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Bagheri-Hosseinabadi Z, Eshkevari SMS, Khalighfard S, Alizadeh AM, Khori V, Amiriani T, Poorkhani A, Sadani S, Esmati E, Lashgari M, Mahmoodi M, Hajizadeh MR. A systematic approach introduced some immune system targets in rectal cancer by considering cell-free DNA methylation in response to radiochemotherapy. Cytokine 2024; 181:156666. [PMID: 38906038 DOI: 10.1016/j.cyto.2024.156666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 05/12/2024] [Accepted: 05/26/2024] [Indexed: 06/23/2024]
Abstract
BACKGROUND This study aims to investigate cell-free DNA (cfDNA) methylation of genes involved in some immune system targets as biomarkers of radioresistance in patients with non-metastatic rectal cancer. METHODS Gene expression (GSE68204, GPL6480, and GSE15781) and DNA methylation profiles (GSE75548 and GSE139404) of rectal cancer patients were obtained from the Gene Expression Omnibus (GEO) database. GEO2R and FunRich software were first used to identify genes with significant expression differences. Enricher softwer was then used to analyze Gene Ontology and detect pathway enrichment of hub genes. Blood samples were then taken from 43 rectal cancer patients. After cfDNA extraction from samples, it was treated with bisulfite and analyzed by methylation-specific PCR. RESULTS 1088 genes with high and 629 with low expression were identified by GEO2R and FunRich software. A total of five high-expression hub genes, including CDH24, FGF18, CCND1, IFITM1, UBE2V1, and three low-expression hub genes, including CBLN2, VIPR2, and IRF4, were identified from UALCAN and DNMIVD databases. Methylation-specific PCR indicated a significant difference in hub gene methylation between cancerous and non-cancerous individuals. Radiochemotherapy significantly affected hub gene methylation. There was a considerable difference in the methylation rate of hub genes between patients who responded to radiochemotherapy and those who did not. CONCLUSIONS Evaluating gene methylation patterns might be an appropriate diagnostic tool to predict radiochemotherapy response and develop targeted therapeutic agents.
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Affiliation(s)
- Zahra Bagheri-Hosseinabadi
- Molecular Medicine Research Center, Research Institute of Basic Medical Sciences, Rafsanjan University of Medical Sciences, Rafsanjan, Iran; Department of Clinical Biochemistry, School of Medicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | | | | | - Ali Mohammad Alizadeh
- Radiation Oncology Research Center, Cancer Institute, Tehran University of Medical Sciences, Tehran, Iran; Cancer Research Center, Cancer Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Vahid Khori
- Ischemic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Taghi Amiriani
- Ischemic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Amirhoushang Poorkhani
- Ischemic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Somayeh Sadani
- Ischemic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ebrahim Esmati
- Radiation Oncology Research Center, Cancer Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Marzih Lashgari
- Radiation Oncology Research Center, Cancer Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehdi Mahmoodi
- Molecular Medicine Research Center, Research Institute of Basic Medical Sciences, Rafsanjan University of Medical Sciences, Rafsanjan, Iran; Department of Clinical Biochemistry, Afzalipour School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohammad Reza Hajizadeh
- Molecular Medicine Research Center, Research Institute of Basic Medical Sciences, Rafsanjan University of Medical Sciences, Rafsanjan, Iran; Department of Clinical Biochemistry, School of Medicine, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
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2
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Joo JE, Mahmood K, Walker R, Georgeson P, Candiloro I, Clendenning M, Como J, Joseland S, Preston S, Graversen L, Wilding M, Field M, Lemon M, Wakeling J, Marfan H, Susman R, Isbister J, Edwards E, Bowman M, Kirk J, Ip E, McKay L, Antill Y, Hopper JL, Boussioutas A, Macrae FA, Dobrovic A, Jenkins MA, Rosty C, Winship IM, Buchanan DD. Identifying primary and secondary MLH1 epimutation carriers displaying low-level constitutional MLH1 methylation using droplet digital PCR and genome-wide DNA methylation profiling of colorectal cancers. Clin Epigenetics 2023; 15:95. [PMID: 37270516 PMCID: PMC10239107 DOI: 10.1186/s13148-023-01511-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/24/2023] [Indexed: 06/05/2023] Open
Abstract
BACKGROUND MLH1 epimutation is characterised by constitutional monoallelic MLH1 promoter hypermethylation, which can cause colorectal cancer (CRC). Tumour molecular profiles of MLH1 epimutation CRCs were used to classify germline MLH1 promoter variants of uncertain significance and MLH1 methylated early-onset CRCs (EOCRCs). Genome-wide DNA methylation and somatic mutational profiles of tumours from two germline MLH1: c.-11C > T and one MLH1: c.-[28A > G; 7C > T] carriers and three MLH1 methylated EOCRCs (< 45 years) were compared with 38 reference CRCs. Methylation-sensitive droplet digital PCR (ddPCR) was used to detect mosaic MLH1 methylation in blood, normal mucosa and buccal DNA. RESULTS Genome-wide methylation-based Consensus Clustering identified four clusters where the tumour methylation profiles of germline MLH1: c.-11C > T carriers and MLH1 methylated EOCRCs clustered with the constitutional MLH1 epimutation CRCs but not with the sporadic MLH1 methylated CRCs. Furthermore, monoallelic MLH1 methylation and APC promoter hypermethylation in tumour were observed in both MLH1 epimutation and germline MLH1: c.-11C > T carriers and MLH1 methylated EOCRCs. Mosaic constitutional MLH1 methylation in MLH1: c.-11C > T carriers and 1 of 3 MLH1 methylated EOCRCs was identified by methylation-sensitive ddPCR. CONCLUSIONS Mosaic MLH1 epimutation underlies the CRC aetiology in MLH1: c.-11C > T germline carriers and a subset of MLH1 methylated EOCRCs. Tumour profiling and ultra-sensitive ddPCR methylation testing can be used to identify mosaic MLH1 epimutation carriers.
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Affiliation(s)
- Jihoon E Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia.
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia.
| | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, VIC, Australia
| | - Romy Walker
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
| | - Peter Georgeson
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
| | - Ida Candiloro
- Beacon Biomarkers Lab, Department of Surgery, Austin Health, University of Melbourne, Heidelberg, VIC, Australia
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
| | - Julia Como
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
| | - Sharelle Joseland
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
| | - Susan Preston
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
| | - Lise Graversen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Mathilda Wilding
- Department of Clinical Genetics, Royal North Shore Hospital, Sydney, NSW, Australia
| | - Michael Field
- Department of Clinical Genetics, Royal North Shore Hospital, Sydney, NSW, Australia
| | - Michelle Lemon
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Janette Wakeling
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
- Tasman Health Care, Southport, QLD, Australia
| | - Helen Marfan
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Rachel Susman
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Joanne Isbister
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Melbourne, VIC, Australia
| | - Emma Edwards
- Familial Cancer Service, Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, NSW, 2145, Australia
| | - Michelle Bowman
- Familial Cancer Service, Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, NSW, 2145, Australia
| | - Judy Kirk
- Familial Cancer Service, Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, NSW, 2145, Australia
| | - Emilia Ip
- Department of Cancer Genetics, Liverpool Hospital, Liverpool, NSW, Australia
| | - Lynne McKay
- The Cabrini Family Cancer Clinic, Cabrini Health, Malvern, VIC, Australia
| | - Yoland Antill
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Melbourne, VIC, Australia
- The Cabrini Family Cancer Clinic, Cabrini Health, Malvern, VIC, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, VIC, Australia
| | - Alex Boussioutas
- Department of Gastroenterology, The Alfred Hospital, Melbourne, Parkville, VIC, 3010, Australia
- Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Finlay A Macrae
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Melbourne, VIC, Australia
- Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Parkville, VIC, Australia
- Department of Medicine, The University of Melbourne, Parkville, Australia
| | - Alexander Dobrovic
- Beacon Biomarkers Lab, Department of Surgery, Austin Health, University of Melbourne, Heidelberg, VIC, Australia
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, VIC, Australia
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
- Envoi Specialist Pathologists, Brisbane, Australia
- University of Queensland, Brisbane, Australia
| | - Ingrid M Winship
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Melbourne, VIC, Australia
- Department of Medicine, The University of Melbourne, Parkville, Australia
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Victorian Comprehensive Cancer Centre, The University of Melbourne, 305 Grattan Street, Parkville, VIC, 3000, Australia
- Victorian Comprehensive Cancer Centre, University of Melbourne Centre for Cancer Research, Parkville, VIC, Australia
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Melbourne, VIC, Australia
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Kawai T, Nyuya A, Mori Y, Tanaka T, Tanioka H, Yasui K, Toshima T, Taniguchi F, Shigeyasu K, Umeda Y, Fujiwara T, Okawaki M, Yamaguchi Y, Goel A, Nagasaka T. Clinical and epigenetic features of colorectal cancer patients with somatic POLE proofreading mutations. Clin Epigenetics 2021; 13:117. [PMID: 34034807 PMCID: PMC8146650 DOI: 10.1186/s13148-021-01104-7] [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: 03/02/2021] [Accepted: 05/17/2021] [Indexed: 01/09/2023] Open
Abstract
Background Mutations in the POLE gene result in an ultra-hypermutated phenotype in colorectal cancer (CRC); however, the molecular characterisation of epigenetic alterations remains unclear. We examined the genetic and epigenetic profiles of POLE-mutant CRC to elucidate the clinicopathological features of the associated genetic and epigenetic alterations. Results Tumour tissues (1,013) obtained from a cohort of patients with CRC were analysed to determine associations between the proofreading domain mutations of POLE with various clinicopathological variables, microsatellite instability (MSI) status, BRAF and KRAS mutations, and the methylation status of key regions of MLH1, MGMT, and SFRP2 promoters by calculating the methylation scores (range 0–6). Only four cases (0.4%) exhibited pathogenic POLE hotspot mutations (two p.P286R [c.857C > G], one p.V411L [c.1231G > C], and p.S459F [c.1376C > T] each), which were mutually exclusive to BRAF and KRAS mutations and MSI. CRC patients were divided into four subgroups: patients with POLE mutations (POLE, 0.4%, n = 4), patients with both MSI and extensive methylation in MLH1 (MSI-M, 2.9%, n = 29), patients with MSI but no extensive methylation in MLH1 (MSI-U, 3.6%, n = 36), and patients without MSI (non-MSI, 93.2%, n = 944). The POLE group was younger at diagnosis (median 52 years, P < 0.0001), with frequent right-sided tumour localisation (frequency of tumours located in the right colon was 100%, 93.1%, 36.1%, and 29.9% in POLE, MSI-M, MSI-U, and non-MSI, respectively; P < 0.0001), and was diagnosed at an earlier stage (frequency of stages I–II was 100%, 72.4%, 77.8%, and 46.6% in POLE, MSI-M, MSI-U, and non-MSI, respectively, P < 0.0001). The mean methylation score in POLE was not different from that in MSI-U and non-MSI, but the methylation signature was distinct from that of the other subgroups. Additionally, although the examined number of POLE-mutant tumours was small, the number of CD8-positive cells increased in tumours with partial methylation in the MLH1 gene. Conclusions CRC patients with POLE proofreading mutations are rare. Such mutations are observed in younger individuals, and tumours are primarily located in the right colon. Diagnosis occurs at an earlier stage, and distinct epigenetic alterations may be associated with CD8 cell infiltration. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01104-7.
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Affiliation(s)
- Takashi Kawai
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Akihiro Nyuya
- Department of Clinical Oncology, Kawasaki Medical School, 577 Matsushima, Kurashiki, 701-0192, Japan
| | - Yoshiko Mori
- Department of Clinical Genetics and Digestive Tract and General Surgery, Saitama Medical Center, Saitama Medical University, Kawagoe, Saitama, 350-8550, Japan
| | - Takehiro Tanaka
- Department of Pathology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Hiroaki Tanioka
- Department of Clinical Oncology, Kawasaki Medical School, 577 Matsushima, Kurashiki, 701-0192, Japan
| | - Kazuya Yasui
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Toshiaki Toshima
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Fumitaka Taniguchi
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Kunitoshi Shigeyasu
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Yuzo Umeda
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Toshiyoshi Fujiwara
- Department of Gastroenterological Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Makoto Okawaki
- Department of Clinical Oncology, Kawasaki Medical School, 577 Matsushima, Kurashiki, 701-0192, Japan
| | - Yoshiyuki Yamaguchi
- Department of Clinical Oncology, Kawasaki Medical School, 577 Matsushima, Kurashiki, 701-0192, Japan
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA, 91016, USA
| | - Takeshi Nagasaka
- Department of Clinical Oncology, Kawasaki Medical School, 577 Matsushima, Kurashiki, 701-0192, Japan.
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Ta TV, Nguyen QN, Chu HH, Truong VL, Vuong LD. RAS/RAF mutations and their associations with epigenetic alterations for distinct pathways in Vietnamese colorectal cancer. Pathol Res Pract 2020; 216:152898. [PMID: 32089414 DOI: 10.1016/j.prp.2020.152898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/27/2020] [Accepted: 02/16/2020] [Indexed: 02/07/2023]
Abstract
KRAS, NRAS, and BRAF are potential tumor-driven genes that are involved in the RAS/RAF/MAPK signaling pathway. RAS/RAF mutations importantly contribute to colorectal tumorigenesis since they remain the activated status of downstream pathways without regulation of the upstream EGFR signal. However, it has not been unclear how epigenetic alterations involved in colorectal tumorigenesis mediated by KRAS, NRAS, or BRAF mutations. Therefore, in this study, we investigated the frequency and distribution of KRAS/NRAS/BRAF mutations in Vietnamese colorectal cancer (CRC) and explored the relationship between genetic and epigenetic abnormalities in 156 tumors of CRC. Somatic mutations of KRAS (exon 2, codon 12/13; exon 3, codon 61), NRAS (exon 2, codon 12/13; exon 3, codon 61), and BRAF (exon 15, codon 600) was determined by Cobas® KRAS Mutation Test, Therascreen NRAS Pyro Kit and Cobas® 4800 BRAF V600 Mutation Test, respectively. Methylation status of BRCA1, MLH1, MGMT, p16, RASSF1A, and APC was detected by methylation-specific PCR. Distribution of each abnormality in clinicopathological features was also analyzed. Results showed the mutation rates of KRAS, NRAS, and BRAF were 41.0 %, 9.6 %, 8.3 % respectively, while the methylation rates of BRCA1, MLH1, MGMT, p16, RASSF1A, and APC were 16.7 %, 16.7 %, 32.7 %, 30.1 %, 30.1 %, and 37.2 % respectively. The distribution of KRAS mutation was mutually exclusive against that of NRAS (p < 0.001) and BRAF (p < 0.001) mutations in CRC. RAS/RAF mutations were more common in adenocarcinoma subtype (p = 0.020), whereas RASSF1A methylation was more frequent in mucinous adenocarcinoma subtype (p = 0.007). In addition, the frequency of having KRAS mutations was significantly higher in MGMT (p = 0.035) or RASSF1A (p = 0.043) methylated cases than in those without methylation. BRAF mutations were positively associated with MLH1 hypermethylation (p = 0.028) but were inversely associated with APC hypermethylation (p = 0.032). Overall, our results show specific interactions of genetic and epigenetic alterations and suggest the presence of independent oncogenic pathways in tumorigenesis of CRC.
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Affiliation(s)
- To Van Ta
- Pathology and Molecular Biology Center, National Cancer Hospital K, 30 Cau Buou Street, Thanh Tri, Hanoi, Viet Nam
| | - Quang Ngoc Nguyen
- Pathology and Molecular Biology Center, National Cancer Hospital K, 30 Cau Buou Street, Thanh Tri, Hanoi, Viet Nam
| | - Ha Hoang Chu
- National Key Laboratory of Gene Technology, Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet Street, Cau Giay, Hanoi, Viet Nam
| | - Van-Long Truong
- Department of Smart Food and Drug, College of BNIT, Inje University, Gimhae 50834, South Korea.
| | - Linh Dieu Vuong
- Pathology and Molecular Biology Center, National Cancer Hospital K, 30 Cau Buou Street, Thanh Tri, Hanoi, Viet Nam.
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Song WY, Zhang X, Zhang Q, Zhang PJ, Zhang R. Clinical value evaluation of serum markers for early diagnosis of colorectal cancer. World J Gastrointest Oncol 2020; 12:219-227. [PMID: 32104552 PMCID: PMC7031148 DOI: 10.4251/wjgo.v12.i2.219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/17/2020] [Accepted: 02/08/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Early screening for colorectal cancer (CRC) is important in clinical practice. However, the currently methods are inadequate because of high cost and low diagnostic value. AIM To develop a new examination method based on the serum biomarker panel for the early detection of CRC. METHODS Three hundred and fifty cases of CRC, 300 cases of colorectal polyps and 360 cases of normal controls. Combined with the results of area under curve (AUC) and correlation analysis, the binary Logistic regression analysis of the remaining indexes which is in accordance with the requirements was carried out, and discriminant analysis, classification tree and artificial neural network analysis were used to analyze the remaining indexes at the same time. RESULTS By comparison of these methods, we obtained the ability to distinguish CRC from healthy control group, malignant disease group and benign disease group. Artificial neural network had the best diagnostic value when compared with binary logistic regression, discriminant analysis, and classification tree. The AUC of CRC and the control group was 0.992 (0.987, 0.997), sensitivity and specificity were 98.9% and 95.6%. The AUC of the malignant disease group and benign group was 0.996 (0.992, 0.999), sensitivity and specificity were 97.4% and 96.7%. CONCLUSION Artificial neural network diagnosis method can improve the sensitivity and specificity of the diagnosis of CRC, and a novel assistant diagnostic method was built for the early detection of CRC.
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Affiliation(s)
- Wen-Yue Song
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning Province, China
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Interventional Therapy Department, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Xin Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Interventional Therapy Department, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Qi Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning Province, China
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Interventional Therapy Department, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Peng-Jun Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Interventional Therapy Department, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Rong Zhang
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang 110016, Liaoning Province, China
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Liang TJ, Wang HX, Zheng YY, Cao YQ, Wu X, Zhou X, Dong SX. APC hypermethylation for early diagnosis of colorectal cancer: a meta-analysis and literature review. Oncotarget 2018; 8:46468-46479. [PMID: 28515349 PMCID: PMC5542282 DOI: 10.18632/oncotarget.17576] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 04/02/2017] [Indexed: 12/27/2022] Open
Abstract
Adenomatous polyposis coli (APC) promoter hypermethylation has been frequently observed in colorectal cancer (CRC). The association between APC promoter methylation and clinicopathological significance in CRC is under investigation. We performed a meta-analysis to quantitatively evaluate the significance of APC methylation in CRC. The study included a total of 24 articles and 2025 CRC patients. The frequency of APC promoter hypermethylation was significantly higher in colorectal adenoma than in normal colorectal tissue, OR was 5.76, 95% CI, 2.45-13.56; p<0.0001, I2=0%. APC promoter more frequently hypermethylated in CRC stage I compared to normal colorectal tissue, OR was 13.42, 95% CI, 3.66-49.20; p<0.0001, I2=31%. The risk of incidence of CRC was significantly correlated to APC promoter hypermethylation, pooled OR was 9.80, 95%CI, 6.07-15.81; p<0.00001, I2=43%. APC methylation was not associated with grade, stage of CRC as well as tumor location, patients’ gender, and smoking behavior. The results indicate that APC promoter hypermethylation is an early event in carcinogenesis of CRC, could be a valuable diagnostic marker for early-stage CRC. APC methylation is not significantly associated with overall survival in patients with CRC. APC is a potential drug target for development of personalized treatment.
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Affiliation(s)
- Tie-Jun Liang
- Department of Digestive Disease, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, China
| | - Hong-Xu Wang
- Department of General Surgery, Jiyang People's Hospital, Jiyang, Shandong, China
| | - Yan-Yan Zheng
- Department of Medical Imaging, Jiyang People's Hospital, Jiyang, Shandong, China
| | - Ying-Qing Cao
- Department of Anus & Intestine Surgery, Taian City Central Hospital, Taian, Shandong, China
| | - Xiaoyu Wu
- Department of Surgical Oncology, The Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xin Zhou
- Department of General Surgery, Jiangsu Cancer Hospital, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shu-Xiao Dong
- Department of Gastrointestinal Surgery, Linyi People's Hospital, Linyi, Shandong, China
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7
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Zhou Z, Zhang H, Lai J, Diao D, Li W, Dang C, Song Y. Relationships between p14ARF Gene Methylation and Clinicopathological Features of Colorectal Cancer: A Meta-Analysis. PLoS One 2016; 11:e0152050. [PMID: 26999279 PMCID: PMC4801177 DOI: 10.1371/journal.pone.0152050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 03/08/2016] [Indexed: 12/31/2022] Open
Abstract
We conducted a meta-analysis to explore the relationships between p14ARF gene methylation and clinicopathological features of colorectal cancer (CRC). Databases, including Pubmed, Embase and Cochrane Library, were searched and, finally, a total of 18 eligible researches encompassing 1988 CRC patients were selected. Combined odds ratios (ORs) with 95% confidence intervals (95% CIs) were evaluated under a fixed effects model for absence of heterogeneity. Significant associations were observed between p14ARF gene methylation and tumor location (OR = 2.35, 95% CI: 1.55–3.55, P = 0.001), microsatellite instability (MSI) status (OR = 3.28, 95% CI: 2.12–5.07, P<0.0001). However, there were no significant associations between p14ARF gene methylation and tumor stage, tumor differentiation. We concluded that p14ARF gene methylation may be significantly associated with tumor location, and MSI status of CRC.
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Affiliation(s)
- Zhangjian Zhou
- Division of Surgical Oncology, The First Affiliated Hospital, Xi'an Jiaotong University, 277 W, Yanta Road, Xi'an, 710061, Shaanxi, China
| | - Hao Zhang
- Division of Surgical Oncology, The First Affiliated Hospital, Xi'an Jiaotong University, 277 W, Yanta Road, Xi'an, 710061, Shaanxi, China
| | - Jianguo Lai
- Division of Surgical Oncology, The First Affiliated Hospital, Xi'an Jiaotong University, 277 W, Yanta Road, Xi'an, 710061, Shaanxi, China
| | - Dongmei Diao
- Division of Surgical Oncology, The First Affiliated Hospital, Xi'an Jiaotong University, 277 W, Yanta Road, Xi'an, 710061, Shaanxi, China
| | - Wenhan Li
- Division of Surgical Oncology, The First Affiliated Hospital, Xi'an Jiaotong University, 277 W, Yanta Road, Xi'an, 710061, Shaanxi, China
| | - Chengxue Dang
- Division of Surgical Oncology, The First Affiliated Hospital, Xi'an Jiaotong University, 277 W, Yanta Road, Xi'an, 710061, Shaanxi, China
| | - Yongchun Song
- Division of Surgical Oncology, The First Affiliated Hospital, Xi'an Jiaotong University, 277 W, Yanta Road, Xi'an, 710061, Shaanxi, China
- * E-mail:
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Savio AJ, Daftary D, Dicks E, Buchanan DD, Parfrey PS, Young JP, Weisenberger D, Green RC, Gallinger S, McLaughlin JR, Knight JA, Bapat B. Promoter methylation of ITF2, but not APC, is associated with microsatellite instability in two populations of colorectal cancer patients. BMC Cancer 2016; 16:113. [PMID: 26884349 PMCID: PMC4756469 DOI: 10.1186/s12885-016-2149-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 02/08/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Aberrant Wnt signaling activation occurs commonly in colorectal carcinogenesis, leading to upregulation of many target genes. APC (adenomatous polyposis coli) is an important component of the β-catenin destruction complex, which regulates Wnt signaling, and is often mutated in colorectal cancer (CRC). In addition to mutational events, epigenetic changes arise frequently in CRC, specifically, promoter hypermethylation which silences tumor suppressor genes. APC and the Wnt signaling target gene ITF2 (immunoglobulin transcription factor 2) incur hypermethylation in various cancers, however, methylation-dependent regulation of these genes in CRC has not been studied in large, well-characterized patient cohorts. The microsatellite instability (MSI) subtype of CRC, featuring DNA mismatch repair deficiency and often promoter hypermethylation of MutL homolog 1 (MLH1), has a favorable outcome and is characterized by different chemotherapeutic responses than microsatellite stable (MSS) tumors. Other epigenetic events distinguishing these subtypes have not yet been fully elucidated. METHODS Here, we quantify promoter methylation of ITF2 and APC by MethyLight in two case-case studies nested in population-based CRC cohorts from the Ontario Familial Colorectal Cancer Registry (n = 330) and the Newfoundland Familial Colorectal Cancer Registry (n = 102) comparing MSI status groups. RESULTS ITF2 and APC methylation are significantly associated with tumor versus normal state (both P < 1.0 × 10(-6)). ITF2 is methylated in 45.8% of MSI cases and 26.9% of MSS cases and is significantly associated with MSI in Ontario (P = 0.002) and Newfoundland (P = 0.005) as well as the MSI-associated feature of MLH1 promoter hypermethylation (P = 6.72 × 10(-4)). APC methylation, although tumor-specific, does not show a significant association with tumor subtype, age, gender, or stage, indicating it is a general tumor-specific CRC biomarker. CONCLUSIONS This study demonstrates, for the first time, MSI-associated ITF2 methylation, and further reveals the subtype-specific epigenetic events modulating Wnt signaling in CRC.
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Affiliation(s)
- Andrea J Savio
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada.
| | - Darshana Daftary
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada.
- Ontario Familial Colorectal Cancer Registry, Toronto, ON, Canada.
| | - Elizabeth Dicks
- Faculty of Medicine, Memorial University of Newfoundland, St John's, Newfoundland, Canada.
| | - Daniel D Buchanan
- Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, VIC, Australia.
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia.
| | - Patrick S Parfrey
- Faculty of Medicine, Memorial University of Newfoundland, St John's, Newfoundland, Canada.
| | - Joanne P Young
- Department of Haematology and Oncology, The Queen Elizabeth Hospital, Woodville, South Australia, Australia.
| | - Daniel Weisenberger
- USC Epigenome Center, University of Southern California, Los Angeles, CA, USA.
| | - Roger C Green
- Faculty of Medicine, Memorial University of Newfoundland, St John's, Newfoundland, Canada.
| | - Steven Gallinger
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada.
- Ontario Familial Colorectal Cancer Registry, Toronto, ON, Canada.
- Department of Surgery, University of Toronto, Toronto, ON, Canada.
| | - John R McLaughlin
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada.
- Ontario Familial Colorectal Cancer Registry, Toronto, ON, Canada.
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
| | - Julia A Knight
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada.
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
| | - Bharati Bapat
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, Canada.
- Department of Pathology, University Health Network, Toronto, ON, Canada.
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Ding Z, Jiang T, Piao Y, Han T, Han Y, Xie X. Meta-analysis of the association between APC promoter methylation and colorectal cancer. Onco Targets Ther 2015; 8:211-22. [PMID: 25632237 PMCID: PMC4304602 DOI: 10.2147/ott.s75827] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Previous studies investigating the association between adenomatous polyposis coli (APC) gene promoter methylation and colorectal cancer (CRC) have yielded conflicting results. The aim of this study was to comprehensively evaluate the potential application of the detection of APC promoter methylation to the prevention and treatment of CRC. PubMed, Embase, and MEDLINE (results updated to October 2014) were searched for relevant studies. The effect size was defined as the weighted odds ratio (OR), which was calculated using either the fixed-effects or random-effects model. Prespecified subgroup and sensitivity analyses were conducted to evaluate potential heterogeneity among the included studies. Nineteen studies comprising 2,426 participants were selected for our meta-analysis. The pooled results of nine studies comprising a total of 740 subjects indicated that APC promoter methylation was significantly associated with CRC risk (pooled OR 5.53; 95% confidence interval [CI] 3.50–8.76; P<0.01). Eleven studies with a total of 1,219 patients evaluated the association between APC promoter methylation and the presence of CRC metastasis, and the pooled OR was 0.80 (95% CI 0.44–1.46; P=0.47). A meta-analysis conducted with four studies with a total of 467 patients found no significant correlation between APC promoter methylation and the presence of colorectal adenoma (pooled OR 1.85; 95% CI 0.67–5.10; P=0.23). No significant correlation between APC promoter methylation and patients’ Dukes’ stage, TNM stage, differentiation grade, age, or sex was identified. In conclusion, APC promoter methylation was found to be significantly associated with a higher risk of developing CRC. The findings indicate that APC promoter methylation may be a potential biomarker for the carcinogenesis of CRC.
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Affiliation(s)
- Zhenyu Ding
- Department of Oncology, General Hospital of Shenyang Military Region, Shenyang City, Liaoning Province, People's Republic of China
| | - Tong Jiang
- Laboratory of Military Health in Cold Region, Center for Disease Control and Prevention of Shenyang Military Region, Shenyang City, Liaoning Province, People's Republic of China
| | - Ying Piao
- Department of Oncology, General Hospital of Shenyang Military Region, Shenyang City, Liaoning Province, People's Republic of China
| | - Tao Han
- Department of Oncology, General Hospital of Shenyang Military Region, Shenyang City, Liaoning Province, People's Republic of China
| | - Yaling Han
- Institute of Cardiovascular Disease, General Hospital of Shenyang Military Region, Shenyang City, Liaoning Province, People's Republic of China
| | - Xiaodong Xie
- Department of Oncology, General Hospital of Shenyang Military Region, Shenyang City, Liaoning Province, People's Republic of China
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Veganzones S, Maestro ML, Rafael S, de la Orden V, Vidaurreta M, Mediero B, Espantaleón M, Cerdán J, Díaz-Rubio E. Combined methylation of p16 and hMLH1 (CMETH2) discriminates a subpopulation with better prognosis in colorectal cancer patients with microsatellite instability tumors. Tumour Biol 2015; 36:3853-61. [DOI: 10.1007/s13277-014-3027-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 12/26/2014] [Indexed: 12/26/2022] Open
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Abstract
Death associated protein kinase 1 (DAPK) is an important serine/theoreine kinase involved in various cellular processes such as apoptosis, autophagy and inflammation. DAPK expression and activity are misregulated in multiple diseases including cancer, neuronal death, stoke, et al. Methylation of the DAPK gene is common in many types of cancer and can lead to loss of DAPK expression. In this review, we summarize the pathological status and functional roles of DAPK in disease and compare the published reagents that can manipulate the expression or activity of DAPK. The pleiotropic functions of DAPK make it an intriguing target and the barriers and opportunities for targeting DAPK for future clinical application are discussed.
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Samaei NM, Yazdani Y, Alizadeh-Navaei R, Azadeh H, Farazmandfar T. Promoter methylation analysis of WNT/β-catenin pathway regulators and its association with expression of DNMT1 enzyme in colorectal cancer. J Biomed Sci 2014; 21:73. [PMID: 25107489 PMCID: PMC4237828 DOI: 10.1186/s12929-014-0073-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 07/27/2014] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Aberrant DNA methylation as the most important reason making epigenetic silencing of genes is a main mechanism of gene inactivation in patients with colorectal cancer. In this study, we decided to identify promoter methylation status of ten genes encoding WNT negative regulators, and measure the expression of DNMT1 enzyme in colorectal cancer samples. RESULTS Aberrant methylation of APC gene was statistically significant associated with age over 50 (p = 0.017), DDK3 with male (p < 0.0001), SFRP4, WIF1, and WNT5a with increasing tumor stage (p = 0.004, p = 0.029, and p = 0.004), SFRP4 and WIF1 with tumor differentiation (p = 0.009 and p = 0.031) and SFRP2 and SFRP5 with histological type (p = 0.001 and p = 0.025). The increasing number of methylated genes correlated with the expression levels of the DNMT1 mRNA. CONCLUSIONS The rate of gene promoter methylation of WNT pathway regulators is high in colorectal cancer cells. Hyper-methylation is associated with increased expression of the DNMT1 enzyme.
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Affiliation(s)
- Nader Mansour Samaei
- Golestan Research Center of Gastroenterology and Hepatology-GRCGH, Golestan University of Medical Sciences, Gorgan, Iran
| | - Yaghoub Yazdani
- Golestan Research Center of Gastroenterology and Hepatology-GRCGH, Golestan University of Medical Sciences, Gorgan, Iran
| | - Reza Alizadeh-Navaei
- Molecular and Cell Biology Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Hossein Azadeh
- Cancer Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Touraj Farazmandfar
- Golestan Research Center of Gastroenterology and Hepatology-GRCGH, Golestan University of Medical Sciences, Gorgan, Iran
- Molecular and Cell Biology Research Center, Mazandaran University of Medical Sciences, Sari, Iran
- Cancer Research Center, Mazandaran University of Medical Sciences, Sari, Iran
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Hokazono K, Ueki T, Nagayoshi K, Nishioka Y, Hatae T, Koga Y, Hirahashi M, Oda Y, Tanaka M. A CpG island methylator phenotype of colorectal cancer that is contiguous with conventional adenomas, but not serrated polyps. Oncol Lett 2014; 8:1937-1944. [PMID: 25289081 PMCID: PMC4186580 DOI: 10.3892/ol.2014.2430] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 07/15/2014] [Indexed: 01/05/2023] Open
Abstract
A subset of colorectal cancers (CRCs) harbor the CpG island methylator phenotype (CIMP), with concurrent multiple promoter hypermethylation of tumor-related genes. A serrated pathway in which CIMP is developed from serrated polyps is proposed. The present study characterized CIMP and morphologically examined precursor lesions of CIMP. In total, 104 CRCs treated between January 1996 and December 2004 were examined. Aberrant promoter methylation of 15 cancer-related genes was analyzed. CIMP status was classified according to the number of methylated genes and was correlated with the clinicopathological features, including the concomitant polyps in and around the tumors. The frequency of aberrant methylation in each CRC showed a bimodal pattern, and the CRCs were classified as CIMP-high (CIMP-H), CIMP-low (CIMP-L) and CIMP-negative (CIMP-N). CIMP-H was associated with aberrant methylation of MLH1 (P=0.005) and with an improved recurrence-free survival (RFS) rate following curative resection compared with CIMP-L/N (five-year RFS rate, 93.8 vs. 67.1%; P=0.044), while CIMP-N tumors were associated with frequent distant metastases at diagnosis (P=0.023). No concomitant serrated lesions were present in the tumors, whereas conventional adenoma was contiguous with 11 (10.6%) of 104 CRCs, including four CIMP-H CRCs. CIMP-H was classified in CRCs by a novel CIMP marker panel and the presence of concomitant tumors revealed that certain CIMP-H CRCs may have arisen from conventional adenomas.
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Affiliation(s)
- Koji Hokazono
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Takashi Ueki
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Kinuko Nagayoshi
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Yasunobu Nishioka
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Tatsunobu Hatae
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Yutaka Koga
- Department of Anatomical Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Minako Hirahashi
- Department of Anatomical Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Yoshinao Oda
- Department of Anatomical Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Masao Tanaka
- Department of Surgery and Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
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Chen YZ, Liu D, Zhao YX, Wang HT, Gao Y, Chen Y. Relationships between p16 gene promoter methylation and clinicopathologic features of colorectal cancer: a meta-analysis of 27 cohort studies. DNA Cell Biol 2014; 33:729-38. [PMID: 24979649 DOI: 10.1089/dna.2013.2253] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Many existing studies have demonstrated that p16 promoter methylation might be correlated with the clinicopathologic features of colorectal cancer (CRC), but individually published results are inconclusive. This meta-analysis aimed to derive a more precise estimation of the relationships between p16 promoter methylation and the clinicopathologic features of CRC. We searched the CISCOM, CINAHL, Web of Science, PubMed, Google Scholar, EBSCO, Cochrane Library, and CBM databases from inception through August 1, 2013. Meta-analysis was performed using the STATA 12.0 software. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated under fixed- or random-effects models. Twenty-seven clinical cohort studies were included with a total of 3311 CRC patients. Our meta-analysis results revealed that p16 promoter methylation was associated with pathological characteristics of CRC (tumor, nodes, metastasis stage: OR=1.55, 95% CI: 1.14-2.13, p=0.006; lymph node metastasis: OR=2.40, 95% CI: 1.37-4.19, p=0.002; histologic grade: OR=2.72, 95% CI: 1.63-4.54, p<0.001; Dukes stage: OR=2.06, 95% CI: 1.57-2.71, p=0.002; tumor size: OR=1.99, 95% CI: 1.03-3.85, p=0.041; location: OR=2.49, 95% CI: 1.95-3.18, p<0.001, respectively). Subgroup analysis by ethnicity suggested that there were also significant correlations between p16 gene promoter methylation and pathological characteristics of CRC among both Caucasian and Asian populations (all p<0.05). Our meta-analysis suggests that promoter methylation of the p16 gene may be strongly correlated with the clinicopathologic features of CRC. Thus, p16 gene promoter methylation may be a potential biomarker for CRC.
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Affiliation(s)
- Yan-Zhi Chen
- Department of Radiotherapy, The Fourth Affiliated Hospital of China Medical University , Shenyang, People's Republic of China
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15
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Li X, Yao X, Wang Y, Hu F, Wang F, Jiang L, Liu Y, Wang D, Sun G, Zhao Y. MLH1 promoter methylation frequency in colorectal cancer patients and related clinicopathological and molecular features. PLoS One 2013; 8:e59064. [PMID: 23555617 PMCID: PMC3612054 DOI: 10.1371/journal.pone.0059064] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 02/12/2013] [Indexed: 02/07/2023] Open
Abstract
Purpose To describe the frequency of MLH1 promoter methylation in colorectal cancer (CRC); to explore the associations between MLH1 promoter methylation and clinicopathological and molecular factors using a systematic review and meta-analysis. Methods A literature search of the PubMed and Embase databases was conducted to identify relevant articles published up to September 7, 2012 that described the frequency of MLH1 promoter methylation or its associations with clinicopathological and molecular factors in CRC. The pooled frequency, odds ratio (OR) and 95% confidence intervals (95% CI) were calculated. Results The pooled frequency of MLH1 promoter methylation in unselected CRC was 20.3% (95% CI: 16.8–24.1%). They were 18.7% (95% CI: 14.7–23.6%) and 16.4% (95% CI: 11.9–22.0%) in sporadic and Lynch syndrome (LS) CRC, respectively. Significant associations were observed between MLH1 promoter methylation and gender (pooled OR = 1.641, 95% CI: 1.215–2.215; P = 0.001), tumor location (pooled OR = 3.804, 95% CI: 2.715–5.329; P<0.001), tumor differentiation (pooled OR = 2.131, 95% CI: 1.464–3.102; P<0.001), MSI (OR: 27.096, 95% CI: 13.717–53.526; P<0.001). Significant associations were also observed between MLH1 promoter methylation and MLH1 protein expression, BRAF mutation (OR = 14.919 (95% CI: 6.427–34.631; P<0.001) and 9.419 (95% CI: 2.613–33.953; P = 0.001), respectively). Conclusion The frequency of MLH1 promoter methylation in unselected CRC was 20.3%. They were 18.7% in sporadic CRC and 16.4% in LS CRC, respectively. MLH1 promoter methylation may be significantly associated with gender, tumor location, tumor differentiation, MSI, MLH1 protein expression, and BRAF mutation.
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Affiliation(s)
- Xia Li
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang Province, P.R. China
| | - Xiaoping Yao
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang Province, P.R. China
| | - Yibaina Wang
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang Province, P.R. China
| | - Fulan Hu
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang Province, P.R. China
| | - Fan Wang
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang Province, P.R. China
| | - Liying Jiang
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang Province, P.R. China
| | - Yupeng Liu
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang Province, P.R. China
| | - Da Wang
- Department of Science and Technology Administration, Harbin Medical University, Harbin, Heilongjiang Province, P.R. China
| | - Guizhi Sun
- Department of Surgery, Cancer Hospital of Harbin Medical University, Harbin, Heilongjiang Province, P.R. China
| | - Yashuang Zhao
- Department of Epidemiology, Public Health College, Harbin Medical University, Harbin, Heilongjiang Province, P.R. China
- * E-mail:
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Promoter CpG island methylation in colorectal cancer:. Epigenomics 2012. [DOI: 10.1017/cbo9780511777271.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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Tanaka N, Huttenhower C, Nosho K, Baba Y, Shima K, Quackenbush J, Haigis KM, Giovannucci E, Fuchs CS, Ogino S. Novel application of structural equation modeling to correlation structure analysis of CpG island methylation in colorectal cancer. THE AMERICAN JOURNAL OF PATHOLOGY 2010; 177:2731-40. [PMID: 21037082 DOI: 10.2353/ajpath.2010.100361] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The CpG island methylator phenotype (CIMP-high, CIMP1) is a distinct phenotype associated with microsatellite instability (MSI) and BRAF mutation in colon cancer. Recent evidence suggests the presence of KRAS mutation-associated CIMP subtype (CIMP-low, CIMP2). We used cluster analysis, principal component analysis (PCA), and structural equation modeling (SEM), a novel strategy, to decipher the correlation structure of CpG island hypermethylation. Using a database of 861 colon and rectal cancers, DNA methylation at 16 CpG islands [CACNA1G, CDKN2A (p16/ink4a), CHFR, CRABP1, HIC1, IGF2, IGFBP3, MGMT, MINT-1, MINT-31, MLH1, NEUROG1, p14 (CDKN2A/arf), RUNX3, SOCS1, and WRN] was quantified by real-time PCR. Tumors were categorized into three groups: Group 1 with wild-type KRAS/BRAF (N = 440); Group 2 with mutant KRAS and wild-type BRAF (N = 308); and Group 3 with wild-type KRAS and mutant BRAF (N = 107). Tumors with mutant KRAS/BRAF (N = 6) were excluded. In unsupervised hierarchical clustering analysis, all but six markers (CACNA1G, IGF2, RUNX3, MGMT, MINT-1, and SOCS1) were differentially clustered with CIMP-high and CIMP-low according to KRAS and BRAF status. In SEM, the correlation structures between CIMP, locus-specific CpG island methylation, and MSI differed according to KRAS and BRAF status, which was consistent with PCA results. In conclusion, KRAS and BRAF mutations appear to differentially influence correlation structure of CpG island methylation. Our novel data suggest two distinct perturbations, resulting in differential locus-specific propensity of CpG methylation.
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Affiliation(s)
- Noriko Tanaka
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
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Chen K, Wang G, Peng L, Liu S, Fu X, Zhou Y, Yu H, Li A, Li J, Zhang S, Bai Y, Zhang Y. CADM1/TSLC1 inactivation by promoter hypermethylation is a frequent event in colorectal carcinogenesis and correlates with late stages of the disease. Int J Cancer 2010; 128:266-73. [PMID: 20340131 DOI: 10.1002/ijc.25356] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Accepted: 03/04/2010] [Indexed: 01/28/2023]
Abstract
Cell adhesion molecule 1 (CADM1/TSLC1), a putative tumor suppressor involving in cell adhesion, proliferation and apoptosis, is frequently inactivated in several carcinomas due to promoter hypermethylation. But alterations of CADM1/TSLC1 in colorectal carcinogenesis and clinical significance have not been elucidated yet. The aim of this study was to determine the role of functional inactivation of CADM1/TSLC1 gene in colorectal tumorigenesis and its potential as a novel epigenetic marker for clinical assessment of patients with colorectal cancer. We measured CADM1/TSLC1 expression levels in 8 colorectal cancer cell lines, 54 primary colorectal carcinomas and their corresponding non-cancerous tissues by reverse transcription polymerase chain reaction, western blot analysis and immunohistochemistry. We analyzed CADM1/TSLC1 promoter methylation status by bisulfite genomic sequencing and the methylation special polymerase chain reaction, and evaluated its correlation with clinicopathological characteristics. All statistical tests were 2-sides. Downregulation of CADM1/TSLC1 expression was observed in 7 of 8 (88%) colorectal cancer cell lines and in 39 of 54 (72%) primary colorectal carcinomas. Hypermethylation of CADM1/TSLC1 promoter region occurred in 6 of 8 (75%) colorectal cancer cell lines and 32 of 54 (59%) primary colorectal carcinomas, and was correlated with advanced colorectal carcinoma. Epigenetic inactivation of CADM1/TSLC1 gene is a frequent alteration in development of colorectal cancer and can be a potential biomarker for molecular staging of patients with colorectal cancer.
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Affiliation(s)
- Kequan Chen
- Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
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Mitomi H, Fukui N, Tanaka N, Kanazawa H, Saito T, Matsuoka T, Yao T. Aberrant p16((INK4a)) methylation is a frequent event in colorectal cancers: prognostic value and relation to mRNA expression and immunoreactivity. J Cancer Res Clin Oncol 2010; 136:323-31. [PMID: 19779933 DOI: 10.1007/s00432-009-0688-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Accepted: 09/14/2009] [Indexed: 01/19/2023]
Abstract
PURPOSE Aberrant p16((INK4a)) promoter methylation is common in colorectal cancer (CRC), but its clinicopathological significance remains controversial. The present study was therefore conducted to analyze p16((INK4a)) methylation and its relationship to clinicopathological features, mRNA levels and immunoreactivity in a series of lesions. METHODS p16((INK4a)) methylation was assessed for normal mucosa (n = 30) and CRC samples (n = 212) by methylation-specific real-time quantitative PCR, and p16((INK4a)) expression by immunostaining in formalin-fixed paraffin-embedded specimens. In addition, fresh DNA (n = 61) was analyzed for relationships to p16((INK4a)) mRNA by reverse-transcription PCR. RESULTS The p16((INK4a)) methylation index of normal mucosa samples ranged from 0 to 2% (mean, 0.23%; median, 0.02%), while the values for tumor samples varied widely from 0 to 100% (mean, 25.7%; median, 7.1%), the difference being statistically significant (P < 0.001). Of 151 paraffin-embedded CRC tissue samples, 51 (34%), 54 (36%), and 46 (30%) were classified as low, intermediate, and high for aberrant methylation of p16((INK4a)). High p16((INK4a)) methylation was significantly associated with large tumor size (P = 0.025). Patients with higher methylation further showed more frequent recurrence as compared with the low-methylation group, and shortened cancer-related survival (Hazard ratio [HR], 3.379; P < 0.001) and recurrence-free survival (HR, 3.962; P < 0.001 on multivariate analysis). A significant inverse relationship was apparent between the p16((INK4a)) methylation and immunoreactivity (P = 0.017). A similar tendency was also observed for the methylation status and the mRNA level (P = 0.195). CONCLUSIONS We conclude that p16((INK4a)) methylation results in transcriptional silencing and defines a group of CRCs with a poor prognosis.
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Affiliation(s)
- Hiroyuki Mitomi
- Department of Human Pathology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan.
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Kim JC, Choi JS, Roh SA, Cho DH, Kim TW, Kim YS. Promoter Methylation of Specific Genes is Associated with the Phenotype and Progression of Colorectal Adenocarcinomas. Ann Surg Oncol 2010; 17:1767-76. [DOI: 10.1245/s10434-009-0901-y] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Indexed: 12/23/2022]
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Mokarram P, Kumar K, Brim H, Naghibalhossaini F, Saberi-firoozi M, Nouraie M, Green R, Lee E, Smoot DT, Ashktorab H. Distinct high-profile methylated genes in colorectal cancer. PLoS One 2009; 4:e7012. [PMID: 19750230 PMCID: PMC2737306 DOI: 10.1371/journal.pone.0007012] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Accepted: 06/17/2009] [Indexed: 12/20/2022] Open
Abstract
Background Mutations and promoters' methylation of a set of candidate cancer genes (CAN genes) are associated with progression of colorectal cancer (CRC). We hypothesized that these genes' promoters are inactivated through epigenetic silencing and may show a different profile in high-risk populations. We investigated the status of CAN gene methylation and CHD5 protein expression in African American CRC tissue microarrays (TMA) using immunohistochemical staining. Methodology/Principal Findings The promoter methylation status of the CAN genes was studied by methylation-specific PCR (MSP) in 51 Iranians (a white population) and 51 African Americans (AA). Microsatellite instability (MSI) was analyzed as well. The differential frequency of methylation for each gene was tested by chi-square analysis between the two groups based on matched age and sex. CHD5 protein expression was evaluated in moderate to well differentiated and poorly differentiated carcinomas compared to matched normal tissue using TMA. In addition, the correlation between these epigenetic biomarkers and various clinicopathological factors, including, age, location, and stage of the disease were analyzed. Seventy-seven and 34% of tumors were distal in Iranian and African American patients, respectively. In both populations, the percentage of methylation was >65% for SYNE1, MMP2, APC2, GPNMB, EVL, PTPRD, and STARD8, whereas methylation was <50% for LGR6, RET, CD109, and RNF. The difference in methylation between the two populations was statistically significant for CHD5, ICAM5 and GPNMB. Thirty-one percent AA tumors showed MSI-H, compared to 28% in Iranians. Conclusions/Significance A significantly higher methylation rate was found for GPNMB, ICAM5, and CHD5 genes in AA patients compared to Iranians. These genes might play a role in the high incidence and aggressiveness of CRC in the AA population. The hypermethylation of the CAN genes can be considered as a marker of colon carcinogenesis.
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Affiliation(s)
- Pooneh Mokarram
- Department of Internal Medicine and Gastroenterology Research Center, Shiraz, Iran University of Medical Sciences, Tehran, Iran
| | - Krishan Kumar
- Department of Medicine and Cancer Center, Howard University, College of Medicine, Washington, D. C., United States of America
| | - Hassan Brim
- Department of Medicine and Cancer Center, Howard University, College of Medicine, Washington, D. C., United States of America
| | - Fakhraddin Naghibalhossaini
- Department of Internal Medicine and Gastroenterology Research Center, Shiraz, Iran University of Medical Sciences, Tehran, Iran
| | - Mehdi Saberi-firoozi
- Department of Internal Medicine and Gastroenterology Research Center, Shiraz, Iran University of Medical Sciences, Tehran, Iran
| | - Mehdi Nouraie
- Department of Medicine and Cancer Center, Howard University, College of Medicine, Washington, D. C., United States of America
| | - Robert Green
- Department of Pathology, Howard University, College of Medicine, Washington, D. C., United States of America
| | - Ed Lee
- Department of Pathology, Howard University, College of Medicine, Washington, D. C., United States of America
| | - Duane T. Smoot
- Department of Medicine and Cancer Center, Howard University, College of Medicine, Washington, D. C., United States of America
| | - Hassan Ashktorab
- Department of Medicine and Cancer Center, Howard University, College of Medicine, Washington, D. C., United States of America
- * E-mail:
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Hsiao SH, Huang THM, Leu YW. Excavating relics of DNA methylation changes during the development of neoplasia. Semin Cancer Biol 2009; 19:198-208. [DOI: 10.1016/j.semcancer.2009.02.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Accepted: 02/15/2009] [Indexed: 12/31/2022]
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JC virus T-antigen in colorectal cancer is associated with p53 expression and chromosomal instability, independent of CpG island methylator phenotype. Neoplasia 2009; 11:87-95. [PMID: 19107235 DOI: 10.1593/neo.81188] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2008] [Revised: 10/16/2008] [Accepted: 10/16/2008] [Indexed: 12/25/2022] Open
Abstract
JC virus has a transforming gene encoding JC virus T-antigen (JCVT). JCVT may inactivate wild-type p53, cause chromosomal instability (CIN), and stabilize beta-catenin. A link between JCVT and CpG island methylator phenotype (CIMP) has been suggested. However, no large-scale study has examined the relations of JCVT with molecular alterations, clinical outcome, or prognosis in colon cancer. We detected JCVT expression (by immunohistochemistry) in 271 (35%) of 766 colorectal cancers. We quantified DNA methylation in eight CIMP-specific promoters (CACNA1G, CDKN2A, CRABP1, IGF2, MLH1, NEUROG1, RUNX3, and SOCS1) and eight other loci (CHFR, HIC1, IGFBP3, MGMT, MINT1, MINT31, p14, WRN) by MethyLight. We examined loss of heterozygosity in 2p, 5q, 17q, and 18q. JCVT was significantly associated with p53 expression (P < .0001), p21 loss (P < .0001), CIN (>/=2 chromosomal segments with LOH; P < .0001), nuclear beta-catenin (P = .006), LINE-1 hypomethylation (P = .002), and inversely with CIMP-high (P = .0005) and microsatellite instability (MSI) (P < .0001), but not with PIK3CA mutation. In multivariate logistic regression analysis, the associations of JCVT with p53 [adjusted odds ratio (OR), 8.45; P < .0001], CIN (adjusted OR, 2.53; P = .003), cyclin D1 (adjusted OR, 1.57; P = .02), LINE-1 hypomethylation (adjusted OR, 1.97 for a 30% decline as a unit; P = .03), BRAF mutation (adjusted OR, 2.20; P = .04), and family history of colorectal cancer (adjusted OR, 0.64; P = .04) remained statistically significant. However, JCVT was no longer significantly associated with CIMP, MSI, beta-catenin, or cyclooxygenase-2 expression in multivariate analysis. JCVT was unrelated with patient survival. In conclusion, JCVT expression in colorectal cancer is independently associated with p53 expression and CIN, which may lead to uncontrolled cell proliferation.
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de Vogel S, Weijenberg MP, Herman JG, Wouters KAD, de Goeij AFPM, van den Brandt PA, de Bruïne AP, van Engeland M. MGMT and MLH1 promoter methylation versus APC, KRAS and BRAF gene mutations in colorectal cancer: indications for distinct pathways and sequence of events. Ann Oncol 2009; 20:1216-22. [PMID: 19164452 DOI: 10.1093/annonc/mdn782] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND To study how caretaker gene silencing relates to gatekeeper mutations in colorectal cancer (CRC), we investigated whether O6-methylguanine DNA methyltransferase (MGMT) and Human Mut-L Homologue 1 (MLH1) promoter hypermethylation are associated with APC, KRAS and BRAF mutations among 734 CRC patients. METHODS We compared MGMT hypermethylation with G:C > A:T mutations in APC and KRAS and with the occurrence of such mutations in CpG or non-CpG dinucleotides in APC. We also compared MLH1 hypermethylation with truncating APC mutations and activating KRAS and BRAF mutations. RESULTS Only 10% of the tumors showed both MGMT and MLH1 hypermethylation. MGMT hypermethylation occurred more frequently in tumors with G:C > A:T KRAS mutations (55%) compared with those without these mutations (38%, P < 0.001). No such difference was observed for G:C > A:T mutations in APC, regardless of whether mutations occurred in CpG or non-CpG dinucleotides. MLH1 hypermethylation was less common in tumors with APC mutations (P = 0.006) or KRAS mutations (P = 0.001), but was positively associated with BRAF mutations (P < 0.001). CONCLUSIONS MGMT hypermethylation is associated with G:C > A:T mutations in KRAS, but not in APC, suggesting that MGMT hypermethylation may succeed APC mutations but precedes KRAS mutations in colorectal carcinogenesis. MLH1-hypermethylated tumors harbor fewer APC and KRAS mutations and more BRAF mutations, suggesting that they develop distinctly from an MGMT methylator pathway.
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Affiliation(s)
- S de Vogel
- Department of Epidemiology, GROW-School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
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Sweeney C, Boucher KM, Samowitz WS, Wolff RK, Albertsen H, Curtin K, Caan BJ, Slattery ML. Oncogenetic tree model of somatic mutations and DNA methylation in colon tumors. Genes Chromosomes Cancer 2009; 48:1-9. [PMID: 18767147 DOI: 10.1002/gcc.20614] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Our understanding of somatic alterations in colon cancer has evolved from a concept of a series of events taking place in a single sequence to a recognition of multiple pathways. An oncogenetic tree is a model intended to describe the pathways and sequence of somatic alterations in carcinogenesis without assuming that tumors will fall in mutually exclusive categories. We applied this model to data on colon tumor somatic alterations. An oncogenetic tree model was built using data on mutations of TP53, KRAS2, APC, and BRAF genes, methylation at CpG sites of MLH1 and TP16 genes, methylation in tumor (MINT) markers, and microsatellite instability (MSI) for 971 colon tumors from a population-based series. Oncogenetic tree analysis resulted in a reproducible tree with three branches. The model represents methylation of MINT markers as initiating a branch and predisposing to MSI, methylation of MHL1 and TP16, and BRAF mutation. APC mutation is the first alteration in an independent branch and is followed by TP53 mutation. KRAS2 mutation was placed a third independent branch, implying that it neither depends on, nor predisposes to, the other alterations. Individual tumors were observed to have alteration patterns representing every combination of one, two, or all three branches. The oncogenetic tree model assumptions are appropriate for the observed heterogeneity of colon tumors, and the model produces a useful visual schematic of the sequence of events in pathways of colon carcinogenesis.
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Affiliation(s)
- Carol Sweeney
- Health Sciences Center, University of Utah, Salt Lake City, UT, USA.
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Iacopetta B, Kawakami K, Watanabe T. Predicting clinical outcome of 5-fluorouracil-based chemotherapy for colon cancer patients: is the CpG island methylator phenotype the 5-fluorouracil-responsive subgroup? Int J Clin Oncol 2008; 13:498-503. [PMID: 19093176 DOI: 10.1007/s10147-008-0854-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Indexed: 12/14/2022]
Abstract
The CpG island methylator phenotype (CIMP+) of colorectal cancer (CRC) occurs predominantly in the proximal colon and is characterized by frequent hypermethylation of gene promoter regions. In this review, we present evidence suggesting CIMP+ represents the subgroup of colon cancers that are responsive to 5-fluorouracil (5-FU)-based treatments. CIMP+ has been associated with survival benefit from 5-FU in a clinical study of CRC, with additional evidence coming from studies on gastric cancer and tumor cell lines. Elevated concentrations of 5-10-methylene tetrahydrofolate (CH(2)FH(4)) occur in CIMP+ tumors and are probably due to low expression levels for gamma-glutamyl hydrolase (GGH). Clinical and in vitro work has previously shown that high CH(2)FH(4) and low GGH expression levels correlate with good response to 5-FU. Methylation-induced silencing of dihydropyrimidine dehydrogenase, the rate-limiting enzyme in 5-FU degradation, may also provide a link between CIMP+ and good response to 5-FU. The CIMP+-related phenotype referred to as microsatellite instability (MSI+) has been widely investigated as a predictive marker of response to 5-FU, with contradictory results. The interpretation of these studies is likely to be confounded by the fact that some MSI+ tumors occur in the background of CIMP+, but a significant proportion of others do not. Further studies on tumors from randomized clinical trials are required to confirm the value of CIMP+ and associated molecular features for the prediction of clinical outcome to 5-FU-based chemotherapy.
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Affiliation(s)
- Barry Iacopetta
- School of Surgery M507, University of Western Australia, Nedlands, 6009, Australia.
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Comprehensive biostatistical analysis of CpG island methylator phenotype in colorectal cancer using a large population-based sample. PLoS One 2008; 3:e3698. [PMID: 19002263 PMCID: PMC2579485 DOI: 10.1371/journal.pone.0003698] [Citation(s) in RCA: 263] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2008] [Accepted: 10/24/2008] [Indexed: 12/18/2022] Open
Abstract
Background The CpG island methylator phenotype (CIMP) is a distinct phenotype associated with microsatellite instability (MSI) and BRAF mutation in colon cancer. Recent investigations have selected 5 promoters (CACNA1G, IGF2, NEUROG1, RUNX3 and SOCS1) as surrogate markers for CIMP-high. However, no study has comprehensively evaluated an expanded set of methylation markers (including these 5 markers) using a large number of tumors, or deciphered the complex clinical and molecular associations with CIMP-high determined by the validated marker panel. Metholodology/Principal Findings DNA methylation at 16 CpG islands [the above 5 plus CDKN2A (p16), CHFR, CRABP1, HIC1, IGFBP3, MGMT, MINT1, MINT31, MLH1, p14 (CDKN2A/ARF) and WRN] was quantified in 904 colorectal cancers by real-time PCR (MethyLight). In unsupervised hierarchical clustering analysis, the 5 markers (CACNA1G, IGF2, NEUROG1, RUNX3 and SOCS1), CDKN2A, CRABP1, MINT31, MLH1, p14 and WRN were generally clustered with each other and with MSI and BRAF mutation. KRAS mutation was not clustered with any methylation marker, suggesting its association with a random methylation pattern in CIMP-low tumors. Utilizing the validated CIMP marker panel (including the 5 markers), multivariate logistic regression demonstrated that CIMP-high was independently associated with older age, proximal location, poor differentiation, MSI-high, BRAF mutation, and inversely with LINE-1 hypomethylation and β-catenin (CTNNB1) activation. Mucinous feature, signet ring cells, and p53-negativity were associated with CIMP-high in only univariate analysis. In stratified analyses, the relations of CIMP-high with poor differentiation, KRAS mutation and LINE-1 hypomethylation significantly differed according to MSI status. Conclusions Our study provides valuable data for standardization of the use of CIMP-high-specific methylation markers. CIMP-high is independently associated with clinical and key molecular features in colorectal cancer. Our data also suggest that KRAS mutation is related with a random CpG island methylation pattern which may lead to CIMP-low tumors.
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Segditsas S, Sieber OM, Rowan A, Setien F, Neale K, Phillips RKS, Ward R, Esteller M, Tomlinson IPM. Promoter hypermethylation leads to decreased APC mRNA expression in familial polyposis and sporadic colorectal tumours, but does not substitute for truncating mutations. Exp Mol Pathol 2008; 85:201-6. [PMID: 18977219 DOI: 10.1016/j.yexmp.2008.09.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Accepted: 09/19/2008] [Indexed: 01/13/2023]
Abstract
Germline mutations in the tumour suppressor APC cause familial adenomatous polyposis (FAP), and somatic mutations are common in sporadic colorectal cancers (CRCs). Hypermethylation of APC promoter 1A has been reported in a substantial proportion of sporadic CRCs and may cause transcriptional silencing. Methylation has been proposed as an alternative to mutation or loss of heterozygosity as a mechanism of gene inactivation. However, the significance of APC methylation has remained unclear, because it has not previously been related to the presence of mono- or bi-allelic mutations at APC. We examined 103 FAP adenomas, 11 attenuated FAP adenomas, 31 sporadic CRCs and 30 CRC cell lines, all with known germline and/or somatic APC mutations. Overall, APC promoter 1A methylation was detected in 27-45% of colorectal tumours and cell lines, but generally not in histologically normal colorectum. In contrast to previous reports, methylation was detected in similar proportions of FAP/AFAP and sporadic CRCs. Importantly, methylation was independent of the presence, number and positions of APC mutations and was not associated with the CpG island methylator phenotype. Methylation resulted in a decrease or loss of 1A isoform mRNA and reduced total APC transcript levels, although expression was retained from promoter 1B. However, neither APC protein levels, nor transcription of a panel of Wnt target genes was associated with methylation status. Our data suggest that APC promoter 1A hypermethylation may influence APC expression levels in a subtle fashion, but methylation does not result in complete gene inactivation or act as a 'second hit'.
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Affiliation(s)
- Stefania Segditsas
- Molecular and Population Genetics Laboratory, London Research Institute, Cancer Research UK, London WC2A 3PX, UK
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Suehiro Y, Wong CW, Chirieac LR, Kondo Y, Shen L, Webb CR, Chan YW, Chan ASY, Chan TL, Wu TT, Rashid A, Hamanaka Y, Hinoda Y, Shannon RL, Wang X, Morris J, Issa JPJ, Yuen ST, Leung SY, Hamilton SR. Epigenetic-genetic interactions in the APC/WNT, RAS/RAF, and P53 pathways in colorectal carcinoma. Clin Cancer Res 2008; 14:2560-9. [PMID: 18451217 DOI: 10.1158/1078-0432.ccr-07-1802] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
PURPOSE Early events in colorectal tumorigenesis include mutation of the adenomatous polyposis coli (APC) gene and epigenetic hypermethylation with transcriptional silencing of the O(6)-methylguanine DNA methyltransferase (MGMT), human mut L homologue 1 (hMLH1), and P16/CDKN2A genes. Epigenetic alterations affect genetic events: Loss of MGMT via hypermethylation reportedly predisposes to guanine-to-adenine or cytosine-to-thymine (G:C-->A:T) transition mutations in KRAS and P53, and silencing of hMLH1 leads to high levels of microsatellite instability (MSI-H)/mutator phenotype, suggesting that epigenetic-genetic subtypes exist. EXPERIMENTAL DESIGN We evaluated the relationships of aberrant methylation of APC, MGMT, hMLH1, P16, N33, and five MINTs to mutations in APC, KRAS, BRAF, and P53 in 208 colorectal carcinomas. RESULTS We found that APC hypermethylation was age related (P = 0.04), in contrast to the other genes, and did not cluster with CpG island methylator phenotype (CIMP) markers. Hypermethylation of APC concurrently with either MGMT or hMLH1 was strongly associated with occurrence of G-to-A transitions in APC [odds ratio (OR), 26.8; P < 0.0002 from multivariable logic regression model], but C-to-T transitions had no associations. There was no relationship of hypermethylation of any gene, including MGMT, with G-to-A or C-to-T transitions in KRAS or P53, although APC hypermethylation was associated with P53 mutation (P < 0.0002). CIMP with MSI-H due to hMLH1 hypermethylation, or CIMP with loss of MGMT expression in non-MSI-H tumors, was associated with BRAF mutation (OR, 4.5; P < 0.0002). CIMP was also associated with BRAF V600E T-to-A transversion (OR, 48.5; P < 0.0002). CONCLUSIONS Our findings suggest that the heterogeneous epigenetic dysregulation of promoter methylation in various genes is interrelated with the occurrence of mutations, as manifested in epigenetic-genetic subgroups of tumors.
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Affiliation(s)
- Yutaka Suehiro
- Department of Pathology, Division of Pathology and Laboratory Medicine, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
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Ang PW, Li WQ, Soong R, Iacopetta B. BRAF mutation is associated with the CpG island methylator phenotype in colorectal cancer from young patients. Cancer Lett 2008; 273:221-4. [PMID: 18778891 DOI: 10.1016/j.canlet.2008.08.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2008] [Revised: 05/12/2008] [Accepted: 08/04/2008] [Indexed: 11/30/2022]
Abstract
This study investigated the relationship between BRAF mutation, the CpG island methylator phenotype (CIMP+) and APC methylation in colorectal cancer (CRC) from young patients. The V600E BRAF mutation was found in 7% of cases and was strongly associated with the tumour features of proximal site, advanced stage and poor histological grade. More than half (53%) the tumours with BRAF mutation were also CIMP+ as evaluated by a standard panel of markers, compared to only 4% of tumours with wildtype BRAF (P<0.0001). In contrast to CIMP+, APC methylation was inversely correlated with BRAF mutation (P=0.02). BRAF mutation and CIMP+ are therefore likely to be involved in an alternate, albeit rare, pathway to APC inactivation during the development of CRC in younger patients.
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Affiliation(s)
- Pei Woon Ang
- School of Surgery M507, University of Western Australia, 35 Stirling Hwy, Nedlands 6009, Australia
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Ogino S, Kawasaki T, Nosho K, Ohnishi M, Suemoto Y, Kirkner GJ, Fuchs CS. LINE-1 hypomethylation is inversely associated with microsatellite instability and CpG island methylator phenotype in colorectal cancer. Int J Cancer 2008; 122:2767-73. [PMID: 18366060 DOI: 10.1002/ijc.23470] [Citation(s) in RCA: 206] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The CpG island methylator phenotype (CIMP) with widespread promoter CpG island methylation is a phenotype in colorectal cancer, associated with microsatellite instability (MSI) and BRAF mutation. Genome-wide hypomethylation may also play an important role in genomic instability. However, the relation between global DNA methylation level and methylation in individual CpG islands remains uncertain. Utilizing 869 population-based colorectal cancers, we measured long interspersed nucleotide element-1 (LINE-1) methylation level by Pyrosequencing, which correlates with global DNA methylation level. We quantified DNA methylation in 8 CIMP-specific promoters (CACNA1G, CDKN2A (p16), CRABP1, IGF2, MLH1, NEUROG1, RUNX3 and SOCS1) by real-time PCR (MethyLight technology). LINE-1 methylation levels in tumors were approximately normally distributed (mean, 61.4%; median, 62.3%; standard deviation, 9.6%). Among the 869 tumors, 128 (15%) were classified as CIMP-high (>or=6/8 methylated promoters). The mean LINE-1 methylation level was higher in CIMP-high tumors (65.1%, p < 0.0001) than non-CIMP-high tumors (60.7%), and higher in MSI-high tumors (64.7%, p < 0.0001) than non-MSI-high tumors (60.7%). When tumors were stratified by MSI/CIMP status, compared to non-MSI-high non-CIMP-high tumors (mean LINE-1 methylation level, 60.4%), the mean LINE-1 methylation level was higher in MSI-high CIMP-high (64.8%, p < 0.0001), MSI-high non-CIMP-high (64.6%, p = 0.03) and non-MSI-high CIMP-high tumors (66.1%, p = 0.0003). In addition, 18q loss of heterozygosity in non-MSI-high tumors was correlated with LINE-1 hypomethylation (p = 0.004). In conclusion, both CIMP-high and MSI-high are inversely associated with LINE-1 hypomethylation, suggesting that CIMP/MSI and genomic hypomethylation may represent different pathways to colorectal cancer. Our data also support a possible link between global hypomethylation and chromosomal instability.
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Affiliation(s)
- Shuji Ogino
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.
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Nagasaka T, Koi M, Kloor M, Gebert J, Vilkin A, Nishida N, Shin SK, Sasamoto H, Tanaka N, Matsubara N, Boland CR, Goel A. Mutations in both KRAS and BRAF may contribute to the methylator phenotype in colon cancer. Gastroenterology 2008; 134:1950-60, 1960.e1. [PMID: 18435933 PMCID: PMC2543132 DOI: 10.1053/j.gastro.2008.02.094] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2007] [Revised: 02/21/2008] [Accepted: 02/28/2008] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Colorectal cancers (CRCs) with the CpG island methylator phenotype (CIMP) often associate with epigenetic silencing of hMLH1 and an activating mutation in the BRAF gene. However, the current CIMP criteria are ambiguous and often result in an underestimation of CIMP frequencies in CRCs. Because BRAF and KRAS belong to same signaling pathway, we hypothesized that not only mutations in BRAF but mutant KRAS may also associate with CIMP in CRC. METHODS We determined the methylation status in a panel of 14 markers (7 canonical CIMP-related loci and 7 new loci), microsatellite instability status, and BRAF/KRAS mutations in a collection of 487 colorectal tissues that included both sporadic and Lynch syndrome patients. RESULTS Methylation analysis of 7 CIMP-related markers revealed that the mean number of methylated loci was highest in BRAF-mutated CRCs (3.6) vs KRAS-mutated (1.2, P < .0001) or BRAF/KRAS wild-type tumors (0.7, P < .0001). However, analyses with 7 additional markers showed that the mean number of methylated loci in BRAF mutant tumors (4.4) was the same as in KRAS mutant CRCs (4.3, P = .8610). Although sporadic microsatellite instability high tumors had the highest average number of methylated markers (8.4), surprisingly, Lynch syndrome CRCs also demonstrated frequent methylation (5.1). CONCLUSIONS CIMP in CRC may result from activating mutations in either BRAF or KRAS, and the inclusion of additional methylation markers that correlate with mutant KRAS may help clarify CIMP in future studies. Additionally, aberrant DNA methylation is a common event not only in sporadic CRC but also in Lynch syndrome CRCs.
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Affiliation(s)
- Takeshi Nagasaka
- Division of Gastroenterology, Department of Internal Medicine and Charles A Sammons Cancer Center and Baylor Research Institute, Baylor University Medical Center, Dallas, TX 75246, USA
| | - Minoru Koi
- Division of Gastroenterology, Department of Internal Medicine and Charles A Sammons Cancer Center and Baylor Research Institute, Baylor University Medical Center, Dallas, TX 75246, USA
| | - Matthias Kloor
- Institute of Molecular Pathology, University of Heidelberg, Heidelberg, Germany
| | - Johannes Gebert
- Institute of Molecular Pathology, University of Heidelberg, Heidelberg, Germany
| | - Alex Vilkin
- Division of Gastroenterology, Department of Internal Medicine and Charles A Sammons Cancer Center and Baylor Research Institute, Baylor University Medical Center, Dallas, TX 75246, USA
| | - Naoshi Nishida
- Division of Gastroenterology, Department of Internal Medicine and Charles A Sammons Cancer Center and Baylor Research Institute, Baylor University Medical Center, Dallas, TX 75246, USA
| | - Sung Kwan Shin
- Division of Gastroenterology, Department of Internal Medicine and Charles A Sammons Cancer Center and Baylor Research Institute, Baylor University Medical Center, Dallas, TX 75246, USA
| | - Hiromi Sasamoto
- Department of Gastroenterological Surgery and Surgical Oncology, Okayama University Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Noriaki Tanaka
- Department of Gastroenterological Surgery and Surgical Oncology, Okayama University Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Nagahide Matsubara
- Department of Gastroenterological Surgery and Surgical Oncology, Okayama University Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - C. Richard Boland
- Division of Gastroenterology, Department of Internal Medicine and Charles A Sammons Cancer Center and Baylor Research Institute, Baylor University Medical Center, Dallas, TX 75246, USA
| | - Ajay Goel
- Division of Gastroenterology, Department of Internal Medicine and Charles A Sammons Cancer Center and Baylor Research Institute, Baylor University Medical Center, Dallas, TX 75246, USA
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CpG island methylator phenotype (CIMP) in cancer: causes and implications. Cancer Lett 2008; 268:177-86. [PMID: 18471961 DOI: 10.1016/j.canlet.2008.03.022] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2008] [Revised: 03/19/2008] [Accepted: 03/19/2008] [Indexed: 12/31/2022]
Abstract
Strong evidence exists for a subgroup of tumours, from a variety of tissue types, exhibiting concordant tumour specific DNA methylation: the "CpG island methylator phenotype" (CIMP). Occurrence of CIMP is associated with a range of genetic and environmental factors, although the molecular causes are not well-understood. Both increased expression and aberrant targeting of DNA methyltransferases (DNMTs) could contribute to the occurrence of CIMP. One under-explored area is the possibility that DNA damage may induce or select for CIMP during carcinogenesis or treatment of tumours with chemotherapy. DNA damaging agents can induce DNA damage at guanine rich regions throughout the genome, including CpG islands. This DNA damage can result in stalled DNA synthesis, which will lead to localised increased DNMT1 concentration and therefore potentially increased DNA methylation at these sites. Chemotherapy can select for cells which have increased tolerance to DNA damage due to increased lesion bypass, in some cases by mechanisms which involve inactivation of genes by CpG island methylation. CIMP has been associated with worse patient prognosis, probably due to increased epigenetic plasticity. Therefore, further clinical testing of the diagnostic and prognostic value of the current CIMP markers, as well as increasing our understanding of the molecular causes underlying CIMP are required.
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Low expression of gamma-glutamyl hydrolase mRNA in primary colorectal cancer with the CpG island methylator phenotype. Br J Cancer 2008; 98:1555-61. [PMID: 18414409 PMCID: PMC2391094 DOI: 10.1038/sj.bjc.6604346] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The CpG island methylator phenotype (CIMP+) in colorectal cancer (CRC) is defined as concomitant and frequent hypermethylation of CpG islands within gene promoter regions. We previously demonstrated that CIMP+ was associated with elevated concentrations of folate intermediates in tumour tissues. In the present study, we investigated whether CIMP+ was associated with a specific mRNA expression pattern for folate- and nucleotide-metabolising enzymes. An exploratory study was conducted on 114 CRC samples from Australia. mRNA levels for 17 genes involved in folate and nucleotide metabolism were measured by real-time RT-PCR. CIMP+ was determined by real-time methylation-specific PCR and compared to mRNA expression. Candidate genes showing association with CIMP+ were further investigated in a replication cohort of 150 CRC samples from Japan. In the exploratory study, low expression of γ-glutamyl hydrolase (GGH) was strongly associated with CIMP+ and CIMP+-related clinicopathological and molecular features. Trends for inverse association between GGH expression and the concentration of folate intermediates were also observed. Analysis of the replication cohort confirmed that GGH expression was significantly lower in CIMP+ CRC. Promoter hypermethylation of GGH was observed in only 5.6% (1 out of 18) CIMP+ tumours and could not account for the low expression level of this gene. CIMP+ CRC is associated with low expression of GGH, suggesting involvement of the folate pathway in the development and/or progression of this phenotype. Further studies of folate metabolism in CIMP+ CRC may help to elucidate the aetiology of these tumours and to predict their response to anti-folates and 5-fluorouracil/leucovorin.
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Abstract
Molecular classification of colorectal cancer is evolving. As our understanding of colorectal carcinogenesis improves, we are incorporating new knowledge into the classification system. In particular, global genomic status [microsatellite instability (MSI) status and chromosomal instability (CIN) status] and epigenomic status [CpG island methylator phenotype (CIMP) status] play a significant role in determining clinical, pathological and biological characteristics of colorectal cancer. In this review, we discuss molecular classification and molecular correlates based on MSI status and CIMP status in colorectal cancer. Studying molecular correlates is important in cancer research because it can 1) provide clues to pathogenesis, 2) propose or support the existence of a new molecular subtype, 3) alert investigators to be aware of potential confounding factors in association studies, and 4) suggest surrogate markers in clinical or research settings.
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Affiliation(s)
- Shuji Ogino
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA.
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Derks S, Postma C, Carvalho B, van den Bosch SM, Moerkerk PTM, Herman JG, Weijenberg MP, de Bruïne AP, Meijer GA, van Engeland M. Integrated analysis of chromosomal, microsatellite and epigenetic instability in colorectal cancer identifies specific associations between promoter methylation of pivotal tumour suppressor and DNA repair genes and specific chromosomal alterations. Carcinogenesis 2007; 29:434-9. [PMID: 18048385 DOI: 10.1093/carcin/bgm270] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Colorectal cancer (CRC) is a complex and heterogeneous disease in which genomic instability and DNA promoter methylation play important roles. The aim of this study was to investigate the relationship between chromosomal instability (CIN), microsatellite instability (MSI) and promoter methylation of CRC-associated genes. Therefore, 71 CRCs were analysed for CIN and MSI by comparative genomic hybridization and the mononucleotide marker BAT-26, respectively. Promoter methylation of the tumour suppressor and DNA repair genes hMLH1, O(6)-MGMT, APC, p14(ARF), p16(INK4A), RASSF1A, GATA-4, GATA-5 and CHFR was analysed using methylation-specific polymerase chain reaction. These integrative analyses showed that in CIN+ CRCs, promoter methylation of GATA-4 and p16(INK4A) was inversely related to chromosomal loss at 15q11-q21 and gain at 20q13, respectively (P values: 3.8 x 10(-2) and 4.5 x 10(-2), respectively). Interestingly, promoter methylation of RASSF1A, GATA-4, GATA-5 and CHFR, as well as a high methylation index (MI), was positively related to chromosomal gain at 8q23-qter (P values: 1.5 x 10(-2), 3.8 x 10(-2), 3.9 x 10(-2), 4.9 x 10(-2) and 8.2 x 10(-3), respectively). MSI was associated with BRAF mutation, promoter methylation of hMLH1, APC and p16(INK4A) and a high MI (total number of methylated genes) (P values: 2.4 x 10(-2), 2.5 x 10(-3), 1.8 x 10(-2), 4.6 x 10(-2) and 1.0 x 10(-2), respectively). Therefore, we conclude that promoter methylation of pivotal tumour suppressor and DNA repair genes is associated with specific patterns of chromosomal changes in CRC, which are different from methylation patterns in MSI tumours.
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Affiliation(s)
- Sarah Derks
- Department of Pathology, GROW - School for Oncology and developmental biology, Maastricht University, Maastricht, 6200 MD, The Netherlands
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Kawasaki T, Nosho K, Ohnishi M, Suemoto Y, Kirkner GJ, Dehari R, Meyerhardt JA, Fuchs CS, Ogino S. Correlation of beta-catenin localization with cyclooxygenase-2 expression and CpG island methylator phenotype (CIMP) in colorectal cancer. Neoplasia 2007; 9:569-77. [PMID: 17710160 PMCID: PMC1939932 DOI: 10.1593/neo.07334] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2007] [Revised: 05/21/2007] [Accepted: 05/21/2007] [Indexed: 11/18/2022] Open
Abstract
The WNT/beta-catenin (CTNNB1) pathway is commonly activated in the carcinogenic process. Cross-talks between the WNT and cyclooxygenase-2 (COX-2 or PTGS2)/prostaglandin pathways have been suggested. The relationship between beta-catenin activation and microsatellite instability (MSI) in colorectal cancer has been controversial. The CpG island methylator phenotype (CIMP or CIMP-high) with widespread promoter methylation is a distinct epigenetic phenotype in colorectal cancer, which is associated with MSI-high. However, no study has examined the relationship between beta-catenin activation and CIMP status. Using 832 population-based colorectal cancer specimens, we assessed beta-catenin localization by immunohistochemistry. We quantified DNA methylation in eight CIMP-specific promoters [CACNA1G, CDKN2A(p16), CRABP1, IGF2, MLH1, NEUROG1, RUNX3, and SOCS1] by real-time polymerase chain reaction (MethyLight). MSI-high, CIMP-high, and BRAF mutation were associated inversely with cytoplasmic and nuclear beta-catenin expressions (i.e., beta-catenin activation) and associated positively with membrane expression. The inverse relation between beta-catenin activation and CIMP was independent of MSI. COX-2 overexpression correlated with cytoplasmic beta-catenin expression (even after tumors were stratified by CIMP status), but did not correlate significantly with nuclear or membrane expression. In conclusion, beta-catenin activation is inversely associated with CIMP-high independent of MSI status. Cytoplasmic beta-catenin is associated with COX-2 overexpression, supporting the role of cytoplasmic beta-catenin in stabilizing PTGS2 (COX-2) mRNA.
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Affiliation(s)
- Takako Kawasaki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Katsuhiko Nosho
- Department of Internal Medicine, Sapporo Medical University, Sapporo, Japan
| | - Mutsuko Ohnishi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Yuko Suemoto
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Gregory J Kirkner
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Reiko Dehari
- Department of Pathology, Kanagawa Cancer Center, Kanagawa, Japan
| | - Jeffrey A Meyerhardt
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Charles S Fuchs
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Shuji Ogino
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
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Iacopetta B, Grieu F, Phillips M, Ruszkiewicz A, Moore J, Minamoto T, Kawakami K. Methylation levels of LINE-1 repeats and CpG island loci are inversely related in normal colonic mucosa. Cancer Sci 2007; 98:1454-60. [PMID: 17640302 PMCID: PMC11158818 DOI: 10.1111/j.1349-7006.2007.00548.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Hypermethylation of CpG island loci within gene promoter regions is a frequent event in colorectal cancer that is often associated with transcriptional silencing and has been referred to as CIMP+. DNA hypomethylation can occur in concert with CIMP+, although these two phenomena appear not to be related in colorectal cancer. The authors investigated here whether the methylation level of LINE-1 repeats, a surrogate marker for genomic methylation, was associated with the level of CpG island methylation in colorectal cancers and in matching normal colonic mucosa from 178 patients. The MethyLight assay was used to quantitate the methylation of CpG islands within the MLH1, P16(INK4A), TIMP3, DAPK, APC, ER and MYOD genes. A real-time, methylation-specific polymerase chain reaction assay was also used to quantitate the methylation of LINE-1 repeats. In colorectal cancer, no associations were seen between methylation levels in LINE-1 repeats and CpG island loci, including a new CpG island panel that was recently proposed for CIMP+. In normal colonic mucosa, however, the methylation level of LINE-1 repeats was inversely correlated with CpG-island methylation of the MLH1, P16, TIMP3, APC, ER and MYOD genes. The methylation level of LINE-1 repeats in normal colonic mucosa also showed significant associations with common polymorphisms in the methylene tetrahydrofolate reductase and methylene tetrahydrofolate dehydrogenase genes involved in methyl group metabolism. Further investigation of genomic and CpG island methylation in normal colonic mucosa and the possible influences of environmental and genetic factors may provide new insights into the development of CIMP+ colorectal cancer.
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Affiliation(s)
- Barry Iacopetta
- School of Surgery and Pathology, WA Institute for Medical Research, University of Western Australia, 35 Stirling Highway, Nedlands 6009, Australia.
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Ahmed FE. Colorectal cancer epigenetics: the role of environmental factors and the search for molecular biomarkers. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS 2007; 25:101-54. [PMID: 17558783 DOI: 10.1080/10590500701399184] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
This review presents an evenhanded evaluation of the role of epigenetics in the development of colorectal cancer, and investigates the extent of environmental influences on modulating this disease. Advances in our understanding of chromatin structure, histone modification, transcriptional activity and DNA methylation have lead to an integrated approach to the role of epigenetics in carcinogenesis. Epigenetic mechanisms appear to permit response of individuals to environment through change in gene expression and are involved in inactivating one of the two X chromosomes in women. Epigenetic changes play an important role in development and can also arise stochastically as individuals age. Because epigenetic alterations are potentially reversible, thereby allowing malignant cells to revert to the normal state, there is potential to develop effective strategies to prevent or even reverse this curable cancer. Moreover, because the methylation status of a specific sequence or the pattern of methylation across the genome can now be measured accurately, molecular biomarkers of screening, diagnosis, prognosis, prediction of treatment and those related to risk assessment can be developed using sophisticated molecular genetic technologies. Although in many cases a high sensitivity and specificity of the detection assays has been achieved, there still remains ample room for improvement in areas of sample preparation, assay design and marker selection.
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Affiliation(s)
- Farid E Ahmed
- Department of Radiation Oncology, Leo W. Jenkins Cancer Center, The Brody School of Medicine, East Carolina University, Greenville, North Carolina 27858, USA.
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