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Liu Y, Zhao Y, Lin L, Yang Q, Zhang L. Differential Expression of Noncoding RNAs Revealed Enhancer RNA AC016735.2 as a Potential Pathogenic Marker of Congenital Microtia Patients. J Craniofac Surg 2024; 35:00001665-990000000-01401. [PMID: 38456687 PMCID: PMC11045553 DOI: 10.1097/scs.0000000000010046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 01/11/2024] [Indexed: 03/09/2024] Open
Abstract
PURPOSE Congenital microtia is a complex maxillofacial malformation with various risk factors. This study aimed to find potential pathogenic noncoding RNAs for congenital microtia patients. METHODS We collected 3 pairs of residual ear cartilage samples and corresponding normal ear cartilage samples from nonsyndromic congenital microtia patients for microarray experiments. The differentially expressed RNAs were screened, and enrichment analysis and correlation expression analysis were performed to elucidate the function of the differentially expressed genes (DEGs). We further investigated the most significantly differentially expressed long noncoding RNA (lncRNA), AC016735.2, through follow-up analyses including RT-qPCR and Western blotting, to validate its differential expression in residual ear cartilage compared with normal ear cartilage. SiRNA was designed to study the regulatory role of AC016735.2, and cell proliferation experiments were conducted to explore its impact on residual ear chondrocytes. RESULTS Analysis of the microarray data revealed a total of 1079 differentially expressed RNAs, including 305 mRNAs and x lncRNAs, using a threshold of FC>1.5 and P<0.05 for mRNA, and FC>1.0 and P<0.05 for lncRNA. Enrichment analysis indicated that these genes are mainly involved in extracellular matrix regulation and embryonic development. AC016735.2 showed the highest differential expression among the eRNAs, being upregulated in residual ear cartilage. It acts in cis to regulate the nearby coding gene ZFP36L2, indirectly affecting downstream genes such as BMP4, TWSG1, COL2A1, and COL9A2. CONCLUSION Significant differences were observed in the expression of lncRNAs and mRNAs between residual ear cartilage and normal auricular cartilage tissues in the same genetic background of congenital microtia. These differentially expressed lncRNAs and mRNAs may play crucial roles in the occurrence and development of microtia through pathways associated with extracellular matrix regulation and gastrulation. Particularly, AC016735.2, an eRNA acting in cis, could serve as a potential pathogenic noncoding gene.
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Affiliation(s)
- Ying Liu
- Ear Reconstruction Department, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Plastic Surgery Department, Beijing Hospital of Integrated Traditional Chinese and Western Medicine, Beijing, China
| | - Yanyong Zhao
- Ear Reconstruction Department, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Lin Lin
- Ear Reconstruction Department, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Qinghua Yang
- Ear Reconstruction Department, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Ling Zhang
- Laser Treatment Department, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
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Abstract
Orofacial clefts (OFCs) are the most common congenital birth defects in humans and immediately recognized at birth. The etiology remains complex and poorly understood and seems to result from multiple genetic and environmental factors along with gene-environment interactions. It can be classified into syndromic (30%) and nonsyndromic (70%) clefts. Nonsyndromic OFCs include clefts without any additional physical or cognitive deficits. Recently, various genetic approaches, such as genome-wide association studies (GWAS), candidate gene association studies, and linkage analysis, have identified multiple genes involved in the etiology of OFCs. This article provides an insight into the multiple genes involved in the etiology of OFCs. Identification of specific genetic causes of clefts helps in a better understanding of the molecular pathogenesis of OFC. In the near future, it helps to provide a more accurate diagnosis, genetic counseling, personalized medicine for better clinical care, and prevention of OFCs.
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Affiliation(s)
- Mahamad Irfanulla Khan
- Department of Orthodontics & Dentofacial Orthopedics, The Oxford Dental College, Bangalore, Karnataka, India
| | - Prashanth CS
- Department of Orthodontics & Dentofacial Orthopedics, DAPM R.V. Dental College, Bangalore, Karnataka, India
| | - Narasimha Murthy Srinath
- Department of Oral & Maxillofacial Surgery, Krishnadevaraya College of Dental Sciences, Bangalore, Karnataka, India
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Gendron C, Schwentker A, van Aalst JA. Genetic Advances in the Understanding of Microtia. J Pediatr Genet 2016; 5:189-197. [PMID: 27895971 DOI: 10.1055/s-0036-1592422] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 09/30/2016] [Indexed: 10/20/2022]
Abstract
Microtia is a genetic condition affecting the external ears and presents clinically along a wide spectrum: minimally affected ears are small with minor shape abnormalities; extremely affected ears lack all identifiable structures, with the most extreme being absence of the entire external ear. Multiple genetic causes have been linked to microtia in both animal models and humans, which are improving our understanding of the condition and may lead to the identification of a unified cause for the condition. Microtia is also a prominent feature of several genetic syndromes, the study of which has provided further insight into the possible causes and genetic mechanisms of the condition. This article reviews our current understanding of microtia including epidemiological characteristics, classification systems, environmental and genetic causative factors leading to microtia. Despite our increased understanding of the genetics of microtia, we do not have a means of preventing the condition and still rely on complex staged, surgical correction.
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Affiliation(s)
- Craig Gendron
- Craniofacial and Pediatric Plastic Surgery, Saskatoon Health Region of Saskatchewan, Saskatoon, Canada
| | - Ann Schwentker
- Division of Plastic Surgery, University of Cincinnati, Cincinnati, Ohio, United States
| | - John A van Aalst
- Division of Plastic Surgery, University of Cincinnati, Cincinnati, Ohio, United States
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Li X, Hu J, Zhang J, Jin Q, Wang DM, Yu J, Zhang Q, Zhang YB. Genome-wide linkage study suggests a susceptibility locus for isolated bilateral microtia on 4p15.32-4p16.2. PLoS One 2014; 9:e101152. [PMID: 24983964 PMCID: PMC4077761 DOI: 10.1371/journal.pone.0101152] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 06/03/2014] [Indexed: 11/19/2022] Open
Abstract
Microtia is a congenital deformity where the external ear is underdeveloped. Genetic investigations have identified many susceptibility genes of microtia-related syndromes. However, no causal genes were reported for isolated microtia, the main form of microtia. We conducted a genome-wide linkage analysis on a 5-generation Chinese pedigree with isolated bilateral microtia. We identified a suggestive linkage locus on 4p15.32-4p16.2 with parametric LOD score of 2.70 and nonparametric linkage score (Zmean) of 12.28 (simulated occurrence per genome scan equal to 0.46 and 0.47, respectively). Haplotype reconstruction analysis of the 4p15.32-4p16.2 region further confined the linkage signal to a 10-Mb segment located between rs12505562 and rs12649803 (9.65-30.24 cM; 5.54-15.58 Mb). Various human organ developmental genes reside in this 10-Mb susceptibility region, such as EVC, EVC2, SLC2A9, NKX3-2, and HMX1. The coding regions of three genes, EVC known for cartilage development and NKX3-2, HMX1 involved in microtia, were selected for sequencing with 5 individuals from the pedigree. Of the 38 identified sequence variants, none segregates along with the disease phenotype. Other genes or DNA sequences of the 10-Mb region warrant for further investigation. In conclusion, we report a susceptibility locus of isolated microtia, and this finding will encourage future studies on the genetic basis of ear deformity.
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Affiliation(s)
- Xin Li
- Beijing Institute of Genomics, Chinese Academy of Sciences and Key Laboratory of Genome Science and Information, Chinese Academy of Sciences, Beijing, P. R. China
- Department of Cardiology, Beijing Anzhen Hospital of the Capital University of Medical Sciences, Beijing, P. R. China
| | - Jintian Hu
- Department of Ear Reconstruction, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Jiao Zhang
- Department of Ear Reconstruction, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Qian Jin
- Department of Ear Reconstruction, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Duen-Mei Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences and Key Laboratory of Genome Science and Information, Chinese Academy of Sciences, Beijing, P. R. China
| | - Jun Yu
- Beijing Institute of Genomics, Chinese Academy of Sciences and Key Laboratory of Genome Science and Information, Chinese Academy of Sciences, Beijing, P. R. China
| | - Qingguo Zhang
- Department of Ear Reconstruction, Plastic Surgery Hospital, Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Yong-Biao Zhang
- Beijing Institute of Genomics, Chinese Academy of Sciences and Key Laboratory of Genome Science and Information, Chinese Academy of Sciences, Beijing, P. R. China
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Luquetti DV, Heike CL, Hing AV, Cunningham ML, Cox TC. Microtia: epidemiology and genetics. Am J Med Genet A 2012; 158A:124-39. [PMID: 22106030 PMCID: PMC3482263 DOI: 10.1002/ajmg.a.34352] [Citation(s) in RCA: 237] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 09/12/2011] [Indexed: 12/26/2022]
Abstract
Microtia is a congenital anomaly of the ear that ranges in severity from mild structural abnormalities to complete absence of the ear, and can occur as an isolated birth defect or as part of a spectrum of anomalies or a syndrome. Microtia is often associated with hearing loss and patients typically require treatment for hearing impairment and surgical ear reconstruction. The reported prevalence varies among regions, from 0.83 to 17.4 per 10,000 births, and the prevalence is considered to be higher in Hispanics, Asians, Native Americans, and Andeans. The etiology of microtia and the cause of this wide variability in prevalence are poorly understood. Strong evidence supports the role of environmental and genetic causes for microtia. Although some studies have identified candidate genetic variants for microtia, no causal genetic mutation has been confirmed. The application of novel strategies in developmental biology and genetics has facilitated elucidation of mechanisms controlling craniofacial development. In this paper we review current knowledge of the epidemiology and genetics of microtia, including potential candidate genes supported by evidence from human syndromes and animal models. We also discuss the possible etiopathogenesis in light of the hypotheses formulated to date: Neural crest cells disturbance, vascular disruption, and altitude.
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Affiliation(s)
- Daniela V Luquetti
- Division of Craniofacial Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, USA.
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Salahshourifar I, Halim AS, Sulaiman WAW, Zilfalil BA. Contribution of 6p24 to non-syndromic cleft lip and palate in a Malay population: association of variants in OFC1. J Dent Res 2011; 90:387-91. [PMID: 21297019 DOI: 10.1177/0022034510391798] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Non-syndromic cleft lip, with or without cleft palate, is a heterogeneous, complex disease with a high incidence in the Asian population. Several association studies have been done on cleft candidate genes, but no reports have been published thus far on the Orofacial Cleft 1 (OFC1) genomic region in an Asian population. This study investigated the association between the OFC1 genomic region and non-syndromic cleft lip with or without cleft palate in 90 Malay father-mother-offspring trios. Results showed a preferential over-transmission of a 101-bp allele of marker D6S470 in the allele- and haplotype-based transmission disequilibrium test (TDT), as well as an excess of maternal transmission. However, no significant p-value was found for a maternal genotype effect in a log-linear model, although single and double doses of the 101-bp allele showed a slightly increased cleft risk (RR = 1.37, 95% CI, 0.527-3.4, p-value = 0.516). Carrying two copies of the 101-bp allele was significantly associated with an increased cleft risk (RR = 2.53, 95% CI, 1.06-6.12, p-value = 0.035). In conclusion, we report evidence of the contribution of the OFC1 genomic region to the etiology of clefts in a Malay population.
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Affiliation(s)
- I Salahshourifar
- Human Genome Center, Universiti Sains Malaysia, Kubang Kerian, 16150, Kelantan, Malaysia
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Colmant C, Brisset S, Tachdjian G, Gautier V, Ftouki M, Laroudie M, Druart L, Frydman R, Picone O. Interstitial deletion 6p22.3-p24.3 characterized by CGH array in a foetus with multiple malformations. Prenat Diagn 2009; 29:908-10. [PMID: 19530104 DOI: 10.1002/pd.2306] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Little HJ, Rorick NK, Su LI, Baldock C, Malhotra S, Jowitt T, Gakhar L, Subramanian R, Schutte BC, Dixon MJ, Shore P. Missense mutations that cause Van der Woude syndrome and popliteal pterygium syndrome affect the DNA-binding and transcriptional activation functions of IRF6. Hum Mol Genet 2009; 18:535-45. [PMID: 19036739 PMCID: PMC2638798 DOI: 10.1093/hmg/ddn381] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Accepted: 11/10/2008] [Indexed: 11/12/2022] Open
Abstract
Cleft lip and cleft palate (CLP) are common disorders that occur either as part of a syndrome, where structures other than the lip and palate are affected, or in the absence of other anomalies. Van der Woude syndrome (VWS) and popliteal pterygium syndrome (PPS) are autosomal dominant disorders characterized by combinations of cleft lip, CLP, lip pits, skin-folds, syndactyly and oral adhesions which arise as the result of mutations in interferon regulatory factor 6 (IRF6). IRF6 belongs to a family of transcription factors that share a highly conserved N-terminal, DNA-binding domain and a less well-conserved protein-binding domain. To date, mutation analyses have suggested a broad genotype-phenotype correlation in which missense and nonsense mutations occurring throughout IRF6 may cause VWS; in contrast, PPS-causing mutations are highly associated with the DNA-binding domain, and appear to preferentially affect residues that are predicted to interact directly with the DNA. Nevertheless, this genotype-phenotype correlation is based on the analysis of structural models rather than on the investigation of the DNA-binding properties of IRF6. Moreover, the effects of mutations in the protein interaction domain have not been analysed. In the current investigation, we have determined the sequence to which IRF6 binds and used this sequence to analyse the effect of VWS- and PPS-associated mutations in the DNA-binding domain of IRF6. In addition, we have demonstrated that IRF6 functions as a co-operative transcriptional activator and that mutations in the protein interaction domain of IRF6 disrupt this activity.
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Affiliation(s)
- Hayley J. Little
- Faculty of Life Sciences, Michael Smith Building
- Dental School, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | | | - Ling-I Su
- Faculty of Life Sciences, Michael Smith Building
| | | | | | - Tom Jowitt
- Faculty of Life Sciences, Michael Smith Building
| | - Lokesh Gakhar
- Department of Biochemistry, University of Iowa, Iowa City, IA, USA
| | | | - Brian C. Schutte
- Department of Pediatrics and Interdisciplinary PhD Program in Genetics
| | - Michael J. Dixon
- Faculty of Life Sciences, Michael Smith Building
- Dental School, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Paul Shore
- Faculty of Life Sciences, Michael Smith Building
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Identification and analysis of a conserved Tcfap2a intronic enhancer element required for expression in facial and limb bud mesenchyme. Mol Cell Biol 2007; 28:315-25. [PMID: 17984226 DOI: 10.1128/mcb.01168-07] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tcfap2a, the gene encoding the mouse AP-2alpha transcription factor, is required for normal development of multiple structures during embryogenesis, including the face and limbs. Using comparative sequence analysis and transgenic-mouse experiments we have identified an intronic enhancer within this gene that directs expression to the face and limb mesenchyme. There are two conserved sequence blocks within this intron, and the larger of these directs tissue-specific activity and is found in all vertebrate Tcfap2a genes analyzed. To assess the role of the enhancer in regulating endogenous mouse Tcfap2a expression, we have deleted this cis-regulatory sequence from the genome. Loss of this element severely impairs Tcfap2a expression in the limb bud mesenchyme but generates only a modest reduction in the facial mesenchyme. The reduction in Tcfap2a transcription is accompanied by altered patterning of the forelimb, resulting in postaxial polydactyly. These results indicate that the major role for this enhancer resides within the limb bud, and it serves to maintain a level of Tcfap2a expression that limits the size of the hand plate and the associated number of digit primordia. The potential role of this cis-acting sequence in modeling the size and shape of the face and limbs during evolution is discussed.
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Klockars T, Suutarla S, Kentala E, Ala-Mello S, Rautio J. Inheritance of microtia in the Finnish population. Int J Pediatr Otorhinolaryngol 2007; 71:1783-8. [PMID: 17868909 DOI: 10.1016/j.ijporl.2007.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2007] [Revised: 07/31/2007] [Accepted: 08/04/2007] [Indexed: 11/15/2022]
Abstract
OBJECTIVE To study the inheritance of microtia in the Finnish population, identify families for genetic linkage analyses and compare the phenotype between sporadic and familial patients. METHODS Retrospective case series and patient questionnaire of 109 microtia patients referred for reconstruction of the earlobe to the Helsinki University Central Hospital during the years 1980-2005. RESULTS 22 out of the 109 patients had a relative with microtia or preauricular tag. The familial and sporadic patients did not differ in microtia phenotype or sex distribution. Urinary system anomalies were statistically more prevalent in familial patients (p<0.01). The analyses of the birthplace of parents or grandparents of familial or sporadic microtia patients resulted in no evidence for founder effect. CONCLUSIONS The prevalence of familial microtia/OAVS in the Finnish population is higher than 20%. The sporadic and familial microtia/OAVS patients do not differ in the phenotype or sex distribution. The mode of inheritance seems to be autosomal dominant with incomplete penetrance.
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Affiliation(s)
- Tuomas Klockars
- Department of Otorhinolaryngology, Kymenlaakso Central Hospital, Kotkantie 41, 48210 Kotka, Finland.
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Colella S, Yau C, Taylor JM, Mirza G, Butler H, Clouston P, Bassett AS, Seller A, Holmes CC, Ragoussis J. QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data. Nucleic Acids Res 2007; 35:2013-25. [PMID: 17341461 PMCID: PMC1874617 DOI: 10.1093/nar/gkm076] [Citation(s) in RCA: 450] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Array-based technologies have been used to detect chromosomal copy number changes (aneuploidies) in the human genome. Recent studies identified numerous copy number variants (CNV) and some are common polymorphisms that may contribute to disease susceptibility. We developed, and experimentally validated, a novel computational framework (QuantiSNP) for detecting regions of copy number variation from BeadArray SNP genotyping data using an Objective Bayes Hidden-Markov Model (OB-HMM). Objective Bayes measures are used to set certain hyperparameters in the priors using a novel re-sampling framework to calibrate the model to a fixed Type I (false positive) error rate. Other parameters are set via maximum marginal likelihood to prior training data of known structure. QuantiSNP provides probabilistic quantification of state classifications and significantly improves the accuracy of segmental aneuploidy identification and mapping, relative to existing analytical tools (Beadstudio, Illumina), as demonstrated by validation of breakpoint boundaries. QuantiSNP identified both novel and validated CNVs. QuantiSNP was developed using BeadArray SNP data but it can be adapted to other platforms and we believe that the OB-HMM framework has widespread applicability in genomic research. In conclusion, QuantiSNP is a novel algorithm for high-resolution CNV/aneuploidy detection with application to clinical genetics, cancer and disease association studies.
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Affiliation(s)
- Stefano Colella
- Genomics Laboratory and Bioinformatics, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, Life Science Interface Doctoral Training Centre, Wolfson Building, Parks Road, Oxford OX1 3QD, Henry Wellcome Centre for Gene Function, Department of Statistics, University of Oxford, Oxford, OX1 3TG, Oxford Medical Genetics Laboratories, The Churchill Hospital, Oxford, OX3 7LJ, UK, Centre for Addiction & Mental Health, University of Toronto, 1001 Queen Street West, Toronto, Ontario M6J 1H4, Canada and MRC Mammalian Genetics Unit, Medical Research Council, Harwell, Oxford, OX11 0RD
| | - Christopher Yau
- Genomics Laboratory and Bioinformatics, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, Life Science Interface Doctoral Training Centre, Wolfson Building, Parks Road, Oxford OX1 3QD, Henry Wellcome Centre for Gene Function, Department of Statistics, University of Oxford, Oxford, OX1 3TG, Oxford Medical Genetics Laboratories, The Churchill Hospital, Oxford, OX3 7LJ, UK, Centre for Addiction & Mental Health, University of Toronto, 1001 Queen Street West, Toronto, Ontario M6J 1H4, Canada and MRC Mammalian Genetics Unit, Medical Research Council, Harwell, Oxford, OX11 0RD
| | - Jennifer M. Taylor
- Genomics Laboratory and Bioinformatics, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, Life Science Interface Doctoral Training Centre, Wolfson Building, Parks Road, Oxford OX1 3QD, Henry Wellcome Centre for Gene Function, Department of Statistics, University of Oxford, Oxford, OX1 3TG, Oxford Medical Genetics Laboratories, The Churchill Hospital, Oxford, OX3 7LJ, UK, Centre for Addiction & Mental Health, University of Toronto, 1001 Queen Street West, Toronto, Ontario M6J 1H4, Canada and MRC Mammalian Genetics Unit, Medical Research Council, Harwell, Oxford, OX11 0RD
| | - Ghazala Mirza
- Genomics Laboratory and Bioinformatics, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, Life Science Interface Doctoral Training Centre, Wolfson Building, Parks Road, Oxford OX1 3QD, Henry Wellcome Centre for Gene Function, Department of Statistics, University of Oxford, Oxford, OX1 3TG, Oxford Medical Genetics Laboratories, The Churchill Hospital, Oxford, OX3 7LJ, UK, Centre for Addiction & Mental Health, University of Toronto, 1001 Queen Street West, Toronto, Ontario M6J 1H4, Canada and MRC Mammalian Genetics Unit, Medical Research Council, Harwell, Oxford, OX11 0RD
| | - Helen Butler
- Genomics Laboratory and Bioinformatics, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, Life Science Interface Doctoral Training Centre, Wolfson Building, Parks Road, Oxford OX1 3QD, Henry Wellcome Centre for Gene Function, Department of Statistics, University of Oxford, Oxford, OX1 3TG, Oxford Medical Genetics Laboratories, The Churchill Hospital, Oxford, OX3 7LJ, UK, Centre for Addiction & Mental Health, University of Toronto, 1001 Queen Street West, Toronto, Ontario M6J 1H4, Canada and MRC Mammalian Genetics Unit, Medical Research Council, Harwell, Oxford, OX11 0RD
| | - Penny Clouston
- Genomics Laboratory and Bioinformatics, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, Life Science Interface Doctoral Training Centre, Wolfson Building, Parks Road, Oxford OX1 3QD, Henry Wellcome Centre for Gene Function, Department of Statistics, University of Oxford, Oxford, OX1 3TG, Oxford Medical Genetics Laboratories, The Churchill Hospital, Oxford, OX3 7LJ, UK, Centre for Addiction & Mental Health, University of Toronto, 1001 Queen Street West, Toronto, Ontario M6J 1H4, Canada and MRC Mammalian Genetics Unit, Medical Research Council, Harwell, Oxford, OX11 0RD
| | - Anne S. Bassett
- Genomics Laboratory and Bioinformatics, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, Life Science Interface Doctoral Training Centre, Wolfson Building, Parks Road, Oxford OX1 3QD, Henry Wellcome Centre for Gene Function, Department of Statistics, University of Oxford, Oxford, OX1 3TG, Oxford Medical Genetics Laboratories, The Churchill Hospital, Oxford, OX3 7LJ, UK, Centre for Addiction & Mental Health, University of Toronto, 1001 Queen Street West, Toronto, Ontario M6J 1H4, Canada and MRC Mammalian Genetics Unit, Medical Research Council, Harwell, Oxford, OX11 0RD
| | - Anneke Seller
- Genomics Laboratory and Bioinformatics, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, Life Science Interface Doctoral Training Centre, Wolfson Building, Parks Road, Oxford OX1 3QD, Henry Wellcome Centre for Gene Function, Department of Statistics, University of Oxford, Oxford, OX1 3TG, Oxford Medical Genetics Laboratories, The Churchill Hospital, Oxford, OX3 7LJ, UK, Centre for Addiction & Mental Health, University of Toronto, 1001 Queen Street West, Toronto, Ontario M6J 1H4, Canada and MRC Mammalian Genetics Unit, Medical Research Council, Harwell, Oxford, OX11 0RD
| | - Christopher C. Holmes
- Genomics Laboratory and Bioinformatics, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, Life Science Interface Doctoral Training Centre, Wolfson Building, Parks Road, Oxford OX1 3QD, Henry Wellcome Centre for Gene Function, Department of Statistics, University of Oxford, Oxford, OX1 3TG, Oxford Medical Genetics Laboratories, The Churchill Hospital, Oxford, OX3 7LJ, UK, Centre for Addiction & Mental Health, University of Toronto, 1001 Queen Street West, Toronto, Ontario M6J 1H4, Canada and MRC Mammalian Genetics Unit, Medical Research Council, Harwell, Oxford, OX11 0RD
| | - Jiannis Ragoussis
- Genomics Laboratory and Bioinformatics, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, Life Science Interface Doctoral Training Centre, Wolfson Building, Parks Road, Oxford OX1 3QD, Henry Wellcome Centre for Gene Function, Department of Statistics, University of Oxford, Oxford, OX1 3TG, Oxford Medical Genetics Laboratories, The Churchill Hospital, Oxford, OX3 7LJ, UK, Centre for Addiction & Mental Health, University of Toronto, 1001 Queen Street West, Toronto, Ontario M6J 1H4, Canada and MRC Mammalian Genetics Unit, Medical Research Council, Harwell, Oxford, OX11 0RD
- *To whom correspondence should be addressed. +44-(0)1865 287526+44-(0)1865 287533
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Suwanrath-Kengpol C, Limprasert P, Mitarnun W. Prenatal diagnosis of deletion of chromosome 6p presenting with hydrops fetalis. Prenat Diagn 2004; 24:887-9. [PMID: 15565585 DOI: 10.1002/pd.1042] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
OBJECTIVE To report the first known case of 6p deletion presenting in utero with hydrops fetalis and multiple anomalies in the second trimester of pregnancy. METHODS A thirty-year-old woman (gravida 3 para 1 abortion 1) was referred to our hospital at 18 weeks of gestation because of suspicion of fetal anomaly on routine ultrasound examination. A detailed anomaly scan revealed a single viable fetus with marked skin edema, marked ascites, pleural effusion, hydronephrosis of left kidney, absence of right kidney, cardiac anomaly and oligohydramnios. The fetal face was not visible due to the fetal position. Fetal karyotyping revealed 46,XX,del(6)(p21.3). The couple opted to terminate the pregnancy. RESULTS A hydropic female fetus was aborted and the autopsy revealed hydrops fetalis with bilateral cleft lips, hydronephrosis of left kidney, absence of right kidney, spleen, and thymus gland, truncus arteriosus, and single umbilical artery. Cord blood and tissue culture confirmed that the fetus had deletion of chromosome 6p. CONCLUSION Deletion of short arm of chromosome 6 can result in hydrops fetalis in early pregnancy.
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Affiliation(s)
- Chitkasaem Suwanrath-Kengpol
- Department of Obstetrics and Gynecology, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand.
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Marazita ML, Field LL, Tunçbilek G, Cooper ME, Goldstein T, Gürsu KG. Genome-scan for loci involved in cleft lip with or without cleft palate in consanguineous families from Turkey. Am J Med Genet A 2003; 126A:111-22. [PMID: 15057975 DOI: 10.1002/ajmg.a.20564] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Cleft lip with or without cleft palate (CL/P) is a common congenital anomaly, with birth prevalence ranging from 1/500 to 1/1,000. A number of genetic loci have shown positive linkage or association results in European Caucasian populations. The purpose of the current study was to assess whether any of those loci have positive results in Turkish Caucasian CL/P families, and to perform a 10 cM genome scan to identify other regions potentially containing cleft susceptibility loci. Eighteen affected individuals with consanguineous parents were identified as part of our on-going studies of orofacial clefts in Ankara, Turkey. Genotyped were 383 genome-scan markers, and 70 additional markers, including markers in six candidate loci or regions on chromosomes 2, 4, 6, 14, 17, and 19 (TGFA, D4S175, F13A1, TGFB3, D17S250, and APOC2) that have been implicated in other studies of families with orofacial clefting. LOD scores (two point and multiple point) and family-based association statistics (TDT) were calculated between each of the markers and CL/P. For the LOD score calculations, an autosomal recessive model was assumed for the inheritance of CL/P. Of the six candidate markers, significant TDT results were obtained with TGFA (P = 0.05). The most statistically significant multipoint results from the linkage genome scan were between putative genes controlling risk of CL/P and regions on chromosomes 4, 10, 12, and 15 (maximum multipoint HLOD's of 1.25, 1.30, 2.73, and 1.28 respectively). These results demonstrate the power of small numbers of families with inbred probands to detect linkage and association.
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Affiliation(s)
- Mary L Marazita
- Center for Craniofacial and Dental Genetics, Division of Oral Biology, School of Dental Medicine, University of Pittsburgh, Suite 500 Cellomics Building, Pittsburgh, 100 Technology Drive, Pittsburgh, PA 15219, USA.
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Abstract
Craniofacial anomalies, and in particular cleft lip and palate, are major human birth defects with a worldwide frequency of 1 in 700 and substantial clinical impact. A wide range of studies in developmental biology has contributed to a better knowledge of how both genes and environmental exposures impact head organogenesis. Specific causes have now been identified for some forms of cleft lip and palate, and we are at the beginning of a time in which the common nonsyndromic forms may also have specific etiologies identified. Mouse models have an especially important role in disclosing cleft etiologies and providing models for environmental cotriggers or interventions. An overview of the gene-environment contributions to nonsyndromic forms of clefting and their implications for developmental biology and clinical counseling is presented.
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Affiliation(s)
- J C Murray
- Department of Pediatrics, University of Iowa, Iowa City 52242, USA
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15
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Topping A, Harris P, Moss ALH. The 6p deletion syndrome: a new orofacial clefting syndrome and its implications for antenatal screening. BRITISH JOURNAL OF PLASTIC SURGERY 2002; 55:68-72. [PMID: 11783973 DOI: 10.1054/bjps.2001.3729] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Foetal genetic screening has become the centre of the ethical debate surrounding the screening of foetuses for chromosomal defects to help create 'eugenic' children with either perceived advantageous characteristics or traits that could be used to medically aid unhealthy siblings. This report highlights the problems facing the medical establishment by citing, by way of example, a case of a genetic abnormality producing a clefting syndrome. The 6p deletion syndrome was first described almost 20 years ago, and the evidence is mounting for its inclusion as an orofacial clefting syndrome. This case report includes a description of the syndrome, the method used for detecting chromosomal aberrations and a comparison with other reports of the syndrome published to date. However, by pursuing a genetic-testing policy at our unit to detect new abnormalities or to help substantiate previously reported abnormalities, the way could be left open for its subsequent abuse by parents and corporations alike, so having implications not only for the individual but also for the unit performing the test. A brief synopsis is therefore also provided regarding the current circumstances of foetal screening in the UK.
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Affiliation(s)
- A Topping
- Department of Plastic and Reconstructive Surgery, St George's Hospital, London, UK
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16
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Shiels C, Islam SA, Vatcheva R, Sasieni P, Sternberg MJ, Freemont PS, Sheer D. PML bodies associate specifically with the MHC gene cluster in interphase nuclei. J Cell Sci 2001; 114:3705-16. [PMID: 11707522 DOI: 10.1242/jcs.114.20.3705] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Promyelocytic leukemia (PML) bodies are nuclear multi-protein domains. The observations that viruses transcribe their genomes adjacent to PML bodies and that nascent RNA accumulates at their periphery suggest that PML bodies function in transcription. We have used immuno-FISH in primary human fibroblasts to determine the 3D spatial organisation of gene-rich and gene-poor chromosomal regions relative to PML bodies. We find a highly non-random association of the gene-rich major histocompatibilty complex (MHC) on chromosome 6 with PML bodies. This association is specific for the centromeric end of the MHC and extends over a genomic region of at least 1.6 megabases. We also show that PML association is maintained when a subsection of this region is integrated into another chromosomal location. This is the first demonstration that PML bodies have specific chromosomal associations and supports a model for PML bodies as part of a functional nuclear compartment.
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Affiliation(s)
- C Shiels
- Human Cytogenetics Laboratory, Imperial Cancer Research Fund, London, WC2A 3PX, UK
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17
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Volpi EV, Chevret E, Jones T, Vatcheva R, Williamson J, Beck S, Campbell RD, Goldsworthy M, Powis SH, Ragoussis J, Trowsdale J, Sheer D. Large-scale chromatin organization of the major histocompatibility complex and other regions of human chromosome 6 and its response to interferon in interphase nuclei. J Cell Sci 2000; 113 ( Pt 9):1565-76. [PMID: 10751148 DOI: 10.1242/jcs.113.9.1565] [Citation(s) in RCA: 315] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The large-scale chromatin organization of the major histocompatibility complex and other regions of chromosome 6 was studied by three-dimensional image analysis in human cell types with major differences in transcriptional activity. Entire gene clusters were visualized by fluorescence in situ hybridization with multiple locus-specific probes. Individual genomic regions showed distinct configurations in relation to the chromosome 6 terrritory. Large chromatin loops containing several megabases of DNA were observed extending outwards from the surface of the domain defined by the specific chromosome 6 paint. The frequency with which a genomic region was observed on an external chromatin loop was cell type dependent and appeared to be related to the number of active genes in that region. Transcriptional up-regulation of genes in the major histocompatibility complex by interferon-gamma led to an increase in the frequency with which this large gene cluster was found on an external chromatin loop. Our data are consistent with an association between large-scale chromatin organization of specific genomic regions and their transcriptional status.
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Affiliation(s)
- E V Volpi
- Human Cytogenetics Laboratory, Imperial Cancer Research Fund, London WC2A 3PX, UK
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18
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Abstract
Blepharoptosis is a relatively common condition that is frequently encountered by the ophthalmic surgeon. Treatment remains somewhat unpredictable, and the choice of one of the various surgical options depends on the cause of the ptosis and the amount of levator function. Recent contributions to the literature on the classification and management of ptosis are reviewed here.
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Affiliation(s)
- P J Sakol
- Penn State Geisinger at Hershey, Pennsylvania, USA
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