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Wang W, Wang M, Jiang H, Wang T, Da R. BRAF non-V600E more frequently co-occurs with IDH1/2 mutations in adult patients with gliomas than in patients harboring BRAF V600E but without a survival advantage. BMC Neurol 2021; 21:195. [PMID: 33980169 PMCID: PMC8114535 DOI: 10.1186/s12883-021-02224-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/05/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The effects of BRAFnon-V600E and BRAFV600E on the outcomes and the molecular characteristics of adult glioma patients are unknown and need to be explored, although BRAFV600E has been extensively studied in pediatric glioma. METHODS Co-occurring mutations and copy number alterations of associated genes in the MAPK and p53 pathways were investigated using data from The Cancer Genome Atlas (TCGA) public database retrieved by cBioPortal. The prognosis of available adult glioma cohorts with BRAFV600E and BRAFnon-V600E mutations were also investigated. RESULTS Ninety patients with BRAFV600E or BRAFnon-V600E were enrolled in this study, and data from 52 nonredundant patients were investigated. Glioblastoma multiform was the most common cancer type, with BRAF non-V600E and BRAFV600E. TP53 (56.00% vs. 7.41%), IDH1/2 (36.00% vs. 3.70%), and ATRX (32.00% vs. 7.41%) exhibited more mutations in BRAFnon-V600E than in BRAFV600E, and TP53 was an independent risk factor (56.00% vs. 7.41%). Both BRAFnon-V600E and BRAFV600E frequently overlapped with CDKN2A/2B homozygous deletions (HDs), but there was no significant difference. Survival analysis showed no difference between the BRAF non-V600E and BRAFV600E cohorts, even after excluding the survival benefit of IDH1/2 mutations and considering the BRAFnon-V600E mutations in the glycine-rich loop (G-loop) and in the activation segment. The estimated mean survival of patients with BRAFnon-V600E & IDH1/2WT with mutations in the G-loop groups was the shortest. CONCLUSIONS BRAFnon-V600E exhibited a stronger association with IDH1/2 mutations than BRAFV600E, but no survival advantage was found.
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Affiliation(s)
- Wei Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Maode Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Haitao Jiang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Tuo Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Rong Da
- Department of Clinical Laboratory, The First Affiliated Hospital of Xi'an Jiaotong University, No.277 Yanta West Road, Xi'an, 710061, Shaanxi, China.
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2
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Da R, Wang M, Jiang H, Wang T, Wang W. BRAF AMP Frequently Co-occurs With IDH1/2, TP53, and ATRX Mutations in Adult Patients With Gliomas and Is Associated With Poorer Survival Than That of Patients Harboring BRAF V600E. Front Oncol 2021; 10:531968. [PMID: 33489866 PMCID: PMC7817544 DOI: 10.3389/fonc.2020.531968] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 11/11/2020] [Indexed: 12/31/2022] Open
Abstract
Abnormal RAS/RAF signaling plays a critical role in glioma. Although it is known that the V600E mutation of v-raf murine viral oncogene homolog B1 (BRAFV600E) and BRAF amplification (BRAFAMP) both result in constitutive activation of the RAS/RAF pathway, whether BRAFV600E and BRAFAMP have different effects on the survival of glioma patients needs to be clarified. Using cBioPortal, we retrieved studies of both mutations and copy number variations of the BRAF gene in CNS/brain tumors and investigated data from 69 nonredundant glioma patients. The BRAF mutation group had significantly more male patients (64.00% vs. 36.84%; P = 0.046) and a higher occurrence of glioblastoma multiforme (66.00% vs. 31.58%; P = 0.013) compared to those in the other group. The BRAFAMP group had significantly more patients with the mutant isocitrate dehydrogenase 1 and 2 (IDH1/2) (73.68% vs. 18.00%; P = 0.000), tumor protein p53 (TP53) (73.68% vs. 30.00%; P = 0.002), and alpha thalassemia/mental retardation syndrome X linked (ATRX) (63.16% vs. 18.00%; P = 0.001) than the mutation group. The BRAFAMP and IDH1/2WT cohort had lower overall survival compared with the BRAFAMP and IDH1/2MT groups (P = 0.001) and the BRAF mutation cohort (P = 0.019), including the BRAFV600E (P = 0.033) and BRAFnon-V600E (P = 0.029) groups, using Kaplan–Meier survival curves and the log rank (Mantel–Cox) test. The BRAFAMP and IDH1/2WT genotype was found to be an independent predictive factor for glioma with BRAF mutation and BRAFAMP using Cox proportional hazard regression analysis (HR = 0.138, P = 0.018). Our findings indicate that BRAFAMP frequently occurs with IDH1/2, TP53, and ATRX mutations. Adult patients with glioma with BRAFAMP and IDH1/2WT had worse prognoses compared with those with BRAF mutation and BRAFAMP and IDH1/2MT. This suggests that the assessment of the status of BRAFAMP and IDH1/2 in adult glioma/glioblastoma patients has prognostic value as these patients have relatively short survival times and may benefit from personalized targeted therapy using BRAF and/or MEK inhibitors.
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Affiliation(s)
- Rong Da
- Department of Clinical Laboratory, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Maode Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Haitao Jiang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Tuo Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Wei Wang
- Department of Neurosurgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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3
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Evolutionary Forces and Codon Bias in Different Flavors of Intrinsic Disorder in the Human Proteome. J Mol Evol 2019; 88:164-178. [DOI: 10.1007/s00239-019-09921-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 11/26/2019] [Indexed: 12/22/2022]
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4
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Dunn GP, Andronesi OC, Cahill DP. From genomics to the clinic: biological and translational insights of mutant IDH1/2 in glioma. Neurosurg Focus 2015; 34:E2. [PMID: 23373447 DOI: 10.3171/2012.12.focus12355] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The characterization of the genomic alterations across all human cancers is changing the way that malignant disease is defined and treated. This paradigm is extending to glioma, where the discovery of recurrent mutations in the isocitrate dehydrogenase 1 (IDH1) gene has shed new light on the molecular landscape in glioma and other IDH-mutant cancers. The IDH1 mutations are present in the vast majority of low-grade gliomas and secondary glioblastomas. Rapidly emerging work on the consequences of mutant IDH1 protein expression suggests that its neomorphic enzymatic activity catalyzing the production of the oncometabolite 2-hydroxyglutarate influences a range of cellular programs that affect the epigenome, transcriptional programs, hypoxia-inducible factor biology, and development. In the brief time since its discovery, knowledge of the IDH mutation status has had significant translational implications, and diagnostic tools are being used to monitor its expression and function. The concept of IDH1-mutant versus IDH1-wild type will become a critical early distinction in diagnostic and treatment algorithms.
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Affiliation(s)
- Gavin P Dunn
- Departments of Neurosurgery, Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
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5
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Malcikova J, Pavlova S, Kozubik KS, Pospisilova S. TP53 Mutation Analysis in Clinical Practice: Lessons From Chronic Lymphocytic Leukemia. Hum Mutat 2014; 35:663-71. [DOI: 10.1002/humu.22508] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 01/03/2014] [Indexed: 01/22/2023]
Affiliation(s)
- Jitka Malcikova
- Central European Institute of Technology; Center of Molecular Medicine, and Faculty of Medicine; Department of Internal Medicine - Hematology and Oncology; Masaryk University; Brno Czech Republic
| | - Sarka Pavlova
- Central European Institute of Technology; Center of Molecular Medicine, and Faculty of Medicine; Department of Internal Medicine - Hematology and Oncology; Masaryk University; Brno Czech Republic
| | - Katerina Stano Kozubik
- Central European Institute of Technology; Center of Molecular Medicine, and Faculty of Medicine; Department of Internal Medicine - Hematology and Oncology; Masaryk University; Brno Czech Republic
| | - Sarka Pospisilova
- Central European Institute of Technology; Center of Molecular Medicine, and Faculty of Medicine; Department of Internal Medicine - Hematology and Oncology; Masaryk University; Brno Czech Republic
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6
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Detection of TP53 R249 Mutation in Iranian Patients with Pancreatic Cancer. JOURNAL OF ONCOLOGY 2013; 2013:738915. [PMID: 24489544 PMCID: PMC3892507 DOI: 10.1155/2013/738915] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/22/2013] [Revised: 10/13/2013] [Accepted: 10/16/2013] [Indexed: 12/13/2022]
Abstract
The TP53 gene encodes tumor protein p53 which play a major role in the etiology of pancreatic cancer. The important role of codon 249 of TP53 for binding of p53 to its sequence-specific consensus site in DNA has been revealed by crystallography's studies, and mutation at this codon was detected in the plasma of some human cancers. The TP53 Mut assessor software within the International Agency for Research on Cancer (IARC) TP53 Database was performed to evaluate every possible mutation at codon 249. DNA was extracted from the plasma of 133 pancreatic cancer patients and 85 noncancer-bearing individuals. Exon 7 in TP53 was amplified, and mutation at R249 was identified by the endonuclease cleavage of HaeIII. The group of patients showed a frequency of 11% (22 of 133 samples) R249 mutation compared to 3.5% (3 of 85 samples) in the group of control which was significant (P = 0.03). This mutation demonstrated statistically significant association with pancreatic cancer risk in unadjusted odds ratio (OR: 3.74, 95% CI: 1.1–13.2; P = 0.041); however when adjusted for confounding factors, it was marginally significant because of lower control samples. These findings demonstrate that mutation at R249 of TP53 can be considered for increasing risk of pancreatic cancer that needs more research.
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7
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Zhao Y, Epstein RJ. Conserved nonsense-prone CpG sites in apoptosis-regulatory genes: conditional stop signs on the road to cell death. Evol Bioinform Online 2013; 9:275-83. [PMID: 23908585 PMCID: PMC3728200 DOI: 10.4137/ebo.s11759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Methylation-prone CpG dinucleotides are strongly conserved in the germline, yet are also predisposed to somatic mutation. Here we quantify the relationship between germline codon mutability and somatic carcinogenesis by comparing usage of the nonsense-prone CGA (→TGA) codons in gene groups that differ in apoptotic function; to this end, suppressor genes were subclassified as either apoptotic (gatekeepers) or repair (caretakers). Mutations affecting CGA codons in sporadic tumors proved to be highly asymmetric. Moreover, nonsense mutations were 3-fold more likely to affect gatekeepers than caretakers. In addition, intragenic CGA clustering nonrandomly affected functionally critical regions of gatekeepers. We conclude that human gatekeeper suppressor genes are enriched for nonsense-prone codons, and submit that this germline vulnerability to tumors could reflect in utero selection for a methylation-dependent capability to short-circuit environmental insults that otherwise trigger apoptosis and fetal loss.
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Affiliation(s)
- Yongzhong Zhao
- Department of Genetics, Mount Sinai School of Medicine, New York, USA
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8
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TP53 aberrations in chronic lymphocytic leukemia. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 792:109-31. [PMID: 24014294 DOI: 10.1007/978-1-4614-8051-8_5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
CLL patients harboring TP53 defects remain the most challenging group in terms of designing rational and effective therapy. Irrespective of the treatment employed-chemotherapy, chemoimmunotherapy, or pure biological drugs-median survival of these patients does not exceed 3-4 years. This adverse outcome is caused by a less effective response to therapeutics acting through DNA damage induction and relying on the subsequent initiation of apoptosis as well as by virtually inevitable aggressive relapse. Patient proportions with TP53 defects at diagnosis or before first therapy were reported within the range 5-15 %, but they increase dramatically in pretreated cohorts (reported up to 44 %), and also in patients with Richter transformation (50 % harbor TP53 defects). Currently, most laboratories monitor TP53 defect as presence of 17p deletion using I-FISH, but 23-45 % of TP53-affected patients were shown to harbor only mutation(s). In other patients with intact TP53, the p53 pathway may be impaired by mutations in ATM gene coding for the p53-regulatory kinase; however, prognosis of ATM-defective patients is not as poor as those with TP53 abnormalities. Though many novel agents are under development, the monoclonal antibody alemtuzumab and allogeneic stem cell transplantation remain the basic treatment options for TP53-affected CLL patients.
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9
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Hashimoto K, Rogozin IB, Panchenko AR. Oncogenic potential is related to activating effect of cancer single and double somatic mutations in receptor tyrosine kinases. Hum Mutat 2012; 33:1566-75. [PMID: 22753356 PMCID: PMC3465464 DOI: 10.1002/humu.22145] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Accepted: 05/29/2012] [Indexed: 01/16/2023]
Abstract
Aberrant activation of receptor tyrosine kinases (RTKs) is a common feature of many cancer cells. It was previously suggested that the mechanisms of kinase activation in cancer might be linked to transitions between active and inactive states. Here, we estimate the effects of single and double cancer mutations on the stability of active and inactive states of the kinase domains from different RTKs. We show that singleton cancer mutations destabilize active and inactive states; however, inactive states are destabilized more than the active ones, leading to kinase activation. We show that there exists a relationship between the estimate of oncogenic potential of cancer mutation and kinase activation. Namely, more frequent mutations have a higher activating effect, which might allow us to predict the activating effect of the mutations from the mutation spectra. Independent evolutionary analysis of mutation spectra complements this observation and finds the same frequency threshold defining mutation hotspots. We analyze double mutations and report a positive epistasis and additional advantage of doublets with respect to cancer cell fitness. The activation mechanisms of double mutations differ from those of single mutations and double mutation spectrum is found to be dissimilar to the mutation spectrum of singletons.
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Affiliation(s)
| | - Igor B. Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Anna R. Panchenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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10
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Dunn GP, Rinne ML, Wykosky J, Genovese G, Quayle SN, Dunn IF, Agarwalla PK, Chheda MG, Campos B, Wang A, Brennan C, Ligon KL, Furnari F, Cavenee WK, Depinho RA, Chin L, Hahn WC. Emerging insights into the molecular and cellular basis of glioblastoma. Genes Dev 2012. [PMID: 22508724 DOI: 10.1101/gad.187922.112.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Glioblastoma is both the most common and lethal primary malignant brain tumor. Extensive multiplatform genomic characterization has provided a higher-resolution picture of the molecular alterations underlying this disease. These studies provide the emerging view that "glioblastoma" represents several histologically similar yet molecularly heterogeneous diseases, which influences taxonomic classification systems, prognosis, and therapeutic decisions.
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Affiliation(s)
- Gavin P Dunn
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
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11
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Dunn GP, Rinne ML, Wykosky J, Genovese G, Quayle SN, Dunn IF, Agarwalla PK, Chheda MG, Campos B, Wang A, Brennan C, Ligon KL, Furnari F, Cavenee WK, Depinho RA, Chin L, Hahn WC. Emerging insights into the molecular and cellular basis of glioblastoma. Genes Dev 2012; 26:756-84. [PMID: 22508724 DOI: 10.1101/gad.187922.112] [Citation(s) in RCA: 415] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Glioblastoma is both the most common and lethal primary malignant brain tumor. Extensive multiplatform genomic characterization has provided a higher-resolution picture of the molecular alterations underlying this disease. These studies provide the emerging view that "glioblastoma" represents several histologically similar yet molecularly heterogeneous diseases, which influences taxonomic classification systems, prognosis, and therapeutic decisions.
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Affiliation(s)
- Gavin P Dunn
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
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12
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Lai A, Kharbanda S, Pope WB, Tran A, Solis OE, Peale F, Forrest WF, Pujara K, Carrillo JA, Pandita A, Ellingson BM, Bowers CW, Soriano RH, Schmidt NO, Mohan S, Yong WH, Seshagiri S, Modrusan Z, Jiang Z, Aldape KD, Mischel PS, Liau LM, Escovedo CJ, Chen W, Nghiemphu PL, James CD, Prados MD, Westphal M, Lamszus K, Cloughesy T, Phillips HS. Evidence for sequenced molecular evolution of IDH1 mutant glioblastoma from a distinct cell of origin. J Clin Oncol 2011; 29:4482-90. [PMID: 22025148 DOI: 10.1200/jco.2010.33.8715] [Citation(s) in RCA: 335] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
PURPOSE Mutation in isocitrate dehydrogenase 1 (IDH1) at R132 (IDH1(R132MUT)) is frequent in low-grade diffuse gliomas and, within glioblastoma (GBM), has been proposed as a marker for GBMs that arise by transformation from lower-grade gliomas, regardless of clinical history. To determine how GBMs arising with IDH1(R132MUT) differ from other GBMs, we undertook a comprehensive comparison of patients presenting clinically with primary GBM as a function of IDH1(R132) mutation status. PATIENTS AND METHODS In all, 618 treatment-naive primary GBMs and 235 lower-grade diffuse gliomas were sequenced for IDH1(R132) and analyzed for demographic, radiographic, anatomic, histologic, genomic, epigenetic, and transcriptional characteristics. RESULTS Investigation revealed a constellation of features that distinguishes IDH1(R132MUT) GBMs from other GBMs (including frontal location and lesser extent of contrast enhancement and necrosis), relates them to lower-grade IDH1(R132MUT) gliomas, and supports the concept that IDH1(R132MUT) gliomas arise from a neural precursor population that is spatially and temporally restricted in the brain. The observed patterns of DNA sequence, methylation, and copy number alterations support a model of ordered molecular evolution of IDH1(R132MUT) GBM in which the appearance of mutant IDH1 protein is an initial event, followed by production of p53 mutant protein, and finally by copy number alterations of PTEN and EGFR. CONCLUSION Although histologically similar, GBMs arising with and without IDH1(R132MUT) appear to represent distinct disease entities that arise from separate cell types of origin as the result of largely nonoverlapping sets of molecular events. Optimal clinical management should account for the distinction between these GBM disease subtypes.
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Affiliation(s)
- Albert Lai
- David Geffen School of Medicine at theUniversity of California at Los Angeles, Los Angeles, CA, USA
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TP53 mutation profile in chronic lymphocytic leukemia: evidence for a disease specific profile from a comprehensive analysis of 268 mutations. Leukemia 2010; 24:2072-9. [PMID: 20861914 DOI: 10.1038/leu.2010.208] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The TP53 mutation profile in chronic lymphocytic leukemia (CLL) and the correlation of TP53 mutations with allele status or associated molecular genetics are currently unknown. We performed a large mutation analysis of TP53 at four centers and characterized the pattern of TP53 mutations in CLL. We report on 268 mutations in 254 patients with CLL. Missense mutations appeared in 74% of cases compared with deletions and insertions (20%), nonsense (4%) and splice site (2%) mutations. The majority (243 of 268) of mutations were located in the DNA-binding domain. Transitions were found in 131 of 268 mutations, with only 41 occurring at methylated CpG sites (15%), suggesting that transitions at CpGs are uncommon. The codons most frequently mutated were at positions 175, 179, 248 and 273; in addition, we detected a common 2-nt deletion in the codon 209. Most mutations (199 of 259) were accompanied by deletion of the other allele (17p-). Interestingly, trisomy 12 (without 17p-) was only found in one of 60 cases with TP53 mutation (without 17p-) compared with 60 of 16 in the cohort without mutation (P=0.006). The mutational profile was not different in the cohorts with and without previous therapy, suggesting that the mechanism underlying the development of mutations may be similar, independent of treatment.
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Xu F, Dong C, Xie C, Ren J. Ultrahighly sensitive homogeneous detection of DNA and microRNA by using single-silver-nanoparticle counting. Chemistry 2010; 16:14225. [PMID: 19938021 DOI: 10.1002/chem.200902555] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA and RNA analysis is of high importance for clinical diagnoses, forensic analysis, and basic studies in the biological and biomedical fields. In this paper, we report the ultrahighly sensitive homogeneous detection of DNA and microRNA by using a novel single-silver-nanoparticle counting (SSNPC) technique. The principle of SSNPC is based on the photon-burst counting of single silver nanoparticles (Ag NPs) in a highly focused laser beam (about 0.5 fL detection volume) due to Brownian motion and the strong resonance Rayleigh scattering of single Ag NPs. We first investigated the performance of the SSNPC system and then developed an ultrasensitive homogeneous detection method for DNA and microRNA based on this single-nanoparticle technique. Sandwich nucleic acid hybridization models were utilized in the assays. In the hybridization process, when two Ag-NP-oligonucleotide conjugates were mixed in a sample containing DNA (or microRNA) targets, the binding of the targets caused the Ag NPs to form dimers (or oligomers), which led to a reduction in the photon-burst counts. The SSNPC method was used to measure the change in the photon-burst counts. The relationship between the change of the photon-burst counts and the target concentration showed a good linearity. This method was used for the assay of sequence-specific DNA fragments and microRNAs. The detection limits were at about the 1 fM level, which is 2-5 orders of magnitude more sensitive than current homogeneous methods.
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Affiliation(s)
- Fagong Xu
- College of Chemistry & Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai 200240, PR China
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15
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Kouidou S, Malousi A, Kyventidis A, Fragou A, Maglaveras N. G:C > A:T mutations and potential epigenetic regulation of p53 in breast cancer. Breast Cancer Res Treat 2007; 106:351-60. [PMID: 17505880 DOI: 10.1007/s10549-007-9514-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Accepted: 01/03/2007] [Indexed: 01/03/2023]
Abstract
Analysis of germline p53 mutations in breast cancer reveals that the Li-Fraumeni and Li-Fraumeni-like syndromes are mostly related to the loss of initiation codon 133 of regulatory TP53 isoforms (Delta133p53). In eight codons of exons 5-8 (including 133), mutations are frequent in Li-Fraumeni-related, but scarce in sporadic breast cancer, while in six more codons they are frequent both in familial and sporadic breast cancers. At the proximity of these codons, we observed in somatic mutation databases, 16 codons (minihotspots mostly in exons 7, 8) which undergo frequent G:C > A:T transitions (non-CpG) in all sporadic cancers. In addition, in sporadic breast cancer we observed 35 adjacent codons in which the following types of mutation are observed: frequent G:C > A:T transitions at CCs/GGs, frequent silent mutations in exons 5,6 and suppressed nonsense mutations (5 codons, few records). Non-CpG G:C > A:T transitions in the 35 codons are rare in familial cancers (p53, BRCA1, or BRCA2-related), but frequent in sporadic cancers in organs where Li-Fraumeni-related carcinogenesis is common e.g. adrenal cortex, soft tissues. These data are in support of the following tissue-specific processes: in sporadic breast cancer (sarcomas etc.), loss of methylation sites (in 35 codons mostly next to codon 133), might lead to loss of silencing of TP53 isoforms which are suppressed in these tissues. On the contrary, "spreading" of cytosine methylation (asymmetric) in a G:C-rich region next to common hotspots (codons 238-252 in minihotspots) and mutagenesis probably destabilizes all tissues. Frequent C > T activation at non-CpG is also observed in prostate sporadic cancer, which similarly to breast, undergoes age-related crisis. The above data reveal that tissue-specific epigenetic regulatory mechanisms might be involved in p53 instability.
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Affiliation(s)
- Sofia Kouidou
- Department of Biological Chemistry, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece.
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Lamolle G, Marin M, Alvarez-Valin F. Silent mutations in the gene encoding the p53 protein are preferentially located in conserved amino acid positions and splicing enhancers. Mutat Res 2006; 600:102-12. [PMID: 16650445 DOI: 10.1016/j.mrfmmm.2006.03.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2005] [Revised: 01/17/2006] [Accepted: 03/17/2006] [Indexed: 02/04/2023]
Abstract
The last release of p53 somatic mutation database contains more than 20,000 of mutation among which 951 are silent (synonymous). This striking amount of silent mutations is much more than what would be expected if synonymous mutations were effectively neutral. The prevalent explanation to reconcile this vast amount of silent mutations with the neutral expectation is that they are just the subproduct of the hypermutability process that affect cancer cells. Some evidences have been presented in this direction, and the explanation has been taken as granted. Assuming that silent mutations are effectively neutral has major implication in the investigation of mutational processes that affect the gene encoding the p53 protein, since on the basis of this assumption they are considered the Null hypothesis, for instance for measuring and comparing among tissues the endogenous mutability. From this it follows that determining whether silent mutations in the p53 gene, and in all disease genes in general, are or not basically mutational noise, is of paramount importance. In this paper we readdress this topic by testing whether there is a relationship between the spatial distribution of silent mutations inside the p53 gene and functional significant features of the gene. For this purpose we divided the population of silent mutations in three groups: those that are found accompanied by other mutations (doublets and multiplest), those that were isolated as singlets, but the same mutation was also isolated as being part of a doublet (or multiplet) in another individual. And the last group is composed by those that were always found as singlets and never as being part of a doublet or a multiplet. This last group was expected to be enriched in functionally significant silent mutations. We found that all silent mutations, but particularly those of the last group, are preferentially located in conserved amino acid positions (i.e. functionally important amino acids) and also tend to be located inside suspected splicing enhancers. Noteworthy, this association remains even after eliminating the possible contribution of mutation hotspots. Besides, we present additional evidence in the direction that these putative splicing enhancers are real functional enhancers.
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Affiliation(s)
- Guillermo Lamolle
- Sección Biomatemática, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, Uruguay
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17
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Belyavskaya VA, Vardosanidze VK, Smirnova OY, Karakin EI, Savkin IV, Gervas PA, Cherdyntseva NV, Voevoda MI. Genetic status of p53 in stomach cancer: Somatic mutations and polymorphism of codon 72. Bull Exp Biol Med 2006; 141:243-6. [PMID: 16984108 DOI: 10.1007/s10517-006-0139-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The incidence of somatic mutagenesis of p53 oncosuppressor protein in malignant tumors of the stomach and genetic polymorphism of p53 were studied in patients with stomach cancer on DNA samples isolated from tumor tissues obtained during surgery. The incidence of Pro/Pro genotype increased in the patients, while the percentage of Arg/Pro heterozygotes was markedly lower compared to long-living persons without cancer. The incidence of p53 somatic mutations in exons 5, 7, 8 was 70.8%; multiple mutations were detected in half of the examined patients. The relationship between the intensity of p53 mutagenesis and histological structure of the tumor was detected. The contribution of p53 genetic status to the risk of stomach cancer can be more effectively evaluated on DNA samples isolated from not only tumor cells, but also from normal tissues. The effects of epigenetic factors determining the intensity of somatic mutagenesis of p53 in tumors should be taken into account.
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18
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Gorlov IP, Gorlova OY, Frazier ML, Amos CI. Missense mutations in cancer suppressor gene TP53 are colocalized with exonic splicing enhancers (ESEs). Mutat Res 2004; 554:175-83. [PMID: 15450416 DOI: 10.1016/j.mrfmmm.2004.04.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2004] [Revised: 04/20/2004] [Accepted: 04/27/2004] [Indexed: 01/10/2023]
Abstract
Mutation databases can be viewed as footprints of functional organization of a gene and thus can be used to infer its functional organization. We studied the association of exonic splicing enhancers (ESEs) with missense mutations in the tumor suppressor gene TP53 using the International Agency for Research on Cancer (IARC) mutation database. The goals of the study were: (i) to verify the hypothesis that deleterious missense mutations are colocalized with ESEs; (ii) to identify potentially functional ESE sites in the open reading frame (ORF) of the TP53. If some sequence functions as a splicing enhancer, then nucleotide substitutions in the site will disturb splicing, abrogate p53 function, and cause an increased susceptibility to cancer. Therefore, among cancers showing p53 mutations, more missense mutations are expected within functional ESE sites as compared to non-functional ESE motifs. Using several statistical tests, we found that missense mutations in TP53 are strongly colocalized with ESEs, and that only a small fraction of ESE sites contributes to the association. There are usually one or two ESEs per exon showing a statistically significant association with missense mutations--so-called significant ESE sites. In many respects significant ESE sites are different from those that do not show association with missense mutations. We found that positions of significant ESE sites are codon-dependent--significant ESEs preferentially start from the first position of a codon, whereas non-significant ESEs show no position dependence. Significant ESEs showed a more limited set of sequences compared to non-significant ESEs. These findings suggest that there is a limited number of missense mutations that influence ESE sites and our analysis provides further insight into the types of sites that harbor exonic enhancer elements.
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Affiliation(s)
- Ivan P Gorlov
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Box 189, 1515 Holcombe Boulevard, Houston 77030, USA
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19
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Affiliation(s)
- Nadir R Farid
- Osancor Biotech Inc, 31 Woodland Drive, Watford, Herts, UK, WD17 3BY
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20
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Abstract
It is clear that mutations cause cancer. The implicated mechanism is Darwinism. That is, a stochastic series of mutations is purported to effect the cellular variability upon which natural selection acts to yield increasingly cancer-like intermediates leading ultimately to malignant clones. It is no wonder then that the neoplastic phenotype is considered "alien," having evolved via random unrehearsed events. Neoplasia, however, has also been depicted as something less than foreign, bordering on familiar. This is because cancer shares proliferative and invasive qualities with the native developmental processes of embryogenesis and adult tissue renewal/repair. A question then arises: If key features of malignancy already naturally exist within well-choreographed programs, why reinvent this phenotype via stochastic multistep schemes rather than reactivate it largely en bloc? Indeed, as will be shown, tissues do harbor a malignant potential capable of reactivation. Specifically, this capability is maintained by stem cells (having inherited such from embryonic precursors)-a phenotype controlled by a microenvironment favoring perpetual rearing by (quiescent) stem cells of proliferative progeny for orderly renewal over neoplasia. Accordingly, normally well-sequestered stem cells, when amid carcinogen/mutagen-induced disruption to local surroundings, produce progeny tending by default toward disorderliness (neoplasia) over renewal. Because such tumor-causing mutations act non-cell autonomously, this cancerous state is potentially reversible but subsequent cell-autonomous mutations can impair particular clonal progeny, already cancerous, from regressing. Thus, a scenario wherein mutations (1) de-repress malignancy non-cell autonomously and then (2) slow its reversion cell autonomously, commonly misinterpreted as Darwinian, may constitute a non-Darwinian mechanism for the genesis of cancers that are stem cell derived.
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Affiliation(s)
- Ivan Bergstein
- Division of Hematology-Oncology, Weill Medical College of Cornell University, New York, New York 10021, USA
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21
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Rodin SN, Rodin AS, Juhasz A, Holmquist GP. Cancerous hyper-mutagenesis in p53 genes is possibly associated with transcriptional bypass of DNA lesions. Mutat Res 2002; 510:153-68. [PMID: 12459451 DOI: 10.1016/s0027-5107(02)00260-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The database of tumor-associated p53 base substitutions includes about 5% of tumors with two or more base substitutions. These multiplet base substitutions in one tumor are evidence for hyper-mutagenesis. Our retrospective analysis of this database indicates that most multiplets arise from a single transient hyper-mutagenic event in one cell that subsequently proliferated into a clonal tumor. The hyper-mutagenesis, 1.8 x 10(-4) substitutions per base pair, is detected as multiple mutations in p53 genes of tumors. It requires one strongly tumorigenic p53 substitution, usually missense, called the driver mutation. The occurrence frequencies of ancillary base substitutions, those that hitch-hike along with the driver mutation, are independent of their amino acid coding properties. In this respect, they act like neutral mutations. In support of this neutrality, we find that the frequency distribution of hitch-hiking CpG transitions along the p53 exons, their mutational spectrum, approximates the spontaneous pre-selection mutational spectrum of most human tissues and is correlated with the mutational spectrum of p53 pseudogenes in mammalian germ cells. The driver substitutions of multiplets predominantly originate along the transcribed strand while the ancillary substitutions tend to originate along the non-transcribed strand. This data is consistent with a model of time-dependent mutagenesis in non-dividing stem cells for generating multiple strand-asymmetric p53 mutations in tumors. By transcriptional bypass of DNA lesions with concomitant misincorporation, transcriptional mutagenesis generates a transient mutant p53 mRNA. The associated mutant p53 protein could allow the host cell a growth advantage, release from G1-arrest. Then, during subsequent DNA replication and misreading of the same lesion, the damaged base along the transcribed DNA strand would serve as the origin of the p53 base substitution that drives the hyper-mutagenic event leading to tumors with multiple p53 mutations.
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Affiliation(s)
- S N Rodin
- Biology Department, Beckman Research Institute of the City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA.
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22
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Abstract
The high frequency of G-->T transversions in the p53 gene is a distinctive feature of lung cancer patients with a smoking history and is commonly believed to reflect the direct mutagenic signature of polycyclic aromatic hydrocarbon (PAH) adducts along the gene. Using the April 2000 update of the p53 mutation database of the International Agency for Research on Cancer together with the primary literature, we confirm that the frequency of p53 G-->T transversions in lung cancer of smokers is about three times higher than their frequency in lung cancer of nonsmokers and in most other smoke-unrelated cancers. In contrast, the frequency of C-->A transversions, the DNA-strand mirror counterpart of G-->T transversions, appears to be similar in virtually all human cancers. Along with other data, this strand bias leads us to suggest that smoking may inhibit repair of G-->T primary lesions on the non-transcribed strand. As to the origin of G-->T primary lesions in the p53 gene, we unexpectedly found that cell lines derived from lung cancers, but not from other cancers, demonstrate significant additional excess of G-->T transversions when compared to p53 mutations in parent primary tumors. A detailed codon-by-codon comparison provides evidence in favor of the in vitro origin of this culture-associated G-->T augmentation. Since in culture lung cancer cell lines are not exposed to the carcinogens from smoke, one would rather ascribe these new G-->T transversions to some other mutagens such as, for example, reactive oxygen and nitrogen species. These results are consistent with our previous report [Proc. Natl. Acad. Sci. U.S.A. 97 (2000) 12244], and suggest that other factors, in addition to the direct mutagenic action of PAH-like carcinogens, contribute to p53 mutation-associated lung malignancy.
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Affiliation(s)
- Sergei N Rodin
- Department of Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA.
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23
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Abstract
The underlying mechanism leading to carcinogenesis involves genomic instability, likely related to aneuploidy. While p53 as a "guardian of the genome" is an appealing candidate as an initiator of genomic instability, its mutations or deletions usually occur late in the course of tumor progression. P53 may, however, become a target of events initiated by genomic instability. P53 is a transcription factor with multifaceted regulatory functions in the cell cycle, DNA repair and apoptosis. Inactivating p53 mutations have been described in some 50% of human cancers. These mutations are not only important in tumor progression but apparently also in the response of some tumors to chemotherapy and radiation treatment, thus to clinical outcome. P53 mutations are found in 14% of malignant thyroid tumors and are more frequent in poorly differentiated and anaplastic tumors. We have examined the mutation rates of p53 as a measure of genomic instability (hypermutability) of malignant thyroid tumors. We also wondered whether radiation enhances this tendency to genomic instability. To those ends we extracted all available entries from the p53 mutations database (http://www.perso@curies.fr), verified, extended where applicable, and supplemented that information from the original published reports. We were able to locate 100 entries. The distribution of the types of p53 aberrations in thyroid cancer was similar to those in the database as a whole. The silent mutation rate of 20%, not different from the expected 25%, is consistent with a random occurrence of these mutations. This silent mutation rate is 130 times that expected and is 7 times that of the p53 database. Moreover the distribution of p53 mutations is compatible with Poisson's distribution, which, when considered in the context of the silent mutation rates, indicates that p53 is particularly hypermutable in thyroid cancer. Epigenetic deamination of CpG dinucleotides at highly transforming DNA-contact residues is a feature of poorly differentiated tumors and thus associated with tumor progression. The rates of p53 mutations in radiation-related thyroid cancers (15.4%) are similar to those in spontaneously arising tumors, although there was a highly significant heterogeneity (p<0.0005) in the residues mutated in the two tumor sets. None of the residues mutated in radiation-related thyroid cancer involved CpG deamination. Based on the evidence of p53 hypermutability, thyroid cancer appears to exhibit remarkable genomic instability. Spontaneous epigenetic mutational events are involved in tumor progression. While thyroid cancer related to radiation exposure does not increase the rates of p53 mutation, they exhibit mutation at residues not involved in p53/DNA interface.
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Affiliation(s)
- N R Farid
- Osancor Biotech Inc., Watford, Herts, UK.
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24
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Frowein J. Hypothesis: chemical carcinogenesis mediated by a transiently active carcinogen receptor. CYTOGENETICS AND CELL GENETICS 2001; 91:102-4. [PMID: 11173839 DOI: 10.1159/000056827] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Biologically active small-molecular-weight compounds are actively transported into the cell nucleus by a specific receptor. This has been widely demonstrated for retinoids, polycyclic hydrocarbons (such as steroids), and dioxin. Thus, it is reasonable to assume that genotoxically active polycyclic hydrocarbons, and possibly all genotoxically active small-molecular-weight substances, exert their transformational effect in the cell nucleus via a specific receptor. I propose that the receptor is activated only at the end of the G(1) phase of the cell cycle and that the carcinogen receptor complex interferes directly with DNA synthesis, leading to mutations. This hypothesis may account for various characteristics of malignant growth, such as the organ specificity of carcinogens and the relationship between cell proliferation and malignant transformation. If so, it could form the basis for establishing a radioreceptor assay for carcinogens.
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25
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Shahedian B, Shi Y, Zou M, Farid NR. Thyroid carcinoma is characterized by genomic instability: evidence from p53 mutations. Mol Genet Metab 2001; 72:155-63. [PMID: 11161841 DOI: 10.1006/mgme.2000.3114] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
p53 is a transcription factor with multifaceted regulatory functions in cell cycle progression, DNA repair, and programmed cell death. Inactivating mutations have been described in 50% of human cancers. These mutations appear to be important in tumor progression and response to chemotherapy and radiation treatment and thus clinical outcome. p53 mutations are found in 14% of malignant thyroid tumors and are more frequent in poorly differentiated and anaplastic tumors. Given that p53 is a late event in the notional multistep pathogenesis of cancer, we examined its mutation rates as a measure of genomic instability (hypermutability) of malignant thyroid tumors and also wondered whether radiation enhances that proclivity to genomic instability. To that end we have extracted all available data from the p53 mutation database (http://www.perso@curie.fr), verified, extended, where applicable, and supplemented that information from published reports. We were able to identify 100 entries. The distribution of the p53 mutational events--deletions/insertions, transitions versus transversion mutations--was similar to that of the database as a whole. The silent mutation rate of 17.8%, not different from the expected 25%, is consistent with a random occurrence of these mutations. The silent mutation rate is 120 times that expected and is 6 times that of the database. Moreover, the distribution of p53 mutations is compatible with Poisson's distribution, which taken with silent mutation rates indicates that p53 is particularly hypermutable in thyroid carcinomas. Epigenetic deamination of CpG dinucleotide at highly oncogenic DNA-contact residues is a feature of poorly differentiated tumors and thus associated with tumor progression. The rates of p53 mutations (15.4%) in radiation-related cancers were very similar to those in apparently spontaneously arising tumors, although there was a highly significant heterogeneity (P < 0.0005) in the residues mutated. None involved CpG deamination. It is apparent that thyroid cancer exhibits remarkable genomic instability evidenced by p53 hypermutability. Spontaneous epigenetic mutational events are involved in tumor progression and while radiation increases the absolute prevalence of thyroid cancer in the susceptible it does not increase the rate of p53 mutation and seemingly targets different non-DNA-contact residues than those in spontaneously arising tumors.
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Affiliation(s)
- B Shahedian
- Oscancor Biothech Inc, Watford, Herts, United Kingdom
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26
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Abstract
Over 10,000 mutations in the TP53 suppressor gene have been recorded in the International Agency for Research on Cancer (IARC) tumor data base. About 4% of these mutations are silent. It is a question whether these mutations play a role in tumor development. In order to approach this question, we asked whether the reported silent mutations are randomly distributed throughout the TP53 gene. The p53 data base was searched exon by exon. From the frequency of codons with no silent mutations, the average number of silent mutations per codon for each exon was calculated using the Poisson distribution. The results indicate the distribution to be non-random. About one-third of all silent mutations occur in "hot-spots" and after subtraction of these hot-spots, the remaining silent mutations are randomly distributed. In addition, the percentage of silent mutations among the total in the silent mutation hot-spots is close to that expected for random mutation. We conclude that most of the silent mutations recorded in tumors play no role in tumor development and that the percentage of silent mutation is an indication of the amount of random mutation during tumorigenesis. Silent mutations occur to a significantly different extent in different tumor types. Tumors of the esophagus and colon have a low frequency of silent mutations, tumors of the prostate have a high frequency.
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Affiliation(s)
- B S Strauss
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 East 58th Street, 60637, Chicago, IL, USA.
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27
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Rodin SN, Rodin AS. Human lung cancer and p53: the interplay between mutagenesis and selection. Proc Natl Acad Sci U S A 2000; 97:12244-9. [PMID: 11035769 PMCID: PMC17326 DOI: 10.1073/pnas.180320897] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
It is an almost consensus opinion that the major carcinogenic risk of tobacco smoke is in its direct mutagenic action on DNA of cancer-related genes. The key data supposedly linking smoke-induced mutations to lung cancer were obtained from the adduct spectrum of the p53 tumor suppressor gene. Results of our analysis of p53 mutations compiled from the International Agency for Research on Cancer p53 database (April 1999 update) and from the literature point to a different causative link. Our new analytical tests focused on complementary base substitutions and showed that it is strand-specific repair of primary lesions and site-specific selection of the resultant mutations that determine the lung cancer-specific hot spots of G:C to T:A transversions along the p53 gene and also their increased abundance in lung tissues as compared with smoke-inaccessible tissues. However, on each of the two strands of p53 DNA, our tests revealed no significant difference between smokers and nonsmokers, either in the frequency of different types of mutations or in the frequency of their occurrence along the p53 gene. Moreover, in both smokers and nonsmokers, there was the same frequency of lung tumors with silent p53 mutations. Accordingly, we offer here a selection-based explanation of why lung cancers with nonsilent p53 mutations are more common in smokers than in nonsmokers. We conclude that physiological stresses (not necessarily genotoxic) aggravated by smoking are the leading risk factor in the p53-associated etiology of lung cancer.
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Affiliation(s)
- S N Rodin
- Biology Department, Beckman Research Institute of the City of Hope, 1450 East Duarte Road, Duarte, CA 91010, USA
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28
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Heinmöller E, Dietmaier W, Zirngibl H, Heinmöller P, Scaringe W, Jauch KW, Hofstädter F, Rüschoff J. Molecular analysis of microdissected tumors and preneoplastic intraductal lesions in pancreatic carcinoma. THE AMERICAN JOURNAL OF PATHOLOGY 2000; 157:83-92. [PMID: 10880379 PMCID: PMC1850206 DOI: 10.1016/s0002-9440(10)64520-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Little or no data exist concerning the inactivation of tumor suppressor genes in intraductal lesions surrounding invasive ductal pancreatic carcinomas. Using a novel improved primer extension and preamplification polymerase chain reaction, we analyzed microdissected paraffin-embedded specimens of pancreatic carcinoma (n = 29) and their corresponding pancreatic intraductal lesions (PIL, n = 331) for loss of heterozygosity (LOH) of p16(INK4), DPC4, and p53 by microsatellite analysis and for p53 protein by immunohistochemistry. LOH at the p16(INK4) locus (9p21) was found in nine of 22 informative tumors (41%), in 15 of 25 tumors (60%) at the DPC4 locus (18q21.1), and in 22 of 27 tumors (81%) at the p53 locus (17p13). Homozygous deletions of p16(INK4) and DPC4 were found in eight of 22 (36%) and four of 25 tumors (16%), respectively. Furthermore, 24 of 29 tumors (83%) revealed considerable intratumoral genetic heterogeneity. In 165 of 277 PILs (60%) having suitable DNA for microsatellite analysis, alterations in at least one tumor suppressor gene were found. In individual PILs, up to three alterations were detected, and p53 LOH occurred even in morphologically normal-appearing ductal epithelium near the tumor. Although deletions of all three tumor suppressor genes were found in PILs without nuclear atypia, there was a tendency toward earlier LOH of p16(INK4) compared to DPC4 and p53 in these lesions. LOH in tumors accompanied positive p53 immunohistochemistry in 81% but only in 38% in PILs.
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Affiliation(s)
| | | | - Hubert Zirngibl
- University Clinic Witten-Herdecke, Wuppertal, Germany; and the Department of Molecular Genetics and Molecular Diagnosis,¶
| | - Petra Heinmöller
- the University Clinic of Regensburg, Regensburg, Germany; the Institute of Pathology,§
| | - William Scaringe
- the City of Hope National Medical Center and Beckman Research Institute, Duarte, California
| | - Karl-Walter Jauch
- the University Clinic of Regensburg, Regensburg, Germany; the Institute of Pathology,§
| | | | - Josef Rüschoff
- Klinikum Kassel, Kassel, Germany; the Department of Surgery,†
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29
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Affiliation(s)
- G P Pfeifer
- Department of Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA.
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