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Kouwenhoven EN, van Bokhoven H, Zhou H. Gene regulatory mechanisms orchestrated by p63 in epithelial development and related disorders. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:590-600. [PMID: 25797018 DOI: 10.1016/j.bbagrm.2015.03.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 03/09/2015] [Accepted: 03/12/2015] [Indexed: 01/30/2023]
Abstract
The transcription factor p63 belongs to the p53 family and is a key regulator in epithelial commitment and development. Mutations in p63 give rise to several epithelial related disorders with defects in skin, limb and orofacial structures. Since the discovery of p63, efforts have been made to identify its target genes using individual gene approaches and to understand p63 function in normal epithelial development and related diseases. Recent genome-wide approaches have identified tens of thousands of potential p63-regulated target genes and regulatory elements, and reshaped the concept of gene regulation orchestrated by p63. These data also provide insights into p63-related disease mechanisms. In this review, we discuss the regulatory role of p63 in normal and diseased epithelial development in light of these novel findings. We also propose future perspectives for dissecting the molecular mechanism of p63-mediated epithelial development and related disorders as well as for potential therapeutic strategies.
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Affiliation(s)
- Evelyn N Kouwenhoven
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.
| | - Hans van Bokhoven
- Radboud university medical center, Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.
| | - Huiqing Zhou
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands; Radboud university medical center, Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands.
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Leslie EJ, Taub MA, Liu H, Steinberg KM, Koboldt DC, Zhang Q, Carlson JC, Hetmanski JB, Wang H, Larson DE, Fulton RS, Kousa YA, Fakhouri WD, Naji A, Ruczinski I, Begum F, Parker MM, Busch T, Standley J, Rigdon J, Hecht JT, Scott AF, Wehby GL, Christensen K, Czeizel AE, Deleyiannis FWB, Schutte BC, Wilson RK, Cornell RA, Lidral AC, Weinstock GM, Beaty TH, Marazita ML, Murray JC. Identification of functional variants for cleft lip with or without cleft palate in or near PAX7, FGFR2, and NOG by targeted sequencing of GWAS loci. Am J Hum Genet 2015; 96:397-411. [PMID: 25704602 PMCID: PMC4375420 DOI: 10.1016/j.ajhg.2015.01.004] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/09/2015] [Indexed: 11/21/2022] Open
Abstract
Although genome-wide association studies (GWASs) for nonsyndromic orofacial clefts have identified multiple strongly associated regions, the causal variants are unknown. To address this, we selected 13 regions from GWASs and other studies, performed targeted sequencing in 1,409 Asian and European trios, and carried out a series of statistical and functional analyses. Within a cluster of strongly associated common variants near NOG, we found that one, rs227727, disrupts enhancer activity. We furthermore identified significant clusters of non-coding rare variants near NTN1 and NOG and found several rare coding variants likely to affect protein function, including four nonsense variants in ARHGAP29. We confirmed 48 de novo mutations and, based on best biological evidence available, chose two of these for functional assays. One mutation in PAX7 disrupted the DNA binding of the encoded transcription factor in an in vitro assay. The second, a non-coding mutation, disrupted the activity of a neural crest enhancer downstream of FGFR2 both in vitro and in vivo. This targeted sequencing study provides strong functional evidence implicating several specific variants as primary contributory risk alleles for nonsyndromic clefting in humans.
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Affiliation(s)
- Elizabeth J Leslie
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA.
| | - Margaret A Taub
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Huan Liu
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA 52242, USA; State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, 430072 Wuhan, China
| | - Karyn Meltz Steinberg
- The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Daniel C Koboldt
- The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Qunyuan Zhang
- Department of Statistical Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Jenna C Carlson
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Jacqueline B Hetmanski
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Hang Wang
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - David E Larson
- The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Robert S Fulton
- The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Youssef A Kousa
- Department of Biochemistry and Molecular Biology, College of Osteopathic Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Walid D Fakhouri
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ali Naji
- Department of Diagnostic and Biomedical Sciences, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Ferdouse Begum
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Margaret M Parker
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Tamara Busch
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Jennifer Standley
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Jennifer Rigdon
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Jacqueline T Hecht
- Department of Pediatrics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Alan F Scott
- Institute of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - George L Wehby
- Department of Health Management and Policy, College of Public Health, University of Iowa, Iowa City, IA 52242, USA
| | - Kaare Christensen
- Department of Epidemiology, Institute of Public Health, University of Southern Denmark, 5230 Odense, Denmark
| | - Andrew E Czeizel
- Foundation for the Community Control of Hereditary Diseases, Budapest 1148, Hungary
| | - Frederic W-B Deleyiannis
- Department of Surgery, Plastic and Reconstructive Surgery, University of Colorado School of Medicine, Denver, CO 80045, USA
| | - Brian C Schutte
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Richard K Wilson
- The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Robert A Cornell
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Andrew C Lidral
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA 52242, USA
| | - George M Weinstock
- The Genome Institute, Washington University School of Medicine, St. Louis, MO 63108, USA; The Jackson Laboratory for Genomic Medicine, Farmington, CT 06117, USA
| | - Terri H Beaty
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA; Department of Human Genetics, Graduate School of Public Health, and Clinical and Translational Science Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Jeffrey C Murray
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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