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Wen SWC, Borg M, Timm S, Hansen TF, Hilberg O, Andersen RF. Methylated Cell-Free Tumor DNA in Sputum as a Tool for Diagnosing Lung Cancer-A Systematic Review and Meta-Analysis. Cancers (Basel) 2024; 16:506. [PMID: 38339257 PMCID: PMC10854681 DOI: 10.3390/cancers16030506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Lung cancer is the leading cause of cancer-related mortality worldwide. Early diagnosis is pivotal for the prognosis. There is a notable overlap between lung cancer and chronic bronchitis, and the potential use of methylated tumor DNA in sputum as a biomarker for lung cancer detection is appealing. This systematic review and meta-analysis followed the PRISMA 2020 statement. A comprehensive search was conducted in Embase, Medline, Web of Science, and the Cochrane Library, using these search strings: Lung cancer, sputum, and methylated tumor DNA. A total of 15 studies met the eligibility criteria. Studies predominantly utilized a case-control design, with sensitivity ranging from 10 to 93% and specificity from 8 to 100%. A meta-analysis of all genes across studies resulted in a summary sensitivity of 54.3% (95% CI 49.4-59.2%) and specificity of 79.7% (95% CI 75.0-83.7%). Notably, two less explored genes (TAC1, SOX17) demonstrated sensitivity levels surpassing 85%. The study's findings highlight substantial variations in the sensitivity and specificity of methylated tumor DNA in sputum for lung cancer detection. Challenges in reproducibility could stem from differences in tumor site, sample acquisition, extraction methods, and methylation measurement techniques. This meta-analysis provides a foundation for prioritizing high-performing genes, calling for a standardization and refinement of methodologies before potential application in clinical trials.
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Affiliation(s)
- Sara Witting Christensen Wen
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
- Department of Regional Health Research, University of Southern Denmark, 5000 Odense, Denmark
| | - Morten Borg
- Department of Medicine, Vejle Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark;
| | - Signe Timm
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
- Department of Regional Health Research, University of Southern Denmark, 5000 Odense, Denmark
| | - Torben Frøstrup Hansen
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
- Department of Regional Health Research, University of Southern Denmark, 5000 Odense, Denmark
| | - Ole Hilberg
- Department of Regional Health Research, University of Southern Denmark, 5000 Odense, Denmark
- Department of Medicine, Vejle Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark;
| | - Rikke Fredslund Andersen
- Department of Biochemistry and Immunology, Vejle Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
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Li P, Liu S, Du L, Mohseni G, Zhang Y, Wang C. Liquid biopsies based on DNA methylation as biomarkers for the detection and prognosis of lung cancer. Clin Epigenetics 2022; 14:118. [PMID: 36153611 PMCID: PMC9509651 DOI: 10.1186/s13148-022-01337-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 09/16/2022] [Indexed: 11/27/2022] Open
Abstract
Lung cancer (LC) is the main cause of cancer-related mortality. Most LC patients are diagnosed in an advanced stage when the symptoms are obvious, and the prognosis is quite poor. Although low-dose computed tomography (LDCT) is a routine clinical examination for early detection of LC, the false-positive rate is over 90%. As one of the intensely studied epigenetic modifications, DNA methylation plays a key role in various diseases, including cancer and other diseases. Hypermethylation in tumor suppressor genes or hypomethylation in oncogenes is an important event in tumorigenesis. Remarkably, DNA methylation usually occurs in the very early stage of malignant tumors. Thus, DNA methylation analysis may provide some useful information about the early detection of LC. In recent years, liquid biopsy has developed rapidly. Liquid biopsy can detect and monitor both primary and metastatic malignant tumors and can reflect tumor heterogeneity. Moreover, it is a minimally invasive procedure, and it causes less pain for patients. This review summarized various liquid biopsies based on DNA methylation for LC. At first, we briefly discussed some emerging technologies for DNA methylation analysis. Subsequently, we outlined cell-free DNA (cfDNA), sputum, bronchoalveolar lavage fluid, bronchial aspirates, and bronchial washings DNA methylation-based liquid biopsy for the early detection of LC. Finally, the prognostic value of DNA methylation in cfDNA and sputum and the diagnostic value of other DNA methylation-based liquid biopsies for LC were also analyzed.
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3
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Leng S, Picchi MA, Meek PM, Jiang M, Bayliss SH, Zhai T, Bayliyev RI, Tesfaigzi Y, Campen MJ, Kang H, Zhu Y, Lan Q, Sood A, Belinsky SA. Wood smoke exposure affects lung aging, quality of life, and all-cause mortality in New Mexican smokers. Respir Res 2022; 23:236. [PMID: 36076291 PMCID: PMC9454202 DOI: 10.1186/s12931-022-02162-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 08/27/2022] [Indexed: 11/10/2022] Open
Abstract
Background The role of wood smoke (WS) exposure in the etiology of chronic obstructive pulmonary disease (COPD), lung cancer (LC), and mortality remains elusive in adults from countries with low ambient levels of combustion-emitted particulate matter. This study aims to delineate the impact of WS exposure on lung health and mortality in adults age 40 and older who ever smoked. Methods We assessed health impact of self-reported “ever WS exposure for over a year” in the Lovelace Smokers Cohort using both objective measures (i.e., lung function decline, LC incidence, and deaths) and two health related quality-of-life questionnaires (i.e., lung disease-specific St. George's Respiratory Questionnaire [SGRQ] and the generic 36-item short-form health survey). Results Compared to subjects without WS exposure, subjects with WS exposure had a more rapid decline of FEV1 (− 4.3 ml/s, P = 0.025) and FEV1/FVC ratio (− 0.093%, P = 0.015), but not of FVC (− 2.4 ml, P = 0.30). Age modified the impacts of WS exposure on lung function decline. WS exposure impaired all health domains with the increase in SGRQ scores exceeding the minimal clinically important difference. WS exposure increased hazard for incidence of LC and death of all-cause, cardiopulmonary diseases, and cancers by > 50% and shortened the lifespan by 3.5 year. We found no evidence for differential misclassification or confounding from socioeconomic status for the health effects of WS exposure. Conclusions We identified epidemiological evidence supporting WS exposure as an independent etiological factor for the development of COPD through accelerating lung function decline in an obstructive pattern. Time-to-event analyses of LC incidence and cancer-specific mortality provide human evidence supporting the carcinogenicity of WS exposure. Supplementary Information The online version contains supplementary material available at 10.1186/s12931-022-02162-y.
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Affiliation(s)
- Shuguang Leng
- Department of Internal Medicine, School of Medicine, University of New Mexico, Albuquerque, NM, 87131, USA. .,Cancer Control and Population Sciences, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, 87131, USA. .,Lung Cancer Program, Lovelace Biomedical Research Institute, Albuquerque, NM, 87108, USA.
| | - Maria A Picchi
- Lung Cancer Program, Lovelace Biomedical Research Institute, Albuquerque, NM, 87108, USA
| | - Paula M Meek
- College of Nursing, University of Utah, Salt Lake City, UT, 84112, USA
| | - Menghui Jiang
- Department of Internal Medicine, School of Medicine, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Samuel H Bayliss
- Department of Internal Medicine, School of Medicine, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Ting Zhai
- Department of Internal Medicine, School of Medicine, University of New Mexico, Albuquerque, NM, 87131, USA.,Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Ruslan I Bayliyev
- Department of Internal Medicine, School of Medicine, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Yohannes Tesfaigzi
- Pulmonary and Critical Care Medicine Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 01255, USA
| | - Matthew J Campen
- Cancer Control and Population Sciences, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, 87131, USA.,College of Pharmacy, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Huining Kang
- Department of Internal Medicine, School of Medicine, University of New Mexico, Albuquerque, NM, 87131, USA.,Cancer Control and Population Sciences, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, 87131, USA
| | - Yiliang Zhu
- Department of Internal Medicine, School of Medicine, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Akshay Sood
- Department of Internal Medicine, School of Medicine, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Steven A Belinsky
- Cancer Control and Population Sciences, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, 87131, USA.,Lung Cancer Program, Lovelace Biomedical Research Institute, Albuquerque, NM, 87108, USA
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Benefits from Adjuvant Chemotherapy in Patients with Resected Non-Small Cell Lung Cancer: Possibility of Stratification by Gene Amplification of ACTN4 According to Evaluation of Metastatic Ability. Cancers (Basel) 2022; 14:cancers14184363. [PMID: 36139525 PMCID: PMC9497297 DOI: 10.3390/cancers14184363] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/01/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
Surgical treatment is the best curative treatment option for patients with non-small cell lung cancer (NSCLC), but some patients have recurrence beyond the surgical margin even after receiving curative surgery. Therefore, therapies with anti-cancer agents also play an important role perioperatively. In this paper, we review the current status of adjuvant chemotherapy in NSCLC and describe promising perioperative therapies, including molecularly targeted therapies and immune checkpoint inhibitors. Previously reported biomarkers of adjuvant chemotherapy for NSCLC are discussed along with their limitations. Adjuvant chemotherapy after resective surgery was most effective in patients with metastatic lesions located just outside the surgical margin; in addition, these metastatic lesions were the most sensitive to adjuvant chemotherapy. Thus, the first step in predicting patients who have sensitivity to adjuvant therapies is to perform a qualified evaluation of metastatic ability using markers such as actinin-4 (ACTN4). In this review, we discuss the potential use of biomarkers in patient stratification for effective adjuvant chemotherapy and, in particular, the use of ACTN4 as a possible biomarker for NSCLC.
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Xie B, Peng F, He F, Cheng Y, Cheng J, Zhou Z, Mao W. DNA methylation influences the CTCF-modulated transcription of RASSF1A in lung cancer cells. Cell Biol Int 2022; 46:1900-1914. [PMID: 35989484 DOI: 10.1002/cbin.11868] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/30/2022] [Accepted: 07/14/2022] [Indexed: 11/05/2022]
Abstract
Ras-association domain family 1A (RASSF1A) is one of the most methylated genes in lung cancer (LC). We investigate whether the high DNA methylation level of RASSF1A can relieve the resistance of RASSF1A to LC by inhibiting RASSF1A's transcription factor binding to RASSF1A. RASSF1A expression in tissues and cells was tested utilizing quantitative real-time polymerase chain reaction (qRT-PCR), and Western blot. RASSF1A expression and RASSF1A methylation level in LC cells exposed to 5-Aza-dc were assessed by qRT-PCR and quantitative methylation-specific PCR. The association between CTCF and RASSF1A was assessed using hTFtarget, ChIP, and luciferase reporter gene analysis. The effects of 5-Aza-dc, CTCF, and RASSF1A on cell biological behaviors and epithelial-mesenchymal transition (EMT)-related markers were assessed by cell function experiments and Western blot. Moreover, we constructed the xenograft tumor and pulmonary nodule metastasis models, and assessed tumor volume and weight. RASSF1A expression and pulmonary nodule metastasis were tested utilizing qRT-PCR, Western blot, and H&E staining. RASSF1A was under-expressed in LC tissues and cells. 5-Aza-dc enhanced RASSF1A level and weakened RASSF1A methylation level in LC cells. RASSF1A silencing neutralized 5-Aza-dc-mediated repressing effects on LC cell biological function and EMT. The loss of CTCF binding to RASSF1A in LC cells was associated with DNA methylation. The effect of 5-Aza-dc on RASSF1A level, LC cell malignant behaviors, and EMT-related factors were strengthened by CTCF upregulation. RASSF1A overexpression suppressed LC tumor growth and pulmonary nodule metastasis in vivo. DNA methylation blocked the modulation of RASSF1A expression by CTCF and relieved the resistance of RASSF1A to LC.
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Affiliation(s)
- Bin Xie
- Department of Respiratory Medicine, Yue Bei People's Hospital, Shaoguan, China
| | - Feng Peng
- Department of Respiratory Medicine, Yue Bei People's Hospital, Shaoguan, China
| | - Fengping He
- Central Laboratory, Yue Bei People's Hospital, Shaoguan, China
| | - Yixing Cheng
- Department of Respiratory Medicine, Huzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Huzhou, Zhejiang, China
| | - Jiangtao Cheng
- Department of Respiratory Medicine, Yue Bei People's Hospital, Shaoguan, China
| | - Zhibing Zhou
- Department of Respiratory Medicine, Yue Bei People's Hospital, Shaoguan, China
| | - Wei Mao
- Department of Respiratory Medicine, Huzhou Traditional Chinese Medicine Hospital Affiliated to Zhejiang Chinese Medical University, Huzhou, Zhejiang, China
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6
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Liu T, Guo W, Luo K, Li L, Dong J, Liu M, Shi X, Wang Z, Zhang J, Yin J, Qiu N, Lu M, Chen D, Jia X, Liu H, Gu Y, Xiong Y, Zheng G, Xu G, He Z, Zhang Z. Smoke-induced SAV1 Gene Promoter Hypermethylation Disrupts YAP Negative Feedback and Promotes Malignant Progression of Non-small Cell Lung Cancer. Int J Biol Sci 2022; 18:4497-4512. [PMID: 35864957 PMCID: PMC9295071 DOI: 10.7150/ijbs.73428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/02/2022] [Indexed: 11/26/2022] Open
Abstract
YAP (gene symbol YAP1) as a potential oncoprotein, is positively correlated with the malignancy of various tumors. However, overexpression of YAP alone in multiple normal tissue cells has failed to induce tumor formation and the underlying mechanism is poorly understood. Herein, we show that YAP activation directly induces transcription of its negative regulator, SAV1, to constitute a negative feedback loop, which plays a vital role in maintaining lung epithelial cell homeostasis and was dysregulated in non-small cell lung cancer (NSCLC). Notably, smoking promotes the hypermethylation of the SAV1 promoter region, which disrupts YAP negative feedback by inactivating the Hippo pathway. Besides, exogenous overexpression of SAV1 can act as a traffic protein, activating the Hippo signaling and concurrently inhibiting the WNT pathway to decrease cancer cell growth. Furthermore, using the lung cancer organoids, we found that lentivirus-mediated SAV1 gene transfer combined with methylation inhibitor and YAP-TEAD inhibitor is a potential feasible clinical medication regimen for the lung cancer patient, especially among the smoking population. Thus, this SAV1 mediated feedback loop provides an efficient mechanism to establish the robustness and homeostasis of YAP regulation and as a potential target of gene therapy for the smoking NSCLC population.
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Affiliation(s)
- Ting Liu
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Key Laboratory of "Translational Medicine on Malignant Tumor Treatment", Guangzhou city, Guangdong, P. R. China
| | - Wei Guo
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Key Laboratory of "Translational Medicine on Malignant Tumor Treatment", Guangzhou city, Guangdong, P. R. China
| | - Kai Luo
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Key Laboratory of "Translational Medicine on Malignant Tumor Treatment", Guangzhou city, Guangdong, P. R. China
| | - Lei Li
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Key Laboratory of "Translational Medicine on Malignant Tumor Treatment", Guangzhou city, Guangdong, P. R. China
| | - Jing Dong
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Key Laboratory of "Translational Medicine on Malignant Tumor Treatment", Guangzhou city, Guangdong, P. R. China
| | - Meijun Liu
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Key Laboratory of "Translational Medicine on Malignant Tumor Treatment", Guangzhou city, Guangdong, P. R. China
| | - Xingyuan Shi
- Department of Central Laboratory, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, P. R. China
| | - Zhiyuan Wang
- Department of Central Laboratory, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, P. R. China
| | - Jianlei Zhang
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Key Laboratory of "Translational Medicine on Malignant Tumor Treatment", Guangzhou city, Guangdong, P. R. China
| | - Jiang Yin
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Key Laboratory of "Translational Medicine on Malignant Tumor Treatment", Guangzhou city, Guangdong, P. R. China
| | - Ni Qiu
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Key Laboratory of "Translational Medicine on Malignant Tumor Treatment", Guangzhou city, Guangdong, P. R. China
| | - Minying Lu
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Key Laboratory of "Translational Medicine on Malignant Tumor Treatment", Guangzhou city, Guangdong, P. R. China
| | - Danyang Chen
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Key Laboratory of "Translational Medicine on Malignant Tumor Treatment", Guangzhou city, Guangdong, P. R. China
| | - Xiaoting Jia
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Key Laboratory of "Translational Medicine on Malignant Tumor Treatment", Guangzhou city, Guangdong, P. R. China
| | - Hao Liu
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Key Laboratory of "Translational Medicine on Malignant Tumor Treatment", Guangzhou city, Guangdong, P. R. China
| | - Yixue Gu
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Key Laboratory of "Translational Medicine on Malignant Tumor Treatment", Guangzhou city, Guangdong, P. R. China
| | - Yan Xiong
- Department of Central Laboratory, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, P. R. China
| | - Guopei Zheng
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Key Laboratory of "Translational Medicine on Malignant Tumor Treatment", Guangzhou city, Guangdong, P. R. China.,The State Key Laboratory of Respiratory, Guangzhou, Guangdong, P. R. China
| | - Gang Xu
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Key Laboratory of "Translational Medicine on Malignant Tumor Treatment", Guangzhou city, Guangdong, P. R. China
| | - Zhimin He
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Key Laboratory of "Translational Medicine on Malignant Tumor Treatment", Guangzhou city, Guangdong, P. R. China
| | - Zhijie Zhang
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou Key Laboratory of "Translational Medicine on Malignant Tumor Treatment", Guangzhou city, Guangdong, P. R. China
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Mohammed F, Baydaa Abed Hussein A, Ahmed T. Evaluation of Methylation Panel in the Promoter Region of p16INK4a , RASSF1A, and MGMT as a Biomarker in Sputum for Lung Cancer. ARCHIVES OF RAZI INSTITUTE 2022; 77:1075-1081. [PMID: 36618318 PMCID: PMC9759213 DOI: 10.22092/ari.2022.357985.2131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/21/2022] [Indexed: 01/10/2023]
Abstract
Lung cancer is the most common cause of cancer death in the world. Effective early detection and appropriate medications can help treat this deadly cancer. Therefore, early detection of lung cancer is of utmost importance, especially in screening high-risk populations (such as smokers) with an urgent need to identify new biomarkers. The present study aimed to demonstrate the potential of using the panel of DNA methylation as a biomarker for the early diagnosis of lung cancer from sputum samples. The methylated promoter of p16INK4a , RASSF1A, and MGMT genes was estimated by the methylation-specific polymerase chain reaction in a sample of 84 lung cancer patients (65 smokers and 19 non-smokers). Based on the results, p16INK4a promoter methylation was significantly associated with smoking habit and lung cancer progression in terms of histological grading and patient staging. The sensitivity and specificity of the p16INK4a gene as a biomarker for lung cancer were 71% and 90%, respectively. The methylated promoter of RASSF1A was less sensitive (48%) as a biomarker for lung cancer with 83%. The results demonstrated a strong association between promoter methylation of RASSF1A and late stages of lung cancer (P=0.0007). The sensitivity of the MGMT gene as a biomarker for lung cancer was 61% with high specificity (92%), compared to other candidate genes in this study. The epigenetic alteration in the promoter region of p16INK4a , RASSF1A, and MGMT genes is highly associated with cancer cell development. It is suggested that the use of these candidate biomarkers can be used as an adjunct to computed tomography screening to diagnose patients at high risk for lung cancer after validation.
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Affiliation(s)
- F Mohammed
- AL-Manara College for Medical Sciences, Department of Pharmacy, Maysan, Iraq
| | - A Baydaa Abed Hussein
- Department of Sciences, College of Basic Education, University of Misan, Maysan, Iraq
| | - T Ahmed
- AL-Manara College for Medical Sciences, Department of Pharmacy, Maysan, Iraq
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8
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High-throughput sample processing for methylation analysis in an automated, enclosed environment. SLAS Technol 2022; 27:172-179. [DOI: 10.1016/j.slast.2021.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Jin Y, Chen Z, Chen Q, Sha L, Shen C. [Role and Significance of Bioactive Substances in Sputum
in the Diagnosis of Lung Cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2021; 24:867-873. [PMID: 34923805 PMCID: PMC8695240 DOI: 10.3779/j.issn.1009-3419.2021.102.46] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
肺癌是我国目前发病率最高的恶性肿瘤之一,其诊断的金标准需要进行组织活检的病理学检查或脱落细胞学检查,二者的有创性和敏感性限制了他们的使用。痰液中含有大量核酸、蛋白质,是肺功能的良好反映物,肺癌组织也会影响痰液中的生物成分,检测其中的生物活性物质可有助于肺癌的诊断。本文综合目前国内外的研究结果,对痰液中可用于肺癌诊断的生物活性物质做一综述。
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Affiliation(s)
- Yuming Jin
- West China School of Medicine, Sichuan University, Chengdu 610041, China
| | - Zixuan Chen
- West China School of Medicine, Sichuan University, Chengdu 610041, China
| | - Quan Chen
- West China School of Medicine, Sichuan University, Chengdu 610041, China
| | - Leihao Sha
- West China School of Medicine, Sichuan University, Chengdu 610041, China
| | - Cheng Shen
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
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10
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Li N, Dhilipkannah P, Jiang F. High-Throughput Detection of Multiple miRNAs and Methylated DNA by Droplet Digital PCR. J Pers Med 2021; 11:jpm11050359. [PMID: 33946992 PMCID: PMC8146424 DOI: 10.3390/jpm11050359] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/14/2021] [Accepted: 04/22/2021] [Indexed: 01/04/2023] Open
Abstract
Altered miRNA expression and DNA methylation have highly active and diverse roles in carcinogenesis. Simultaneous detection of the molecular aberrations may have a synergistic effect on the diagnosis of malignancies. Herein, we develop a high-throughput assay for detecting multiple miRNAs and DNA methylation using droplet digital PCR (ddPCR) coupled with a 96-microwell plate. The microplate-based ddPCR could absolutely and reproducibly quantify 15 miRNAs and 14 DNA methylation sites with a high sensitivity (one copy/µL and 0.1%, respectively). Analyzing sputum and plasma of 40 lung cancer patients and 36 cancer-free smokers by this approach identified an integrated biomarker panel consisting of two sputum miRNAs (miRs-31-5p and 210-3p), one sputum DNA methylation (RASSF1A), and two plasma miRNAs (miR-21-5p and 126) for the diagnosis of lung cancer with higher sensitivity and specificity compared with a single type of biomarker. The diagnostic value of the integrated biomarker panel for the early detection of lung cancer was confirmed in a different cohort of 36 lung cancer patients and 39 cancer-free smokers. The high-throughput assay for quantification of multiple molecular aberrations across sputum and plasma could improve the early detection of lung cancer.
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11
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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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12
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Liu B, Ricarte Filho J, Mallisetty A, Villani C, Kottorou A, Rodgers K, Chen C, Ito T, Holmes K, Gastala N, Valyi-Nagy K, David O, Gaba RC, Ascoli C, Pasquinelli M, Feldman LE, Massad MG, Wang TH, Jusue-Torres I, Benedetti E, Winn RA, Brock MV, Herman JG, Hulbert A. Detection of Promoter DNA Methylation in Urine and Plasma Aids the Detection of Non-Small Cell Lung Cancer. Clin Cancer Res 2020; 26:4339-4348. [PMID: 32430478 PMCID: PMC7442601 DOI: 10.1158/1078-0432.ccr-19-2896] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/16/2020] [Accepted: 05/14/2020] [Indexed: 12/15/2022]
Abstract
PURPOSE Low-dose CT screening can reduce lung cancer-related mortality. However, CT screening has an FDR of nearly 96%. We sought to assess whether urine samples can be a source for DNA methylation-based detection of non-small cell lung cancer (NSCLC). EXPERIMENTAL DESIGN This nested case-control study of subjects with suspicious nodules on CT imaging obtained plasma and urine samples preoperatively. Cases (n = 74) had pathologic confirmation of NSCLC. Controls (n = 27) had a noncancer diagnosis. We detected promoter methylation in plasma and urine samples using methylation on beads and quantitative methylation-specific real-time PCR for cancer-specific genes (CDO1, TAC1, HOXA7, HOXA9, SOX17, and ZFP42). RESULTS DNA methylation at cancer-specific loci was detected in both plasma and urine, and was more frequent in patients with cancer compared with controls for all six genes in plasma and in CDO1, TAC1, HOXA9, and SOX17 in urine. Univariate and multivariate logistic regression analysis showed that methylation detection in each one of six genes in plasma and CDO1, TAC1, HOXA9, and SOX17 in urine were significantly associated with the diagnosis of NSCLC, independent of age, race, and smoking pack-years. When methylation was detected for three or more genes in both plasma and urine, the sensitivity and specificity for lung cancer diagnosis were 73% and 92%, respectively. CONCLUSIONS DNA methylation-based biomarkers in plasma and urine could be useful as an adjunct to CT screening to guide decision-making regarding further invasive procedures in patients with pulmonary nodules.
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Affiliation(s)
- Bin Liu
- Cancer Center, University of Illinois at Chicago, Chicago, Illinois
| | | | - Apurva Mallisetty
- Department of Surgery, University of Illinois at Chicago College of Medicine, Chicago, Illinois
| | - Cassandra Villani
- Department of Surgery, University of Illinois at Chicago College of Medicine, Chicago, Illinois
| | - Anastasia Kottorou
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Clinical and Molecular Oncology Laboratory, Medical School, University of Patras, Patras, Greece
| | - Kristen Rodgers
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Chen Chen
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P.R. China
| | - Tomoaki Ito
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Surgery, Juntendo University Shizuoka Hospital, Juntendo University School of Medicine, Shizuoka, Japan
| | - Kyla Holmes
- Cancer Center, University of Illinois at Chicago, Chicago, Illinois
| | - Nicole Gastala
- Department of Family Medicine, Mile Square Health Center, University of Illinois at Chicago College of Medicine, Chicago, Illinois
| | - Klara Valyi-Nagy
- Department of Pathology, University of Illinois at Chicago College of Medicine, Chicago, Illinois
| | - Odile David
- Department of Pathology, University of Illinois at Chicago College of Medicine, Chicago, Illinois
| | - Ron C Gaba
- Department of Radiology, University of Illinois at Chicago College of Medicine, Chicago, Illinois
| | - Christian Ascoli
- Department of Pulmonary, University of Illinois at Chicago College of Medicine, Chicago, Illinois
| | - Mary Pasquinelli
- Department of Pulmonary, University of Illinois at Chicago College of Medicine, Chicago, Illinois
| | - Lawrence E Feldman
- Department of Hematology and Oncology, University of Illinois at Chicago College of Medicine, Chicago, Illinois
| | - Malek G Massad
- Department of Surgery, University of Illinois at Chicago College of Medicine, Chicago, Illinois
| | - Tza-Huei Wang
- Department of Biomedical Engineering and Institute for Nano Biotechnology, The Johns Hopkins University, School of Medicine, Baltimore, Maryland
| | - Ignacio Jusue-Torres
- Department of Neurological Surgery, Loyola University Stritch School of Medicine, Maywood, Illinois
| | - Enrico Benedetti
- Department of Surgery, University of Illinois at Chicago College of Medicine, Chicago, Illinois
| | - Robert A Winn
- Cancer Center, University of Illinois at Chicago, Chicago, Illinois
- Department of Pulmonary, University of Illinois at Chicago College of Medicine, Chicago, Illinois
| | - Malcolm V Brock
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Sidney Kimmel Cancer Center, Department of Oncology, The Johns Hopkins University, School of Medicine, Baltimore, Maryland
| | - James G Herman
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.
| | - Alicia Hulbert
- Cancer Center, University of Illinois at Chicago, Chicago, Illinois.
- Department of Surgery, University of Illinois at Chicago College of Medicine, Chicago, Illinois
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13
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Epigenetic Silencing of LMX1A Contributes to Cancer Progression in Lung Cancer Cells. Int J Mol Sci 2020; 21:ijms21155425. [PMID: 32751497 PMCID: PMC7432919 DOI: 10.3390/ijms21155425] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/16/2020] [Accepted: 07/27/2020] [Indexed: 12/15/2022] Open
Abstract
Epigenetic modification is considered a major mechanism of the inactivation of tumor suppressor genes that finally contributes to carcinogenesis. LIM homeobox transcription factor 1α (LMX1A) is one of the LIM-homeobox-containing genes that is a critical regulator of growth and differentiation. Recently, LMX1A was shown to be hypermethylated and functioned as a tumor suppressor in cervical cancer, ovarian cancer, and gastric cancer. However, its role in lung cancer has not yet been clarified. In this study, we used public databases, methylation-specific PCR (MSP), reverse transcription PCR (RT-PCR), and bisulfite genomic sequencing to show that LMX1A was downregulated or silenced due to promoter hypermethylation in lung cancers. Treatment of lung cancer cells with the demethylating agent 5-aza-2'-deoxycytidine restored LMX1A expression. In the lung cancer cell lines H23 and H1299, overexpression of LMX1A did not affect cell proliferation but suppressed colony formation and invasion. These suppressive effects were reversed after inhibition of LMX1A expression in an inducible expression system in H23 cells. The quantitative RT-PCR (qRT-PCR) data showed that LMX1A could modulate epithelial mesenchymal transition (EMT) through E-cadherin (CDH1) and fibronectin (FN1). NanoString gene expression analysis revealed that all aberrantly expressed genes were associated with processes related to cancer progression, including angiogenesis, extracellular matrix (ECM) remodeling, EMT, cancer metastasis, and hypoxia-related gene expression. Taken together, these data demonstrated that LMX1A is inactivated through promoter hypermethylation and functions as a tumor suppressor. Furthermore, LMX1A inhibits non-small cell lung cancer (NSCLC) cell invasion partly through modulation of EMT, angiogenesis, and ECM remodeling.
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14
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Yang L, Zhang J, Yang G, Xu H, Lin J, Shao L, Li J, Guo C, Du Y, Guo L, Li X, Han-Zhang H, Wang C, Chuai S, Ye J, Kang Q, Liu H, Ying J, Wang Y. The prognostic value of a Methylome-based Malignancy Density Scoring System to predict recurrence risk in early-stage Lung Adenocarcinoma. Theranostics 2020; 10:7635-7644. [PMID: 32685009 PMCID: PMC7359091 DOI: 10.7150/thno.44229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 06/01/2020] [Indexed: 12/11/2022] Open
Abstract
Current NCCN guidelines do not recommend the use of adjuvant chemotherapy for stage IA lung adenocarcinoma patients with R0 surgery. However, 25% to 40% of patients with stage IA disease experience recurrence. Stratifying patients according to the recurrence risk may tailor adjuvant therapy and surveillance imaging for those with a higher risk. However, prognostic markers are often identified by comparing high-risk and low-risk cases which might introduce bias due to the widespread interpatient heterogeneity. Here, we developed a scoring system quantifying the degree of field cancerization in adjacent normal tissues and revealed its association with disease-free survival (DFS). Methods: We recruited a cohort of 44 patients with resected stage IA lung adenocarcinoma who did not receive adjuvant therapy. Both tumor and adjacent normal tissues were obtained from each patient and subjected to capture-based targeted genomic and epigenomic profiling. A novel methylome-based scoring system namely malignancy density ratio (MD ratio) was developed based on 39 patients by comparing tumor and corresponding adjacent normal tissues of each patient. A MD score was then obtained by Wald statistics. The correlations of MD ratio, MD score, and genomic features with clinical outcome were investigated. Results: Patients with a high-risk MD ratio showed a significantly shorter postsurgical DFS compared with those with a low-risk MD ratio (HR=4.47, P=0.01). The MD ratio was not associated with T stage (P=1), tumor cell fraction (P=0.748) nor inflammatory status (p=0.548). Patients with a high-risk MD score also demonstrated an inferior DFS (HR=4.69, P=0.039). In addition, multivariate analysis revealed EGFR 19 del (HR=5.39, P=0.012) and MD score (HR= 7.90, P=0.01) were independent prognostic markers. Conclusion: The novel methylome-based scoring system, developed by comparing the signatures between tumor and corresponding adjacent normal tissues of individual patients, largely minimizes the bias of interpatient heterogeneity and reveals a robust prognostic value in patients with resected lung adenocarcinoma.
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15
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Tessema M, Tassew DD, Yingling CM, Do K, Picchi MA, Wu G, Petersen H, Randell S, Lin Y, Belinsky SA, Tesfaigzi Y. Identification of novel epigenetic abnormalities as sputum biomarkers for lung cancer risk among smokers and COPD patients. Lung Cancer 2020; 146:189-196. [PMID: 32559455 DOI: 10.1016/j.lungcan.2020.05.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/09/2020] [Accepted: 05/12/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVES Smoking is a common risk factor for chronic obstructive pulmonary disease (COPD) and lung cancer. Although COPD patients have higher risk of lung cancer compared to non-COPD smokers, the molecular links between these diseases are not well-defined. This study aims to identify genes that are downregulated by cigarette smoke and commonly repressed in COPD and lung cancer. MATERIALS AND METHODS Primary human airway epithelial cells (HAEC) were exposed to cigarette-smoke-extract (CSE) for 10-weeks and significantly suppressed genes were identified by transcriptome array. Epigenetic abnormalities of these genes in lung adenocarcinoma (LUAD) from patients with or without COPD were determined using genome-wide and gene-specific assays and by in vitro treatment of cell lines with trichostatin-A or 5-aza-2-deoxycytidine. RESULTS The ten most commonly downregulated genes following chronic CSE exposure of HAEC and show promoter hypermethylation in LUAD were selected. Among these, expression of CCNA1, SNCA, and ZNF549 was significantly reduced in lung tissues from COPD compared with non-COPD cases while expression of CCNA1 and SNCA was further downregulated in tumors with COPD. The promoter regions of all three genes were hypermethylated in LUAD but not normal or COPD lungs. The reduced expression and aberrant promoter hypermethylation of these genes in LUAD were independently validated using data from the Cancer Genome Atlas project. Importantly, SNCA and ZNF549 methylation detected in sputum DNA from LUAD (52% and 38%) cases were more prevalent compared to cancer-free smokers (26% and 15%), respectively (p < 0.02). CONCLUSIONS Our data show that suppression of CCNA1, SNCA, and ZNF549 in lung cancer and COPD occurs with or without promoter hypermethylation, respectively. Detecting methylation of these and previously identified genes in sputum of cancer-free smokers may serve as non-invasive biomarkers for early detection of lung cancer among high risk smokers including COPD patients.
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Affiliation(s)
- Mathewos Tessema
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, M, USA.
| | - Dereje D Tassew
- COPD Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA; Currently, Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Christin M Yingling
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, M, USA
| | - Kieu Do
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, M, USA
| | - Maria A Picchi
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, M, USA
| | - Guodong Wu
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, M, USA
| | - Hans Petersen
- COPD Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Scott Randell
- Department of Cell and Molecular Physiology, The University of North Carolina, Chapel Hill, NC, USA
| | - Yong Lin
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, M, USA
| | - Steven A Belinsky
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, M, USA
| | - Yohannes Tesfaigzi
- COPD Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA; Currently, Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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16
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Wang Z, Zhang L, Li L, Li X, Xu Y, Wang M, Liang L, Jiao P, Li Y, He S, Du J, He L, Tang M, Sun M, Yang L, Di J, Zhu G, Shi H, Liu D. Sputum Cell-Free DNA: Valued Surrogate Sample for Detection of EGFR Mutation in Patients with Advanced Lung Adenocarcinoma. J Mol Diagn 2020; 22:934-942. [PMID: 32407801 DOI: 10.1016/j.jmoldx.2020.04.208] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 03/24/2020] [Accepted: 04/13/2020] [Indexed: 12/16/2022] Open
Abstract
Sputum is a common cytologic sample type, but its potential use in EGFR mutation detection in patients with lung cancer is not fully evaluated. This study established an improved sputum cell-free DNA (cfDNA) extraction method study and applied a super-amplification refractory mutation system to detect the EGFR mutation status in sputum cfDNA. The sputum sediments were used for cytology evaluation. The study included 102 lung adenocarcinoma patients; 65 patients (63.7%) were positive for EGFR mutations in tumor samples. EGFR mutation status was positive in 30 patients (29.4%) by sputum cfDNA testing, achieving an overall sensitivity and specificity of 46.2% and 100%, respectively. Comparison of EGFR mutation status in tumor samples revealed that the sensitivity of testing sputum cfDNA in 40 patients with stage I to IIIA versus 62 patients with stage IIIB to IV was 24% (6/25) versus 65.0% (26/40). Through cytology evaluation, the sputum specimens from 62 advanced patients were classified into three categories: 10 were unsatisfactory; 34 were satisfactory but had no malignant cells; and 18 had malignant cells. The sensitivities of these three categories were 0% (0/8), 71.4% (15/21), and 100% (11/11), respectively. These findings revealed that with the improved cfDNA extraction method and sputum cytology evaluation, sputum cfDNA is a valuable surrogate sample type for detecting clinical EGFR mutations in advanced lung adenocarcinoma patients.
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Affiliation(s)
- Zheng Wang
- Department of Pathology, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
| | - Lin Zhang
- Department of Pathology, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
| | - Lin Li
- Department of Oncology, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
| | - Xiaoguang Li
- Minimally Invasive Tumor Therapies Center, National Center of Gerontology, Beijing, People's Republic of China
| | - Yan Xu
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, People's Republic of China
| | - Mengzhao Wang
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, People's Republic of China
| | - Li Liang
- Department of Cancer Chemotherapy and Radiation Sickness, Peking University Third Hospital, Beijing, People's Republic of China
| | - Peng Jiao
- Department of Thoracic Surgery, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
| | - Yuanming Li
- Minimally Invasive Tumor Therapies Center, National Center of Gerontology, Beijing, People's Republic of China
| | - Shurong He
- Department of Pathology, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
| | - Jun Du
- Department of Pathology, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
| | - Lei He
- Department of Pathology, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
| | - Min Tang
- Department of Oncology, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
| | - Mingjun Sun
- Department of Pathology, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
| | - Li Yang
- Department of Pathology, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
| | - Jing Di
- Department of Pathology, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
| | - Guanshan Zhu
- Amoy Diagnostics Co, Ltd, Xiamen, People's Republic of China
| | - Hong Shi
- Department of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.
| | - Dongge Liu
- Department of Pathology, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China.
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17
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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.
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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
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18
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Teneng I, Picchi MA, Leng S, Dagucon CP, Ramalingam S, Tellez CS, Belinsky SA. DNA-PKc deficiency drives pre-malignant transformation by reducing DNA repair capacity in concert with reprogramming the epigenome in human bronchial epithelial cells. DNA Repair (Amst) 2019; 79:1-9. [PMID: 31055244 PMCID: PMC6551272 DOI: 10.1016/j.dnarep.2019.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/11/2019] [Accepted: 04/13/2019] [Indexed: 12/14/2022]
Abstract
The expression of DNA-dependent protein kinase catalytic subunit (DNA-PKc) is highly variable in smokers and reduced enzyme activity has been associated with risk for lung cancer. An in vitro model of lung pre-malignancy was used to evaluate the role of double-strand break DNA repair capacity in transformation of hTERT/CDK4 immortalized human bronchial epithelial cells (HBECs) and reprograming of the epigenome. Here we show that knockdown of DNA-PKc to levels simulating haploinsufficiency dramatically reduced DNA repair capacity following challenge with bleomycin and significantly increased transformation efficiency of HBEC lines exposed weekly for 12 weeks to this radiomimetic. Transformed HBEC lines with wild type or knockdown of DNA-PKc showed altered expression of more than 1,000 genes linked to major cell regulatory pathways involved in lung cancer. While lung cancer driver mutations were not detected in transformed clones, more than 300 genes that showed reduced expression associated with promoter methylation in transformed clones or predictive for methylation in malignant tumors were identified. These studies support reduced DNA repair capacity as a key factor in the initiation and clonal expansion of pre-neoplastic cells and double-strand break DNA damage as causal for epigenetic mediated silencing of many lung cancer-associated genes. The fact that DNA damage, repair, and epigenetic silencing of genes are causal for many other cancers that include colon and prostate extends the generalizability and impact of these findings.
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Affiliation(s)
- Ivo Teneng
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Maria A Picchi
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Shuguang Leng
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | | | - Suresh Ramalingam
- Department of Hematology and Oncology, Emory University School of Medicine, Winship Cancer Institute, Atlanta, GA, USA
| | - Carmen S Tellez
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Steven A Belinsky
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA.
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19
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Abstract
While lung cancer has been the leading cause of cancer-related deaths for many years in the United States, incidence and mortality statistics - among other measures - vary widely worldwide. The aim of this study was to review the evidence on lung cancer epidemiology, including data of international scope with comparisons of economically, socially, and biologically different patient groups. In industrialized nations, evolving social and cultural smoking patterns have led to rising or plateauing rates of lung cancer in women, lagging the long-declining smoking and cancer incidence rates in men. In contrast, emerging economies vary widely in smoking practices and cancer incidence but commonly also harbor risks from environmental exposures, particularly widespread air pollution. Recent research has also revealed clinical, radiologic, and pathologic correlates, leading to greater knowledge in molecular profiling and targeted therapeutics, as well as an emphasis on the rising incidence of adenocarcinoma histology. Furthermore, emergent evidence about the benefits of lung cancer screening has led to efforts to identify high-risk smokers and development of prediction tools. This review also includes a discussion on the epidemiologic characteristics of special groups including women and nonsmokers. Varying trends in smoking largely dictate international patterns in lung cancer incidence and mortality. With declining smoking rates in developed countries and knowledge gains made through molecular profiling of tumors, the emergence of new risk factors and disease features will lead to changes in the landscape of lung cancer epidemiology.
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Affiliation(s)
- Julie A. Barta
- Division of Pulmonary and Critical Care Medicine, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, US
| | - Charles A. Powell
- Division of Pulmonary, Critical Care, and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, US
| | - Juan P. Wisnivesky
- Division of Pulmonary, Critical Care, and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, US
- Division of General Internal Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, US
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20
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Leng S, Diergaarde B, Picchi MA, Wilson DO, Gilliland FD, Yuan JM, Siegfried JM, Belinsky SA. Gene Promoter Hypermethylation Detected in Sputum Predicts FEV 1 Decline and All-Cause Mortality in Smokers. Am J Respir Crit Care Med 2018; 198:187-196. [PMID: 29437466 PMCID: PMC6058990 DOI: 10.1164/rccm.201708-1659oc] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2017] [Accepted: 02/12/2018] [Indexed: 02/07/2023] Open
Abstract
RATIONALE Gene promoter hypermethylation detected in sputum assesses the extent of field cancerization and predicts lung cancer (LC) risk in ever-smokers. A rapid decline of FEV1 is a major driver for development of airway obstruction. OBJECTIVES To assess the effects of methylation of 12 genes on FEV1 decline and of FEV1 decline on subsequent LC incidence using two independent, longitudinal cohorts (i.e., LSC [Lovelace Smokers Cohort] and PLuSS [Pittsburgh Lung Screening Study]). METHODS Gene methylation was measured in sputum using two-stage nested methylation-specific PCR. The linear mixed effects model was used to assess the effects of studied variables on FEV1 decline. MEASUREMENTS AND MAIN RESULTS A dose-dependent relationship between number of genes methylated and FEV1 decline was identified, with smokers with three or more methylated genes having 27.8% and 10.3% faster FEV1 decline than smokers with zero to two methylated genes in the LSC and PLuSS cohort, respectively (all P < 0.01). High methylation in sputum was associated with a shorter latency for LC incidence (log-rank P = 0.0048) and worse all-cause mortality (log-rank P < 0.0001). Smokers with subsequent LC incidence had a more rapid annual decline of FEV1 (by 5.2 ml, P = 0.038) than smoker control subjects. CONCLUSIONS Gene methylation detected in sputum predicted FEV1 decline, LC incidence, and all-cause mortality in smokers. Rapid FEV1 decline may be a risk factor for LC incidence in smokers, which may explain a greater prevalence of airway obstruction seen in patients with LC.
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Affiliation(s)
- Shuguang Leng
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
- Cancer Control Research Program and
- School of Public Health, Qingdao University, Qingdao, Shandong, China
| | - Brenda Diergaarde
- Department of Human Genetics and
- Cancer Epidemiology and Prevention Program
- Lung Cancer Program, and
| | - Maria A. Picchi
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - David O. Wilson
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Frank D. Gilliland
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California; and
| | - Jian-Min Yuan
- Department of Epidemiology, Graduate School of Public Health, and
- Division of Cancer Control and Population Sciences, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | | | - Steven A. Belinsky
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
- Cancer Control Research Program and
- Cancer Genetics and Epigenetics Program, University of New Mexico Comprehensive Cancer Center, Albuquerque, New Mexico
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21
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Su Y, Fang HB, Jiang F. An epigenetic classifier for early stage lung cancer. Clin Epigenetics 2018; 10:68. [PMID: 29796119 PMCID: PMC5964676 DOI: 10.1186/s13148-018-0502-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 05/14/2018] [Indexed: 12/19/2022] Open
Abstract
Background Methylated genes detected in sputum are promise biomarkers for lung cancer. Yet the current PCR technologies for quantification of DNA methylation and diagnostic value of the sputum biomarkers are not sufficient to be used for lung cancer early detection. The emerging droplet digital PCR (ddPCR) is a straightforward means for precise, direct, and absolute quantification of nucleic acids. Here, we investigate whether ddPCR can sensitively and robustly quantify DNA methylation in sputum for more precise diagnosis of lung cancer. Results First, the analytic performance of methylation-specific ddPCR (ddMSP) and quantitative methylation-specific PCR (qMSP) is determined in methylated and unmethylated DNA samples. Second, 29 genes, previously proposed as potential sputum biomarkers for lung cancer, are analyzed by using ddMSP in a training set of 127 lung cancer patients and 159 controls. ddMSP has higher sensitivity, precision, and reproducibility for quantification of methylation compared with qMSP (all p < 0.05). A classifier comprising four sputum methylation biomarkers for lung cancer is developed by using ddMSP, producing 86.6% sensitivity and 90.6% specificity, independent of stage and histology of lung cancer (all p > 0.05). The classifier has higher accuracy compared with sputum cytology (88.8 vs. 70.6%, p < 0.01). The diagnostic performance is confirmed in a testing set of 89 cases and 107 controls. Conclusions ddMSP is a robust tool for reliable quantification of DNA methylation in sputum, and the epigenetic classifier could help diagnose lung cancer at the early stage.
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Affiliation(s)
- Yun Su
- 1Department of Surgery, Jiangsu Province Hospital of Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing, 210023 China
| | - Hong Bin Fang
- 2Department of Biostatistics, Bioinformatics and Biomathematics, Georgetown University Medical Center, 4000 Reservoir Road, N.W, Washington D.C., 20057 USA
| | - Feng Jiang
- 3Department of Pathology, University of Maryland School of Medicine, Baltimore, MD USA
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22
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Dong X, Shi M, Lee M, Toro R, Gravina S, Han W, Yasuda S, Wang T, Zhang Z, Vijg J, Suh Y, Spivack SD. Global, integrated analysis of methylomes and transcriptomes from laser capture microdissected bronchial and alveolar cells in human lung. Epigenetics 2018; 13:264-274. [PMID: 29465290 DOI: 10.1080/15592294.2018.1441650] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Gene regulatory analysis of highly diverse human tissues in vivo is essentially constrained by the challenge of performing genome-wide, integrated epigenetic and transcriptomic analysis in small selected groups of specific cell types. Here we performed genome-wide bisulfite sequencing and RNA-seq from the same small groups of bronchial and alveolar cells isolated by laser capture microdissection from flash-frozen lung tissue of 12 donors and their peripheral blood T cells. Methylation and transcriptome patterns differed between alveolar and bronchial cells, while each of these epithelia showed more differences from mesodermally-derived T cells. Differentially methylated regions (DMRs) between alveolar and bronchial cells tended to locate at regulatory regions affecting promoters of 4,350 genes. A large number of pathways enriched for these DMRs including GTPase signal transduction, cell death, and skeletal muscle. Similar patterns of transcriptome differences were observed: 4,108 differentially expressed genes (DEGs) enriched in GTPase signal transduction, inflammation, cilium assembly, and others. Prioritizing using DMR-DEG regulatory network, we highlighted genes, e.g., ETS1, PPARG, and RXRG, at prominent alveolar vs. bronchial cell discriminant nodes. Our results show that multi-omic analysis of small, highly specific cells is feasible and yields unique physiologic loci distinguishing human lung cell types in situ.
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Affiliation(s)
- Xiao Dong
- a Department of Genetics , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA
| | - Miao Shi
- b Department of Medicine , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA
| | - Moonsook Lee
- a Department of Genetics , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA
| | - Rafael Toro
- a Department of Genetics , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA
| | - Silvia Gravina
- a Department of Genetics , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA
| | - Weiguo Han
- b Department of Medicine , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA
| | - Shoya Yasuda
- c Department of Computational Intelligence and Systems Science , Tokyo Institute of Technology , 4259 Nagatsuta-cho, Midori-ku, Yokohama , Kanagawa 226-8502 , Japan
| | - Tao Wang
- d Department of Epidemiology & Population Health , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA
| | - Zhengdong Zhang
- a Department of Genetics , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA
| | - Jan Vijg
- a Department of Genetics , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA.,e Department of Ophthalmology & Visual Sciences , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA
| | - Yousin Suh
- a Department of Genetics , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA.,b Department of Medicine , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA.,e Department of Ophthalmology & Visual Sciences , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA
| | - Simon D Spivack
- a Department of Genetics , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA.,b Department of Medicine , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA.,d Department of Epidemiology & Population Health , Albert Einstein College of Medicine , 1301 Morris Park Ave, Bronx , New York 10461 , USA
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23
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de Antonellis P, De Luca A, Normanno N. Gene methylation in liquid biopsy and risk of recurrence in lung cancer. J Thorac Dis 2018; 10:1286-1289. [PMID: 29707279 DOI: 10.21037/jtd.2018.02.84] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Pasqualino de Antonellis
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Antonella De Luca
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
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24
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Kim H, Wang X, Jin P. Developing DNA methylation-based diagnostic biomarkers. J Genet Genomics 2018; 45:87-97. [PMID: 29496486 DOI: 10.1016/j.jgg.2018.02.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 01/29/2018] [Accepted: 02/12/2018] [Indexed: 02/06/2023]
Abstract
An emerging paradigm shift for disease diagnosis is to rely on molecular characterization beyond traditional clinical and symptom-based examinations. Although genetic alterations and transcription signature were first introduced as potential biomarkers, clinical implementations of these markers are limited due to low reproducibility and accuracy. Instead, epigenetic changes are considered as an alternative approach to disease diagnosis. Complex epigenetic regulation is required for normal biological functions and it has been shown that distinctive epigenetic disruptions could contribute to disease pathogenesis. Disease-specific epigenetic changes, especially DNA methylation, have been observed, suggesting its potential as disease biomarkers for diagnosis. In addition to specificity, the feasibility of detecting disease-associated methylation marks in the biological specimens collected noninvasively, such as blood samples, has driven the clinical studies to validate disease-specific DNA methylation changes as a diagnostic biomarker. Here, we highlight the advantages of DNA methylation signature for diagnosis in different diseases and discuss the statistical and technical challenges to be overcome before clinical implementation.
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Affiliation(s)
- Hyerim Kim
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Xudong Wang
- Department of Gastroenterological Surgery, The Second Hospital, Jilin University, Changchun 130041, China.
| | - Peng Jin
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA.
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25
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Leng S, Picchi MA, Kang H, Wu G, Filipczak PT, Juri DE, Zhang X, Gauderman WJ, Gilliland FD, Belinsky SA. Dietary Nutrient Intake, Ethnicity, and Epigenetic Silencing of Lung Cancer Genes Detected in Sputum in New Mexican Smokers. Cancer Prev Res (Phila) 2017; 11:93-102. [PMID: 29118161 DOI: 10.1158/1940-6207.capr-17-0196] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 09/19/2017] [Accepted: 10/30/2017] [Indexed: 12/17/2022]
Abstract
Lung cancer gene methylation detected in sputum assesses field cancerization and predicts lung cancer incidence. Hispanic smokers have higher lung cancer susceptibility compared with non-Hispanic whites (NHW). We aimed to identify novel dietary nutrients affecting lung cancer gene methylation and determine the degree of ethnic disparity in methylation explained by diet. Dietary intakes of 139 nutrients were assessed using a validated Harvard food frequency questionnaire in 327 Hispanics and 1,502 NHWs from the Lovelace Smokers Cohort. Promoter methylation of 12 lung cancer genes was assessed in sputum DNA. A global association was identified between dietary intake and gene methylation (Ppermutation = 0.003). Seventeen nutrient measurements were identified with magnitude of association with methylation greater than that seen for folate. A stepwise approach identified B12, manganese, sodium, and saturated fat as the minimally correlated set of nutrients whose optimal intakes could reduce the methylation by 36% (Ppermutation < 0.001). Six protective nutrients included vitamin D, B12, manganese, magnesium, niacin, and folate. Approximately 42% of ethnic disparity in methylation was explained by insufficient intake of protective nutrients in Hispanics compared with NHWs. Functional validation of protective nutrients showed an enhanced DNA repair capacity toward double-strand DNA breaks, a mechanistic biomarker strongly linked to acquisition of lung cancer gene methylation in smokers. Dietary intake is a major modifiable factor for preventing promoter methylation of lung cancer genes in smokers' lungs. Complex dietary supplements could be developed on the basis of these protective nutrients for lung cancer chemoprevention in smokers. Hispanic smokers may benefit the most from this complex for reducing their lung cancer susceptibility. Cancer Prev Res; 11(2); 93-102. ©2017 AACR.
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Affiliation(s)
- Shuguang Leng
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico. .,Cancer Control (CaC) Research Program, University of New Mexico Cancer Center, Albuquerque, New Mexico
| | - Maria A Picchi
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Huining Kang
- Department of Internal Medicine and UNM Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Guodong Wu
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Piotr T Filipczak
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Daniel E Juri
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Xiequn Zhang
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - W James Gauderman
- Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Frank D Gilliland
- Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Steven A Belinsky
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico. .,Cancer Control (CaC) Research Program, University of New Mexico Cancer Center, Albuquerque, New Mexico
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26
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Fusco N, Fumagalli C, Guerini-Rocco E. Looking for sputum biomarkers in lung cancer secondary prevention: where are we now? J Thorac Dis 2017; 9:4277-4279. [PMID: 29268490 DOI: 10.21037/jtd.2017.10.22] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Nicola Fusco
- Division of Pathology, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy.,Department of Biomedical, Surgical, and Dental Sciences, University of Milan, Milan, Italy
| | | | - Elena Guerini-Rocco
- Division of Pathology, European Institute of Oncology, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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27
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Duruisseaux M, Esteller M. Lung cancer epigenetics: From knowledge to applications. Semin Cancer Biol 2017; 51:116-128. [PMID: 28919484 DOI: 10.1016/j.semcancer.2017.09.005] [Citation(s) in RCA: 183] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 09/12/2017] [Accepted: 09/13/2017] [Indexed: 12/17/2022]
Abstract
Lung cancer is the leading cause of cancer-related mortality worldwide. Advances in our understanding of the genomics of lung cancer have led to substantial progress in the treatment of specific molecular subsets. Immunotherapy also emerges as a major breakthrough in lung cancer treatment. However, challenges remain as a consensual approach for early lung cancer detection remains elusive while primary or secondary drug resistance eventually leads to treatment failure in all patients with advanced disease. Furthermore, a large portion of patients are still treated with conventional chemotherapy that is only modestly effective. The last two decades have seen exponential developments in the epigenetic understanding of lung cancer. Epigenetic alterations in DNA methylation, non-coding RNA expression, chromatin modeling and post transcriptional regulators are key events in each step of lung cancer pathogenesis. Here, we review the central role epigenetic disruptions play in lung cancer carcinogenesis and the acquisition of cancerous phenotype and aggressive behavior as well as in the resistance to therapy. Epigenetic disruptions could represent reliable biomarkers for lung cancer risk assessment, early diagnosis, prognosis stratification, molecular classification and prediction of treatment efficacy. The therapeutic potential of epigenetics targeted drugs in combination with chemotherapy, targeted therapy and/or immunotherapy is currently being intensively investigated. We suggest that integration of tissue-derived or circulating epigenetic biomarkers and epidrugs in clinical trial design will translate epigenetic knowledge of lung cancer into the clinic and improve lung cancer patient outcomes.
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Affiliation(s)
- Michaël Duruisseaux
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain and Centro de Investigación Biomédica en Red de Cáncer (CIBERONC); Department of Respiratory Medecine, Hôpital Louis-Pradel, Hospices civils de Lyon, 28 avenue du Doyen Lépine, 69677, Lyon cedex, France.
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain and Centro de Investigación Biomédica en Red de Cáncer (CIBERONC); Instituciò Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Catalonia, Spain; Department of Physiological Sciences II, School of Medicine, University of Barcelona, 08036, Barcelona, Catalonia, Spain.
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28
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Belinsky SA, Leng S, Wu G, Thomas CL, Picchi MA, Lee SJ, Aisner S, Ramalingam S, Khuri FR, Karp DD. Gene Methylation Biomarkers in Sputum and Plasma as Predictors for Lung Cancer Recurrence. Cancer Prev Res (Phila) 2017; 10:635-640. [PMID: 28904059 DOI: 10.1158/1940-6207.capr-17-0177] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/20/2017] [Accepted: 08/31/2017] [Indexed: 12/25/2022]
Abstract
Detection of methylated genes in exfoliated cells from the lungs of smokers provides an assessment of the extent of field cancerization, is a validated biomarker for predicting lung cancer, and provides some discrimination when interrogated in blood. The potential utility of this 8-gene methylation panel for predicting tumor recurrence has not been assessed. The Eastern Cooperative Oncology Group initiated a prevention trial (ECOG-ACRIN5597) that enrolled resected stage I non-small cell lung cancer patients who were randomized 2:1 to receive selenized yeast versus placebo for 4 years. We conducted a correlative biomarker study to assess prevalence for methylation of the 8-gene panel in longitudinally collected sputum and blood after tumor resection to determine whether selenium alters their methylation profile and whether this panel predicts local and/or distant recurrence. Patients (N = 1,561) were enrolled into the prevention trial; 565 participated in the biomarker study with 122 recurrences among that group. Assessing the association between recurrence and risk of gene methylation longitudinally for up to 48 months showed a 1.4-fold increase in OR for methylation in sputum in the placebo group independent of location (local or distant). Kaplan-Meier curves evaluating the association between number of methylated genes and time to recurrence showed no increased risk in sputum, while a significant HR of 1.5 was seen in plasma. Methylation detection in sputum and blood is associated with risk for recurrence. Cancer Prev Res; 10(11); 635-40. ©2017 AACR.
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Affiliation(s)
- Steven A Belinsky
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico.
| | - Shuguang Leng
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Guodong Wu
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Cynthia L Thomas
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Maria A Picchi
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Sandra J Lee
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Seena Aisner
- Rutgers New Jersey Medical School, Newark, New Jersey
| | - Suresh Ramalingam
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, Georgia
| | - Fadlo R Khuri
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, Georgia
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29
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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.
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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
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30
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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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31
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Hulbert A, Jusue-Torres I, Stark A, Chen C, Rodgers K, Lee B, Griffin C, Yang A, Huang P, Wrangle J, Belinsky SA, Wang TH, Yang SC, Baylin SB, Brock MV, Herman JG. Early Detection of Lung Cancer Using DNA Promoter Hypermethylation in Plasma and Sputum. Clin Cancer Res 2017; 23:1998-2005. [PMID: 27729459 PMCID: PMC6366618 DOI: 10.1158/1078-0432.ccr-16-1371] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 09/17/2016] [Accepted: 09/20/2016] [Indexed: 12/12/2022]
Abstract
Purpose: CT screening can reduce death from lung cancer. We sought to improve the diagnostic accuracy of lung cancer screening using ultrasensitive methods and a lung cancer-specific gene panel to detect DNA methylation in sputum and plasma.Experimental Design: This is a case-control study of subjects with suspicious nodules on CT imaging. Plasma and sputum were obtained preoperatively. Cases (n = 150) had pathologic confirmation of node-negative (stages I and IIA) non-small cell lung cancer. Controls (n = 60) had non-cancer diagnoses. We detected promoter methylation using quantitative methylation-specific real-time PCR and methylation-on-beads for cancer-specific genes (SOX17, TAC1, HOXA7, CDO1, HOXA9, and ZFP42).Results: DNA methylation was detected in plasma and sputum more frequently in people with cancer compared with controls (P < 0.001) for five of six genes. The sensitivity and specificity for lung cancer diagnosis using the best individual genes was 63% to 86% and 75% to 92% in sputum, respectively, and 65% to 76% and 74% to 84% in plasma, respectively. A three-gene combination of the best individual genes has sensitivity and specificity of 98% and 71% using sputum and 93% and 62% using plasma. Area under the receiver operating curve for this panel was 0.89 [95% confidence interval (CI), 0.80-0.98] in sputum and 0.77 (95% CI, 0.68-0.86) in plasma. Independent blinded random forest prediction models combining gene methylation with clinical information correctly predicted lung cancer in 91% of subjects using sputum detection and 85% of subjects using plasma detection.Conclusions: High diagnostic accuracy for early-stage lung cancer can be obtained using methylated promoter detection in sputum or plasma. Clin Cancer Res; 23(8); 1998-2005. ©2016 AACR.
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Affiliation(s)
- Alicia Hulbert
- Sidney Kimmel Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ignacio Jusue-Torres
- Department of Neurosurgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alejandro Stark
- Department of Mechanical Engineering, The Johns Hopkins University, Baltimore, Maryland
| | - Chen Chen
- Sidney Kimmel Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Thoracic Surgery, Second Xiangya Hospital of Central South University, Changsha, Hunan, PR China
| | - Kristen Rodgers
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Beverly Lee
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Candace Griffin
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Andrew Yang
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Peng Huang
- Sidney Kimmel Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Biostatistics, The Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - John Wrangle
- Department of Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Steven A Belinsky
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Tza-Huei Wang
- Sidney Kimmel Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Mechanical Engineering, The Johns Hopkins University, Baltimore, Maryland
- Department of Biomedical Engineering and Institute for NanoBioTechnology, The Johns Hopkins University, School of Medicine, Baltimore, Maryland
| | - Stephen C Yang
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Stephen B Baylin
- Sidney Kimmel Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Malcolm V Brock
- Sidney Kimmel Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - James G Herman
- Sidney Kimmel Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland.
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
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Gaballah IF, Helal SF, Mourad BH. Early detection of lung cancer potential among Egyptian wood workers. INTERNATIONAL JOURNAL OF OCCUPATIONAL AND ENVIRONMENTAL HEALTH 2017; 23:120-127. [PMID: 29359635 PMCID: PMC6060858 DOI: 10.1080/10773525.2018.1428265] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 01/11/2018] [Indexed: 01/08/2023]
Abstract
Wood dust is known to be a human carcinogen, with a considerable risk of lung cancer. The increased cancer risk is likely induced through its genotoxic effects resulting from oxidative DNA damage. This study aimed at assessing the genotoxicity of wood dust and demonstrating the role of sputum PCR as a screening tool for early prediction of lung cancer among wood workers. The study was carried out in the carpentry section of a modernized factory involved with the manufacture of wooden furniture in Greater Cairo, Egypt. Environmental assessment of respirable wood dust concentrations was done. Frequency of chromosomal aberrations (CA%) and sister chromatid exchanges (SCE%) in peripheral blood lymphocytes (PBL) was assessed and comet assays were performed in samples from among the study population (n = 86). Levels of superoxide dismutase (SOD) and glutathione peroxidase (GPx) enzymes were measured. The polymerase chain reaction (PCR) was used to study hypermethylation of p16 and ̸or O6-methylguanine-DNA methyltransferase (MGMT) gene promoters in sputum DNA. The concentrations of respirable wood dust exceeded the Egyptian and international permissible limits with highest levels generated by sawing operations. Laboratory investigations revealed statistically significantly higher frequencies of CA and SCE as well as increased comet tail length associated with significant decrement in the levels of SOD and GPx among exposed group. A statistically significant elevation in the extent of hypermethylation was detected for the p16 and MGMT gene promoters in the sputum DNA of studied wood workers. The study results support the conclusion that prolonged unprotected occupational exposure to wood dust is associated with possible genotoxicity and oxidative stress that might raise the risk for carcinogenesis including lung cancer.
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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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Lu Y, Li S, Zhu S, Gong Y, Shi J, Xu L. Methylated DNA/RNA in Body Fluids as Biomarkers for Lung Cancer. Biol Proced Online 2017; 19:2. [PMID: 28331435 PMCID: PMC5356409 DOI: 10.1186/s12575-017-0051-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 03/02/2017] [Indexed: 12/21/2022] Open
Abstract
DNA/RNA methylation plays an important role in lung cancer initiation and progression. Liquid biopsy makes use of cells, nucleotides and proteins released from tumor cells into body fluids to help with cancer diagnosis and prognosis. Methylation of circulating tumor DNA (ctDNA) has gained increasing attention as biomarkers for lung cancer. Here we briefly introduce the biological basis and detection method of ctDNA methylation, and review various applications of methylated DNA in body fluids in lung cancer screening, diagnosis, prognosis, monitoring and treatment prediction. We also discuss the emerging role of RNA methylation as biomarkers for cancer.
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Affiliation(s)
- Yan Lu
- No.2 oncology department, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, No.110, Ganhe Rd, Shanghai, China
| | - Shulin/Sl Li
- MD Anderson Cancer Center, the university of Texas, 1840 Old Spanish Trail, Houston, TX USA
| | - Shiguo/Sg Zhu
- Department of Immunology and Pathogenic Biology, School of Basic Medical Sciences, Shanghai University of Traditional Chinese Medicine, 1200 Cai Lun Rd, Shanghai, China
| | - Yabin/Yb Gong
- No.2 oncology department, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, No.110, Ganhe Rd, Shanghai, China
| | - Jun/J Shi
- No.2 oncology department, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, No.110, Ganhe Rd, Shanghai, China
| | - Ling/L Xu
- No.2 oncology department, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, No.110, Ganhe Rd, Shanghai, China
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Identification of Methylation-Driven, Differentially Expressed STXBP6 as a Novel Biomarker in Lung Adenocarcinoma. Sci Rep 2017; 7:42573. [PMID: 28198450 PMCID: PMC5309775 DOI: 10.1038/srep42573] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 01/12/2017] [Indexed: 02/06/2023] Open
Abstract
DNA methylation is an essential epigenetic marker associated with the silencing of gene expression. Although various genome-wide studies revealed aberrantly methylated gene targets as molecular biomarkers for early detection, the survival rate of lung cancer patients is still poor. In order to identify methylation-driven biomarkers, genome-wide changes in DNA methylation and differential expression in 32 pairs of lung adenocarcinoma and adjacent normal lung tissue in non-smoking women were examined. This concurrent analysis identified 21 negatively correlated probes (r ≤ −0.5), corresponding to 17 genes. Examining the endogenous expression in lung cancer cell lines, five of the genes were found to be significantly down-regulated. Furthermore, in tumor cells alone, 5-aza-2′-deoxycytidine treatment increased the expression levels of STXBP6 in a dose dependent manner and pyrosequencing showed higher percentage of methylation in STXBP6 promoter. Functional analysis revealed that overexpressed STXBP6 in A549 and H1299 cells significantly decreased cell proliferation, colony formation, and migration, and increased apoptosis. Finally, significantly lower survival rates (P < 0.05) were observed when expression levels of STXBP6 were low. Our results provide a basis for the genetic etiology of lung adenocarcinoma by demonstrating the possible role of hypermethylation of STXBP6 in poor clinical outcomes in lung cancer patients.
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Duppel U, Woenckhaus M, Schulz C, Merk J, Dietmaier W. Quantitative detection of TUSC3 promoter methylation -a potential biomarker for prognosis in lung cancer. Oncol Lett 2016; 12:3004-3012. [PMID: 27698890 PMCID: PMC5038372 DOI: 10.3892/ol.2016.4927] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 06/17/2016] [Indexed: 11/06/2022] Open
Abstract
Aberrant promoter methylation of tumor relevant genes frequently occurs in early steps of carcinogenesis and during tumor progression. Epigenetic alterations could be used as potential biomarkers for early detection and for prediction of prognosis and therapy response in lung cancer. The present study quantitatively analyzed the methylation status of known and potential gatekeeper and tumor suppressor genes [O-6-methylguanine-DNA methyltransferase (MGMT), Ras association domain family member 1A (RASSF1A), Ras protein activator like 1 (RASAL1), programmed cell death 4 (PDCD4), metastasis suppressor 1 (MTSS1) and tumor suppressor candidate 3 (TUSC3)] in 42 lung cancers and in corresponding non-malignant bronchus and lung tissue using bisulfite-conversion independent methylation-quantification of endonuclease-resistant DNA (MethyQESD). Methylation status was associated with clinical and pathological parameters. No methylation was found in the promoter regions of PDCD4 and MTSS1 of either compartment. MGMT, RASSF1A and RASAL1 showed sporadic (up to 26.2%) promoter methylation. The promoter of TUSC3, however, was frequently methylated in the tumor (59.5%), benign bronchus (67.9%) and alveolar lung (31.0%) tissues from each tumor patient. The methylation status of TUSC3 was significantly associated with smaller tumor size (P=0.008) and a longer overall survival (P=0.013). Pooled blood DNA of healthy individuals did not show any methylation of either gene. Therefore, methylation of TUSC3 shows prognostic and pathobiological relevance in lung cancer. Furthermore, quantitative detection of TUSC3 promoter methylation appears to be a promising tool for early detection and prediction of prognosis in lung cancer. However, additional studies are required to confirm this finding.
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Affiliation(s)
- Uta Duppel
- Institute of Pathology, University of Regensburg, D-93053 Regensburg, Bavaria, Germany
| | | | - Christian Schulz
- Department of Internal Medicine II, University Hospital Regensburg, D-93053 Regensburg, Bavaria, Germany
| | - Johannes Merk
- Department of Thoracic Surgery, University Hospital Regensburg, D-93053 Regensburg, Bavaria, Germany
| | - Wolfgang Dietmaier
- Institute of Pathology, University of Regensburg, D-93053 Regensburg, Bavaria, Germany
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Dong N, Shi L, Wang DC, Chen C, Wang X. Role of epigenetics in lung cancer heterogeneity and clinical implication. Semin Cell Dev Biol 2016; 64:18-25. [PMID: 27575638 DOI: 10.1016/j.semcdb.2016.08.029] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 08/24/2016] [Indexed: 12/15/2022]
Abstract
Lung cancer, as a highly heterogeneous disease, can be initiated and progressed through the interaction between permanent genetic mutations and dynamic epigenetic alterations. However, the mediating mechanisms of epigenetics in cancer heterogeneity remain unclear. The evolution of cancer, the existence of cancer stem cells (CSCs) and the phenomenon of epithelial-mesenchymal transition (EMT) have been reported to be involved in lung cancer heterogeneity. In this review, we briefly recap the definition of heterogeneity and concept of epigenetics, highlight the potential roles and mechanisms of epigenetic regulation in heterogeneity of lung cancer, and summarize the diagnostic and therapeutic implications of epigenetic alterations in lung cancer, especially the role of DNA methylation and histone acetylation. Deep understanding of epigenetic regulation in cancer heterogeneity is instrumental to the design of novel therapeutic approaches that target lung cancer.
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Affiliation(s)
- Nian Dong
- Department of Pulmonary Medicine, The First affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, China
| | - Lin Shi
- Zhongshan Hospital, Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Clinical Bioinformatics; Zhongshan Hospital Institute of Clinical Science of Fudan University, Shanghai, China
| | - Diane C Wang
- Department of Pulmonary Medicine, The First affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, China
| | - Chengshui Chen
- Department of Pulmonary Medicine, The First affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, China.
| | - Xiangdong Wang
- Department of Pulmonary Medicine, The First affiliated Hospital, Wenzhou Medical University, Wenzhou, 325000, China; Zhongshan Hospital, Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Clinical Bioinformatics; Zhongshan Hospital Institute of Clinical Science of Fudan University, Shanghai, China.
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Tellez CS, Juri DE, Do K, Picchi MA, Wang T, Liu G, Spira A, Belinsky SA. miR-196b Is Epigenetically Silenced during the Premalignant Stage of Lung Carcinogenesis. Cancer Res 2016; 76:4741-51. [PMID: 27302168 DOI: 10.1158/0008-5472.can-15-3367] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 05/16/2016] [Indexed: 02/06/2023]
Abstract
miRNA silencing by promoter hypermethylation may represent a mechanism by which lung cancer develops and progresses, but the miRNAs involved during malignant transformation are unknown. We previously established a model of premalignant lung cancer wherein we treated human bronchial epithelial cells (HBEC) with low doses of tobacco carcinogens. Here, we demonstrate that next-generation sequencing of carcinogen-transformed HBECs treated with the demethylating agent 5-aza-2'deoxycytidine revealed miR-196b and miR-34c-5p to be epigenetic targets. Bisulfite sequencing confirmed dense promoter hypermethylation indicative of silencing in multiple malignant cell lines and primary tumors. Chromatin immunoprecipitation studies further demonstrated an enrichment in repressive histone marks on the miR-196b promoter during HBEC transformation. Restoration of miR-196b expression by transfecting transformed HBECs with specific mimics led to cell-cycle arrest mediated in part through transcriptional regulation of the FOS oncogene, and miR-196b reexpression also significantly reduced the growth of tumor xenografts. Luciferase assays demonstrated that forced expression of miR-196b inhibited the FOS promoter and AP-1 reporter activity. Finally, a case-control study revealed that methylation of miR-196b in sputum was strongly associated with lung cancer (OR = 4.7, P < 0.001). Collectively, these studies highlight miR-196b as a tumor suppressor whose silencing early in lung carcinogenesis may provide a selective growth advantage to premalignant cells. Targeted delivery of miR-196b could therefore serve as a preventive or therapeutic strategy for the management of lung cancer. Cancer Res; 76(16); 4741-51. ©2016 AACR.
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Affiliation(s)
- Carmen S Tellez
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico.
| | - Daniel E Juri
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Kieu Do
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Maria A Picchi
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico
| | - Teresa Wang
- Department of Medicine, Boston University, Boston, Massachusetts
| | - Gang Liu
- Department of Medicine, Boston University, Boston, Massachusetts
| | - Avrum Spira
- Department of Medicine, Boston University, Boston, Massachusetts
| | - Steven A Belinsky
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico.
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Epigenetic Repression of CCDC37 and MAP1B Links Chronic Obstructive Pulmonary Disease to Lung Cancer. J Thorac Oncol 2016. [PMID: 26200272 DOI: 10.1097/jto.0000000000000592] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Lung cancer and chronic obstructive pulmonary disease (COPD) share environmental risk factors. COPD also increases the risk of lung cancer; however, the molecular mechanisms are unclear. METHODS An epigenome-wide association study of lung tumors and cancer-free lung tissue (CFLT) pairs from non-small-cell lung cancer cases with (n = 18) or without (n = 17) COPD was conducted using the HumanMethylation450 beadchip (HM450K). COPD-associated methylation of top-ranked genes was confirmed in a larger sample set, independently validated, and their potential as sputum-based biomarkers was investigated. RESULTS Methylation of CCDC37 and MAP1B was more prevalent in lung tumors from COPD than non-COPD cases [54 of 71 (76%) versus 20 of 46 (43%), p = 0.0013] and [48 of 71 (68%) versus 17 of 46 (37%), p = 0.0035], respectively, after adjustment for age, sex, smoking status, and tumor histology. HM450K probes across CCDC37 and MAP1B promoters showed higher methylation in tumors than CFLT with the highest methylation seen in tumors from COPD cases (p < 0.05). These results were independently validated using The Cancer Genome Atlas data. CCDC37 methylation was more prevalent in sputum from COPD than non-COPD smokers (p < 0.005) from two cohorts. CCDC37 and MAP1B expression was dramatically repressed in tumors and CFLT from COPD than non-COPD cases, p less than 0.02. CONCLUSIONS The reduced expression of CCDC37 and MAP1B associated with COPD likely predisposes these genes to methylation that in turn, may contribute to lung cancer.
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Verma M. The Role of Epigenomics in the Study of Cancer Biomarkers and in the Development of Diagnostic Tools. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 867:59-80. [PMID: 26530360 DOI: 10.1007/978-94-017-7215-0_5] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Epigenetics plays a key role in cancer development. Genetics alone cannot explain sporadic cancer and cancer development in individuals with no family history or a weak family history of cancer. Epigenetics provides a mechanism to explain the development of cancer in such situations. Alterations in epigenetic profiling may provide important insights into the etiology and natural history of cancer. Because several epigenetic changes occur before histopathological changes, they can serve as biomarkers for cancer diagnosis and risk assessment. Many cancers may remain asymptomatic until relatively late stages; in managing the disease, efforts should be focused on early detection, accurate prediction of disease progression, and frequent monitoring. This chapter describes epigenetic biomarkers as they are expressed during cancer development and their potential use in cancer diagnosis and prognosis. Based on epigenomic information, biomarkers have been identified that may serve as diagnostic tools; some such biomarkers also may be useful in identifying individuals who will respond to therapy and survive longer. The importance of analytical and clinical validation of biomarkers is discussed, along with challenges and opportunities in this field.
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Affiliation(s)
- Mukesh Verma
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute (NCI), National Institutes of Health (NIH), Suite# 4E102. 9609 Medical Center Drive, MSC 9763, Bethesda, MD, 20892-9726, USA.
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Diaz-Lagares A, Mendez-Gonzalez J, Hervas D, Saigi M, Pajares MJ, Garcia D, Crujerias AB, Pio R, Montuenga LM, Zulueta J, Nadal E, Rosell A, Esteller M, Sandoval J. A Novel Epigenetic Signature for Early Diagnosis in Lung Cancer. Clin Cancer Res 2016; 22:3361-71. [DOI: 10.1158/1078-0432.ccr-15-2346] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 01/16/2016] [Indexed: 11/16/2022]
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Molecular genetic approaches in the diagnosis of lung cancer. КЛИНИЧЕСКАЯ ПРАКТИКА 2015. [DOI: 10.17816/clinpract83261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
It is an acute problem for the 21st century to find effective and inexpensive methods for early detection of lung cancer. Patients, suspected of having a malignant disease of lungs, generally undergo clinical studies such as CT scans of the chest and bronchoscopy. The latter is mainly used to confirm the diagnosis. However, even when the signs, symptoms and radiological findings indicate that clinical diagnosis of malignant lung disease is evident, additional invasive procedures for obtaining the biological material suitable for the final confirmation of the presence of malignant cells are required. Currently, there is a clear understanding of the need to find biomarkers able to detect pre-clinical stage of cancer cells using minimally invasive procedures.
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Sathe A, Zhang YA, Ma X, Ray P, Cadinu D, Wang YW, Yao X, Liu X, Tang H, Wang Y, Huang Y, Liu C, Gu J, Akerman M, Mo Y, Cheng C, Xuan Z, Chen L, Xiao G, Xie Y, Girard L, Wang H, Lam S, Wistuba II, Zhang L, Gazdar AF, Zhang MQ. SCT Promoter Methylation is a Highly Discriminative Biomarker for Lung and Many Other Cancers. ACTA ACUST UNITED AC 2015; 1:30-33. [PMID: 33758771 DOI: 10.1109/lls.2015.2488438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Aberrant DNA methylation has long been implicated in cancers. In this work we present a highly discriminative DNA methylation biomarker for non-small cell lung cancers and fourteen other cancers. Based on 69 NSCLC cell lines and 257 cancer-free lung tissues we identified a CpG island in SCT gene promoter which was verified by qMSP experiment in 15 NSCLC cell lines and 3 immortalized human respiratory epithelium cells. In addition, we found that SCT promoter was methylated in 23 cancer cell lines involving >10 cancer types profiled by ENCODE. We found that SCT promoter is hyper-methylated in primary tumors from TCGA lung cancer cohort. Additionally, we found that SCT promoter is methylated at high frequencies in fifteen malignancies and is not methylated in~1000 non-cancerous tissues across >30 organ types. Our study indicates that SCT promoter methylation is a highly discriminative biomarker for lung and many other cancers.
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Affiliation(s)
- Adwait Sathe
- Center for Systems Biology, Department of Molecular and Cell Biology, The University of Texas at Dallas, 800 W Campbell Rd., Richardson, TX, 75080, USA
| | - Yu-An Zhang
- The Hamon Center for Therapeutic Oncology Research and Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Xiaotu Ma
- Center for Systems Biology, Department of Molecular and Cell Biology, The University of Texas at Dallas, 800 W Campbell Rd., Richardson, TX, 75080, USA
| | - Pradipta Ray
- Center for Systems Biology, Department of Molecular and Cell Biology, The University of Texas at Dallas, 800 W Campbell Rd., Richardson, TX, 75080, USA
| | - Daniela Cadinu
- Center for Systems Biology, Department of Molecular and Cell Biology, The University of Texas at Dallas, 800 W Campbell Rd., Richardson, TX, 75080, USA
| | - Yi-Wei Wang
- The Hamon Center for Therapeutic Oncology Research and Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Xiao Yao
- Center for Systems Biology, Department of Molecular and Cell Biology, The University of Texas at Dallas, 800 W Campbell Rd., Richardson, TX, 75080, USA
| | - Xiaoyun Liu
- The Hamon Center for Therapeutic Oncology Research and Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Hao Tang
- Department of Clinical Science, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Yunfei Wang
- Center for Systems Biology, Department of Molecular and Cell Biology, The University of Texas at Dallas, 800 W Campbell Rd., Richardson, TX, 75080, USA
| | - Ying Huang
- Center for Systems Biology, Department of Molecular and Cell Biology, The University of Texas at Dallas, 800 W Campbell Rd., Richardson, TX, 75080, USA
| | - Changning Liu
- Center for Systems Biology, Department of Molecular and Cell Biology, The University of Texas at Dallas, 800 W Campbell Rd., Richardson, TX, 75080, USA
| | - Jin Gu
- Division of Bioinformatics, Center for Synthetic and Systems Biology, TNLIST, Tsinghua University, Beijing 100084, China
| | - Martin Akerman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Yifan Mo
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Chao Cheng
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Zhenyu Xuan
- Center for Systems Biology, Department of Molecular and Cell Biology, The University of Texas at Dallas, 800 W Campbell Rd., Richardson, TX, 75080, USA
| | - Lei Chen
- Laboratory of Signal Transduction, Eastern Hepatobiliary Surgery Hospital, SMMU, Shanghai 200438, China
| | - Guanghua Xiao
- Department of Clinical Science, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Yang Xie
- Department of Clinical Science, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Luc Girard
- The Hamon Center for Therapeutic Oncology Research and Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Hongyang Wang
- Laboratory of Signal Transduction, Eastern Hepatobiliary Surgery Hospital, SMMU, Shanghai 200438, China
| | - Stephen Lam
- BC Cancer Research Center, BC Cancer Agency, Vancouver, BC V521L3, Canada
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, Thoracic/Head and Neck Medical Oncology, The University of Texas, MD Anderson Cancer Center, Houston TX 77030, USA
| | - Li Zhang
- Center for Systems Biology, Department of Molecular and Cell Biology, The University of Texas at Dallas, 800 W Campbell Rd., Richardson, TX, 75080, USA
| | - Adi F Gazdar
- The Hamon Center for Therapeutic Oncology Research and Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Michael Q Zhang
- Center for Systems Biology, Department of Molecular and Cell Biology, The University of Texas at Dallas, 800 W Campbell Rd., Richardson, TX, 75080, USA.,Division of Bioinformatics, Center for Synthetic and Systems Biology, TNLIST, Tsinghua University, Beijing 100084, China
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Bergougnoux A, Claustres M, De Sario A. Nasal epithelial cells: a tool to study DNA methylation in airway diseases. Epigenomics 2015; 7:119-26. [PMID: 25687471 DOI: 10.2217/epi.14.65] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
A number of chronic airway diseases are characterized by high inflammation and unbalanced activation of the immune response, which lead to tissue damage and progressive reduction of the pulmonary function. Because they are exposed to various environmental stimuli, lung cells are prone to epigenomic changes. Many genes responsible for the immune response and inflammation are tightly regulated by DNA methylation, which suggests that alteration of the epigenome in lung cells may have a considerable impact on the penetrance and/or the severity of airway diseases. A major hurdle in clinical epigenomic studies is to gather appropriate biospecimens. Herein, we show that nasal epithelial cells are suitable to analyze DNA methylation in human diseases primarily affecting the lower airway tract.
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Affiliation(s)
- Anne Bergougnoux
- Laboratory Genetics of Rare Diseases, INSERM U827, Montpellier, France
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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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Wood SL, Pernemalm M, Crosbie PA, Whetton AD. Molecular histology of lung cancer: from targets to treatments. Cancer Treat Rev 2015; 41:361-75. [PMID: 25825324 DOI: 10.1016/j.ctrv.2015.02.008] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 02/02/2015] [Accepted: 02/13/2015] [Indexed: 01/06/2023]
Abstract
Lung cancer is the leading cause of cancer-related death worldwide with a 5-year survival rate of less than 15%, despite significant advances in both diagnostic and therapeutic approaches. Combined genomic and transcriptomic sequencing studies have identified numerous genetic driver mutations that are responsible for the development of lung cancer. In addition, molecular profiling studies identify gene products and their mutations which predict tumour responses to targeted therapies such as protein tyrosine kinase inhibitors and also can offer explanation for drug resistance mechanisms. The profiling of circulating micro-RNAs has also provided an ability to discriminate patients in terms of prognosis/diagnosis and high-throughput DNA sequencing strategies are beginning to elucidate cell signalling pathway mutations associated with oncogenesis, including potential stem cell associated pathways, offering the promise that future therapies may target this sub-population, preventing disease relapse post treatment and improving patient survival. This review provides an assessment of molecular profiling within lung cancer concerning molecular mechanisms, treatment options and disease-progression. Current areas of development within lung cancer profiling are discussed (i.e. profiling of circulating tumour cells) and future challenges for lung cancer treatment addressed such as detection of micro-metastases and cancer stem cells.
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Affiliation(s)
- Steven L Wood
- Faculty Institute of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Wolfson Molecular Imaging Centre, Manchester M20 3LJ, UK.
| | - Maria Pernemalm
- Faculty Institute of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Wolfson Molecular Imaging Centre, Manchester M20 3LJ, UK; Karolinska Institutet, Department of Oncology and Pathology, SciLifeLab, Tomtebodavägen 23A, 17165 Solna, Sweden
| | - Philip A Crosbie
- Faculty Institute of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Wolfson Molecular Imaging Centre, Manchester M20 3LJ, UK
| | - Anthony D Whetton
- Faculty Institute of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, Wolfson Molecular Imaging Centre, Manchester M20 3LJ, UK
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Li W, Liu HY, Jia ZR, Qiao PP, Pi XT, Chen J, Deng LH. Advances in the early detection of lung cancer using analysis of volatile organic compounds: from imaging to sensors. Asian Pac J Cancer Prev 2015; 15:4377-84. [PMID: 24969857 DOI: 10.7314/apjcp.2014.15.11.4377] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
According to the World Health Organization (WHO), 1.37 million people died of lung cancer all around the world in 2008, occupying the first place in all cancer-related deaths. However, this number might be decreased if patients were detected earlier and treated appropriately. Unfortunately, traditional imaging techniques are not sufficiently satisfactory for early detection of lung cancer because of limitations. As one alternative, breath volatile organic compounds (VOCs) may reflect the biochemical status of the body and provide clues to some diseases including lung cancer at early stage. Early detection of lung cancer based on breath analysis is becoming more and more valued because it is non-invasive, sensitive, inexpensive and simple. In this review article, we analyze the limitations of traditional imaging techniques in the early detection of lung cancer, illustrate possible mechanisms of the production of VOCs in cancerous cells, present evidence that supports the detection of such disease using breath analysis, and summarize the advances in the study of E-noses based on gas sensitive sensors. In conclusion, the analysis of breath VOCs is a better choice for the early detection of lung cancer compared to imaging techniques. We recommend a more comprehensive technique that integrates the analysis of VOCs and non-VOCs in breath. In addition, VOCs in urine may also be a trend in research on the early detection of lung cancer.
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Affiliation(s)
- Wang Li
- Key Laboratory of Biorheology Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China E-mail :
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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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49
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Leng S, Liu Y, Weissfeld JL, Thomas CL, Han Y, Picchi MA, Edlund CK, Willink RP, Gaither Davis AL, Do KC, Nukui T, Zhang X, Burki EA, Van Den Berg D, Romkes M, Gauderman WJ, Crowell RE, Tesfaigzi Y, Stidley CA, Amos CI, Siegfried JM, Gilliland FD, Belinsky SA. 15q12 variants, sputum gene promoter hypermethylation, and lung cancer risk: a GWAS in smokers. J Natl Cancer Inst 2015; 107:djv035. [PMID: 25713168 DOI: 10.1093/jnci/djv035] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Lung cancer is the leading cause of cancer-related mortality worldwide. Detection of promoter hypermethylation of tumor suppressor genes in exfoliated cells from the lung provides an assessment of field cancerization that in turn predicts lung cancer. The identification of genetic determinants for this validated cancer biomarker should provide novel insights into mechanisms underlying epigenetic reprogramming during lung carcinogenesis. METHODS A genome-wide association study using generalized estimating equations and logistic regression models was conducted in two geographically independent smoker cohorts to identify loci affecting the propensity for cancer-related gene methylation that was assessed by a 12-gene panel interrogated in sputum. All statistical tests were two-sided. RESULTS Two single nucleotide polymorphisms (SNPs) at 15q12 (rs73371737 and rs7179575) that drove gene methylation were discovered and replicated with rs73371737 reaching genome-wide significance (P = 3.3×10(-8)). A haplotype carrying risk alleles from the two 15q12 SNPs conferred 57% increased risk for gene methylation (P = 2.5×10(-9)). Rs73371737 reduced GABRB3 expression in lung cells and increased risk for smoking-induced chronic mucous hypersecretion. Furthermore, subjects with variant homozygote of rs73371737 had a two-fold increase in risk for lung cancer (P = .0043). Pathway analysis identified DNA double-strand break repair by homologous recombination (DSBR-HR) as a major pathway affecting susceptibility for gene methylation that was validated by measuring chromatid breaks in lymphocytes challenged by bleomycin. CONCLUSIONS A functional 15q12 variant was identified as a risk factor for gene methylation and lung cancer. The associations could be mediated by GABAergic signaling that drives the smoking-induced mucous cell metaplasia. Our findings also substantiate DSBR-HR as a critical pathway driving epigenetic gene silencing.
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Affiliation(s)
- Shuguang Leng
- : Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM (SL, YL, CLT, MAP, RPW, KCD, XZ, EAB, YT, SAB); Department of Epidemiology, Graduate School of Public Health (JLW) and Department of Medicine (TN, MR), University of Pittsburgh, Pittsburgh, PA; Center for Genomic Medicine, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH (YH, CIA); Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA (CKE, DVDB, WJG, FDG); Department of Pharmacology & Chemical Biology, Hillman Cancer Center of the University of Pittsburgh Medical Center, Pittsburgh, PA (ALGD, JMS); Department of Internal Medicine, University of New Mexico, Albuquerque, NM (REC, CAS); Department of Pharmacology, University of Minnesota, Minneapolis, MN (JMS)
| | - Yushi Liu
- : Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM (SL, YL, CLT, MAP, RPW, KCD, XZ, EAB, YT, SAB); Department of Epidemiology, Graduate School of Public Health (JLW) and Department of Medicine (TN, MR), University of Pittsburgh, Pittsburgh, PA; Center for Genomic Medicine, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH (YH, CIA); Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA (CKE, DVDB, WJG, FDG); Department of Pharmacology & Chemical Biology, Hillman Cancer Center of the University of Pittsburgh Medical Center, Pittsburgh, PA (ALGD, JMS); Department of Internal Medicine, University of New Mexico, Albuquerque, NM (REC, CAS); Department of Pharmacology, University of Minnesota, Minneapolis, MN (JMS)
| | - Joel L Weissfeld
- : Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM (SL, YL, CLT, MAP, RPW, KCD, XZ, EAB, YT, SAB); Department of Epidemiology, Graduate School of Public Health (JLW) and Department of Medicine (TN, MR), University of Pittsburgh, Pittsburgh, PA; Center for Genomic Medicine, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH (YH, CIA); Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA (CKE, DVDB, WJG, FDG); Department of Pharmacology & Chemical Biology, Hillman Cancer Center of the University of Pittsburgh Medical Center, Pittsburgh, PA (ALGD, JMS); Department of Internal Medicine, University of New Mexico, Albuquerque, NM (REC, CAS); Department of Pharmacology, University of Minnesota, Minneapolis, MN (JMS)
| | - Cynthia L Thomas
- : Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM (SL, YL, CLT, MAP, RPW, KCD, XZ, EAB, YT, SAB); Department of Epidemiology, Graduate School of Public Health (JLW) and Department of Medicine (TN, MR), University of Pittsburgh, Pittsburgh, PA; Center for Genomic Medicine, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH (YH, CIA); Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA (CKE, DVDB, WJG, FDG); Department of Pharmacology & Chemical Biology, Hillman Cancer Center of the University of Pittsburgh Medical Center, Pittsburgh, PA (ALGD, JMS); Department of Internal Medicine, University of New Mexico, Albuquerque, NM (REC, CAS); Department of Pharmacology, University of Minnesota, Minneapolis, MN (JMS)
| | - Younghun Han
- : Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM (SL, YL, CLT, MAP, RPW, KCD, XZ, EAB, YT, SAB); Department of Epidemiology, Graduate School of Public Health (JLW) and Department of Medicine (TN, MR), University of Pittsburgh, Pittsburgh, PA; Center for Genomic Medicine, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH (YH, CIA); Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA (CKE, DVDB, WJG, FDG); Department of Pharmacology & Chemical Biology, Hillman Cancer Center of the University of Pittsburgh Medical Center, Pittsburgh, PA (ALGD, JMS); Department of Internal Medicine, University of New Mexico, Albuquerque, NM (REC, CAS); Department of Pharmacology, University of Minnesota, Minneapolis, MN (JMS)
| | - Maria A Picchi
- : Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM (SL, YL, CLT, MAP, RPW, KCD, XZ, EAB, YT, SAB); Department of Epidemiology, Graduate School of Public Health (JLW) and Department of Medicine (TN, MR), University of Pittsburgh, Pittsburgh, PA; Center for Genomic Medicine, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH (YH, CIA); Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA (CKE, DVDB, WJG, FDG); Department of Pharmacology & Chemical Biology, Hillman Cancer Center of the University of Pittsburgh Medical Center, Pittsburgh, PA (ALGD, JMS); Department of Internal Medicine, University of New Mexico, Albuquerque, NM (REC, CAS); Department of Pharmacology, University of Minnesota, Minneapolis, MN (JMS)
| | - Christopher K Edlund
- : Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM (SL, YL, CLT, MAP, RPW, KCD, XZ, EAB, YT, SAB); Department of Epidemiology, Graduate School of Public Health (JLW) and Department of Medicine (TN, MR), University of Pittsburgh, Pittsburgh, PA; Center for Genomic Medicine, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH (YH, CIA); Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA (CKE, DVDB, WJG, FDG); Department of Pharmacology & Chemical Biology, Hillman Cancer Center of the University of Pittsburgh Medical Center, Pittsburgh, PA (ALGD, JMS); Department of Internal Medicine, University of New Mexico, Albuquerque, NM (REC, CAS); Department of Pharmacology, University of Minnesota, Minneapolis, MN (JMS)
| | - Randall P Willink
- : Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM (SL, YL, CLT, MAP, RPW, KCD, XZ, EAB, YT, SAB); Department of Epidemiology, Graduate School of Public Health (JLW) and Department of Medicine (TN, MR), University of Pittsburgh, Pittsburgh, PA; Center for Genomic Medicine, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH (YH, CIA); Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA (CKE, DVDB, WJG, FDG); Department of Pharmacology & Chemical Biology, Hillman Cancer Center of the University of Pittsburgh Medical Center, Pittsburgh, PA (ALGD, JMS); Department of Internal Medicine, University of New Mexico, Albuquerque, NM (REC, CAS); Department of Pharmacology, University of Minnesota, Minneapolis, MN (JMS)
| | - Autumn L Gaither Davis
- : Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM (SL, YL, CLT, MAP, RPW, KCD, XZ, EAB, YT, SAB); Department of Epidemiology, Graduate School of Public Health (JLW) and Department of Medicine (TN, MR), University of Pittsburgh, Pittsburgh, PA; Center for Genomic Medicine, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH (YH, CIA); Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA (CKE, DVDB, WJG, FDG); Department of Pharmacology & Chemical Biology, Hillman Cancer Center of the University of Pittsburgh Medical Center, Pittsburgh, PA (ALGD, JMS); Department of Internal Medicine, University of New Mexico, Albuquerque, NM (REC, CAS); Department of Pharmacology, University of Minnesota, Minneapolis, MN (JMS)
| | - Kieu C Do
- : Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM (SL, YL, CLT, MAP, RPW, KCD, XZ, EAB, YT, SAB); Department of Epidemiology, Graduate School of Public Health (JLW) and Department of Medicine (TN, MR), University of Pittsburgh, Pittsburgh, PA; Center for Genomic Medicine, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH (YH, CIA); Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA (CKE, DVDB, WJG, FDG); Department of Pharmacology & Chemical Biology, Hillman Cancer Center of the University of Pittsburgh Medical Center, Pittsburgh, PA (ALGD, JMS); Department of Internal Medicine, University of New Mexico, Albuquerque, NM (REC, CAS); Department of Pharmacology, University of Minnesota, Minneapolis, MN (JMS)
| | - Tomoko Nukui
- : Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM (SL, YL, CLT, MAP, RPW, KCD, XZ, EAB, YT, SAB); Department of Epidemiology, Graduate School of Public Health (JLW) and Department of Medicine (TN, MR), University of Pittsburgh, Pittsburgh, PA; Center for Genomic Medicine, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH (YH, CIA); Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA (CKE, DVDB, WJG, FDG); Department of Pharmacology & Chemical Biology, Hillman Cancer Center of the University of Pittsburgh Medical Center, Pittsburgh, PA (ALGD, JMS); Department of Internal Medicine, University of New Mexico, Albuquerque, NM (REC, CAS); Department of Pharmacology, University of Minnesota, Minneapolis, MN (JMS)
| | - Xiequn Zhang
- : Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM (SL, YL, CLT, MAP, RPW, KCD, XZ, EAB, YT, SAB); Department of Epidemiology, Graduate School of Public Health (JLW) and Department of Medicine (TN, MR), University of Pittsburgh, Pittsburgh, PA; Center for Genomic Medicine, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH (YH, CIA); Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA (CKE, DVDB, WJG, FDG); Department of Pharmacology & Chemical Biology, Hillman Cancer Center of the University of Pittsburgh Medical Center, Pittsburgh, PA (ALGD, JMS); Department of Internal Medicine, University of New Mexico, Albuquerque, NM (REC, CAS); Department of Pharmacology, University of Minnesota, Minneapolis, MN (JMS)
| | - Elizabeth A Burki
- : Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM (SL, YL, CLT, MAP, RPW, KCD, XZ, EAB, YT, SAB); Department of Epidemiology, Graduate School of Public Health (JLW) and Department of Medicine (TN, MR), University of Pittsburgh, Pittsburgh, PA; Center for Genomic Medicine, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH (YH, CIA); Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA (CKE, DVDB, WJG, FDG); Department of Pharmacology & Chemical Biology, Hillman Cancer Center of the University of Pittsburgh Medical Center, Pittsburgh, PA (ALGD, JMS); Department of Internal Medicine, University of New Mexico, Albuquerque, NM (REC, CAS); Department of Pharmacology, University of Minnesota, Minneapolis, MN (JMS)
| | - David Van Den Berg
- : Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM (SL, YL, CLT, MAP, RPW, KCD, XZ, EAB, YT, SAB); Department of Epidemiology, Graduate School of Public Health (JLW) and Department of Medicine (TN, MR), University of Pittsburgh, Pittsburgh, PA; Center for Genomic Medicine, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH (YH, CIA); Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA (CKE, DVDB, WJG, FDG); Department of Pharmacology & Chemical Biology, Hillman Cancer Center of the University of Pittsburgh Medical Center, Pittsburgh, PA (ALGD, JMS); Department of Internal Medicine, University of New Mexico, Albuquerque, NM (REC, CAS); Department of Pharmacology, University of Minnesota, Minneapolis, MN (JMS)
| | - Marjorie Romkes
- : Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM (SL, YL, CLT, MAP, RPW, KCD, XZ, EAB, YT, SAB); Department of Epidemiology, Graduate School of Public Health (JLW) and Department of Medicine (TN, MR), University of Pittsburgh, Pittsburgh, PA; Center for Genomic Medicine, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH (YH, CIA); Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA (CKE, DVDB, WJG, FDG); Department of Pharmacology & Chemical Biology, Hillman Cancer Center of the University of Pittsburgh Medical Center, Pittsburgh, PA (ALGD, JMS); Department of Internal Medicine, University of New Mexico, Albuquerque, NM (REC, CAS); Department of Pharmacology, University of Minnesota, Minneapolis, MN (JMS)
| | - W James Gauderman
- : Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM (SL, YL, CLT, MAP, RPW, KCD, XZ, EAB, YT, SAB); Department of Epidemiology, Graduate School of Public Health (JLW) and Department of Medicine (TN, MR), University of Pittsburgh, Pittsburgh, PA; Center for Genomic Medicine, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH (YH, CIA); Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA (CKE, DVDB, WJG, FDG); Department of Pharmacology & Chemical Biology, Hillman Cancer Center of the University of Pittsburgh Medical Center, Pittsburgh, PA (ALGD, JMS); Department of Internal Medicine, University of New Mexico, Albuquerque, NM (REC, CAS); Department of Pharmacology, University of Minnesota, Minneapolis, MN (JMS)
| | - Richard E Crowell
- : Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM (SL, YL, CLT, MAP, RPW, KCD, XZ, EAB, YT, SAB); Department of Epidemiology, Graduate School of Public Health (JLW) and Department of Medicine (TN, MR), University of Pittsburgh, Pittsburgh, PA; Center for Genomic Medicine, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH (YH, CIA); Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA (CKE, DVDB, WJG, FDG); Department of Pharmacology & Chemical Biology, Hillman Cancer Center of the University of Pittsburgh Medical Center, Pittsburgh, PA (ALGD, JMS); Department of Internal Medicine, University of New Mexico, Albuquerque, NM (REC, CAS); Department of Pharmacology, University of Minnesota, Minneapolis, MN (JMS)
| | - Yohannes Tesfaigzi
- : Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM (SL, YL, CLT, MAP, RPW, KCD, XZ, EAB, YT, SAB); Department of Epidemiology, Graduate School of Public Health (JLW) and Department of Medicine (TN, MR), University of Pittsburgh, Pittsburgh, PA; Center for Genomic Medicine, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH (YH, CIA); Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA (CKE, DVDB, WJG, FDG); Department of Pharmacology & Chemical Biology, Hillman Cancer Center of the University of Pittsburgh Medical Center, Pittsburgh, PA (ALGD, JMS); Department of Internal Medicine, University of New Mexico, Albuquerque, NM (REC, CAS); Department of Pharmacology, University of Minnesota, Minneapolis, MN (JMS)
| | - Christine A Stidley
- : Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM (SL, YL, CLT, MAP, RPW, KCD, XZ, EAB, YT, SAB); Department of Epidemiology, Graduate School of Public Health (JLW) and Department of Medicine (TN, MR), University of Pittsburgh, Pittsburgh, PA; Center for Genomic Medicine, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH (YH, CIA); Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA (CKE, DVDB, WJG, FDG); Department of Pharmacology & Chemical Biology, Hillman Cancer Center of the University of Pittsburgh Medical Center, Pittsburgh, PA (ALGD, JMS); Department of Internal Medicine, University of New Mexico, Albuquerque, NM (REC, CAS); Department of Pharmacology, University of Minnesota, Minneapolis, MN (JMS)
| | - Christopher I Amos
- : Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM (SL, YL, CLT, MAP, RPW, KCD, XZ, EAB, YT, SAB); Department of Epidemiology, Graduate School of Public Health (JLW) and Department of Medicine (TN, MR), University of Pittsburgh, Pittsburgh, PA; Center for Genomic Medicine, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH (YH, CIA); Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA (CKE, DVDB, WJG, FDG); Department of Pharmacology & Chemical Biology, Hillman Cancer Center of the University of Pittsburgh Medical Center, Pittsburgh, PA (ALGD, JMS); Department of Internal Medicine, University of New Mexico, Albuquerque, NM (REC, CAS); Department of Pharmacology, University of Minnesota, Minneapolis, MN (JMS)
| | - Jill M Siegfried
- : Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM (SL, YL, CLT, MAP, RPW, KCD, XZ, EAB, YT, SAB); Department of Epidemiology, Graduate School of Public Health (JLW) and Department of Medicine (TN, MR), University of Pittsburgh, Pittsburgh, PA; Center for Genomic Medicine, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH (YH, CIA); Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA (CKE, DVDB, WJG, FDG); Department of Pharmacology & Chemical Biology, Hillman Cancer Center of the University of Pittsburgh Medical Center, Pittsburgh, PA (ALGD, JMS); Department of Internal Medicine, University of New Mexico, Albuquerque, NM (REC, CAS); Department of Pharmacology, University of Minnesota, Minneapolis, MN (JMS)
| | - Frank D Gilliland
- : Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM (SL, YL, CLT, MAP, RPW, KCD, XZ, EAB, YT, SAB); Department of Epidemiology, Graduate School of Public Health (JLW) and Department of Medicine (TN, MR), University of Pittsburgh, Pittsburgh, PA; Center for Genomic Medicine, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH (YH, CIA); Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA (CKE, DVDB, WJG, FDG); Department of Pharmacology & Chemical Biology, Hillman Cancer Center of the University of Pittsburgh Medical Center, Pittsburgh, PA (ALGD, JMS); Department of Internal Medicine, University of New Mexico, Albuquerque, NM (REC, CAS); Department of Pharmacology, University of Minnesota, Minneapolis, MN (JMS)
| | - Steven A Belinsky
- : Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM (SL, YL, CLT, MAP, RPW, KCD, XZ, EAB, YT, SAB); Department of Epidemiology, Graduate School of Public Health (JLW) and Department of Medicine (TN, MR), University of Pittsburgh, Pittsburgh, PA; Center for Genomic Medicine, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH (YH, CIA); Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA (CKE, DVDB, WJG, FDG); Department of Pharmacology & Chemical Biology, Hillman Cancer Center of the University of Pittsburgh Medical Center, Pittsburgh, PA (ALGD, JMS); Department of Internal Medicine, University of New Mexico, Albuquerque, NM (REC, CAS); Department of Pharmacology, University of Minnesota, Minneapolis, MN (JMS).
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Abstract
Idiopathic pulmonary fibrosis (IPF) is a lethal chronic lung disorder with no effective treatment and a prognosis worse than that of lung cancer. Despite extensive research efforts, its etiology and pathogenesis still remain largely unknown. Current experimental evidence has shifted the disease paradigm from chronic inflammation towards the premise of abnormal epithelial wound repair in response to repeated epigenetic injurious stimuli in genetically predisposed individuals. Epigenetics is defined as the study of heritable changes in gene function by factors other than an individual's DNA sequence, providing valuable information regarding adaption of genes to environmental changes. Although cancer is the most studied disease with relevance to epigenetic modifications, recent data support the idea that epigenomic alterations may lead to variable disease phenotypes, including fibroproliferative lung disorders such as IPF. This review article summarizes the latest experimental and translational epigenetic studies in the research field of chronic lung disorders, mainly focusing on IPF, highlights current methodology limitations, and underlines future directions and perspectives.
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Affiliation(s)
- Argyrios Tzouvelekis
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, 300 Cedar St., TAC-441 South, P.O. Box 208057, New Haven, CT 06520, USA
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