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Yu Y, Xue W, Liu Z, Chen S, Wang J, Peng Q, Xu L, Liu X, Cui C, Fan JB. A novel DNA methylation marker to identify lymph node metastasis of colorectal cancer. Front Oncol 2022; 12:1000823. [PMID: 36313642 PMCID: PMC9614158 DOI: 10.3389/fonc.2022.1000823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/22/2022] [Indexed: 11/13/2022] Open
Abstract
Lymph node metastasis (LNM) of colorectal cancer (CRC) is an important factor for both prognosis and treatment. Given the deficiencies of conventional tests, we aim to discover novel DNA methylation markers to efficiently identify LNM status of CRC. In this study, genome-wide methylation sequencing was performed in a cohort (n=30) using fresh CRC tissue to discover differentially methylated markers. These markers were subsequently validated with fluorescence quantitative PCR in a cohort (n=221), and the optimal marker was compared to conventional diagnostic methods. Meanwhile, immunohistochemistry was used to verify the effectiveness of the antibody corresponding to this marker in a cohort (n=56). LBX2 achieved an AUC of 0.87, specificity of 87.3%, sensitivity of 75.7%, and accuracy of 81.9%, which outperformed conventional methods including imaging (CT, PET-CT) with an AUC of 0.52, CA199 with an AUC of 0.58, CEA with an AUC of 0.56. LBX2 was also superior to clinicopathological indicators including the depth of tumor invasion and lymphatic invasion with an AUC of 0.61and 0.63 respectively. Moreover, the AUC of LBX2 antibody was 0.84, which was also better than these conventional methods. In conclusion, A novel methylation marker LBX2 could be used as a simple, cost-effective, and reliable diagnostic method for LNM of CRC.
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Affiliation(s)
- Yingdian Yu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Wenyuan Xue
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zefeng Liu
- Department of General Surgery, Zhujiang Hosipital, Southern Medical University, Guangzhou, China
| | - Shang Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Jun Wang
- AnchorDx Medical Co., Ltd., International Bio-Island, Guangzhou, China
| | - Quanzhou Peng
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Linhao Xu
- AnchorDx Medical Co., Ltd., International Bio-Island, Guangzhou, China
| | - Xin Liu
- AnchorDx Medical Co., Ltd., International Bio-Island, Guangzhou, China
| | - Chunhui Cui
- Department of General Surgery, Zhujiang Hosipital, Southern Medical University, Guangzhou, China
- *Correspondence: Jian-Bing Fan, ; Chunhui Cui,
| | - Jian-Bing Fan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- AnchorDx Medical Co., Ltd., International Bio-Island, Guangzhou, China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- *Correspondence: Jian-Bing Fan, ; Chunhui Cui,
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Li J, Li H, Run ZC, Wang ZL, Jiang T, An Y, Li Z. RASSF1A methylation as a biomarker for detection of colorectal cancer and hepatocellular carcinoma. World J Gastrointest Oncol 2022; 14:1574-1584. [PMID: 36160746 PMCID: PMC9412931 DOI: 10.4251/wjgo.v14.i8.1574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/02/2022] [Accepted: 07/22/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Studies have validated the potential of methylated cell-free DNA as a biomarker in various tumors, and methylated DNA in plasma may be a potential biomarker for cancer.
AIM To evaluate the diagnostic value of RASSF1A methylation in plasma for colorectal cancer (CRC) and hepatocellular carcinoma (HCC).
METHODS A total of 92 CRC patients, 67 colorectal polyp (CRP) patients, 63 HCC patients, and 66 liver cirrhosis (LC) patients were enrolled. The plasma DNA was subjected to DNA extraction, double-strand DNA concentration determination, bisulfite conversion, purification, single-strand DNA concentration determination, and digital polymerase chain reaction (PCR) detection. The methylation rate was calculated. The diagnostic value was evaluated by the area under the curve (AUC).
RESULTS The age and sex in the CRC and CRP groups and the HCC and LC groups were also matched. The DNA methylation rate of RASSF1A in plasma in the CRC group was 2.87 ± 1.80, and that in the CRP group was 1.50 ± 0.64. DNA methylation of RASSF1A in plasma showed a significant difference between the CRC and CRP groups. The AUC of RASSF1A methylation for discriminating the CRC and CRP groups was 0.82 (0.76-0.88). The AUCs of T1, T2, T3 and T4 CRC and CRP were 0.83 (0.72-0.95), 0.87 (0.78-0.95), 0.86 (0.77-0.95), and 0.75 (0.64-0.85), respectively. The DNA methylation rate of RASSF1A in plasma in the HCC group was 4.45 ± 2.93, and that in the LC group was 2.46 ± 2.07. DNA methylation of RASSF1A in plasma for the HCC and LC groups showed a significant difference. The AUC of RASSF1A methylation for discriminating the HCC and LC groups was 0.70 (0.60-0.79). The AUCs of T1, T2, T3 and T4 HCC and LC were 0.80 (0.61, 1.00), 0.74 (0.59-0.88), 0.60 (0.42-0.79), and 0.68 (0.53-0.82), respectively.
CONCLUSION RASSF1A methylation in plasma detected by digital PCR may be a potential biomarker for CRC and HCC.
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Affiliation(s)
- Jian Li
- Department of General Surgery, Affiliated Tumor Hospital of Zhengzhou University, Henan Tumor Hospital, Zhengzhou 450000, Henan Province, China
| | - Huan Li
- Department of Gastroenterology, Sixth Medical Center of Chinese PLA General Hospital, Beijing 100048, China
| | - Zeng-Ci Run
- Department of General Surgery, Affiliated Tumor Hospital of Zhengzhou University, Henan Tumor Hospital, Zhengzhou 450000, Henan Province, China
| | - Zhen-Lei Wang
- Department of General Surgery, Affiliated Tumor Hospital of Zhengzhou University, Henan Tumor Hospital, Zhengzhou 450000, Henan Province, China
| | - Tao Jiang
- Medicine Innovation Research Division of Chinese PLA General Hospital, Beijing 100853, China
| | - Yang An
- Faculty of Hepato-Pancreato-Biliary Surgery, Sixth Medical Center of Chinese PLA General Hospital, Beijing 100048, China
| | - Zhi Li
- Department of General Surgery, Affiliated Tumor Hospital of Zhengzhou University, Henan Tumor Hospital, Zhengzhou 450000, Henan Province, China
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Oh SJ, Lee MG, Moon JR, Lee CK, Chi SG, Kim HJ. Ras association domain family 1 isoform A suppresses colonic tumor cell growth through p21 WAF1 activation in a p53-dependent manner. J Gastroenterol Hepatol 2019; 34:890-898. [PMID: 30226276 DOI: 10.1111/jgh.14469] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 09/02/2018] [Accepted: 09/06/2018] [Indexed: 01/06/2023]
Abstract
BACKGROUND AND AIM Despite the frequent loss of Ras association domain family 1 isoform A (RASSF1A) expression in various cancers, the precise mechanism underlying its tumor-suppressive effect is not fully understood. To elucidate the growth-inhibitory role for RASSF1A in colorectal tumorigenesis, this study investigated the RASSF1A regulation of the p53-p21WAF1 pathway. METHODS Ras association domain family 1 isoform A effect on cellular growth was tested in three human colon cancer cell lines by flow cytometry, cell counting, and [3 H]-thymidine incorporation assay. HCT116 p53+/+ and p53-/- isogenic sublines were utilized to determine the p53 dependence of RASSF1A effect on p21WAF1 . Cycloheximide chase experiment and immunoprecipitation assay were carried out to define RASSF1A effect on p53 stability and mouse double minute 2 (MDM2) homolog ubiquitination. RESULTS Ras association domain family 1 isoform A expression inhibits colonic cell proliferation by preventing the G1 to S phase transition of the cell cycle. The RASSF1A-induced G1 cell cycle arrest is accompanied by the increase in the level of p21WAF1 mRNA expression. The p21WAF -inducing activity of RASSF1A was substantially higher in HCT116 p53+/+ cell compared with isogenic p53-/- cells. The cycloheximide chase assay revealed that RASSF1A expression leads to p53 stabilization and MDM2 homolog degradation. Using p53-/- and p21WAF1-/- subline cells, this study finally validated a crucial role of the p53-p21WAF1 axis in RASSF1A-mediated growth inhibition. CONCLUSIONS RASSF1A suppresses colonic tumor growth through the activation of the p53-p21WAF1 pathway. This finding supports that RASSF1A could be a valuable marker for the assessment of colorectal cancer development and progression.
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Affiliation(s)
- Shin Ju Oh
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Kyung Hee University School of Medicine, Seoul, Korea
| | - Min-Goo Lee
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Jung Rock Moon
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Kyung Hee University School of Medicine, Seoul, Korea
| | - Chang Kyun Lee
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Kyung Hee University School of Medicine, Seoul, Korea
| | - Sung-Gil Chi
- Department of Life Sciences, Korea University, Seoul, Korea
| | - Hyo Jong Kim
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Kyung Hee University School of Medicine, Seoul, Korea
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Liu D, Peng H, Sun Q, Zhao Z, Yu X, Ge S, Wang H, Fang H, Gao Q, Liu J, Wu L, Song M, Wang Y. The Indirect Efficacy Comparison of DNA Methylation in Sputum for Early Screening and Auxiliary Detection of Lung Cancer: A Meta-Analysis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2017. [PMID: 28644424 PMCID: PMC5551117 DOI: 10.3390/ijerph14070679] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Background: DNA methylation in sputum has been an attractive candidate biomarker for the non-invasive screening and detection of lung cancer. Materials and Methods: Databases including PubMed, Ovid, Cochrane library, Web of Science databases, Chinese Biological Medicine (CBM), Chinese National Knowledge Infrastructure (CNKI), Wanfang, Vip Databases and Google Scholar were searched to collect the diagnostic trials on aberrant DNA methylation in the screening and detection of lung cancer published until 1 December 2016. Indirect comparison meta-analysis was used to evaluate the diagnostic value of the included candidate genes. Results: The systematic literature search yielded a total of 33 studies including a total of 4801 subjects (2238 patients with lung cancer and 2563 controls) and covering 32 genes. We identified that methylated genes in sputum samples for the early screening and auxiliary detection of lung cancer yielded an overall sensitivity of 0.46 (0.41–0.50) and specificity of 0.83 (0.80–0.86). Combined indirect comparisons identified the superior gene of SOX17 (sensitivity: 0.84, specificity: 0.88), CDO1 (sensitivity: 0.78, specificity: 0.67), ZFP42 (sensitivity: 0.87, specificity: 0.63) and TAC1 (sensitivity: 0.86, specificity: 0.75). Conclusions: The present meta-analysis demonstrates that methylated SOX17, CDO1, ZFP42, TAC1, FAM19A4, FHIT, MGMT, p16, and RASSF1A are potential superior biomarkers for the screening and auxiliary detection of lung cancer.
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Affiliation(s)
- Di Liu
- Beijing Municipal Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China.
| | - Hongli Peng
- Beijing Municipal Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China.
| | - Qi Sun
- Beijing Municipal Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China.
| | - Zhongyao Zhao
- Beijing Municipal Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China.
| | - Xinwei Yu
- Beijing Municipal Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China.
- School of Medical and Health Sciences, Edith Cowan University, Perth 6027, Australia.
| | - Siqi Ge
- Beijing Municipal Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China.
- School of Medical and Health Sciences, Edith Cowan University, Perth 6027, Australia.
| | - Hao Wang
- Beijing Municipal Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China.
| | - Honghong Fang
- Beijing Municipal Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China.
| | - Qing Gao
- Beijing Municipal Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China.
| | - Jiaonan Liu
- Beijing Municipal Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China.
| | - Lijuan Wu
- Beijing Municipal Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China.
| | - Manshu Song
- Beijing Municipal Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China.
| | - Youxin Wang
- Beijing Municipal Key Laboratory of Clinical Epidemiology, School of Public Health, Capital Medical University, Beijing 100069, China.
- School of Medical and Health Sciences, Edith Cowan University, Perth 6027, Australia.
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Lim Y, Wan Y, Vagenas D, Ovchinnikov DA, Perry CFL, Davis MJ, Punyadeera C. Salivary DNA methylation panel to diagnose HPV-positive and HPV-negative head and neck cancers. BMC Cancer 2016; 16:749. [PMID: 27663357 PMCID: PMC5034533 DOI: 10.1186/s12885-016-2785-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/15/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous group of tumours with a typical 5 year survival rate of <40 %. DNA methylation in tumour-suppressor genes often occurs at an early stage of tumorigenesis, hence DNA methylation can be used as an early tumour biomarker. Saliva is an ideal diagnostic medium to detect early HNSCC tumour activities due to its proximity to tumour site, non-invasiveness and ease of sampling. We test the hypothesis that the surveillance of DNA methylation in five tumour-suppressor genes (RASSF1α, p16 INK4a , TIMP3, PCQAP/MED15) will allow us to diagnose HNSCC patients from a normal healthy control group as well as to discriminate between Human Papillomavirus (HPV)-positive and HPV-negative patients. METHODS Methylation-specific PCR (MSP) was used to determine the methylation levels of RASSF1α, p16 INK4a , TIMP3 and PCQAP/MED15 in DNA isolated from saliva. Statistical analysis was carried out using non-parametric Mann-Whitney's U-test for individually methylated genes. A logistic regression analysis was carried out to determine the assay sensitivity when combing the five genes. Further, a five-fold cross-validation with a bootstrap procedure was carried out to determine how well the panel will perform in a real clinical scenario. RESULTS Salivary DNA methylation levels were not affected by age. Salivary DNA methylation levels for RASSF1α, p16 INK4a , TIMP3 and PCQAP/MED15 were higher in HPV-negative HNSCC patients (n = 88) compared with a normal healthy control group (n = 122) (sensitivity of 71 % and specificity of 80 %). Conversely, DNA methylation levels for these genes were lower in HPV-positive HNSCC patients (n = 45) compared with a normal healthy control group (sensitivity of 80 % and specificity of 74 %), consistent with the proposed aetiology of HPV-positive HNSCCs. CONCLUSIONS Salivary DNA tumour-suppressor methylation gene panel has the potential to detect early-stage tumours in HPV-negative HNSCC patients. HPV infection was found to deregulate the methylation levels in HPV-positive HNSCC patients. Large-scale double-blinded clinical trials are crucial before this panel can potentially be integrated into a clinical setting.
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Affiliation(s)
- Yenkai Lim
- The School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, GPO Box 2434, 60 Musk Avenue, Kelvin Grove, Brisbane, QLD, 4059, Australia
| | - Yunxia Wan
- The School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, GPO Box 2434, 60 Musk Avenue, Kelvin Grove, Brisbane, QLD, 4059, Australia
| | - Dimitrios Vagenas
- The School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, GPO Box 2434, 60 Musk Avenue, Kelvin Grove, Brisbane, QLD, 4059, Australia
| | - Dmitry A Ovchinnikov
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - Chris F L Perry
- Department of Otolaryngology, Princess Alexandra Hospital, 199 Ipswich Road, Woolloongabba, Brisbane, QLD, 4102, Australia.,School of Medicine, University of Queensland, 288 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Melissa J Davis
- Department of Biomedical Engineering, University of Melbourne, Parkville, Melbourne, VIC, 3010, Australia
| | - Chamindie Punyadeera
- The School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, GPO Box 2434, 60 Musk Avenue, Kelvin Grove, Brisbane, QLD, 4059, Australia.
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Klacz J, Wierzbicki PM, Wronska A, Rybarczyk A, Stanislawowski M, Slebioda T, Olejniczak A, Matuszewski M, Kmiec Z. Decreased expression of RASSF1A tumor suppressor gene is associated with worse prognosis in clear cell renal cell carcinoma. Int J Oncol 2015; 48:55-66. [PMID: 26648328 PMCID: PMC4734610 DOI: 10.3892/ijo.2015.3251] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/09/2015] [Indexed: 12/27/2022] Open
Abstract
Clear-cell renal cell carcinoma (ccRCC) is the most common subtype of RCC (70-80%) and is associated with poor prognosis in 40% of cases mainly due to metastasis in the course of the disease. RASSF1, with its isoforms RASSF1A and RASSF1C, is a tumor suppressor gene which has not been fully analyzed in ccRCC yet. The epigenetic downregulation of RASSF1A is commonly associated with promoter hypermethylation. The aim of the present study was to compare the ccRCC outcomes with the expression of RASSF1A and RASSF1C. Tissues were obtained from 86 ccRCC patients. RASSF1A and RASSF1C mRNA levels were assessed in tumor and matched normal kidney tissue, and in 12 samples of local metastases by quantitative PCR (qPCR). RASSF1A and RASSF1C proteins levels were semi-quantified in 58 samples by western blot analysis and their tissue localization was assessed by immunohistochemistry. Hypermethylation of RASSF1A promoter was measured by high-resolution-melting methylation-specific qPCR. RASSF1A mRNA levels were 4 and 5 times lower in 66% of tumor and 75% metastasized samples. RASSF1A hypermethylation was found in 40% of analyzed T cases. RASSF1A protein expression was 5 or 20 times decreased in 70% tumor and 75% metastatic samples, respectively. RASSF1A hypermethylation, mRNA and protein levels were associated with TNM progression and higher Fuhrman's grading. Decreased RASSF1A expression, hypermethylation, TNM and Fuhrman's grading were associated with poorer overall survival (OS). Cox hazard ratio (HR) analysis revealed predictor role of RASSF1A mRNA levels on OS and progression-free survival (PFS) in relation to Fuhrman's grading (OS HR=2.25, PFS HR=2.93). RASSF1C levels were increased in ccRCC; no correlations with clinicopathological variables were found. We conclude that RASSF1C gene is not involved in ccRCC progression and we propose that the measurements of RASSF1A mRNA levels in paired tumor-normal kidney tissue could serve as a new prognostic factor in ccRCC.
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Affiliation(s)
- Jakub Klacz
- Department of Urology, Faculty of Medicine, Medical University of Gdansk, Gdansk 80-211, Poland
| | - Piotr M Wierzbicki
- Department of Histology, Faculty of Medicine, Medical University of Gdansk, Gdansk 80-211, Poland
| | - Agata Wronska
- Department of Histology, Faculty of Medicine, Medical University of Gdansk, Gdansk 80-211, Poland
| | - Agnieszka Rybarczyk
- Department of Histology, Faculty of Medicine, Medical University of Gdansk, Gdansk 80-211, Poland
| | - Marcin Stanislawowski
- Department of Histology, Faculty of Medicine, Medical University of Gdansk, Gdansk 80-211, Poland
| | - Tomasz Slebioda
- Department of Histology, Faculty of Medicine, Medical University of Gdansk, Gdansk 80-211, Poland
| | - Agata Olejniczak
- Department of Histology, Faculty of Medicine, Medical University of Gdansk, Gdansk 80-211, Poland
| | - Marcin Matuszewski
- Department of Urology, Faculty of Medicine, Medical University of Gdansk, Gdansk 80-211, Poland
| | - Zbigniew Kmiec
- Department of Histology, Faculty of Medicine, Medical University of Gdansk, Gdansk 80-211, Poland
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Grawenda AM, O'Neill E. Clinical utility of RASSF1A methylation in human malignancies. Br J Cancer 2015; 113:372-81. [PMID: 26158424 PMCID: PMC4522630 DOI: 10.1038/bjc.2015.221] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 05/11/2015] [Accepted: 05/13/2015] [Indexed: 02/06/2023] Open
Abstract
The high frequency of RASSF1A methylation has been noted in a vast number of patients in a broad spectrum of malignancies, suggesting that RASSF1A inactivation is associated with cancer pathogenesis. However, whether this recurrent incidence of RASSF1A hypermethylation in human malignancies and its association with more aggressive tumour phenotype is a frequent event across different cancer types has not yet been discussed. In this review, we interrogated existing evidence for association of RASSF1A hypermethylation with clinicopathological characteristics that can indicate more invasive lesions.
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Affiliation(s)
- A M Grawenda
- CRUK/MRC Oxford Institute, Department of Oncology, University of Oxford, Oxford, UK
| | - E O'Neill
- CRUK/MRC Oxford Institute, Department of Oncology, University of Oxford, Oxford, UK
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Coppedè F, Grossi E, Lopomo A, Spisni R, Buscema M, Migliore L. Application of artificial neural networks to link genetic and environmental factors to DNA methylation in colorectal cancer. Epigenomics 2015; 7:175-86. [PMID: 25942531 DOI: 10.2217/epi.14.77] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
AIMS We applied artificial neural networks (ANNs) to understand the connections among polymorphisms of genes involved in folate metabolism, clinico-pathological features and promoter methylation levels of MLH1, APC, CDKN2A(INK4A), MGMT and RASSF1A in 83 sporadic colorectal cancer (CRC) tissues, and to link dietary and lifestyle factors with gene promoter methylation. MATERIALS & METHODS Promoter methylation was assessed by means of methylation-sensitive high-resolution melting and genotyping by PCR-RFLP technique. Data were analyzed with the Auto Contractive Map, a special kind of ANN able to define the strength of the association of each variable with all the others and to visually show the map of the main connections. RESULTS We observed a strong connection between the low methylation levels of the five CRC genes and the MTR 2756AA genotype. Several other connections were revealed, including those between dietary and lifestyle factors and the methylation levels of CRC genes. CONCLUSION ANNs revealed the complexity of the interconnections among factors linked to DNA methylation in CRC.
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Affiliation(s)
- Fabio Coppedè
- Department of Translational Research & New Technologies in Medicine & Surgery, Division of Medical Genetics, University of Pisa, Medical School, Via Roma 55, 56126 Pisa, Italy
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He Z, Duan H, Zhang B, Li M, Chen L, Zhang B, Zhu X, Gao C, Li J, Zhang X, Zhang J, Wang S, Zeng X, Li D, Xing X, Zhang Z, Ma L, Bai Q, Liu C, Xiao Y, Zheng Y, Chen W. CpG site-specific RASSF1a hypermethylation is associated with occupational PAH exposure and genomic instability. Toxicol Res (Camb) 2015. [DOI: 10.1039/c5tx00013k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Previous studies have shown an etiologic link between exposure to PAHs and lung cancer development.
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