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Szegedi K, Szabó Z, Kállai J, Király J, Szabó E, Bereczky Z, Juhász É, Dezső B, Szász C, Zsebik B, Flaskó T, Halmos G. Potential Role of VHL, PTEN, and BAP1 Mutations in Renal Tumors. J Clin Med 2023; 12:4538. [PMID: 37445575 DOI: 10.3390/jcm12134538] [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: 05/24/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023] Open
Abstract
The genetic profiling of renal tumors has revealed genomic regions commonly affected by structural changes and a general genetic heterogeneity. The VHL, PTEN, and BAP1 genes are often mutated in renal tumors. The frequency and clinical relevance of these mutations in renal tumors are still being researched. In our study, we investigated VHL, PTEN, and BAP1 genes and the sequencing of 24 samples of patients with renal tumors, revealing that VHL was mutated at a noticeable frequency (25%). Six of the investigated samples showed mutations, and one genetic polymorphism (rs779805) was detected in both heterozygote and homozygote forms. PTEN gene mutation was observed in only one sample, and one specimen showed genetic polymorphism. In the case of the BAP1 gene, all of the samples were wild types. Interestingly, VHL mutation was detected in two female patients diagnosed with AML and in one with oncocytoma. We assume that VHL or PTEN mutations may contribute to the development of human renal cancer. However, the overall mutation rate was low in all specimens investigated, and the development and prognosis of the disease were not exclusively associated with these types of genetic alterations.
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Affiliation(s)
- Krisztián Szegedi
- Department of Urology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Doctoral School of Pharmaceutical Sciences, University of Debrecen, 4032 Debrecen, Hungary
| | - Zsuzsanna Szabó
- Department of Biopharmacy, Faculty of Pharmacy, University of Debrecen, 4032 Debrecen, Hungary
| | - Judit Kállai
- Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - József Király
- Department of Biopharmacy, Faculty of Pharmacy, University of Debrecen, 4032 Debrecen, Hungary
| | - Erzsébet Szabó
- Department of Biopharmacy, Faculty of Pharmacy, University of Debrecen, 4032 Debrecen, Hungary
| | - Zsuzsanna Bereczky
- Division of Clinical Laboratory Science, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Éva Juhász
- Department of Pediatrics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Balázs Dezső
- Department of Pathology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
- Department of Oral Pathology and Microbiology, Faculty of Dentistry, University of Debrecen, 4032 Debrecen, Hungary
| | - Csaba Szász
- Department of Pathology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Barbara Zsebik
- Department of Biopharmacy, Faculty of Pharmacy, University of Debrecen, 4032 Debrecen, Hungary
| | - Tibor Flaskó
- Department of Urology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Gábor Halmos
- Department of Biopharmacy, Faculty of Pharmacy, University of Debrecen, 4032 Debrecen, Hungary
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Boratto SDF, Cardoso PAS, Priolli DG, Botelho RV, Goldenberg A, Bianco B, Waisberg J. von Hippel-Lindau Syndrome: Genetic Study of Case With a Rare Pathogenic Variant With Optic Nerve Hemangioblastoma, a Rare Phenotypic Expression. Front Oncol 2020; 10:139. [PMID: 32117777 PMCID: PMC7033541 DOI: 10.3389/fonc.2020.00139] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 01/27/2020] [Indexed: 12/19/2022] Open
Abstract
von Hippel-Lindau syndrome (VHLS) is a rare, autosomal dominant genetic disease with high penetrance and variable phenotypic expression caused by variants in the VHL gene. VHLS is associated with the presence of vascular tumors, often hemangioblastoma of the central nervous system, retina, or spinal cord and, less frequently, pancreatic cystic neoplasm, pancreatic neuroendocrine tumor, clear cell carcinoma of the kidney, endolymphatic sac tumor, pheochromocytoma, and paraganglioma. The authors report a case of a patient with VHLS with a rare pathogenic variant in the VHL gene and with an optic nerve hemangioblastoma, a rare phenotypic expression. Case report: A 49-year-old woman was diagnosed with cystic neoplasm of the pancreas, renal cell carcinoma of the right kidney, and hemangioblastoma of the left optic nerve. The patient's family history revealed siblings with VHLS manifestations. The index case was her mother who died at age 63 of clear cell renal carcinoma. The information was obtained by consulting the patient's medical register and by interviews with the patient and her relatives. The presence of left optic nerve hemangioblastoma was suggested by CT scan of the skull and orbit. The sequencing of the VHL gene was performed in the peripheral blood by the polymerase chain reaction (PCR) technique, and the duplication and deletion research was performed using the multiplex ligation-dependent probe amplification (MPLA) technique. The presence of a rare pathogenic variant c.263G> A (p.Trp88Ter) was observed in heterozygosity in the VHL gene that determined a premature stop codon. CT scan of the skull and orbits suggested the presence of HB in the optic nerve of the left eye. The results of the CT scan of the skull and orbits show thickening with tortuosity of the left optic nerve, with a small area of nodular enhancement. The right optic nerve had a conserved aspect. Conclusion: This is the fourth case described of this rare pathogenic variant of the VHL gene, according to the Human Gene Mutation Database and VHLdb database records and with an optic nerve hemangioblastoma of the optic nerve, a very rare phenotypic expression of the VHLS.
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Affiliation(s)
| | - Pedro Augusto Soffner Cardoso
- Department of Surgery, Faculdade De Medicina Do ABC, Santo André, Brazil.,Department of Surgery, State Public Servant Hospital (IAMSPE), São Paulo, Brazil
| | - Denise Gonçalves Priolli
- Postgraduate Programme Stricto Sensu in Health Science, Sao Francisco University Medical School, Bragança Paulista, Brazil
| | | | - Alberto Goldenberg
- Department of Surgery, Escola Paulista de Medicina, São Paulo Federal University, São Paulo, Brazil
| | - Bianca Bianco
- Department of Collective Health, Faculdade De Medicina Do ABC, Santo André, Brazil
| | - Jaques Waisberg
- Department of Surgery, Faculdade De Medicina Do ABC, Santo André, Brazil.,Department of Surgery, State Public Servant Hospital (IAMSPE), São Paulo, Brazil
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3
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Zhang M, Wang J, Jiang J, Zhan X, Ling Y, Lu Z, Guo J, Gao X. Von Hippel-Lindau disease type 2 in a Chinese family with a VHL p.W88X truncation. Endocrine 2015; 48:83-8. [PMID: 25069792 DOI: 10.1007/s12020-014-0368-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 07/16/2014] [Indexed: 12/18/2022]
Abstract
Von Hippel-Lindau (VHL) disease is an autosomal dominant syndrome caused by germline mutations in the synonymous VHL gene encoding a tumor suppressor. Affected individuals are susceptible to various benign and malignant tumors. Based on the phenotypes, VHL disease is classified as type 1 and type 2. Here, we describe a Chinese family diagnosed as VHL disease type 2, with different metabolic status of tumors on FDG PET-CT. Genetic analysis revealed a germline c.264G>A point mutation, resulting in premature termination at codon 88 (p.W88X). This pedigree represents a rare link between p.W88X nonsense mutation (genotype) and VHL disease type 2 (phenotype), which has not been previously described. This is also the first nonsense mutation to manifest as VHL disease type 2 in ethnic Chinese. We also reviewed the literature and provided an outline of mutations associated with VHL disease in China.
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Affiliation(s)
- Min Zhang
- Department of Endocrinology and Metabolism, Qingpu Branch of Zhongshan Hospital, Fudan University, Shanghai, People's Republic of China
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Kanda RK, Quinlivan ML, Gershon AA, Nichols RA, Breuer J. Population diversity in batches of the varicella Oka vaccine. Vaccine 2011; 29:3293-8. [PMID: 21349363 DOI: 10.1016/j.vaccine.2011.02.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 01/27/2011] [Accepted: 02/07/2011] [Indexed: 10/18/2022]
Abstract
The Oka vaccine is a live attenuated vaccine for the prevention of varicella. Although the vaccine differs from the progenitor virus by over 40 mutations, only three of these are fixed, the rest being a mixture of the wildtype and the vaccine allele. To examine the extent of this variability between two of the three commercially available vaccine preparations, we analysed the vaccine/wildtype allele frequencies present at fifteen vaccine loci in five preparations each from two different manufacturers of the vOka vaccine. Our results suggest that differences in manufacturing processes between the two companies have resulted in significant variation in the frequencies of the vaccine/wildtype alleles in their vaccines. Yet despite these differences, the allele frequencies in the vaccines from the two companies are strongly correlated. We discuss the significance of these findings and the role of evolutionary processes that influence the production of this live attenuated vaccine.
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Affiliation(s)
- R K Kanda
- Department of Infection, The Windeyer Institute, University College London, 46 Cleveland Street, London WC1T 4JF, England, UK.
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5
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Carr IM, Robinson JI, Dimitriou R, Markham AF, Morgan AW, Bonthron DT. Inferring relative proportions of DNA variants from sequencing electropherograms. Bioinformatics 2009; 25:3244-50. [PMID: 19819885 DOI: 10.1093/bioinformatics/btp583] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- I M Carr
- Leeds Institute of Molecular Medicine, Wellcome Trust Brenner Building, University of Leeds, St James's University Hospital, Beckett Street, Leeds LS9 7TF, UK.
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Dicks E, Teague JW, Stephens P, Raine K, Yates A, Mattocks C, Tarpey P, Butler A, Menzies A, Richardson D, Jenkinson A, Davies H, Edkins S, Forbes S, Gray K, Greenman C, Shepherd R, Stratton MR, Futreal PA, Wooster R. AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes. Bioinformatics 2007; 23:1689-91. [PMID: 17485433 PMCID: PMC5947781 DOI: 10.1093/bioinformatics/btm152] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
UNLABELLED The undertaking of large-scale DNA sequencing screens for somatic variants in human cancers requires accurate and rapid processing of traces for variants. Due to their often aneuploid nature and admixed normal tissue, heterozygous variants found in primary cancers are often subtle and difficult to detect. To address these issues, we have developed a mutation detection algorithm, AutoCSA, specifically optimized for the high throughput screening of cancer samples. AVAILABILITY http://www.sanger.ac.uk/genetics/CGP/Software/AutoCSA.
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Affiliation(s)
- E. Dicks
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - J. W. Teague
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - P. Stephens
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - K. Raine
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - A. Yates
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - C. Mattocks
- NGRL (Wessex), Salisbury District Hospital, Salisbury, SP2 8BJ, UK
| | - P. Tarpey
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - A. Butler
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - A. Menzies
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - D. Richardson
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - A. Jenkinson
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - H. Davies
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - S. Edkins
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - S. Forbes
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - K. Gray
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - C. Greenman
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - R. Shepherd
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - M. R. Stratton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - P. A. Futreal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - R. Wooster
- Cancer Genome Project, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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7
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Huang JS, Huang CJ, Chen SK, Chien CC, Chen CW, Lin CM. Associations between VHL genotype and clinical phenotype in familial von Hippel-Lindau disease. Eur J Clin Invest 2007; 37:492-500. [PMID: 17537157 DOI: 10.1111/j.1365-2362.2007.01806.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND Von Hippel-Lindau (VHL) disease is an autosomal dominant hereditary disorder associated with tumours and cysts in the central nervous system (CNS) and other visceral organs. Germline mutations in the VHL gene on chromosome 3p25-26 are considered the cause of this disease. MATERIALS AND METHODS We studied six patients with VHL disease and their relatives. Loss of heterozygosity (LOH) was determined by five flanking microsatellite polymorphic markers in the VHL locus. Multiplex ligation-dependent probe amplification (MLPA) and quantitative real-time polymerase chain reaction (qPCR) amplification were used to detect the genomic deletions. Single-strand conformation polymorphism (SSCP) analysis was applied to test for sequence variations. RESULTS Three germline deletions in the VHL gene (142.9, 53.3 and 3.3 kb) were found by MLPA. These deletions were defined clearly by qPCR analyses. The142.9 kb germline deletion was significantly associated with patients with CNS haemangioblastomas (P < 0.01 by Fisher's exact test), and one missense mutation (Gln209Arg) was detected from a patient with a pancreatic cyst in the same family. LOH was also detected from a patient with bilateral renal cell carcinomas. CONCLUSION Diverse genetic conditions are associated with the clinical manifestations of VHL disease. Genomic deletions that can be detected by MLPA or qPCR are major causes for this syndrome. Missense mutations and LOH accompanying the disease lead to complex clinical symptoms and genotypic determination can facilitate a clinical diagnosis because of their strong association.
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Affiliation(s)
- J S Huang
- Department of Neurosurgery, Cathay General Hospital, Taipei, Taiwan
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8
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Quinlivan ML, Gershon AA, Al Bassam MM, Steinberg SP, LaRussa P, Nichols RA, Breuer J. Natural selection for rash-forming genotypes of the varicella-zoster vaccine virus detected within immunized human hosts. Proc Natl Acad Sci U S A 2007; 104:208-12. [PMID: 17182747 PMCID: PMC1765436 DOI: 10.1073/pnas.0605688104] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2006] [Indexed: 11/18/2022] Open
Abstract
The Oka vaccine strain is a live attenuated virus that is routinely administered to children in the United States and Europe to prevent chickenpox. It is effective and safe but occasionally produces a rash. The vaccine virus has accumulated mutations during its attenuation, but the rashes are not explained by their reversion, unlike complications reported for other viral vaccines. Indeed, most of the novel mutations distinguishing the Oka vaccine from the more virulent parental virus have not actually become fixed. Because the parental alleles are still present, the vaccine is polymorphic at >30 loci and therefore contains a mixture of related viruses. The inoculation of >40 million patients has consequently created a highly replicated evolutionary experiment that we have used to assess the competitive ability of these different viral genotypes in a human host. Using virus recovered from rash vesicles, we show that two vaccine mutations, causing amino acid substitutions in the major transactivating protein IE62, are outcompeted by the ancestral alleles. Standard interpretations of varicella disease severity concentrate on the undeniably important effects of host genotype and immune status, yet our results allow us to demonstrate that the viral genotype is associated with virulence and to identify the key sites. We propose that these loci have pleiotropic effects on the immunogenic properties of the virus, rash formation, and its epidemiological spread, which mould the evolution of its virulence. These findings are of practical importance for reducing the incidence of vaccine-associated rash and promoting public acceptance of the vaccine.
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Affiliation(s)
- Mark L. Quinlivan
- *Centre for Infectious Disease, Institute for Cell and Molecular Science, Queen Mary's School of Medicine and Dentistry, 4 Newark Street, London E1 2AT, United Kingdom
| | - Anne A. Gershon
- Columbia University College of Physicians and Surgeons, 650 West 168th Street, Black Building 4-427, New York, NY 10032; and
| | - Mahmoud M. Al Bassam
- *Centre for Infectious Disease, Institute for Cell and Molecular Science, Queen Mary's School of Medicine and Dentistry, 4 Newark Street, London E1 2AT, United Kingdom
| | - Sharon P. Steinberg
- Columbia University College of Physicians and Surgeons, 650 West 168th Street, Black Building 4-427, New York, NY 10032; and
| | - Philip LaRussa
- Columbia University College of Physicians and Surgeons, 650 West 168th Street, Black Building 4-427, New York, NY 10032; and
| | - Richard A. Nichols
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Judith Breuer
- *Centre for Infectious Disease, Institute for Cell and Molecular Science, Queen Mary's School of Medicine and Dentistry, 4 Newark Street, London E1 2AT, United Kingdom
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Blow MJ, Grocock RJ, van Dongen S, Enright AJ, Dicks E, Futreal PA, Wooster R, Stratton MR. RNA editing of human microRNAs. Genome Biol 2006; 7:R27. [PMID: 16594986 PMCID: PMC1557993 DOI: 10.1186/gb-2006-7-4-r27] [Citation(s) in RCA: 253] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2005] [Revised: 01/30/2005] [Accepted: 03/06/2006] [Indexed: 12/31/2022] Open
Abstract
A survey of RNA editing of miRNAs from ten human tissues indicates that RNA editing increases the diversity of miRNAs and their targets. Background MicroRNAs (miRNAs) are short RNAs of around 22 nucleotides that regulate gene expression. The primary transcripts of miRNAs contain double-stranded RNA and are therefore potential substrates for adenosine to inosine (A-to-I) RNA editing. Results We have conducted a survey of RNA editing of miRNAs from ten human tissues by sequence comparison of PCR products derived from matched genomic DNA and total cDNA from the same individual. Six out of 99 (6%) miRNA transcripts from which data were obtained were subject to A-to-I editing in at least one tissue. Four out of seven edited adenosines were in the mature miRNA and were predicted to change the target sites in 3' untranslated regions. For a further six miRNAs, we identified A-to-I editing of transcripts derived from the opposite strand of the genome to the annotated miRNA. These miRNAs may have been annotated to the wrong genomic strand. Conclusion Our results indicate that RNA editing increases the diversity of miRNAs and their targets, and hence may modulate miRNA function.
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Affiliation(s)
- Matthew J Blow
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Russell J Grocock
- Computational and Functional Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Stijn van Dongen
- Computational and Functional Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Anton J Enright
- Computational and Functional Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Ed Dicks
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - P Andrew Futreal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Richard Wooster
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Michael R Stratton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
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10
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Blow MJ, Grocock RJ, van Dongen S, Enright AJ, Dicks E, Futreal PA, Wooster R, Stratton MR. RNA editing of human microRNAs. Genome Biol 2006. [PMID: 16594986 DOI: 10.1186/gb-2006-7-4-r17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are short RNAs of around 22 nucleotides that regulate gene expression. The primary transcripts of miRNAs contain double-stranded RNA and are therefore potential substrates for adenosine to inosine (A-to-I) RNA editing. RESULTS We have conducted a survey of RNA editing of miRNAs from ten human tissues by sequence comparison of PCR products derived from matched genomic DNA and total cDNA from the same individual. Six out of 99 (6%) miRNA transcripts from which data were obtained were subject to A-to-I editing in at least one tissue. Four out of seven edited adenosines were in the mature miRNA and were predicted to change the target sites in 3' untranslated regions. For a further six miRNAs, we identified A-to-I editing of transcripts derived from the opposite strand of the genome to the annotated miRNA. These miRNAs may have been annotated to the wrong genomic strand. CONCLUSION Our results indicate that RNA editing increases the diversity of miRNAs and their targets, and hence may modulate miRNA function.
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Affiliation(s)
- Matthew J Blow
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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11
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Blow MJ, Grocock RJ, van Dongen S, Enright AJ, Dicks E, Futreal PA, Wooster R, Stratton MR. RNA editing of human microRNAs. Genome Biol 2006. [PMID: 16594986 DOI: 10.1186/gb-20060704-r27] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are short RNAs of around 22 nucleotides that regulate gene expression. The primary transcripts of miRNAs contain double-stranded RNA and are therefore potential substrates for adenosine to inosine (A-to-I) RNA editing. RESULTS We have conducted a survey of RNA editing of miRNAs from ten human tissues by sequence comparison of PCR products derived from matched genomic DNA and total cDNA from the same individual. Six out of 99 (6%) miRNA transcripts from which data were obtained were subject to A-to-I editing in at least one tissue. Four out of seven edited adenosines were in the mature miRNA and were predicted to change the target sites in 3' untranslated regions. For a further six miRNAs, we identified A-to-I editing of transcripts derived from the opposite strand of the genome to the annotated miRNA. These miRNAs may have been annotated to the wrong genomic strand. CONCLUSION Our results indicate that RNA editing increases the diversity of miRNAs and their targets, and hence may modulate miRNA function.
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Affiliation(s)
- Matthew J Blow
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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12
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Giménez-Bachs JM, Salinas-Sánchez AS, Sánchez-Sánchez F, Lorenzo-Romero JG, Donate-Moreno MJ, Pastor-Navarro H, García-Olmo DC, Escribano-Martínez J, Virseda-Rodríguez JA. Determination of vhl gene mutations in sporadic renal cell carcinoma. Eur Urol 2005; 49:1051-7. [PMID: 16387411 DOI: 10.1016/j.eururo.2005.10.028] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2005] [Revised: 08/31/2005] [Accepted: 10/20/2005] [Indexed: 11/22/2022]
Abstract
OBJECTIVE Characterization of the molecular status of the vhl gene and its relationship to the usual prognostic factors could help establish new diagnostic and therapeutic strategies. This study determines the presence of vhl gene mutations in tumor tissue from patients with sporadic renal cell carcinoma, the relationship between the mutations and classic prognostic factors, and the possible impact on protein function. MATERIALS AND METHOD Cross-sectional analytical study investigating vhl gene mutations in tumor tissue by PCR testing of the gene exons and automatic sequencing in 96 patients with sporadic renal cell carcinoma. The characteristics of the mutations detected, as well as their relationship with various clinical and pathological parameters and the possible impact on protein function, were analyzed. RESULTS Twenty-two mutations were found in 21 patients (21.9%); 68.2% were point mutations. The mutations were associated only with tumor histotype and were located in protein functional domains. Three mutations were detected in the intron position; 73.7% were considered relevant to protein function. CONCLUSION The percentage of vhl gene mutations in sporadic renal cell carcinoma was relatively low, mutations were seen more often in clear cell carcinoma and were not related to the classic clinical prognostic factors. Mutations of the vhl gene produce important changes in the protein, causing it to lose its tumor suppressor function.
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13
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Zhang LY, Ibbotson RE, Orchard JA, Gardiner AC, Seear RV, Chase AJ, Oscier DG, Cross NCP. P2X7 polymorphism and chronic lymphocytic leukaemia: lack of correlation with incidence, survival and abnormalities of chromosome 12. Leukemia 2003; 17:2097-100. [PMID: 12931211 DOI: 10.1038/sj.leu.2403125] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The P2X7 receptor, a plasma membrane ATP-gated ion channel that plays a role in lymphocyte apoptosis, has been suggested as an important contributory factor to the pathogenesis of chronic lymphocytic leukaemia (CLL). The P2X7 gene resides on chromosome 12 and is polymorphic in the population at large (1513A/C) with the A and C alleles encoding fully active and nonfunctional proteins, respectively. We have evaluated the significance of this polymorphism by genotyping 144 patients with CLL and 348 healthy controls using a tetraprimer ARMS assay. We found no significant difference in allele frequency between patients and controls. Although patients with the C allele (A/C heterozygotes or C/C homozygotes) had a marginally shorter survival than those who were homozygous for the A allele, this difference was not significant for either the patient group considered as a whole or for IgVH-mutated/unmutated subsets. Finally, no association was found between trisomy 12 and P2X7 genotype. We conclude that the influence, if any, of P2X7 genotype on susceptibility to CLL or clinical outcome is small.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Child
- Chromosome Aberrations
- Chromosomes, Human, Pair 12
- DNA Primers
- Genotype
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/epidemiology
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/mortality
- Middle Aged
- Polymerase Chain Reaction
- Polymorphism, Genetic
- Receptors, Purinergic P2/genetics
- Receptors, Purinergic P2X7
- Reference Values
- Survival Analysis
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Affiliation(s)
- L Y Zhang
- Wessex Regional Genetics Laboratory, Salisbury, UK
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14
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Baralle D, Mattocks C, Kalidas K, Elmslie F, Whittaker J, Lees M, Ragge N, Patton MA, Winter RM, ffrench-Constant C. Different mutations in the NF1 gene are associated with Neurofibromatosis-Noonan syndrome (NFNS). Am J Med Genet A 2003; 119A:1-8. [PMID: 12707950 DOI: 10.1002/ajmg.a.20023] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The association of the Noonan phenotype with neurofibromatosis type 1 (NF1) was first noted by Allanson et al. [Am J Med Genet 1985;21:457-462.] and 30 further cases have subsequently been reported. It has been suggested that this phenotype is more common than previously appreciated, as Colley et al. [Clin Genet 1996;49:59-64.] examined 94 sequentially identified patients with NF1 from their genetic register and found Noonan features in 12. A 3-bp deletion of exon 17 of the NF1 neurofibromin gene was described in one family by Carey et al. [Proc Greenwood Genet Center 1997;17:52-53]. However, it remains unclear whether Neurofibromatosis-Noonan syndrome (NFNS) represents a form of NF1 (with mutations in the NF1 neurofibromin gene) or a separate syndrome. We have used a new, rapid sequence analysis technique-comparative sequence analysis (CSA)-to examine the NF1 gene in six patients with NFNS. None of the six patients had the previously identified mutation, nor did we observe other mutations within this exon. However, two other mutations were found: in exon 25, a 3-bp deletion 4312 del GAA, and in exon 23-2, a 2-bp insertion 4095 ins TG. The PTPN11 gene, now known to cause over 50% of Noonan syndrome was also examined in four cases of NFNS, and no mutations were found. These results show that NFNS can in some cases result from different mutations in the NF1 gene and therefore represents a variant form of NF1.
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Affiliation(s)
- Diana Baralle
- Department of Medical Genetics, Addenbrooke's Hospital, Cambridge, United Kingdom.
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15
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Abstract
Most mutation detection techniques are unsuitable for routine use on solid tumours. Important parameters include sensitivity, specificity, efficiency, use of existing resources, and cost. In the UK, < 0.2% of service genetics laboratory activity involves mutation analysis in tumours (usually for family studies), mainly because it is time consuming/labour intensive (thus expensive) and DNA extracted from formalin fixed, paraffin wax embedded tissue is of low quality and yield. The small size of DNA fragments obtained from tissue blocks limits the polymerase chain reaction, the basis of most mutation detection methods. Other, biological, factors include: (1) heterogeneity of mutations within and between tumours, (2) variation in type and site of mutations in any one gene, (3) normal tissue harbouring mutations, (4) few genes are mutated in most of any one tumour type, and (5) few clinically useful correlations with genetic changes have been found. Present research is centred on correlating single gene mutations with various clinicopathological features, but the pattern of mutations in a combination of genes will probably prove more useful. Microsatellite instability, however, appears to be worth testing for in both familial and sporadic tumours, particularly of the colorectum.
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Affiliation(s)
- I M Frayling
- Department of Medical Genetics, Addenbrooke's Hospital, Cambridge, UK.
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