, Stanford University School of MedicineStanfordUnited States
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3
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Curtis SW, Carlson JC, Beaty TH, Murray JC, Weinberg SM, Marazita ML, Cotney JL, Cutler DJ, Epstein MP, Leslie EJ. Rare variant modifier analysis identifies variants in SEC24D associated with orofacial cleft subtypes. Hum Genet 2023; 142:1531-1541. [PMID: 37676273 DOI: 10.1007/s00439-023-02596-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/18/2023] [Indexed: 09/08/2023]
Abstract
As one of the most common structural birth defects, orofacial clefts (OFCs) have been studied for decades, and recent studies have demonstrated that there are genetic differences between the different phenotypic presentations of OFCs. However, the contribution of rare genetic variation genome-wide to different subtypes of OFCs has been understudied, with most studies focusing on common genetic variation or rare variation within targeted regions of the genome. Therefore, we used whole-genome sequencing data from the Gabriella Miller Kids First Pediatric Research Program to conduct a gene-based burden analysis to test for genetic modifiers of cleft lip (CL) vs cleft lip and palate (CLP). We found that there was a significantly increased burden of rare variants in SEC24D in CL cases compared to CLP cases (p = 6.86 [Formula: see text] 10-7). Of the 15 variants within SEC24D, 53.3% were synonymous, but overlapped a known craniofacial enhancer. We then tested whether these variants could alter predicted transcription factor binding sites (TFBS), and found that the rare alleles destroyed binding sites for 9 transcription factors (TFs), including Pax1 (p = 0.0009), and created binding sites for 23 TFs, including Pax6 (p = 6.12 [Formula: see text] 10-5) and Pax9 (p = 0.0001), which are known to be involved in normal craniofacial development, suggesting a potential mechanism by which these synonymous variants could have a functional impact. Overall, this study indicates that rare genetic variation may contribute to the phenotypic heterogeneity of OFCs and suggests that regulatory variation may also contribute and warrant further investigation in future studies of genetic variants controlling risk to OFC.
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Affiliation(s)
- Sarah W Curtis
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Jenna C Carlson
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, 15621, USA
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
| | - Seth M Weinberg
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Mary L Marazita
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Justin L Cotney
- Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT, 06030, USA
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Michael P Epstein
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Elizabeth J Leslie
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA.
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4
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Yankee TN, Oh S, Winchester EW, Wilderman A, Robinson K, Gordon T, Rosenfeld JA, VanOudenhove J, Scott DA, Leslie EJ, Cotney J. Integrative analysis of transcriptome dynamics during human craniofacial development identifies candidate disease genes. Nat Commun 2023; 14:4623. [PMID: 37532691 PMCID: PMC10397224 DOI: 10.1038/s41467-023-40363-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/25/2023] [Indexed: 08/04/2023] Open
Abstract
Craniofacial disorders arise in early pregnancy and are one of the most common congenital defects. To fully understand how craniofacial disorders arise, it is essential to characterize gene expression during the patterning of the craniofacial region. To address this, we performed bulk and single-cell RNA-seq on human craniofacial tissue from 4-8 weeks post conception. Comparisons to dozens of other human tissues revealed 239 genes most strongly expressed during craniofacial development. Craniofacial-biased developmental enhancers were enriched +/- 400 kb surrounding these craniofacial-biased genes. Gene co-expression analysis revealed that regulatory hubs are enriched for known disease causing genes and are resistant to mutation in the normal healthy population. Combining transcriptomic and epigenomic data we identified 539 genes likely to contribute to craniofacial disorders. While most have not been previously implicated in craniofacial disorders, we demonstrate this set of genes has increased levels of de novo mutations in orofacial clefting patients warranting further study.
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Affiliation(s)
- Tara N Yankee
- Graduate Program in Genetics and Developmental Biology, UConn Health, Farmington, CT, 06030, USA
| | - Sungryong Oh
- University of Connecticut School of Medicine, Department of Genetics and Genome Sciences, Farmington, CT, 06030, USA
| | | | - Andrea Wilderman
- Graduate Program in Genetics and Developmental Biology, UConn Health, Farmington, CT, 06030, USA
| | - Kelsey Robinson
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Tia Gordon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Baylor Genetics Laboratory, Houston, TX, 77021, USA
| | - Jennifer VanOudenhove
- University of Connecticut School of Medicine, Department of Genetics and Genome Sciences, Farmington, CT, 06030, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Elizabeth J Leslie
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Justin Cotney
- University of Connecticut School of Medicine, Department of Genetics and Genome Sciences, Farmington, CT, 06030, USA.
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, 06269, USA.
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5
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Alvizi L, Nani D, Brito LA, Kobayashi GS, Passos-Bueno MR, Mayor R. Neural crest E-cadherin loss drives cleft lip/palate by epigenetic modulation via pro-inflammatory gene-environment interaction. Nat Commun 2023; 14:2868. [PMID: 37225711 DOI: 10.1038/s41467-023-38526-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 05/05/2023] [Indexed: 05/26/2023] Open
Abstract
Gene-environment interactions are believed to play a role in multifactorial phenotypes, although poorly described mechanistically. Cleft lip/palate (CLP), the most common craniofacial malformation, has been associated with both genetic and environmental factors, with little gene-environment interaction experimentally demonstrated. Here, we study CLP families harbouring CDH1/E-Cadherin variants with incomplete penetrance and we explore the association of pro-inflammatory conditions to CLP. By studying neural crest (NC) from mouse, Xenopus and humans, we show that CLP can be explained by a 2-hit model, where NC migration is impaired by a combination of genetic (CDH1 loss-of-function) and environmental (pro-inflammatory activation) factors, leading to CLP. Finally, using in vivo targeted methylation assays, we demonstrate that CDH1 hypermethylation is the major target of the pro-inflammatory response, and a direct regulator of E-cadherin levels and NC migration. These results unveil a gene-environment interaction during craniofacial development and provide a 2-hit mechanism to explain cleft lip/palate aetiology.
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Affiliation(s)
- Lucas Alvizi
- Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK.
| | - Diogo Nani
- Centro de Estudos do Genoma Humano e Celulas-Tronco, Departamento de Genetica e Biologia Evolutiva, Instituto de Biociencias, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Luciano Abreu Brito
- Centro de Estudos do Genoma Humano e Celulas-Tronco, Departamento de Genetica e Biologia Evolutiva, Instituto de Biociencias, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Gerson Shigeru Kobayashi
- Centro de Estudos do Genoma Humano e Celulas-Tronco, Departamento de Genetica e Biologia Evolutiva, Instituto de Biociencias, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Maria Rita Passos-Bueno
- Centro de Estudos do Genoma Humano e Celulas-Tronco, Departamento de Genetica e Biologia Evolutiva, Instituto de Biociencias, Universidade de Sao Paulo, Sao Paulo, Brazil.
| | - Roberto Mayor
- Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK.
- Center for Integrative Biology, Faculty of Sciences, Universidad Mayor, Santiago, Chile.
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6
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Curtis SW, Carlson JC, Beaty TH, Murray JC, Weinberg SM, Marazita ML, Cotney JL, Cutler DJ, Epstein MP, Leslie EJ. Rare genetic variants in SEC24D modify orofacial cleft phenotypes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.24.23287714. [PMID: 37034635 PMCID: PMC10081436 DOI: 10.1101/2023.03.24.23287714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
As one of the most common structural birth defects, orofacial clefts (OFCs) have been studied for decades, and recent studies have demonstrated that there are genetic differences between the different phenotypic presentations of OFCs. However, the contribution of rare genetic variation genome-wide to different subtypes of OFCs has been understudied, with most studies focusing on common genetic variation or rare variation within targeted regions of the genome. Therefore, we used whole-genome sequencing data from the Gabriella Miller Kids First Pediatric Research Program to conduct a gene-based burden analysis to test for genetic modifiers of cleft lip (CL) vs cleft lip and palate (CLP). We found that there was a significantly increased burden of rare variants in SEC24D in CL cases compared to CLP cases (p=6.86×10-7). Of the 15 variants within SEC24D, 53.3% were synonymous, but overlapped a known craniofacial enhancer. We then tested whether these variants could alter predicted transcription factor binding sites (TFBS), and found that the rare alleles destroyed binding sites for 9 transcription factors (TFs), including Pax1 (p=0.0009), and created binding sites for 23 TFs, including Pax6 (p=6.12×10-5) and Pax9 (p= 0.0001), which are known to be involved in normal craniofacial development, suggesting a potential mechanism by which these synonymous variants could have a functional impact. Overall, this study demonstrates that rare genetic variation contributes to the phenotypic heterogeneity of OFCs and suggests that regulatory variation may also contribute and warrant further investigation in future studies of genetic variants controlling risk to OFC.
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Affiliation(s)
- Sarah W Curtis
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Jenna C Carlson
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, 15621, USA
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205,USA
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
| | - Seth M Weinberg
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Mary L Marazita
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Justin L Cotney
- Department of Genetics and Genome Sciences, University of Connecticut, CT, 06030, USA
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
| | - Michael P Epstein
- Department of Human Genetics, Emory University, Atlanta, GA, 30322, USA
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7
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Ishorst N, Henschel L, Thieme F, Drichel D, Sivalingam S, Mehrem SL, Fechtner AC, Fazaal J, Welzenbach J, Heimbach A, Maj C, Borisov O, Hausen J, Raff R, Hoischen A, Dixon M, Rada-Iglesias A, Bartusel M, Rojas-Martinez A, Aldhorae K, Braumann B, Kruse T, Kirschneck C, Spanier G, Reutter H, Nowak S, Gölz L, Knapp M, Buness A, Krawitz P, Nöthen MM, Nothnagel M, Becker T, Ludwig KU, Mangold E. Identification of de novo variants in nonsyndromic cleft lip with/without cleft palate patients with low polygenic risk scores. Mol Genet Genomic Med 2023; 11:e2109. [PMID: 36468602 PMCID: PMC10009911 DOI: 10.1002/mgg3.2109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/04/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Nonsyndromic cleft lip with/without cleft palate (nsCL/P) is a congenital malformation of multifactorial etiology. Research has identified >40 genome-wide significant risk loci, which explain less than 40% of nsCL/P heritability. Studies show that some of the hidden heritability is explained by rare penetrant variants. METHODS To identify new candidate genes, we searched for highly penetrant de novo variants (DNVs) in 50 nsCL/P patient/parent-trios with a low polygenic risk for the phenotype (discovery). We prioritized DNV-carrying candidate genes from the discovery for resequencing in independent cohorts of 1010 nsCL/P patients of diverse ethnicities and 1574 population-matched controls (replication). Segregation analyses and rare variant association in the replication cohort, in combination with additional data (genome-wide association data, expression, protein-protein-interactions), were used for final prioritization. CONCLUSION In the discovery step, 60 DNVs were identified in 60 genes, including a variant in the established nsCL/P risk gene CDH1. Re-sequencing of 32 prioritized genes led to the identification of 373 rare, likely pathogenic variants. Finally, MDN1 and PAXIP1 were prioritized as top candidates. Our findings demonstrate that DNV detection, including polygenic risk score analysis, is a powerful tool for identifying nsCL/P candidate genes, which can also be applied to other multifactorial congenital malformations.
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Affiliation(s)
- Nina Ishorst
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Leonie Henschel
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Frederic Thieme
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Dmitriy Drichel
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Sugirthan Sivalingam
- Core Unit for Bioinformatic Analysis, Medical Faculty, University of Bonn, Bonn, Germany.,Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany.,Institute of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Sarah L Mehrem
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Ariane C Fechtner
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Julia Fazaal
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Julia Welzenbach
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - André Heimbach
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Oleg Borisov
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Jonas Hausen
- Core Unit for Bioinformatic Analysis, Medical Faculty, University of Bonn, Bonn, Germany.,Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany.,Institute of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Ruth Raff
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Michael Dixon
- Faculty of Biology, Medicine & Health, University of Manchester, Manchester, UK
| | - Alvaro Rada-Iglesias
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/University of Cantabria, Santander, Spain
| | - Michaela Bartusel
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico.,Centro de Investigacion y Desarrollo en Ciencias de la Salud, Universidad Autonoma de Nuevo Leon, Monterrey, Mexico
| | - Khalid Aldhorae
- Department of Orthodontics, College of Dentistry, Thamar University, Thamar, Yemen.,Department of Orthodontics, College of Dentistry, University of Ibn al-Nafis for Medical Sciences, Sanaa, Yemen
| | - Bert Braumann
- Faculty of Medicine and University Hospital Cologne, Department of Orthodontics, University of Cologne, Cologne, Germany
| | - Teresa Kruse
- Faculty of Medicine and University Hospital Cologne, Department of Orthodontics, University of Cologne, Cologne, Germany
| | | | - Gerrit Spanier
- Department of Cranio-Maxillofacial Surgery, University Hospital Regensburg, Regensburg, Germany
| | - Heiko Reutter
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany.,Division of Neonatology and Pediatric Intensive Care, Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Erlangen, Germany
| | - Stefanie Nowak
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Lina Gölz
- Department of Orthodontics, University of Erlangen-Nürnberg, Erlangen, Germany.,Department of Orthodontics, University of Bonn, Bonn, Germany
| | - Michael Knapp
- Institute of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Andreas Buness
- Core Unit for Bioinformatic Analysis, Medical Faculty, University of Bonn, Bonn, Germany.,Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany.,Institute of Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Michael Nothnagel
- Cologne Center for Genomics, University of Cologne, Cologne, Germany.,University Hospital Cologne, Cologne, Germany
| | - Tim Becker
- Institute of Community Medicine, University of Greifswald, Greifswald, Germany
| | - Kerstin U Ludwig
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Elisabeth Mangold
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
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8
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Zieger HK, Weinhold L, Schmidt A, Holtgrewe M, Juranek SA, Siewert A, Scheer AB, Thieme F, Mangold E, Ishorst N, Brand FU, Welzenbach J, Beule D, Paeschke K, Krawitz PM, Ludwig KU. Prioritization of non-coding elements involved in non-syndromic cleft lip with/without cleft palate through genome-wide analysis of de novo mutations. HGG ADVANCES 2023; 4:100166. [PMID: 36589413 PMCID: PMC9795529 DOI: 10.1016/j.xhgg.2022.100166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Non-syndromic cleft lip with/without cleft palate (nsCL/P) is a highly heritable facial disorder. To date, systematic investigations of the contribution of rare variants in non-coding regions to nsCL/P etiology are sparse. Here, we re-analyzed available whole-genome sequence (WGS) data from 211 European case-parent trios with nsCL/P and identified 13,522 de novo mutations (DNMs) in nsCL/P cases, 13,055 of which mapped to non-coding regions. We integrated these data with DNMs from a reference cohort, with results of previous genome-wide association studies (GWASs), and functional and epigenetic datasets of relevance to embryonic facial development. A significant enrichment of nsCL/P DNMs was observed at two GWAS risk loci (4q28.1 (p = 8 × 10-4) and 2p21 (p = 0.02)), suggesting a convergence of both common and rare variants at these loci. We also mapped the DNMs to 810 position weight matrices indicative of transcription factor (TF) binding, and quantified the effect of the allelic changes in silico. This revealed a nominally significant overrepresentation of DNMs (p = 0.037), and a stronger effect on binding strength, for DNMs located in the sequence of the core binding region of the TF Musculin (MSC). Notably, MSC is involved in facial muscle development, together with a set of nsCL/P genes located at GWAS loci. Supported by additional results from single-cell transcriptomic data and molecular binding assays, this suggests that variation in MSC binding sites contributes to nsCL/P etiology. Our study describes a set of approaches that can be applied to increase the added value of WGS data.
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Affiliation(s)
- Hanna K. Zieger
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Leonie Weinhold
- Institute for Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn 53127, Germany
| | - Axel Schmidt
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Manuel Holtgrewe
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany
| | - Stefan A. Juranek
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn 53127, Germany
| | - Anna Siewert
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Annika B. Scheer
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Frederic Thieme
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Elisabeth Mangold
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Nina Ishorst
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Fabian U. Brand
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Bonn 53127, Germany
| | - Julia Welzenbach
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health, Berlin 10117, Germany
- Max Delbrück Center for Molecular Medicine, Berlin 13125, Germany
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn 53127, Germany
| | - Peter M. Krawitz
- Institute for Medical Biometry, Informatics and Epidemiology, University Hospital Bonn, Bonn 53127, Germany
| | - Kerstin U. Ludwig
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn 53127, Germany
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9
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Hammond NL, Dixon MJ. Revisiting the embryogenesis of lip and palate development. Oral Dis 2022; 28:1306-1326. [PMID: 35226783 PMCID: PMC10234451 DOI: 10.1111/odi.14174] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/17/2022] [Accepted: 02/23/2022] [Indexed: 12/13/2022]
Abstract
Clefts of the lip and palate (CLP), the major causes of congenital facial malformation globally, result from failure of fusion of the facial processes during embryogenesis. With a prevalence of 1 in 500-2500 live births, CLP causes major morbidity throughout life as a result of problems with facial appearance, feeding, speaking, obstructive apnoea, hearing and social adjustment and requires complex, multi-disciplinary care at considerable cost to healthcare systems worldwide. Long-term outcomes for affected individuals include increased mortality compared with their unaffected siblings. The frequent occurrence and major healthcare burden imposed by CLP highlight the importance of dissecting the molecular mechanisms driving facial development. Identification of the genetic mutations underlying syndromic forms of CLP, where CLP occurs in association with non-cleft clinical features, allied to developmental studies using appropriate animal models is central to our understanding of the molecular events underlying development of the lip and palate and, ultimately, how these are disturbed in CLP.
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Affiliation(s)
- Nigel L. Hammond
- Faculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUK
| | - Michael J. Dixon
- Faculty of Biology, Medicine and HealthUniversity of ManchesterManchesterUK
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10
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Peng L, Niu Z, Chen J, Wan T, Wu D, Yang Y, Wang G, Yang L, Huang W, Chen Z. Association of genetic polymorphisms of VAX1, MAFB, and NTN1 with nonsyndromic cleft lip with or without cleft palate in Chinese population. Mol Genet Genomics 2022; 297:553-559. [PMID: 35212839 DOI: 10.1007/s00438-022-01871-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 02/08/2022] [Indexed: 12/09/2022]
Abstract
Nonsyndromic cleft lip with or without palate (NSCL/P) is a common birth defect involving genetic factors. We conducted this case-control study to verify the association of ten single-nucleotide polymorphisms (SNPs) of six genes (VAX1, MAFB, PAX7, ABCA4, NTN1, and NOG) with NSCL/P in the Chinese population. The study included 249 NSCL/P patients, 62 nonsyndromic cleft palate only (NSCPO) patients and 480 controls. Three loci, namely, VAX1 rs7078160, MAFB rs11696257, and NTN1 rs4791774, were associated with NSCL/P (Bonferroni method adjusted p values were 0.020, 0.00031, and 0.030, respectively). We also found that the disease risk of individuals carrying both VAX1 rs7078160 and NTN1 rs4791774 was higher than those carrying only one of them (p = 4.50 × 10-4 and 6.03 × 10-3, respectively). SNPs of genes VAX1 rs7078160, MAFB rs11696257, and NTN1 rs4791774 increased NSCL/P risk in the Chinese population.
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Affiliation(s)
- Li Peng
- Department of Orthodontics, Shanghai Key Laboratory of Stomatology, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhenmin Niu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China.
| | - Jiapei Chen
- Department of Orthodontics, Shanghai Key Laboratory of Stomatology, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Teng Wan
- Department of Oral and Maxillofacial Surgery, Shanghai Key Laboratory of Stomatology, Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dandan Wu
- Department of Oral and Maxillofacial Surgery, Shanghai Key Laboratory of Stomatology, Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yusheng Yang
- Department of Oral and Maxillofacial Surgery, Shanghai Key Laboratory of Stomatology, Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guomin Wang
- Department of Oral and Maxillofacial Surgery, Shanghai Key Laboratory of Stomatology, Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin Yang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Wei Huang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China.
| | - Zhenqi Chen
- Department of Orthodontics, Shanghai Key Laboratory of Stomatology, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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11
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Ruff KLM, Hollstein R, Fazaal J, Thieme F, Gehlen J, Mangold E, Knapp M, Welzenbach J, Ludwig KU. Allele-specific transcription factor binding in a cellular model of orofacial clefting. Sci Rep 2022; 12:1807. [PMID: 35110662 PMCID: PMC8810875 DOI: 10.1038/s41598-022-05876-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 01/17/2022] [Indexed: 11/09/2022] Open
Abstract
Non-syndromic cleft lip with/without cleft palate (nsCL/P) is a frequent congenital malformation with multifactorial etiology. While recent genome-wide association studies (GWAS) have identified several nsCL/P risk loci, the functional effects of the associated non-coding variants are largely unknown. Furthermore, additional risk loci remain undetected due to lack of power. As genetic variants might alter binding of transcription factors (TF), we here hypothesized that the integration of data from TF binding sites, expression analyses and nsCL/P GWAS might help to (i) identify functionally relevant variants at GWAS loci, and (ii) highlight novel risk variants that have been previously undetected. Analysing the craniofacial TF TFAP2A in human embryonic palatal mesenchyme (HEPM) cells, we identified 2845 TFAP2A ChIP-seq peaks, several of which were located near nsCL/P candidate genes (e.g. MSX1 and SPRY2). Comparison with independent data suggest that 802 of them might be specific to craniofacial development, and genes near these peaks are enriched in processes relevant to nsCL/P. Integration with nsCL/P GWAS data, however, did not show robust evidence for co-localization of common nsCL/P risk variants with TFAP2A ChIP-seq peaks. This data set represents a new resource for the analyses of craniofacial processes, and similar approaches with additional cell lines and TFs could be applied to generate further insights into nsCL/P etiology.
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Affiliation(s)
- Katharina L M Ruff
- School of Medicine and University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Ronja Hollstein
- School of Medicine and University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Julia Fazaal
- School of Medicine and University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Frederic Thieme
- School of Medicine and University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Jan Gehlen
- Centre for Human Genetics, University of Marburg, Marburg, Germany
| | - Elisabeth Mangold
- School of Medicine and University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Michael Knapp
- Institute for Medical Biometry, Informatics and Epidemiology IMBIE, University of Bonn, Bonn, Germany
| | - Julia Welzenbach
- School of Medicine and University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Kerstin U Ludwig
- School of Medicine and University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany.
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12
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Leslie EJ. Genetic models and approaches to study orofacial clefts. Oral Dis 2021; 28:1327-1338. [PMID: 34923716 DOI: 10.1111/odi.14109] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/08/2021] [Accepted: 12/16/2021] [Indexed: 11/26/2022]
Abstract
INTRODUCTION Orofacial clefts (OFCs) are common craniofacial birth defects with heterogeneous phenotype and etiology. Geneticists have applied nearly every available method and technology to further our understanding of the genetic architectures of OFCs. OBJECTIVE This review describes the evidence for a genetic etiology in OFCs, statistical genetic approaches employed to identify genetic causes, and how the results have shaped our current understanding of the genetic architectures of syndromic and nonsyndromic OFCs. CONCLUSION There has been rapid progress towards elucidating the genetic architectures of OFCs due to the availability of large collections of DNA samples from cases, controls, and families with OFCs and the consistent adoption of new methodologies and novel statistical approaches as they are developed. Genetic studies have identified rare and common variants influencing risk of OFCs in both Mendelian and complex forms of OFCs, blurring the distinctions traditional categories used in genetic studies and clinical medicine.
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13
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Avasthi KK, Muthuswamy S, Asim A, Agarwal A, Agarwal S. Identification of Novel Genomic Variations in Susceptibility to Nonsyndromic Cleft Lip and Palate Patients. Pediatr Rep 2021; 13:650-657. [PMID: 34941638 PMCID: PMC8703930 DOI: 10.3390/pediatric13040077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/27/2021] [Accepted: 12/01/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Nonsyndromic cleft lip with or without palate (NSCL/P) is a multifactorial and common birth malformation caused by genetic and environmental factors, as well as by teratogens. Genome-wide association studies found genetic variations with modulatory effects of NSCL/P formation in Chinese and Iranian populations. We aimed to identify the susceptibility of single-nucleotide polymorphisms (SNPs) to nonsyndromic cleft lip with or without palate in the Indian population. MATERIAL AND METHODS The present study was conducted on NSCL/P cases and controls. Genomic DNA was extracted from peripheral blood and Axiom- Precision Medicine Research Array (PMRA) was performed. The Axiom-PMRA covers 902,527 markers and several thousand novel risk variants. Quality control-passed samples were included for candidate genetic variation identification, gene functional enrichment, and pathway and network analysis. RESULTS The genome-wide association study identified fourteen novel candidate gene SNPs that showed the most significant association with the risk of NSCL/P, and eight were predicted to have regulatory sequences. CONCLUSION The GWAS study showed novel candidate genetic variations in NSCL/P formations. These findings contribute to the understanding of genetic predisposition to nonsyndromic cleft lip with or without palate.
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Affiliation(s)
- Kapil Kumar Avasthi
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS), Lucknow 226014, India; (K.K.A.); (A.A.)
| | - Srinivasan Muthuswamy
- Department of Life Sciences, National Institute of Technology, Rourkela 769001, Odisha, India;
| | - Ambreen Asim
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS), Lucknow 226014, India; (K.K.A.); (A.A.)
| | - Amit Agarwal
- Department of Burn and Plastic Surgery, Vivekananda Polyclinic and Institute of Medical Sciences, Lucknow 226007, India;
| | - Sarita Agarwal
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGIMS), Lucknow 226014, India; (K.K.A.); (A.A.)
- Correspondence: ; Tel.: +91-0522-2494356
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14
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Ray D, Venkataraghavan S, Zhang W, Leslie EJ, Hetmanski JB, Weinberg SM, Murray JC, Marazita ML, Ruczinski I, Taub MA, Beaty TH. Pleiotropy method reveals genetic overlap between orofacial clefts at multiple novel loci from GWAS of multi-ethnic trios. PLoS Genet 2021; 17:e1009584. [PMID: 34242216 PMCID: PMC8270211 DOI: 10.1371/journal.pgen.1009584] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/06/2021] [Indexed: 12/19/2022] Open
Abstract
Based on epidemiologic and embryologic patterns, nonsyndromic orofacial clefts- the most common craniofacial birth defects in humans- are commonly categorized into cleft lip with or without cleft palate (CL/P) and cleft palate alone (CP), which are traditionally considered to be etiologically distinct. However, some evidence of shared genetic risk in IRF6, GRHL3 and ARHGAP29 regions exists; only FOXE1 has been recognized as significantly associated with both CL/P and CP in genome-wide association studies (GWAS). We used a new statistical approach, PLACO (pleiotropic analysis under composite null), on a combined multi-ethnic GWAS of 2,771 CL/P and 611 CP case-parent trios. At the genome-wide significance threshold of 5 × 10-8, PLACO identified 1 locus in 1q32.2 (IRF6) that appears to increase risk for one OFC subgroup but decrease risk for the other. At a suggestive significance threshold of 10-6, we found 5 more loci with compelling candidate genes having opposite effects on CL/P and CP: 1p36.13 (PAX7), 3q29 (DLG1), 4p13 (LIMCH1), 4q21.1 (SHROOM3) and 17q22 (NOG). Additionally, we replicated the recognized shared locus 9q22.33 (FOXE1), and identified 2 loci in 19p13.12 (RAB8A) and 20q12 (MAFB) that appear to influence risk of both CL/P and CP in the same direction. We found locus-specific effects may vary by racial/ethnic group at these regions of genetic overlap, and failed to find evidence of sex-specific differences. We confirmed shared etiology of the two OFC subtypes comprising CL/P, and additionally found suggestive evidence of differences in their pathogenesis at 2 loci of genetic overlap. Our novel findings include 6 new loci of genetic overlap between CL/P and CP; 3 new loci between pairwise OFC subtypes; and 4 loci not previously implicated in OFCs. Our in-silico validation showed PLACO is robust to subtype-specific effects, and can achieve massive power gains over existing approaches for identifying genetic overlap between disease subtypes. In summary, we found suggestive evidence for new genetic regions and confirmed some recognized OFC genes either exerting shared risk or with opposite effects on risk to OFC subtypes.
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Affiliation(s)
- Debashree Ray
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail: (DR); (THB)
| | - Sowmya Venkataraghavan
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Wanying Zhang
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Elizabeth J. Leslie
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Jacqueline B. Hetmanski
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Seth M. Weinberg
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jeffrey C. Murray
- Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa, United States of America
| | - Mary L. Marazita
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Margaret A. Taub
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Terri H. Beaty
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail: (DR); (THB)
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15
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Welzenbach J, Hammond NL, Nikolić M, Thieme F, Ishorst N, Leslie EJ, Weinberg SM, Beaty TH, Marazita ML, Mangold E, Knapp M, Cotney J, Rada-Iglesias A, Dixon MJ, Ludwig KU. Integrative approaches generate insights into the architecture of non-syndromic cleft lip with or without cleft palate. HGG ADVANCES 2021; 2:100038. [PMID: 35047836 PMCID: PMC8756534 DOI: 10.1016/j.xhgg.2021.100038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 05/27/2021] [Indexed: 12/15/2022] Open
Abstract
Non-syndromic cleft lip with or without cleft palate (nsCL/P) is a common congenital facial malformation with a multifactorial etiology. Genome-wide association studies (GWASs) have identified multiple genetic risk loci. However, functional interpretation of these loci is hampered by the underrepresentation in public resources of systematic functional maps representative of human embryonic facial development. To generate novel insights into the etiology of nsCL/P, we leveraged published GWAS data on nsCL/P as well as available chromatin modification and expression data on mid-facial development. Our analyses identified five novel risk loci, prioritized candidate target genes within associated regions, and highlighted distinct pathways. Furthermore, the results suggest the presence of distinct regulatory effects of nsCL/P risk variants throughout mid-facial development and shed light on its regulatory architecture. Our integrated data provide a platform to advance hypothesis-driven molecular investigations of nsCL/P and other human facial defects.
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Affiliation(s)
- Julia Welzenbach
- Institute of Human Genetics, University Hospital Bonn, Medical Faculty, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Nigel L. Hammond
- Faculty of Biology, Medicine, and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9PT, UK
| | - Miloš Nikolić
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Frederic Thieme
- Institute of Human Genetics, University Hospital Bonn, Medical Faculty, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Nina Ishorst
- Institute of Human Genetics, University Hospital Bonn, Medical Faculty, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Elizabeth J. Leslie
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Seth M. Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Terri H. Beaty
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Psychiatry and Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Elisabeth Mangold
- Institute of Human Genetics, University Hospital Bonn, Medical Faculty, Venusberg-Campus 1, 53127 Bonn, Germany
| | - Michael Knapp
- Institute of Medical Biometry, Informatics, and Epidemiology, University Hospital Bonn, Bonn, Germany
| | - Justin Cotney
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - Alvaro Rada-Iglesias
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), University of Cantabria, Cantabria, Spain
| | - Michael J. Dixon
- Faculty of Biology, Medicine, and Health, Manchester Academic Health Sciences Centre, University of Manchester, Manchester M13 9PT, UK
| | - Kerstin U. Ludwig
- Institute of Human Genetics, University Hospital Bonn, Medical Faculty, Venusberg-Campus 1, 53127 Bonn, Germany
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16
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Machado RA, Martelli-Junior H, Reis SRDA, Küchler EC, Scariot R, das Neves LT, Coletta RD. Identification of Novel Variants in Cleft Palate-Associated Genes in Brazilian Patients With Non-syndromic Cleft Palate Only. Front Cell Dev Biol 2021; 9:638522. [PMID: 34307341 PMCID: PMC8297955 DOI: 10.3389/fcell.2021.638522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/30/2021] [Indexed: 12/17/2022] Open
Abstract
The identification of genetic risk factors for non-syndromic oral clefts is of great importance for better understanding the biological processes related to this heterogeneous and complex group of diseases. Herein we applied whole-exome sequencing to identify potential variants related to non-syndromic cleft palate only (NSCPO) in the multiethnic Brazilian population. Thirty NSCPO samples and 30 sex- and genetic ancestry-matched healthy controls were pooled (3 pools with 10 samples for each group) and subjected to whole-exome sequencing. After filtering, the functional affects, individually and through interactions, of the selected variants and genes were assessed by bioinformatic analyses. As a group, 399 variants in 216 genes related to palatogenesis/cleft palate, corresponding to 6.43%, were exclusively identified in the NSCPO pools. Among those genes are 99 associated with syndromes displaying cleft palate in their clinical spectrum and 92 previously related to cleft lip palate. The most significantly biological processes and pathways overrepresented in the NSCPO-identified genes were associated with the folic acid metabolism, highlighting the interaction between LDL receptor-related protein 6 (LRP6) and 5-methyltetrahydrofolate-homocysteine methyltransferase (MTR) that interconnect two large networks. This study yields novel data on characterization of specific variants and complex processes and pathways related to NSCPO, including many variants in genes of the folate/homocysteine pathway, and confirms that variants in genes related to syndromic cleft palate and cleft lip-palate may cause NSCPO.
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Affiliation(s)
- Renato Assis Machado
- Department of Oral Diagnosis, School of Dentistry, University of Campinas (FOP), Piracicaba, Brazil.,Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, Brazil
| | - Hercílio Martelli-Junior
- Stomatology Clinic, School of Dental, State University of Montes Claros, Montes Claros, Brazil.,Center for Rehabilitation of Craniofacial Anomalies, School of Dental, UNIFENAS - Universidade José do Rosario Vellano, Alfenas, Brazil
| | | | | | - Rafaela Scariot
- Department of Oral and Maxillofacial Surgery, School of Health Science, Federal University of Paraná, Curitiba, Brazil
| | - Lucimara Teixeira das Neves
- Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, Brazil.,Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo (FOB), Bauru, Brazil
| | - Ricardo D Coletta
- Department of Oral Diagnosis, School of Dentistry, University of Campinas (FOP), Piracicaba, Brazil
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17
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Young JI, Slifer S, Hecht JT, Blanton SH. DNA Methylation Variation Is Identified in Monozygotic Twins Discordant for Non-syndromic Cleft Lip and Palate. Front Cell Dev Biol 2021; 9:656865. [PMID: 34055787 PMCID: PMC8149607 DOI: 10.3389/fcell.2021.656865] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
Non-syndromic cleft lip with or without cleft palate (NSCLP) is the most common craniofacial birth defect. The etiology of NSCLP is complex with multiple genes and environmental factors playing causal roles. Although studies have identified numerous genetic markers associated with NSCLP, the role of epigenetic variation remains relatively unexplored. Because of their identical DNA sequences, monozygotic (MZ) twins discordant for NSCLP are an ideal model for examining the potential contribution of DNA methylation to non-syndromic orofacial clefting. In this study, we compared the patterns of whole genome DNA methylation in six MZ twin pairs discordant for NSCLP. Differentially methylated positions (DMPs) and regions (DMRs) were identified in NSCLP candidate genes, including differential methylation in MAFB and ZEB2 in two independent MZ twin pairs. In addition to DNA methylation differences in NSCLP candidate genes, we found common differential methylation in genes belonging to the Hippo signaling pathway, implicating this mechanosensory pathway in the etiology of NSCLP. The results of this novel approach using MZ twins discordant for NSCLP suggests that differential methylation is one mechanism contributing to NSCLP, meriting future studies on the role of DNA methylation in familial and sporadic NSCLP.
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Affiliation(s)
- Juan I. Young
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Susan Slifer
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Jacqueline T. Hecht
- McGovern Medical School, University of Texas Health Science Center, Houston, TX, United States
| | - Susan H. Blanton
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States
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18
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Danescu A, Rens EG, Rehki J, Woo J, Akazawa T, Fu K, Edelstein-Keshet L, Richman JM. Symmetry and fluctuation of cell movements in neural crest-derived facial mesenchyme. Development 2021; 148:dev.193755. [PMID: 33757991 PMCID: PMC8126411 DOI: 10.1242/dev.193755] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 03/05/2021] [Indexed: 12/13/2022]
Abstract
In the face, symmetry is established when bilateral streams of neural crest cells leave the neural tube at the same time, follow identical migration routes and then give rise to the facial prominences. However, developmental instability exists, particularly surrounding the steps of lip fusion. The causes of instability are unknown but inability to cope with developmental fluctuations are a likely cause of congenital malformations, such as non-syndromic orofacial clefts. Here, we tracked cell movements over time in the frontonasal mass, which forms the facial midline and participates in lip fusion, using live-cell imaging of chick embryos. Our mathematical examination of cell velocity vectors uncovered temporal fluctuations in several parameters, including order/disorder, symmetry/asymmetry and divergence/convergence. We found that treatment with a Rho GTPase inhibitor completely disrupted the temporal fluctuations in all measures and blocked morphogenesis. Thus, we discovered that genetic control of symmetry extends to mesenchymal cell movements and that these movements are of the type that could be perturbed in asymmetrical malformations, such as non-syndromic cleft lip. This article has an associated ‘The people behind the papers’ interview. Highlighted Article: Live imaging of the chick embryo face followed by mathematical analysis of mesenchymal cell tracks captures novel fluctuations between states of order/disorder as well as symmetry/asymmetry, revealing developmental instabilities that are part of normal morphogenesis.
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Affiliation(s)
- Adrian Danescu
- Life Sciences Institute, 2350 Health Sciences Mall, University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - Elisabeth G Rens
- Department of Mathematics, University of British Columbia, 1986 Mathematics Road, Vancouver, V6T 1Z2, Canada
| | - Jaspreet Rehki
- Life Sciences Institute, 2350 Health Sciences Mall, University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - Johnathan Woo
- Life Sciences Institute, 2350 Health Sciences Mall, University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - Takashi Akazawa
- Life Sciences Institute, 2350 Health Sciences Mall, University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - Katherine Fu
- Life Sciences Institute, 2350 Health Sciences Mall, University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - Leah Edelstein-Keshet
- Department of Mathematics, University of British Columbia, 1986 Mathematics Road, Vancouver, V6T 1Z2, Canada
| | - Joy M Richman
- Life Sciences Institute, 2350 Health Sciences Mall, University of British Columbia, Vancouver, V6T 1Z3, Canada
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19
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Curtis SW, Chang D, Lee MK, Shaffer JR, Indencleef K, Epstein MP, Cutler DJ, Murray JC, Feingold E, Beaty TH, Claes P, Weinberg SM, Marazita ML, Carlson JC, Leslie EJ. The PAX1 locus at 20p11 is a potential genetic modifier for bilateral cleft lip. HGG ADVANCES 2021; 2:100025. [PMID: 33817668 PMCID: PMC8018676 DOI: 10.1016/j.xhgg.2021.100025] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/22/2021] [Indexed: 12/12/2022] Open
Abstract
Nonsyndromic orofacial clefts (OFCs) are a common birth defect and are phenotypically heterogenous in the structure affected by the cleft - cleft lip (CL) and cleft lip and palate (CLP) - as well as other features, such as the severity of the cleft. Here, we focus on bilateral and unilateral clefts as one dimension of OFC severity, because the genetic architecture of these subtypes is not well understood. We tested for subtype-specific genetic associations in 44 bilateral CL (BCL) cases, 434 unilateral CL (UCL) cases, 530 bilateral CLP cases (BCLP), 1123 unilateral CLP (UCLP) cases, and unrelated controls (N = 1626), using a mixed-model approach. While no novel loci were found, the genetic architecture of UCL was distinct compared to BCL, with 44.03% of suggestive loci having different effects between the two subtypes. To further understand the subtype-specific genetic risk factors, we performed a genome-wide scan for modifiers and found a significant modifier locus on 20p11 (p=7.53×10-9), 300kb downstream of PAX1, that associated with higher odds of BCL vs. UCL, and replicated in an independent cohort (p=0.0018) with no effect in BCLP (p>0.05). We further found that this locus was associated with normal human nasal shape. Taken together, these results suggest bilateral and unilateral clefts may have different genetic architectures. Moreover, our results suggest BCL, the rarest form of OFC, may be genetically distinct from the other OFC subtypes. This expands our understanding of modifiers for OFC subtypes and further elucidates the genetic mechanisms behind the phenotypic heterogeneity in OFCs.
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Affiliation(s)
- Sarah W. Curtis
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Daniel Chang
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Myoung Keun Lee
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - John R. Shaffer
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15621, USA
| | - Karlijne Indencleef
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
| | | | - David J. Cutler
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Jeffrey C. Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA 52242, USA
| | - Eleanor Feingold
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15621, USA
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Terri H. Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Peter Claes
- Medical Imaging Research Center, University Hospitals Leuven, Leuven, Belgium
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Seth M. Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15621, USA
| | - Jenna C. Carlson
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15621, USA
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15261, USA
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20
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Clinical characterization of 266 patients and family members with cleft lip and/or palate with associated malformations and syndromes. Clin Oral Investig 2021; 25:5531-5540. [PMID: 33760974 PMCID: PMC8370934 DOI: 10.1007/s00784-021-03863-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 02/25/2021] [Indexed: 12/02/2022]
Abstract
Objectives To clinically characterize patients and family members with cleft lip and/or palate (CL/P) and associated congenital malformations or syndromes and propose possible inheritance patterns. Materials and methods An observational study of patients with CL/P, including medical and family history and intra- and extra-oral examination of their family members, was performed. Results Two hundred sixty-six patients, 1257 family members, and 42 pedigrees were included in the study. The distribution of patients according to the cleft type was 57.9% with CLP, 25.2% with cleft palate (CPO), and 12.8% with cleft lip with/without alveolus (CL/A). Seventy-four (27.8%) patients had associated malformations, and 24 (9.2%) a syndrome. The skeletal (27.7%), cardiovascular (19.3%) systems, and eyes (22.9%) were most commonly affected. Pierre Robin Sequence (7 patients) and van der Woude (4) were the most common syndromes. The majority of patients with CPO (19/24) had an associate syndrome. The families had an average of 2.45 affected members. Conclusion Individual and interfamilial phenotypic variability in patients with CL/P makes the understanding of etiopathogenesis challenging. Clinical relevance The overall prevalence of individuals with CL/P and their pedigrees with associated malformations and syndromes emphasize the need for early identification, interdisciplinary, and long-term planning. Supplementary Information The online version contains supplementary material available at 10.1007/s00784-021-03863-2.
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21
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Indencleef K, Hoskens H, Lee MK, White JD, Liu C, Eller RJ, Naqvi S, Wehby GL, Moreno Uribe LM, Hecht JT, Long RE, Christensen K, Deleyiannis FW, Walsh S, Shriver MD, Richmond S, Wysocka J, Peeters H, Shaffer JR, Marazita ML, Hens G, Weinberg SM, Claes P. The Intersection of the Genetic Architectures of Orofacial Clefts and Normal Facial Variation. Front Genet 2021; 12:626403. [PMID: 33692830 PMCID: PMC7937973 DOI: 10.3389/fgene.2021.626403] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/26/2021] [Indexed: 01/06/2023] Open
Abstract
Unaffected relatives of individuals with non-syndromic cleft lip with or without cleft palate (NSCL/P) show distinctive facial features. The presence of this facial endophenotype is potentially an expression of underlying genetic susceptibility to NSCL/P in the larger unselected population. To explore this hypothesis, we first partitioned the face into 63 partially overlapping regions representing global-to-local facial morphology and then defined endophenotypic traits by contrasting the 3D facial images from 264 unaffected parents of individuals with NSCL/P versus 3,171 controls. We observed distinct facial features between parents and controls across 59 global-to-local facial segments at nominal significance (p ≤ 0.05) and 52 segments at Bonferroni corrected significance (p < 1.2 × 10-3), respectively. Next, we quantified these distinct facial features as univariate traits in another dataset of 8,246 unaffected European individuals and performed a genome-wide association study. We identified 29 independent genetic loci that were associated (p < 5 × 10-8) with at least one of the tested endophenotypic traits, and nine genetic loci also passed the study-wide threshold (p < 8.47 × 10-10). Of the 29 loci, 22 were in proximity of loci previously associated with normal facial variation, 18 were near genes that show strong evidence in orofacial clefting (OFC), and another 10 showed some evidence in OFC. Additionally, polygenic risk scores for NSCL/P showed associations with the endophenotypic traits. This study thus supports the hypothesis of a shared genetic architecture of normal facial development and OFC.
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Affiliation(s)
- Karlijne Indencleef
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
| | - Hanne Hoskens
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Myoung Keun Lee
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Julie D. White
- Department of Anthropology, Pennsylvania State University, State College, PA, United States
| | - Chenxing Liu
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Ryan J. Eller
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN, United States
| | - Sahin Naqvi
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, United States
| | - George L. Wehby
- Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, IA, United States
| | - Lina M. Moreno Uribe
- Department of Orthodontics & The Iowa Institute for Oral Health Research, College of Dentistry, University of Iowa, Iowa City, IA, United States
| | - Jacqueline T. Hecht
- Department of Pediatrics, McGovern Medical School and School of Dentistry, UT Health at Houston, Houston, TX, United States
| | - Ross E. Long
- Lancaster Cleft Palate Clinic, Lancaster, PA, United States
| | - Kaare Christensen
- Department of Epidemiology, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | | | - Susan Walsh
- Department of Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN, United States
| | - Mark D. Shriver
- Department of Anthropology, Pennsylvania State University, State College, PA, United States
| | - Stephen Richmond
- Applied Clinical Research and Public Health, School of Dentistry, Cardiff University, Cardiff, United Kingdom
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, United States
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, United States
| | - Hilde Peeters
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - John R. Shaffer
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Mary L. Marazita
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Greet Hens
- Department of Otorhinolaryngology, KU Leuven, Leuven, Belgium
| | - Seth M. Weinberg
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Anthropology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Peter Claes
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
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22
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Bonfante B, Faux P, Navarro N, Mendoza-Revilla J, Dubied M, Montillot C, Wentworth E, Poloni L, Varón-González C, Jones P, Xiong Z, Fuentes-Guajardo M, Palmal S, Chacón-Duque JC, Hurtado M, Villegas V, Granja V, Jaramillo C, Arias W, Barquera R, Everardo-Martínez P, Sánchez-Quinto M, Gómez-Valdés J, Villamil-Ramírez H, Silva de Cerqueira CC, Hünemeier T, Ramallo V, Liu F, Weinberg SM, Shaffer JR, Stergiakouli E, Howe LJ, Hysi PG, Spector TD, Gonzalez-José R, Schüler-Faccini L, Bortolini MC, Acuña-Alonzo V, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Thauvin-Robinet C, Faivre L, Costedoat C, Balding D, Cox T, Kayser M, Duplomb L, Yalcin B, Cotney J, Adhikari K, Ruiz-Linares A. A GWAS in Latin Americans identifies novel face shape loci, implicating VPS13B and a Denisovan introgressed region in facial variation. SCIENCE ADVANCES 2021; 7:eabc6160. [PMID: 33547071 PMCID: PMC7864580 DOI: 10.1126/sciadv.abc6160] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 12/17/2020] [Indexed: 05/25/2023]
Abstract
To characterize the genetic basis of facial features in Latin Americans, we performed a genome-wide association study (GWAS) of more than 6000 individuals using 59 landmark-based measurements from two-dimensional profile photographs and ~9,000,000 genotyped or imputed single-nucleotide polymorphisms. We detected significant association of 32 traits with at least 1 (and up to 6) of 32 different genomic regions, more than doubling the number of robustly associated face morphology loci reported until now (from 11 to 23). These GWAS hits are strongly enriched in regulatory sequences active specifically during craniofacial development. The associated region in 1p12 includes a tract of archaic adaptive introgression, with a Denisovan haplotype common in Native Americans affecting particularly lip thickness. Among the nine previously unidentified face morphology loci we identified is the VPS13B gene region, and we show that variants in this region also affect midfacial morphology in mice.
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Affiliation(s)
- Betty Bonfante
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille 13005, France
| | - Pierre Faux
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille 13005, France
| | - Nicolas Navarro
- Biogéosciences, UMR 6282 CNRS, EPHE, Université Bourgogne Franche-Comté, Dijon 21078, France
- EPHE, PSL University, Paris 75014, France
| | - Javier Mendoza-Revilla
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
- Unit of Human Evolutionary Genetics, Institut Pasteur, Paris 75015, France
| | - Morgane Dubied
- Biogéosciences, UMR 6282 CNRS, EPHE, Université Bourgogne Franche-Comté, Dijon 21078, France
| | - Charlotte Montillot
- INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France
| | - Emma Wentworth
- Department of Genetics and Genome Sciences, University of Connecticut Health, Farmington, CT 06030, USA
| | - Lauriane Poloni
- Biogéosciences, UMR 6282 CNRS, EPHE, Université Bourgogne Franche-Comté, Dijon 21078, France
- EPHE, PSL University, Paris 75014, France
| | - Ceferino Varón-González
- Institut de Systématique, Évolution, Biodiversité, ISYEB-UMR 7205-CNRS, MNHN, UPMC, EPHE, UA, Muséum National d'Histoire Naturelle, Sorbonne Universités, Paris 75005, France
| | - Philip Jones
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Ziyi Xiong
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam 3015GD, Netherlands
| | - Macarena Fuentes-Guajardo
- Departamento de Tecnología Médica, Facultad de Ciencias de la Salud, Universidad de Tarapacá, Arica 1000000, Chile
| | - Sagnik Palmal
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille 13005, France
| | - Juan Camilo Chacón-Duque
- Division of Vertebrates and Anthropology, Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Valeria Villegas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Vanessa Granja
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Claudia Jaramillo
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - William Arias
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Rodrigo Barquera
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City 14050, Mexico
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History (MPI-SHH), Jena 07745, Germany
| | - Paola Everardo-Martínez
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City 14050, Mexico
| | - Mirsha Sánchez-Quinto
- Forensic Science, Faculty of Medicine, UNAM (Universidad Nacional Autónoma de México), Mexico City 06320, Mexico
| | - Jorge Gómez-Valdés
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City 14050, Mexico
| | - Hugo Villamil-Ramírez
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico
| | | | - Tábita Hünemeier
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP 05508-090, Brazil
| | - Virginia Ramallo
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brasil
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn U9129ACD, Argentina
| | - Fan Liu
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam 3015GD, Netherlands
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100864, China
- University of Chinese Academy of Sciences, Beijing 100864, China
| | - Seth M Weinberg
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Department of Anthropology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - John R Shaffer
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Evie Stergiakouli
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol BS1 2LY, UK
- School of Oral and Dental Sciences, University of Bristol, Bristol BS1 2LY, UK
| | - Laurence J Howe
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol BS1 2LY, UK
| | - Pirro G Hysi
- Department of Twin Research and Genetic Epidemiology, King's College London, London WC2R 2LS, UK
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London WC2R 2LS, UK
| | - Rolando Gonzalez-José
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico, CONICET, Puerto Madryn U9129ACD, Argentina
| | - Lavinia Schüler-Faccini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brasil
| | - Maria-Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 90040-060, Brasil
| | - Victor Acuña-Alonzo
- Molecular Genetics Laboratory, National School of Anthropology and History, Mexico City 14050, Mexico
| | - Samuel Canizales-Quinteros
- Unidad de Genomica de Poblaciones Aplicada a la Salud, Facultad de Química, UNAM-Instituto Nacional de Medicina Genómica, Mexico City 4510, Mexico
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 31, Perú
| | - Gabriel Bedoya
- GENMOL (Genética Molecular), Universidad de Antioquia, Medellín 5001000, Colombia
| | - Francisco Rothhammer
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Arica 1000000, Chile
| | - Christel Thauvin-Robinet
- INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France
- Centre de Référence Maladies Rares "Anomalies du Développement et Syndromes Malformatifs" de l'Est, Centre de Génétique, FHU TRANSLAD, CHU Dijon, Dijon 21000, France
| | - Laurence Faivre
- INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France
- Centre de Référence Maladies Rares "Anomalies du Développement et Syndromes Malformatifs" de l'Est, Centre de Génétique, FHU TRANSLAD, CHU Dijon, Dijon 21000, France
| | | | - David Balding
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
- Melbourne Integrative Genomics, Schools of BioSciences and Mathematics & Statistics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Timothy Cox
- Department of Oral and Craniofacial Sciences, School of Dentistry and Department of Pediatrics, School of Medicine, University of Missouri, Kansas City, MO 64108, USA
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam 3015GD, Netherlands
| | - Laurence Duplomb
- INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France
| | - Binnaz Yalcin
- INSERM UMR 1231 Génétique des Anomalies du Développement, Université Bourgogne Franche-Comté, Dijon 21000, France
| | - Justin Cotney
- Department of Genetics and Genome Sciences, University of Connecticut Health, Farmington, CT 06030, USA
| | - Kaustubh Adhikari
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK.
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Andrés Ruiz-Linares
- Aix-Marseille Université, CNRS, EFS, ADES, Marseille 13005, France.
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, London WC1E 6BT, UK
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, China
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23
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Martinelli M, Palmieri A, Carinci F, Scapoli L. Non-syndromic Cleft Palate: An Overview on Human Genetic and Environmental Risk Factors. Front Cell Dev Biol 2020; 8:592271. [PMID: 33195260 PMCID: PMC7606870 DOI: 10.3389/fcell.2020.592271] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/28/2020] [Indexed: 12/27/2022] Open
Abstract
The epithelial and mesenchymal cells involved in early embryonic facial development are guided by complex regulatory mechanisms. Any factor perturbing the growth, approach and fusion of the frontonasal and maxillary processes could result in orofacial clefts that represent the most common craniofacial malformations in humans. The rarest and, probably for this reason, the least studied form of cleft involves only the secondary palate, which is posterior to the incisive foramen. The etiology of cleft palate only is multifactorial and involves both genetic and environmental risk factors. The intention of this review is to give the reader an overview of the efforts made by researchers to shed light on the underlying causes of this birth defect. Most of the scientific papers suggesting potential environmental and genetic causes of non-syndromic cleft palate are summarized in this review, including genome-wide association and gene–environment interaction studies.
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Affiliation(s)
- Marcella Martinelli
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Annalisa Palmieri
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Francesco Carinci
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Luca Scapoli
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum - University of Bologna, Bologna, Italy
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24
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He M, Zuo X, Liu H, Wang W, Zhang Y, Fu Y, Zhen Q, Yu Y, Pan Y, Qin C, Li B, Yang R, Wu J, Huang Z, Ge H, Wu H, Xu Q, Zuo Y, Chen W, Qin Y, Liu Z, Chen S, Zhang H, Zhou F, Yan H, Yu Y, Yong L, Chen G, Liang B, Cornell RA, Zong L, Wang L, Zou D, Sun L, Bian Z. Genome-wide Analyses Identify a Novel Risk Locus for Nonsyndromic Cleft Palate. J Dent Res 2020; 99:1461-1468. [PMID: 32758111 DOI: 10.1177/0022034520943867] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The 3 major subphenotypes observed in patients with nonsyndromic orofacial clefts (NSOFCs) are nonsyndromic cleft lip only (NSCLO), nonsyndromic cleft lip with palate (NSCLP), and nonsyndromic cleft palate only (NSCPO). However, the genetic architecture underlying NSCPO is largely unknown. Here we performed a 2-stage genome-wide association study (GWAS) on NSCPO and replication analyses of selected variants in other NSOFCs from the Chinese Han population. We identified a novel locus (15q24.3) and a known locus (1q32.2) where variants in or near the gene reached genome-wide significance (2.80 × 10-13 < P < 1.72 × 10-08) in a test for association with NSCPO in a case-control design. Although a variant from 15q24.3 was found to be significantly associated with both NSCPO and NSCLP, the direction of estimated effects on risk were opposite. Our functional annotation of the risk alleles within 15q24.3 coupled with previously established roles of the candidate genes within identified risk loci in periderm development, embryonic patterning, and/or regulation of cellular processes supports their involvement in palate development and the pathogenesis of cleft palate. Our study advances the understanding of the genetic basis of NSOFCs and provides novel insights into the pathogenesis of NSCPO.
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Affiliation(s)
- M He
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei, China
| | - X Zuo
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Key Laboratory of Major Autoimmune Diseases, Anhui Province, Hefei, China
| | - H Liu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei, China
| | - W Wang
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Key Laboratory of Major Autoimmune Diseases, Anhui Province, Hefei, China
| | - Y Zhang
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Key Laboratory of Major Autoimmune Diseases, Anhui Province, Hefei, China
| | - Y Fu
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei, China
| | - Q Zhen
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Key Laboratory of Major Autoimmune Diseases, Anhui Province, Hefei, China
| | - Y Yu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei, China
| | - Y Pan
- Jiangsu Key Laboratory of Oral Diseases, School of Stomatology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - C Qin
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei, China
| | - B Li
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Key Laboratory of Major Autoimmune Diseases, Anhui Province, Hefei, China
| | - R Yang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei, China
| | - J Wu
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Key Laboratory of Major Autoimmune Diseases, Anhui Province, Hefei, China
| | - Z Huang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei, China
| | - H Ge
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Key Laboratory of Major Autoimmune Diseases, Anhui Province, Hefei, China
| | - H Wu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei, China
| | - Q Xu
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Key Laboratory of Major Autoimmune Diseases, Anhui Province, Hefei, China
| | - Y Zuo
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei, China
| | - W Chen
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Key Laboratory of Major Autoimmune Diseases, Anhui Province, Hefei, China
| | - Y Qin
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei, China
| | - Z Liu
- Stomatological Hospital of Nanyang, Nanyang, Henan, China
| | - S Chen
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Key Laboratory of Major Autoimmune Diseases, Anhui Province, Hefei, China
| | - H Zhang
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Key Laboratory of Major Autoimmune Diseases, Anhui Province, Hefei, China
| | - F Zhou
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Key Laboratory of Major Autoimmune Diseases, Anhui Province, Hefei, China
| | - H Yan
- Stomatological Hospital of Xiangyang, Xiangyang, Hubei, China
| | - Y Yu
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Key Laboratory of Major Autoimmune Diseases, Anhui Province, Hefei, China
| | - L Yong
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Key Laboratory of Major Autoimmune Diseases, Anhui Province, Hefei, China
| | - G Chen
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Key Laboratory of Major Autoimmune Diseases, Anhui Province, Hefei, China
| | - B Liang
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Key Laboratory of Major Autoimmune Diseases, Anhui Province, Hefei, China
| | - R A Cornell
- Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, Iowa City, IA, USA
| | - L Zong
- Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
| | - L Wang
- Jiangsu Key Laboratory of Oral Diseases, School of Stomatology, Nanjing Medical University, Nanjing, Jiangsu, China
| | - D Zou
- Department of Oral Surgery, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology, National Clinical Research Center of Stomatology, Shanghai, China
| | - L Sun
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, China.,Key Laboratory of Major Autoimmune Diseases, Anhui Province, Hefei, China
| | - Z Bian
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, Hubei, China
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25
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Nakatomi M, Ludwig KU, Knapp M, Kist R, Lisgo S, Ohshima H, Mangold E, Peters H. Msx1 deficiency interacts with hypoxia and induces a morphogenetic regulation during mouse lip development. Development 2020; 147:dev189175. [PMID: 32467233 DOI: 10.1242/dev.189175] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/16/2020] [Indexed: 12/19/2022]
Abstract
Nonsyndromic clefts of the lip and palate are common birth defects resulting from gene-gene and gene-environment interactions. Mutations in human MSX1 have been linked to orofacial clefting and we show here that Msx1 deficiency causes a growth defect of the medial nasal process (Mnp) in mouse embryos. Although this defect alone does not disrupt lip formation, Msx1-deficient embryos develop a cleft lip when the mother is transiently exposed to reduced oxygen levels or to phenytoin, a drug known to cause embryonic hypoxia. In the absence of interacting environmental factors, the Mnp growth defect caused by Msx1 deficiency is modified by a Pax9-dependent 'morphogenetic regulation', which modulates Mnp shape, rescues lip formation and involves a localized abrogation of Bmp4-mediated repression of Pax9 Analyses of GWAS data revealed a genome-wide significant association of a Gene Ontology morphogenesis term (including assigned roles for MSX1, MSX2, PAX9, BMP4 and GREM1) specifically for nonsyndromic cleft lip with cleft palate. Our data indicate that MSX1 mutations could increase the risk for cleft lip formation by interacting with an impaired morphogenetic regulation that adjusts Mnp shape, or through interactions that inhibit Mnp growth.
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Affiliation(s)
- Mitsushiro Nakatomi
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne NE1 3BZ, UK
- Division of Anatomy, Department of Health Promotion, Kyushu Dental University, Kitakyushu 803-8580, Japan
| | - Kerstin U Ludwig
- Institute of Human Genetics, University Hospital Bonn, 53127 Bonn, Germany
| | - Michael Knapp
- Institute of Medical Biometry, Informatics and Epidemiology, University of Bonn, 53127 Bonn, Germany
| | - Ralf Kist
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne NE1 3BZ, UK
- School of Dental Sciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4BW, UK
| | - Steven Lisgo
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne NE1 3BZ, UK
| | - Hayato Ohshima
- Division of Anatomy and Cell Biology of the Hard Tissue, Department of Tissue Regeneration and Reconstruction, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8514, Japan
| | - Elisabeth Mangold
- Institute of Human Genetics, University Hospital Bonn, 53127 Bonn, Germany
| | - Heiko Peters
- Biosciences Institute, Newcastle University, International Centre for Life, Newcastle upon Tyne NE1 3BZ, UK
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26
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Craniofacial Analysis May Indicate Co-Occurrence of Skeletal Malocclusions and Associated Risks in Development of Cleft Lip and Palate. J Dev Biol 2020; 8:jdb8010002. [PMID: 32012961 PMCID: PMC7151201 DOI: 10.3390/jdb8010002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/21/2020] [Accepted: 01/23/2020] [Indexed: 12/22/2022] Open
Abstract
Non-syndromic orofacial clefts encompass a range of morphological changes affecting the oral cavity and the craniofacial skeleton, of which the genetic and epigenetic etiologic factors remain largely unknown. The objective of this study is to explore the contribution of underlying dentofacial deformities (also known as skeletal malocclusions) in the craniofacial morphology of non-syndromic cleft lip and palate patients (nsCLP). For that purpose, geometric morphometric analysis was performed using full skull cone beam computed tomography (CBCT) images of patients with nsCLP (n = 30), normocephalic controls (n = 60), as well as to sex- and ethnicity- matched patients with an equivalent dentofacial deformity (n = 30). Our outcome measures were shape differences among the groups quantified via principal component analysis and associated principal component loadings, as well as mean shape differences quantified via a Procrustes distance among groups. According to our results, despite the shape differences among all three groups, the nsCLP group shares many morphological similarities in the maxilla and mandible with the dentofacial deformity group. Therefore, the dentoskeletal phenotype in nsCLP could be the result of the cleft and the coexisting dentofacial deformity and not simply the impact of the cleft.
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27
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Saleem K, Zaib T, Sun W, Fu S. Assessment of candidate genes and genetic heterogeneity in human non syndromic orofacial clefts specifically non syndromic cleft lip with or without palate. Heliyon 2019; 5:e03019. [PMID: 31886431 PMCID: PMC6921104 DOI: 10.1016/j.heliyon.2019.e03019] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 11/25/2019] [Accepted: 12/06/2019] [Indexed: 12/26/2022] Open
Abstract
Non syndromic orofacial clefts specifically non-syndromic cleft lip/palate are one of the most common craniofacial malformation among birth defects in human having multifactorial etiology with an incidence of 1:700/1000. On the basis of association with other congenital malformations or their presence as isolated anomaly, OFC can be classified as syndromic (30%) and nonsyndromic (70%) respectively. The major cause of disease demonstrates complex interplay between genetic and environmental factors. The pathogenic mechanism of underlying factors have been provided by different genetic studies on large-scale with significant recent advances in genotyping technologies usually based on linkage or genome wide association studies (GWAS). On the basis of recent studies, new tools to identify causative genes involved in NSCL/P reported approximately more than 30 genetic risk loci that are responsible for pathogenesis of facial deformation. Despite these findings, it is still uncertain that how much of variance in NSCL/P predisposing factors can be explain by identified risk loci, as they all together accounts for only 20%-25% of NSCL/P heritability. So there is need of further findings about the problem of rare low frequency coding variants and other missing responsive factors or genetic modifiers. This review will described those potential genes and loci reported in different studies whose involvement in pathogenesis of nonsyndromic OFC has wide scientific evidence.
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Affiliation(s)
- Komal Saleem
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China.,Key Laboratory of Preservation of Human Genetics Resources and Disease Control in China (Harbin Medical University), Ministry of Education, China
| | - Tahir Zaib
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China.,Key Laboratory of Preservation of Human Genetics Resources and Disease Control in China (Harbin Medical University), Ministry of Education, China
| | - Wenjing Sun
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China.,Key Laboratory of Preservation of Human Genetics Resources and Disease Control in China (Harbin Medical University), Ministry of Education, China
| | - Songbin Fu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China.,Key Laboratory of Preservation of Human Genetics Resources and Disease Control in China (Harbin Medical University), Ministry of Education, China
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28
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van Rooij IALM, Ludwig KU, Welzenbach J, Ishorst N, Thonissen M, Galesloot TE, Ongkosuwito E, Bergé SJ, Aldhorae K, Rojas-Martinez A, Kiemeney LALM, Vermeesch JR, Brunner H, Roeleveld N, Devriendt K, Dormaar T, Hens G, Knapp M, Carels C, Mangold E. Non-Syndromic Cleft Lip with or without Cleft Palate: Genome-Wide Association Study in Europeans Identifies a Suggestive Risk Locus at 16p12.1 and Supports SH3PXD2A as a Clefting Susceptibility Gene. Genes (Basel) 2019; 10:genes10121023. [PMID: 31817908 PMCID: PMC6947597 DOI: 10.3390/genes10121023] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/04/2019] [Accepted: 12/05/2019] [Indexed: 01/16/2023] Open
Abstract
Non-syndromic cleft lip with or without cleft palate (nsCL/P) ranks among the most common human congenital malformations, and has a multifactorial background in which both exogenous and genetic risk factors act in concert. The present report describes a genome-wide association study (GWAS) involving a total of 285 nsCL/P patients and 1212 controls from the Netherlands and Belgium. Twenty of the 40 previously reported nsC/LP susceptibility loci were replicated, which underlined the validity of this sample. SNV-based analysis of the data identified an as yet unreported suggestive locus at chromosome 16p12.1 (p-value of the lead SNV: 4.17 × 10-7). This association was replicated in two of three patient/control replication series (Central European and Yemeni). Gene analysis of the GWAS data prioritized SH3PXD2A at chromosome 10q24.33 as a candidate gene for nsCL/P. To date, support for this gene as a cleft gene has been restricted to data from zebrafish and a knockout mouse model. The present GWAS was the first to implicate SH3PXD2A in non-syndromic cleft formation in humans. In summary, although performed in a relatively small sample, the present GWAS generated novel insights into nsCL/P etiology.
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Affiliation(s)
- Iris ALM van Rooij
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud university medical center, 6500 HB Nijmegen, The Netherlands; (I.A.v.R.); (T.E.G.); (L.A.K.); (N.R.)
| | - Kerstin U Ludwig
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; (K.U.L.); (J.W.); (N.I.)
| | - Julia Welzenbach
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; (K.U.L.); (J.W.); (N.I.)
| | - Nina Ishorst
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; (K.U.L.); (J.W.); (N.I.)
| | - Michelle Thonissen
- Department of Dentistry, Radboud Institute for Health Sciences, Section of Orthodontics and Craniofacial Biology, Radboud university medical center, 6500 HB Nijmegen, The Netherlands; (M.T.); (E.O.)
| | - Tessel E Galesloot
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud university medical center, 6500 HB Nijmegen, The Netherlands; (I.A.v.R.); (T.E.G.); (L.A.K.); (N.R.)
| | - Edwin Ongkosuwito
- Department of Dentistry, Radboud Institute for Health Sciences, Section of Orthodontics and Craniofacial Biology, Radboud university medical center, 6500 HB Nijmegen, The Netherlands; (M.T.); (E.O.)
| | - Stefaan J Bergé
- Department of Oral and Maxillofacial Surgery, Radboud university medical center, 6500 HB Nijmegen, The Netherlands;
| | - Khalid Aldhorae
- Orthodontic Department, College of Dentistry, Thamar University, Thamar, Yemen;
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, School of Medicine, and Universidad Autonoma de Nuevo Leon, Centro de Investigación y Desarrollo en Ciencias de la Salud, Monterrey 64460, Mexico;
| | - Lambertus ALM Kiemeney
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud university medical center, 6500 HB Nijmegen, The Netherlands; (I.A.v.R.); (T.E.G.); (L.A.K.); (N.R.)
- Department of Urology, Radboud Institute for Health Sciences, Radboud university medical center, 6500 HB Nijmegen, The Netherlands
| | | | - Han Brunner
- Department of Human Genetics, and Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6500 HB Nijmgen, The Netherlands;
- Department of Clinical Genetics, and GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, 6202 AZ Maastricht, The Netherlands
| | - Nel Roeleveld
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud university medical center, 6500 HB Nijmegen, The Netherlands; (I.A.v.R.); (T.E.G.); (L.A.K.); (N.R.)
| | - Koen Devriendt
- Center for Human Genetics, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium;
| | - Titiaan Dormaar
- Department of Imaging and Pathology, KU Leuven, 3000 Leuven, Belgium;
- Oral and Maxillofacial Surgery, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Greet Hens
- Department of Neurosciences, Experimental Otorhinolaryngology, KU Leuven, 3000 Leuven, Belgium;
| | - Michael Knapp
- Institute of Medical Biometry, Informatics and Epidemiology, University of Bonn, 53127 Bonn, Germany;
| | - Carine Carels
- Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium (C.C.)
- Department of Human Genetics, and Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, 6500 HB Nijmgen, The Netherlands;
- Orthodontics, University Hospitals KU Leuven, 3000 Leuven, Belgium
| | - Elisabeth Mangold
- Institute of Human Genetics, University of Bonn, 53127 Bonn, Germany; (K.U.L.); (J.W.); (N.I.)
- Correspondence: ; Tel.: +49-228-28751008
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29
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The functional variant of NTN1 contributes to the risk of nonsyndromic cleft lip with or without cleft palate. Eur J Hum Genet 2019; 28:453-460. [PMID: 31780810 PMCID: PMC7080719 DOI: 10.1038/s41431-019-0549-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/22/2019] [Accepted: 10/29/2019] [Indexed: 11/09/2022] Open
Abstract
Previous genome-wide association study of nonsyndromic cleft lip with or without cleft palate (NSCL/P) identified a susceptible variant (rs4791774). We hypothesized that the functional single nucleotide polymorphism (SNP) may be in linkage disequilibrium with this lead SNP. The potential functional SNP (rs4791331) was identified by bioinformatic analysis. A case–control study with 891 orofacial cleft cases and 830 controls was designed to investigate its association with orofacial cleft. The allele-specific DNA-protein binding preference was predicted by JASPAR database. Cell proliferation, cycle and apoptosis, luciferase activity and netrin-1 (NTN1) expression were examined after transfection with the rs4791331 C/T vector in HEK-293 and HEPM cell lines. Forty-six lip tissues of NSCL/P patients were collected to detect NTN1 expression. ntn1a knockout zebrafish models were generated by CRISPR/Cas9 and observed with micro-CT. In the case–control study, the rs4791331-T allele was associated with an increased risk of nonsyndromic orofacial cleft (OR = 1.41, 95% CI = 1.19–1.68), as well as the subgroups cleft lip only (OR = 1.46, 95% CI = 1.14–1.87) and cleft lip and palate (OR = 1.58, 95% CI = 1.27–1.96). The T allele of rs4791331 exhibited anti-apoptotic effects and promoted cell cycle progression at the G1/S transition. Decreased enhancer activity and reduced NTN1 expression following transfection of the T allele were observed. Carriers of the CT/TT genotypes showed significantly lower expression of NTN1 than CC carriers. The ntn1a−/− zebrafish showed relatively wider intermaxillary fissures. These results indicate that rs4791331 (C > T) disrupted motif binding and led to abnormal expression of NTN1, which may be involved in the development of NSCL/P.
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30
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Xiong Z, Dankova G, Howe LJ, Lee MK, Hysi PG, de Jong MA, Zhu G, Adhikari K, Li D, Li Y, Pan B, Feingold E, Marazita ML, Shaffer JR, McAloney K, Xu SH, Jin L, Wang S, de Vrij FMS, Lendemeijer B, Richmond S, Zhurov A, Lewis S, Sharp GC, Paternoster L, Thompson H, Gonzalez-Jose R, Bortolini MC, Canizales-Quinteros S, Gallo C, Poletti G, Bedoya G, Rothhammer F, Uitterlinden AG, Ikram MA, Wolvius E, Kushner SA, Nijsten TEC, Palstra RJTS, Boehringer S, Medland SE, Tang K, Ruiz-Linares A, Martin NG, Spector TD, Stergiakouli E, Weinberg SM, Liu F, Kayser M. Novel genetic loci affecting facial shape variation in humans. eLife 2019; 8:e49898. [PMID: 31763980 PMCID: PMC6905649 DOI: 10.7554/elife.49898] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 11/22/2019] [Indexed: 12/14/2022] Open
Abstract
The human face represents a combined set of highly heritable phenotypes, but knowledge on its genetic architecture remains limited, despite the relevance for various fields. A series of genome-wide association studies on 78 facial shape phenotypes quantified from 3-dimensional facial images of 10,115 Europeans identified 24 genetic loci reaching study-wide suggestive association (p < 5 × 10-8), among which 17 were previously unreported. A follow-up multi-ethnic study in additional 7917 individuals confirmed 10 loci including six unreported ones (padjusted < 2.1 × 10-3). A global map of derived polygenic face scores assembled facial features in major continental groups consistent with anthropological knowledge. Analyses of epigenomic datasets from cranial neural crest cells revealed abundant cis-regulatory activities at the face-associated genetic loci. Luciferase reporter assays in neural crest progenitor cells highlighted enhancer activities of several face-associated DNA variants. These results substantially advance our understanding of the genetic basis underlying human facial variation and provide candidates for future in-vivo functional studies.
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Affiliation(s)
- Ziyi Xiong
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
- Department of EpidemiologyErasmus MC University Medical Center RotterdamRotterdamNetherlands
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of GenomicsUniversity of Chinese Academy of Sciences (CAS)BeijingChina
| | - Gabriela Dankova
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Laurence J Howe
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
| | - Myoung Keun Lee
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
| | - Pirro G Hysi
- Department of Twin Research and Genetic EpidemiologyKing’s College LondonLondonUnited Kingdom
| | - Markus A de Jong
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
- Department of Oral & Maxillofacial Surgery, Special Dental Care, and OrthodonticsErasmus MC University Medical Center RotterdamRotterdamNetherlands
- Department of Biomedical Data SciencesLeiden University Medical CenterLeidenNetherlands
| | - Gu Zhu
- QIMR Berghofer Medical Research InstituteBrisbaneAustralia
| | - Kaustubh Adhikari
- Department of Genetics, Evolution, and EnvironmentUniversity College LondonLondonUnited Kingdom
| | - Dan Li
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
| | - Yi Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of GenomicsUniversity of Chinese Academy of Sciences (CAS)BeijingChina
| | - Bo Pan
- Department of Auricular ReconstructionPlastic Surgery HospitalBeijingChina
| | - Eleanor Feingold
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
- Department of Human GeneticsUniversity of PittsburghPittsburghUnited States
| | - John R Shaffer
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
- Department of Human GeneticsUniversity of PittsburghPittsburghUnited States
| | | | - Shu-Hua Xu
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
| | - Li Jin
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life SciencesFudan UniversityShanghaiChina
| | - Sijia Wang
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
| | - Femke MS de Vrij
- Department of PsychiatryErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Bas Lendemeijer
- Department of PsychiatryErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Stephen Richmond
- Applied Clinical Research and Public Health, University Dental SchoolCardiff UniversityCardiffUnited Kingdom
| | - Alexei Zhurov
- Applied Clinical Research and Public Health, University Dental SchoolCardiff UniversityCardiffUnited Kingdom
| | - Sarah Lewis
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
| | - Gemma C Sharp
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
- School of Oral and Dental SciencesUniversity of BristolBristolUnited Kingdom
| | - Lavinia Paternoster
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
| | - Holly Thompson
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
| | - Rolando Gonzalez-Jose
- Instituto Patagonico de Ciencias Sociales y Humanas, CENPAT-CONICETPuerto MadrynArgentina
| | | | - Samuel Canizales-Quinteros
- UNAM-Instituto Nacional de Medicina Genomica, Facultad de QuımicaUnidad de Genomica de Poblaciones Aplicada a la SaludMexico CityMexico
| | - Carla Gallo
- Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y FilosofıaUniversidad Peruana Cayetano HerediaLimaPeru
| | - Giovanni Poletti
- Laboratorios de Investigacion y Desarrollo, Facultad de Ciencias y FilosofıaUniversidad Peruana Cayetano HerediaLimaPeru
| | - Gabriel Bedoya
- GENMOL (Genetica Molecular)Universidad de AntioquiaMedellınColombia
| | | | - André G Uitterlinden
- Department of EpidemiologyErasmus MC University Medical Center RotterdamRotterdamNetherlands
- Department of Internal MedicineErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - M Arfan Ikram
- Department of EpidemiologyErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Eppo Wolvius
- Department of Oral & Maxillofacial Surgery, Special Dental Care, and OrthodonticsErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Steven A Kushner
- Department of PsychiatryErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Tamar EC Nijsten
- Department of DermatologyErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Robert-Jan TS Palstra
- Department of BiochemistryErasmus MC University Medical Center RotterdamRotterdamNetherlands
| | - Stefan Boehringer
- Department of Biomedical Data SciencesLeiden University Medical CenterLeidenNetherlands
| | | | - Kun Tang
- CAS Key Laboratory of Computational BiologyChinese Academy of Sciences (CAS)ShanghaiChina
- CAS-MPG Partner Institute for Computational Biology (PICB)Chinese Academy of Sciences (CAS)ShanghaiChina
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological SciencesChinese Academy of Sciences (CAS)ShanghaiChina
| | - Andres Ruiz-Linares
- State Key Laboratory of Genetic Engineering, School of Life SciencesFudan UniversityShanghaiChina
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life SciencesFudan UniversityShanghaiChina
- Aix-Marseille Université, CNRS, EFS, ADESMarseilleFrance
| | | | - Timothy D Spector
- Department of Twin Research and Genetic EpidemiologyKing’s College LondonLondonUnited Kingdom
| | - Evie Stergiakouli
- Medical Research Council Integrative Epidemiology Unit, Population Health SciencesUniversity of BristolBristolUnited Kingdom
- School of Oral and Dental SciencesUniversity of BristolBristolUnited Kingdom
| | - Seth M Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral BiologyUniversity of PittsburghPittsburghUnited States
- Department of Human GeneticsUniversity of PittsburghPittsburghUnited States
- Department of AnthropologyUniversity of PittsburghPittsburghUnited States
| | - Fan Liu
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of GenomicsUniversity of Chinese Academy of Sciences (CAS)BeijingChina
| | - Manfred Kayser
- Department of Genetic IdentificationErasmus MC University Medical Center RotterdamRotterdamNetherlands
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31
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Huang L, Jia Z, Shi Y, Du Q, Shi J, Wang Z, Mou Y, Wang Q, Zhang B, Wang Q, Ma S, Lin H, Duan S, Yin B, Lin Y, Wang Y, Jiang D, Hao F, Zhang L, Wang H, Jiang S, Xu H, Yang C, Li C, Li J, Shi B, Yang Z. Genetic factors define CPO and CLO subtypes of nonsyndromicorofacial cleft. PLoS Genet 2019; 15:e1008357. [PMID: 31609978 PMCID: PMC6812857 DOI: 10.1371/journal.pgen.1008357] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 10/24/2019] [Accepted: 08/07/2019] [Indexed: 02/05/2023] Open
Abstract
Nonsyndromic orofacial cleft (NSOFC) is a severe birth defect that occurs early in embryonic development and includes the subtypes cleft palate only (CPO), cleft lip only (CLO) and cleft lip with cleft palate (CLP). Given a lack of specific genetic factor analysis for CPO and CLO, the present study aimed to dissect the landscape of genetic factors underlying the pathogenesis of these two subtypes using 6,986 cases and 10,165 controls. By combining a genome-wide association study (GWAS) for specific subtypes of CPO and CLO, as well as functional gene network and ontology pathway analysis, we identified 18 genes/loci that surpassed genome-wide significance (P < 5 × 10−8) responsible for NSOFC, including nine for CPO, seven for CLO, two for both conditions and four that contribute to the CLP subtype. Among these 18 genes/loci, 14 are novel and identified in this study and 12 contain developmental transcription factors (TFs), suggesting that TFs are the key factors for the pathogenesis of NSOFC subtypes. Interestingly, we observed an opposite effect of the genetic variants in the IRF6 gene for CPO and CLO. Moreover, the gene expression dosage effect of IRF6 with two different alleles at the same single-nucleotide polymorphism (SNP) plays important roles in driving CPO or CLO. In addition, PAX9 is a key TF for CPO. Our findings define subtypes of NSOFC using genetic factors and their functional ontologies and provide a clue to improve their diagnosis and treatment in the future. Although GWAS have discovered 43 genes/loci associated with NSOFC, most previous studies used mixed samples of CL/P subtypes rather than CPO or CLO separately. Our findings define the CPO and CLO subtypes using genetic factors and their functional ontologies based on CPO and CLO GWAS data. In this study, we identified 18 genes/loci that contribute to CPO, CLO or CLP. Fourteen of them are novel and identified, and 12 contain developmental transcription factors (TFs), suggesting that TFs are the key factors for the pathogenesis of NSOFC subtypes. We observed an opposite effect in the strongest associated locus IRF6 for CPO and CLO; this information was omitted by previous CL/P GWAS. Furthermore, we reveal that the gene expression dosage of IRF6 plays important roles in driving CPO or CLO. In addition, we found that PAX9 is a strong genetic factor for CPO. These results suggest that transcription factors are the key genetic reason for the pathogenesis of NSOFC subtypes.
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Affiliation(s)
- Lulin Huang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Clinical Laboratory, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhonglin Jia
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yi Shi
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Clinical Laboratory, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- Institute of Chengdu Biology, and Sichuan Translational Medicine Hospital, Chinese Academy of Sciences, Chengdu, China
| | - Qin Du
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Clinical Laboratory, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- Institute of Chengdu Biology, and Sichuan Translational Medicine Hospital, Chinese Academy of Sciences, Chengdu, China
- Department of Stomatology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Jiayu Shi
- Division of Growth and Development and Section of Orthodontics, School of Dentistry, University of California, Los Angeles, United States of America
| | - Ziyan Wang
- Department of basic medicine, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yandong Mou
- Department of Stomatology, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Qingwei Wang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Clinical Laboratory, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- Institute of Chengdu Biology, and Sichuan Translational Medicine Hospital, Chinese Academy of Sciences, Chengdu, China
| | - Bihe Zhang
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Qing Wang
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Shi Ma
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Clinical Laboratory, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - He Lin
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Clinical Laboratory, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Shijun Duan
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Bin Yin
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yansong Lin
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yiru Wang
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Dan Jiang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Clinical Laboratory, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Fang Hao
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Clinical Laboratory, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Lin Zhang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Clinical Laboratory, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Haixin Wang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Clinical Laboratory, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Suyuan Jiang
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Huijuan Xu
- Institute of Chengdu Biology, and Sichuan Translational Medicine Hospital, Chinese Academy of Sciences, Chengdu, China
| | - Chengwei Yang
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Chenghao Li
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jingtao Li
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Bing Shi
- State Key Laboratory of Oral Diseases and National Clinical Research Center for Oral Diseases and Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhenglin Yang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Clinical Laboratory, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- Institute of Chengdu Biology, and Sichuan Translational Medicine Hospital, Chinese Academy of Sciences, Chengdu, China
- Department of basic medicine, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- * E-mail:
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Wilderman A, VanOudenhove J, Kron J, Noonan JP, Cotney J. High-Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development. Cell Rep 2019; 23:1581-1597. [PMID: 29719267 PMCID: PMC5965702 DOI: 10.1016/j.celrep.2018.03.129] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/05/2017] [Accepted: 03/28/2018] [Indexed: 11/29/2022] Open
Abstract
Defects in patterning during human embryonic development frequently result in craniofacial abnormalities. The gene regulatory programs that build the craniofacial complex are likely controlled by information located between genes and within intronic sequences. However, systematic identification of regulatory sequences important for forming the human face has not been performed. Here, we describe comprehensive epigenomic annotations from human embryonic craniofacial tissues and systematic comparisons with multiple tissues and cell types. We identified thousands of tissue-specific craniofacial regulatory sequences and likely causal regions for rare craniofacial abnormalities. We demonstrate significant enrichment of common variants associated with orofacial clefting in enhancers active early in embryonic development, while those associated with normal facial variation are enriched near the end of the embryonic period. These data are provided in easily accessible formats for both craniofacial researchers and clinicians to aid future experimental design and interpretation of noncoding variation in those affected by craniofacial abnormalities.
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Affiliation(s)
- Andrea Wilderman
- Graduate Program in Genetics and Developmental Biology, UConn Health, Farmington, CT 06030, USA; Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA
| | | | - Jeffrey Kron
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA
| | - James P Noonan
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Kavli Institute for Neuroscience, Yale University, New Haven, CT 06520, USA
| | - Justin Cotney
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA.
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Carlson JC, Anand D, Butali A, Buxo CJ, Christensen K, Deleyiannis F, Hecht JT, Moreno LM, Orioli IM, Padilla C, Shaffer JR, Vieira AR, Wehby GL, Weinberg SM, Murray JC, Beaty TH, Saadi I, Lachke SA, Marazita ML, Feingold E, Leslie EJ. A systematic genetic analysis and visualization of phenotypic heterogeneity among orofacial cleft GWAS signals. Genet Epidemiol 2019; 43:704-716. [PMID: 31172578 PMCID: PMC6687557 DOI: 10.1002/gepi.22214] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 03/29/2019] [Accepted: 04/17/2019] [Indexed: 12/17/2022]
Abstract
Phenotypic heterogeneity is a hallmark of complex traits, and genetic studies of such traits may focus on them as a single diagnostic entity or by analyzing specific components. For example, in orofacial clefting (OFC), three subtypes-cleft lip (CL), cleft lip and palate (CLP), and cleft palate (CP) have been studied separately and in combination. To further dissect the genetic architecture of OFCs and how a given associated locus may be contributing to distinct subtypes of a trait we developed a framework for quantifying and interpreting evidence of subtype-specific or shared genetic effects in complex traits. We applied this technique to create a "cleft map" of the association of 30 genetic loci with three OFC subtypes. In addition to new associations, we found loci with subtype-specific effects (e.g., GRHL3 [CP], WNT5A [CLP]), as well as loci associated with two or all three subtypes. We cross-referenced these results with mouse craniofacial gene expression datasets, which identified additional promising candidate genes. However, we found no strong correlation between OFC subtypes and expression patterns. In aggregate, the cleft map revealed that neither subtype-specific nor shared genetic effects operate in isolation in OFC architecture. Our approach can be easily applied to any complex trait with distinct phenotypic subgroups.
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Affiliation(s)
- Jenna C. Carlson
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
| | - Azeez Butali
- Department of Oral Pathology, Radiology and Medicine, University of Iowa, IA 52242, USA
| | - Carmen J. Buxo
- Dental and Craniofacial Genomics Core, School of Dental Medicine, University of Puerto Rico, San Juan, Puerto Rico, 00936, USA
| | - Kaare Christensen
- Department of Epidemiology, Institute of Public Health, University of Southern Denmark, Odense, DK-5230, Denmark
| | | | - Jacqueline T. Hecht
- Department of Pediatrics, McGovern Medical School and School of Dentistry UT Health at Houston, Houston, TX, 77030, USA
| | - Lina M. Moreno
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Ieda M. Orioli
- INAGEMP (National Institute of Population Medical Genetics), Porto Alegre, 91501-970, Brazil
- ECLAMC (Latin American Collaborative Study of Congenital Malformations) at Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Carmencita Padilla
- Department of Pediatrics, College of Medicine; Institute of Human Genetics, National Institutes of Health; University of the Philippines Manila, Manila, 1000, The Philippines
- Philippine Genome Center, University of the Philippines System, Quezon City, 1101, The Philippines
| | - John R. Shaffer
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh PA,15219, USA
| | - Alexandre R. Vieira
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh PA,15219, USA
| | - George L. Wehby
- Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, IA, 52242, USA
| | - Seth M. Weinberg
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh PA,15219, USA
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, and Clinical and Translational Science, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15219, USA
| | - Jeffrey C. Murray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa,52242, USA
| | - Terri H. Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore MD, 21205, USA
| | - Irfan Saadi
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160 USA
| | - Salil A. Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE 19716 USA
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19716 USA
| | - Mary L. Marazita
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh PA,15219, USA
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, and Clinical and Translational Science, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15219, USA
| | - Eleanor Feingold
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, and Clinical and Translational Science, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15219, USA
| | - Elizabeth J. Leslie
- Department of Human Genetics, Emory University School of Medicine, Emory University, Atlanta, GA, 30322, USA
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Meng P, Zhao H, Huang W, Zhang Y, Zhong W, Zhang M, Jia P, Zhou Z, Maimaitili G, Chen F, Zhang J, Lin J. Three GLI2 mutations combined potentially underlie non-syndromic cleft lip with or without cleft palate in a Chinese pedigree. Mol Genet Genomic Med 2019; 7:e714. [PMID: 31386309 PMCID: PMC6732289 DOI: 10.1002/mgg3.714] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 02/03/2019] [Accepted: 04/16/2019] [Indexed: 12/28/2022] Open
Abstract
Background Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is the most common craniofacial birth defect. Its etiology is complex and it has a lifelong influence on affected individuals. Despite many studies, the pathogenic gene alleles are not completely clear. Here, we recruited a Chinese NSCL/P family and explored the candidate causative variants in this pedigree. Methods We performed whole‐exome sequencing on two patients and two unaffected subjects of this family. Variants were screened based on bioinformatics analysis to identify the potential etiological alleles. Species conservation analysis, mutation function prediction, and homology protein modeling were also performed to preliminarily evaluate the influence of the mutations. Results We identified three rare mutations that are located on a single chromatid (c.2684C > T_p.Ala895Val, c.4350G > T_p.Gln1450His, and c.4622C > A_p.Ser1541Tyr) in GLI2 as candidate causative variants. All of these three mutations were predicted to be deleterious, and they affect amino acids that are conserved in many species. The mutation c.2684C > T was predicted to affect the structure of the GLI2 protein. Conclusion Our results further demonstrate that GLI2 variants play a role in the pathogenesis of NSCL/P, and the three rare missense mutations combined are probably the potential disease‐causing variants in this family.
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Affiliation(s)
- Peiqi Meng
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, PR China
| | - Huaxiang Zhao
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, PR China
| | - Wenbin Huang
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, PR China
| | - Yunfan Zhang
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, PR China
| | - Wenjie Zhong
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, PR China
| | - Mengqi Zhang
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, PR China
| | - Peizeng Jia
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, PR China
| | - Zhibo Zhou
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, PR China
| | - Gulibaha Maimaitili
- Department of Stomatology, The Fifth Affiliated Hospital of Xinjiang Medical University, Urumqi, PR China
| | - Feng Chen
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, PR China
| | - Jieni Zhang
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, PR China
| | - Jiuxiang Lin
- Department of Orthodontics, Peking University School and Hospital of Stomatology, Beijing, PR China
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Lin-Shiao E, Lan Y, Welzenbach J, Alexander KA, Zhang Z, Knapp M, Mangold E, Sammons M, Ludwig KU, Berger SL. p63 establishes epithelial enhancers at critical craniofacial development genes. SCIENCE ADVANCES 2019; 5:eaaw0946. [PMID: 31049400 PMCID: PMC6494499 DOI: 10.1126/sciadv.aaw0946] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/19/2019] [Indexed: 05/15/2023]
Abstract
The transcription factor p63 is a key mediator of epidermal development. Point mutations in p63 in patients lead to developmental defects, including orofacial clefting. To date, knowledge on how pivotal the role of p63 is in human craniofacial development is limited. Using an inducible transdifferentiation model, combined with epigenomic sequencing and multicohort meta-analysis of genome-wide association studies data, we show that p63 establishes enhancers at craniofacial development genes to modulate their transcription. Disease-specific substitution mutation in the DNA binding domain or sterile alpha motif protein interaction domain of p63, respectively, eliminates or reduces establishment of these enhancers. We show that enhancers established by p63 are highly enriched for single-nucleotide polymorphisms associated with nonsyndromic cleft lip ± cleft palate (CL/P). These orthogonal approaches indicate a strong molecular link between p63 enhancer function and CL/P, illuminating molecular mechanisms underlying this developmental defect and revealing vital regulatory elements and new candidate causative genes.
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Affiliation(s)
- Enrique Lin-Shiao
- Departments of Cell and Developmental Biology and Epigenetics Institute, Philadelphia, PA 19104, USA
- Biochemistry and Molecular Biophysics, Biomedical Sciences Graduate Program, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Yemin Lan
- Departments of Cell and Developmental Biology and Epigenetics Institute, Philadelphia, PA 19104, USA
| | - Julia Welzenbach
- Institute of Human Genetics, University Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Katherine A Alexander
- Departments of Cell and Developmental Biology and Epigenetics Institute, Philadelphia, PA 19104, USA
| | - Zhen Zhang
- Departments of Cell and Developmental Biology and Epigenetics Institute, Philadelphia, PA 19104, USA
| | - Michael Knapp
- Institute of Medical Biometry, Informatics and Epidemiology, University of Bonn, Bonn, Germany
| | - Elisabeth Mangold
- Institute of Human Genetics, University Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Morgan Sammons
- Departments of Cell and Developmental Biology and Epigenetics Institute, Philadelphia, PA 19104, USA
| | - Kerstin U Ludwig
- Institute of Human Genetics, University Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Shelley L Berger
- Departments of Cell and Developmental Biology and Epigenetics Institute, Philadelphia, PA 19104, USA
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Xu Z, Lie RT, Wilcox AJ, Saugstad OD, Taylor JA. A comparison of DNA methylation in newborn blood samples from infants with and without orofacial clefts. Clin Epigenetics 2019; 11:40. [PMID: 30832715 PMCID: PMC6399917 DOI: 10.1186/s13148-019-0638-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 02/20/2019] [Indexed: 01/08/2023] Open
Abstract
Background Isolated orofacial clefts are among the most common congenital birth defects. Although the underlying biological mechanisms remain largely unknown, clefts are thought to be complex disorders influenced by genetic, environmental, and potentially epigenetic factors. Methods In blood samples from 2- to 3-day-old infants (n = 747) collected in a nationwide population-based study of orofacial clefts in Norway, we measured DNA methylation profiles for more than 450,000 CpGs and then conducted epigenome-wide association analyses (EWAS). We tested methylation profile difference at each CpG between controls (n = 436) and each of the cleft subtypes (92 cleft lip only, CLO; 84 cleft palate only, CPO; 132 cleft lip and palate, CLP). We also compared controls to various combinations of case groups and compared case subtypes to each other. Finally, using the EWAS results, we searched for larger differentially methylated regions (DMRs) associated with orofacial clefts. Results In EWAS comparing controls to individual cleft subtypes, we found no significant associations at a Bonferroni P value threshold of 10−7. After pooling case groups, we found two significantly differentially methylated CpGs: cg09696939 near gene BICC1 is associated with CLO+CLP (P = 9.58 × 10−8); cg26985354 in gene CLASRP is associated with CPO+CLP (P = 7.38 × 10−8). In DMR analysis, we identified a total of 56 significant regions when comparing controls to individual cleft subtypes (10 for CLO, 6 for CPO, 41 for CLP). Only one DMR is shared among the three cleft groups. In combined case group analysis, we found 26 DMRs for CLP+CLO, 31 for CLP+CPO, and 37 when all subtypes are combined. Finally, in case-case comparisons of subtypes, we identified 10 DMRs when comparing CLP to CPO, 9 in CLP compared to CLO, and 13 in CLP compared to CPO. Conclusions We identified two individual CpGs and multiple DMRs that differ between controls and cleft case subtypes. Although we find some evidence for the possible role of DNA methylation in etiology of orofacial clefts, our study does not support previous reports of widespread differences in blood DNA methylation between babies with and without facial clefts. Electronic supplementary material The online version of this article (10.1186/s13148-019-0638-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zongli Xu
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - 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
| | - Allen J Wilcox
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Ola Didrik Saugstad
- Department of Pediatric Research, Oslo University Hospital, Oslo, Norway.,Department of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA. .,Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, NIH, P.O. Box 12233, Mail Drop A3-05, Research Triangle Park, NC, 27709, USA.
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Shaffer JR, LeClair J, Carlson JC, Feingold E, Buxó CJ, Christensen K, Deleyiannis FW, Field LL, Hecht JT, Moreno L, Orioli IM, Padilla C, Vieira AR, Wehby GL, Murray JC, Weinberg SM, Marazita ML, Leslie EJ. Association of low-frequency genetic variants in regulatory regions with nonsyndromic orofacial clefts. Am J Med Genet A 2019; 179:467-474. [PMID: 30582786 PMCID: PMC6374160 DOI: 10.1002/ajmg.a.61002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/06/2018] [Accepted: 11/01/2018] [Indexed: 01/24/2023]
Abstract
Genome-wide scans have shown that common risk alleles for orofacial clefts (OFC) tend to be located in noncoding regulatory elements and cumulatively explain only part of the heritability of OFCs. Low-frequency variants may account for some of the "missing" heritability. Therefore, we scanned low-frequency variants located within putative craniofacial enhancers to identify novel OFC risk variants and implicate new regulatory elements in OFC pathogenesis. Analyses were performed in a multiethnic sample of 1,995 cases of cleft lip with or without cleft palate (CL/P), 221 cases with cleft palate (CP) only, and 1,576 unaffected controls. One hundred and nineteen putative craniofacial enhancers identified from ChIP-Seq studies in craniofacial tissues or cell lines contained multiple low-frequency (0.01-1%) variants, which we genotyped in participants using a custom Illumina panel. Two complementary statistical approaches, sequence kernel association test and combined multivariate and collapsing, were used to test association of the aggregated low-frequency variants across each enhancer region with CL/P and CP. We discovered a significant association between CP and a branchial arch enhancer near FOXP1 (mm60; p-value = .0002). Additionally, we observed a suggestive association between CL/P and a forebrain enhancer near FOXE1 (hs1717; p-value = .001). These findings suggest that low-frequency variants in craniofacial enhancer regions contribute to the complex etiology of nonsyndromic OFCs.
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Affiliation(s)
- John R. Shaffer
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, 15219 USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261 USA
| | - Jessica LeClair
- formerly of Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Jenna C. Carlson
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, 15219 USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261 USA
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Eleanor Feingold
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261 USA
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Carmen J. Buxó
- Dental and Craniofacial Genomics Core, School of Dental Medicine, University of Puerto Rico, San Juan, Puerto Rico, 00936, USA
| | - Kaare Christensen
- Department of Epidemiology, Institute of Public Health, University of Southern Denmark, Odense, DK-5000, Denmark
| | - Frederic W.B. Deleyiannis
- Department of Surgery, Plastic and Reconstructive Surgery, University of Colorado School of Medicine, Denver, CO, 80045, USA
| | - L. Leigh Field
- Department of Medical Genetics, University of British Columbia, Vancouver, V6H 3N1, Canada
| | - Jacqueline T. Hecht
- Department of Pediatrics, McGovern Medical School and School of Dentistry UT Health at Houston, Houston, TX, 77030, USA
| | - Lina Moreno
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Ieda M. Orioli
- Department of Genetics, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, 21941-617, Brazil
- ECLAMC (Latin American Collaborative Study of Congenital Malformations) at INAGEMP (National Institute of Population Medical Genetics), Rio de Janeiro, 21941-617, Brazil
| | - Carmencita Padilla
- Department of Pediatrics, College of Medicine; and Institute of Human Genetics, National Institutes of Health; University of the Philippines Manila, Manila, The Philippines, 1000; and Philippine Genome Center, University of the Philippines System, Manila, The Philippines 1101
| | - Alexandre R. Vieira
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, 15219 USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261 USA
| | - George L. Wehby
- Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, IA, 52246, USA
| | - Jeffrey C. Murray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, Iowa, 52242, USA
| | - Seth M. Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, 15219 USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261 USA
- Department of Anthropology, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, 15219 USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15261 USA
- Clinical and Translational Science, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Elizabeth J. Leslie
- Department of Human Genetics, Emory University School of Medicine, Emory University, Atlanta, GA, 30322
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Li B, Ma L, Zhang C, Zhou Z, Yuan H, Jiang H, Pan Y, Tan Q. Associations of genetic variants in endocytic trafficking of epidermal growth factor receptor super pathway with risk of nonsyndromic cleft lip with or without cleft palate. Mol Genet Genomic Med 2018; 6:1157-1167. [PMID: 30411541 PMCID: PMC6305670 DOI: 10.1002/mgg3.497] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/03/2018] [Accepted: 10/02/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The genetic etiology of nonsyndromic cleft lip with or without cleft palate (NSCL/P) has not been fully clarified to date. Epidermal growth factor receptor (EGFR) was reportedly involved in its biological establishment and regulation of cell migration during the embryonic stage. METHODS We selected a super pathway of endocytic trafficking of EGFR and investigated the associations of single-nucleotide polymorphisms (SNPs) in the super pathway with the risk of NSCL/P by analyzing our published genome-wide association study (GWAS) data from 504 NSCL/P individuals and 455 controls. After the false discovery rate (FDR) control, we conducted linkage disequilibrium (LD) analyses and conditional regression analyses to obtain independent lead SNPs. We performed LD analyses between the lead SNPs and the reported SNPs to find novel ones from our study. We annotated the lead SNPs and investigated their mapped genes in silico. RESULTS A total of 82 SNPs showed a statistical association with the risk of NSCL/P after FDR control. They contained three reported SNPs which were g.117068049G>A (rs7078160), g.117086783C>G (rs10886040), and g.117101266G>T (rs17095681). Four independent lead SNPs were obtained, including g.116979803 T>C (rs1905539) and g.117037960A>G (rs7902502) at 10q25.3, g.35720163G>C (rs75656820) at 17q12, and g.156864512G>A (rs1800877) at 1q23.1. Three of them were in low LD (r2 < 0.5) with the reported SNPs except g.117037960A>G (rs7902502), so these three were newly identified. Lead SNPs were mapped to three genes: SHTN1, AP2B1, and NTRK1. The three genes were relatively more highly expressed in the human craniofacial region and in the proximal maxillary location during the craniofacial development stage of the embryonic mouse. CONCLUSION Our results suggested that SHTN1, AP2B1, and NTRK1 might be associated with the development of NSCL/P.
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Affiliation(s)
- Bing Li
- Department of Burns and Plastic Surgery, The Drum Tower Clinical Medical College, Nanjing Medical University, Nanjing, China.,Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Lan Ma
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Chi Zhang
- Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Zhixuan Zhou
- Department of Polyclinic, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Hua Yuan
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Hongbing Jiang
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Yongchu Pan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Qian Tan
- Department of Burns and Plastic Surgery, The Drum Tower Clinical Medical College, Nanjing Medical University, Nanjing, China.,Department of Burns and Plastic Surgery, Affiliated Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
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39
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Indencleef K, Roosenboom J, Hoskens H, White JD, Shriver MD, Richmond S, Peeters H, Feingold E, Marazita ML, Shaffer JR, Weinberg SM, Hens G, Claes P. Six NSCL/P Loci Show Associations With Normal-Range Craniofacial Variation. Front Genet 2018; 9:502. [PMID: 30410503 PMCID: PMC6210408 DOI: 10.3389/fgene.2018.00502] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 10/05/2018] [Indexed: 12/17/2022] Open
Abstract
Objectives: Orofacial clefting is one of the most prevalent craniofacial malformations. Previous research has demonstrated that unaffected relatives of patients with non-syndromic cleft lip with/without cleft palate (NSCL/P) show distinctive facial features, which can be an expression of underlying NSCL/P susceptibility genes. These results support the hypothesis that genes involved in the occurrence of a cleft also play a role in normal craniofacial development. In this study, we investigated the influence of genetic variants associated with NSCL/P on normal-range variation in facial shape. Methods: A literature review of genome wide association studies (GWAS) investigating the genetic etiology of NSCL/P was performed, resulting in a list of 75 single nucleotide polymorphisms (SNPs) located in 38 genetic loci. Genotype data were available for 65 of these selected SNPs in three datasets with a combined sample size of 7,418 participants of European ancestry, whose 3D facial images were also available. The effect of each SNP was tested using a multivariate canonical correlation analysis (CCA) against 63 hierarchically-constructed facial segments in each of the three datasets and meta-analyzed. This allowed for the investigation of associations between SNPs known to be involved in NSCL/P and normal-range facial shape variations in a global-to-local perspective, without preselecting specific facial shape features or characteristics. Results: Six NSCL/P SNPs showed significant associations with variation in normal-range facial morphology. rs6740960 showed significant effects in the chin area (p = 3.71 × 10−28). This SNP lies in a non-coding area. Another SNP, rs227731 near the NOG gene, showed a significant effect in the philtrum area (p = 1.96 × 10−16). Three SNPs showed significant effects on the shape of the nose. rs742071 (p = 8.71 × 10−14), rs34246903 (p = 6.87 × 10−12), and rs10512248 (p = 8.4 × 10−9). Respectively, these SNPs are annotated to PAX7, MSX1, and PTCH1. Finally, rs7590268, an intron variant of THADA, showed an effect in the shape of the supraorbital ridge (p = 3.84 × 10−7). Conclusions: This study provides additional evidence NSCL/P-associated genetic variants influence normal-range craniofacial morphology, with significant effects observed for the chin, the nose, the supraorbital ridges and the philtrum area.
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Affiliation(s)
- Karlijne Indencleef
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium.,Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
| | - Jasmien Roosenboom
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Hanne Hoskens
- Medical Imaging Research Center, UZ Leuven, Leuven, Belgium.,Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Julie D White
- Department of Anthropology, The Pennsylvania State University, University Park, PA, United States
| | - Mark D Shriver
- Department of Anthropology, The Pennsylvania State University, University Park, PA, United States
| | - Stephen Richmond
- Applied Clinical Research and Public Health, School of Dentistry, Cardiff University, College of Biomedical and Life Sciences, Heath Park, Cardiff, United Kingdom
| | - Hilde Peeters
- Department of Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Eleanor Feingold
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Mary L Marazita
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - John R Shaffer
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Seth M Weinberg
- Department of Oral Biology, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Greet Hens
- Department of Otorhinolaryngology, University Hospitals Leuven, Leuven, Belgium
| | - Peter Claes
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium.,Medical Imaging Research Center, UZ Leuven, Leuven, Belgium
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40
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Howe LJ, Lee MK, Sharp GC, Davey Smith G, St Pourcain B, Shaffer JR, Ludwig KU, Mangold E, Marazita ML, Feingold E, Zhurov A, Stergiakouli E, Sandy J, Richmond S, Weinberg SM, Hemani G, Lewis SJ. Investigating the shared genetics of non-syndromic cleft lip/palate and facial morphology. PLoS Genet 2018; 14:e1007501. [PMID: 30067744 PMCID: PMC6089455 DOI: 10.1371/journal.pgen.1007501] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 08/13/2018] [Accepted: 06/19/2018] [Indexed: 01/06/2023] Open
Abstract
There is increasing evidence that genetic risk variants for non-syndromic cleft lip/palate (nsCL/P) are also associated with normal-range variation in facial morphology. However, previous analyses are mostly limited to candidate SNPs and findings have not been consistently replicated. Here, we used polygenic risk scores (PRS) to test for genetic overlap between nsCL/P and seven biologically relevant facial phenotypes. Where evidence was found of genetic overlap, we used bidirectional Mendelian randomization (MR) to test the hypothesis that genetic liability to nsCL/P is causally related to implicated facial phenotypes. Across 5,804 individuals of European ancestry from two studies, we found strong evidence, using PRS, of genetic overlap between nsCL/P and philtrum width; a 1 S.D. increase in nsCL/P PRS was associated with a 0.10 mm decrease in philtrum width (95% C.I. 0.054, 0.146; P = 2x10-5). Follow-up MR analyses supported a causal relationship; genetic variants for nsCL/P homogeneously cause decreased philtrum width. In addition to the primary analysis, we also identified two novel risk loci for philtrum width at 5q22.2 and 7p15.2 in our Genome-wide Association Study (GWAS) of 6,136 individuals. Our results support a liability threshold model of inheritance for nsCL/P, related to abnormalities in development of the philtrum.
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Affiliation(s)
- Laurence J. Howe
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, United Kingdom
- Institute of Cardiovascular Science, University College London, London, United Kingdom
- * E-mail: (LJH); (SJL)
| | - Myoung Keun Lee
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Gemma C. Sharp
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, United Kingdom
- Bristol Dental School, University of Bristol, Bristol, United Kingdom
| | - George Davey Smith
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Beate St Pourcain
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, United Kingdom
- Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
| | - John R. Shaffer
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | | | | | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Eleanor Feingold
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Alexei Zhurov
- Department of Applied Clinical Research and Public Health, School of Dentistry, University of Cardiff, Cardiff, United Kingdom
| | - Evie Stergiakouli
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, United Kingdom
- Bristol Dental School, University of Bristol, Bristol, United Kingdom
| | - Jonathan Sandy
- Bristol Dental School, University of Bristol, Bristol, United Kingdom
| | - Stephen Richmond
- Department of Applied Clinical Research and Public Health, School of Dentistry, University of Cardiff, Cardiff, United Kingdom
| | - Seth M. Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Gibran Hemani
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Sarah J. Lewis
- Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, United Kingdom
- Bristol Dental School, University of Bristol, Bristol, United Kingdom
- * E-mail: (LJH); (SJL)
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41
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Affiliation(s)
- Seth M. Weinberg
- Department of Oral Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
- Department of Anthropology, University of Pittsburgh, Pittsburgh, Pennsylvania, United Staes of America
- * E-mail:
| | - Robert Cornell
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa, United States America
| | - Elizabeth J. Leslie
- Department of Human Genetics, Emory University, Atlanta, Georgia, United States of America
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42
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Claes P, Roosenboom J, White JD, Swigut T, Sero D, Li J, Lee MK, Zaidi A, Mattern BC, Liebowitz C, Pearson L, González T, Leslie EJ, Carlson JC, Orlova E, Suetens P, Vandermeulen D, Feingold E, Marazita ML, Shaffer JR, Wysocka J, Shriver MD, Weinberg SM. Genome-wide mapping of global-to-local genetic effects on human facial shape. Nat Genet 2018; 50:414-423. [PMID: 29459680 PMCID: PMC5937280 DOI: 10.1038/s41588-018-0057-4] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 01/03/2018] [Indexed: 11/08/2022]
Abstract
Genome-wide association scans of complex multipartite traits like the human face typically use preselected phenotypic measures. Here we report a data-driven approach to phenotyping facial shape at multiple levels of organization, allowing for an open-ended description of facial variation while preserving statistical power. In a sample of 2,329 persons of European ancestry, we identified 38 loci, 15 of which replicated in an independent European sample (n = 1,719). Four loci were completely new. For the others, additional support (n = 9) or pleiotropic effects (n = 2) were found in the literature, but the results reported here were further refined. All 15 replicated loci highlighted distinctive patterns of global-to-local genetic effects on facial shape and showed enrichment for active chromatin elements in human cranial neural crest cells, suggesting an early developmental origin of the facial variation captured. These results have implications for studies of facial genetics and other complex morphological traits.
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Affiliation(s)
- Peter Claes
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium.
- Medical Imaging Research Center, MIRC, UZ Leuven, Leuven, Belgium.
- Murdoch Childrens Research Institute, Melbourne, Victoria, Australia.
| | - Jasmien Roosenboom
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Julie D White
- Department of Anthropology, Penn State University, University Park, PA, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Dzemila Sero
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, MIRC, UZ Leuven, Leuven, Belgium
| | - Jiarui Li
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, MIRC, UZ Leuven, Leuven, Belgium
| | - Myoung Keun Lee
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Arslan Zaidi
- Department of Anthropology, Penn State University, University Park, PA, USA
| | - Brooke C Mattern
- Department of Anthropology, Penn State University, University Park, PA, USA
| | - Corey Liebowitz
- Department of Anthropology, Penn State University, University Park, PA, USA
| | - Laurel Pearson
- Department of Anthropology, Penn State University, University Park, PA, USA
| | - Tomás González
- Department of Anthropology, Penn State University, University Park, PA, USA
| | - Elizabeth J Leslie
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jenna C Carlson
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ekaterina Orlova
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Paul Suetens
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, MIRC, UZ Leuven, Leuven, Belgium
| | - Dirk Vandermeulen
- Department of Electrical Engineering, ESAT/PSI, KU Leuven, Leuven, Belgium
- Medical Imaging Research Center, MIRC, UZ Leuven, Leuven, Belgium
| | - Eleanor Feingold
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - John R Shaffer
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Mark D Shriver
- Department of Anthropology, Penn State University, University Park, PA, USA.
| | - Seth M Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA, USA.
- Department of Anthropology, University of Pittsburgh, Pittsburgh, PA, USA.
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43
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Gowans LJJ, Oseni G, Mossey PA, Adeyemo WL, Eshete MA, Busch TD, Donkor P, Obiri-Yeboah S, Plange-Rhule G, Oti AA, Owais A, Olaitan PB, Aregbesola BS, Oginni FO, Bello SA, Audu R, Onwuamah C, Agbenorku P, Ogunlewe MO, Abdur-Rahman LO, Marazita ML, Adeyemo AA, Murray JC, Butali A. Novel GREM1 Variations in Sub-Saharan African Patients With Cleft Lip and/or Cleft Palate. Cleft Palate Craniofac J 2018; 55:736-742. [PMID: 29489415 DOI: 10.1177/1055665618754948] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE Cleft lip and/or cleft palate (CL/P) are congenital anomalies of the face and have multifactorial etiology, with both environmental and genetic risk factors playing crucial roles. Though at least 40 loci have attained genomewide significant association with nonsyndromic CL/P, these loci largely reside in noncoding regions of the human genome, and subsequent resequencing studies of neighboring candidate genes have revealed only a limited number of etiologic coding variants. The present study was conducted to identify etiologic coding variants in GREM1, a locus that has been shown to be largely associated with cleft of both lip and soft palate. PATIENTS AND METHOD We resequenced DNA from 397 sub-Saharan Africans with CL/P and 192 controls using Sanger sequencing. Following analyses of the sequence data, we observed 2 novel coding variants in GREM1. These variants were not found in the 192 African controls and have never been previously reported in any public genetic variant database that includes more than 5000 combined African and African American controls or from the CL/P literature. RESULTS The novel variants include p.Pro164Ser in an individual with soft palate cleft only and p.Gly61Asp in an individual with bilateral cleft lip and palate. The proband with the p.Gly61Asp GREM1 variant is a van der Woude (VWS) case who also has an etiologic variant in IRF6 gene. CONCLUSION Our study demonstrated that there is low number of etiologic coding variants in GREM1, confirming earlier suggestions that variants in regulatory elements may largely account for the association between this locus and CL/P.
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Affiliation(s)
- Lord Jephthah Joojo Gowans
- 1 Cleft Clinic, Komfo Anokye Teaching Hospital and Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Ganiyu Oseni
- 2 Department of Plastic Surgery, Ladoke Akintola University of Science and Technology, Osogbo, Nigeria
| | - Peter A Mossey
- 3 Department of Orthodontics, University of Dundee, Dundee, United Kingdom
| | - Wasiu Lanre Adeyemo
- 4 Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos, Nigeria
| | - Mekonen A Eshete
- 5 Addis Ababa University, School of Public Health, Addis Ababa, Ethiopia
| | - Tamara D Busch
- 6 Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Peter Donkor
- 1 Cleft Clinic, Komfo Anokye Teaching Hospital and Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Solomon Obiri-Yeboah
- 1 Cleft Clinic, Komfo Anokye Teaching Hospital and Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Gyikua Plange-Rhule
- 1 Cleft Clinic, Komfo Anokye Teaching Hospital and Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Alexander A Oti
- 1 Cleft Clinic, Komfo Anokye Teaching Hospital and Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Arwa Owais
- 7 Department of Pediatric Dentistry, University of Iowa, Iowa City, IA, USA
| | - Peter B Olaitan
- 2 Department of Plastic Surgery, Ladoke Akintola University of Science and Technology, Osogbo, Nigeria
| | - Babatunde S Aregbesola
- 8 Department of Oral and Maxillofacial Surgery, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Fadekemi O Oginni
- 8 Department of Oral and Maxillofacial Surgery, Obafemi Awolowo University, Ile-Ife, Nigeria
| | | | - Rosemary Audu
- 10 Department of Virology, Nigerian Institute of Medical Research, Lagos, Nigeria
| | - Chika Onwuamah
- 10 Department of Virology, Nigerian Institute of Medical Research, Lagos, Nigeria
| | - Pius Agbenorku
- 1 Cleft Clinic, Komfo Anokye Teaching Hospital and Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Mobolanle O Ogunlewe
- 4 Department of Oral and Maxillofacial Surgery, University of Lagos, Lagos, Nigeria
| | - Lukman O Abdur-Rahman
- 11 Division of Pediatric Surgery, Department of Surgery, University of Ilorin, Ilorin, Nigeria
| | - Mary L Marazita
- 12 Center for Craniofacial and Dental Genetics, Department of Oral Biology, University of Pittsburgh, Pittsburgh, PA, USA.,13 Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - A A Adeyemo
- 14 National Human Genome Research Institute, Bethesda, MD, USA
| | - Jeffrey C Murray
- 6 Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Azeez Butali
- 15 Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, IA, USA
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44
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FOXE1 Mutation Screening in a Case with Cleft Lip, Hypothyroidism, and Thyroid Carcinoma: A New Syndrome? Case Rep Genet 2017; 2017:6390545. [PMID: 28928994 PMCID: PMC5591984 DOI: 10.1155/2017/6390545] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 07/19/2017] [Accepted: 07/30/2017] [Indexed: 01/30/2023] Open
Abstract
A 26-year-old woman is referred to the Internal Medicine consultation due to increases in laboratory studies associated with Papillary Thyroid Carcinoma (PTC) that was confirmed by histopathological studies. Her clinical history revealed that, at 3 months of age, she was successfully treated with surgery for cleft lip (CL) and at the age of 24 years was diagnosed with hypothyroidism. Single nucleotide polymorphisms (SNPs) in FOXE1 and its promoter regions have been associated with various etiologies related to the thyroid, including orofacial clefting, specially cleft palate (CP) and CL, hypothyroidism (HT), and thyroid cancer. The association of CL, HT, and PTC might be component of a new syndrome; however FOXE1 coding region, which has been involved with these entities, has not exhibited mutations or SNPs. Further study of other genes may help in better characterization of the possible syndrome.
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45
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Bandoli G, Palmsten K, Forbess Smith CJ, Chambers CD. A Review of Systemic Corticosteroid Use in Pregnancy and the Risk of Select Pregnancy and Birth Outcomes. Rheum Dis Clin North Am 2017; 43:489-502. [PMID: 28711148 PMCID: PMC5604866 DOI: 10.1016/j.rdc.2017.04.013] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The evidence to date regarding corticosteroid exposure in pregnancy and select pregnancy and birth outcomes is limited and inconsistent. The authors provide a narrative review of published literature summarizing the findings for oral clefts, preterm birth, birth weight, preeclampsia, and gestational diabetes mellitus. Whenever possible, the results are limited to oral or systemic administration with a further focus on use in autoimmune disease. Although previous studies of corticosteroid exposure in pregnancy reported an increased risk of oral clefts in the offspring, more recent studies have not replicated these findings.
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Affiliation(s)
- Gretchen Bandoli
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, Mail Code 0828, La Jolla, CA 92093-0412, USA.
| | - Kristin Palmsten
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, Mail Code 0828, La Jolla, CA 92093-0412, USA
| | - Chelsey J Forbess Smith
- Department of Rheumatology, University of California, San Diego, 9500 Gilman Drive, Mail Code 0656, La Jolla, CA 92093-0412, USA
| | - Christina D Chambers
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, Mail Code 0828, La Jolla, CA 92093-0412, USA
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46
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Moreno Uribe LM, Fomina T, Munger RG, Romitti PA, Jenkins MM, Gjessing HK, Gjerdevik M, Christensen K, Wilcox AJ, Murray JC, Lie RT, Wehby GL. A Population-Based Study of Effects of Genetic Loci on Orofacial Clefts. J Dent Res 2017; 96:1322-1329. [PMID: 28662356 DOI: 10.1177/0022034517716914] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Prior genome-wide association studies for oral clefts have focused on clinic-based samples with unclear generalizability. Prior samples were also small for investigating effects by cleft type and exclusively studied isolated clefts (those occurring without other birth defects). We estimated the effects of 17 top loci on cleft types in both isolated and nonisolated cases in the largest consortium to date of European-descent population-based studies. Our analytic approach focused on a mother-child dyad case-control design, but it also allowed analyzing mother-only or child-only genotypes to maximize power. Our total sample included 1,875 cases with isolated clefts, 459 cases with nonisolated clefts, and 3,749 controls. After correcting for multiple testing, we observed significant associations between fetal single-nucleotide polymorphisms (SNPs) at IRF6, PAX7, 8q21.3, 8q24, KIAA1598-VAX1, and MAFB and isolated cleft lip only (CLO) and cleft lip and palate (CLP). Significant associations were observed between isolated CLO and fetal SNPs near TPM1 and NOG1 and between CLP and fetal SNPs at ABCA4-ARHGAP29, THADA, FOXE1, and SPRY2. Overall, effects were similar for isolated CLO and CLP, except for ABCA4-ARHGAP29. A protective effect was observed for the fetal NOG1 SNP on cleft palate only, opposite in direction to the effect on CLO. For most fetal SNPs, a dose-response allelic effect was observed. No evidence of parent-of-origin or maternal genome effects was observed. Overall, effect direction and magnitude were similar between isolated and nonisolated clefts, suggesting that several loci are modifiers of cleft risk in both isolated and nonisolated forms. Our results provide reliable estimates of the effects of top loci on risks of oral clefts in a population of European descent.
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Affiliation(s)
- L M Moreno Uribe
- 1 Department of Orthodontics and Dows Institute, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - T Fomina
- 2 Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - R G Munger
- 3 Department of Nutrition and Food Sciences, Utah State University, Logan, UT, USA
| | - P A Romitti
- 4 Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, IA, USA
| | - M M Jenkins
- 5 National Center on Birth Defects and Developmental Disabilities, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - H K Gjessing
- 2 Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,6 Norwegian Institute of Public Health, Bergen and Oslo, Norway
| | - M Gjerdevik
- 2 Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,6 Norwegian Institute of Public Health, Bergen and Oslo, Norway
| | - K Christensen
- 7 Department of Public Health, University of Southern Denmark; Department of Clinical Genetics and Department of Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | - A J Wilcox
- 8 Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, USA
| | - J C Murray
- 9 Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - R T Lie
- 2 Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,6 Norwegian Institute of Public Health, Bergen and Oslo, Norway
| | - G L Wehby
- 10 Departments of Health Management and Policy, Economics, and Preventive and Community Dentistry, and Public Policy Center, University of Iowa, Iowa City, IA, USA
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47
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Sharp GC, Ho K, Davies A, Stergiakouli E, Humphries K, McArdle W, Sandy J, Davey Smith G, Lewis SJ, Relton CL. Distinct DNA methylation profiles in subtypes of orofacial cleft. Clin Epigenetics 2017; 9:63. [PMID: 28603561 PMCID: PMC5465456 DOI: 10.1186/s13148-017-0362-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/26/2017] [Indexed: 11/13/2022] Open
Abstract
Background Epigenetic data could help identify risk factors for orofacial clefts, either by revealing a causal role for epigenetic mechanisms in causing clefts or by capturing information about causal genetic or environmental factors. Given the evidence that different subtypes of orofacial cleft have distinct aetiologies, we explored whether children with different cleft subtypes showed distinct epigenetic profiles. Methods In whole-blood samples from 150 children from the Cleft Collective cohort study, we measured DNA methylation at over 450,000 sites on the genome. We then carried out epigenome-wide association studies (EWAS) to test the association between methylation at each site and cleft subtype (cleft lip only (CLO) n = 50; cleft palate only (CPO) n = 50; cleft lip and palate (CLP) n = 50). We also compared methylation in the blood to methylation in the lip or palate tissue using genome-wide data from the same 150 children and conducted an EWAS of CLO compared to CLP in lip tissue. Results We found four genomic regions in blood differentially methylated in CLO compared to CLP, 17 in CPO compared to CLP and 294 in CPO compared to CLO. Several regions mapped to genes that have previously been implicated in the development of orofacial clefts (for example, TBX1, COL11A2, HOXA2, PDGFRA), and over 250 associations were novel. Methylation in blood correlated with that in lip/palate at some regions. There were 14 regions differentially methylated in the lip tissue from children with CLO and CLP, with one region (near KIAA0415) showing up in both the blood and lip EWAS. Conclusions Our finding of distinct methylation profiles in different orofacial cleft (OFC) subtypes represents a promising first step in exploring the potential role of epigenetic modifications in the aetiology of OFCs and/or as clinically useful biomarkers of OFC subtypes. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0362-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gemma C Sharp
- MRC Integrative Epidemiology Unit, School of Oral and Dental Sciences, University of Bristol, Bristol, England
| | - Karen Ho
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, England
| | - Amy Davies
- School of Oral and Dental Sciences, University of Bristol, Bristol, England
| | - Evie Stergiakouli
- MRC Integrative Epidemiology Unit, School of Oral and Dental Sciences, University of Bristol, Bristol, England
| | - Kerry Humphries
- School of Oral and Dental Sciences, University of Bristol, Bristol, England
| | - Wendy McArdle
- School of Social and Community Medicine, University of Bristol, Bristol, England
| | - Jonathan Sandy
- School of Oral and Dental Sciences, University of Bristol, Bristol, England
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, England
| | - Sarah J Lewis
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, England
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, England
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