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Smits JPH, Qu J, Pardow F, van den Brink NJM, Rodijk-Olthuis D, van Vlijmen-Willems IMJJ, van Heeringen SJ, Zeeuwen PLJM, Schalkwijk J, Zhou H, van den Bogaard EH. The Aryl Hydrocarbon Receptor Regulates Epidermal Differentiation through Transient Activation of TFAP2A. J Invest Dermatol 2024; 144:2013-2028.e2. [PMID: 38401701 DOI: 10.1016/j.jid.2024.01.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/26/2024]
Abstract
The aryl hydrocarbon receptor (AHR) is an evolutionary conserved environmental sensor identified as an indispensable regulator of epithelial homeostasis and barrier organ function. Molecular signaling cascade and target genes upon AHR activation and their contribution to cell and tissue function are however not fully understood. Multiomics analyses using human skin keratinocytes revealed that upon ligand activation, AHR binds open chromatin to induce expression of transcription factors, for example, TFAP2A, as a swift response to environmental stimuli. The terminal differentiation program, including upregulation of barrier genes, FLG and keratins, was mediated by TFAP2A as a secondary response to AHR activation. The role of AHR-TFAP2A axis in controlling keratinocyte terminal differentiation for proper barrier formation was further confirmed using CRISPR/Cas9 in human epidermal equivalents. Overall, the study provides additional insights into the molecular mechanism behind AHR-mediated barrier function and identifies potential targets for the treatment of skin barrier diseases.
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Affiliation(s)
- Jos P H Smits
- Department of Dermatology, Radboud Research Institute for Medical Innovation, Radboudumc, Nijmegen, The Netherlands; Department of Dermatology, University Hospital Düsseldorf, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Jieqiong Qu
- Department of Molecular Developmental Biology, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Felicitas Pardow
- Department of Dermatology, Radboud Research Institute for Medical Innovation, Radboudumc, Nijmegen, The Netherlands; Department of Molecular Developmental Biology, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Noa J M van den Brink
- Department of Dermatology, Radboud Research Institute for Medical Innovation, Radboudumc, Nijmegen, The Netherlands
| | - Diana Rodijk-Olthuis
- Department of Dermatology, Radboud Research Institute for Medical Innovation, Radboudumc, Nijmegen, The Netherlands
| | | | - Simon J van Heeringen
- Department of Molecular Developmental Biology, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Patrick L J M Zeeuwen
- Department of Dermatology, Radboud Research Institute for Medical Innovation, Radboudumc, Nijmegen, The Netherlands
| | - Joost Schalkwijk
- Department of Dermatology, Radboud Research Institute for Medical Innovation, Radboudumc, Nijmegen, The Netherlands
| | - Huiqing Zhou
- Department of Molecular Developmental Biology, Faculty of Science, Radboud University, Nijmegen, The Netherlands; Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands.
| | - Ellen H van den Bogaard
- Department of Dermatology, Radboud Research Institute for Medical Innovation, Radboudumc, Nijmegen, The Netherlands.
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Yang J, Li J, Qin C, Fu X. A WAP-Based Concept Acquisition Teaching Model in Cleft Lip and Palate Phenotype and Embryonic Development: Functionality and Usability Study. Cleft Palate Craniofac J 2024; 61:1499-1508. [PMID: 37165772 DOI: 10.1177/10556656231174433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
OBJECTIVE Taking advantage of the broad coverage of Wireless Application Protocol (WAP), we developed a Content Management System (CMS)-programmed mobile learning application. This application can help the undergraduate to obtain a comprehensive understanding of concepts in Cleft lip and palate Phenotype, and Embryonic development (CPE). The present study aims to evaluate the feasibility and efficacy of the concept acquisition teaching model on the basis of WAP in a practical undergraduate course of CPE. DESIGN The concept acquisition teaching model based on WAP was programmed by CMS, covering definitions of various cleft lip and palate, the mechanisms underlying the phenotypes, practical medical cases, as well as corresponding tests after learning. SETTING The CPE concept acquisition teaching model was distributed to a total of 524 undergraduate students and 46 tutors participated in CPE teaching from seven highly ranked schools of stomatology in China since April 2022. PARTICIPANTS 524 undergraduate students and 46 tutors from seven highly ranked schools of stomatology in China. INTERVENTIONS The CPE concept acquisition teaching model. MAIN OUTCOME MEASURES The effectiveness of the CPE teaching model. RESULTS The response rate to the survey was 100%. The grading of the questionnaires indicated that the students were satisfied with the usability, practicality, and outcome, whereas the tutors were more positive with the contents, cooperation, and outcome. CONCLUSIONS The present study demonstrated the feasibility and efficacy of the WAP-based concept acquisition teaching model of CPE and a high level of satisfaction among undergraduate students and tutors who major in Stomatology.
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Affiliation(s)
- Jiegang 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, China
- The Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Jian Li
- The Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Chuanqi 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, China
- The Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Xiazhou Fu
- 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, China
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Antiguas A, Dunnwald M. A novel noncanonical function for IRF6 in the recycling of E-cadherin. Mol Biol Cell 2024; 35:ar102. [PMID: 38809584 PMCID: PMC11244161 DOI: 10.1091/mbc.e23-11-0430] [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: 11/13/2023] [Revised: 05/17/2024] [Accepted: 05/22/2024] [Indexed: 05/30/2024] Open
Abstract
Interferon Regulatory Factor 6 (IRF6) is a transcription factor essential for keratinocyte cell-cell adhesions. Previously, we found that recycling of E-cadherin was defective in the absence of IRF6, yet total E-cadherin levels were not altered, suggesting a previously unknown, nontranscriptional function for IRF6. IRF6 protein contains a DNA binding domain (DBD) and a protein binding domain (PBD). The transcriptional function of IRF6 depends on its DBD and PBD, however, whether the PBD is necessary for the interaction with cytoplasmic proteins has yet to be demonstrated. Here, we show that an intact PBD is required for recruitment of cell-cell adhesion proteins at the plasma membrane, including the recycling of E-cadherin. Colocalizations and coimmunoprecipitations reveal that IRF6 forms a complex in recycling endosomes with Rab11, Myosin Vb, and E-cadherin, and that the PBD is required for this interaction. These data indicate that IRF6 is a novel effector of the endosomal recycling of E-cadherin and demonstrate a non-transcriptional function for IRF6 in regulating cell-cell adhesions.
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Affiliation(s)
- Angelo Antiguas
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA, 52245
| | - Martine Dunnwald
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA, 52245
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Alhazmi N, Alamoud KA, Albalawi F, Alalola B, Farook FF. The application of zebrafish model in the study of cleft lip and palate development: A systematic review. Heliyon 2024; 10:e28322. [PMID: 38533046 PMCID: PMC10963633 DOI: 10.1016/j.heliyon.2024.e28322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 03/28/2024] Open
Abstract
Objective Craniofacial growth and development are more than a scientific curiosity; it is of tremendous interest to clinicians. Insights into the genetic etiology of cleft lip and palate development are essential for improving diagnosis and treatment planning. The purpose of this systematic review was to utilize a zebrafish model to highlight the role of the IRF6 gene in cleft lip and palate development in humans. Data This review adhered to the guidelines outlined in the PRISMA statement. Nine studies were included in the analysis. Sources This study used major scientific databases such as MEDLINE, EMBASE, Web of Science, and the Zebrafish Information Network and yielded 1275 articles. Two reviewers performed the screening using COVIDENCE™ independently, and a third reviewer resolved any conflicts. Study selection After applying the inclusion and exclusion criteria and screening, nine studies were included in the analysis. The Systematic Review Center for Laboratory Animal Experimentation's (SYRCLE's) risk-of-bias tool was used to assess the quality of the included studies. Results The main outcome supports the role of the IRF6 gene in zebrafish periderm development and embryogenesis, and IRF6 variations result in cleft lip and palate development. The overall SYRCLE risk of bias was low-medium. Conclusion In conclusion, this review indicated the critical role of the IRF6 gene and its downstream genes (GRHL3, KLF17, and ESRP1/2) in the development of cleft lip and palate in zebrafish models. Genetic mutation zebrafish models provide a high level of insights into zebrafish craniofacial development. Clinical relevance this review provides a productive avenue for understanding the powerful and conserved zebrafish model for investigating the pathogenesis of human cleft lip and palate.
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Affiliation(s)
- Nora Alhazmi
- Preventive Dental Science Department, College of Dentistry, King Saud bin Abdulaziz University for Health Sciences, Riyadh, 14611, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, 11481, Saudi Arabia
- Ministry of the National Guard Health Affairs, Riyadh, 11426, Saudi Arabia
| | - Khalid A. Alamoud
- Preventive Dental Science Department, College of Dentistry, King Saud bin Abdulaziz University for Health Sciences, Riyadh, 14611, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, 11481, Saudi Arabia
- Ministry of the National Guard Health Affairs, Riyadh, 11426, Saudi Arabia
| | - Farraj Albalawi
- Preventive Dental Science Department, College of Dentistry, King Saud bin Abdulaziz University for Health Sciences, Riyadh, 14611, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, 11481, Saudi Arabia
- Ministry of the National Guard Health Affairs, Riyadh, 11426, Saudi Arabia
| | - Bassam Alalola
- Preventive Dental Science Department, College of Dentistry, King Saud bin Abdulaziz University for Health Sciences, Riyadh, 14611, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, 11481, Saudi Arabia
- Ministry of the National Guard Health Affairs, Riyadh, 11426, Saudi Arabia
| | - Fathima F. Farook
- Preventive Dental Science Department, College of Dentistry, King Saud bin Abdulaziz University for Health Sciences, Riyadh, 14611, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, 11481, Saudi Arabia
- Ministry of the National Guard Health Affairs, Riyadh, 11426, Saudi Arabia
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Sinha BK, Kumar D, Meher P, Kumari S, Prakash K, Gourinath S, Kashav T. Biophysical and functional characterization of N-terminal domain of Human Interferon Regulatory Factor 6. Mol Biol Rep 2024; 51:380. [PMID: 38429584 DOI: 10.1007/s11033-024-09205-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/02/2024] [Indexed: 03/03/2024]
Abstract
BACKGROUND Interferon regulatory factor 6 (IRF6) has a key function in palate fusion during palatogenesis during embryonic development, and mutations in IRF6 cause orofacial clefting disorders. METHODS AND RESULTS The in silico analysis of IRF6 is done to obtain leads for the domain boundaries and subsequently the sub-cloning of the N-terminal domain of IRF6 into the pGEX-2TK expression vector and successfully optimized the overexpression and purification of recombinant glutathione S-transferase-fused NTD-IRF6 protein under native conditions. After cleavage of the GST tag, NTD-IRF6 was subjected to protein folding studies employing Circular Dichroism and Intrinsic fluorescence spectroscopy at variable pH, temperature, and denaturant. CD studies showed predominantly alpha-helical content and the highest stability of NTD-IRF6 at pH 9.0. A comparison of native and renatured protein depicts loss in the secondary structural content. Intrinsic fluorescence and quenching studies have identified that tryptophan residues are majorly present in the buried areas of the protein and a small fraction was on or near the protein surface. Upon the protein unfolding with a higher concentration of denaturant urea, the peak of fluorescence intensity decreased and red shifted, confirming that tryptophan residues are majorly present in a more polar environment. While regulating IFNβ gene expression during viral infection, the N-terminal domain binds to the promoter region of Virus Response Element-Interferon beta (VRE-IFNβ). Along with the protein folding analysis, this study also aimed to identify the DNA-binding activity and determine the binding affinities of NTD-IRF6 with the VRE-IFNβ promoter region. The protein-DNA interaction is specific as demonstrated by gel retardation assay and the kinetics of molecular interactions as quantified by Biolayer Interferometry showed a strong affinity with an affinity constant (KD) value of 7.96 × 10-10 M. CONCLUSION NTD-IRF6 consists of a mix of α-helix and β-sheets that show temperature-dependent cooperative unfolding between 40 °C and 55 °C. Urea-induced unfolding shows moderate tolerance to urea as the mid-transition concentration of urea (Cm) is 3.2 M. The tryptophan residues are majorly buried as depicted by fluorescence quenching studies. NTD-IRF6 has a specific and high affinity toward the promoter region of VRE-IFNβ.
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Affiliation(s)
- Binita Kumari Sinha
- Department of Life Science, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar, 824236, India
| | - Devbrat Kumar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Priyabrata Meher
- Department of Life Science, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar, 824236, India
| | - Shilpi Kumari
- Department of Biochemical Engineering and Biotechnology, IIT Delhi, New Delhi, India
| | - Krishna Prakash
- Department of Biotechnology, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar, India
| | | | - Tara Kashav
- Department of Life Science, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, Bihar, 824236, India.
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Ghazali N, Rahman NA, Kannan TP, Ahmad A, Sulong S. Identification of copy neutral loss of heterozygosity on chromosomes 1p, 1q, and 6p among nonsyndromic cleft lip and/or without cleft palate with hypodontia. BMC Oral Health 2023; 23:945. [PMID: 38031027 PMCID: PMC10685534 DOI: 10.1186/s12903-023-03464-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 09/27/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND Nonsyndromic cleft lip and/or without cleft palate (NSCL/P) with or without hypodontia is a common developmental aberration in humans and animals. This study aimed to identify the loss of heterozygosity (LOH) involved in hypodontia and NSCL/P pathogenesis. METHODS This is a cross-sectional study that conducted genome-wide copy number analysis using CytoScan 750K array on salivary samples from Malay subjects with NSCL/P with or without hypodontia aged 7-13 years. To confirm the significant results, simple logistic regression was employed to conduct statistical data analysis using SPSS software. RESULTS The results indicated the most common recurrent copy neutral LOH (cnLOH) observed at 1p33-1p32.3, 1q32.2-1q42.13 and 6p12.1-6p11.1 loci in 8 (13%), 4 (7%), and 3 (5%) of the NSCL/P subjects, respectively. The cnLOHs at 1p33-1p32.3 (D1S197), 1q32.2-1q42.13 (D1S160), and 6p12.1-6p11.1 (D1S1661) were identified observed in NSCL/P and noncleft children using microsatellite analysis markers as a validation analysis. The regions affected by the cnLOHs at 1p33-1p32.3, 1q32.2-1q42.13, and 6p12.1-6p11.1 loci contained selected genes, namely FAF1, WNT3A and BMP5, respectively. There was a significant association between the D1S197 (1p33-32.3) markers containing the FAF1 gene among NSCL/P subjects with or without hypodontia compared with the noncleft subjects (p-value = 0.023). CONCLUSION The results supported the finding that the genetic aberration on 1p33-32.3 significantly contributed to the development of NSCL/P with or without hypodontia. These results have an exciting prospect in the promising field of individualized preventive oral health care.
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Affiliation(s)
- Norliana Ghazali
- School of Dental Sciences, Universiti Sains Malaysia (USM), Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Normastura Abd Rahman
- School of Dental Sciences, Universiti Sains Malaysia (USM), Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
| | - Thirumulu Ponnuraj Kannan
- School of Dental Sciences, Universiti Sains Malaysia (USM), Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Azlina Ahmad
- School of Dental Sciences, Universiti Sains Malaysia (USM), Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Sarina Sulong
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia (USM), Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia
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Zhang S, Chen Q, Yang C, Shi J, Lin Y, Duan S, Shi B, Jia Z. Association between variants around IRF6 and non-syndromic orofacial cleft in Western Han Chinese. Oral Dis 2023; 29:1115-1127. [PMID: 34894020 DOI: 10.1111/odi.14100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/21/2021] [Accepted: 11/25/2021] [Indexed: 02/05/2023]
Abstract
OBJECTIVES Considering limitations of previous studies and differences across populations and subtypes, this study aimed to identify new potential SNPs around IRF6 associated with non-syndromic orofacial cleft (NSOC) in Western Han Chinese. MATERIALS AND METHODS We recruited 376 NSOC case-parent trios, including 125 non-syndromic cleft lip only (NSCLO) trios, 151 non-syndromic cleft lip and palate (NSCLP) trios, and 100 non-syndromic cleft palate only (NSCPO) trios. Twenty-two single-nucleotide polymorphisms (SNPs) were genotyped using MassARRAY method. Hardy-Weinberg equilibrium test, allelic transmission disequilibrium test (TDT) analysis, sliding-window haplotype TDT analysis, and tests for parent-of-origin effect were performed using the PLINK software. Pairwise linkage disequilibrium (LD) was computed using the Haploview program. RESULTS In TDT analysis, allele A at rs17015217 (p = 0.00011, OR = 0.61 and 95% CI: 0.47-0.78) and allele T at rs12080691 (p = 0.00011, OR = 0.61 and 95% CI: 0.47-0.78) were under-transmitted among NSCLO trios but over-transmitted among NSCPO trios. Haplotypes showing evidence of under-transmission in NSCLO trios were over-transmitted in NSCPO trios. In tests for parent-of-origin effects, T allele at rs12080691 presented paternal under-transmission among NSCLO trios but over-transmission among NSCPO trios. CONCLUSIONS Allele A at rs17015217 and allele T at rs12080691 are associated with NSCLO and NSCPO with potential to have opposite effects on two subtypes in this sample from Western Han Chinese.
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Affiliation(s)
- Sidi Zhang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, China
| | - Qianming Chen
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, China
| | - Chao Yang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, China
| | - Jiayu Shi
- Division of Growth and Development and Section of Orthodontics, School of Dentistry, University of California, Los Angeles, California, USA
| | - Yansong Lin
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, China
| | - Shijun Duan
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, China
| | - Bing Shi
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, China
| | - Zhonglin Jia
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & Department of cleft lip and palate, West China Hospital of Stomatology, Sichuan University, China
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Créton M, Wagener F, Massink M, Fennis W, Bloemen M, Schols J, Aarts M, van der Molen AM, van Haaften G, van den Boogaard MJ. Concurrent de novo ZFHX4 variant and 16q24.1 deletion in a patient with orofacial clefting; a potential role of ZFHX4 and USP10. Am J Med Genet A 2023; 191:1083-1088. [PMID: 36595458 DOI: 10.1002/ajmg.a.63101] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/25/2022] [Accepted: 12/13/2022] [Indexed: 01/04/2023]
Abstract
A girl with a unilateral cleft lip, alveolus and palate, tooth agenesis, and mild dysmorphic features, without a specific underlying syndrome diagnosis, was genotypically characterized and phenotypically described. Cleft gene panel analysis, single-nucleotide polymorphism (SNP) array, whole genome sequencing (WGS), whole exome sequencing, and quantitative PCR (Q-PCR) analysis were used as diagnostic tests. SNP array revealed a maternal deletion at 16q24.1, encompassing the cleft candidate gene USP10. WES revealed an additional de novo Loss-of-Function variant (p.(Asn838fs)) in the Zinc-Finger-Homeobox-4 (ZFHX4) gene. Q-PCR was performed to explore the effect of the ZFHX4 variant and the deletion in 16q24.1. The mRNA expression of a selection of putative target genes involved in orofacial clefting showed a lowered expression of USP10 (52%), CRISPLD2 (31%), and CRISPLD1 (1%) compared to the control. IRF6 showed no difference in gene expression. This case supports ZFHX4 as a novel cleft gene and suggests USP10 may contribute to the etiology of orofacial clefts in humans.
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Affiliation(s)
- Marijn Créton
- Department of Dentistry - Orthodontics and Craniofacial Biology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Frank Wagener
- Department of Dentistry - Orthodontics and Craniofacial Biology, Radboud University Medical Centre, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Maarten Massink
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Willem Fennis
- Department of Oral-Maxillofacial Surgery, Prosthodontics and Special Dental Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marjon Bloemen
- Department of Dentistry - Orthodontics and Craniofacial Biology, Radboud University Medical Centre, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Jan Schols
- Department of Dentistry - Orthodontics and Craniofacial Biology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Miranda Aarts
- Department of Dentistry - Orthodontics and Craniofacial Biology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Aebele Mink van der Molen
- Department of Plastic Surgery, Wilhelmina Children's Hospital, University of Utrecht, Utrecht, The Netherlands
| | - Gijs van Haaften
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
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Collier AE, Piekos SN, Liu A, Pattison JM, Felix F, Bailetti AA, Sedov E, Gaddam S, Zhen H, Oro AE. GRHL2 and AP2a coordinate early surface ectoderm lineage commitment during development. iScience 2023; 26:106125. [PMID: 36843855 PMCID: PMC9950457 DOI: 10.1016/j.isci.2023.106125] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/09/2022] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Ectodermal dysplasias including skin abnormalities and cleft lip/palate result from improper surface ectoderm (SE) patterning. However, the connection between SE gene regulatory networks and disease remains poorly understood. Here, we dissect human SE differentiation with multiomics and establish GRHL2 as a key mediator of early SE commitment, which acts by skewing cell fate away from the neural lineage. GRHL2 and master SE regulator AP2a balance early cell fate output, with GRHL2 facilitating AP2a binding to SE loci. In turn, AP2a restricts GRHL2 DNA binding away from de novo chromatin contacts. Integration of these regulatory sites with ectodermal dysplasia-associated genomic variants annotated within the Biomedical Data Commons identifies 55 loci previously implicated in craniofacial disorders. These include ABCA4/ARHGAP29 and NOG regulatory regions where disease-linked variants directly affect GRHL2/AP2a binding and gene transcription. These studies elucidate the logic underlying SE commitment and deepen our understanding of human oligogenic disease pathogenesis.
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Affiliation(s)
- Ann E. Collier
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
| | - Samantha N. Piekos
- Stem Cell Biology and Regenerative Medicine Graduate Program, Stanford University, Stanford, CA USA
| | - Angela Liu
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
- Stem Cell Biology and Regenerative Medicine Graduate Program, Stanford University, Stanford, CA USA
| | | | - Franco Felix
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
- Stem Cell Biology and Regenerative Medicine Graduate Program, Stanford University, Stanford, CA USA
| | | | - Egor Sedov
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
| | - Sadhana Gaddam
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
| | - Hanson Zhen
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
| | - Anthony E. Oro
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
- Stem Cell Biology and Regenerative Medicine Graduate Program, Stanford University, Stanford, CA USA
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Siewert A, Reiz B, Krug C, Heggemann J, Mangold E, Dickten H, Ludwig KU. Analysis of candidate genes for cleft lip ± cleft palate using murine single-cell expression data. Front Cell Dev Biol 2023; 11:1091666. [PMID: 37169019 PMCID: PMC10165499 DOI: 10.3389/fcell.2023.1091666] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 04/03/2023] [Indexed: 05/13/2023] Open
Abstract
Introduction: Cleft lip ± cleft palate (CL/P) is one of the most common birth defects. Although research has identified multiple genetic risk loci for different types of CL/P (i.e., syndromic or non-syndromic forms), determining the respective causal genes and understanding the relevant functional networks remain challenging. The recent introduction of single-cell RNA sequencing (scRNA-seq) has provided novel opportunities to study gene expression patterns at cellular resolution. The aims of our study were to: (i) aggregate available scRNA-seq data from embryonic mice and provide this as a resource for the craniofacial community; and (ii) demonstrate the value of these data in terms of the investigation of the gene expression patterns of CL/P candidate genes. Methods and Results: First, two published scRNA-seq data sets from embryonic mice were re-processed, i.e., data representing the murine time period of craniofacial development: (i) facial data from embryonic day (E) E11.5; and (ii) whole embryo data from E9.5-E13.5 from the Mouse Organogenesis Cell Atlas (MOCA). Marker gene expression analyses demonstrated that at E11.5, the facial data were a high-resolution representation of the MOCA data. Using CL/P candidate gene lists, distinct groups of genes with specific expression patterns were identified. Among others we identified that a co-expression network including Irf6, Grhl3 and Tfap2a in the periderm, while it was limited to Irf6 and Tfap2a in palatal epithelia, cells of the ectodermal surface, and basal cells at the fusion zone. The analyses also demonstrated that additional CL/P candidate genes (e.g., Tpm1, Arid3b, Ctnnd1, and Wnt3) were exclusively expressed in Irf6+ facial epithelial cells (i.e., as opposed to Irf6- epithelial cells). The MOCA data set was finally used to investigate differences in expression profiles for candidate genes underlying different types of CL/P. These analyses showed that syndromic CL/P genes (syCL/P) were expressed in significantly more cell types than non-syndromic CL/P candidate genes (nsCL/P). Discussion: The present study illustrates how scRNA-seq data can empower research on craniofacial development and disease.
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Affiliation(s)
- Anna Siewert
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | | | - Carina Krug
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Julia Heggemann
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Elisabeth Mangold
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | | | - Kerstin U. Ludwig
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
- *Correspondence: Kerstin U. Ludwig,
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11
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Schierz IAM, Amoroso S, Antona V, Giuffrè M, Piro E, Serra G, Corsello G. Novel de novo missense mutation in the interferon regulatory factor 6 gene in an Italian infant with IRF6-related disorder. Ital J Pediatr 2022; 48:132. [PMID: 35906647 PMCID: PMC9338470 DOI: 10.1186/s13052-022-01330-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/19/2022] [Indexed: 11/18/2022] Open
Abstract
Background Congenital maxillomandibular syngnathia is a rare craniofacial anomaly leading to difficulties in feeding, breathing and ability to thrive. The fusion may consist of soft tissue union (synechiae) to hard tissue union. Isolated cases of maxillomandibular fusion are extremely rare, it is most often syndromic in etiology. Case presentation Clinical management of a female newborn with oromaxillofacial abnormities (synechiae, cleft palate, craniofacial dysmorphisms, dental anomaly) and extraoral malformations (skinfold overlying the nails of both halluces, syndactyly, abnormal external genitalia) is presented. The associated malformations addressed to molecular genetic investigations revealing an interferon regulatory factor 6 (IRF6)-related disorder (van der Woude syndrome/popliteal pterygium syndrome). A novel de novo heterozygous mutation in exon 4 of IRF6 gene on chromosome 1q32.2, precisely c.262A > G (p.Asn88Asp), was found. Similarities are discussed with known asparagine missense mutations in the same codon, which may alter IRF6 gene function by reduced DNA-binding ability. A concomitant maternal Xp11.22 duplication involving two microRNA genes could contribute to possible epigenetic effects. Conclusions Our reported case carrying a novel mutation can contribute to expand understandings of molecular mechanisms underlying synechiae and orofacial clefting and to correct diagnosing of incomplete or overlapping features in IRF6-related disorders. Additional multidisciplinary evaluations to establish the phenotypical extent of the IRF6-related disorder and to address family counseling should not only be focused on the surgical corrections of syngnathia and cleft palate, but also involve comprehensive otolaryngologic, audiologic, logopedic, dental, orthopedic, urological and psychological evaluations.
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Affiliation(s)
- Ingrid Anne Mandy Schierz
- Neonatal Intensive Care Unit, Department of Health Promotion, Mother-Child Care, Internal Medicine and Medical Specialties "G. D'Alessandro", University Hospital "P. Giaccone", Via Alfonso Giordano n. 3, 90127, Palermo, Italy.
| | - Salvatore Amoroso
- Pediatric Surgery Unit, Children's Hospital, ARNAS Civico - Di Cristina - Benfratelli, Palermo, Italy
| | - Vincenzo Antona
- Neonatal Intensive Care Unit, Department of Health Promotion, Mother-Child Care, Internal Medicine and Medical Specialties "G. D'Alessandro", University Hospital "P. Giaccone", Via Alfonso Giordano n. 3, 90127, Palermo, Italy
| | - Mario Giuffrè
- Neonatal Intensive Care Unit, Department of Health Promotion, Mother-Child Care, Internal Medicine and Medical Specialties "G. D'Alessandro", University Hospital "P. Giaccone", Via Alfonso Giordano n. 3, 90127, Palermo, Italy
| | - Ettore Piro
- Neonatal Intensive Care Unit, Department of Health Promotion, Mother-Child Care, Internal Medicine and Medical Specialties "G. D'Alessandro", University Hospital "P. Giaccone", Via Alfonso Giordano n. 3, 90127, Palermo, Italy
| | - Gregorio Serra
- Neonatal Intensive Care Unit, Department of Health Promotion, Mother-Child Care, Internal Medicine and Medical Specialties "G. D'Alessandro", University Hospital "P. Giaccone", Via Alfonso Giordano n. 3, 90127, Palermo, Italy
| | - Giovanni Corsello
- Neonatal Intensive Care Unit, Department of Health Promotion, Mother-Child Care, Internal Medicine and Medical Specialties "G. D'Alessandro", University Hospital "P. Giaccone", Via Alfonso Giordano n. 3, 90127, Palermo, Italy
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12
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Alade A, Awotoye W, Butali A. Genetic and epigenetic studies in non-syndromic oral clefts. Oral Dis 2022; 28:1339-1350. [PMID: 35122708 DOI: 10.1111/odi.14146] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/11/2022] [Accepted: 01/20/2022] [Indexed: 11/28/2022]
Abstract
The etiology of non-syndromic oral clefts (NSOFC) is complex with genetics, genomics, epigenetics, and stochastics factors playing a role. Several approaches have been applied to understand the etiology of non-syndromic oral clefts. These include linkage, candidate gene association studies, genome-wide association studies, whole-genome sequencing, copy number variations, and epigenetics. In this review, we shared these approaches, genes, and loci reported in some studies.
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Affiliation(s)
- Azeez Alade
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, Iowa, USA
- Iowa Institute for Oral Health Research, University of Iowa, Iowa City, Iowa, USA
- Department of Epidemiology, College of Public Health, University of Iowa, Iowa City, Iowa, USA
| | - Waheed Awotoye
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, Iowa, USA
- Iowa Institute for Oral Health Research, University of Iowa, Iowa City, Iowa, USA
| | - Azeez Butali
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, Iowa, USA
- Iowa Institute for Oral Health Research, University of Iowa, Iowa City, Iowa, USA
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13
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Geetha-Loganathan P, Abramyan J, Buchtová M. Editorial: Cellular Mechanisms During Normal and Abnormal Craniofacial Development. Front Cell Dev Biol 2022; 10:872038. [PMID: 35345852 PMCID: PMC8957218 DOI: 10.3389/fcell.2022.872038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 02/18/2022] [Indexed: 11/22/2022] Open
Affiliation(s)
| | - John Abramyan
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, United States
| | - Marcela Buchtová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia.,Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czechia
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14
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Lan Y, Jiang R. Mouse models in palate development and orofacial cleft research: Understanding the crucial role and regulation of epithelial integrity in facial and palate morphogenesis. Curr Top Dev Biol 2022; 148:13-50. [PMID: 35461563 PMCID: PMC9060390 DOI: 10.1016/bs.ctdb.2021.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cleft lip and cleft palate are common birth defects resulting from genetic and/or environmental perturbations of facial development in utero. Facial morphogenesis commences during early embryogenesis, with cranial neural crest cells interacting with the surface ectoderm to form initially partly separate facial primordia consisting of the medial and lateral nasal prominences, and paired maxillary and mandibular processes. As these facial primordia grow around the primitive oral cavity and merge toward the ventral midline, the surface ectoderm undergoes a critical differentiation step to form an outer layer of flattened and tightly connected periderm cells with a non-stick apical surface that prevents epithelial adhesion. Formation of the upper lip and palate requires spatiotemporally regulated inter-epithelial adhesions and subsequent dissolution of the intervening epithelial seam between the maxillary and medial/lateral nasal processes and between the palatal shelves. Proper regulation of epithelial integrity plays a paramount role during human facial development, as mutations in genes encoding epithelial adhesion molecules and their regulators have been associated with syndromic and non-syndromic orofacial clefts. In this chapter, we summarize mouse genetic studies that have been instrumental in unraveling the mechanisms regulating epithelial integrity and periderm differentiation during facial and palate development. Since proper epithelial integrity also plays crucial roles in wound healing and cancer, understanding the mechanisms regulating epithelial integrity during facial development have direct implications for improvement in clinical care of craniofacial patients.
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Affiliation(s)
- Yu Lan
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States; Division of Plastic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Rulang Jiang
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States; Division of Plastic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.
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15
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Uncovering the Pathogenesis of Orofacial Clefts Using Bioinformatics Analysis. J Craniofac Surg 2022; 33:1971-1975. [PMID: 35142735 DOI: 10.1097/scs.0000000000008560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/27/2022] [Indexed: 11/26/2022] Open
Abstract
OBJECTIVE Many genes have been found to be associated with the occurrence of the orofacial clefts (OFC). The links between these pathogenic genes are rarely studied. In this study, bioinformatics analysis were performed in order to find associations between OFC-related genes and provide new ideas for etiology study of OFCs. METHODS Orofacial clefts-related genes were searched and identified from the Online Mendelian Inheritance of Man (OMIM.org). These genes were then analyzed by bioinformatics methods, including protein-protein interaction network, functional enrichment analysis, module analysis, and hub genes analysis. RESULTS After searching the database of OMIM.org and removing duplicate results, 279 genes were finally obtained. These genes were involved to 369 pathways in biological process, 56 in cell component, 64 in molecular function, and 45 in the Kyoto Encyclopedia of Genes and Genomes. Most identified genes were significantly enriched in embryonic appendage morphogenesis (29.17%), embryonic limb morphogenesis (6.06%), and limb development (4.33%) for biological process (Fig. 5A); ciliary tip (42.86%), MKS complex (28.57%), ciliary basal body (14.29%), and ciliary membrane (14.29%) for cell component. The top 10 hub genes were identified, including SHH, GLI2, PTCH1, SMAD4, FGFR1, BMP4, SOX9, SOX2, RUNX2, and CDH1. CONCLUSIONS Bioinformatics methods were used to analyze OFC-related genes in this study, including hub gene identifying and analysis, protein-protein interaction network construction, and functional enrichment analysis. Several potential mechanisms related to occurrence of OFCs were also discussed. These results may be helpful for further studies of the etiology of OFC.
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16
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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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17
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Jaruga A, Ksiazkiewicz J, Kuzniarz K, Tylzanowski P. Orofacial Cleft and Mandibular Prognathism-Human Genetics and Animal Models. Int J Mol Sci 2022; 23:ijms23020953. [PMID: 35055138 PMCID: PMC8779325 DOI: 10.3390/ijms23020953] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/24/2021] [Accepted: 01/13/2022] [Indexed: 12/12/2022] Open
Abstract
Many complex molecular interactions are involved in the process of craniofacial development. Consequently, the network is sensitive to genetic mutations that may result in congenital malformations of varying severity. The most common birth anomalies within the head and neck are orofacial clefts (OFCs) and prognathism. Orofacial clefts are disorders with a range of phenotypes such as the cleft of the lip with or without cleft palate and isolated form of cleft palate with unilateral and bilateral variations. They may occur as an isolated abnormality (nonsyndromic-NSCLP) or coexist with syndromic disorders. Another cause of malformations, prognathism or skeletal class III malocclusion, is characterized by the disproportionate overgrowth of the mandible with or without the hypoplasia of maxilla. Both syndromes may be caused by the presence of environmental factors, but the majority of them are hereditary. Several mutations are linked to those phenotypes. In this review, we summarize the current knowledge regarding the genetics of those phenotypes and describe genotype-phenotype correlations. We then present the animal models used to study these defects.
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Affiliation(s)
- Anna Jaruga
- Laboratory of Molecular Genetics, Department of Biomedical Sciences, Medical University of Lublin, Chodzki 1, 20-093 Lublin, Poland; (A.J.); (J.K.)
| | - Jakub Ksiazkiewicz
- Laboratory of Molecular Genetics, Department of Biomedical Sciences, Medical University of Lublin, Chodzki 1, 20-093 Lublin, Poland; (A.J.); (J.K.)
- Center for Molecular and Vascular Biology, Department of Cardiovascular Sciences, University of Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Krystian Kuzniarz
- Department of Maxillofacial Surgery, Medical University of Lublin, Staszica 11, 20-081 Lublin, Poland;
| | - Przemko Tylzanowski
- Laboratory of Molecular Genetics, Department of Biomedical Sciences, Medical University of Lublin, Chodzki 1, 20-093 Lublin, Poland; (A.J.); (J.K.)
- Department of Development and Regeneration, University of Leuven, Herestraat 49, 3000 Leuven, Belgium
- Correspondence:
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18
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Seelan RS, Pisano MM, Greene RM. MicroRNAs as epigenetic regulators of orofacial development. Differentiation 2022; 124:1-16. [DOI: 10.1016/j.diff.2022.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 12/30/2021] [Accepted: 01/13/2022] [Indexed: 11/03/2022]
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19
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Parisi L, Knapp PO, Girousi E, Rihs S, La Scala GC, Schnyder I, Stähli A, Sculean A, Bosshardt DD, Katsaros C, Degen M. A Living Cell Repository of the Cranio-/Orofacial Region to Advance Research and Promote Personalized Medicine. Front Cell Dev Biol 2021; 9:682944. [PMID: 34179013 PMCID: PMC8222786 DOI: 10.3389/fcell.2021.682944] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/11/2021] [Indexed: 12/12/2022] Open
Abstract
The prevalence of congenital anomalies in newborns is estimated to be as high as 6%, many of which involving the cranio-/orofacial region. Such malformations, including several syndromes, are usually identified prenatally, at birth, or rarely later in life. The lack of clinically relevant human cell models of these often very rare conditions, the societal pressure to avoid the use of animal models and the fact that the biological mechanisms between rodents and human are not necessarily identical, makes studying cranio-/orofacial anomalies challenging. To overcome these limitations, we are developing a living cell repository of healthy and diseased cells derived from the cranio-/orofacial region. Ultimately, we aim to make patient-derived cells, which retain the molecular and genetic characteristics of the original anomaly or disease in vitro, available for the scientific community. We report our efforts in establishing a human living cell bank derived from the cranio-/orofacial region of otherwise discarded tissue samples, detail our strategy, processes and quality checks. Such specific cell models have a great potential for discovery and translational research and might lead to a better understanding and management of craniofacial anomalies for the benefit of all affected individuals.
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Affiliation(s)
- Ludovica Parisi
- Laboratory for Oral Molecular Biology, Dental Research Center, Department of Orthodontics and Dentofacial Orthopedics, University of Bern, Bern, Switzerland
| | - Patrick O Knapp
- Laboratory for Oral Molecular Biology, Dental Research Center, Department of Orthodontics and Dentofacial Orthopedics, University of Bern, Bern, Switzerland
| | - Eleftheria Girousi
- Laboratory for Oral Molecular Biology, Dental Research Center, Department of Orthodontics and Dentofacial Orthopedics, University of Bern, Bern, Switzerland
| | - Silvia Rihs
- Laboratory for Oral Molecular Biology, Dental Research Center, Department of Orthodontics and Dentofacial Orthopedics, University of Bern, Bern, Switzerland
| | - Giorgio C La Scala
- Division of Pediatric Surgery, Department of Pediatrics, University Hospital of Geneva, Geneva, Switzerland
| | - Isabelle Schnyder
- University Clinic for Pediatric Surgery, Bern University Hospital, Bern, Switzerland
| | - Alexandra Stähli
- Department of Periodontology, School of Dental Medicine, University of Bern, Bern, Switzerland
| | - Anton Sculean
- Department of Periodontology, School of Dental Medicine, University of Bern, Bern, Switzerland
| | - Dieter D Bosshardt
- Department of Periodontology, School of Dental Medicine, University of Bern, Bern, Switzerland.,Robert K. Schenk Laboratory of Oral Histology, Dental Research Center, University of Bern, Bern, Switzerland
| | - Christos Katsaros
- Laboratory for Oral Molecular Biology, Dental Research Center, Department of Orthodontics and Dentofacial Orthopedics, University of Bern, Bern, Switzerland
| | - Martin Degen
- Laboratory for Oral Molecular Biology, Dental Research Center, Department of Orthodontics and Dentofacial Orthopedics, University of Bern, Bern, Switzerland
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20
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Peng Q, Qin W, Li S, Huang M, Rao C, Lu X. A Novel IRF6 Frameshift Mutation in a Large Chinese Pedigree With Van der Woude syndrome. Cleft Palate Craniofac J 2021; 59:548-553. [PMID: 33906476 DOI: 10.1177/10556656211010909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
AIMS Van der Woude syndrome (VWS) is one of the most common craniofacial anomalies, causing significant functional and psychological burden to the patients. This study aimed to identify the genetic cause of VWS in a Chinese family. METHODS Whole genome sequencing (WGS) was performed to screen for pathogenic mutations. Various Bioinformatics tools were used to assess the pathogenicity of the variants. Cosegregation analysis of the candidate variant was carried out. Interpretation of variants was performed according to the American College of Medical Genetics and Genomics guidelines. RESULTS A novel frameshift duplication c.373_374dupAA (p.Asn125Lys fs*43) was identified in exon 4 of the interferon regulatory factor 6 (IRF6) gene in all 3 affected members, which were not found in unaffected family members. The novel mutation leads to a frameshift and a premature stop codon which caused putative truncated protein. Protein alignment indicated high evolutionary conservation of the p.N125 residue, and this mutation was predicted by online tools to be damaging and deleterious. CONCLUSIONS This study demonstrates that the novel mutation c.373_374dupAA (p.Asn125Lysfs*43) in the IRF6 gene corresponds to the VWS in this family. The discovery of this pathogenic variant enriches the genotypic spectrum of IRF6 gene and contributes to genetic diagnosis and counseling of families with VWS.
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Affiliation(s)
- Qi Peng
- Department of Medical and Molecular Genetics, Dongguan Institute of Pediatrics, Dongguan, Guangdong, China.,Medical Laboratory, Dongguan Children's Hospital, Dongguan, Guangdong, China.,Key Laboratory for Children's Genetics and Infectious Diseases of Dongguan, Dongguan, Guangdong, China
| | - Wenyan Qin
- CapitalBio Technology Corporation, Beijing, China
| | - Siping Li
- Department of Medical and Molecular Genetics, Dongguan Institute of Pediatrics, Dongguan, Guangdong, China.,Medical Laboratory, Dongguan Children's Hospital, Dongguan, Guangdong, China.,Key Laboratory for Children's Genetics and Infectious Diseases of Dongguan, Dongguan, Guangdong, China
| | - Meihua Huang
- Department of Stomatology, Dongguan Eighth People's Hospital, Dongguan, Guangdong, China
| | - Chunbao Rao
- Department of Medical and Molecular Genetics, Dongguan Institute of Pediatrics, Dongguan, Guangdong, China.,Medical Laboratory, Dongguan Children's Hospital, Dongguan, Guangdong, China.,Key Laboratory for Children's Genetics and Infectious Diseases of Dongguan, Dongguan, Guangdong, China
| | - Xiaomei Lu
- Department of Medical and Molecular Genetics, Dongguan Institute of Pediatrics, Dongguan, Guangdong, China.,Medical Laboratory, Dongguan Children's Hospital, Dongguan, Guangdong, China.,Key Laboratory for Children's Genetics and Infectious Diseases of Dongguan, Dongguan, Guangdong, China
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21
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Goering JP, Isai DG, Czirok A, Saadi I. Isolation and Time-Lapse Imaging of Primary Mouse Embryonic Palatal Mesenchyme Cells to Analyze Collective Movement Attributes. J Vis Exp 2021. [PMID: 33645552 DOI: 10.3791/62151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Development of the palate is a dynamic process, which involves vertical growth of bilateral palatal shelves next to the tongue followed by elevation and fusion above the tongue. Defects in this process lead to cleft palate, a common birth defect. Recent studies have shown that palatal shelf elevation involves a remodeling process that transforms the orientation of the shelf from a vertical to a horizontal one. The role of the palatal shelf mesenchymal cells in this dynamic remodeling has been difficult to study. Time-lapse-imaging-based quantitative analysis has been recently used to show that primary mouse embryonic palatal mesenchymal (MEPM) cells can self-organize into a collective movement. Quantitative analyses could identify differences in mutant MEPM cells from a mouse model with palate elevation defects. This paper describes methods to isolate and culture MEPM cells from E13.5 embryos-specifically for time-lapse imaging-and to determine various cellular attributes of collective movement, including measures for stream formation, shape alignment, and persistence of direction. It posits that MEPM cells can serve as a proxy model for studying the role of palatal shelf mesenchyme during the dynamic process of elevation. These quantitative methods will allow investigators in the craniofacial field to assess and compare collective movement attributes in control and mutant cells, which will augment the understanding of mesenchymal remodeling during palatal shelf elevation. Furthermore, MEPM cells provide a rare mesenchymal cell model for investigation of collective cell movement in general.
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Affiliation(s)
- Jeremy P Goering
- Department of Anatomy and Cell Biology, University of Kansas Medical Center
| | - Dona Greta Isai
- Department of Anatomy and Cell Biology, University of Kansas Medical Center
| | - Andras Czirok
- Department of Anatomy and Cell Biology, University of Kansas Medical Center; Department of Biological Physics, Eotvos University;
| | - Irfan Saadi
- Department of Anatomy and Cell Biology, University of Kansas Medical Center;
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22
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Carroll SH, Macias Trevino C, Li EB, Kawasaki K, Myers N, Hallett SA, Alhazmi N, Cotney J, Carstens RP, Liao EC. An Irf6- Esrp1/2 regulatory axis controls midface morphogenesis in vertebrates. Development 2020; 147:dev194498. [PMID: 33234718 PMCID: PMC7774891 DOI: 10.1242/dev.194498] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/02/2020] [Indexed: 12/25/2022]
Abstract
Irf6 and Esrp1 are important for palate development across vertebrates. In zebrafish, we found that irf6 regulates the expression of esrp1 We detailed overlapping Irf6 and Esrp1/2 expression in mouse orofacial epithelium. In zebrafish, irf6 and esrp1/2 share expression in periderm, frontonasal ectoderm and oral epithelium. Genetic disruption of irf6 and esrp1/2 in zebrafish resulted in cleft of the anterior neurocranium. The esrp1/2 mutant also developed cleft of the mouth opening. Lineage tracing of cranial neural crest cells revealed that the cleft resulted not from migration defect, but from impaired chondrogenesis. Analysis of aberrant cells within the cleft revealed expression of sox10, col1a1 and irf6, and these cells were adjacent to krt4+ and krt5+ cells. Breeding of mouse Irf6; Esrp1; Esrp2 compound mutants suggested genetic interaction, as the triple homozygote and the Irf6; Esrp1 double homozygote were not observed. Further, Irf6 heterozygosity reduced Esrp1/2 cleft severity. These studies highlight the complementary analysis of Irf6 and Esrp1/2 in mouse and zebrafish, and identify a unique aberrant cell population in zebrafish expressing sox10, col1a1 and irf6 Future work characterizing this cell population will yield additional insight into cleft pathogenesis.
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Affiliation(s)
- Shannon H. Carroll
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Shriners Hospital for Children, Boston, MA 02114, USA
| | - Claudio Macias Trevino
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Harvard Medical School, Boston, MA 02115, USA
| | | | - Kenta Kawasaki
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Shriners Hospital for Children, Boston, MA 02114, USA
| | - Nikita Myers
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Shawn A. Hallett
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nora Alhazmi
- Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Justin Cotney
- Department of Genetics and Genome Sciences, University of Connecticut Health, CT 06030, USA
| | - Russ P. Carstens
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eric C. Liao
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Shriners Hospital for Children, Boston, MA 02114, USA
- Harvard Medical School, Boston, MA 02115, USA
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23
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A Novel IRF6 Variant Detected in a Family With Nonsyndromic Cleft Lip and Palate by Whole Exome Sequencing. J Craniofac Surg 2020; 32:265-269. [PMID: 33136784 DOI: 10.1097/scs.0000000000007000] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
ABSTRACT Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is the most common congenital craniofacial malformation, and its harmful effects on affected individuals and families are apparent. The causative genes and their mechanisms are not completely clear, although several studies have been conducted. Accordingly, in the present study, we recruited a Han Chinese family with hereditary NSCL/P to explore the possible causative variants of this disease using whole exome sequencing. Bioinformatics screening and analysis, mutation function prediction, species conservation analysis, and homology protein modeling were used to identify the variants and evaluate their influence. A mutation in the interferon regulatory factor 6 (IRF6) gene (c.961C>T; p.Val321Met) was detected as a candidate causative variant and predicted to be deleterious. The codon was found to be conserved in many species, and the residue change caused by this mutation changed the structure of IRF6 to a certain degree. The findings suggest that this IRF6 variant is probably the pathogenic cause of NSCL/P in this family. Our results further provide evidence that IRF6 variants play a role in the etiology of NSCL/P.
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24
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Association Between IRF6 Variants and Nonsyndromic Cleft Lip With or Without Cleft Palate in Chile. Reprod Sci 2020; 27:1857-1862. [DOI: 10.1007/s43032-020-00203-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/02/2020] [Indexed: 10/24/2022]
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25
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Degen M, Girousi E, Feldmann J, Parisi L, La Scala GC, Schnyder I, Schaller A, Katsaros C. A Novel Van der Woude Syndrome-Causing IRF6 Variant Is Subject to Incomplete Non-sense-Mediated mRNA Decay Affecting the Phenotype of Keratinocytes. Front Cell Dev Biol 2020; 8:583115. [PMID: 33117810 PMCID: PMC7552806 DOI: 10.3389/fcell.2020.583115] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/03/2020] [Indexed: 01/02/2023] Open
Abstract
Van der Woude syndrome (VWS) is a genetic syndrome that leads to typical phenotypic traits, including lower lip pits and cleft lip/palate (CLP). The majority of VWS-affected patients harbor a pathogenic variant in the gene encoding for the transcription factor interferon regulatory factor 6 (IRF6), a crucial regulator of orofacial development, epidermal differentiation and tissue repair. However, most of the underlying mechanisms leading from pathogenic IRF6 gene variants to phenotypes observed in VWS remain poorly understood and elusive. The availability of one VWS individual within our cohort of CLP patients allowed us to identify a novel VWS-causing IRF6 variant and to functionally characterize it. Using VWS patient-derived keratinocytes, we reveal that most of the mutated IRF6_VWS transcripts are subject to a non-sense-mediated mRNA decay mechanism, resulting in IRF6 haploinsufficiency. While moderate levels of IRF6_VWS remain detectable in the VWS keratinocytes, our data illustrate that the IRF6_VWS protein, which lacks part of its protein-binding domain and its whole C-terminus, is noticeably less stable than its wild-type counterpart. Still, it maintains transcription factor function. As we report and characterize a so far undescribed VWS-causing IRF6 variant, our results shed light on the physiological as well as pathological role of IRF6 in keratinocytes. This acquired knowledge is essential for a better understanding of the molecular mechanisms leading to VWS and CLP.
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Affiliation(s)
- Martin Degen
- Laboratory for Oral Molecular Biology, Dental Research Center, Department of Orthodontics and Dentofacial Orthopedics, University of Bern, Bern, Switzerland
| | - Eleftheria Girousi
- Laboratory for Oral Molecular Biology, Dental Research Center, Department of Orthodontics and Dentofacial Orthopedics, University of Bern, Bern, Switzerland
| | - Julia Feldmann
- Laboratory for Oral Molecular Biology, Dental Research Center, Department of Orthodontics and Dentofacial Orthopedics, University of Bern, Bern, Switzerland
| | - Ludovica Parisi
- Laboratory for Oral Molecular Biology, Dental Research Center, Department of Orthodontics and Dentofacial Orthopedics, University of Bern, Bern, Switzerland
| | - Giorgio C La Scala
- Division of Pediatric Surgery, Department of Pediatrics, University Hospital of Geneva, Geneva, Switzerland
| | - Isabelle Schnyder
- University Clinic for Pediatric Surgery, Bern University Hospital, Bern, Switzerland
| | - André Schaller
- Division of Human Genetics, Bern University Hospital, Bern, Switzerland
| | - Christos Katsaros
- Laboratory for Oral Molecular Biology, Dental Research Center, Department of Orthodontics and Dentofacial Orthopedics, University of Bern, Bern, Switzerland
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26
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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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27
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Hall EG, Wenger LW, Wilson NR, Undurty-Akella SS, Standley J, Augustine-Akpan EA, Kousa YA, Acevedo DS, Goering JP, Pitstick L, Natsume N, Paroya SM, Busch TD, Ito M, Mori A, Imura H, Schultz-Rogers LE, Klee EW, Babovic-Vuksanovic D, Kroc SA, Adeyemo WL, Eshete MA, Bjork BC, Suzuki S, Murray JC, Schutte BC, Butali A, Saadi I. SPECC1L regulates palate development downstream of IRF6. Hum Mol Genet 2020; 29:845-858. [PMID: 31943082 PMCID: PMC7104672 DOI: 10.1093/hmg/ddaa002] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 12/13/2019] [Accepted: 01/02/2020] [Indexed: 12/23/2022] Open
Abstract
SPECC1L mutations have been identified in patients with rare atypical orofacial clefts and with syndromic cleft lip and/or palate (CL/P). These mutations cluster in the second coiled-coil and calponin homology domains of SPECC1L and severely affect the ability of SPECC1L to associate with microtubules. We previously showed that gene-trap knockout of Specc1l in mouse results in early embryonic lethality. We now present a truncation mutant mouse allele, Specc1lΔC510, that results in perinatal lethality. Specc1lΔC510/ΔC510 homozygotes showed abnormal palate rugae but did not show cleft palate. However, when crossed with a gene-trap allele, Specc1lcGT/ΔC510 compound heterozygotes showed a palate elevation delay with incompletely penetrant cleft palate. Specc1lcGT/ΔC510 embryos exhibit transient oral epithelial adhesions at E13.5, which may delay shelf elevation. Consistent with oral adhesions, we show periderm layer abnormalities, including ectopic apical expression of adherens junction markers, similar to Irf6 hypomorphic mutants and Arhgap29 heterozygotes. Indeed, SPECC1L expression is drastically reduced in Irf6 mutant palatal shelves. Finally, we wanted to determine if SPECC1L deficiency also contributed to non-syndromic (ns) CL/P. We sequenced 62 Caucasian, 89 Filipino, 90 Ethiopian, 90 Nigerian and 95 Japanese patients with nsCL/P and identified three rare coding variants (p.Ala86Thr, p.Met91Iso and p.Arg546Gln) in six individuals. These variants reside outside of SPECC1L coiled-coil domains and result in milder functional defects than variants associated with syndromic clefting. Together, our data indicate that palate elevation is sensitive to deficiency of SPECC1L dosage and function and that SPECC1L cytoskeletal protein functions downstream of IRF6 in palatogenesis.
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Affiliation(s)
- Everett G Hall
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Luke W Wenger
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Nathan R Wilson
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Sraavya S Undurty-Akella
- Department of Pediatrics, Craniofacial Anomalies Research Center, University of Iowa, Iowa City, IA 52242, USA
| | - Jennifer Standley
- Department of Pediatrics, Craniofacial Anomalies Research Center, University of Iowa, Iowa City, IA 52242, USA
| | - Eno-Abasi Augustine-Akpan
- Department of Oral Pathology, Radiology and Medicine/Dow Institute for Dental Research, College of Dentistry, University of Iowa, Iowa City, IA 52242, USA
| | - Youssef A Kousa
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Diana S Acevedo
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Jeremy P Goering
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Lenore Pitstick
- Department of Biochemistry, Midwestern University, Downers Grove, IL 60515, USA
| | - Nagato Natsume
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, Aichi Gakuin University Hospital, 2-11 Suemori-Dori, Nagoya, Chikusa-ku, Japan
| | - Shahnawaz M Paroya
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Tamara D Busch
- Department of Pediatrics, Craniofacial Anomalies Research Center, University of Iowa, Iowa City, IA 52242, USA
| | - Masaaki Ito
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, Aichi Gakuin University Hospital, 2-11 Suemori-Dori, Nagoya, Chikusa-ku, Japan
| | - Akihiro Mori
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, Aichi Gakuin University Hospital, 2-11 Suemori-Dori, Nagoya, Chikusa-ku, Japan
| | - Hideto Imura
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, Aichi Gakuin University Hospital, 2-11 Suemori-Dori, Nagoya, Chikusa-ku, Japan
| | | | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Sarah A Kroc
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Wasiu L Adeyemo
- Department of Oral and Maxillofacial Surgery, College of Medicine, University of Lagos, Lagos, PMB 12003, Nigeria
| | - Mekonen A Eshete
- Department of Plastic and Reconstructive Surgery, Addis Ababa University, Addis Ababa, PO Box 26493, Ethiopia
| | - Bryan C Bjork
- Department of Biochemistry, Midwestern University, Downers Grove, IL 60515, USA
| | - Satoshi Suzuki
- Department of Pediatrics, Craniofacial Anomalies Research Center, University of Iowa, Iowa City, IA 52242, USA
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, Aichi Gakuin University Hospital, 2-11 Suemori-Dori, Nagoya, Chikusa-ku, Japan
| | - Jeffrey C Murray
- Department of Pediatrics, Craniofacial Anomalies Research Center, University of Iowa, Iowa City, IA 52242, USA
| | - Brian C Schutte
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
- Department of Pediatrics and Human Development, Michigan State University, East Lansing, MI 48824, USA
| | - Azeez Butali
- Department of Oral Pathology, Radiology and Medicine/Dow Institute for Dental Research, College of Dentistry, University of Iowa, Iowa City, IA 52242, USA
| | - Irfan Saadi
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
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28
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Kousa YA, Zhu H, Fakhouri WD, Lei Y, Kinoshita A, Roushangar RR, Patel NK, Agopian AJ, Yang W, Leslie EJ, Busch TD, Mansour TA, Li X, Smith AL, Li EB, Sharma DB, Williams TJ, Chai Y, Amendt BA, Liao EC, Mitchell LE, Bassuk AG, Gregory S, Ashley-Koch A, Shaw GM, Finnell RH, Schutte BC. The TFAP2A-IRF6-GRHL3 genetic pathway is conserved in neurulation. Hum Mol Genet 2020; 28:1726-1737. [PMID: 30689861 DOI: 10.1093/hmg/ddz010] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 11/26/2018] [Accepted: 12/31/2018] [Indexed: 02/06/2023] Open
Abstract
Mutations in IRF6, TFAP2A and GRHL3 cause orofacial clefting syndromes in humans. However, Tfap2a and Grhl3 are also required for neurulation in mice. Here, we found that homeostasis of Irf6 is also required for development of the neural tube and associated structures. Over-expression of Irf6 caused exencephaly, a rostral neural tube defect, through suppression of Tfap2a and Grhl3 expression. Conversely, loss of Irf6 function caused a curly tail and coincided with a reduction of Tfap2a and Grhl3 expression in tail tissues. To test whether Irf6 function in neurulation was conserved, we sequenced samples obtained from human cases of spina bifida and anencephaly. We found two likely disease-causing variants in two samples from patients with spina bifida. Overall, these data suggest that the Tfap2a-Irf6-Grhl3 genetic pathway is shared by two embryologically distinct morphogenetic events that previously were considered independent during mammalian development. In addition, these data suggest new candidates to delineate the genetic architecture of neural tube defects and new therapeutic targets to prevent this common birth defect.
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Affiliation(s)
- Youssef A Kousa
- Departments of Biochemistry and Molecular Biology.,Division of Neurology, Childrens National Health System.,Center for Neuroscience Research, The Childrens Research Institute, Washington, DC, USA
| | - Huiping Zhu
- Dell Pediatric Research Institute, Department of Nutritional Sciences, University of Texas at Austin, Austin, TX, USA
| | - Walid D Fakhouri
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Yunping Lei
- Dell Pediatric Research Institute, Department of Nutritional Sciences, University of Texas at Austin, Austin, TX, USA
| | - Akira Kinoshita
- Department of Human Genetics, Nagasaki University, Nagasaki, Japan
| | | | | | - A J Agopian
- Human Genetics Center, Division of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Houston, TX, USA
| | - Wei Yang
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Elizabeth J Leslie
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Tamer A Mansour
- Genetics PhD Program.,Department of Clinical Pathology, School of Medicine, University of Mansoura, Mansoura, Egypt.,Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Xiao Li
- Anatomy and Cell Biology, University of Iowa, Iowa City, IA, USA
| | | | - Edward B Li
- Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Dhruv B Sharma
- Center for Statistical Training & Consulting, Michigan State University, East Lansing, MI, USA
| | - Trevor J Williams
- Department of Craniofacial Biology, University of Colorado Denver at Anschutz Medical Campus, Aurora, CO, USA
| | - Yang Chai
- Center for Craniofacial Molecular Biology, Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA
| | - Brad A Amendt
- Anatomy and Cell Biology, University of Iowa, Iowa City, IA, USA
| | - Eric C Liao
- Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Laura E Mitchell
- Human Genetics Center, Division of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Houston, TX, USA
| | | | - Simon Gregory
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Allison Ashley-Koch
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, USA
| | - Gary M Shaw
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Richard H Finnell
- Dell Pediatric Research Institute, Department of Nutritional Sciences, University of Texas at Austin, Austin, TX, USA
| | - Brian C Schutte
- Departments of Biochemistry and Molecular Biology.,Microbiology and Molecular Genetics.,Genetics PhD Program.,Pediatrics and Human Development
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29
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Maili L, Letra A, Silva R, Buchanan EP, Mulliken JB, Greives MR, Teichgraeber JF, Blackwell SJ, Ummer R, Weber R, Chiquet B, Blanton SH, Hecht JT. PBX-WNT-P63-IRF6 pathway in nonsyndromic cleft lip and palate. Birth Defects Res 2019; 112:234-244. [PMID: 31825181 DOI: 10.1002/bdr2.1630] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/18/2019] [Accepted: 11/21/2019] [Indexed: 01/01/2023]
Abstract
Nonsyndromic cleft lip and palate (NSCLP) is one of the most common craniofacial anomalies in humans, affecting more than 135,000 newborns worldwide. NSCLP has a multifactorial etiology with more than 50 genes postulated to play an etiologic role. The genetic pathway comprised of Pbx-Wnt-p63-Irf6 genes was shown to control facial morphogenesis in mice and proposed as a regulatory pathway for NSCLP. Based on these findings, we investigated whether variation in PBX1, PBX2, and TP63, and their proposed interactions were associated with NSCLP. Fourteen single nucleotide variants (SNVs) in/nearby PBX1, PBX2, and TP63 were genotyped in 780 NSCLP families of nonHispanic white (NHW) and Hispanic ethnicities. Family-based association tests were performed for individual SNVs stratified by ethnicity and family history of NSCLP. Gene-gene interactions were also tested. A significant association was found for PBX2 rs3131300 and NSCLP in combined Hispanic families (p = .003) while nominal association was found for TP63 rs9332461 in multiplex Hispanic families (p = .005). Significant haplotype associations were observed for PBX2 in NHW (p = .0002) and Hispanic families (p = .003), and for TP63 in multiplex Hispanic families (.003). An independent case-control group was used to validate findings, and significant associations were found with PBX1 rs6426870 (p = .007) and TP63 rs9332461 (p = .03). Gene-gene interactions were detected between PBX1/PBX2/TP63 with IRF6 in NHW families, and between PBX1 with WNT9B in both NHW and Hispanic families (p < .0018). This study provides the first evidence for a role of PBX1 and PBX2, additional evidence for the role of TP63, and support for the proposed PBX-WNT-TP63-IRF6 regulatory pathway in the etiology of NSCLP.
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Affiliation(s)
- Lorena Maili
- Department of Pediatrics, University of Texas Health Science Center McGovern Medical School at Houston, Houston, Texas
| | - Ariadne Letra
- Department of Diagnostic and Biomedical Sciences, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas.,Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas
| | - Renato Silva
- Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas.,Department of Endodontics, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas
| | - Edward P Buchanan
- Department of Plastic Surgery, Texas Children's Hospital, Houston, Texas
| | | | - Matthew R Greives
- Department of Pediatric Surgery, University of Texas Health Science Center McGovern Medical School at Houston, Houston, Texas
| | - John F Teichgraeber
- Department of Pediatric Surgery, University of Texas Health Science Center McGovern Medical School at Houston, Houston, Texas
| | | | - Rohit Ummer
- Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas
| | - Ryan Weber
- Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas
| | - Brett Chiquet
- Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas.,Department of Pediatric Dentistry, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas
| | - Susan H Blanton
- Dr. John T. MacDonald Foundation Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Jacqueline T Hecht
- Department of Pediatrics, University of Texas Health Science Center McGovern Medical School at Houston, Houston, Texas.,Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry at Houston, Houston, Texas
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30
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Azevedo CDMS, Machado RA, Martelli-Júnior H, Reis SRDA, Persuhn DC, Coletta RD, Rangel ALCA. Exploring GRHL3 polymorphisms and SNP-SNP interactions in the risk of non-syndromic oral clefts in the Brazilian population. Oral Dis 2019; 26:145-151. [PMID: 31564061 DOI: 10.1111/odi.13204] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/27/2019] [Accepted: 09/20/2019] [Indexed: 01/02/2023]
Abstract
OBJECTIVE To investigate the association of single-nucleotide polymorphisms (SNP) in grainyhead-like 3 (GRHL3) and to verify its possible interactions with others genes responsible for craniofacial development in the risk of non-syndromic oral cleft (NSOC). METHODS Applying TaqMan allelic discrimination assays, we evaluated GRHL3 SNPs (rs10903078, rs41268753, and rs4648975) in an ancestry-structured case-control sample composed of 1,127 Brazilian participants [272 non-syndromic cleft palate only (NSCPO), 242 non-syndromic cleft lip only (NSCLO), 319 non-syndromic cleft lip and palate (NSCLP), and 294 healthy controls]. Additionally, SNP-SNP interactions of GRHL3 and previously reported variants in FAM49A, FOXE1, NTN1, and VAX1 were verified in non-syndromic cleft lip with or without cleft palate (NSCL ± P). To eliminate false-positive associations, Bonferroni correction or 1,000 permutation method was applied. RESULTS The multiple logistic regression analysis showed that the CC genotype of rs10903078 (p = .03) and the haplotype C-C formed by the SNPs rs10903078 and rs41268753 (p = .04) were associated with NSCLO, but the p-values did not withstand Bonferroni correction. However, SNP-SNP test revealed significant interactions between GRHL3 SNPs and FAM49A (rs7552), FOXE1 (rs3758249), VAX1 (rs7078160 and rs751231), and NTN1 (rs9891446). CONCLUSIONS Our results confirm the importance of GRHL3 and its interactions with previously NSOC-associated genes, including FAM49A, FOXE1, NTN1, and VAX1, in the pathogenesis of NSOC in the Brazilian population.
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Affiliation(s)
| | - Renato Assis Machado
- Department of Oral Diagnosis, School of Dentistry, University of Campinas, Piracicaba, Brazil
| | - Hercílio Martelli-Júnior
- Dental School, Stomatology Clinic, State University of Montes Claros, Montes Claros, Brazil.,Center for Rehabilitation of Craniofacial Anomalies, Dental School, University of José Rosario Vellano, Alfenas, Brazil
| | | | | | - Ricardo D Coletta
- Department of Oral Diagnosis, School of Dentistry, University of Campinas, Piracicaba, Brazil
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31
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Mendes SMDA, Espinosa DDSG, Moreira PEDO, Marques D, Fagundes NCF, Ribeiro-Dos-Santos Â. miRNAs as biomarkers of orofacial clefts: A systematic review. J Oral Pathol Med 2019; 49:201-209. [PMID: 31479540 DOI: 10.1111/jop.12950] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/05/2019] [Accepted: 08/11/2019] [Indexed: 01/26/2023]
Abstract
Orofacial clefts are facial malformations caused by the improper development of the lips and palate. Many genetic and epigenetic molecules have been involved in the mechanisms of orofacial clefts, one of which are miRNAs. This systematic review aimed to identify miRNAs associated to non-syndromic orofacial clefts in humans. After applying a series of criteria, four studies were selected for analysis. In total, one hundred miRNAs were observed in the literature, of which 57 were reported as upregulated and 43 as downregulated in all orofacial cleft classifications. Moreover, nine miRNAs were differentially expressed only in cleft palate patients, which might suggest distinct regulatory mechanisms for the etiology of cleft lips and palates. We suggest broader population sampling in order to include diverse ethnic groups in the future, as well as analyses toward identifying miRNA target genes and pathways. We highlight the need for experimental validation and of these results to allow further translational approaches and clinical applications.
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Affiliation(s)
- Sissy Maria Dos Anjos Mendes
- Laboratory of Human and Medical Genetics, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil.,Postgraduate Program in Genetics and Molecular Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | | | | | - Diego Marques
- Laboratory of Human and Medical Genetics, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil.,Postgraduate Program in Genetics and Molecular Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | | | - Ândrea Ribeiro-Dos-Santos
- Laboratory of Human and Medical Genetics, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil.,Postgraduate Program in Genetics and Molecular Biology, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
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32
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Shibano M, Watanabe A, Takano N, Mishima H, Kinoshita A, Yoshiura KI, Shibahara T. Target Capture/Next-Generation Sequencing for Nonsyndromic Cleft Lip and Palate in the Japanese Population. Cleft Palate Craniofac J 2019; 57:80-87. [PMID: 31337262 DOI: 10.1177/1055665619857650] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
OBJECTIVE The pathogenesis of nonsyndromic cleft lip with or without cleft palate (NSCL ± P) and nonsyndromic cleft palate only (NSCP) may be associated with genetic factors. Although some predisposing genes/loci have been reported, their attributable risk is too small to be clinically meaningful. To clarify the genetic causes and mechanisms of NSCL±P or NSCP, we conducted mutation analysis of target genes using a next-generation sequencing (NGS) approach. METHODS The target genes, IRF6, WNT5A, WNT9B, TP63, MSX1, TFAP2A, PAX9, DLX3, DLX4, and MN1, were selected based on previous reports of potential associations with the development of NSCL±P or NSCP from genome-wide association studies and candidate gene analyses. Mutation analysis was conducted using NGS on 74 Japanese trios (patient and parents) and 18 Japanese patients only families. RESULTS We detected single-nucleotide variants (SNVs) for 7 genes: IRF6, DLX4, WNT5A, TFAP2A, WNT9B, TP63, and PAX9. The SNVs found on IRF6 and DLX4 were missense mutations, whereas those identified on WNT5A, TFAP2A, WNT9B, TP63, and PAX9 were rare variants in the noncoding region; no de novo mutation was identified in the trio samples. The amino acid change on DLX4 was detected within the highly conserved homeodomain and was predicted to have a deleterious impact on the protein function by in silico analysis. CONCLUSIONS The DLX4 missense mutation c.359C>T (Pro120Leu) was found in 1 Japanese patient with NSCL±P and was located in the homeodomain region. This mutation likely plays a role in the development of NSCL±P in the Japanese population.
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Affiliation(s)
- Masayasu Shibano
- Department of Oral and Maxillofacial Surgery, Tokyo Dental College, Tokyo, Japan
| | - Akira Watanabe
- Department of Oral and Maxillofacial Surgery, Tokyo Dental College, Tokyo, Japan
| | - Nobuo Takano
- Oral Cancer Center, Tokyo Dental College, Chiba, Japan
| | - Hiroyuki Mishima
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Akira Kinoshita
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Koh-Ichiro Yoshiura
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Takahiko Shibahara
- Department of Oral and Maxillofacial Surgery, Tokyo Dental College, Tokyo, Japan
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33
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Haaland ØA, Romanowska J, Gjerdevik M, Lie RT, Gjessing HK, Jugessur A. A genome-wide scan of cleft lip triads identifies parent-of-origin interaction effects between ANK3 and maternal smoking, and between ARHGEF10 and alcohol consumption. F1000Res 2019; 8:960. [PMID: 31372216 PMCID: PMC6662680 DOI: 10.12688/f1000research.19571.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/16/2019] [Indexed: 01/08/2023] Open
Abstract
Background: Although both genetic and environmental factors have been reported to influence the risk of isolated cleft lip with or without cleft palate (CL/P), the exact mechanisms behind CL/P are still largely unaccounted for. We recently developed new methods to identify parent-of-origin (PoO) interactions with environmental exposures (PoOxE) and now apply them to data from a genome-wide association study (GWAS) of families with children born with isolated CL/P. Methods: Genotypes from 1594 complete triads and 314 dyads (1908 nuclear families in total) with CL/P were available for the current analyses. Of these families, 1024 were Asian, 825 were European and 59 had other ancestries. After quality control, 341,191 SNPs remained from the original 569,244. The exposures were maternal cigarette smoking, use of alcohol, and use of vitamin supplements in the periconceptional period. Our new methodology detects if PoO effects are different across environmental strata and is implemented in the R-package Haplin. Results: Among Europeans, there was evidence of a PoOxSmoke effect for ANK3 with three SNPs (rs3793861, q=0.20, p=2.6e-6; rs7087489, q=0.20, p=3.1e-6; rs4310561, q=0.67, p=4.0e-5) and a PoOxAlcohol effect for ARHGEF10 with two SNPs (rs2294035, q=0.32, p=2.9e-6; rs4876274, q=0.76, p=1.3e-5). Conclusion: Our results indicate that the detected PoOxE effects have a plausible biological basis, and thus warrant replication in other independent cleft samples. Our demonstration of the feasibility of identifying complex interactions between relevant environmental exposures and PoO effects offers new avenues for future research aimed at unravelling the complex etiology of cleft lip defects.
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Affiliation(s)
- Øystein Ariansen Haaland
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
| | - Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Computational Biology Unit, University of Bergen, Bergen, N-5020, Norway
| | - Miriam Gjerdevik
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Skøyen, Oslo, Skøyen, N-0213, Norway
| | - Rolv Terje Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Skøyen, Oslo, N-0213, Norway
| | - Håkon Kristian Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Skøyen, Oslo, N-0213, Norway
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Skøyen, Oslo, Skøyen, N-0213, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Skøyen, Oslo, N-0213, Norway
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34
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Haaland ØA, Romanowska J, Gjerdevik M, Lie RT, Gjessing HK, Jugessur A. A genome-wide scan of cleft lip triads identifies parent-of-origin interaction effects between ANK3 and maternal smoking, and between ARHGEF10 and alcohol consumption. F1000Res 2019; 8:960. [PMID: 31372216 PMCID: PMC6662680 DOI: 10.12688/f1000research.19571.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/17/2019] [Indexed: 12/21/2022] Open
Abstract
Background: Although both genetic and environmental factors have been reported to influence the risk of isolated cleft lip with or without cleft palate (CL/P), the exact mechanisms behind CL/P are still largely unaccounted for. We recently developed new methods to identify parent-of-origin (PoO) interactions with environmental exposures (PoOxE) and applied them to families with children born with isolated cleft palate only. Here, we used the same genome-wide association study (GWAS) dataset and methodology to screen for PoOxE effects in the larger sample of CL/P triads. Methods: Genotypes from 1594 complete triads and 314 dyads (1908 nuclear families in total) with CL/P were available for the current analyses. Of these families, 1024 were Asian, 825 were European and 59 had other ancestries. After quality control, 341,191 SNPs remained from the original 569,244. The exposures were maternal cigarette smoking, use of alcohol, and use of vitamin supplements in the periconceptional period. The methodology applied in the analyses is implemented in the R-package Haplin. Results: Among Europeans, there was evidence of a PoOxSmoke effect for ANK3 with three SNPs (rs3793861, q=0.20, p=2.6e-6; rs7087489, q=0.20, p=3.1e-6; rs4310561, q=0.67, p=4.0e-5) and a PoOxAlcohol effect for ARHGEF10 with two SNPs (rs2294035, q=0.32, p=2.9e-6; rs4876274, q=0.76, p=1.3e-5). Conclusion: Our results indicate that the detected PoOxE effects have a plausible biological basis, and thus warrant replication in other independent cleft samples. Our demonstration of the feasibility of identifying complex interactions between relevant environmental exposures and PoO effects offers new avenues for future research aimed at unravelling the complex etiology of cleft lip defects.
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Affiliation(s)
- Øystein Ariansen Haaland
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
| | - Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Computational Biology Unit, University of Bergen, Bergen, N-5020, Norway
| | - Miriam Gjerdevik
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Skøyen, Oslo, Skøyen, N-0213, Norway
| | - Rolv Terje Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Skøyen, Oslo, N-0213, Norway
| | - Håkon Kristian Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Skøyen, Oslo, N-0213, Norway
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, N-5020, Norway
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Skøyen, Oslo, Skøyen, N-0213, Norway
- Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Skøyen, Oslo, N-0213, Norway
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35
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Li H, Jones KL, Hooper JE, Williams T. The molecular anatomy of mammalian upper lip and primary palate fusion at single cell resolution. Development 2019; 146:dev.174888. [PMID: 31118233 DOI: 10.1242/dev.174888] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 05/13/2019] [Indexed: 12/19/2022]
Abstract
The mammalian lip and primary palate form when coordinated growth and morphogenesis bring the nasal and maxillary processes into contact, and the epithelia co-mingle, remodel and clear from the fusion site to allow mesenchyme continuity. Although several genes required for fusion have been identified, an integrated molecular and cellular description of the overall process is lacking. Here, we employ single cell RNA sequencing of the developing mouse face to identify ectodermal, mesenchymal and endothelial populations associated with patterning and fusion of the facial prominences. This analysis indicates that key cell populations at the fusion site exist within the periderm, basal epithelial cells and adjacent mesenchyme. We describe the expression profiles that make each population unique, and the signals that potentially integrate their behaviour. Overall, these data provide a comprehensive high-resolution description of the various cell populations participating in fusion of the lip and primary palate, as well as formation of the nasolacrimal groove, and they furnish a powerful resource for those investigating the molecular genetics of facial development and facial clefting that can be mined for crucial mechanistic information concerning this prevalent human birth defect.
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Affiliation(s)
- Hong Li
- Department of Craniofacial Biology, University of Colorado School of Dental Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Kenneth L Jones
- Department of Pediatrics, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Joan E Hooper
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA
| | - Trevor Williams
- Department of Craniofacial Biology, University of Colorado School of Dental Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA
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36
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Craniofacial malformations and their association with brain development: the importance of a multidisciplinary approach for treatment. Odontology 2019; 108:1-15. [PMID: 31172336 DOI: 10.1007/s10266-019-00433-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 05/22/2019] [Indexed: 02/08/2023]
Abstract
The craniofacial complex develops mainly in the first trimester of pregnancy, but its final shaping and the development of the teeth extend into the second and third trimesters. It is intimately connected with the development of the brain because of the crucial role the cranial neural crest cells play and the fact that many signals which control craniofacial development originate in the brain and vice versa. As a result, malformations of one organ may affect the development of the other. Similarly, there are developmental connections between the craniofacial complex and the teeth. Craniofacial anomalies are either isolated, resulting from abnormal development of the first two embryonic pharyngeal arches, or part of multiple malformation syndromes affecting many other organs. They may stem from gene mutations, chromosomal aberrations or from environmental causes induced by teratogens. The craniofacial morphologic changes are generally cosmetic, but they often interfere with important functions such as chewing, swallowing and respiration. In addition, they may cause hearing or visual impairment. In this review we discussed only a small number of craniofacial malformations and barely touched upon related anomalies of dentition. Following a brief description of the craniofacial development, we discussed oral clefts, craniofacial microsomia, teratogens that may interfere with craniofacial development resulting in different malformations, the genetically determined craniosynostoses syndromes and few other relatively common syndromes that, in addition to the craniofacial complex, also affect other organs. The understanding of these malformations is important in dentistry as dentists play an integral role in their diagnosis and multidisciplinary treatment.
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37
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Reynolds K, Kumari P, Sepulveda Rincon L, Gu R, Ji Y, Kumar S, Zhou CJ. Wnt signaling in orofacial clefts: crosstalk, pathogenesis and models. Dis Model Mech 2019; 12:12/2/dmm037051. [PMID: 30760477 PMCID: PMC6398499 DOI: 10.1242/dmm.037051] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Diverse signaling cues and attendant proteins work together during organogenesis, including craniofacial development. Lip and palate formation starts as early as the fourth week of gestation in humans or embryonic day 9.5 in mice. Disruptions in these early events may cause serious consequences, such as orofacial clefts, mainly cleft lip and/or cleft palate. Morphogenetic Wnt signaling, along with other signaling pathways and transcription regulation mechanisms, plays crucial roles during embryonic development, yet the signaling mechanisms and interactions in lip and palate formation and fusion remain poorly understood. Various Wnt signaling and related genes have been associated with orofacial clefts. This Review discusses the role of Wnt signaling and its crosstalk with cell adhesion molecules, transcription factors, epigenetic regulators and other morphogenetic signaling pathways, including the Bmp, Fgf, Tgfβ, Shh and retinoic acid pathways, in orofacial clefts in humans and animal models, which may provide a better understanding of these disorders and could be applied towards prevention and treatments.
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Affiliation(s)
- Kurt Reynolds
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, CA 95616, USA
| | - Priyanka Kumari
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA
| | - Lessly Sepulveda Rincon
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA
| | - Ran Gu
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA
| | - Yu Ji
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, CA 95616, USA
| | - Santosh Kumar
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA
| | - Chengji J Zhou
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA .,Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817, USA.,Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, CA 95616, USA
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38
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Kousa YA, Fuller E, Schutte BC. IRF6 and AP2A Interaction Regulates Epidermal Development. J Invest Dermatol 2018; 138:2578-2588. [DOI: 10.1016/j.jid.2018.05.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 05/08/2018] [Accepted: 05/29/2018] [Indexed: 12/29/2022]
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39
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Razaghi-Moghadam Z, Namipashaki A, Farahmand S, Ansari-Pour N. Systems genetics of nonsyndromic orofacial clefting provides insights into its complex aetiology. Eur J Hum Genet 2018; 27:226-234. [PMID: 30254216 DOI: 10.1038/s41431-018-0263-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 07/22/2018] [Accepted: 08/09/2018] [Indexed: 12/14/2022] Open
Abstract
Nonsyndromic oral clefting (NSOC) is although one of the most common congenital disorders worldwide, its underlying molecular basis remains elusive. This process has been hindered by the overwhelmingly high level of heterogeneity observed. Given that hitherto multiple loci and genes have been associated with NSOC, and that complex diseases are usually polygenic and show a considerable level of missing heritability, we used a systems genetics approach to reconstruct the NSOC network by integrating human-based physical and regulatory interactome with whole-transcriptome microarray data. We show that the network component contains 53% (23/43) of the curated NSOC-implicated gene set and displays a highly significant propinquity (P < 0.0001) between genes implicated at the genomic level and those differentially expressed at the transcriptome level. In addition, we identified bona fide candidate genes based on topological features and dysregulation (e.g. ANGPTL4), and similarly prioritised genes at GWA loci (e.g. MYC and CREBBP), thus providing further insight into the underlying heterogeneity of NSOC. Gene ontology analysis results were consistent with the NSOC network being associated with embryonic organ morphogenesis and also hinted at an aetiological overlap between NSOC and cancer. We therefore recommend this approach to be applied to other heterogeneous complex diseases to not only provide a molecular framework to unify genes which may seem as disparate entities linked to the same disease, but to also predict and prioritise candidate genes for further validation, thus addressing the missing heritability.
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Affiliation(s)
- Zahra Razaghi-Moghadam
- Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran.,Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Atefeh Namipashaki
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Saman Farahmand
- College of Science and Mathematics, University of Massachusetts Boston, Boston, Massachusetts, USA
| | - Naser Ansari-Pour
- Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran. .,Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LF, UK.
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40
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Welsh IC, Hart J, Brown JM, Hansen K, Rocha Marques M, Aho RJ, Grishina I, Hurtado R, Herzlinger D, Ferretti E, Garcia-Garcia MJ, Selleri L. Pbx loss in cranial neural crest, unlike in epithelium, results in cleft palate only and a broader midface. J Anat 2018; 233:222-242. [PMID: 29797482 PMCID: PMC6036936 DOI: 10.1111/joa.12821] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2018] [Indexed: 01/21/2023] Open
Abstract
Orofacial clefting represents the most common craniofacial birth defect. Cleft lip with or without cleft palate (CL/P) is genetically distinct from cleft palate only (CPO). Numerous transcription factors (TFs) regulate normal development of the midface, comprising the premaxilla, maxilla and palatine bones, through control of basic cellular behaviors. Within the Pbx family of genes encoding Three Amino-acid Loop Extension (TALE) homeodomain-containing TFs, we previously established that in the mouse, Pbx1 plays a preeminent role in midfacial morphogenesis, and Pbx2 and Pbx3 execute collaborative functions in domains of coexpression. We also reported that Pbx1 loss from cephalic epithelial domains, on a Pbx2- or Pbx3-deficient background, results in CL/P via disruption of a regulatory network that controls apoptosis at the seam of frontonasal and maxillary process fusion. Conversely, Pbx1 loss in cranial neural crest cell (CNCC)-derived mesenchyme on a Pbx2-deficient background results in CPO, a phenotype not yet characterized. In this study, we provide in-depth analysis of PBX1 and PBX2 protein localization from early stages of midfacial morphogenesis throughout development of the secondary palate. We further establish CNCC-specific roles of PBX TFs and describe the developmental abnormalities resulting from their loss in the murine embryonic secondary palate. Additionally, we compare and contrast the phenotypes arising from PBX1 loss in CNCC with those caused by its loss in the epithelium and show that CNCC-specific Pbx1 deletion affects only later secondary palate morphogenesis. Moreover, CNCC mutants exhibit perturbed rostro-caudal organization and broadening of the midfacial complex. Proliferation defects are pronounced in CNCC mutants at gestational day (E)12.5, suggesting altered proliferation of mutant palatal progenitor cells, consistent with roles of PBX factors in maintaining progenitor cell state. Although the craniofacial skeletal abnormalities in CNCC mutants do not result from overt patterning defects, osteogenesis is delayed, underscoring a critical role of PBX factors in CNCC morphogenesis and differentiation. Overall, the characterization of tissue-specific Pbx loss-of-function mouse models with orofacial clefting establishes these strains as unique tools to further dissect the complexities of this congenital craniofacial malformation. This study closely links PBX TALE homeodomain proteins to the variation in maxillary shape and size that occurs in pathological settings and during evolution of midfacial morphology.
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Affiliation(s)
- Ian C Welsh
- Program in Craniofacial Biology, Departments of Orofacial Sciences and Anatomy, Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - James Hart
- Department of Cell and Developmental Biology, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Joel M Brown
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Karissa Hansen
- Program in Craniofacial Biology, Departments of Orofacial Sciences and Anatomy, Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Marcelo Rocha Marques
- Program in Craniofacial Biology, Departments of Orofacial Sciences and Anatomy, Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Robert J Aho
- Program in Craniofacial Biology, Departments of Orofacial Sciences and Anatomy, Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Irina Grishina
- Department of Cell and Developmental Biology, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Romulo Hurtado
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Doris Herzlinger
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Elisabetta Ferretti
- Department of Cell and Developmental Biology, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | | | - Licia Selleri
- Program in Craniofacial Biology, Departments of Orofacial Sciences and Anatomy, Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College of Cornell University, New York, NY, USA
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41
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Skare Ø, Lie RT, Haaland ØA, Gjerdevik M, Romanowska J, Gjessing HK, Jugessur A. Analysis of Parent-of-Origin Effects on the X Chromosome in Asian and European Orofacial Cleft Triads Identifies Associations with DMD, FGF13, EGFL6, and Additional Loci at Xp22.2. Front Genet 2018. [PMID: 29520293 PMCID: PMC5827165 DOI: 10.3389/fgene.2018.00025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background: Although both the mother's and father's alleles are present in the offspring, they may not operate at the same level. These parent-of-origin (PoO) effects have not yet been explored on the X chromosome, which motivated us to develop new methods for detecting such effects. Orofacial clefts (OFCs) exhibit sex-specific differences in prevalence and are examples of traits where a search for various types of effects on the X chromosome might be relevant. Materials and Methods: We upgraded our R-package Haplin to enable genome-wide analyses of PoO effects, as well as power simulations for different statistical models. 14,486 X-chromosome SNPs in 1,291 Asian and 1,118 European case-parent triads of isolated OFCs were available from a previous GWAS. For each ethnicity, cleft lip with or without cleft palate (CL/P) and cleft palate only (CPO) were analyzed separately using two X-inactivation models and a sliding-window approach to haplotype analysis. In addition, we performed analyses restricted to female offspring. Results: Associations were identified in "Dystrophin" (DMD, Xp21.2-p21.1), "Fibroblast growth factor 13" (FGF13, Xq26.3-q27.1) and "EGF-like domain multiple 6" (EGFL6, Xp22.2), with biologically plausible links to OFCs. Unlike EGFL6, the other associations on chromosomal region Xp22.2 had no apparent connections to OFCs. However, the Xp22.2 region itself is of potential interest because it contains genes for clefting syndromes [for example, "Oral-facial-digital syndrome 1" (OFD1) and "Midline 1" (MID1)]. Overall, the identified associations were highly specific for ethnicity, cleft subtype and X-inactivation model, except for DMD in which associations were identified in both CPO and CL/P, in the model with X-inactivation and in Europeans only. Discussion/Conclusion: The specificity of the associations for ethnicity, cleft subtype and X-inactivation model underscores the utility of conducting subanalyses, despite the ensuing need to adjust for additional multiple testing. Further investigations are needed to confirm the associations with DMD, EGF16, and FGF13. Furthermore, chromosomal region Xp22.2 appears to be a hotspot for genes implicated in clefting syndromes and thus constitutes an exciting direction to pursue in future OFCs research. More generally, the new methods presented here are readily adaptable to the study of X-linked PoO effects in other outcomes that use a family-based design.
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Affiliation(s)
- Øivind Skare
- Department of Occupational Medicine and Epidemiology, National Institute of Occupational Health, Oslo, Norway
| | - Rolv T Lie
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway
| | - Øystein A Haaland
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Miriam Gjerdevik
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
| | - Julia Romanowska
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Håkon K Gjessing
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Centre for Fertility and Health (CeFH), Norwegian Institute of Public Health, Oslo, Norway.,Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
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Abstract
Development of the mammalian secondary palate involves highly dynamic morphogenetic processes, including outgrowth of palatal shelves from the oral side of the embryonic maxillary prominences, elevation of the initially vertically oriented palatal shelves to the horizontal position above the embryonic tongue, and subsequently adhesion and fusion of the paired palatal shelves at the midline to separate the oral cavity from the nasal cavity. Perturbation of any of these processes could cause cleft palate, a common birth defect that significantly affects patients' quality of life even after surgical treatment. In addition to identifying a large number of genes required for palate development, recent studies have begun to unravel the extensive cross-regulation of multiple signaling pathways, including Sonic hedgehog, bone morphogenetic protein, fibroblast growth factor, transforming growth factor β, and Wnt signaling, and multiple transcription factors during palatal shelf growth and patterning. Multiple studies also provide new insights into the gene regulatory networks and/or dynamic cellular processes underlying palatal shelf elevation, adhesion, and fusion. Here we summarize major recent advances and integrate the genes and molecular pathways with the cellular and morphogenetic processes of palatal shelf growth, patterning, elevation, adhesion, and fusion.
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Affiliation(s)
- C Li
- 1 Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Y Lan
- 1 Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,2 Division of Plastic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - R Jiang
- 1 Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,2 Division of Plastic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
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43
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Kousa YA, Roushangar R, Patel N, Walter A, Marangoni P, Krumlauf R, Klein OD, Schutte BC. IRF6 and SPRY4 Signaling Interact in Periderm Development. J Dent Res 2017; 96:1306-1313. [PMID: 28732181 DOI: 10.1177/0022034517719870] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Rare mutations in IRF6 and GRHL3 cause Van der Woude syndrome, an autosomal dominant orofacial clefting disorder. Common variants in IRF6 and GRHL3 also contribute risk for isolated orofacial clefting. Similarly, variants within genes that encode receptor tyrosine kinase (RTK) signaling components, including members of the FGF pathway, EPHA3 and SPRY2, also contribute risk for isolated orofacial clefting. In the mouse, loss of Irf6 or perturbation of Fgf signaling leads to abnormal oral epithelial adhesions and cleft palate. Oral adhesions can result from a disruption of periderm formation. Here, we find that IRF6 and SPRY4 signaling interact in periderm function. We crossed Irf6 heterozygous ( Irf6+/-) mice with transgenic mice that express Spry4 in the basal epithelial layer ( TgKRT14::Spry4). While embryos with either of these mutations can have abnormal oral adhesions, using a new quantitative assay, we observed a nonadditive effect of abnormal oral epithelial adhesions in the most severely affected double mutant embryos ( Irf6+/-;TgKRT14::Spry4). At the molecular level, the sites of abnormal oral adhesions maintained periderm-like cells that express keratin 6, but we observed abnormal expression of GRHL3. Together, these data suggest that Irf6 and RTK signaling interact in regulating periderm differentiation and function, as well as provide a rationale to screen for epistatic interactions between variants in IRF6 and RTK signaling pathway genes in human orofacial clefting populations.
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Affiliation(s)
- Y A Kousa
- 1 Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - R Roushangar
- 1 Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - N Patel
- 2 Pediatrics and Human Development, Michigan State University, East Lansing, MI, USA
| | - A Walter
- 2 Pediatrics and Human Development, Michigan State University, East Lansing, MI, USA
| | - P Marangoni
- 3 Departments of Orofacial Sciences and Pediatrics and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - R Krumlauf
- 4 Stowers Institute for Medical Research, Kansas City, MO, USA.,5 Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - O D Klein
- 3 Departments of Orofacial Sciences and Pediatrics and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - B C Schutte
- 2 Pediatrics and Human Development, Michigan State University, East Lansing, MI, USA.,6 Departments of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
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44
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Kousa YA, Moussa D, Schutte BC. IRF6 expression in basal epithelium partially rescues Irf6 knockout mice. Dev Dyn 2017. [PMID: 28643456 DOI: 10.1002/dvdy.24537] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Mutations in IRF6, CHUK (IKKA), and RIPK4 can lead to a disease spectrum that includes cutaneous, limb, and craniofacial malformations. Loss of these alleles in the mouse leads to perinatal lethality and severe cutaneous, limb, and craniofacial defects also. Genetic rescue in the mouse has been shown for Ikka and Ripk4. RESULTS Here, we show partial genetic rescue of Irf6 knockout embryos using the KRT14 promoter to drive Irf6 expression in the basal epithelium. In contrast to Irf6 knockout embryos, rescue embryos survive the immediate perinatal period. Macroscopic examination reveals rescue of skin adhesions between the axial and appendicular skeleton. Unexpectedly, KRT14-driven Irf6 expression does not completely rescue orofacial clefting and adhesions between the palate and tongue, suggesting the importance of cell-autonomous IRF6 expression in periderm. Like knockout embryos, Irf6 rescue embryos also have persistent esophageal adhesions, which likely contribute to postnatal demise. CONCLUSIONS Together, these data suggest that targeted expression of IRF6 can significantly reduce disease severity, but that a minimum level of Irf6 in both periderm and basal epithelial cells is necessary for orofacial development. Therefore, homologous human and mouse phenotypes are observed for IRF6, IKKA, and RIPK4. In this work, we show that altering the expression level of IRF6 dramatically modified this phenotype in utero. Developmental Dynamics 246:670-681, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Youssef A Kousa
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan.,Pediatric Residency Program, Children's National Health System, Washington, DC
| | - Dina Moussa
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan
| | - Brian C Schutte
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan.,Department of Pediatrics and Human Development, Michigan State University, East Lansing, Michigan
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45
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Hooper JE, Feng W, Li H, Leach SM, Phang T, Siska C, Jones KL, Spritz RA, Hunter LE, Williams T. Systems biology of facial development: contributions of ectoderm and mesenchyme. Dev Biol 2017; 426:97-114. [PMID: 28363736 PMCID: PMC5530582 DOI: 10.1016/j.ydbio.2017.03.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 03/23/2017] [Accepted: 03/23/2017] [Indexed: 12/17/2022]
Abstract
The rapid increase in gene-centric biological knowledge coupled with analytic approaches for genomewide data integration provides an opportunity to develop systems-level understanding of facial development. Experimental analyses have demonstrated the importance of signaling between the surface ectoderm and the underlying mesenchyme are coordinating facial patterning. However, current transcriptome data from the developing vertebrate face is dominated by the mesenchymal component, and the contributions of the ectoderm are not easily identified. We have generated transcriptome datasets from critical periods of mouse face formation that enable gene expression to be analyzed with respect to time, prominence, and tissue layer. Notably, by separating the ectoderm and mesenchyme we considerably improved the sensitivity compared to data obtained from whole prominences, with more genes detected over a wider dynamic range. From these data we generated a detailed description of ectoderm-specific developmental programs, including pan-ectodermal programs, prominence- specific programs and their temporal dynamics. The genes and pathways represented in these programs provide mechanistic insights into several aspects of ectodermal development. We also used these data to identify co-expression modules specific to facial development. We then used 14 co-expression modules enriched for genes involved in orofacial clefts to make specific mechanistic predictions about genes involved in tongue specification, in nasal process patterning and in jaw development. Our multidimensional gene expression dataset is a unique resource for systems analysis of the developing face; our co-expression modules are a resource for predicting functions of poorly annotated genes, or for predicting roles for genes that have yet to be studied in the context of facial development; and our analytic approaches provide a paradigm for analysis of other complex developmental programs.
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Affiliation(s)
- Joan E Hooper
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA; Computational Bioscience Program, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA.
| | - Weiguo Feng
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA; Department of Craniofacial Biology, University of Colorado School of Dental Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA.
| | - Hong Li
- Department of Craniofacial Biology, University of Colorado School of Dental Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA.
| | - Sonia M Leach
- Department of Biomedical Research, National Jewish Health, 1400 Jackson Street, Denver, CO 80206, USA.
| | - Tzulip Phang
- Computational Bioscience Program, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA; Department of Medicine, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA.
| | - Charlotte Siska
- Computational Bioscience Program, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA.
| | - Kenneth L Jones
- Department of Pediatrics, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA.
| | - Richard A Spritz
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, 12800 E 17th Avenue, Aurora, CO 80045, USA.
| | - Lawrence E Hunter
- Computational Bioscience Program, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA; Department of Pharmacology, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA.
| | - Trevor Williams
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA; Department of Craniofacial Biology, University of Colorado School of Dental Medicine, 12801 E 17th Avenue, Aurora, CO 80045, USA.
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46
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Kousa YA, Mansour TA, Seada H, Matoo S, Schutte BC. Shared molecular networks in orofacial and neural tube development. Birth Defects Res 2017; 109:169-179. [DOI: 10.1002/bdra.23598] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Revised: 10/17/2016] [Accepted: 10/21/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Youssef A. Kousa
- Pediatric Residency Program; Children's National Health System; Washington DC
| | - Tamer A. Mansour
- Department of Population Health and Reproduction; University of California; Davis California
- Department of Clinical Pathology, College of Medicine; Mansoura University; Egypt
| | - Haitham Seada
- Department of Computer Science and Engineering, Computational Optimization and Innovation Laboratory; Michigan State University; East Lansing Michigan
| | - Samaneh Matoo
- Department of Modern Science; Islamic Azad University-Tehran Medical Branch; Tehran Iran
| | - Brian C. Schutte
- Department of Microbiology and Molecular Genetics and the Department of Pediatrics and Human Development; Michigan State University; East Lansing Michigan
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47
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Xiao Y, Taub MA, Ruczinski I, Begum F, Hetmanski JB, Schwender H, Leslie EJ, Koboldt DC, Murray JC, Marazita ML, Beaty TH. Evidence for SNP-SNP interaction identified through targeted sequencing of cleft case-parent trios. Genet Epidemiol 2016; 41:244-250. [PMID: 28019042 DOI: 10.1002/gepi.22023] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 07/21/2016] [Accepted: 09/27/2016] [Indexed: 11/07/2022]
Abstract
Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is the most common craniofacial birth defect in humans, affecting 1 in 700 live births. This malformation has a complex etiology where multiple genes and several environmental factors influence risk. At least a dozen different genes have been confirmed to be associated with risk of NSCL/P in previous studies. However, all the known genetic risk factors cannot fully explain the observed heritability of NSCL/P, and several authors have suggested gene-gene (G × G) interaction may be important in the etiology of this complex and heterogeneous malformation. We tested for G × G interactions using common single nucleotide polymorphic (SNP) markers from targeted sequencing in 13 regions identified by previous studies spanning 6.3 Mb of the genome in a study of 1,498 NSCL/P case-parent trios. We used the R-package trio to assess interactions between polymorphic markers in different genes, using a 1 degree of freedom (1df) test for screening, and a 4 degree of freedom (4df) test to assess statistical significance of epistatic interactions. To adjust for multiple comparisons, we performed permutation tests. The most significant interaction was observed between rs6029315 in MAFB and rs6681355 in IRF6 (4df P = 3.8 × 10-8 ) in case-parent trios of European ancestry, which remained significant after correcting for multiple comparisons. However, no significant interaction was detected in trios of Asian ancestry.
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Affiliation(s)
- Yanzi Xiao
- Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Margaret A Taub
- Department of Biostatistics, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Ingo Ruczinski
- Department of Biostatistics, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Ferdouse Begum
- Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Jacqueline B Hetmanski
- Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Holger Schwender
- Mathematical Institute, Heinrich Heine University, Düsseldorf, Germany
| | - Elizabeth J Leslie
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel C Koboldt
- The Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Jeffrey C Murray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Terri H Beaty
- Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
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48
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Khandelwal KD, Ishorst N, Zhou H, Ludwig KU, Venselaar H, Gilissen C, Thonissen M, van Rooij IALM, Dreesen K, Steehouwer M, van de Vorst M, Bloemen M, van Beusekom E, Roosenboom J, Borstlap W, Admiraal R, Dormaar T, Schoenaers J, Vander Poorten V, Hens G, Verdonck A, Bergé S, Roeleveldt N, Vriend G, Devriendt K, Brunner HG, Mangold E, Hoischen A, van Bokhoven H, Carels CEL. Novel IRF6 Mutations Detected in Orofacial Cleft Patients by Targeted Massively Parallel Sequencing. J Dent Res 2016; 96:179-185. [PMID: 27834299 DOI: 10.1177/0022034516678829] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Common variants in interferon regulatory factor 6 ( IRF6) have been associated with nonsyndromic cleft lip with or without cleft palate (NSCL/P) as well as with tooth agenesis (TA). These variants contribute a small risk towards the 2 congenital conditions and explain only a small percentage of heritability. On the other hand, many IRF6 mutations are known to be a monogenic cause of disease for syndromic orofacial clefting (OFC). We hypothesize that IRF6 mutations in some rare instances could also cause nonsyndromic OFC. To find novel rare variants in IRF6 responsible for nonsyndromic OFC and TA, we performed targeted multiplex sequencing using molecular inversion probes (MIPs) in 1,072 OFC patients, 67 TA patients, and 706 controls. We identified 3 potentially pathogenic de novo mutations in OFC patients. In addition, 3 rare missense variants were identified, for which pathogenicity could not unequivocally be shown, as all variants were either inherited from an unaffected parent or the parental DNA was not available. Retrospective investigation of the patients with these variants revealed the presence of lip pits in one of the patients with a de novo mutation suggesting a Van der Woude syndrome (VWS) phenotype, whereas, in other patients, no lip pits were identified.
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Affiliation(s)
- K D Khandelwal
- 1 Department of Orthodontics and Craniofacial Biology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - N Ishorst
- 2 Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany.,3 Institute of Human Genetics, Biomedical Center, University of Bonn, Bonn, Germany
| | - H Zhou
- 4 Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,5 Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - K U Ludwig
- 2 Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany.,3 Institute of Human Genetics, Biomedical Center, University of Bonn, Bonn, Germany
| | - H Venselaar
- 6 Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - C Gilissen
- 4 Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,7 Department of Cognitive Neurosciences, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - M Thonissen
- 1 Department of Orthodontics and Craniofacial Biology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - I A L M van Rooij
- 8 Radboud Institute for Health Sciences, Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
| | - K Dreesen
- 1 Department of Orthodontics and Craniofacial Biology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - M Steehouwer
- 4 Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - M van de Vorst
- 4 Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - M Bloemen
- 1 Department of Orthodontics and Craniofacial Biology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - E van Beusekom
- 4 Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - J Roosenboom
- 9 Department of Neurosciences, Experimental Otorhinolaryngology, AGORA-Research Group, KU Leuven, Leuven, Belgium
| | - W Borstlap
- 10 Department of Oral and Maxillofacial Surgery, Radboud University Medical Center, Nijmegen, The Netherlands; Cleft Palate Craniofacial Centre, Radboud University Medical Center, Nijmegen, The Netherlands
| | - R Admiraal
- 11 Hearing & Genes Division, Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen. GA, The Netherlands; Cleft Palate Craniofacial Centre, Radboud University Medical Center, Nijmegen, The Netherlands
| | - T Dormaar
- 12 Department of Oral and Maxillofacial Surgery, University Hospitals Leuven, Leuven, Belgium; Leuven Cleft Lip and Palate Team, KU Leuven, Leuven, Belgium
| | - J Schoenaers
- 12 Department of Oral and Maxillofacial Surgery, University Hospitals Leuven, Leuven, Belgium; Leuven Cleft Lip and Palate Team, KU Leuven, Leuven, Belgium
| | - V Vander Poorten
- 13 Otorhinolaryngology-Head and Neck Surgery, University Hospitals Leuven, Belgium; Leuven Cleft Lip and Palate Team, University Hospitals KU Leuven, Leuven, Belgium
| | - G Hens
- 13 Otorhinolaryngology-Head and Neck Surgery, University Hospitals Leuven, Belgium; Leuven Cleft Lip and Palate Team, University Hospitals KU Leuven, Leuven, Belgium
| | - A Verdonck
- 14 Department of Orthodontics, University Hospitals Leuven, Belgium; Leuven Cleft Lip and Palate Team, AGORA-Research Group, University Hospitals KU Leuven, Leuven, Belgium
| | - S Bergé
- 10 Department of Oral and Maxillofacial Surgery, Radboud University Medical Center, Nijmegen, The Netherlands; Cleft Palate Craniofacial Centre, Radboud University Medical Center, Nijmegen, The Netherlands
| | - N Roeleveldt
- 8 Radboud Institute for Health Sciences, Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
| | - G Vriend
- 6 Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - K Devriendt
- 15 Department of Clinical Genetics, Center for Human Genetics, University Hospitals KU Leuven, Leuven, Belgium
| | - H G Brunner
- 4 Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - E Mangold
- 3 Institute of Human Genetics, Biomedical Center, University of Bonn, Bonn, Germany
| | - A Hoischen
- 4 Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,7 Department of Cognitive Neurosciences, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - H van Bokhoven
- 4 Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,7 Department of Cognitive Neurosciences, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - C E L Carels
- 4 Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,16 Department of Oral Health Sciences, AGORA-Research Group, University Hospitals KU Leuven, Leuven, Belgium
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49
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Orr DJA, Teeling EC, Puechmaille SJ, Finarelli JA. Patterns of orofacial clefting in the facial morphology of bats: a possible naturally occurring model of cleft palate. J Anat 2016; 229:657-672. [PMID: 27346883 PMCID: PMC5055088 DOI: 10.1111/joa.12510] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/17/2016] [Indexed: 12/21/2022] Open
Abstract
A normal feature of the facial anatomy of many species of bat is the presence of bony discontinuities or clefts, which bear a remarkable similarity to orofacial clefts that occur in humans as a congenital pathology. These clefts occur in two forms: a midline cleft between the two premaxillae (analogous to the rare midline craniofacial clefts in humans) and bilateral paramedian clefts between the premaxilla and the maxillae (analogous to the typical cleft lip and palate in humans). Here, we describe the distribution of orofacial clefting across major bat clades, exploring the relationship of the different patterns of clefting to feeding mode, development of the vomeronasal organ, development of the nasolacrimal duct and mode of emission of the echolocation call in different bat groups. We also present the results of detailed radiographic and soft tissue dissections of representative examples of the two types of cleft. The midline cleft has arisen independently multiple times in bat phylogeny, whereas the paramedian cleft has arisen once and is a synapomorphy uniting the Rhinolophidae and Hipposideridae. In all cases examined, the bony cleft is filled in by a robust fibrous membrane, continuous with the periosteum of the margins of the cleft. In the paramedian clefts, this membrane splits to enclose the premaxilla but forms a loose fold laterally between the premaxilla and maxilla, allowing the premaxilla and nose-leaf to pivot dorsoventrally in the sagittal plane under the action of facial muscles attached to the nasal cartilages. It is possible that this is a specific adaptation for echolocation and/or aerial insectivory. Given the shared embryological location of orofacial clefts in bats and humans, it is likely that aspects of the developmental control networks that produce cleft lip and palate in humans may also be implicated in the formation of these clefts as a normal feature in some bats. A better understanding of craniofacial development in bats with and without clefts may therefore suggest avenues for research into abnormal craniofacial development in humans.
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Affiliation(s)
- David J A Orr
- Department of Plastic and Reconstructive Surgery, Our Lady's Children's Hospital, Dublin, Ireland.
- School of Medicine, Trinity College Dublin, Dublin, Ireland.
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- UCD Earth Institute, University College Dublin, Dublin, Ireland
| | - Sébastien J Puechmaille
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Zoology Institute, Ernst-Moritz-Arndt University, Greifswald, Germany
| | - John A Finarelli
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- UCD Earth Institute, University College Dublin, Dublin, Ireland
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Tooth agenesis and orofacial clefting: genetic brothers in arms? Hum Genet 2016; 135:1299-1327. [PMID: 27699475 PMCID: PMC5065589 DOI: 10.1007/s00439-016-1733-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 09/21/2016] [Indexed: 12/16/2022]
Abstract
Tooth agenesis and orofacial clefts represent the most common developmental anomalies and their co-occurrence is often reported in patients as well in animal models. The aim of the present systematic review is to thoroughly investigate the current literature (PubMed, EMBASE) to identify the genes and genomic loci contributing to syndromic or non-syndromic co-occurrence of tooth agenesis and orofacial clefts, to gain insight into the molecular mechanisms underlying their dual involvement in the development of teeth and facial primordia. Altogether, 84 articles including phenotype and genotype description provided 9 genomic loci and 26 gene candidates underlying the co-occurrence of the two congenital defects: MSX1, PAX9, IRF6, TP63, KMT2D, KDM6A, SATB2, TBX22, TGFα, TGFβ3, TGFβR1, TGFβR2, FGF8, FGFR1, KISS1R, WNT3, WNT5A, CDH1, CHD7, AXIN2, TWIST1, BCOR, OFD1, PTCH1, PITX2, and PVRL1. The molecular pathways, cellular functions, tissue-specific expression and disease association were investigated using publicly accessible databases (EntrezGene, UniProt, OMIM). The Gene Ontology terms of the biological processes mediated by the candidate genes were used to cluster them using the GOTermMapper (Lewis-Sigler Institute, Princeton University), speculating on six super-clusters: (a) anatomical development, (b) cell division, growth and motility, (c) cell metabolism and catabolism, (d) cell transport, (e) cell structure organization and (f) organ/system-specific processes. This review aims to increase the knowledge on the mechanisms underlying the co-occurrence of tooth agenesis and orofacial clefts, to pave the way for improving targeted (prenatal) molecular diagnosis and finally to reflect on therapeutic or ultimately preventive strategies for these disabling conditions in the future.
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