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Dąbrowska J, Biedziak B, Bogdanowicz A, Mostowska A. Identification of Novel Risk Variants of Non-Syndromic Cleft Palate by Targeted Gene Panel Sequencing. J Clin Med 2023; 12:2051. [PMID: 36902838 PMCID: PMC10004578 DOI: 10.3390/jcm12052051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Non-syndromic cleft palate (ns-CP) has a genetically heterogeneous aetiology. Numerous studies have suggested a crucial role of rare coding variants in characterizing the unrevealed component of genetic variation in ns-CP called the "missing heritability". Therefore, this study aimed to detect low-frequency variants that are implicated in ns-CP aetiology in the Polish population. For this purpose, coding regions of 423 genes associated with orofacial cleft anomalies and/or involved with facial development were screened in 38 ns-CP patients using the next-generation sequencing technology. After multistage selection and prioritisation, eight novel and four known rare variants that may influence an individual's risk of ns-CP were identified. Among detected alternations, seven were located in novel candidate genes for ns-CP, including COL17A1 (c.2435-1G>A), DLG1 (c.1586G>C, p.Glu562Asp), NHS (c.568G>C, p.Val190Leu-de novo variant), NOTCH2 (c.1997A>G, p.Tyr666Cys), TBX18 (c.647A>T, p.His225Leu), VAX1 (c.400G>A, p.Ala134Thr) and WNT5B (c.716G>T, p.Arg239Leu). The remaining risk variants were identified within genes previously linked to ns-CP, confirming their contribution to this anomaly. This list included ARHGAP29 (c.1706G>A, p.Arg569Gln), FLNB (c.3605A>G, Tyr1202Cys), IRF6 (224A>G, p.Asp75Gly-de novo variant), LRP6 (c.481C>A, p.Pro161Thr) and TP63 (c.353A>T, p.Asn118Ile). In summary, this study provides further insights into the genetic components contributing to ns-CP aetiology and identifies novel susceptibility genes for this craniofacial anomaly.
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Affiliation(s)
- Justyna Dąbrowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, 6 Swiecickiego Street, 60-781 Poznan, Poland
| | - Barbara Biedziak
- Department of Orthodontics and Craniofacial Anomalies, Poznan University of Medical Sciences, 60-812 Poznan, Poland
| | - Agnieszka Bogdanowicz
- Department of Orthodontics and Craniofacial Anomalies, Poznan University of Medical Sciences, 60-812 Poznan, Poland
| | - Adrianna Mostowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, 6 Swiecickiego Street, 60-781 Poznan, Poland
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2
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Iwaya C, Suzuki A, Iwata J. MicroRNAs and Gene Regulatory Networks Related to Cleft Lip and Palate. Int J Mol Sci 2023; 24:3552. [PMID: 36834963 PMCID: PMC9958963 DOI: 10.3390/ijms24043552] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/04/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Cleft lip and palate is one of the most common congenital birth defects and has a complex etiology. Either genetic or environmental factors, or both, are involved at various degrees, and the type and severity of clefts vary. One of the longstanding questions is how environmental factors lead to craniofacial developmental anomalies. Recent studies highlight non-coding RNAs as potential epigenetic regulators in cleft lip and palate. In this review, we will discuss microRNAs, a type of small non-coding RNAs that can simultaneously regulate expression of many downstream target genes, as a causative mechanism of cleft lip and palate in humans and mice.
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Affiliation(s)
- Chihiro Iwaya
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Akiko Suzuki
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
| | - Junichi Iwata
- Department of Diagnostic & Biomedical Sciences, School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- Center for Craniofacial Research, The University of Texas Health Science Center at Houston, Houston, TX 77054, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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3
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Funato N. Craniofacial Phenotypes and Genetics of DiGeorge Syndrome. J Dev Biol 2022; 10:jdb10020018. [PMID: 35645294 PMCID: PMC9149807 DOI: 10.3390/jdb10020018] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/11/2022] [Accepted: 05/11/2022] [Indexed: 02/06/2023] Open
Abstract
The 22q11.2 deletion is one of the most common genetic microdeletions, affecting approximately 1 in 4000 live births in humans. A 1.5 to 2.5 Mb hemizygous deletion of chromosome 22q11.2 causes DiGeorge syndrome (DGS) and velocardiofacial syndrome (VCFS). DGS/VCFS are associated with prevalent cardiac malformations, thymic and parathyroid hypoplasia, and craniofacial defects. Patients with DGS/VCFS manifest craniofacial anomalies involving the cranium, cranial base, jaws, pharyngeal muscles, ear-nose-throat, palate, teeth, and cervical spine. Most craniofacial phenotypes of DGS/VCFS are caused by proximal 1.5 Mb microdeletions, resulting in a hemizygosity of coding genes, microRNAs, and long noncoding RNAs. TBX1, located on chromosome 22q11.21, encodes a T-box transcription factor and is a candidate gene for DGS/VCFS. TBX1 regulates the fate of progenitor cells in the cranial and pharyngeal apparatus during embryogenesis. Tbx1-null mice exhibit the most clinical features of DGS/VCFS, including craniofacial phenotypes. Despite the frequency of DGS/VCFS, there has been a limited review of the craniofacial phenotypes of DGC/VCFS. This review focuses on these phenotypes and summarizes the current understanding of the genetic factors that impact DGS/VCFS-related phenotypes. We also review DGS/VCFS mouse models that have been designed to better understand the pathogenic processes of DGS/VCFS.
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Affiliation(s)
- Noriko Funato
- Department of Signal Gene Regulation, Advanced Therapeutic Sciences, Medical and Dental Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
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4
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Raterman ST, Metz JR, Wagener FADTG, Von den Hoff JW. Zebrafish Models of Craniofacial Malformations: Interactions of Environmental Factors. Front Cell Dev Biol 2020; 8:600926. [PMID: 33304906 PMCID: PMC7701217 DOI: 10.3389/fcell.2020.600926] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/23/2020] [Indexed: 11/13/2022] Open
Abstract
The zebrafish is an appealing model organism for investigating the genetic (G) and environmental (E) factors, as well as their interactions (GxE), which contribute to craniofacial malformations. Here, we review zebrafish studies on environmental factors involved in the etiology of craniofacial malformations in humans including maternal smoking, alcohol consumption, nutrition and drug use. As an example, we focus on the (cleft) palate, for which the zebrafish ethmoid plate is a good model. This review highlights the importance of investigating ExE interactions and discusses the variable effects of exposure to environmental factors on craniofacial development depending on dosage, exposure time and developmental stage. Zebrafish also promise to be a good tool to study novel craniofacial teratogens and toxin mixtures. Lastly, we discuss the handful of studies on gene–alcohol interactions using mutant sensitivity screens and reverse genetic techniques. We expect that studies addressing complex interactions (ExE and GxE) in craniofacial malformations will increase in the coming years. These are likely to uncover currently unknown mechanisms with implications for the prevention of craniofacial malformations. The zebrafish appears to be an excellent complementary model with high translational value to study these complex interactions.
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Affiliation(s)
- S T Raterman
- Radboud Institute of Molecular Life Sciences, Nijmegen, Netherlands.,Department of Dentistry-Orthodontics and Craniofacial Biology, Radboud University Medical Center, Nijmegen, Netherlands.,Department of Animal Ecology and Physiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - J R Metz
- Department of Animal Ecology and Physiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, Netherlands
| | - Frank A D T G Wagener
- Radboud Institute of Molecular Life Sciences, Nijmegen, Netherlands.,Department of Dentistry-Orthodontics and Craniofacial Biology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Johannes W Von den Hoff
- Radboud Institute of Molecular Life Sciences, Nijmegen, Netherlands.,Department of Dentistry-Orthodontics and Craniofacial Biology, Radboud University Medical Center, Nijmegen, Netherlands
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5
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Reynolds K, Zhang S, Sun B, Garland M, Ji Y, Zhou CJ. Genetics and signaling mechanisms of orofacial clefts. Birth Defects Res 2020; 112:1588-1634. [PMID: 32666711 PMCID: PMC7883771 DOI: 10.1002/bdr2.1754] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/11/2020] [Accepted: 06/15/2020] [Indexed: 12/31/2022]
Abstract
Craniofacial development involves several complex tissue movements including several fusion processes to form the frontonasal and maxillary structures, including the upper lip and palate. Each of these movements are controlled by many different factors that are tightly regulated by several integral morphogenetic signaling pathways. Subject to both genetic and environmental influences, interruption at nearly any stage can disrupt lip, nasal, or palate fusion and result in a cleft. Here, we discuss many of the genetic risk factors that may contribute to the presentation of orofacial clefts in patients, and several of the key signaling pathways and underlying cellular mechanisms that control lip and palate formation, as identified primarily through investigating equivalent processes in animal models, are examined.
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Affiliation(s)
- Kurt Reynolds
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817
- Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817
- Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) graduate group, University of California, Davis, CA 95616
| | - Shuwen Zhang
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817
- Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817
| | - Bo Sun
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817
- Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817
| | - Michael Garland
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817
- Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817
| | - Yu Ji
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817
- Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817
- Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) graduate group, University of California, Davis, CA 95616
| | - Chengji J. Zhou
- Department of Biochemistry and Molecular Medicine, University of California at Davis, School of Medicine, Sacramento, CA 95817
- Institute for Pediatric Regenerative Medicine of Shriners Hospitals for Children, University of California at Davis, School of Medicine, Sacramento, CA 95817
- Biochemistry, Molecular, Cellular, and Developmental Biology (BMCDB) graduate group, University of California, Davis, CA 95616
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6
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Saad MN, Mabrouk MS, Eldeib AM, Shaker OG. Studying the effects of haplotype partitioning methods on the RA-associated genomic results from the North American Rheumatoid Arthritis Consortium (NARAC) dataset. J Adv Res 2019; 18:113-126. [PMID: 30891314 PMCID: PMC6403413 DOI: 10.1016/j.jare.2019.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/03/2019] [Accepted: 01/14/2019] [Indexed: 12/16/2022] Open
Abstract
Haplotype blocks methods plays a complementary role to the single-SNP approaches. CIT, FGT, SSLD, and single-SNP methods should be applied to discover the markers. Selection of the method used for the association has an impact on the biomarkers. SSLD method detected more significant SNPs than CIT, FGT, and single-SNP methods. The 383 SNPs discovered by all methods are significantly associated with RA.
The human genome, which includes thousands of genes, represents a big data challenge. Rheumatoid arthritis (RA) is a complex autoimmune disease with a genetic basis. Many single-nucleotide polymorphism (SNP) association methods partition a genome into haplotype blocks. The aim of this genome wide association study (GWAS) was to select the most appropriate haplotype block partitioning method for the North American Rheumatoid Arthritis Consortium (NARAC) dataset. The methods used for the NARAC dataset were the individual SNP approach and the following haplotype block methods: the four-gamete test (FGT), confidence interval test (CIT), and solid spine of linkage disequilibrium (SSLD). The measured parameters that reflect the strength of the association between the biomarker and RA were the P-value after Bonferroni correction and other parameters used to compare the output of each haplotype block method. This work presents a comparison among the individual SNP approach and the three haplotype block methods to select the method that can detect all the significant SNPs when applied alone. The GWAS results from the NARAC dataset obtained with the different methods are presented. The individual SNP, CIT, FGT, and SSLD methods detected 541, 1516, 1551, and 1831 RA-associated SNPs respectively, and the individual SNP, FGT, CIT, and SSLD methods detected 65, 156, 159, and 450 significant SNPs respectively, that were not detected by the other methods. Three hundred eighty-three SNPs were discovered by the haplotype block methods and the individual SNP approach, while 1021 SNPs were discovered by all three haplotype block methods. The 383 SNPs detected by all the methods are promising candidates for studying RA susceptibility. A hybrid technique involving all four methods should be applied to detect the significant SNPs associated with RA in the NARAC dataset, but the SSLD method may be preferred because of its advantages when only one method was used.
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Affiliation(s)
- Mohamed N Saad
- Biomedical Engineering Department, Faculty of Engineering, Minia University, Minia, Egypt
| | - Mai S Mabrouk
- Biomedical Engineering Department, Faculty of Engineering, Misr University for Science and Technology, 6th of October City, Egypt
| | - Ayman M Eldeib
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Giza, Egypt
| | - Olfat G Shaker
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
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7
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Clements CC, Wenger TL, Zoltowski AR, Bertollo JR, Miller JS, de Marchena AB, Mitteer LM, Carey JC, Yerys BE, Zackai EH, Emanuel BS, McDonald-McGinn DM, Schultz RT. Critical region within 22q11.2 linked to higher rate of autism spectrum disorder. Mol Autism 2017; 8:58. [PMID: 29090080 PMCID: PMC5658953 DOI: 10.1186/s13229-017-0171-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 09/27/2017] [Indexed: 11/26/2022] Open
Abstract
Background Previous studies have reported no clear critical region for medical comorbidities in children with deletions or duplications of 22q11.2. The purpose of this study was to evaluate whether individuals with small nested deletions or duplications of the LCR-A to B region of 22q11.2 show an elevated rate of autism spectrum disorder (ASD) compared to individuals with deletions or duplications that do not include this region. Methods We recruited 46 patients with nested deletions (n = 33) or duplications (n = 13) of 22q11.2, including LCR-A to B (ndel = 11), LCR-A to C (ndel = 4), LCR-B to D (ndel = 14; ndup = 8), LCR-C to D (ndel = 4; ndup = 2), and smaller nested regions (n = 3). Parent questionnaire, record review, and, for a subset, in-person evaluation were used for ASD diagnostic classification. Rates of ASD in individuals with involvement of LCR-B to LCR-D were compared with Fisher’s exact test to LCR-A to LCR-B for deletions, and to a previously published sample of LCR-A to LCR-D for duplications. The rates of medical comorbidities and psychiatric diagnoses were determined from questionnaires and chart review. We also report group mean differences on psychiatric questionnaires. Results Individuals with deletions involving LCR-A to B showed a 39–44% rate of ASD compared to 0% in individuals whose deletions did not involve LCR-A to B. We observed similar rates of medical comorbidities in individuals with involvement of LCR-A to B and LCR-B to D for both duplications and deletions, consistent with prior studies. Conclusions Children with nested deletions of 22q11.2 may be at greater risk for autism spectrum disorder if the region includes LCR-A to LCR-B. Replication is needed. Electronic supplementary material The online version of this article (10.1186/s13229-017-0171-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Caitlin C Clements
- Center for Autism Research, The Children's Hospital of Philadelphia, 2716 South Street, Philadelphia, PA 19104 USA.,Department of Psychology, University of Pennsylvania, 3720 Walnut Street, Philadelphia, PA 19104 USA
| | - Tara L Wenger
- Center for Autism Research, The Children's Hospital of Philadelphia, 2716 South Street, Philadelphia, PA 19104 USA.,Department of Pediatrics, Seattle Children's Hospital, 4800 Sand Point Way NE, Seattle, WA 98105 USA
| | - Alisa R Zoltowski
- Center for Autism Research, The Children's Hospital of Philadelphia, 2716 South Street, Philadelphia, PA 19104 USA.,Vanderbilt Brain Institute, Vanderbilt University School of Medicine, 465 21st Avenue South, Nashville, TN 37232 USA
| | - Jennifer R Bertollo
- Center for Autism Research, The Children's Hospital of Philadelphia, 2716 South Street, Philadelphia, PA 19104 USA
| | - Judith S Miller
- Center for Autism Research, The Children's Hospital of Philadelphia, 2716 South Street, Philadelphia, PA 19104 USA.,Department of Psychiatry, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104 USA
| | - Ashley B de Marchena
- Center for Autism Research, The Children's Hospital of Philadelphia, 2716 South Street, Philadelphia, PA 19104 USA.,Department of Behavioral and Social Science, University of the Sciences, 600 South 43rd Street, Philadelphia, PA 19104 USA
| | - Lauren M Mitteer
- Department of Pediatrics, The Children's Hospital of Philadelphia, 3400 Civic Center Boulevard, Philadelphia, PA 19104 USA
| | - John C Carey
- Department of Pediatrics, University of Utah, Salt Lake City, UT 84108 USA
| | - Benjamin E Yerys
- Center for Autism Research, The Children's Hospital of Philadelphia, 2716 South Street, Philadelphia, PA 19104 USA.,Department of Psychiatry, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104 USA
| | - Elaine H Zackai
- Department of Pediatrics, The Children's Hospital of Philadelphia, 3400 Civic Center Boulevard, Philadelphia, PA 19104 USA
| | - Beverly S Emanuel
- Department of Pediatrics, The Children's Hospital of Philadelphia, 3400 Civic Center Boulevard, Philadelphia, PA 19104 USA
| | - Donna M McDonald-McGinn
- Department of Pediatrics, The Children's Hospital of Philadelphia, 3400 Civic Center Boulevard, Philadelphia, PA 19104 USA
| | - Robert T Schultz
- Center for Autism Research, The Children's Hospital of Philadelphia, 2716 South Street, Philadelphia, PA 19104 USA.,Department of Psychiatry, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA 19104 USA.,Department of Pediatrics, The Children's Hospital of Philadelphia, 3400 Civic Center Boulevard, Philadelphia, PA 19104 USA
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8
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Schoen C, Aschrafi A, Thonissen M, Poelmans G, Von den Hoff JW, Carels CEL. MicroRNAs in Palatogenesis and Cleft Palate. Front Physiol 2017; 8:165. [PMID: 28420997 PMCID: PMC5378724 DOI: 10.3389/fphys.2017.00165] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 03/06/2017] [Indexed: 01/01/2023] Open
Abstract
Palatogenesis requires a precise spatiotemporal regulation of gene expression, which is controlled by an intricate network of transcription factors and their corresponding DNA motifs. Even minor perturbations of this network may cause cleft palate, the most common congenital craniofacial defect in humans. MicroRNAs (miRNAs), a class of small regulatory non-coding RNAs, have elicited strong interest as key regulators of embryological development, and as etiological factors in disease. MiRNAs function as post-transcriptional repressors of gene expression and are therefore able to fine-tune gene regulatory networks. Several miRNAs are already identified to be involved in congenital diseases. Recent evidence from research in zebrafish and mice indicates that miRNAs are key factors in both normal palatogenesis and cleft palate formation. Here, we provide an overview of recently identified molecular mechanisms underlying palatogenesis involving specific miRNAs, and discuss how dysregulation of these miRNAs may result in cleft palate.
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Affiliation(s)
- Christian Schoen
- Department of Orthodontics and Craniofacial Biology, Radboud University Medical CenterNijmegen, Netherlands
| | - Armaz Aschrafi
- Laboratory of Molecular Biology, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of HealthBethesda, MD, USA
| | - Michelle Thonissen
- Department of Orthodontics and Craniofacial Biology, Radboud University Medical CenterNijmegen, Netherlands
| | - Geert Poelmans
- Department of Human Genetics, Radboud University Medical CenterNijmegen, Netherlands.,Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical CenterNijmegen, Netherlands.,Department of Molecular Animal Physiology, Donders Institute for Brain, Cognition and Behaviour, Radboud Institute for Molecular Life Sciences, Radboud UniversityNijmegen, Netherlands
| | - Johannes W Von den Hoff
- Department of Orthodontics and Craniofacial Biology, Radboud University Medical CenterNijmegen, Netherlands
| | - Carine E L Carels
- Department of Orthodontics and Craniofacial Biology, Radboud University Medical CenterNijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical CenterNijmegen, Netherlands.,Department of Oral Health Sciences, University Hospitals-KU LeuvenLeuven, Belgium
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9
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Scariati E, Padula MC, Schaer M, Eliez S. Long-range dysconnectivity in frontal and midline structures is associated to psychosis in 22q11.2 deletion syndrome. J Neural Transm (Vienna) 2016; 123:823-39. [PMID: 27094177 DOI: 10.1007/s00702-016-1548-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 04/04/2016] [Indexed: 12/23/2022]
Abstract
Patients affected by 22q11.2 deletion syndrome (22q11DS) present a characteristic cognitive and psychiatric profile and have a genetic predisposition to develop schizophrenia. Although brain morphological alterations have been shown in the syndrome, they do not entirely account for the complex clinical picture of the patients with 22q11DS and for their high risk of psychotic symptoms. Since Friston proposed the "disconnection hypothesis" in 1998, schizophrenia is commonly considered as a disorder of brain connectivity. In this study, we review existing evidence pointing to altered brain structural and functional connectivity in 22q11DS, with a specific focus on the role of dysconnectivity in the emergence of psychotic symptoms. We show that widespread alterations of structural and functional connectivity have been described in association with 22q11DS. Moreover, alterations involving long-range association tracts as well as midline structures, such as the corpus callosum and the cingulate gyrus, have been associated with psychotic symptoms in this population. These results suggest common mechanisms for schizophrenia in syndromic and non-syndromic populations. Future directions for investigations are also discussed.
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Affiliation(s)
- E Scariati
- Office Médico-Pédagogique, Department of Psychiatry, University of Geneva, Rue David-Dufour 1, Case Postale 50, 1211, Genève 8, Switzerland.
| | - M C Padula
- Office Médico-Pédagogique, Department of Psychiatry, University of Geneva, Rue David-Dufour 1, Case Postale 50, 1211, Genève 8, Switzerland.
| | - M Schaer
- Office Médico-Pédagogique, Department of Psychiatry, University of Geneva, Rue David-Dufour 1, Case Postale 50, 1211, Genève 8, Switzerland.,Stanford Cognitive and Systems Neuroscience Laboratory, Stanford University, Stanford, CA, USA
| | - S Eliez
- Office Médico-Pédagogique, Department of Psychiatry, University of Geneva, Rue David-Dufour 1, Case Postale 50, 1211, Genève 8, Switzerland.,Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
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10
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Conte F, Oti M, Dixon J, Carels CEL, Rubini M, Zhou H. Systematic analysis of copy number variants of a large cohort of orofacial cleft patients identifies candidate genes for orofacial clefts. Hum Genet 2015; 135:41-59. [PMID: 26561393 PMCID: PMC4698300 DOI: 10.1007/s00439-015-1606-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/15/2015] [Indexed: 12/16/2022]
Abstract
Orofacial clefts (OFCs) represent a large fraction of human birth defects and are one of the most common phenotypes affected by large copy number variants (CNVs). Due to the limited number of CNV patients in individual centers, CNV analyses of a large number of OFC patients are challenging. The present study analyzed 249 genomic deletions and 226 duplications from a cohort of 312 OFC patients reported in two publicly accessible databases of chromosome imbalance and phenotype in humans, DECIPHER and ECARUCA. Genomic regions deleted or duplicated in multiple patients were identified, and genes in these overlapping CNVs were prioritized based on the number of genes encompassed by the region and gene expression in embryonic mouse palate. Our analyses of these overlapping CNVs identified two genes known to be causative for human OFCs, SATB2 and MEIS2, and 12 genes (DGCR6, FGF2, FRZB, LETM1, MAPK3, SPRY1, THBS1, TSHZ1, TTC28, TULP4, WHSC1, WHSC2) that are associated with OFC or orofacial development. Additionally, we report 34 deleted and 24 duplicated genes that have not previously been associated with OFCs but are associated with the BMP, MAPK and RAC1 pathways. Statistical analyses show that the high number of overlapping CNVs is not due to random occurrence. The identified genes are not located in highly variable genomic regions in healthy populations and are significantly enriched for genes that are involved in orofacial development. In summary, we report a CNV analysis pipeline of a large cohort of OFC patients and identify novel candidate OFC genes.
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Affiliation(s)
- Federica Conte
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands.,Medical Genetic Unit, Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, Ferrara, Italy
| | - Martin Oti
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Jill Dixon
- Faculty of Medical and Human Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Carine E L Carels
- Department of Orthodontics and Craniofacial Biology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Michele Rubini
- Medical Genetic Unit, Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, Ferrara, Italy.
| | - Huiqing Zhou
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands. .,Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
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Meechan DW, Maynard TM, Tucker ES, Fernandez A, Karpinski BA, Rothblat LA, LaMantia AS. Modeling a model: Mouse genetics, 22q11.2 Deletion Syndrome, and disorders of cortical circuit development. Prog Neurobiol 2015; 130:1-28. [PMID: 25866365 DOI: 10.1016/j.pneurobio.2015.03.004] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 03/24/2015] [Accepted: 03/29/2015] [Indexed: 12/21/2022]
Abstract
Understanding the developmental etiology of autistic spectrum disorders, attention deficit/hyperactivity disorder and schizophrenia remains a major challenge for establishing new diagnostic and therapeutic approaches to these common, difficult-to-treat diseases that compromise neural circuits in the cerebral cortex. One aspect of this challenge is the breadth and overlap of ASD, ADHD, and SCZ deficits; another is the complexity of mutations associated with each, and a third is the difficulty of analyzing disrupted development in at-risk or affected human fetuses. The identification of distinct genetic syndromes that include behavioral deficits similar to those in ASD, ADHC and SCZ provides a critical starting point for meeting this challenge. We summarize clinical and behavioral impairments in children and adults with one such genetic syndrome, the 22q11.2 Deletion Syndrome, routinely called 22q11DS, caused by micro-deletions of between 1.5 and 3.0 MB on human chromosome 22. Among many syndromic features, including cardiovascular and craniofacial anomalies, 22q11DS patients have a high incidence of brain structural, functional, and behavioral deficits that reflect cerebral cortical dysfunction and fall within the spectrum that defines ASD, ADHD, and SCZ. We show that developmental pathogenesis underlying this apparent genetic "model" syndrome in patients can be defined and analyzed mechanistically using genomically accurate mouse models of the deletion that causes 22q11DS. We conclude that "modeling a model", in this case 22q11DS as a model for idiopathic ASD, ADHD and SCZ, as well as other behavioral disorders like anxiety frequently seen in 22q11DS patients, in genetically engineered mice provides a foundation for understanding the causes and improving diagnosis and therapy for these disorders of cortical circuit development.
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Affiliation(s)
- Daniel W Meechan
- Institute for Neuroscience, Department of Pharmacology & Physiology, The George Washington University, Washington, DC, United States
| | - Thomas M Maynard
- Institute for Neuroscience, Department of Pharmacology & Physiology, The George Washington University, Washington, DC, United States
| | - Eric S Tucker
- Department of Neurobiology and Anatomy, Neuroscience Graduate Program, and Center for Neuroscience, West Virginia University School of Medicine, Morgantown, West Virginia
| | - Alejandra Fernandez
- Institute for Neuroscience, Department of Pharmacology & Physiology, The George Washington University, Washington, DC, United States
| | - Beverly A Karpinski
- Institute for Neuroscience, Department of Pharmacology & Physiology, The George Washington University, Washington, DC, United States
| | - Lawrence A Rothblat
- Institute for Neuroscience, Department of Pharmacology & Physiology, The George Washington University, Washington, DC, United States; Department of Psychology, The George Washington University, Washington, DC, United States
| | - Anthony-S LaMantia
- Institute for Neuroscience, Department of Pharmacology & Physiology, The George Washington University, Washington, DC, United States.
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12
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Liu S, Higashihori N, Yahiro K, Moriyama K. Retinoic acid inhibits histone methyltransferase Whsc1 during palatogenesis. Biochem Biophys Res Commun 2015; 458:525-530. [DOI: 10.1016/j.bbrc.2015.01.148] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 01/30/2015] [Indexed: 12/29/2022]
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Dykes IM, van Bueren KL, Ashmore RJ, Floss T, Wurst W, Szumska D, Bhattacharya S, Scambler PJ. HIC2 is a novel dosage-dependent regulator of cardiac development located within the distal 22q11 deletion syndrome region. Circ Res 2014; 115:23-31. [PMID: 24748541 DOI: 10.1161/circresaha.115.303300] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
RATIONALE 22q11 deletion syndrome arises from recombination between low-copy repeats on chromosome 22. Typical deletions result in hemizygosity for TBX1 associated with congenital cardiovascular disease. Deletions distal to the typically deleted region result in a similar cardiac phenotype but lack in extracardiac features of the syndrome, suggesting that a second haploinsufficient gene maps to this interval. OBJECTIVE The transcription factor HIC2 is lost in most distal deletions, as well as in a minority of typical deletions. We used mouse models to test the hypothesis that HIC2 hemizygosity causes congenital heart disease. METHODS AND RESULTS We created a genetrap mouse allele of Hic2. The genetrap reporter was expressed in the heart throughout the key stages of cardiac morphogenesis. Homozygosity for the genetrap allele was embryonic lethal before embryonic day E10.5, whereas the heterozygous condition exhibited a partially penetrant late lethality. One third of heterozygous embryos had a cardiac phenotype. MRI demonstrated a ventricular septal defect with over-riding aorta. Conditional targeting indicated a requirement for Hic2 within the Nkx2.5+ and Mesp1+ cardiovascular progenitor lineages. Microarray analysis revealed increased expression of Bmp10. CONCLUSIONS Our results demonstrate a novel role for Hic2 in cardiac development. Hic2 is the first gene within the distal 22q11 interval to have a demonstrated haploinsufficient cardiac phenotype in mice. Together our data suggest that HIC2 haploinsufficiency likely contributes to the cardiac defects seen in distal 22q11 deletion syndrome.
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Affiliation(s)
- Iain M Dykes
- From the Molecular Medicine Unit, Institute of Child Health, University College London, London, United Kingdom (I.M.D., K.L.v.B., R.J.A., P.J.S.); Institute of Developmental Genetics (T.F., W.W.) and Technische Universität München-Weihenstephan, Institute of Developmental Genetics (T.F., W.W.), Helmholtz Zentrum München, Neuherberg/Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Site Munich, Munich, Germany (W.W.); Munich Cluster for Systems Neurology (SyNergy), Adolf Butenandt Institute, Ludwig-Maximilians-Universität München, Munich, Germany (W.W.); and Departments of Cardiovascular Medicine (D.S., S.B.) and Cardiovascular Medicine (I.M.D.), University of Oxford, Wellcome Trust Centre for Human Genetics, Headington, Oxford, United Kingdom
| | - Kelly Lammerts van Bueren
- From the Molecular Medicine Unit, Institute of Child Health, University College London, London, United Kingdom (I.M.D., K.L.v.B., R.J.A., P.J.S.); Institute of Developmental Genetics (T.F., W.W.) and Technische Universität München-Weihenstephan, Institute of Developmental Genetics (T.F., W.W.), Helmholtz Zentrum München, Neuherberg/Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Site Munich, Munich, Germany (W.W.); Munich Cluster for Systems Neurology (SyNergy), Adolf Butenandt Institute, Ludwig-Maximilians-Universität München, Munich, Germany (W.W.); and Departments of Cardiovascular Medicine (D.S., S.B.) and Cardiovascular Medicine (I.M.D.), University of Oxford, Wellcome Trust Centre for Human Genetics, Headington, Oxford, United Kingdom
| | - Rebekah J Ashmore
- From the Molecular Medicine Unit, Institute of Child Health, University College London, London, United Kingdom (I.M.D., K.L.v.B., R.J.A., P.J.S.); Institute of Developmental Genetics (T.F., W.W.) and Technische Universität München-Weihenstephan, Institute of Developmental Genetics (T.F., W.W.), Helmholtz Zentrum München, Neuherberg/Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Site Munich, Munich, Germany (W.W.); Munich Cluster for Systems Neurology (SyNergy), Adolf Butenandt Institute, Ludwig-Maximilians-Universität München, Munich, Germany (W.W.); and Departments of Cardiovascular Medicine (D.S., S.B.) and Cardiovascular Medicine (I.M.D.), University of Oxford, Wellcome Trust Centre for Human Genetics, Headington, Oxford, United Kingdom
| | - Thomas Floss
- From the Molecular Medicine Unit, Institute of Child Health, University College London, London, United Kingdom (I.M.D., K.L.v.B., R.J.A., P.J.S.); Institute of Developmental Genetics (T.F., W.W.) and Technische Universität München-Weihenstephan, Institute of Developmental Genetics (T.F., W.W.), Helmholtz Zentrum München, Neuherberg/Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Site Munich, Munich, Germany (W.W.); Munich Cluster for Systems Neurology (SyNergy), Adolf Butenandt Institute, Ludwig-Maximilians-Universität München, Munich, Germany (W.W.); and Departments of Cardiovascular Medicine (D.S., S.B.) and Cardiovascular Medicine (I.M.D.), University of Oxford, Wellcome Trust Centre for Human Genetics, Headington, Oxford, United Kingdom
| | - Wolfgang Wurst
- From the Molecular Medicine Unit, Institute of Child Health, University College London, London, United Kingdom (I.M.D., K.L.v.B., R.J.A., P.J.S.); Institute of Developmental Genetics (T.F., W.W.) and Technische Universität München-Weihenstephan, Institute of Developmental Genetics (T.F., W.W.), Helmholtz Zentrum München, Neuherberg/Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Site Munich, Munich, Germany (W.W.); Munich Cluster for Systems Neurology (SyNergy), Adolf Butenandt Institute, Ludwig-Maximilians-Universität München, Munich, Germany (W.W.); and Departments of Cardiovascular Medicine (D.S., S.B.) and Cardiovascular Medicine (I.M.D.), University of Oxford, Wellcome Trust Centre for Human Genetics, Headington, Oxford, United Kingdom
| | - Dorota Szumska
- From the Molecular Medicine Unit, Institute of Child Health, University College London, London, United Kingdom (I.M.D., K.L.v.B., R.J.A., P.J.S.); Institute of Developmental Genetics (T.F., W.W.) and Technische Universität München-Weihenstephan, Institute of Developmental Genetics (T.F., W.W.), Helmholtz Zentrum München, Neuherberg/Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Site Munich, Munich, Germany (W.W.); Munich Cluster for Systems Neurology (SyNergy), Adolf Butenandt Institute, Ludwig-Maximilians-Universität München, Munich, Germany (W.W.); and Departments of Cardiovascular Medicine (D.S., S.B.) and Cardiovascular Medicine (I.M.D.), University of Oxford, Wellcome Trust Centre for Human Genetics, Headington, Oxford, United Kingdom
| | - Shoumo Bhattacharya
- From the Molecular Medicine Unit, Institute of Child Health, University College London, London, United Kingdom (I.M.D., K.L.v.B., R.J.A., P.J.S.); Institute of Developmental Genetics (T.F., W.W.) and Technische Universität München-Weihenstephan, Institute of Developmental Genetics (T.F., W.W.), Helmholtz Zentrum München, Neuherberg/Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Site Munich, Munich, Germany (W.W.); Munich Cluster for Systems Neurology (SyNergy), Adolf Butenandt Institute, Ludwig-Maximilians-Universität München, Munich, Germany (W.W.); and Departments of Cardiovascular Medicine (D.S., S.B.) and Cardiovascular Medicine (I.M.D.), University of Oxford, Wellcome Trust Centre for Human Genetics, Headington, Oxford, United Kingdom
| | - Peter J Scambler
- From the Molecular Medicine Unit, Institute of Child Health, University College London, London, United Kingdom (I.M.D., K.L.v.B., R.J.A., P.J.S.); Institute of Developmental Genetics (T.F., W.W.) and Technische Universität München-Weihenstephan, Institute of Developmental Genetics (T.F., W.W.), Helmholtz Zentrum München, Neuherberg/Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Site Munich, Munich, Germany (W.W.); Munich Cluster for Systems Neurology (SyNergy), Adolf Butenandt Institute, Ludwig-Maximilians-Universität München, Munich, Germany (W.W.); and Departments of Cardiovascular Medicine (D.S., S.B.) and Cardiovascular Medicine (I.M.D.), University of Oxford, Wellcome Trust Centre for Human Genetics, Headington, Oxford, United Kingdom.
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Cirillo E, Giardino G, Gallo V, Puliafito P, Azzari C, Bacchetta R, Cardinale F, Cicalese MP, Consolini R, Martino S, Martire B, Molinatto C, Plebani A, Scarano G, Soresina A, Cancrini C, Rossi P, Digilio MC, Pignata C. Intergenerational and intrafamilial phenotypic variability in 22q11.2 deletion syndrome subjects. BMC MEDICAL GENETICS 2014; 15:1. [PMID: 24383682 PMCID: PMC3893549 DOI: 10.1186/1471-2350-15-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 12/27/2013] [Indexed: 12/23/2022]
Abstract
BACKGROUND 22q11.2 deletion syndrome (22q11.2DS) is a common microdeletion syndrome, which occurs in approximately 1:4000 births. Familial autosomal dominant recurrence of the syndrome is detected in about 8-28% of the cases. Aim of this study is to evaluate the intergenerational and intrafamilial phenotypic variability in a cohort of familial cases carrying a 22q11.2 deletion. METHODS Thirty-two 22q11.2DS subjects among 26 families were enrolled. RESULTS Second generation subjects showed a significantly higher number of features than their transmitting parents (212 vs 129, P = 0.0015). Congenital heart defect, calcium-phosphorus metabolism abnormalities, developmental and speech delay were more represented in the second generation (P < 0.05). Ocular disorders were more frequent in the parent group. No significant difference was observed for the other clinical variables. Intrafamilial phenotypic heterogeneity was identified in the pedigrees. In 23/32 families, a higher number of features were found in individuals from the second generation and a more severe phenotype was observed in almost all of them, indicating the worsening of the phenotype over generations. Both genetic and epigenetic mechanisms may be involved in the phenotypic variability. CONCLUSIONS Second generation subjects showed a more complex phenotype in comparison to those from the first generation. Both ascertainment bias related to patient selection or to the low rate of reproductive fitness of adults with a more severe phenotype, and several not well defined molecular mechanism, could explain intergenerational and intrafamilial phenotypic variability in this syndrome.
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Affiliation(s)
- Emilia Cirillo
- Department of Translational Medicine, “Federico II” University, Naples, Italy
| | - Giuliana Giardino
- Department of Translational Medicine, “Federico II” University, Naples, Italy
| | - Vera Gallo
- Department of Translational Medicine, “Federico II” University, Naples, Italy
| | - Pamela Puliafito
- Department of Pediatrics, (DPUO), University of Rome Tor Vergata, Rome, Italy
| | - Chiara Azzari
- Department of Pediatrics, Anna Meyer Children’s University Hospital, Florence, Italy
| | - Rosa Bacchetta
- San Raffaele Telethon Institute for Gene Therapy (HSR-TIGET), Milan; Pediatric ImmunoHematology IRCCS San Raffaele Hospital, Milan, Italy
| | - Fabio Cardinale
- Department of Pediatrics, Giovanni XXIII Pediatric Hospital, Bari, Italy
| | | | - Rita Consolini
- Department of Internal and Experimental Medicine, University of Pisa, Pisa, Italy
| | | | - Baldassarre Martire
- Department of Biomedicine and Evolutive Aging, University of Bari, Bari, Italy
| | | | - Alessandro Plebani
- A. Nocivelli Institute for Molecular Medicine, Pediatric Clinic, University of Brescia, Brescia, Italy
| | | | - Annarosa Soresina
- A. Nocivelli Institute for Molecular Medicine, Pediatric Clinic, University of Brescia, Brescia, Italy
| | - Caterina Cancrini
- Department of Pediatrics, (DPUO), University of Rome Tor Vergata, Rome, Italy
| | - Paolo Rossi
- Department of Pediatrics, (DPUO), University of Rome Tor Vergata, Rome, Italy
| | | | - Claudio Pignata
- Department of Translational Medicine, “Federico II” University, Naples, Italy
- Department of Translational Medical Sciences, Unit of Pediatric Immunology, “Federico II” University, via S. Pansini, 5-80131 Naples, Italy
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15
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Zeitz MJ, Lerner PP, Ay F, Van Nostrand E, Heidmann JD, Noble WS, Hoffman AR. Implications of COMT long-range interactions on the phenotypic variability of 22q11.2 deletion syndrome. Nucleus 2013; 4:487-93. [PMID: 24448439 DOI: 10.4161/nucl.27364] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
22q11.2 deletion syndrome (22q11DS) results from a hemizygous microdeletion on chromosome 22 and is characterized by extensive phenotypic variability. Penetrance of signs, including congenital heart, craniofacial, and neurobehavioral abnormalities, varies widely and is not well correlated with genotype. The three-dimensional structure of the genome may help explain some of this variability. The physical interaction profile of a given gene locus with other genetic elements, such as enhancers and co-regulated genes, contributes to its regulation. Thus, it is possible that regulatory interactions with elements outside the deletion region are disrupted in the disease state and modulate the resulting spectrum of symptoms. COMT, a gene within the commonly deleted ~3 Mb region has been implicated as a contributor to the neurological features frequently found in 22q11DS patients. We used this locus as bait in a 4C-seq experiment to investigate genome-wide interaction profiles in B lymphocyte and fibroblast cell lines derived from both 22q11DS and unaffected individuals. All normal B lymphocyte lines displayed local, conserved chromatin looping interactions with regions that are lost in atypical and distal deletions, which may mediate similarities between typical, atypical, and distal 22q11 deletion phenotypes. There are also distinct clusterings of cis interactions based on disease state. We identified regions of differential trans interactions present in normal, and lost in deletion-carrying, B lymphocyte cell lines. This data suggests that hemizygous chromosomal deletions such as 22q11DS can have widespread effects on chromatin organization, and may contribute to the inherent phenotypic variability.
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Affiliation(s)
- Michael J Zeitz
- Veterans Affairs Palo Alto Health Care System; Stanford University Medical School; Palo Alto, CA USA; Department of Genome Sciences; University of Washington; Seattle, WA USA; Department of Genetics and Department of Developmental Biology; Stanford University Medical Center; Stanford, CA USA; Department of Computer Science and Engineering; University of Washington; Seattle, WA USA
| | - Paula P Lerner
- Veterans Affairs Palo Alto Health Care System; Stanford University Medical School; Palo Alto, CA USA
| | - Ferhat Ay
- Department of Genome Sciences; University of Washington; Seattle, WA USA
| | - Eric Van Nostrand
- Department of Genetics and Department of Developmental Biology; Stanford University Medical Center; Stanford, CA USA
| | - Julia D Heidmann
- Veterans Affairs Palo Alto Health Care System; Stanford University Medical School; Palo Alto, CA USA
| | - William S Noble
- Department of Genome Sciences; University of Washington; Seattle, WA USA; Department of Computer Science and Engineering; University of Washington; Seattle, WA USA
| | - Andrew R Hoffman
- Veterans Affairs Palo Alto Health Care System; Stanford University Medical School; Palo Alto, CA USA
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Chen CP, Huang JP, Chen YY, Chern SR, Wu PS, Su JW, Chen YT, Chen WL, Wang W. Chromosome 22q11.2 deletion syndrome: prenatal diagnosis, array comparative genomic hybridization characterization using uncultured amniocytes and literature review. Gene 2013; 527:405-9. [DOI: 10.1016/j.gene.2013.06.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 06/03/2013] [Accepted: 06/04/2013] [Indexed: 12/31/2022]
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