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Al Zoubi MS, Otoum R, Alorjani MS, Al Bashir S, Al Trad B, Abualrja MI, Al-Khatib SM, Al-Batayneh K. TP53, SPOP and PIK3CA Genes Status in Prostate Cancer. Asian Pac J Cancer Prev 2020; 21:3365-3371. [PMID: 33247697 PMCID: PMC8033120 DOI: 10.31557/apjcp.2020.21.11.3365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Indexed: 11/25/2022] Open
Abstract
Recent advances in molecular biology make the identification of prostate cancer (PC) subsets a priority for more understanding of the molecular pathogenesis and treatment options. Genetic alterations in many genes such as TP53, SPOP and PIK3CA genes have been reported in PC with variable frequencies worldwide. We aimed to investigate genetic alterations in the hotspot lesions of TP53, SPOP and PIK3CA genes by direct sequencing and the expression of TP53 and PIK3CA by RT-PCR in prostate cancer, and to explore the correlation between TP53, SPOP and PIK3CA alterations and tumorigenesis of prostate cancer. Seventy-nine FFPE prostate samples from patients who underwent radical prostatectomy were obtained, subjected to genomic DNA extraction and sequenced for mutations in exons 5, 6, 7 and 8 of TP53 gene, exons 4 and 5 of SPOP gene and exons 9 and 20 of PIK3CA gene. RT-PCR was performed for the expression evaluation of the PIK3CA gene. Our results showed a high frequency of TP53 mutations (11/79, 13.9 %) in the selected population. On the other hand, SPOP and PIK3CA genes did not show any genetic alteration in the sequenced exons. PIK3CA gene overexpression was detected in 6% of the cohort by RT-PCR. TP53 mutation is the most frequent genetic alteration and likely has a major role in the pathogenesis of PC in the Jordanian population.
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Affiliation(s)
- Mazhar Salim Al Zoubi
- Department of Basic Medical Sciences, Faculty of Medicine, Yarmouk University, Irbid 211-63, Jordan
| | - Raed Otoum
- Department of Biological Sciences, Faculty of Science, Yarmouk University, Irbid 211-63, Jordan
| | - Mohammed S Alorjani
- Departments of Pathology and Microbiology, Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Samir Al Bashir
- Departments of Pathology and Microbiology, Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Bahaa Al Trad
- Department of Biological Sciences, Faculty of Science, Yarmouk University, Irbid 211-63, Jordan
| | - Manal Issam Abualrja
- Department of Basic Medical Sciences, Faculty of Medicine, Yarmouk University, Irbid 211-63, Jordan
| | - Sohaib M Al-Khatib
- Departments of Pathology and Microbiology, Faculty of Medicine, Jordan University of Science and Technology, Irbid, Jordan
| | - Khalid Al-Batayneh
- Department of Biological Sciences, Faculty of Science, Yarmouk University, Irbid 211-63, Jordan
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Tsai KN, Chen GW, Chen CYC. A Novel Algorithm for Identification of Activated Cryptic 5′ Splice Sites. J Biomol Struct Dyn 2012; 29:1089-99. [DOI: 10.1080/073911012010525033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Roca X, Sachidanandam R, Krainer AR. Intrinsic differences between authentic and cryptic 5' splice sites. Nucleic Acids Res 2003; 31:6321-33. [PMID: 14576320 PMCID: PMC275472 DOI: 10.1093/nar/gkg830] [Citation(s) in RCA: 113] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2003] [Revised: 08/25/2003] [Accepted: 09/11/2003] [Indexed: 11/14/2022] Open
Abstract
Cryptic splice sites are used only when use of a natural splice site is disrupted by mutation. To determine the features that distinguish authentic from cryptic 5' splice sites (5'ss), we systematically analyzed a set of 76 cryptic 5'ss derived from 46 human genes. These cryptic 5'ss have a similar frequency distribution in exons and introns, and are usually located close to the authentic 5'ss. Statistical analysis of the strengths of the 5'ss using the Shapiro and Senapathy matrix revealed that authentic 5'ss have significantly higher score values than cryptic 5'ss, which in turn have higher values than the mutant ones. beta-Globin provides an interesting exception to this rule, so we chose it for detailed experimental analysis in vitro. We found that the sequences of the beta-globin authentic and cryptic 5'ss, but not their surrounding context, determine the correct 5'ss choice, although their respective scores do not reflect this functional difference. Our analysis provides a statistical basis to explain the competitive advantage of authentic over cryptic 5'ss in most cases, and should facilitate the development of tools to reliably predict the effect of disease-associated 5'ss-disrupting mutations at the mRNA level.
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Affiliation(s)
- Xavier Roca
- Cold Spring Harbor Laboratory, PO Box 100, Cold Spring Harbor, NY 11724, USA
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Phelan CM, Liu L, Ruttledge MH, Müntzning K, Ridderheim PA, Collins VP. Chromosome 17 abnormalities and lack of TP53 mutations in paediatric central nervous system tumours. Hum Genet 1995; 96:684-90. [PMID: 8522328 DOI: 10.1007/bf00210300] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Central nervous system (CNS) tumours are the most common solid tumours in children. Cytogenetic and molecular genetic studies of these neoplasms have previously shown abnormalities of chromosome 17, implicating genes on this autosome in tumorigenesis. To identify mutations in the TP53 tumour suppressor gene (17p13.1), we have sequenced the five highly conserved regions of this gene in 29 mixed paediatric CNS tumors. No mutations were detected by this analysis. In order to identify other candidate disease loci on chromosome 17, we have carried out a detailed deletion mapping analysis using 16 polymorphic DNA markers on 19 of the above tumours and an additional four cases. Abnormalities of chromosome 17 occurred in nine cases (39%), six of which were primitive neuroectodermal tumour (PNET)-medulloblastomas. These findings suggest that it is unlikely that the TP53 gene is directly involved in the development of common paediatric brain tumours. This is in contrast to findings from adult brain and other tumour types. Moreover, the frequency of chromosome 17 aberrations, especially in PNET-medulloblastomas, suggests that other genes on this chromosome contribute to tumourigenesis.
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Affiliation(s)
- C M Phelan
- Ludwig Institute for Cancer Research, Karolinska Hospital, Stockholm, Sweden
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Peller S, Kopilova Y, Slutzki S, Halevy A, Kvitko K, Rotter V. A novel polymorphism in intron 6 of the human p53 gene: a possible association with cancer predisposition and susceptibility. DNA Cell Biol 1995; 14:983-90. [PMID: 8534372 DOI: 10.1089/dna.1995.14.983] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We present a novel polymorphic 8-bp sequence in intron 6 of the p53 gene that maps between bp 55 and 62 of the 3' end of exon 6. Of normal blood samples, 32% were heterozygotic for this polymorphism and display a NN' genotype, whereas 68% of the population is homozygotic for the N genotype. The rare homozygotic genotype N' was detected only in four blood samples of cancer patients. Peripheral blood of gastrointestinal (GI) and breast tumor patients demonstrated a higher incidence of heterozygosity (50%) than that of normal individuals. Analysis of the distribution of this polymorphism in tumor samples showed loss of heterozygosity (LOH). This LOH during tumor progression could exhibit preference to each one of the polymorphic alleles. The rare presentation of one allele and the increased incidence of heterozygosity in carcinoma patients may suggest an association between this polymorphism with cancer predisposition and susceptibility. The fact that genetic alterations occurring in noncoding regions may play a role in tumor development only further increases the extent of involvement of p53 in carcinogenesis.
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Affiliation(s)
- S Peller
- Department of Hematology, Assaf Harofeh Medical Center, Zerifin, Israel
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Peller S, Halevy A, Slutzki S, Kopilova Y, Rotter V. p53 mutations in matched primary and metastatic human tumors. Mol Carcinog 1995; 13:166-72. [PMID: 7619219 DOI: 10.1002/mc.2940130306] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Mutations in the p53 tumor suppressor gene have been found to be the most frequent genetic alterations in human malignancies. To further examine the idea that neoplastic progression is associated with mutations in the p53 gene, we analyzed matched primary and metastatic tumor samples. The samples included 15 pairs of breast cancer and metastases to lymph nodes, four pairs of gastrointestinal adenocarcinomas and metastases to liver, one colon adenocarcinoma and metastasis to a lymph node, and one lung carcinoma and metastasis in the pleura. Genomic DNA or cDNA from each tumor sample was amplified by the polymerase chain reaction and labeled by using one biotinylated primer. The DNA strands were separated with magnetic streptavidin beads and sequenced directly. p53 mutations were detected in 11 of 21 patients (52%) in either primary tumors, metastases, or both. In six of these patients the primary tumor and matched metastasis shared the same single mutation. In the other patients an additional mutation in the primary tumor only or a mutation in the metastasis only was observed. Our data suggest that tumor development and progression toward metastasis involves structural alterations in the p53 gene that occur early in carcinogenesis. In some cases, genetic changes in metastatic spreading may also include the appearance of a mutation in a metastasis derived from a primary tumor expressing wild-type p53, a selection of metastatic cells with a single mutation from a primary tumor expressing two different mutations, or loss of heterozygosity.
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Affiliation(s)
- S Peller
- Department of Hematology, Assaf Harofeh Medical Center, Zerifin, Israel
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Lin SY, Chen PH, Yang MJ, Chen TC, Chang CP, Chang JG. Ras oncogene and p53 gene hotspot mutations in colorectal cancers. J Gastroenterol Hepatol 1995; 10:119-24. [PMID: 7787154 DOI: 10.1111/j.1440-1746.1995.tb01064.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Ras oncogene and p53 gene mutations are frequently observed in colorectal cancers. The role of co-operation between these two genes in the tumorigenesis of colorectal cancer was evaluated. Point mutations in K-ras oncogene and hotspot codons of p53 gene of colorectal cancers were evaluated by naturally created or amplified created restriction site method. Nine of 42 cases (21.4%) of colorectal cancer showed K-ras oncogene mutations. Six of 42 cases (14.3%) of colorectal cancer showed p53 gene hotspot point mutations. The low frequency of p53 gene mutation in this series may be due to racial difference or different hotspot codons. When six cases with mutated p53 gene were examined, only one (16.7%) showed concurrent K-ras oncogene codon 12 and p53 gene codon 248 mutations. We concluded that the co-operation between ras oncogene and p53 gene hotspot point mutations in the tumorigenesis of colorectal cancer in Chinese was not common. Other factors such as adenomatous polyposis coli gene mutations, oncogene activation or tumour suppression gene inactivation may be involved.
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Affiliation(s)
- S Y Lin
- Department of Molecular Medicine and Clinical Pathology, Taipei Municipal Jen-Ai Hospital, Taiwan, ROC
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Soussi T, Legros Y, Lubin R, Ory K, Schlichtholz B. Multifactorial analysis of p53 alteration in human cancer: a review. Int J Cancer 1994; 57:1-9. [PMID: 8150526 DOI: 10.1002/ijc.2910570102] [Citation(s) in RCA: 248] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- T Soussi
- Unité 301 INSERM, Institut de Génétique Moléculaire, Paris, France
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Affiliation(s)
- C H Spruck
- Urologic Cancer Research Laboratory, Kenneth Norris Jr. Comprehensive Cancer Center, University of Southern California, Los Angeles 90033
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Laurent-Puig P, Flejou JF, Fabre M, Bedossa P, Belghiti J, Gayral F, Franco D. Overexpression of p53: a rare event in a large series of white patients with hepatocellular carcinoma. Hepatology 1992. [PMID: 1330867 DOI: 10.1002/hep.1840160511] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Mutant p53 has been found in a wide variety of human malignancies including carcinomas of the lung, breast and colon. Because of the controversial mutational rate of the p53 gene in hepatocellular carcinoma, a large series of liver tumors from white patients with different risk factors was examined immunohistochemically for expression of the p53 mutant to assess its prevalence and the relationships between p53 overexpression and clinicopathological data. Nine of 58 specimens were found to have detectable evidence of p53 gene mutation by virtue of the immunohistochemical detection of mutant p53 protein. The p53 mutation was more frequent in patients with serological hepatitis B and C markers than in patients without these markers (p = 0.046). The prevalence of p53-positive tumors was also significantly higher in the group of tumors with invaded portal branches than in the group without (p = 0.02). Our results showed that p53-positive hepatocellular carcinoma is a rare finding in patients exposed to a low dietary aflatoxin intake and that p53 mutation seems to occur at a late stage of the tumoral process and could contribute to an aggressive tumoral phenotype.
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Affiliation(s)
- P Laurent-Puig
- Department of Gastroenterology, Hôpital Bicêtre, Le Kremlin-Bicêtre, France
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