1
|
Vaidyanathan A, Mathew M, Radhakrishnan S, Rout CS, Chakraborty B. Theoretical Insight on the Biosensing Applications of 2D Materials. J Phys Chem B 2020; 124:11098-11122. [PMID: 33232607 DOI: 10.1021/acs.jpcb.0c08539] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The research on the design of efficient, reliable, and cost-effective biosensors is expanding given its high demand in various fields such as health care, environmental surveillance, agriculture, diagnostics, industries, and so forth. In the last decade, various fascinating and interesting 2D materials with extraordinary properties have been experimentally synthesized and theoretically predicted. 2D materials have been explored for the sensing of different biomolecules because of their large surface area and strong interaction with different biomolecules. Theoretical simulations can bring important insight on the interaction of biomolecules on 2D materials, charge transfer, orbital interactions, and so forth and may play an important role in the development of efficient biosensors. Quantum simulation techniques, such as density functional theory (DFT), are very powerful and are gaining popularity especially with the advent of high-speed computing facilities. This review article provides theoretical insight regarding the interaction of various biomolecules on different 2D materials and the charge transfer between the biomolecules and 2D materials leading to electrochemical signals, which can then provide experimentalists the useful design parameters for fabrication of biosensors. It also includes an overview of quantum simulations, use of the DFT method for simulating biomolecules on 2D materials, parameters obtained from theoretical simulations and sensitivity, and limitations of computational techniques for sensing biomolecules on 2D materials. Furthermore, this review summarizes the recent work in first-principles investigation of 2D materials for the purpose of biomolecule sensing. Beyond the traditional graphene or 2D transition-metal dichalcogenides, some novel and recently proposed 2D materials such as pentagraphene, haeckelite, MXenes, and so forth which have exhibited good sensing applications have also been highlighted.
Collapse
Affiliation(s)
- Antara Vaidyanathan
- Department of Chemistry, Ramnarain Ruia Autonomous College, Matunga, Mumbai 400019, India
| | - Minu Mathew
- Centre for Nano and Material Science, Jain University, Jain Global Campus, Jakkasandra, Ramanagara, Bangalore 562112, India
| | - Sithara Radhakrishnan
- Centre for Nano and Material Science, Jain University, Jain Global Campus, Jakkasandra, Ramanagara, Bangalore 562112, India
| | - Chandra Sekhar Rout
- Centre for Nano and Material Science, Jain University, Jain Global Campus, Jakkasandra, Ramanagara, Bangalore 562112, India
| | - Brahmananda Chakraborty
- High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India.,Homi Bhabha National Institute, Mumbai 400094, India
| |
Collapse
|
2
|
Liu Y, Feng Y, Hou T, Lizaso A, Xu F, Xing P, Wang H, Kang Q, Zhang L, Shi Y, Hu X. Investigation on the potential of circulating tumor DNA methylation patterns as prognostic biomarkers for lung squamous cell carcinoma. Transl Lung Cancer Res 2020; 9:2356-2366. [PMID: 33489798 PMCID: PMC7815356 DOI: 10.21037/tlcr-20-1070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Background Aberrant epigenetic modifications play a key role in lung tumorigenesis. In our study, we aimed to explore the clinical implications of baseline circulating tumor DNA (ctDNA) somatic and methylation profiles in patients with lung squamous cell carcinoma (LUSC). Methods A total of 26 patients with LUSC of various stages were included in this study. Somatic mutations and methylation levels were profiled from the plasma-derived ctDNA obtained at the time of diagnosis using unique molecular identifier (UMI)-based targeted sequencing and bisulfite sequencing, respectively. The correlation between baseline ctDNA mutation and methylation profile, and overall survival (OS), were analyzed. Results Somatic mutations were detected in 80.8% (20/26) of the patients. Patients harboring somatic mutations with maximum allelic fraction (maxAF) of >5% had significantly shorter OS compared to those with maxAF ≤5% (7.1 vs. 54.6 months; P=0.020). ctDNA methylation level was found to be strongly correlated with maxAF (Pearson correlation =0.934; P<0.001). Consistent with maxAF, higher methylation levels were also associated with poorer OS (hazard ratio =2.377; 95% CI: 1.283–4.405; P=0.006). Moreover, a total of 1,956 ctDNA methylation blocks were differentially methylated in patients with maxAF >0 (P<0.05). Least absolute shrinkage and selection operator (LASSO) regression analysis revealed a significant correlation between methylation signatures from 5 methylation blocks and OS (hazard ratio =183.20, 95% CI: 2.74–12,243.32; P=0.015). These 5 methylation blocks could serve as an alternative to maxAF and can be explored as prognostic biomarkers. Conclusions Our study identified several ctDNA methylation blocks that can potentially predict the prognosis of LUSC at the time of diagnosis.
Collapse
Affiliation(s)
- Yutao Liu
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yu Feng
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ting Hou
- Burning Rock Biotech, Guangzhou, China
| | | | - Feng Xu
- Burning Rock Biotech, Guangzhou, China
| | - Puyuan Xing
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hongyu Wang
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | | | - Lu Zhang
- Burning Rock Biotech, Guangzhou, China
| | - Yuankai Shi
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xingsheng Hu
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| |
Collapse
|
3
|
Tan X, Zhang S, Gao H, He W, Xu M, Wu Q, Ni X, Jiang H. Hypermethylation of the PTTG1IP promoter leads to low expression in early-stage non-small cell lung cancer. Oncol Lett 2019; 18:1278-1286. [PMID: 31423188 PMCID: PMC6607221 DOI: 10.3892/ol.2019.10400] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 04/15/2019] [Indexed: 12/25/2022] Open
Abstract
Despite the clinical requirement for early diagnosis, the early events in lung cancer and their mechanisms are not fully understood. Pituitary tumor transforming gene 1 binding factor (PTTG1IP) is a tumor-associated gene; however, to the best of our knowledge, its association with lung cancer has not been reported. The present study analyzed PTTG1IP expression in early-stage non-small cell lung cancer (NSCLC) samples and investigated its epigenetic regulatory mechanisms. The results revealed that the mRNA level of PTTG1IP in NSCLC tissues was significantly downregulated by 43% compared with that in adjacent tissues. In addition, overexpression of this gene significantly inhibited cell proliferation. According to data from The Cancer Genome Atlas, a significant negative correlation was identified between the PTTG1IP gene methylation level and expression level in lung adenocarcinoma and lung squamous cell carcinoma cases. Reduced representation bisulfite sequencing (RRBS) analysis of six paired early-stage NSCLC tissue samples indicated that the CpG island shore of the PTTG1IP promoter is hypermethylated in lung cancer tissues, which was further validated in 12 paired early-stage NSCLC samples via bisulfite amplicon sequencing. Following treatment with 5-aza-2′-deoxycytidine to reduce DNA methylation in the promoter region, the PTTG1IP mRNA level increased, indicating that the PTTG1IP promoter DNA methylation level negatively regulates PTTG1IP transcription. In conclusion, in early-stage NSCLC, the PTTG1IP gene is regulated by DNA methylation in its promoter region, which may participate in the development and progression of lung cancer.
Collapse
Affiliation(s)
- Xiaoming Tan
- Department of Respiratory Disease, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, P.R. China
| | - Sufen Zhang
- NHC Key Laboratory of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai 200032, P.R. China
| | - Huifang Gao
- NHC Key Laboratory of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai 200032, P.R. China
| | - Wanhong He
- NHC Key Laboratory of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai 200032, P.R. China
| | - Minjie Xu
- NHC Key Laboratory of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai 200032, P.R. China
| | - Qihan Wu
- NHC Key Laboratory of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai 200032, P.R. China
| | - Xiaohua Ni
- NHC Key Laboratory of Reproduction Regulation, Shanghai Institute of Planned Parenthood Research, Fudan University, Shanghai 200032, P.R. China
| | - Handong Jiang
- Department of Respiratory Disease, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, P.R. China
| |
Collapse
|
4
|
Li L, Fu K, Zhou W, Snyder M. Applying circulating tumor DNA methylation in the diagnosis of lung cancer. PRECISION CLINICAL MEDICINE 2019; 2:45-56. [PMID: 35694699 PMCID: PMC8985769 DOI: 10.1093/pcmedi/pbz003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/17/2019] [Accepted: 03/14/2019] [Indexed: 02/05/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide. Low dose computed tomography (LDCT) is commonly used for disease screening, with identified candidate cancerous regions further diagnosed using tissue biopsy. However, existing techniques are all invasive and unavoidably cause multiple complications. In contrast, liquid biopsy is a noninvasive, ideal surrogate for tissue biopsy that can identify circulating tumor DNA (ctDNA) containing tumorigenic signatures. It has been successfully implemented to assist treatment decisions and disease outcome prediction. ctDNA methylation, a type of lipid biopsy that profiles critical epigenetic alterations occurring during carcinogenesis, has gained increasing attention. Indeed, aberrant ctDNA methylation occurs at early stages in lung malignancy and therefore can be used as an alternative for the early diagnosis of lung cancer. In this review, we give a brief synopsis of the biological basis and detecting techniques of ctDNA methylation. We then summarize the latest progress in use of ctDNA methylation as a diagnosis biomarker. Lastly, we discuss the major issues that limit application of ctDNA methylation in the clinic, and propose possible solutions to enhance its usage.
Collapse
Affiliation(s)
- Lei Li
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, USA
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, 37 Guoxuexiang, Chengdu, China
| | - Kai Fu
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, USA
| | - Wenyu Zhou
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, USA
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, USA
| |
Collapse
|
5
|
Franczak C, Filhine-Tresarrieu P, Gilson P, Merlin JL, Au L, Harlé A. Technical considerations for circulating tumor DNA detection in oncology. Expert Rev Mol Diagn 2019; 19:121-135. [DOI: 10.1080/14737159.2019.1568873] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Claire Franczak
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Vandoeuvre les Nancy, France
| | | | - Pauline Gilson
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Université de Lorraine, CNRS UMR 7039 CRAN, Nancy, France
| | - Jean-Louis Merlin
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Université de Lorraine, CNRS UMR 7039 CRAN, Nancy, France
| | - Lewis Au
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Alexandre Harlé
- Service de Biopathologie, Institut de Cancérologie de Lorraine, Université de Lorraine, CNRS UMR 7039 CRAN, Nancy, France
| |
Collapse
|
6
|
Abstract
Cell-free DNA can be evaluated for the epigenetic component. Epigenetic alterations consist of changes in gene functions that do not involve changes in DNA sequence. The mainly studied epigenetic alteration is DNA methylation occurring at CpG islands in the promoter regions for which several literature data showed clinical relevance. This chapter is an overview of the epigenetic alterations detected in cell-free DNA.
Collapse
|
7
|
|
8
|
Roointan A, Ahmad Mir T, Ibrahim Wani S, Mati-Ur-Rehman, Hussain KK, Ahmed B, Abrahim S, Savardashtaki A, Gandomani G, Gandomani M, Chinnappan R, Akhtar MH. Early detection of lung cancer biomarkers through biosensor technology: A review. J Pharm Biomed Anal 2018; 164:93-103. [PMID: 30366148 DOI: 10.1016/j.jpba.2018.10.017] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 10/05/2018] [Accepted: 10/07/2018] [Indexed: 02/07/2023]
Abstract
Lung cancer is undoubtedly one of the most serious health issues of the 21 st century. It is the second leading cause of cancer-related deaths in both men and women worldwide, accounting for about 1.5 million deaths annually. Despite advances in the treatment of lung cancer with new pharmaceutical products and technological improvements, morbidity and mortality rates remains a significant challenge for the cancer biologists and oncologists. The vast majority of lung cancer patients present with advanced-stage of pathological process that ultimately leads to poor prognosis and a five-year survival rate less than 20%. Early and accurate screening and analysis using cost-effective means are urgently needed to effectively diagnose the disease, improve the survival rate or to reduce mortality and morbidity associated with lung cancer patients. Thus, the only hope for early recognition of risk factors and timely diagnosis and treatment of lung cancer is biosensors technology. Novel biosensing based diagnostics approaches for predicting metastatic risks are likely to have significant therapeutic and clinical impact in the near future. This article systematically provides a brief overview of various biosensing platforms for identification of lung cancer disease biomarkers, with a specific focus on recent advancements in electrochemical and optical biosensors, analytical performances of different biosensors, challenges and further research opportunities for routine clinical analysis.
Collapse
Affiliation(s)
- Amir Roointan
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Tanveer Ahmad Mir
- Division of Biomedical System Engineering, Graduate School of Science and Engineering for Education, University of Toyama, Toyama, Japan; Department of Chemistry and Institute of BioPhysio Sensor Technology (IBST), Pusan National University, Busan, 46241, South Korea; Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, Al Takhassusi Road, Riyadh, 11533, Saudi Arabia; Toyama Nanotechnology Manufacturing Cluster, Toyama, Japan.
| | - Shadil Ibrahim Wani
- Department of Immunology and Molecular Medicine,Sher-i-Kashmir Institute of Medical Sciences, Srinagar, India
| | - Mati-Ur-Rehman
- Department of Radiological Sciences, Graduate school of Medicine and Pharmaceutical Sciences, University of Toyama, Japan
| | - Khalil Khadim Hussain
- Department of Chemistry and Institute of BioPhysio Sensor Technology (IBST), Pusan National University, Busan, 46241, South Korea; Department of pharmacy, University of central Punjab 1-Khayaban-e-Jinnah, Johar Town, Lahore, Pakistan
| | - Bilal Ahmed
- Department of Intellectual Information Engineering, Graduate School of Science and Engineering for Education, University of Toyama, Toyama, Japan
| | - Shugufta Abrahim
- Department of Intellectual Information Engineering, Graduate School of Science and Engineering for Education, University of Toyama, Toyama, Japan
| | - Amir Savardashtaki
- Department of Environmental Sciences, Cyprus International University, Nicosia, Cyprus
| | - Ghazaal Gandomani
- Department of Bioengineering, Biotechnology Research Center, Cyprus International University, Nicosia, Cyprus
| | - Molood Gandomani
- Department of pharmacy, University of central Punjab 1-Khayaban-e-Jinnah, Johar Town, Lahore, Pakistan
| | - Raja Chinnappan
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, Al Takhassusi Road, Riyadh, 11533, Saudi Arabia
| | - Mahmood H Akhtar
- Department of Chemistry and Institute of BioPhysio Sensor Technology (IBST), Pusan National University, Busan, 46241, South Korea
| |
Collapse
|
9
|
Novel method to detect the lung cancer biomarker volatiles using hydrogen vacant silicane nanosheets: A DFT investigation. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.06.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
10
|
Zhang P, Zhu Y, Li Y, Zhu S, Ma R, Zhao M, Li J. Forensic evaluation of STR typing reliability in lung cancer. Leg Med (Tokyo) 2017; 30:38-41. [PMID: 29154002 DOI: 10.1016/j.legalmed.2017.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/26/2017] [Accepted: 11/10/2017] [Indexed: 01/07/2023]
Abstract
Short tandem repeats (STR) analysis is the gold standard method in the forensics field for personal identification and paternity testing. In cancerous tissues, STR markers are gaining attention, with some studies showing increased instability. Lung cancer, which is one of the most commonmalignancies, has become the most lethal among all cancers. In certain situations, lung cancer tissues may be the only resource available for forensic analysis. Therefore, evaluating the reliability of STR markers in lung cancer tissues is required to avoid false exclusions. In this study, 75 lung cancer tissue samples were examined to evaluate the reliability of various STR markers. Out of the 75 examined samples, 24 of the cancerous samples (32%) showed genetic alterations on at least one STR loci, totaling 55 times. The most common type of STR variation was a partial loss of heterozygosity, with the D5S818 loci having the highest variation frequency and no alterations detected on the D2S441 and Penta E loci. Moreover, STR variation frequencies were shown to increase with an increased patient age and increased clinical and pathological characteristics, thus an older patient with an advanced stage of progression exhibited a higher variation frequency. Overall, this study provides forensic scientists with further insight into STR analysis relating to lung cancer tissue.
Collapse
Affiliation(s)
- Peng Zhang
- Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Ying Zhu
- Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China
| | - Yongguo Li
- Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China; Chongqing Engineering Research Center for Criminal Investigation Technology, Chongqing 400016, China
| | - Shisheng Zhu
- Faculty of Medical Technology, Chongqing Medical and Pharmaceutical College, Chongqing 401331, China
| | - Ruoxiang Ma
- Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China; Chongqing Engineering Research Center for Criminal Investigation Technology, Chongqing 400016, China
| | - Minzhu Zhao
- Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China; Chongqing Engineering Research Center for Criminal Investigation Technology, Chongqing 400016, China
| | - Jianbo Li
- Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing 400016, China.
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Leng S, Wu G, Klinge DM, Thomas CL, Casas E, Picchi MA, Stidley CA, Lee SJ, Aisner S, Siegfried JM, Ramalingam S, Khuri FR, Karp DD, Belinsky SA. Gene methylation biomarkers in sputum as a classifier for lung cancer risk. Oncotarget 2017; 8:63978-63985. [PMID: 28969046 PMCID: PMC5609978 DOI: 10.18632/oncotarget.19255] [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: 03/14/2017] [Accepted: 06/05/2017] [Indexed: 01/01/2023] Open
Abstract
CT screening for lung cancer reduces mortality, but will cost Medicare ∼2 billion dollars due in part to high false positive rates. Molecular biomarkers could augment current risk stratification used to select smokers for screening. Gene methylation in sputum reflects lung field cancerization that remains in lung cancer patients post-resection. This population was used in conjunction with cancer-free smokers to evaluate classification accuracy of a validated eight-gene methylation panel in sputum for cancer risk. Sputum from resected lung cancer patients (n=487) and smokers from Lovelace (n=1380) and PLuSS (n=718) cohorts was studied for methylation of an 8-gene panel. Area under a receiver operating characteristic curve was calculated to assess the prediction performance in logistic regressions with different sets of variables. The prevalence for methylation of all genes was significantly increased in the ECOG-ACRIN patients compared to cancer-free smokers as evident by elevated odds ratios that ranged from 1.6 to 8.9. The gene methylation panel showed lung cancer prediction accuracy of 82–86% and with addition of clinical variables improved to 87–90%. With sensitivity at 95%, specificity increased from 25% to 54% comparing clinical variables alone to their inclusion with methylation. The addition of methylation biomarkers to clinical variables would reduce false positive screens by ruling out one-third of smokers eligible for CT screening and could increase cancer detection rates through expanding risk assessment criteria.
Collapse
Affiliation(s)
- Shuguang Leng
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Guodong Wu
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Donna M Klinge
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Cynthia L Thomas
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Elia Casas
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Maria A Picchi
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Christine A Stidley
- Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Sandra J Lee
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Seena Aisner
- Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Jill M Siegfried
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - Suresh Ramalingam
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Fadlo R Khuri
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | | | - Steven A Belinsky
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| |
Collapse
|
13
|
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.
Collapse
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.
| |
Collapse
|
14
|
Abstract
The aim of future research in this area is to provide the mechanistic understanding and the tools for effective prevention, early diagnosis, and therapy of lung cancer. With the established causal link between cigarette smoking and the risk of developing lung cancer, the most effective prevention is certainly not to smoke. A much better mechanistic understanding of lung cancer and its variability will support the development and evaluation of potentially reduced risk products for those who maintain smoking as well as for the development of early diagnostic tools and targeted therapies. Because of the complexity of lung cancer and the long duration for its development, nonclinical and clinical research efforts need to complement each other. Recent promising advances in this research area are the understanding of the interaction between genotoxic and epigenetic effects of smoking, the development of laboratory animal models for lung tumorigenesis by smoke inhalation, the unraveling of molecular pathways and signatures in clinical lung cancer research useful for developing diagnostic tools and therapeutic approaches, and the first successful therapy for lung cancer—although less suitable for smokers. The above—in combination with emerging data sets from explorative non-clinical and clinical studies as well as improved modeling approaches—are setting the stage for accelerated progress towards developing successful early diagnostic tools and therapies as well as for the assessment of new consumer products with potentially reduced risk.
Collapse
|
15
|
Wang M, Liu H, Liu Z, Yi X, Bickeboller H, Hung RJ, Brennan P, Landi MT, Caporaso N, Christiani DC, Doherty JA, Amos CI, Wei Q. Genetic variant in DNA repair gene GTF2H4 is associated with lung cancer risk: a large-scale analysis of six published GWAS datasets in the TRICL consortium. Carcinogenesis 2016; 37:888-896. [PMID: 27288692 PMCID: PMC5008248 DOI: 10.1093/carcin/bgw070] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 05/27/2016] [Accepted: 06/07/2016] [Indexed: 12/15/2022] Open
Abstract
DNA repair pathways maintain genomic integrity and stability, and dysfunction of DNA repair leads to cancer. We hypothesize that functional genetic variants in DNA repair genes are associated with risk of lung cancer. We performed a large-scale meta-analysis of 123,371 single nucleotide polymorphisms (SNPs) in 169 DNA repair genes obtained from six previously published genome-wide association studies (GWASs) of 12160 lung cancer cases and 16838 controls. We calculated odds ratios (ORs) with 95% confidence intervals (CIs) using the logistic regression model and used the false discovery rate (FDR) method for correction of multiple testing. As a result, 14 SNPs had a significant odds ratio (OR) for lung cancer risk with P FDR < 0.05, of which rs3115672 in MSH5 (OR = 1.20, 95% CI = 1.14-1.27) and rs114596632 in GTF2H4 (OR = 1.19, 95% CI = 1.12-1.25) at 6q21.33 were the most statistically significant (P combined = 3.99×10(-11) and P combined = 5.40×10(-10), respectively). The MSH5 rs3115672, but not GTF2H4 rs114596632, was strongly correlated with MSH5 rs3131379 in that region (r (2) = 1.000 and r (2) = 0.539, respectively) as reported in a previous GWAS. Importantly, however, the GTF2H4 rs114596632 T, but not MSH5 rs3115672 T, allele was significantly associated with both decreased DNA repair capacity phenotype and decreased mRNA expression levels. These provided evidence that functional genetic variants of GTF2H4 confer susceptibility to lung cancer.
Collapse
Affiliation(s)
- Meilin Wang
- Duke Cancer Institute, Duke University Medical Center, 905 Lasalle Street, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 21116, China
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, 905 Lasalle Street, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Zhensheng Liu
- Duke Cancer Institute, Duke University Medical Center, 905 Lasalle Street, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xiaohua Yi
- Duke Cancer Institute, Duke University Medical Center, 905 Lasalle Street, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Heike Bickeboller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Rayjean J. Hung
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai hospital, Toronto, Ontario, Canada
| | - Paul Brennan
- Genetic Epidemiology Group, International Agency for Research on Cancer, 69372 Lyon, France
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Neil Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - David C. Christiani
- Department of Environmental Health and
- Department of Epidemiology, Harvard University School of Public Health, Boston, MA 02115, USA and
| | - Jennifer Anne Doherty
- Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH 03756, USA
| | - The TRICL Research Team
- Duke Cancer Institute, Duke University Medical Center, 905 Lasalle Street, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 21116, China
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, 37073 Göttingen, Germany
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai hospital, Toronto, Ontario, Canada
- Genetic Epidemiology Group, International Agency for Research on Cancer, 69372 Lyon, France
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
- Department of Environmental Health and
- Department of Epidemiology, Harvard University School of Public Health, Boston, MA 02115, USA and
- Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH 03756, USA
| | - Christopher I. Amos
- Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH 03756, USA
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, 905 Lasalle Street, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| |
Collapse
|
16
|
Ma M, Zhu H, Zhang C, Sun X, Gao X, Chen G. "Liquid biopsy"-ctDNA detection with great potential and challenges. ANNALS OF TRANSLATIONAL MEDICINE 2015; 3:235. [PMID: 26539452 DOI: 10.3978/j.issn.2305-5839.2015.09.29] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Circulating tumor DNA (ctDNA) is now being extensively studied as it is a noninvasive "real-time" biomarker that can provide diagnostic and prognostic information before, during treatment and at progression. These include DNA mutations, epigenetic alterations and other forms of tumor-specific abnormalities such as microsatellite instability (MSI) and loss of heterozygosity (LOH). ctDNA is of great value in the process of cancer treatment. However, up to date, there is no strict standard considering the exact biomarker because the development and progression of cancer is extremely complicated. Also, results of the studies evaluating ctDNA are not consistent due to the different detection methods and processing. The major challenge is still assay sensitivity and specificity for analysis of ctDNA. This review mainly focuses on the tumor specific DNA mutations, epigenetic alterations as well as detecting methods of ctDNA. The advantages and disadvantages will also be discussed.
Collapse
Affiliation(s)
- Mingwei Ma
- 1 Department of Radiation Oncology, Peking University First Hospital, No.7, Xishiku Str., Xicheng District, Beijing 100034, China ; 2 Department of Radiation Oncology, The First Affiliated Hospital, Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, China ; 3 Department of General Surgery, Affiliated Drum Tower Hospital of Nanjing University Medical School, 321 Zhongshan Road, Nanjing 210008, China
| | - Hongcheng Zhu
- 1 Department of Radiation Oncology, Peking University First Hospital, No.7, Xishiku Str., Xicheng District, Beijing 100034, China ; 2 Department of Radiation Oncology, The First Affiliated Hospital, Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, China ; 3 Department of General Surgery, Affiliated Drum Tower Hospital of Nanjing University Medical School, 321 Zhongshan Road, Nanjing 210008, China
| | - Chi Zhang
- 1 Department of Radiation Oncology, Peking University First Hospital, No.7, Xishiku Str., Xicheng District, Beijing 100034, China ; 2 Department of Radiation Oncology, The First Affiliated Hospital, Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, China ; 3 Department of General Surgery, Affiliated Drum Tower Hospital of Nanjing University Medical School, 321 Zhongshan Road, Nanjing 210008, China
| | - Xinchen Sun
- 1 Department of Radiation Oncology, Peking University First Hospital, No.7, Xishiku Str., Xicheng District, Beijing 100034, China ; 2 Department of Radiation Oncology, The First Affiliated Hospital, Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, China ; 3 Department of General Surgery, Affiliated Drum Tower Hospital of Nanjing University Medical School, 321 Zhongshan Road, Nanjing 210008, China
| | - Xianshu Gao
- 1 Department of Radiation Oncology, Peking University First Hospital, No.7, Xishiku Str., Xicheng District, Beijing 100034, China ; 2 Department of Radiation Oncology, The First Affiliated Hospital, Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, China ; 3 Department of General Surgery, Affiliated Drum Tower Hospital of Nanjing University Medical School, 321 Zhongshan Road, Nanjing 210008, China
| | - Gang Chen
- 1 Department of Radiation Oncology, Peking University First Hospital, No.7, Xishiku Str., Xicheng District, Beijing 100034, China ; 2 Department of Radiation Oncology, The First Affiliated Hospital, Nanjing Medical University, 300 Guangzhou Road, Nanjing 210029, China ; 3 Department of General Surgery, Affiliated Drum Tower Hospital of Nanjing University Medical School, 321 Zhongshan Road, Nanjing 210008, China
| |
Collapse
|
17
|
Warton K, Samimi G. Methylation of cell-free circulating DNA in the diagnosis of cancer. Front Mol Biosci 2015; 2:13. [PMID: 25988180 PMCID: PMC4428375 DOI: 10.3389/fmolb.2015.00013] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/07/2015] [Indexed: 01/04/2023] Open
Abstract
A range of molecular alterations found in tumor cells, such as DNA mutations and DNA methylation, is reflected in cell-free circulating DNA (circDNA) released from the tumor into the blood, thereby making circDNA an ideal candidate for the basis of a blood-based cancer diagnosis test. In many cancer types, mutations driving tumor development and progression are present in a wide range of oncogenes and tumor suppressor genes. However, even when a gene is consistently mutated in a particular cancer, the mutations can be spread over very large regions of its sequence, making evaluation difficult. This diversity of sequence changes in tumor DNA presents a challenge for the development of blood tests based on DNA mutations for cancer diagnosis. Unlike mutations, DNA methylation that can be consistently measured, as it tends to occur in specific regions of the DNA called CpG islands. Since DNA methylation is reflected within circDNA, detection of tumor-specific DNA methylation in patient plasma is a feasible approach for the development of a blood-based test. Aberrant circDNA methylation has been described in most cancer types and is actively being investigated for clinical applications. A commercial blood test for colorectal cancer based on the methylation of the SEPT9 promoter region in circDNA is under review for approval by the Federal Drug Administration (FDA) for clinical use. In this paper, we review the state of research in circDNA methylation as an application for blood-based diagnostic tests in colorectal, breast, lung, pancreatic and ovarian cancers, and we consider some of the future directions and challenges in this field. There are a number of potential circDNA biomarkers currently under investigation, and experience with SEPT9 shows that the time to clinical translation can be relatively rapid, supporting the promise of circDNA as a biomarker.
Collapse
Affiliation(s)
- Kristina Warton
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre and St Vincent's Clinical School, University of New South Wales Sydney, NSW, Australia
| | - Goli Samimi
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre and St Vincent's Clinical School, University of New South Wales Sydney, NSW, Australia
| |
Collapse
|
18
|
Wang X, Ling L, Su H, Cheng J, Jin L. Aberrant methylation of genes in sputum samples as diagnostic biomarkers for non-small cell lung cancer: a meta-analysis. Asian Pac J Cancer Prev 2015; 15:4467-74. [PMID: 24969871 DOI: 10.7314/apjcp.2014.15.11.4467] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We aimed to comprehensively review the evidence for using sputum DNA to detect non-small cell lung cancer (NSCLC). MATERIALS AND METHODS We searched PubMed, Science Direct, Web of Science, Chinese Biological Medicine (CBM), Chinese National Knowledge Infrastructure (CNKI), Wanfang, Vip Databases and Google Scholar from 2003 to 2013. The meta-analysis was carried out using a random-effect model with sensitivity, specificity, diagnostic odd ratios (DOR), summary receiver operating characteristic curves (ROC curves), area under the curve (AUC), and 95% confidence intervals (CI) as effect measurements. RESULTS There were twenty-two studies meeting the inclusion criteria for the meta-analysis. Combined sensitivity and specificity were 0.62 (95%CI: 0.59-0.65) and 0.73 (95%CI: 0.70-0.75), respectively. The DOR was 10.3 (95%CI: 5.88-18.1) and the AUC was 0.78. CONCLUSIONS The overall accuracy of the test was currently not strong enough for the detection of NSCLC for clinical application. Discovery and evaluation of additional biomarkers with improved sensitivity and specificity from studies rated high quality deserve further attention.
Collapse
Affiliation(s)
- Xu Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei 230032, Anhui Province, China E-mail :
| | | | | | | | | |
Collapse
|
19
|
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]
|
20
|
Kang I, Wang Y, Reagan C, Fu Y, Wang MX, Gu LQ. Designing DNA interstrand lock for locus-specific methylation detection in a nanopore. Sci Rep 2013; 3:2381. [PMID: 24135881 PMCID: PMC3798886 DOI: 10.1038/srep02381] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 07/12/2013] [Indexed: 12/31/2022] Open
Abstract
DNA methylation is an important epigenetic regulation of gene transcription. Locus-specific DNA methylation can be used as biomarkers in various diseases including cancer. Many methods have been developed for genome-wide methylation analysis, but molecular diagnotics needs simple tools to determine methylation states at individual CpG sites in a gene fragment. In this report, we utilized the nanopore single-molecule sensor to investigate a base-pair specific metal ion/nucleic acids interaction, and explored its potential application in locus-specific DNA methylation analysis. We identified that divalent Mercury ion (Hg2+) can selectively bind a uracil-thymine mismatch (U-T) in a dsDNA. The Hg2+ binding creates a reversible interstrand lock, called MercuLock, which enhances the hybridization strength by two orders of magnitude. Such MercuLock cannot be formed in a 5-methylcytosine-thymine mismatch (mC-T). By nanopore detection of dsDNA stability, single bases of uracil and 5-methylcytosine can be distinguished. Since uracil is converted from cytosine by bisulfite treatment, cytosine and 5′-methylcytosine can be discriminated. We have demonstrated the methylation analysis of multiple CpGs in a p16 gene CpG island. This single-molecule assay may have potential in detection of epigenetic cancer biomarkers in biofluids, with an ultimate goal for early diagnosis of cancer.
Collapse
Affiliation(s)
- Insoon Kang
- Department of Bioengineering and Dalton Cardiovascular Research Center
| | | | | | | | | | | |
Collapse
|
21
|
Pallis AG, Syrigos KN. Lung cancer in never smokers: disease characteristics and risk factors. Crit Rev Oncol Hematol 2013; 88:494-503. [PMID: 23921082 DOI: 10.1016/j.critrevonc.2013.06.011] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Revised: 06/07/2013] [Accepted: 06/28/2013] [Indexed: 12/16/2022] Open
Abstract
It is estimated that approximately 25% of all lung cancer cases are observed in never-smokers and its incidence is expected to increase due to smoking prevention programs. Risk factors for the development of lung cancer described include second-hand smoking, radon exposure, occupational exposure to carcinogens and to cooking oil fumes and indoor coal burning. Other factors reported are infections (HPV and Mycobacterium tuberculosis), hormonal and diatery factors and diabetes mellitus. Having an affected relative also increases the risk for lung cancer while recent studies have identified several single nucleotide polymorphisms associated with increased risk for lung cancer development in never smokers. Distinct clinical, pathology and molecular characteristics are observed in lung cancer in never smokers; more frequently is observed in females and adenocarcinoma is the predominant histology while it has a different pattern of molecular alterations. The purpose of this review is to summarize our current knowledge of this disease.
Collapse
|
22
|
Quintans JSS, Antoniolli AR, Onofre FMB, Onofre ASC. Detection of lung cancer using multiple genetic markers--a systematic review. Diagn Cytopathol 2013; 41:834-42. [PMID: 23513001 DOI: 10.1002/dc.22978] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 01/01/2013] [Indexed: 11/08/2022]
Abstract
Lung cancer is the leading cause of cancer deaths worldwide, and has one of the lowest survival rates of any solid tumor. In recent years, several attempts have been conducted to improve an early or accelerated diagnosis due to better overall prognosis after therapy. The aim of this study was evaluating the use of genetic markers for diagnosis of lung cancer. This study was conducted in accordance to Transparent Reporting of Systematic Reviews and Meta-Analyses. Three Internet sources were used to search: MEDLINE-PubMed, EMBASE, and LILACS. The databases were searched for studies conducted in the period up to and including May 10, 2011. The following inclusion criteria were applied: lung cancer studies, and the use of genetic markers for diagnosis. Studies using animal models, review articles, meta-analyses, abstracts, conference proceedings, editorials/letters, case reports, incorrect study population, inadequate data, and cytology was not obtained, were excluded. A total of 1,901 abstracts/citations were identified for preliminary review. From 24 final selected studies, 17 referred to chromosomal markers diagnosis, eight to genes as marker, and one to both subjects. Fluorescence in situ hybridization (FISH) was applied in all studies. Despite the limitations of this study, application of genetic markers to lung cancer diagnosis seems to have prognosis value irrespective of detection methodology used. FISH was the main technique applied to diagnose genetics alterations and revealed a high specificity, although some authors reported low sensitivity.
Collapse
|
23
|
Qiu X, Qiao Y, Liu B, Li Y, You J, Zhou Q. [Advances of DNA methylation in early diagnosis of lung cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2012; 15:234-41. [PMID: 22510510 PMCID: PMC5999983 DOI: 10.3779/j.issn.1009-3419.2012.04.08] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Lung cancer is the leading cause of cancer-related death and thus a major health problem nowadays. No early diagnostic method is ideal up to now. Changes in DNA methylation occur on early stage of lung cancer. Detection of DNA methylation is expected to be an important method in early diagosis of lung cancer.
Collapse
Affiliation(s)
- Xiaoming Qiu
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, Tianjin 300052, China
| | | | | | | | | | | |
Collapse
|
24
|
Jin H, Lee HC, Park SS, Jeong YS, Kim SY. Serum cancer biomarker discovery through analysis of gene expression data sets across multiple tumor and normal tissues. J Biomed Inform 2011; 44:1076-85. [DOI: 10.1016/j.jbi.2011.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 08/05/2011] [Accepted: 08/09/2011] [Indexed: 01/13/2023]
|
25
|
Yasuda H, Soejima K, Nakayama S, Kawada I, Nakachi I, Yoda S, Satomi R, Ikemura S, Terai H, Sato T, Watanabe H, Naoki K, Hayashi Y, Ishizaka A. Bronchoscopic microsampling is a useful complementary diagnostic tool for detecting lung cancer. Lung Cancer 2011; 72:32-8. [PMID: 20813423 DOI: 10.1016/j.lungcan.2010.07.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Revised: 07/24/2010] [Accepted: 07/30/2010] [Indexed: 10/19/2022]
Abstract
PURPOSE Bronchoscopic microsampling (BMS) is a novel and direct method with which to obtain epithelial lining fluid (ELF) from the lungs. Analysis of DNA hypermethylation of tumor suppressor genes (TSGs) is expected to be a sensitive tool for the early detection of lung cancer. It has been reported that the existence of EGFR mutations and EML4-ALK gene rearrangements are related to the sensitivity of corresponding kinase inhibitors. We aimed to evaluate the suitability of ELF as a sample for analyzing molecular changes specific for lung cancer. PATIENTS AND METHODS We collected ELF from 61 lung cancer patients by BMS from the airway close to the peripheral lung nodule and purified the nucleic acids. We performed methylation specific PCR in each ELF as well as matched serum and tumor tissue for TSGs for DNA methylation analysis. We also examined EGFR mutations and EML4-ALK rearrangement. RESULTS The sensitivity for detecting DNA hypermethylation in ELF vs serum was 74.1% vs 18.5%. We found 60.1% of patients had at least one hypermethylation in ELF, while only 27.9% had it in serum. Of note, DNA hypermethylation was detected even in stage I patients (60.0%) and the detection rate was almost the same level in each stage. We also found the sensitivity for detecting EGFR mutation in ELF vs serum was 58.3% vs 8.3%. We detected an EML4-ALK fusion gene using ELF in one patient. CONCLUSIONS BMS is an alternative method to detect cancer specific genetic and epigenetic alterations and will be a useful complementary diagnostic tool for lung cancer. SUMMARY Investigation of genetic and epigenetic changes associated with lung cancer has clinical importance for its diagnosis and management. The clinical usefulness of bronchoscopic microsampling (BMS) in lung cancer has not yet been evaluated. This study demonstrates that BMS could be useful for detecting lung cancer specific molecular changes and valuable for early diagnosis and determination of treatment options for lung cancer.
Collapse
Affiliation(s)
- Hiroyuki Yasuda
- Department of Pulmonary Medicine, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Kim CE, Tchou-Wong KM, Rom WN. Sputum-based molecular biomarkers for the early detection of lung cancer: limitations and promise. Cancers (Basel) 2011; 3:2975-89. [PMID: 24212941 PMCID: PMC3759181 DOI: 10.3390/cancers3032975] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Revised: 07/11/2011] [Accepted: 07/12/2011] [Indexed: 12/31/2022] Open
Abstract
Lung cancer is the leading cause of cancer deaths, with an overall survival of 15% at five years. Biomarkers that can sensitively and specifically detect lung cancer at early stage are crucial for improving this poor survival rate. Sputum has been the target for the discovery of non-invasive biomarkers for lung cancer because it contains airway epithelial cells, and molecular alterations identified in sputum are most likely to reflect tumor-associated changes or field cancerization caused by smoking in the lung. Sputum-based molecular biomarkers include morphology, allelic imbalance, promoter hypermethylation, gene mutations and, recently, differential miRNA expression. To improve the sensitivity and reproducibility of sputum-based biomarkers, we recommend standardization of processing protocols, bronchial epithelial cell enrichment, and identification of field cancerization biomarkers.
Collapse
Affiliation(s)
- Connie E. Kim
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine. 462 First Avenue, NBV 7N24, New York, NY 10016, USA; E-Mails: (C.E.K.); (K.-M.T.-W.)
| | - Kam-Meng Tchou-Wong
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine. 462 First Avenue, NBV 7N24, New York, NY 10016, USA; E-Mails: (C.E.K.); (K.-M.T.-W.)
- Department of Environmental Medicine, New York University School of Medicine, 57 Old Forge Road, Tuxedo, NY 10987, USA
| | - William N. Rom
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine. 462 First Avenue, NBV 7N24, New York, NY 10016, USA; E-Mails: (C.E.K.); (K.-M.T.-W.)
- Department of Environmental Medicine, New York University School of Medicine, 57 Old Forge Road, Tuxedo, NY 10987, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: 212-263-6479; Fax: 212-263-8442
| |
Collapse
|
27
|
Abstract
The presence of DNA and RNA circulating in human plasma and serum is described. The known sources of the DNA/RNA in blood, the ability of these nucleic acids to enter other cells and to express in the recipient cells are considered along with their relationship to metastases. The possible role(s) of the DNA/RNA in personalized clinical diagnosis, monitoring of treatment and prognosis in oncology are discussed.
Collapse
Affiliation(s)
- Peter Brian Gahan
- Anatomy & Human Sciences, King’s College London, London Bridge, London, SE1 1UL UK
| |
Collapse
|
28
|
Carozzi FM, Bisanzi S, Falini P, Sani C, Venturini G, Lopes Pegna A, Bianchi R, Ronchi C, Picozzi G, Mascalchi M, Carrozzi L, Baliva F, Pistelli F, Tavanti L, Falaschi F, Grazzini M, Innocenti F, Paci E. Molecular profile in body fluids in subjects enrolled in a randomised trial for lung cancer screening: Perspectives of integrated strategies for early diagnosis. Lung Cancer 2010; 68:216-21. [DOI: 10.1016/j.lungcan.2009.06.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2009] [Revised: 05/22/2009] [Accepted: 06/20/2009] [Indexed: 01/27/2023]
|
29
|
Common 5p15.33 and 6p21.33 variants influence lung cancer risk. Nat Genet 2008; 40:1407-9. [PMID: 18978787 DOI: 10.1038/ng.273] [Citation(s) in RCA: 447] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Accepted: 09/29/2008] [Indexed: 12/14/2022]
Abstract
We conducted a genome-wide association (GWA) study of lung cancer comparing 511,919 SNP genotypes in 1,952 cases and 1,438 controls. The most significant association was attained at 15q25.1 (rs8042374; P = 7.75 x 10(-12)), confirming recent observations. Pooling data with two other GWA studies (5,095 cases, 5,200 controls) and with replication in an additional 2,484 cases and 3,036 controls, we identified two newly associated risk loci mapping to 6p21.33 (rs3117582, BAT3-MSH5; P(combined) = 4.97 x 10(-10)) and 5p15.33 (rs401681, CLPTM1L; P(combined) = 7.90 x 10(-9)).
Collapse
|
30
|
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.
Collapse
|
31
|
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.
Collapse
Affiliation(s)
- H-S Hsu
- Division of Thoracic Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
| | | | | | | | | | | | | |
Collapse
|
32
|
Abstract
In general, DNA methylation acts in concert with other epigenetic processes, including histone modifications, chromatin remodeling and microRNAs, to shape the overall chromatin structure of the nucleus and potentially modify its functional state. Aberrant DNA methylation events can occur in a number of human diseases but we are only just beginning to appreciate the scope and magnitude of this process in human health. As one example, in contrast to normal cells, the cancer methylome is characterized by reciprocal hypermethylation of specific regulatory regions of genes along with an overall decrease in the quantity of 5-methylcytosine throughout the remainder of the genome. Currently, near genome-wide technologies are available and have been utilized to examine the extent of DNA methylation in discovery-based studies involving several physiological and disease states. Although early in the process, DNA methylation is being explored as a biomarker to be used in clinical practice for early detection of disease, tumor classification and for predicting disease outcome or recurrence. This perspective focuses on the current and future states of the use of DNA methylation biomarkers in disease diagnosis, prognosis and classification, with a particular emphasis on cancer.
Collapse
Affiliation(s)
- Huidong Shi
- University of Missouri-Columbia, School of Medicine, Department of Pathology and Anatomical Sciences, Columbia, MO 65212, USA.
| | | | | |
Collapse
|
33
|
Heaphy CM, Bisoffi M, Griffith JK. Diagnostic significance of allelic imbalance in cancer. EXPERT OPINION ON MEDICAL DIAGNOSTICS 2007; 1:159-68. [PMID: 23489303 DOI: 10.1517/17530059.1.2.159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Allelic imbalance (AI), a deviation from the normal 1:1 ratio of maternal and paternal alleles, occurs in virtually all solid and blood-borne malignancies. The frequency and spectrum of AI in a tumor cell reflects the karyotypic complexity of the cancer genome. Hence, many investigations have assessed the extent of AI to analyze differences between normal and tumor tissues in a variety of different organs. In this review, the authors describe established and emerging technologies used to assess the extent of AI in human tissues, and their application in the diagnosis of cancer. The four major methods to be reviewed represent powerful and widely used tools for the identification of allelic imbalances accompanying cancer initiation and progression. These are fluorescent in situ hybridization, comparative genomic hybridization, single nucleotide polymorphism arrays and the use of microsatellite markers. For each method, the authors provide a brief description of the approach and elaborate on specific studies that highlight its utility in the diagnosis of human cancers.
Collapse
Affiliation(s)
- Christopher M Heaphy
- Graduate Research Assistant, University of New Mexico School of Medicine, Department of Biochemistry and Molecular Biology, MSC08 4670, 1 University of New Mexico, Albuquerque, New Mexico 87131-0001, USA +1 505 272 5090 ; +1 505 272 6587 ;
| | | | | |
Collapse
|
34
|
Abstract
PURPOSE OF REVIEW Biomarkers for lung cancer may be used for risk stratification, early detection, treatment selection, prognostication and monitoring for recurrence. All these areas of clinical management would benefit from sensitive and specific, noninvasive, cost-effective biomarkers. RECENT FINDINGS Significant progress has been made in understanding the steps involved in lung carcinogenesis and in the development of novel technologies for biomarker discovery. Over the last 3 years research into prospective lung cancer biomarkers has proliferated, especially in the areas of early detection and prognostication. The most active areas of research have been in promoter methylation, proteomics and genomics. Many investigators are adopting panels of serum biomarkers in an attempt to increase sensitivity. The development of targeted lung cancer therapy has engendered interest in markers to identify the optimal candidates for these therapies. SUMMARY Much progress has been made in the last 3 years in the identification and validation of new biomarkers for the early diagnosis of lung cancer. The biomarkers require additional studies before they can be used clinically. Markers to identify lung cancer patients who may benefit from targeted therapy have been developed more rapidly and may be used now in some clinical situations.
Collapse
Affiliation(s)
- Alissa K Greenberg
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, New York University School of Medicine, New York, New York, USA.
| | | |
Collapse
|
35
|
Herceg Z, Hainaut P. Genetic and epigenetic alterations as biomarkers for cancer detection, diagnosis and prognosis. Mol Oncol 2007; 1:26-41. [PMID: 19383285 PMCID: PMC5543860 DOI: 10.1016/j.molonc.2007.01.004] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Revised: 01/31/2007] [Accepted: 01/31/2007] [Indexed: 02/06/2023] Open
Abstract
The development of cancer is driven by the accumulation of scores of alterations affecting the structure and function of the genome. Equally important in this process are genetic alterations and epigenetic changes. Whereas the former disrupt normal patterns of gene expression, sometimes leading to the expression of abnormal, constitutively active proteins, the latter deregulate the mechanisms such as transcriptional control leading to the inappropriate silencing or activation of cancer-associated genes. Both types of changes are inheritable at the cellular level, thus contributing to the clonal expansion of cancer cells. In this review, we summarize current knowledge on how genetic alterations in oncogenes or tumour suppressor genes, as well as epigenetic changes, can be exploited in the clinics as biomarkers for cancer detection, diagnosis and prognosis. We propose a rationale for identifying alterations that may have a functional impact within a background of "passenger" alterations that may occur solely as the consequence of deregulated genetic and epigenetic stability. Such functional alterations may represent candidates for targeted therapeutic approaches.
Collapse
Affiliation(s)
- Zdenko Herceg
- Group of Molecular Carcinogenesis and Biomarkers, International Agency for Research on Cancer, 150 Cours Albert Thomas, Lyon Cedex F-69008, Rhone-Alpes, France.
| | | |
Collapse
|
36
|
Pasrija T, Srinivasan R, Behera D, Majumdar S. Telomerase activity in sputum and telomerase and its components in biopsies of advanced lung cancer. Eur J Cancer 2007; 43:1476-82. [PMID: 17531468 DOI: 10.1016/j.ejca.2007.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2006] [Revised: 03/13/2007] [Accepted: 04/05/2007] [Indexed: 11/16/2022]
Abstract
PURPOSE In this study, we explored the diagnostic utility of sputum telomerase activity as a non-invasive biomarker of lung cancer. In biopsies of lung cancer, the relationship of telomerase activity to telomerase reverse transcriptase (hTERT) and telomerase RNA component (hTERC) and to c-Myc expression was also evaluated. METHODS Paired biopsy and sputum samples were evaluated for telomerase activity by the telomerase repeat amplification protocol (TRAP) assay in 34 cases of lung cancer and in 30 control subjects without any evidence of lung cancer. hTERT and hTERC transcript expression was evaluated in 42 cases of lung cancer and compared to telomerase activity and c-Myc transcript expression. RESULTS Telomerase activity was present in 85.2% of biopsies and in 67.6% of paired sputum with a good concordance. Three out of the 30 negative controls showed a weak telomerase activity, all of whom had sarcoidosis. Thus, sputum telomerase activity had sensitivity, specificity, Negative Predictive Value and Positive Predictive Value of 67.6%, 90%, 71% and 88.46%, respectively. The hTERT levels correlated to the telomerase activity but not to the c-Myc oncogene expression. CONCLUSIONS In lung cancer, sputum telomerase activity is a candidate non-invasive biomarker of malignancy.
Collapse
Affiliation(s)
- Teena Pasrija
- Department of Pulmonary Medicine, Postgraduate Institute of Medical Education and Research, Education and Research, Sector 12, Chandigarh 160 012, India
| | | | | | | |
Collapse
|