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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] [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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Wilderman A, VanOudenhove J, Kron J, Noonan JP, Cotney J. High-Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development. Cell Rep 2019; 23:1581-1597. [PMID: 29719267 PMCID: PMC5965702 DOI: 10.1016/j.celrep.2018.03.129] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/05/2017] [Accepted: 03/28/2018] [Indexed: 11/29/2022] Open
Abstract
Defects in patterning during human embryonic development frequently result in craniofacial abnormalities. The gene regulatory programs that build the craniofacial complex are likely controlled by information located between genes and within intronic sequences. However, systematic identification of regulatory sequences important for forming the human face has not been performed. Here, we describe comprehensive epigenomic annotations from human embryonic craniofacial tissues and systematic comparisons with multiple tissues and cell types. We identified thousands of tissue-specific craniofacial regulatory sequences and likely causal regions for rare craniofacial abnormalities. We demonstrate significant enrichment of common variants associated with orofacial clefting in enhancers active early in embryonic development, while those associated with normal facial variation are enriched near the end of the embryonic period. These data are provided in easily accessible formats for both craniofacial researchers and clinicians to aid future experimental design and interpretation of noncoding variation in those affected by craniofacial abnormalities.
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Affiliation(s)
- Andrea Wilderman
- Graduate Program in Genetics and Developmental Biology, UConn Health, Farmington, CT 06030, USA; Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA
| | | | - Jeffrey Kron
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA
| | - James P Noonan
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Kavli Institute for Neuroscience, Yale University, New Haven, CT 06520, USA
| | - Justin Cotney
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06030, USA; Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA.
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Edelhoff D, Probst F, Ehrenfeld M, Prandtner O, Schweiger J, Liebermann A. Interdisciplinary full-mouth rehabilitation for redefining esthetics, function, and orofacial harmony. J ESTHET RESTOR DENT 2019; 31:179-189. [PMID: 30609191 DOI: 10.1111/jerd.12455] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 11/05/2018] [Accepted: 12/03/2018] [Indexed: 11/29/2022]
Abstract
OBJECTIVE In severe congenital or acquired orofacial anomalies, both dental esthetics and function are usually compromised. In particular, the esthetic ideas of the final desired appearance may differ from patient to patient, as the human esthetic sensibility differs significantly. Especially in complex cases, digital technology today offers outstanding improvements and simplifications in craniomaxillofacial surgical and prosthetic treatments, leading to a wide range of planning and pretreatment options. CLINICAL CONSIDERATIONS This case report describes a patient-oriented interdisciplinary craniomaxillofacial surgical and prosthetic treatment with noninvasive tooth-colored splints, a Le Fort I osteotomy, and a full-mouth rehabilitation to meet the patient's demand for better function as well as orofacial esthetics and harmony. CONCLUSIONS By means of the digitally planned Le Fort I intervention and completion of the prosthetic rehabilitation, it was possible to optimize esthetics and facial harmony. CLINICAL SIGNIFICANCE In complex cases, digital technology today offers outstanding improvements and simplifications in craniomaxillofacial surgery and prosthetic treatments, leading to a wide range of planning and pretreatment options. Computer-aided design/computer-aided manufacturing technology enables the fabrication of tooth-colored flexible polycarbonate splints that offer a noninvasive, removable, functional, and esthetic solution. In intricate cases involving craniomaxillofacial anomalies, often together with necessary orofacial surgeries or prosthetic treatments due to moderate to severe tooth wear, such digital preprosthetic treatment and planning options represent an important enhancement with more predictable results.
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Affiliation(s)
- Daniel Edelhoff
- Department of Prosthetic Dentistry, University Hospital, LMU Munich, Munich, Germany
| | - Florian Probst
- Department of Oral and Maxillofacial Surgery and Facial Plastic Surgery, University Hospital, Munich, Germany
| | - Michael Ehrenfeld
- Department of Oral and Maxillofacial Surgery and Facial Plastic Surgery, University Hospital, Munich, Germany
| | | | - Josef Schweiger
- Department of Prosthetic Dentistry, University Hospital, LMU Munich, Munich, Germany
| | - Anja Liebermann
- Department of Prosthetic Dentistry, University Hospital, LMU Munich, Munich, Germany
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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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Beaty TH, Marazita ML, Leslie EJ. Genetic factors influencing risk to orofacial clefts: today's challenges and tomorrow's opportunities. F1000Res 2016; 5:2800. [PMID: 27990279 PMCID: PMC5133690 DOI: 10.12688/f1000research.9503.1] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/18/2016] [Indexed: 12/18/2022] Open
Abstract
Orofacial clefts include cleft lip (CL), cleft palate (CP), and cleft lip and palate (CLP), which combined represent the largest group of craniofacial malformations in humans with an overall prevalence of one per 1,000 live births. Each of these birth defects shows strong familial aggregation, suggesting a major genetic component to their etiology. Genetic studies of orofacial clefts extend back centuries, but it has proven difficult to define any single etiologic mechanism because many genes appear to influence risk. Both linkage and association studies have identified several genes influencing risk, but these differ across families and across populations. Genome-wide association studies have identified almost two dozen different genes achieving genome-wide significance, and there are broad classes of 'causal genes' for orofacial clefts: a few genes strongly associated with risk and possibly directly responsible for Mendelian syndromes which include orofacial clefts as a key phenotypic feature of the syndrome, and multiple genes with modest individual effects on risk but capable of disrupting normal craniofacial development under the right circumstances (which may include exposure to environmental risk factors). Genomic sequencing studies are now underway which will no doubt reveal additional genes/regions where variants (sequence and structural) can play a role in controlling risk to orofacial clefts. The real challenge to medicine and public health is twofold: to identify specific genes and other etiologic factors in families with affected members and then to devise effective interventions for these different biological mechanisms controlling risk to complex and heterogeneous birth defects such as orofacial clefts.
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Affiliation(s)
- Terri H Beaty
- Department of Epidemiology, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Mary L Marazita
- Department of Oral Biology and Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, 15219, USA
| | - Elizabeth J Leslie
- Department of Oral Biology and Center for Craniofacial and Dental Genetics, University of Pittsburgh, Pittsburgh, PA, 15219, USA
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