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Hong Y, Kim WJ. DNA Methylation Markers in Lung Cancer. Curr Genomics 2020; 22:79-87. [PMID: 34220295 PMCID: PMC8188581 DOI: 10.2174/1389202921999201013164110] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 08/04/2020] [Accepted: 08/18/2020] [Indexed: 01/05/2023] Open
Abstract
Lung cancer is the most common cancer and the leading cause of cancer-related morbidity and mortality worldwide. As early symptoms of lung cancer are minimal and non-specific, many patients are diagnosed at an advanced stage. Despite a concerted effort to diagnose lung cancer early, no biomarkers that can be used for lung cancer screening and prognosis prediction have been established so far. As global DNA demethylation and gene-specific promoter DNA methylation are present in lung cancer, DNA methylation biomarkers have become a major area of research as potential alternative diagnostic methods to detect lung cancer at an early stage. This review summarizes the emerging DNA methylation changes in lung cancer tumorigenesis, focusing on biomarkers for early detection and their potential clinical applications in lung cancer.
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Affiliation(s)
- Yoonki Hong
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon, South Korea
| | - Woo Jin Kim
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon, South Korea
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DNA Methylation as a Noninvasive Epigenetic Biomarker for the Detection of Cancer. DISEASE MARKERS 2017; 2017:3726595. [PMID: 29038612 PMCID: PMC5605861 DOI: 10.1155/2017/3726595] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 07/10/2017] [Accepted: 08/07/2017] [Indexed: 12/30/2022]
Abstract
In light of the high incidence and mortality rates of cancer, early and accurate diagnosis is an important priority for assigning optimal treatment for each individual with suspected illness. Biomarkers are crucial in the screening of patients with a high risk of developing cancer, diagnosing patients with suspicious tumours at the earliest possible stage, establishing an accurate prognosis, and predicting and monitoring the response to specific therapies. Epigenetic alterations are innovative biomarkers for cancer, due to their stability, frequency, and noninvasive accessibility in bodily fluids. Epigenetic modifications are also reversible and potentially useful as therapeutic targets. Despite this, there is still a lack of accurate biomarkers for the conclusive diagnosis of most cancer types; thus, there is a strong need for continued investigation to expand this area of research. In this review, we summarise current knowledge on methylated DNA and its implications in cancer to explore its potential as an epigenetic biomarker to be translated for clinical application. We propose that the identification of biomarkers with higher accuracy and more effective detection methods will enable improved clinical management of patients and the intervention at early-stage disease.
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Peng M, Chen C, Hulbert A, Brock MV, Yu F. Non-blood circulating tumor DNA detection in cancer. Oncotarget 2017; 8:69162-69173. [PMID: 28978187 PMCID: PMC5620327 DOI: 10.18632/oncotarget.19942] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 07/25/2017] [Indexed: 01/01/2023] Open
Abstract
Tumor DNA contains specific somatic alterations that are crucial for the diagnosis and treatment of cancer. Due to the spatial and temporal intra-tumor heterogeneity, multi-sampling is needed to adequately characterize the somatic alterations. Tissue biopsy, however, is limited by the restricted access to sample and the challenges to recapitulate the tumor clonal diversity. Non-blood circulating tumor DNA are tumor DNA fragments presents in non-blood body fluids, such as urine, saliva, sputum, stool, pleural fluid, and cerebrospinal fluid (CSF). Recent studies have demonstrated the presence of tumor DNA in these non-blood body fluids and their application to the diagnosis, screening, and monitoring of cancers. Non-blood circulating tumor DNA has an enormous potential for large-scale screening of local neoplasms because of its non-invasive nature, close proximity to the tumors, easiness and it is an economically viable option. It permits longitudinal assessments and allows sequential monitoring of response and progression. Enrichment of tumor DNA of local cancers in non-blood body fluids may help to archive a higher sensitivity than in plasma ctDNA. The direct contact of cancerous cells and body fluid may facilitate the detection of tumor DNA. Furthermore, normal DNA always dilutes the plasma ctDNA, which may be aggravated by inflammation and injury when very high amounts of normal DNA are released into the circulation. Altogether, our review indicate that non-blood circulating tumor DNA presents an option where the disease can be tracked in a simple and less-invasive manner, allowing for serial sampling informing of the tumor heterogeneity and response to treatment.
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Affiliation(s)
- Muyun Peng
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P.R China
| | - Chen Chen
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P.R China
| | - Alicia Hulbert
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Malcolm V Brock
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Fenglei Yu
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P.R China
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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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Analysis of DNA Methylation Status in Bodily Fluids for Early Detection of Cancer. Int J Mol Sci 2017; 18:ijms18040735. [PMID: 28358330 PMCID: PMC5412321 DOI: 10.3390/ijms18040735] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 03/24/2017] [Accepted: 03/26/2017] [Indexed: 02/07/2023] Open
Abstract
Epigenetic alterations by promoter DNA hypermethylation and gene silencing in cancer have been reported over the past few decades. DNA hypermethylation has great potential to serve as a screening marker, a prognostic marker, and a therapeutic surveillance marker in cancer clinics. Some bodily fluids, such as stool or urine, were obtainable without any invasion to the body. Thus, such bodily fluids were suitable samples for high throughput cancer surveillance. Analyzing the methylation status of bodily fluids around the cancer tissue may, additionally, lead to the early detection of cancer, because several genes in cancer tissues are reported to be cancer-specifically hypermethylated. Recently, several studies that analyzed the methylation status of DNA in bodily fluids were conducted, and some of the results have potential for future development and further clinical use. In fact, a stool DNA test was approved by the U.S. Food and Drug Administration (FDA) for the screening of colorectal cancer. Another promising methylation marker has been identified in various bodily fluids for several cancers. We reviewed studies that analyzed DNA methylation in bodily fluids as a less-invasive cancer screening.
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Fumagalli C, Bianchi F, Raviele PR, Vacirca D, Bertalot G, Rampinelli C, Lazzeroni M, Bonanni B, Veronesi G, Fusco N, Barberis M, Guerini-Rocco E. Circulating and tissue biomarkers in early-stage non-small cell lung cancer. Ecancermedicalscience 2017; 11:717. [PMID: 28194229 PMCID: PMC5295844 DOI: 10.3332/ecancer.2017.717] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVE We sought to characterise circulating and tissue tumour biomarkers of patients who developed early-stage non-small cell lung cancer (NSCLC) during long-term follow-up of a chemoprevention trial (NCT00321893). MATERIALS AND METHODS Blood and sputum samples were collected from 202 high-risk asymptomatic individuals with CT-detected stable lung nodules. Real-time PCR was performed on plasma to quantify free circulating DNA. Baseline serum was investigated with a previously validated test based on 13 circulating miRNAs (miR-Test). Promoter methylation status of p16, RASSF1a and RARβ2 and telomerase activity were assessed in sputum samples. DNA was extracted from each tumour developed during follow-up and subjected to a mutation survey using the LungCarta panel on the Sequenom MassARRAY platform. RESULTS During follow-up (9 years) six individuals underwent surgery for stage I NSCLC with a median time of disease onset of 20.5 months. MiR-Test scores were positive (range: 0.14-7.24) in four out of six baseline pre-disease onset sera. No association was identified between free circulating DNA or sputum biomarkers and disease onset. All tumours harboured at least one somatic mutation in well-known cancer genes, including KRAS (n = 4), BRAF (n = 1), and TP53 (n = 3). CONCLUSION Circulating miRNA tests may represent valuable tools to detect clinically-silent tumours. Early-stage lung adenocarcinomas harbour recurrent genetic events similar to those described in advanced-stage NSCLCs.
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Affiliation(s)
- Caterina Fumagalli
- Division of Pathology, European Institute of Oncology, Via Giuseppe Ripamonti 435, 20141, Milan, Italy
| | - Fabrizio Bianchi
- Institute for Stem-cell Biology, Regenerative Medicine and Innovative Therapies (ISBReMIT), IRCCS Casa Sollievo della Sofferenza, Viale Cappuccini 1, 71013, San Giovanni Rotondo, Foggia, Italy
| | - Paola Rafaniello Raviele
- Division of Pathology, European Institute of Oncology, Via Giuseppe Ripamonti 435, 20141, Milan, Italy
| | - Davide Vacirca
- Division of Pathology, European Institute of Oncology, Via Giuseppe Ripamonti 435, 20141, Milan, Italy
| | - Giovanni Bertalot
- Molecular Medicine Programme IEO, European Institute of Oncology, Via Giuseppe Ripamonti 435, 20141, Milan, Italy
| | - Cristiano Rampinelli
- Department of Radiology, European Institute of Oncology, Via Giuseppe Ripamonti 435, 20141, Milan, Italy
| | - Matteo Lazzeroni
- Division of Cancer Prevention and Genetics, European Institute of Oncology, Via Giuseppe Ripamonti 435, 20141, Milan, Italy
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, European Institute of Oncology, Via Giuseppe Ripamonti 435, 20141, Milan, Italy
| | - Giulia Veronesi
- Division of Thoracic Surgery, Humanitas Research Hospital, Via Manzoni 56, 20089, Rozzano Milan, Italy
| | - Nicola Fusco
- Division of Pathology, Fondazione IRCCS Ca' Granda - Ospedale Maggiore Policlinico, University of Milan, Via Francesco Sforza 35, 20122, Milan, Italy
| | - Massimo Barberis
- Division of Pathology, European Institute of Oncology, Via Giuseppe Ripamonti 435, 20141, Milan, Italy
| | - Elena Guerini-Rocco
- Division of Pathology, European Institute of Oncology, Via Giuseppe Ripamonti 435, 20141, Milan, Italy
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Ahmad A. Epigenetics in Personalized Management of Lung Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 890:111-22. [PMID: 26703801 DOI: 10.1007/978-3-319-24932-2_6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In last several years, the focus on the origin and progression of human cancers has shifted from genetic to epigenetic regulation, with particular attention to methylation and acetylation events that have profound effect on the eventual expression of oncogenes and the suppression of tumor suppressors. A few drugs targeting these epigenetic changes have already been approved for treatment, albeit not for lung cancer. With the recent advances in the push towards personalized therapy, questions have been asked about the possible targeting of epigenetic events for personalized lung cancer therapy. Some progress has been made but a lot needs to be done. In this chapter, a succinct review of these topics is provided.
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Affiliation(s)
- Aamir Ahmad
- Karmanos Cancer Institute, Wayne State University, Detroit, MI, 48201, USA.
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Mehta A, Dobersch S, Romero-Olmedo AJ, Barreto G. Epigenetics in lung cancer diagnosis and therapy. Cancer Metastasis Rev 2015; 34:229-41. [DOI: 10.1007/s10555-015-9563-3] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Gao L, Xie E, Yu T, Chen D, Zhang L, Zhang B, Wang F, Xu J, Huang P, Liu X, Fang B, Pan S. Methylated APC and RASSF1A in multiple specimens contribute to the differential diagnosis of patients with undetermined solitary pulmonary nodules. J Thorac Dis 2015; 7:422-32. [PMID: 25922721 DOI: 10.3978/j.issn.2072-1439.2015.01.24] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 10/22/2014] [Indexed: 12/18/2022]
Abstract
BACKGROUND Inactivation of tumor-suppressor gene (TSG) by promoter hypermethylation has been reported in many tumor types, including lung cancer. This study was designed to determine the methylated APC and RASSF1A genes in tumor tissue, serum and plasma of patients with early stage lung cancer. METHODS Eighty-nine patients with undetermined solitary pulmonary nodules detected upon CT-scan were recruited in this study. DNA samples were extracted from biopsy tissues, serum and plasma and QMSP of APC and RASSF1A was carried out after bisulfite conversion. The 89 patients consist of 58 stage I lung cancer patients and 31 benign lung disease according to pathological report. Twenty-six cancer patients had matched biopsy tumor tissue, serum and plasma samples. RESULTS The methylation rates of APC and RASSF1A were 59.0% and 66.1% in biopsy tissues, 42.5% and 52.5% in serum, and 24.1% and 43.1% in plasma of cancer patients. For RASSF1A, different samples all showed a significant difference between cancer group and benign group (P<0.05). However, APC gene only explored the P value less than 0.05 in plasma result. Towards the 26 lung cancer patients with three matched samples, methylation rate in each sample type was more than 50.0% and displayed no difference. CONCLUSIONS Evaluation of APC and RASSF1A promoter methylation by using QMSP appears to be very useful for the differential diagnosis of patients with undetermined solitary pulmonary nodules. Our results also suggested that plasma might be the best sample for clinical detection of early stage lung.
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Affiliation(s)
- Li Gao
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical, Department of Laboratory Medicine, Nanjing 210029, China ; 3 Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 4 Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Erfu Xie
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical, Department of Laboratory Medicine, Nanjing 210029, China ; 3 Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 4 Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tongfu Yu
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical, Department of Laboratory Medicine, Nanjing 210029, China ; 3 Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 4 Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dan Chen
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical, Department of Laboratory Medicine, Nanjing 210029, China ; 3 Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 4 Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lixia Zhang
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical, Department of Laboratory Medicine, Nanjing 210029, China ; 3 Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 4 Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bingfeng Zhang
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical, Department of Laboratory Medicine, Nanjing 210029, China ; 3 Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 4 Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Fang Wang
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical, Department of Laboratory Medicine, Nanjing 210029, China ; 3 Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 4 Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jian Xu
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical, Department of Laboratory Medicine, Nanjing 210029, China ; 3 Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 4 Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Peijun Huang
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical, Department of Laboratory Medicine, Nanjing 210029, China ; 3 Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 4 Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xisheng Liu
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical, Department of Laboratory Medicine, Nanjing 210029, China ; 3 Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 4 Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bingliang Fang
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical, Department of Laboratory Medicine, Nanjing 210029, China ; 3 Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 4 Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shiyang Pan
- 1 Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 2 National Key Clinical, Department of Laboratory Medicine, Nanjing 210029, China ; 3 Department of Radiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China ; 4 Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Hubers AJ, Heideman DAM, Burgers SA, Herder GJM, Sterk PJ, Rhodius RJ, Smit HJ, Krouwels F, Welling A, Witte BI, Duin S, Koning R, Comans EFI, Steenbergen RDM, Postmus PE, Meijer GA, Snijders PJF, Smit EF, Thunnissen E. DNA hypermethylation analysis in sputum for the diagnosis of lung cancer: training validation set approach. Br J Cancer 2015; 112:1105-13. [PMID: 25719833 PMCID: PMC4366885 DOI: 10.1038/bjc.2014.636] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 10/06/2014] [Accepted: 12/01/2014] [Indexed: 01/22/2023] Open
Abstract
Background: Lung cancer has the highest mortality of all cancers. The aim of this study was to examine DNA hypermethylation in sputum and validate its diagnostic accuracy for lung cancer. Methods: DNA hypermethylation of RASSF1A, APC, cytoglobin, 3OST2, PRDM14, FAM19A4 and PHACTR3 was analysed in sputum samples from symptomatic lung cancer patients and controls (learning set: 73 cases, 86 controls; validation set: 159 cases, 154 controls) by quantitative methylation-specific PCR. Three statistical models were used: (i) cutoff based on Youden's J index, (ii) cutoff based on fixed specificity per marker of 96% and (iii) risk classification of post-test probabilities. Results: In the learning set, approach (i) showed that RASSF1A was best able to distinguish cases from controls (sensitivity 42.5%, specificity 96.5%). RASSF1A, 3OST2 and PRDM14 combined demonstrated a sensitivity of 82.2% with a specificity of 66.3%. Approach (ii) yielded a combination rule of RASSF1A, 3OST2 and PHACTR3 (sensitivity 67.1%, specificity 89.5%). The risk model (approach iii) distributed the cases over all risk categories. All methods displayed similar and consistent results in the validation set. Conclusions: Our findings underscore the impact of DNA methylation markers in symptomatic lung cancer diagnosis. RASSF1A is validated as diagnostic marker in lung cancer.
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Affiliation(s)
- A J Hubers
- Department of Pathology, VU University Medical Center, De Boelelaan 1117, Amsterdam 1081 HV, The Netherlands
| | - D A M Heideman
- Department of Pathology, VU University Medical Center, De Boelelaan 1117, Amsterdam 1081 HV, The Netherlands
| | - S A Burgers
- Department of Thoracic Oncology, NKI-Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - G J M Herder
- Department of Pulmonary Diseases, Sint Antonius Hospital, Nieuwegein, The Netherlands
| | - P J Sterk
- Department of Pulmonary Diseases, Academic Medical Center, Amsterdam, The Netherlands
| | - R J Rhodius
- Department of Pulmonary Diseases, Academic Medical Center, Amsterdam, The Netherlands
| | - H J Smit
- Department of Pulmonary Diseases, Sint Lucas Andreas Hospital, Amsterdam, The Netherlands
| | - F Krouwels
- Department of Pulmonary Diseases, Spaarne Hospital, Hoofddorp, The Netherlands
| | - A Welling
- Department of Pulmonary Diseases, Medisch Centrum Alkmaar, Alkmaar, The Netherlands
| | - B I Witte
- Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands
| | - S Duin
- Department of Pathology, VU University Medical Center, De Boelelaan 1117, Amsterdam 1081 HV, The Netherlands
| | - R Koning
- Department of Pathology, VU University Medical Center, De Boelelaan 1117, Amsterdam 1081 HV, The Netherlands
| | - E F I Comans
- Department of Nuclear Medicine, VU University Medical Center, Amsterdam, The Netherlands
| | - R D M Steenbergen
- Department of Pathology, VU University Medical Center, De Boelelaan 1117, Amsterdam 1081 HV, The Netherlands
| | - P E Postmus
- Department of Pulmonary Diseases, VU University Medical Center, Amsterdam, The Netherlands
| | - G A Meijer
- Department of Pathology, VU University Medical Center, De Boelelaan 1117, Amsterdam 1081 HV, The Netherlands
| | - P J F Snijders
- Department of Pathology, VU University Medical Center, De Boelelaan 1117, Amsterdam 1081 HV, The Netherlands
| | - E F Smit
- Department of Pulmonary Diseases, VU University Medical Center, Amsterdam, The Netherlands
| | - E Thunnissen
- Department of Pathology, VU University Medical Center, De Boelelaan 1117, Amsterdam 1081 HV, The Netherlands
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11
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Kim Y, Kim DH. CpG island hypermethylation as a biomarker for the early detection of lung cancer. Methods Mol Biol 2015; 1238:141-171. [PMID: 25421659 DOI: 10.1007/978-1-4939-1804-1_8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Lung cancer is the most frequent cause of cancer-related deaths and causes over one million deaths worldwide each year. Despite significant strides in the diagnosis and treatment of lung cancer, the prognosis is extremely poor, with the overall 5-year survival rates still remaining around 15 %. This is largely due to occult metastatic dissemination, which appears in approximately two-thirds of patients at the time of detection. Thus, the development of efficient diagnostic methods to enable the early detection of cancer for these patients is clearly imperative.One promising approach is the identification of lung cancer-specific biomarkers at an early stage. The de novo methylation of CpG islands within the promoters of tumor suppressor genes is one of the most frequently acquired epigenetic changes during the pathogenesis of lung cancer and usually associated with transcriptional downregulation of a gene. The analysis of DNA methylation patterns in sputum, bronchial fluid, plasma, or serum could become a powerful tool for the accurate and early diagnosis of lung cancer with unparalleled specificity and sensitivity.
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Affiliation(s)
- Yujin Kim
- Department of Molecular Cell Biology, Sungkyunkwan University of School of Medicine, Suwon, 440-746, Korea
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Barrow TM, Michels KB. Epigenetic epidemiology of cancer. Biochem Biophys Res Commun 2014; 455:70-83. [PMID: 25124661 DOI: 10.1016/j.bbrc.2014.08.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 07/15/2014] [Accepted: 08/01/2014] [Indexed: 02/06/2023]
Abstract
Epigenetic epidemiology includes the study of variation in epigenetic traits and the risk of disease in populations. Its application to the field of cancer has provided insight into how lifestyle and environmental factors influence the epigenome and how epigenetic events may be involved in carcinogenesis. Furthermore, it has the potential to bring benefit to patients through the identification of diagnostic markers that enable the early detection of disease and prognostic markers that can inform upon appropriate treatment strategies. However, there are a number of challenges associated with the conduct of such studies, and with the identification of biomarkers that can be applied to the clinical setting. In this review, we delineate the challenges faced in the design of epigenetic epidemiology studies in cancer, including the suitability of blood as a surrogate tissue and the capture of genome-wide DNA methylation. We describe how epigenetic epidemiology has brought insight into risk factors associated with lung, breast, colorectal and bladder cancer and review relevant research. We discuss recent findings on the identification of epigenetic diagnostic and prognostic biomarkers for these cancers.
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Affiliation(s)
- Timothy M Barrow
- Institute for Prevention and Tumor Epidemiology, Freiburg Medical Center, University of Freiburg, 79106, Germany; German Consortium for Translational Cancer Research (DKTK), Heidelberg, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Karin B Michels
- Institute for Prevention and Tumor Epidemiology, Freiburg Medical Center, University of Freiburg, 79106, Germany; Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA.
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Hubers AJ, Brinkman P, Boksem RJ, Rhodius RJ, Witte BI, Zwinderman AH, Heideman DAM, Duin S, Koning R, Steenbergen RDM, Snijders PJF, Smit EF, Sterk PJ, Thunnissen E. Combined sputum hypermethylation and eNose analysis for lung cancer diagnosis. J Clin Pathol 2014; 67:707-11. [PMID: 24915850 DOI: 10.1136/jclinpath-2014-202414] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
AIMS The aim of this study is to explore DNA hypermethylation analysis in sputum and exhaled breath analysis for their complementary, non-invasive diagnostic capacity in lung cancer. METHODS Sputum samples and exhaled breath were prospectively collected from 20 lung cancer patients and 31 COPD controls (Set 1). An additional 18 lung cancer patients and 8 controls only collected exhaled breath as validation set (Set 2). DNA hypermethylation of biomarkers RASSF1A, cytoglobin, APC, FAM19A4, PHACTR3, 3OST2 and PRDM14 was considered, and breathprints from exhaled breath samples were created using an electronic nose (eNose). RESULTS Both DNA hypermethylation markers in sputum and eNose were independently able to distinguish lung cancer patients from controls. The combination of RASSF1A and 3OST2 hypermethylation had a sensitivity of 85% with a specificity of 74%. eNose had a sensitivity of 80% with a specificity of 48%. Sensitivity for lung cancer diagnosis increased to 100%, when RASSF1A hypermethylation was combined with eNose, with specificity of 42%. Both methods showed to be complementary to each other (p≤0.011). eNose results were reproducible in Set 2. CONCLUSIONS When used in concert, RASSF1A hypermethylation in sputum and exhaled breath analysis are complementary for lung cancer diagnosis, with 100% sensitivity in this series. This finding should be further validated.
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Affiliation(s)
- A Jasmijn Hubers
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Paul Brinkman
- Department of Respiratory Medicine, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Remco J Boksem
- Department of Respiratory Medicine, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Robert J Rhodius
- Department of Respiratory Medicine, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Birgit I Witte
- Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands
| | - Aeilko H Zwinderman
- Department of Clinical Epidemiology and Biostatistics, Academic Medical Center, Amsterdam, The Netherlands
| | | | - Sylvia Duin
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Remco Koning
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Peter J F Snijders
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Egbert F Smit
- Department of Pulmonary Diseases, VU University Medical Center, Amsterdam, The Netherlands
| | - Peter J Sterk
- Department of Respiratory Medicine, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Erik Thunnissen
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
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Hua F, Fang N, Li X, Zhu S, Zhang W, Gu J. A meta-analysis of the relationship between RARβ gene promoter methylation and non-small cell lung cancer. PLoS One 2014; 9:e96163. [PMID: 24796328 PMCID: PMC4010458 DOI: 10.1371/journal.pone.0096163] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 04/04/2014] [Indexed: 02/07/2023] Open
Abstract
Background Hypermethylation of CpG islands in tumor suppressor gene plays an important role in carcinogenesis. Many studies have demonstrated that hypermethylation in promoter region of RARβ gene could be found with high prevalence in tumor tissue and autologous controls such as corresponding non-tumor lung tissue, sputum and plasma of the NSCLC patients. But with the small number subjects included in the individual studie, the statistical power is limited. Accordingly, we performed this meta-analysis to further asses the relationship of methylation prevalence between the cancer tissue and atuologous controls (corresponding non-tumor lung tissue, sputum and plasma). Methods The published articles about RARβ gene promoter hypermethyltion were identified using a systematic search strategy in PubMed, EMBASE and CNKI databases. The pooled odds ratio (OR) of RARβ promoter methylation in lung cancer tissue versus autologous controls were calculated. Results Finally, eleven articles, including 1347 tumor tissue samples and 1137 autologous controls were included in this meta-analysis. The pooled odds ratio of RARβ promoter methylation in cancer tissue was 3.60 (95%CI: 2.46–5.27) compared to autologous controls with random-effect model. Strong and significant correlation between tumor tissue and autologous controls of RARβ gene promoter hypermethylation prevalence across studies (Correlation coefficient 0.53) was found. Conclusion RARβ promoter methylation may play an important role in carcinogenesis of the NSCLC. With significant methylation prevalence correlation between tumor tissue and autologous of this gene, methylation detection may be a potential method for searching biomarker for NSCLC.
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Affiliation(s)
- Feng Hua
- Department of surgery oncology, Shandong cancer hospital, Jinan, China
| | - Nianzhen Fang
- Tianjin Medical University General Hospital, Tianjin Lung Cancer Institute, Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin, China
| | - Xuebing Li
- Tianjin Medical University General Hospital, Tianjin Lung Cancer Institute, Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin, China
| | - Siwei Zhu
- Department of Oncology, Tianjin Union Medical Center, Tianjin, China
| | - Weisan Zhang
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin, China
- * E-mail: (J-DG); (W-SZ)
| | - Jundong Gu
- Tianjin Medical University General Hospital, Tianjin Lung Cancer Institute, Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin, China
- Department of Oncology, Tianjin Union Medical Center, Tianjin, China
- * E-mail: (J-DG); (W-SZ)
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Hubers AJ, van der Drift MA, Prinsen CFM, Witte BI, Wang Y, Shivapurkar N, Stastny V, Bolijn AS, Hol BEA, Feng Z, Dekhuijzen PNR, Gazdar AF, Thunnissen E. Methylation analysis in spontaneous sputum for lung cancer diagnosis. Lung Cancer 2014; 84:127-33. [PMID: 24598366 DOI: 10.1016/j.lungcan.2014.01.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 01/20/2014] [Accepted: 01/22/2014] [Indexed: 02/03/2023]
Abstract
OBJECTIVES Lung cancer is the most fatal cancer in the developed world due to presence of metastases at time of diagnosis. The aim of this study is to examine DNA hypermethylation in sputum compared to sputum cytology for the diagnosis of lung cancer. A novel risk analysis is introduced, using the distinction between diagnostic and risk markers. METHODS Two independent sets were randomly composed from a prospectively collected sputum bank (Set 1: n = 98 lung cancer patients, n = 90 controls; Set 2: n = 60 lung cancer patients, n = 445 controls). Sputum cytology was performed for all samples. The following DNA hypermethylation markers were tested in both sets: RASSF1A, APC and cytoglobin (CYGB). Two statistical analyses were conducted: multivariate logistic regression and a risk classification model based on post-test probabilities. RESULTS In multivariate analysis, RASSF1A was the best of the three markers in discriminating lung cancer cases from controls in both sets (sensitivity 41-52%, specificity 94-96%). The risk model showed that 36% of lung cancer patients were defined as "high risk" (≥ 60% chance on lung cancer) based on RASSF1A hypermethylation in Set 1. The model was reproducible in Set 2. Risk markers (APC, CYGB) have less diagnostic value. Sensitivity of cytology for lung cancer diagnosis was 22%. RASSF1A hypermethylation yielded a sensitivity of 45%. The combined sensitivity for RASSF1A with cytological diagnosis increased to 52% with similar specificity (94%). CONCLUSION In a diagnostic setting, hypermethylation analysis in sputum is possible when a diagnostic marker is used. However, risk markers are insufficient for this purpose.
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Affiliation(s)
- A Jasmijn Hubers
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Miep A van der Drift
- Department of Pulmonology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Clemens F M Prinsen
- Department of Pathology, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Birgit I Witte
- Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands
| | - Yinghui Wang
- Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Narayan Shivapurkar
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, USA
| | - Victor Stastny
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, USA
| | - Anne S Bolijn
- Department of Pathology, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Bernard E A Hol
- Department of Pulmonology, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Ziding Feng
- Fred Hutchinson Cancer Research Center, Seattle, USA
| | - P N Richard Dekhuijzen
- Department of Pulmonology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Adi F Gazdar
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, USA
| | - Erik Thunnissen
- Department of Pathology, Canisius-Wilhelmina Hospital, Nijmegen, The Netherlands.
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Fleischhacker M, Dietrich D, Liebenberg V, Field JK, Schmidt B. The role of DNA methylation as biomarkers in the clinical management of lung cancer. Expert Rev Respir Med 2014; 7:363-83. [DOI: 10.1586/17476348.2013.814397] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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17
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Liloglou T, Bediaga NG, Brown BR, Field JK, Davies MP. Epigenetic biomarkers in lung cancer. Cancer Lett 2014; 342:200-12. [DOI: 10.1016/j.canlet.2012.04.018] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 04/18/2012] [Accepted: 04/22/2012] [Indexed: 12/31/2022]
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Hubers AJ, Prinsen CFM, Sozzi G, Witte BI, Thunnissen E. Molecular sputum analysis for the diagnosis of lung cancer. Br J Cancer 2013; 109:530-7. [PMID: 23868001 PMCID: PMC3738145 DOI: 10.1038/bjc.2013.393] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 05/08/2013] [Accepted: 06/21/2013] [Indexed: 12/20/2022] Open
Abstract
Lung cancer is the leading cause of cancer mortality rate worldwide, mainly because of the presence of metastatic disease at the time of diagnosis. Early detection of lung cancer improves prognosis, and towards this end, large screening trials in high-risk individuals have been conducted since the past century. Despite all efforts, the need for novel (complementary) lung cancer diagnostic and screening methods still exists. In this review, we focus on the assessment of lung cancer-related biomarkers in sputum in the past decennium. Besides cytology, mutation and microRNA analysis, special attention has been paid to DNA promoter hypermethylation, of which all available literature is summarised without time restriction. A model is proposed to aid in the distinction between diagnostic and risk markers. Research on the use of sputum for non-invasive detection of early-stage lung cancer has brought new insights and advanced molecular techniques. The sputum shows a promising potential for routine diagnostic and possibly screening purposes.
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Affiliation(s)
- A J Hubers
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
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Association between P(16INK4a) promoter methylation and non-small cell lung cancer: a meta-analysis. PLoS One 2013; 8:e60107. [PMID: 23577085 PMCID: PMC3618325 DOI: 10.1371/journal.pone.0060107] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 02/21/2013] [Indexed: 12/02/2022] Open
Abstract
Background Aberrant methylation of CpG islands acquired in tumor cells in promoter regions plays an important role in carcinogenesis. Accumulated evidence demonstrates P16INK4a gene promoter hypermethylation is involved in non-small cell lung carcinoma (NSCLC), indicating it may be a potential biomarker for this disease. The aim of this study is to evaluate the frequency of P16INK4a gene promoter methylation between cancer tissue and autologous controls by summarizing published studies. Methods By searching Medline, EMBSE and CNKI databases, the open published studies about P16INK4a gene promoter methylation and NSCLC were identified using a systematic search strategy. The pooled odds of P16INK4A promoter methylation in lung cancer tissue versus autologous controls were calculated by meta-analysis method. Results Thirty-four studies, including 2 652 NSCLC patients with 5 175 samples were included in this meta-analysis. Generally, the frequency of P16INK4A promoter methylation ranged from 17% to 80% (median 44%) in the lung cancer tissue and 0 to 80% (median 15%) in the autologous controls, which indicated the methylation frequency in cancer tissue was much higher than that in autologous samples. We also find a strong and significant correlation between tumor tissue and autologous controls of P16INK4A promoter methylation frequency across studies (Correlation coefficient 0.71, 95% CI:0.51–0.83, P<0.0001). And the pooled odds ratio of P16INK4A promoter methylation in cancer tissue was 3.45 (95% CI: 2.63–4.54) compared to controls under random-effect model. Conclusion Frequency of P16INK4a promoter methylation in cancer tissue was much higher than that in autologous controls, indicating promoter methylation plays an important role in carcinogenesis of the NSCLC. Strong and significant correlation between tumor tissue and autologous samples of P16INK4A promoter methylation demonstrated a promising biomarker for NSCLC.
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20
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How Kit A, Nielsen HM, Tost J. DNA methylation based biomarkers: practical considerations and applications. Biochimie 2012; 94:2314-37. [PMID: 22847185 DOI: 10.1016/j.biochi.2012.07.014] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 07/16/2012] [Indexed: 02/06/2023]
Abstract
A biomarker is a molecular target analyzed in a qualitative or quantitative manner to detect and diagnose the presence of a disease, to predict the outcome and the response to a specific treatment allowing personalized tailoring of patient management. Biomarkers can belong to different types of biochemical molecules such as proteins, DNA, RNA or lipids, whereby protein biomarkers have been the most extensively studied and used, notably in blood-based protein quantification tests or immunohistochemistry. The rise of interest in epigenetic mechanisms has allowed the identification of a new type of biomarker, DNA methylation, which is of great potential for many applications. This stable and heritable covalent modification mostly affects cytosines in the context of a CpG dinucleotide in humans. It can be detected and quantified by a number of technologies including genome-wide screening methods as well as locus- or gene-specific high-resolution analysis in different types of samples such as frozen tissues and FFPE samples, but also in body fluids such as urine, plasma, and serum obtained through non-invasive procedures. In some cases, DNA methylation based biomarkers have proven to be more specific and sensitive than commonly used protein biomarkers, which could clearly justify their use in clinics. However, very few of them are at the moment used in clinics and even less commercial tests are currently available. The objective of this review is to discuss the advantages of DNA methylation as a biomarker, the practical considerations for their development, and their use in disease detection, prediction of outcome or treatment response, through multiple examples mainly focusing on cancer, but also to evoke their potential for complex diseases and prenatal diagnostics.
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Affiliation(s)
- Alexandre How Kit
- Laboratory for Functional Genomics, Fondation Jean Dausset - CEPH, 27 rue Juliette Dodu, 75010 Paris, France
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Scesnaite A, Jarmalaite S, Mutanen P, Anttila S, Nyberg F, Benhamou S, Boffetta P, Husgafvel-Pursiainen K. Similar DNA methylation pattern in lung tumours from smokers and never-smokers with second-hand tobacco smoke exposure. Mutagenesis 2012; 27:423-9. [PMID: 22217548 DOI: 10.1093/mutage/ger092] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Tobacco smoke causes lung cancer in smokers and in never-smokers exposed to second-hand tobacco smoke (SHS). Nonetheless, molecular mechanisms of lung cancer in SHS-exposed never-smokers are still elusive. We studied lung cancers from current smokers (n = 109), former smokers (n = 56) and never-smokers (n = 47) for promoter hypermethylation of five tumour suppressor genes--p16, RARB, RASSF1, MGMT and DAPK1--using methylation-specific polymerase chain reaction. Lung tumours from ever-smokers suggested an increased risk of p16 hypermethylation as compared to never-smokers (P = 0.073), with former smokers having the highest frequency of p16 hypermethylation (P = 0.044 versus current smokers and P = 0.009 versus never-smokers). In the never-smoking group, p16 hypermethylation was seen in lung tumours from SHS-exposed individuals (4/33; 12%) but in none of the non-exposed individuals (0/9). The overall occurrence of hypermethylation (measured both as methylation index and as number of genes affected) was similar in those ever exposed to tobacco smoke (smokers, SHS-exposed never-smokers) and differed from non-exposed never-smokers. In multivariate analysis, p16 hypermethylation was more prevalent in lung tumours from male than female patients (P = 0.018) and in squamous cell carcinomas than in adenocarcinomas (P = 0.025). Occurrence of TP53 mutation in the tumour was associated with hypermethylation of at least one gene (P = 0.027). In all, our data suggest that promoter hypermethylation pattern in SHS-exposed never-smokers resembles that observed in smokers. Association between TP53 mutation, a hallmark of smokers' lung cancer, and methylation of one or more of the lung cancer-related genes studied, provides further evidence for common tobacco smoke-related origin for both types of molecular alterations.
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Affiliation(s)
- Asta Scesnaite
- Faculty of Natural Sciences, Vilnius University, Ciurlionio 21, LT03101 Vilnius, Lithuania
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Sun W, Zaboli D, Wang H, Liu Y, Arnaoutakis D, Khan T, Khan Z, Koch W, Califano JA. Detection of TIMP3 promoter hypermethylation in salivary rinse as an independent predictor of local recurrence-free survival in head and neck cancer. Clin Cancer Res 2012; 18:1082-91. [PMID: 22228635 PMCID: PMC3288549 DOI: 10.1158/1078-0432.ccr-11-2392] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
PURPOSE To validate a panel of methylation-based salivary rinse biomarkers (P16, CCNA1, DCC, TIMP3, MGMT, DAPK, and MINT31) previously shown to be independently associated with poor overall survival and local recurrence in a larger, separate cohort of patients with head and neck squamous cell carcinoma (HNSCC). EXPERIMENTAL DESIGN One hundred ninety-seven patients were included. All pretreatment saliva DNA samples were evaluated for the methylation status of the gene promoters by quantitative methylation-specific PCR. The main outcome measures were overall survival, local recurrence-free survival, and disease-free survival. RESULTS In univariate analyses, the detection of hypermethylation of CCNA1, MGMT, and MINT31 was significantly associated with poor overall survival; the detection of hypermethylation of TIMP3 was significantly associated with local recurrence-free survival; and the detection of hypermethylation of MINT31 was significantly associated with poor disease-free survival. In multivariate analyses, detection of hypermethylation at any single marker was not predictive of overall survival in patients with HNSCC; detection of hypermethylation of TIMP3 in salivary rinse had an independent, significant association with local recurrence-free survival (HR = 2.51; 95% CI: 1.10-5.68); and none of the studied markers was significantly associated with disease-free survival. CONCLUSION The detection of promoter hypermethylation of the seven genes in salivary rinse as an independent prognostic indicator of overall survival in patients with HNSCC was not validated. Detection of promoter hypermethylation of TIMP3 in pretreatment salivary rinse is independently associated with local recurrence-free survival in patients with HNSCC and may be a valuable salivary rinse biomarker for HNSCC recurrence.
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Affiliation(s)
- Wenyue Sun
- Department of Otolaryngology-Head and Neck Surgery, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - David Zaboli
- Department of Otolaryngology-Head and Neck Surgery, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Hao Wang
- Division of Oncology Biostatistics, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Yan Liu
- Department of Surgery, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Demetri Arnaoutakis
- Department of Otolaryngology-Head and Neck Surgery, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Tanbir Khan
- Department of Otolaryngology-Head and Neck Surgery, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Zubair Khan
- Department of Otolaryngology-Head and Neck Surgery, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Wayne Koch
- Department of Otolaryngology-Head and Neck Surgery, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Joseph A. Califano
- Department of Otolaryngology-Head and Neck Surgery, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins Medical Institutions, Baltimore, Maryland
- Milton J. Dance Head and Neck Center, Greater Baltimore Medical Center, Baltimore, Maryland
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Hwang SH, Kim KU, Kim JE, Kim HH, Lee MK, Lee CH, Lee SY, Oh T, An S. Detection of HOXA9 gene methylation in tumor tissues and induced sputum samples from primary lung cancer patients. Clin Chem Lab Med 2011; 49:699-704. [PMID: 21480815 DOI: 10.1515/cclm.2011.108] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
BACKGROUND Lung cancer is a leading cause of cancer deaths. Unfortunately, no effective early screening modality exists for lung cancer. We aimed to evaluate the prevalence of HOXA9 promoter methylation in tissue and induced sputum samples from Korean patients with lung cancer. METHODS Using pyrosequencing, HOXA9 methylation was analyzed for 40 pairs of primary lung cancer and normal tissues and 185 induced sputum specimens, including 76 patients with lung cancer. RESULTS The methylation of HOXA9 in lung cancer tissue was significantly higher compared with normal tissues (67.4% ± 17.6% vs. 23.6% ± 10.3%, respectively; p<0.001). With a cut-off of >45.6% of HOXA9 gene methylation in tissues, the sensitivity was 90.5% and the specificity was 97.5%. In induced sputum specimens, the HOXA9 gene in lung cancer patients was significantly more hypermethylated compared with patients with benign lung diseases and the healthy group (23.4% ± 15.9%, 14.9% ± 7.9%, and 9.7% ± 5.0%, respectively; p<0.001). CONCLUSIONS The HOXA9 gene was hypermethylated in 32 of 40 tumors (80%), especially in early stages of lung cancer. HOXA9 methylation could be a potential biomarker to aid early detection and prognosis.
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Affiliation(s)
- Sang-Hyun Hwang
- Department of Laboratory Medicine, Pusan National University Hospital, School of Medicine Pusan National University, Busan, Republic of Korea
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Begum S, Brait M, Dasgupta S, Ostrow KL, Zahurak M, Carvalho AL, Califano JA, Goodman SN, Westra WH, Hoque MO, Sidransky D. An epigenetic marker panel for detection of lung cancer using cell-free serum DNA. Clin Cancer Res 2011; 17:4494-503. [PMID: 21610147 DOI: 10.1158/1078-0432.ccr-10-3436] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
PURPOSE We investigated the feasibility of detecting aberrant DNA methylation of some novel and known genes in the serum of lung cancer patients. EXPERIMENTAL DESIGN To determine the analytic sensitivity, we examined the tumor and the matched serum DNA for aberrant methylation of 15 gene promoters from 10 patients with primary lung tumors by using quantitative methylation-specific PCR. We then tested this 15-gene set to identify the more useful DNA methylation changes in the serum of a limited number of lung cancer patients and controls. In an independent set, we tested the six most promising genes (APC, CDH1, MGMT, DCC, RASSF1A, and AIM1) for further elucidation of the diagnostic application of this panel of markers. RESULTS Promoter hypermethylation of at least one of the genes studied was detected in all 10 lung primary tumors. In majority of cases, aberrant methylation in serum DNA was accompanied by methylation in the matched tumor samples. In the independent set, using a single gene that had 100% specificity (DCC), 35.5% (95% CI: 25-47) of the 76 lung cancer patients were correctly identified. For patients without methylated DCC, addition of a logistic regression score that was based on the five remaining genes improved sensitivity from 35.5% to 75% (95% CI: 64-84) but decreased the specificity from 100% to 73% (95% CI: 54-88). CONCLUSION This approach needs to be evaluated in a larger test set to determine the role of this gene set in early detection and surveillance of lung cancer.
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Affiliation(s)
- Shahnaz Begum
- Department of Otolaryngology and Head and Neck Surgery, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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Ma YT, Collins SI, Young LS, Murray PG, Woodman CBJ. Smoking initiation is followed by the early acquisition of epigenetic change in cervical epithelium: a longitudinal study. Br J Cancer 2011; 104:1500-4. [PMID: 21487403 PMCID: PMC3101930 DOI: 10.1038/bjc.2011.113] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND To prove a causal link between an epigenetic change and an environmental or behavioural risk factor for a given disease, it is first necessary to show that the onset of exposure precedes the first detection of that epigenetic change in subjects who are still free of disease. METHODS Towards this end, a cohort of women aged 15-19 years, recruited soon after they first had sexual intercourse, were used to provide sequential observations on the relationship between cigarette smoking and the detection in cervical cytological samples of methylated forms of CDKN2A (p16) using nested methylation-specific polymerase chain reaction. RESULTS Among women who remained cytologically normal and who tested negative for human papillomavirus DNA in cervical smears during follow-up, those who first started to smoke during follow-up had an increased risk of acquiring CDKN2A methylation compared with never-smokers (odds ratio=3.67; 95% confidence interval 1.09-12.33; P=0.04). CONCLUSION Smoking initiation is associated with the appearance of methylated forms of CDKN2A.
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Affiliation(s)
- Y T Ma
- Cancer Research UK Institute for Cancer Studies, School of Cancer Sciences, University of Birmingham, Birmingham, Edgbaston, B15 2TT, UK
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Hypermethylation of CCND2 May Reflect a Smoking-Induced Precancerous Change in the Lung. JOURNAL OF ONCOLOGY 2011; 2011:950140. [PMID: 21577262 PMCID: PMC3090638 DOI: 10.1155/2011/950140] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 01/12/2011] [Accepted: 01/26/2011] [Indexed: 11/25/2022]
Abstract
It remains unknown whether tobacco smoke induces DNA hypermethylation as an early event in carcinogenesis or as a late event, specific to overt cancer tissue. Using MethyLight assays, we analyzed 316 lung tissue samples from 151 cancer-free subjects (121 ever-smokers and 30 never-smokers) for hypermethylation of 19 genes previously observed to be hypermethylated in nonsmall cell lung cancers. Only APC (39%), CCND2 (21%), CDH1 (7%), and RARB (4%) were hypermethylated in >2% of these cancer-free subjects. CCND2 was hypermethylated more frequently in ever-smokers (26%) than in never-smokers (3%). CCND2 hypermethylation was also associated with increased age and upper lobe sample location. APC was frequently hypermethylated in both ever-smokers (41%) and never-smokers (30%). BVES, CDH13, CDKN2A (p16), CDKN2B, DAPK1, IGFBP3, IGSF4, KCNH5, KCNH8, MGMT, OPCML, PCSK6, RASSF1, RUNX, and TMS1 were rarely hypermethylated (<2%) in all subjects. Hypermethylation of CCND2 may reflect a smoking-induced precancerous change in the lung.
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Ostrow KL, Hoque MO, Loyo M, Brait M, Greenberg A, Siegfried JM, Grandis JR, Gaither Davis A, Bigbee WL, Rom W, Sidransky D. Molecular analysis of plasma DNA for the early detection of lung cancer by quantitative methylation-specific PCR. Clin Cancer Res 2010; 16:3463-72. [PMID: 20592015 DOI: 10.1158/1078-0432.ccr-09-3304] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
PURPOSE Aberrant promoter hypermethylation of tumor suppressor genes is a promising marker for lung cancer detection. We investigated the likelihood of detecting aberrant DNA methylation of tumor suppressor genes in plasma samples of patients with abnormalities of the lung detected upon computed tomography (CT) scan. EXPERIMENTAL DESIGN In a small evaluation cohort, four gene promoters (DCC, Kif1a, NISCH, and Rarb) were found to be methylated with increased frequency in samples from cancer patients specifically. We then examined DNA from 93 plasma samples from patients with abnormal findings in the lung detected upon CT scan for aberrant methylation of these four gene promoters by quantitative fluorogenic real-time PCR. The patients were divided into two groups, ground glass opacity (n = 23) and cancerous tumors (n = 70). Plasma DNA from age-matched nodule-free individuals were used as controls (n = 80). RESULTS In plasma, 73% of patients with cancerous tumors showed methylation of at least one gene with a specificity of 71% (P = 0.0001). Only 22% patients with ground glass opacity exhibited methylation of at least one gene. When smoking history was taken into account, 72% of cancer patients with no smoking history or those who smoked <20 pack-years showed methylation of at least one gene with 100% specificity (P = 0.05) when compared with matched controls. Among heavy smokers with 20+ pack-years of smoking history, 30% of the control group and 73% of the patients with cancerous tumors showed methylation (P = 0.0001). CONCLUSIONS These biomarkers can distinguish between cancerous and noncancerous abnormal CT findings.
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Affiliation(s)
- Kimberly Laskie Ostrow
- Department of Otolaryngology-Head and Neck Cancer Research Division, Johns Hopkins School of Medicine, Baltimore, Maryland 21231, USA
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Tessema M, Klinge DM, Yingling CM, Do K, Van Neste L, Belinsky SA. Re-expression of CXCL14, a common target for epigenetic silencing in lung cancer, induces tumor necrosis. Oncogene 2010; 29:5159-70. [PMID: 20562917 PMCID: PMC2940978 DOI: 10.1038/onc.2010.255] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Chemokines are important regulators of directional cell migration and tumor metastasis. A genome-wide transcriptome array designed to uncover novel genes silenced by methylation in lung cancer identified the CXC-subfamily of chemokines. Expression of eleven of the sixteen known human CXC-chemokines was increased in lung adenocarcinoma cell lines after treatment with 5-aza-2deoxycytidine (DAC). Tumor-specific methylation leading to silencing of CXCL5, 12 and 14 was found in over 75% of primary lung adenocarcinomas and DAC treatment restored expression of each silenced gene. Forced expression of CXCL14 in H23 cells where this gene is silenced by methylation increased cell death in vitro and dramatically reduced in vivo growth of lung tumor xenografts through necrosis of up to 90% of the tumor mass. CXCL14 re-expression had a profound effect on the genome altering the transcription of over 1,000 genes, including increased expression of 30 cell cycle inhibitor and pro-apoptosis genes. In addition, CXCL14 methylation in sputum from asymptomatic early stage lung cancer cases was associated with a 2.9-fold elevated risk for this disease compared to controls, substantiating its potential as a biomarker for early detection of lung cancer. Together these findings identify CXCL14 as an important tumor suppressor gene epigenetically silenced during lung carcinogenesis.
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Affiliation(s)
- M Tessema
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
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Anglim PP, Alonzo TA, Laird-Offringa IA. DNA methylation-based biomarkers for early detection of non-small cell lung cancer: an update. Mol Cancer 2008; 7:81. [PMID: 18947422 PMCID: PMC2585582 DOI: 10.1186/1476-4598-7-81] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Accepted: 10/23/2008] [Indexed: 12/19/2022] Open
Abstract
Lung cancer is the number one cancer killer in the United States. This disease is clinically divided into two sub-types, small cell lung cancer, (10–15% of lung cancer cases), and non-small cell lung cancer (NSCLC; 85–90% of cases). Early detection of NSCLC, which is the more common and less aggressive of the two sub-types, has the highest potential for saving lives. As yet, no routine screening method that enables early detection exists, and this is a key factor in the high mortality rate of this disease. Imaging and cytology-based screening strategies have been employed for early detection, and while some are sensitive, none have been demonstrated to reduce lung cancer mortality. However, mortality might be reduced by developing specific molecular markers that can complement imaging techniques. DNA methylation has emerged as a highly promising biomarker and is being actively studied in multiple cancers. The analysis of DNA methylation-based biomarkers is rapidly advancing, and a large number of potential biomarkers have been identified. Here we present a detailed review of the literature, focusing on DNA methylation-based markers developed using primary NSCLC tissue. Viable markers for clinical diagnosis must be detectable in 'remote media' such as blood, sputum, bronchoalveolar lavage, or even exhaled breath condensate. We discuss progress on their detection in such media and the sensitivity and specificity of the molecular marker panels identified to date. Lastly, we look to future advancements that will be made possible with the interrogation of the epigenome.
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Affiliation(s)
- Paul P Anglim
- Departments of Surgery and of Biochemistry and Molecular Biology, Keck School of Medicine, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90089-9176, USA.
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Baryshnikova E, Destro A, Infante MV, Cavuto S, Cariboni U, Alloisio M, Ceresoli GL, Lutman R, Brambilla G, Chiesa G, Ravasi G, Roncalli M. Molecular alterations in spontaneous sputum of cancer-free heavy smokers: results from a large screening program. Clin Cancer Res 2008; 14:1913-9. [PMID: 18347195 DOI: 10.1158/1078-0432.ccr-07-1741] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE The high mortality rate for lung cancer is likely to be reduced by the development of a panel of sensitive biological markers able to identify early-stage lung cancers or subjects at high risk. The aim of this study was to establish the frequency of K-ras and p53 mutations and p16(INK4A), RASSF1A, and NORE1A hypermethylation in sputum of a large cohort of cancer-free heavy smokers and to assess whether these markers are suitable for a routine use in the clinical practice for the early diagnosis of pulmonary cancer. EXPERIMENTAL DESIGN Sputum samples were collected from 820 heavy smokers. Inclusion criteria consisted of radiologic and cytologic absence of pulmonary lesions, age at least 60 years, male gender, and a smoking history of at least 20 pack-years. RESULTS The analysis identified 56 individuals (6.9%) with one molecular alteration. p53 mutation and p16(INK4A), RASSF1A, and NORE1A methylation frequencies were 1.9%, 5.1%, 0.8%, and 1.0%, respectively; no K-ras mutations were found. One patient with p53 mutations was diagnosed with an early-stage lung cancer after 3-years of follow-up. The molecular analysis of bronchoscopy samples confirmed in half of the cases alterations present in sputum without revealing additional molecular changes. CONCLUSIONS Genetic and epigenetic abnormalities can be detected in cancer-free heavy smokers. Although the predictive value of the cancer risk is still to be established as it requires not less than 5 years of follow-up, p53 and p16(INK4A) are more promising candidates than K-ras, RASSF1A, and NORE1A for the pulmonary molecular screening of heavy smokers healthy individuals.
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van der Drift MA, Prinsen CFM, Hol BEA, Bolijn AS, Jeunink MAF, Dekhuijzen PNR, Thunnissen FBJM. Can free DNA be detected in sputum of lung cancer patients? Lung Cancer 2008; 61:385-90. [PMID: 18313165 DOI: 10.1016/j.lungcan.2008.01.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2007] [Revised: 12/24/2007] [Accepted: 01/12/2008] [Indexed: 11/28/2022]
Abstract
SUMMARY Free DNA is present in the serum of cancer patients in a higher concentration than that in non-cancer patients. Free DNA in sputum may originate from malignant or inflammatory diseases. The aim of the study was to examine the presence of free DNA in sputum and the relationship to lung cancer. The contribution of inflammatory cells was established as well. The amount of free and cellular DNA in sputum was determined using real-time beta-globin PCR in 28 lung cancer patients and 68 controls. Free DNA was present in sputum samples of the cancer patients and controls. We found no differences in DNA concentration in sputum of patients with and without lung cancer. For all patients combined the amount of free DNA was related to the amount of inflammation. Further, we found increased hypermethylation of RASSF1A in lung cancer patients compared to controls to show that tumour related DNA is present in sputum. In conclusion, free DNA can be detected in sputum of lung cancer patients. The amount of free DNA is related to the amount of inflammation, but not to the presence of lung cancer.
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Affiliation(s)
- M A van der Drift
- Department of Pulmonology, Radboud University Nijmegen Medical Centre, Nijmegen, Dekkerswald, Groesbeek, The Netherlands.
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Hsu HS, Chen TP, Wen CK, Hung CH, Chen CY, Chen JT, Wang YC. Multiple genetic and epigenetic biomarkers for lung cancer detection in cytologically negative sputum and a nested case-control study for risk assessment. J Pathol 2008; 213:412-9. [PMID: 17973238 DOI: 10.1002/path.2246] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The purpose of this study was to define a biomarker panel for detection of cancer cells in cytologically negative sputum and to evaluate the panel for assessment of lung cancer risk. We examined 19 genetic and epigenetic markers using a sensitive fluorescence-based method in cytologically negative sputum and in lung tumour tissues from 82 lung cancer patients. We also used these markers to test the sputum of 37 cancer-free individuals who were matched by age, sex, and smoking habit. Based on the concordance of biomarkers in lung tumours and corresponding sputum, and the low prevalence in cancer-free individuals, we selected seven markers for a nested case-control study: microsatellite instability of D9S942; loss of heterozygosity of D9S286, D9S942, GATA49D12, and D13S170; and methylation of p16INK4a and RARbeta. Based on the assumption that a lung cancer cell has alterations in two or more of the seven biomarkers, we compared the pattern of biomarker alteration in lung tumours and corresponding sputum. Our comparison yielded a sensitivity of 82%, specificity of 75%, and concordance of 79%. Three cancer-free individuals were considered to have an elevated risk based on the criterion that their sputum showed alteration in two of the seven biomarkers. One individual was indeed diagnosed as having lung cancer 18 months after sputum collection. In the nested case-control study, six biomarkers showed significantly increased odds ratios ranging from 3.14 to 11.24. Our study defines a biomarker panel for detection of cancer cells in cytologically negative sputum and verifies its use for risk assessment of lung cancer. In combination with conventional diagnostic tools, this multiple genetic and epigenetic panel should improve the detection or risk assessment of lung cancer.
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Affiliation(s)
- H-S Hsu
- Division of Thoracic Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
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The impact of genetic markers on the diagnosis of lung cancer: a current perspective. J Thorac Oncol 2008; 2:1044-51. [PMID: 17975498 DOI: 10.1097/jto.0b013e318158eed4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Lung cancer is the leading worldwide source of cancer-related death. It is acknowledged that prognosis and treatment outcomes in lung cancer might be improved by increasing the effectiveness of early-stage diagnosis. Several recently published studies have produced intriguing results regarding the detection of biomarkers in tumor samples, but also in easily accessible specimens such as sputum, plasma, and exhaled breath condensate. This review presents advances in genetic diagnostics of lung cancer, with particular reference to the clinical usefulness of individual biomarkers, specimens, and methods. The adequacy of their sensitivity and specificity for cancer screening and early detection is discussed in detail.
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Aberrant p16 promoter methylation among Greek lung cancer patients and smokers: correlation with smoking. Eur J Cancer Prev 2007; 16:396-402. [PMID: 17923809 DOI: 10.1097/01.cej.0000236260.26265.d6] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Genetic and environmental factors (dietary and smoking) influence lung cancer epidemiology and induce epigenetic modifications that should be assessed in individual populations. We analyzed p16 methylation among Greek non-small cell lung carcinoma patients and smokers using two-stage methylation-specific polymerase chain reaction. One hundred and fifty specimens from cancerous and adjacent non-cancerous tissue, bronchial washings and sputum from patients and 48 specimens, mostly sputum, from disease-free smokers were included. p16 methylation was very frequent in biopsies (82.85%) and bronchial washings (non-small cell lung carcinoma, 80.35%; small cell lung carcinoma, 16.66%) from patients, but also in adjacent non-cancerous tissue (45.71%). Concordance of p16 methylation and positivity by cytological examination was 51.78%. Methylation was also observed in sputum from asymptomatic cytology-negative smokers (22.5%) and chronic obstructive pulmonary disease patients (three of eight). Among disease-free individuals, methylation correlated only with heavy smoking (>50 pack-years, P<0.001) and differed among male and female disease-free smokers. In summary, p16 methylation is very frequent among non-small cell lung carcinoma patients, and correlates with heavy cigarette consumption only in disease-free smokers.
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Feng Q, Yu M, Kiviat NB. Molecular biomarkers for cancer detection in blood and bodily fluids. Crit Rev Clin Lab Sci 2007; 43:497-560. [PMID: 17050080 DOI: 10.1080/10408360600922632] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cancer is a major and increasing public health problem worldwide. Traditionally, the diagnosis and staging of cancer, as well as the evaluation of response to therapy have been primarily based on morphology, with relatively few cancer biomarkers currently in use. Conventional biomarker studies have been focused on single genes or discrete pathways, but this approach has had limited success because of the complex and heterogeneous nature of many cancers. The completion of the human genome project and the development of new technologies have greatly facilitated the identification of biomarkers for assessment of cancer risk, early detection of primary cancers, monitoring cancer treatment, and detection of recurrence. This article reviews the various approaches used for development of such markers and describes markers of potential clinical interest in major types of cancer. Finally, we discuss the reasons why so few cancer biomarkers are currently available for clinical use.
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Affiliation(s)
- Qinghua Feng
- Department of Pathology, School of Medicine, University of Washington, Seattle, Washington 98109, USA.
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