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Jeddi F, Faghfuri E, Mehranfar S, Soozangar N. The common bisulfite-conversion-based techniques to analyze DNA methylation in human cancers. Cancer Cell Int 2024; 24:240. [PMID: 38982390 PMCID: PMC11234524 DOI: 10.1186/s12935-024-03405-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 06/11/2024] [Indexed: 07/11/2024] Open
Abstract
DNA methylation is an important molecular modification that plays a key role in the expression of cancer genes. Evaluation of epigenetic changes, hypomethylation and hypermethylation, in specific genes are applied for cancer diagnosis. Numerous studies have concentrated on describing DNA methylation patterns as biomarkers for cancer diagnosis monitoring and predicting response to cancer therapy. Various techniques for detecting DNA methylation status in cancers are based on sodium bisulfite treatment. According to the application of these methods in research and clinical studies, they have a number of advantages and disadvantages. The current review highlights sodium bisulfite treatment-based techniques, as well as, the advantages, drawbacks, and applications of these methods in the evaluation of human cancers.
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Affiliation(s)
- Farhad Jeddi
- Zoonoses Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
- Department of Genetics and Pathology, School of Medicine, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Elnaz Faghfuri
- Digestive Diseases Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Sahar Mehranfar
- Department of Genetics and Immunology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Narges Soozangar
- Zoonoses Research Center, Ardabil University of Medical Sciences, Ardabil, Iran.
- Digestive Diseases Research Center, Ardabil University of Medical Sciences, Ardabil, Iran.
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Zhao J, Lu Y, Ren X, Bian T, Feng J, Sun H, Liu L, She B, Liu Y, Ke H. Association of the SHOX2 and RASSF1A methylation levels with the pathological evolution of early-stage lung adenocarcinoma. BMC Cancer 2024; 24:687. [PMID: 38840077 PMCID: PMC11154976 DOI: 10.1186/s12885-024-12452-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 05/30/2024] [Indexed: 06/07/2024] Open
Abstract
Background The methylation of SHOX2 and RASSF1A shows promise as a potential biomarker for the early screening of lung cancer, offering a solution to remedy the limitations of morphological diagnosis. The aim of this study is to diagnose lung adenocarcinoma by measuring the methylation levels of SHOX2 and RASSF1A, and provide an accurate pathological diagnosis to predict the invasiveness of lung cancer prior to surgery.Material and methods The methylation levels of SHOX2 and RASSF1A were quantified using a LungMe® test kit through methylation-specific PCR (MS-PCR). The diagnostic efficacy of SHOX2 and RASSF1A and the cutoff values were validated using ROC curve analysis. The hazardous factors influencing the invasiveness of lung adenocarcinoma were calculated using multiple regression.Results: The cutoff values of SHOX2 and RASSF1A were 8.3 and 12.0, respectively. The sensitivities of LungMe® in IA, MIA and AIS patients were 71.3% (122/171), 41.7% (15/36), and 16.1% (5/31) under the specificity of 94.1% (32/34) for benign lesions. Additionally, the methylation level of SHOX2, RASSF1A and LungMe® correlated with the high invasiveness of clinicopathological features, such as age, gender, tumor size, TNM stage, pathological type, pleural invasion and STAS. The tumor size, age, CTR values and LungMe® methylation levels were identified as independent hazardous factors influencing the invasiveness of lung adenocarcinoma.Conclusion: SHOX2 and RASSF1A combined methylation can be used as an early detection indicator of lung adenocarcinoma. SHOX2 and RASSF1A combined (LungMe®) methylation is significantly correlated to age, gender, tumor size, TNM stage, pathological type, pleural invasion and STAS. The SHOX2 and RASSF1A methylation levels, tumor size and CTR values could predict the invasiveness of the tumor prior to surgery, thereby providing guidance for the surgical procedure.
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Affiliation(s)
- Jiaping Zhao
- Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China
- Medical School of Nantong University, Nantong University, ChongChuan District, NanTong, 226001, Jiangsu, China
| | - Yu Lu
- Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China
- Medical School of Nantong University, Nantong University, ChongChuan District, NanTong, 226001, Jiangsu, China
| | - Xiaosha Ren
- Department of Academic Development, Shanghai methyldia technology Co. Ltd, No. 412 Huiqing Road , Shanghai, 201203, China
| | - Tingting Bian
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China
| | - Jia Feng
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China
| | - Hui Sun
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China
| | - Lei Liu
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China
| | - Bin She
- Department of Academic Development, Shanghai methyldia technology Co. Ltd, No. 412 Huiqing Road , Shanghai, 201203, China
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China
- Tellgen Corporation Co. Ltd, No. 115, Lane 572, Bibo Road, Pilot Free Trade Zone, Shanghai, 201203, China
| | - Yifei Liu
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China.
| | - Honggang Ke
- Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China.
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Xie B, Dong W, He F, Peng F, Zhang H, Wang W. The Combination of SHOX2 and RASSF1A DNA Methylation Had a Diagnostic Value in Pulmonary Nodules and Early Lung Cancer. Oncology 2024; 102:759-774. [PMID: 38262380 DOI: 10.1159/000534275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 09/19/2023] [Indexed: 01/25/2024]
Abstract
INTRODUCTION The study explored the effects of SHOX2 and RASSF1A DNA methylation in lung cancer (LC). METHOD Bronchoalveolar lavage fluid (BALF) samples as well as LC and normal adjacent tissues were collected from 72 LC patients and 35 patients with benign pulmonary nodules. Quantitative analysis of SHOX2 and RASSF1A DNA methylation was performed in benign pulmonary nodules and different stages of LC. The diagnostic value of SHOX2 and RASSF1A DNA methylation in LC and benign pulmonary nodules was determined by receiver operating characteristics analysis. Gain/loss-of-function experiments were constructed in LC cells and mouse models of xenograft and pulmonary nodule metastasis. The levels of SHOX2 and transfer-associated genes were tested through quantitative reverse transcription polymerase chain reaction and Western blot. Malignant phenotype of LC cells was assessed by functional experiment. The tumor volume and weight of mice in xenograft models were measured. Pulmonary nodule metastasis was determined through HE staining assay. 5-azacytidine appeared as a positive control drug. RESULT SHOX2 DNA methylation or RASSF1A DNA methylation had diagnostic efficiency in pulmonary nodules and early LC, with the two combined having better diagnostic value. SHOX2 expression was upregulated in LC. Similar to 5-azacytidine, SHOX2 knockdown inhibited LC cell viability, migration, and invasion in vitro as well as restrained LC tumorigenesis and pulmonary nodule metastasis in vivo, whereas overexpressed SHOX2 had the opposite effects. CONCLUSION The combination of SHOX2 and RASSF1A DNA methylation had a diagnostic value in pulmonary nodules and early LC. SHOX2 positively modulated the tumorigenesis and metastasis of LC by regulating DNA methylation processes.
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Affiliation(s)
- Bin Xie
- Department of Respiratory Medicine, Yue Bei People's Hospital, Shaoguan, China
| | - Wenyan Dong
- Department of Geriatric Medicine, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Fengping He
- Central Laboratory, Yue Bei People's Hospital, Shaoguan, China
| | - Feng Peng
- Department of Respiratory Medicine, Yue Bei People's Hospital, Shaoguan, China
| | - Honghua Zhang
- Department of Respiratory Medicine, Yue Bei People's Hospital, Shaoguan, China
| | - Wei Wang
- Medical Integration and Practice Center of Shandong University, Jinan, China
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Zhang J, Yao H, Lai C, Sun X, Yang X, Li S, Guo Y, Luo J, Wen Z, Tang K. A novel multimodal prediction model based on DNA methylation biomarkers and low-dose computed tomography images for identifying early-stage lung cancer. Chin J Cancer Res 2023; 35:511-525. [PMID: 37969955 PMCID: PMC10643339 DOI: 10.21147/j.issn.1000-9604.2023.05.08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/17/2023] [Indexed: 11/17/2023] Open
Abstract
Objective DNA methylation alterations are early events in carcinogenesis and immune signalling in lung cancer. This study aimed to develop a model based on short stature homeobox 2 gene (SHOX2)/prostaglandin E receptor 4 gene (PTGER4) DNA methylation in plasma, appearance subtype of pulmonary nodules (PNs) and low-dose computed tomography (LDCT) images to distinguish early-stage lung cancers. Methods We developed a multimodal prediction model with a training set of 257 individuals. The performance of the multimodal prediction model was further validated in an independent validation set of 42 subjects. In addition, we explored the association between SHOX2/PTGER4 DNA methylation and driver gene mutations in lung cancer based on data from The Cancer Genome Atlas (TCGA) portal. Results There were significant differences between the early-stage lung cancers and benign groups in the methylation levels. The area under a receiver operator characteristic curve (AUC) of SHOX2 in patients with solid nodules, mixed ground-glass opacity nodules and pure ground-glass opacity nodules were 0.693, 0.497 and 0.864, respectively, while the AUCs of PTGER4 were 0.559, 0.739 and 0.619, respectively. With the highest AUC of 0.894, the novel multimodal prediction model outperformed the Mayo Clinic model (0.519) and LDCT-based deep learning model (0.842) in the independent validation set. Database analysis demonstrated that patients with SHOX2/PTGER4 DNA hypermethylation were enriched in TP53 mutations. Conclusions The present multimodal prediction model could more efficiently distinguish early-stage lung cancer from benign PNs. A prognostic index based on DNA methylation and lung cancer driver gene alterations may separate the patients into groups with good or poor prognosis.
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Affiliation(s)
- Jing Zhang
- Division of Pulmonary and Critical Care Medicine, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Haohua Yao
- Department of Urology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Chunliu Lai
- Division of Pulmonary and Critical Care Medicine, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Xue Sun
- Department of Respiratory and Critical Care Medicine, the Fourth People’s Hospital of Shenyang, Shenyang 110031, China
| | - Xiujuan Yang
- Department of Pharmacy, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Shurong Li
- Department of Radiology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Yubiao Guo
- Division of Pulmonary and Critical Care Medicine, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Junhang Luo
- Department of Urology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Zhihua Wen
- Department of Radiology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Kejing Tang
- Division of Pulmonary and Critical Care Medicine, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
- Department of Pharmacy, the First Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510080, China
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Wu X, Chen H, You C, Peng Z. A potential immunotherapeutic and prognostic biomarker for multiple tumors including glioma: SHOX2. Hereditas 2023; 160:21. [PMID: 37170390 PMCID: PMC10173633 DOI: 10.1186/s41065-023-00279-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/06/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND Short stature homeobox 2 (SHOX2) is significant gene in the development and progression of multiple types of tumors. Nonetheless, the biological role of SHOX2 within pan-cancer datasets has not been investigated. Thus, comprehensive bioinformatics analyses of pan-cancer datasets were conducted to explore how SHOX2 regulates tumorigenesis. METHODS A variety of tumor datasets and online analytical tools, including SangerBox, TIMER2, LinkedOmic, GEPIA2 and cBioPortal, were applied to explore SHOX2 expression in various tumors. To ascertain the connections between SHOX2 expression and genetic alterations, SHOX2-related genes and tumor immunity, the pan-cancer datasets were examined. In vitro assays were applied to verify the biological functions of SHOX2 in glioma cells via CCK-8, wound healing, Transwell and colony formation assays. RESULTS Analyses found that SHOX2 was overexpressed in multiple cancer types. SHOX2 expression level was significantly correlated with isocitrate dehydrogenase (IDH), 1p/19q, O6-methylguanine DNA methyltransferase (MGMT) status and new types of glioma patients. High mRNA expression levels of SHOX2 were associated with a poor prognosis in multiple tumor patients. KEGG enrichment analysis showed that SHOX2-related genes were associated with cell cycle and DNA damage repair. Genetic alterations of SHOX2 were identified in multiple types of cancers, including duplications and deep mutations. Immune analysis showed that SHOX2 was closely correlated with the tumor mutation burden (TMB), microsatellite instability (MSI), neoantigen and neoantigens and immune checkpoint (ICP) in a variety of tumors and could influence the immunotherapy sensitivity of cancers. CCK-8, wound healing, Transwell and colony formation experiments showed that SHOX2 knockdown inhibited glioma cell proliferation, migration, invasion and colony formation abilities. CONCLUSION SHOX2 was overexpressed in multiple cancer types in TCGA cohort. SHOX2 knockdown inhibited glioma cell proliferation, migration and colony formation ability. Our study showed that SHOX2 may be an immunotherapeutic and promising prognostic biomarker in certain types of tumors.
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Affiliation(s)
- Xiaocong Wu
- Department of Neurosurgery, Sichuan Friendship Hospital, 96 Shangshahepu Street, Jinjiang District, Chengdu, Sichuan, 610066, China
| | - Hui Chen
- Department of Neurosurgery, Sichuan Friendship Hospital, 96 Shangshahepu Street, Jinjiang District, Chengdu, Sichuan, 610066, China
| | - Chao You
- Department of Neurosurgery, West China Hospital, Sichuan University, 37 Guoxue Lane, Wuhou District, Chengdu, Sichuan, 610041, China.
| | - Zongjun Peng
- Department of Neurosurgery, Sichuan Friendship Hospital, 96 Shangshahepu Street, Jinjiang District, Chengdu, Sichuan, 610066, China.
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Zeng S, Lin C, Huang Y. miR-375 Combined with SHOX2 Methylation has Higher Diagnostic Efficacy for Non-Small-Cell Lung Cancer. Mol Biotechnol 2022:10.1007/s12033-022-00604-y. [DOI: 10.1007/s12033-022-00604-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 11/07/2022] [Indexed: 12/05/2022]
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Gao H, Yang J, He L, Wang W, Liu Y, Hu Y, Ge M, Ding J, Ye Q. The Diagnostic Potential of SHOX2 and RASSF1A DNA Methylation in Early Lung Adenocarcinoma. Front Oncol 2022; 12:849024. [PMID: 35837113 PMCID: PMC9273978 DOI: 10.3389/fonc.2022.849024] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectiveMethylation of the promoters of SHOX2 and RASSF1A are potentially informative biomarkers for the diagnosis of early lung adenocarcinoma (LUAD). Abnormal methylation of SHOX2 and RASSF1A promoters may promote the occurrence and facilitate the progression of LUAD.Materials and MethodsWe selected 54 patients with early LUAD and 31 patients with benign lung nodules as a NJDT cohort and evaluated their DNA methylation and mRNA sequencing levels. The DNA methylation sequencing, mRNA sequencing, and clinical data for patients with LUAD were obtained from The Cancer Genome Atlas, and served as a TCGA cohort. We evaluated the diagnostic potential of a SHOX2 and RASSF1A combined promoter methylation assay for detection of early LUAD in the NJDT cohort. Then we explored the promoter methylation levels of SHOX2 and RASSF1A and their gene expression between normal and tumor samples at different stages in both cohorts. Pathways enriched between tumor and normal samples of methylation-positive patients in the NJDT cohort were analyzed.ResultsIn the NJDT cohort, the sensitivity of the combined promoter methylation assay on tumor samples was 74.07%, the sensitivity on paired tumor and paracancerous samples was 77.78%, and the specificities in both contexts were 100%. The combined promoter methylation-positive patients had clinicopathologic features including older age, larger tumors, deeper invasion, and higher Ki-67 expression. In both cohorts, SHOX2 expression increased and RASSF1A expression decreased in tumor samples. The promoter methylation level of SHOX2 and RASSF1A was significantly higher in tumor samples at stage I-II than that in normal samples. The promoter methylation levels of these two genes were both negative associated with their expression in early tumor samples. In the NJDT cohort, methylation-positive patients of both individual SHOX2 and RASSF1A assays exhibited upregulation of folate acid metabolism and nucleotide metabolism in tumor samples. The SHOX2 methylation-positive and RASSF1A methylation-positive patients showed the downregulation of pathways related to cell proliferation and apoptosis and pathways involved in DNA repair, cell growth and cell adhesion, respectively.ConclusionThe combined promoter methylation assay for SHOX2 and RASSF1A can be used for screening and diagnosis of early LUAD, with good sensitivity and specificity. The promoter methylation levels of SHOX2 and RASSF1A were associated with their abnormal mRNA expression, and affected DNA instability, cell proliferation, apoptosis and tumor microenvironment in patients with LUAD.
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Affiliation(s)
- Hong Gao
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
- Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Jun Yang
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Lu He
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Wei Wang
- Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Intelligent Pathology Institute, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yanhong Liu
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
- Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Yue Hu
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
- Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Meiling Ge
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
- Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Jie Ding
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
- Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Qing Ye
- Department of Pathology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Intelligent Pathology Institute, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- *Correspondence: Qing Ye,
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Bao Y, Gabrielpillai J, Dietrich J, Zarbl R, Strieth S, Schröck F, Dietrich D. Fibroblast growth factor (FGF), FGF receptor (FGFR), and cyclin D1 (CCND1) DNA methylation in head and neck squamous cell carcinomas is associated with transcriptional activity, gene amplification, human papillomavirus (HPV) status, and sensitivity to tyrosine kinase inhibitors. Clin Epigenetics 2021; 13:228. [PMID: 34933671 PMCID: PMC8693503 DOI: 10.1186/s13148-021-01212-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 12/08/2021] [Indexed: 12/11/2022] Open
Abstract
Background Dysregulation of fibroblast growth factor receptor (FGFR) signaling pathway has been observed in head and neck squamous cell carcinoma (HNSCC) and is a promising therapeutic target for selective tyrosine kinase inhibitors (TKIs). Potential predictive biomarkers for response to FGFR-targeted therapies are urgently needed. Understanding the epigenetic regulation of FGF pathway related genes, i.e. FGFRs, FGFs, and CCND1, could enlighten the way towards biomarker-selected FGFR-targeted therapies. Methods We performed DNA methylation analysis of the encoding genes FGFR1, FGFR2, FGFR3, FGFR4, FGF1-14, FGF16-23, and CCND1 at single CpG site resolution (840 CpG sites) employing The Cancer Genome Research Atlas (TCGA) HNSCC cohort comprising N = 530 tumor tissue and N = 50 normal adjacent tissue samples. We correlated DNA methylation to mRNA expression with regard to human papilloma virus (HPV) and gene amplification status. Moreover, we investigated the correlation of methylation with sensitivity to the selective FGFR inhibitors PD 173074 and AZD4547 in N = 40 HPV(−) HNSCC cell lines. Results We found sequence-contextually nuanced CpG methylation patterns in concordance with epigenetically regulated genes. High methylation levels were predominantly found in the promoter flank and gene body region, while low methylation levels were present in the central promoter region for most of the analyzed CpG sites. FGFRs, FGFs, and CCND1 methylation differed significantly between tumor and normal adjacent tissue and was associated with HPV and gene amplification status. CCND1 promoter methylation correlated with CCND1 amplification. For most of the analyzed CpG sites, methylation levels correlated to mRNA expression in tumor tissue. Furthermore, we found significant correlations of DNA methylation of specific CpG sites with response to the FGFR1/3–selective inhibitors PD 173074 and AZD4547, predominantly within the transcription start site of CCND1. Conclusions Our results suggest an epigenetic regulation of CCND1, FGFRs, and FGFs via DNA methylation in HNSCC and warrants further investigation of DNA methylation as a potential predictive biomarker for response to selective FGFR inhibitors in clinical trials. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01212-4.
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Affiliation(s)
- Yilin Bao
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center Bonn (UKB), Sigmund-Freud-Str. 25, 53105, Bonn, Germany.,Department of Otolaryngology, Head and Neck Surgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jennis Gabrielpillai
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center Bonn (UKB), Sigmund-Freud-Str. 25, 53105, Bonn, Germany
| | - Jörn Dietrich
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center Bonn (UKB), Sigmund-Freud-Str. 25, 53105, Bonn, Germany
| | - Romina Zarbl
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center Bonn (UKB), Sigmund-Freud-Str. 25, 53105, Bonn, Germany
| | - Sebastian Strieth
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center Bonn (UKB), Sigmund-Freud-Str. 25, 53105, Bonn, Germany
| | - Friederike Schröck
- Department of Psychiatry and Psychotherapy, University Hospital Bonn, Bonn, Germany
| | - Dimo Dietrich
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center Bonn (UKB), Sigmund-Freud-Str. 25, 53105, Bonn, Germany.
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Xu J, Song J, Wang T, Zhu W, Zuo L, Wu J, Guo J, Yang X. A combination of methylation and protein markers is capable of detecting gastric cancer detection by combined markers. Epigenomics 2021; 13:1557-1570. [PMID: 34632818 DOI: 10.2217/epi-2021-0080] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: This study aimed to validate a combination of mSEPT9, mRNF180 and CA724 for gastric cancer (GC) detection. Patients & methods: The performance of mSEPT9, mRNF180 and CA724 was examined in a prospective cohort study with 518 participants (151 with GC, 56 with atrophic gastritis, 87 with other gastrointestinal diseases and 224 with no evidence of disease). Results: mSEPT9, mRNF180 or CA724 alone detected 48.3, 37.1 and 43.1% of GC, respectively. The combination of mSEPT9 and mRNF180 detected 60.3% of GC, and the combination of all three markers detected 68.6% of GC. The detection sensitivity of mSEPT9 and mRNF180 was significantly higher for gastric body and in elder subjects. mSEPT9 was correlated with poorer GC survival. Conclusion: The combination of mSEPT9, mRNF180 and CA724 was adequately sensitive for GC detection. The blood mSEPT9 was predictive for GC prognosis.
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Affiliation(s)
- Jianbiao Xu
- Department of General Surgery II, The First People's Hospital of Yunnan Province, Kunming, Yunnan, 650032, PR China
| | - Jianlin Song
- Department of General Surgery II, The First People's Hospital of Yunnan Province, Kunming, Yunnan, 650032, PR China
| | - Tongmin Wang
- Department of General Surgery II, The First People's Hospital of Yunnan Province, Kunming, Yunnan, 650032, PR China
| | - Wenchuan Zhu
- Department of General Surgery II, The First People's Hospital of Yunnan Province, Kunming, Yunnan, 650032, PR China
| | - Liangyu Zuo
- Department of General Surgery II, The First People's Hospital of Yunnan Province, Kunming, Yunnan, 650032, PR China
| | - Jinzhi Wu
- Department of General Surgery II, The First People's Hospital of Yunnan Province, Kunming, Yunnan, 650032, PR China
| | - Jianhui Guo
- Department of General Surgery II, The First People's Hospital of Yunnan Province, Kunming, Yunnan, 650032, PR China
| | - Xiaochun Yang
- Department of Ophthalmology, The First People's Hospital of Yunnan Province, Kunming, Yunnan, 650032, PR China
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Teng Y, Loveless R, Benson EM, Sun L, Shull AY, Shay C. SHOX2 cooperates with STAT3 to promote breast cancer metastasis through the transcriptional activation of WASF3. J Exp Clin Cancer Res 2021; 40:274. [PMID: 34465361 PMCID: PMC8406721 DOI: 10.1186/s13046-021-02083-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 08/24/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Metastasis is most often the root cause of cancer-related death. Human short stature homeobox 2 (SHOX2), a homeodomain transcription factor, is a novel inducer of epithelial-to-mesenchymal transition in breast cancer cells, though its exact role and underlying mechanisms in metastasis are not well understood. METHODS TCGA analysis was performed to identify the clinical relevance of SHOX2 in breast cancer. Gene depletion was achieved by short hairpin RNA and small interfering RNA. Molecular regulations and alterations were assessed by Western blotting, immunoprecipitation, immunohistochemistry, qRT-PCR, chromatin immunoprecipitation coupled with qPCR (ChIP-qPCR), and ChIP/re-ChIP. The impact of SHOX2 signaling on tumor growth and metastasis was evaluated in orthotopic breast tumor mice. RESULTS The expression level of SHOX2 is strongly associated with poor distant metastasis-free survival in breast cancer patients and inactivation of SHOX2 suppresses breast tumor growth and metastasis in mice. In breast cancer cells, SHOX2 directly activates Wiskott-Aldridge syndrome protein family member 3 (WASF3), a metastasis-promoting gene, at the transcriptional level, leading to a significant increase in metastatic potential. Mechanistically, SHOX2 activates signal transducer and activator of transcription 3 (STAT3) and recruits it to the WASF3 promoter, where STAT3 cooperates with SHOX2 to form a functional immunocomplex to promote WASF3 transcriptional activity in breast cancer cells. WASF3 knockdown abrogates SHOX2-induced metastasis, but not SHOX2-dependent tumorigenesis. CONCLUSIONS These findings provide a critical link between the SHOX2-STAT3-WASF3 signaling axis and metastasis and suggest that the targeting of this signaling node may represent a valuable alternative strategy for combating breast cancer metastasis.
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Affiliation(s)
- Yong Teng
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University School of Medicine, 201 Dowman Dr, GA, 30322, Atlanta, USA.
- Department of Oral Biology and Diagnostic Sciences, Georgia Cancer Center, Augusta University, 30912, Augusta, GA, USA.
| | - Reid Loveless
- Department of Oral Biology and Diagnostic Sciences, Georgia Cancer Center, Augusta University, 30912, Augusta, GA, USA
| | - Elayne M Benson
- Department of Biology, Presbyterian College, 29325, Clinton, SC, USA
| | - Li Sun
- Department of Oral Biology and Diagnostic Sciences, Georgia Cancer Center, Augusta University, 30912, Augusta, GA, USA
| | - Austin Y Shull
- Department of Biology, Presbyterian College, 29325, Clinton, SC, USA
| | - Chloe Shay
- Emory Children's Center, Emory University School of Medicine, 30322, Atlanta, GA, USA
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11
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Wu J, Li P. Detection of short stature homeobox 2 and RAS-associated domain family 1 subtype A DNA methylation in interventional pulmonology. World J Clin Cases 2021; 9:5391-5397. [PMID: 34307592 PMCID: PMC8281403 DOI: 10.12998/wjcc.v9.i20.5391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/07/2021] [Accepted: 05/20/2021] [Indexed: 02/06/2023] Open
Abstract
One of the most important aspects of interventional pulmonology is to obtain tissue or liquid samples of the chest to diagnose a respiratory disease; however, it is still possible to obtain insufficient tissue or cytologic specimens. Indeed, methylation detection is an effective method by which to establish a diagnosis. This review focuses on the clinical application of short stature homeobox 2 and RAS-associated domain family 1 subtype A DNA methylation detection in interventional pulmonology, including bronchoscopic fluid biopsy, transbronchial needle aspiration, and pleural effusion.
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Affiliation(s)
- Jian Wu
- Department of Anesthesiology, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning Province, China
| | - Peng Li
- Department of Pulmonary and Critical Care Medicine, Shengjing Hospital of China Medical University, Shenyang 110004, Liaoning Province, China
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12
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Huang W, Huang H, Zhang S, Wang X, Ouyang J, Lin Z, Chen P. A Novel Diagnosis Method Based on Methylation Analysis of SHOX2 and Serum Biomarker for Early Stage Lung Cancer. Cancer Control 2021; 27:1073274820969703. [PMID: 33167712 PMCID: PMC7791477 DOI: 10.1177/1073274820969703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Objectives: Lung cancer (LC) is often accompanied by significant methylation
abnormalities. This study aimed to develop a decision tree (DT) accompanied
the stature homeobox 2 gene (SHOX2) / prostaglandin E receptor 4 (PTGER4)
gene DNA methylation with traditional tumor marker in the differential
diagnosis of benign and malignant lung nodule. Methods: We performed a study with 104 patients enrolled in the LC group and 36
patients in the benign lung diseases group. All the clinical data of these
patients were collected through electronic medical record. Total Methylation
(TM) status of both SHOX2 and PTGER4 was defined as methylation levels of
SHOX2 plus methylation levels of PTGER4. One-way analysis was used to
compare the concentrations of serum samples and t-test was used to compare
pairwise mean values between groups. Receiver operating curve (ROC) was used
to evaluate the diagnostic value. Furthermore, the strategy was validated in
19 LC patients and 11 patients with benign lung diseases. Results: There were significant differences between the concentration of
neuron-specific enolase (NSE), carcinoembryonic antigen (CEA), cytokeratin
19 fragments (CYFRA21 -1) and the methylation levels of SHOX2, PTGER4 and TM
in lung benign diseases and cancer group. The AUCs of NSE, CEA, CYFRA21 -1,
Methylation SHOX2, Methylation PTGER4 and TM were 0.721 (95% CI:
0.627–0.816), 0.753 (95% CI: 0.673–0.833) and 0.778(95% CI: 0.700–0.856),
0.851(0.786-0.916), 0.847(0.780-0.913) and 0.861(0.800-0.922) respectively.
We developed a DT model with TM and CYFRA21 -1 used in this study, and the
area under the curve (AUC) of DT was 0.921 and the sensitivity up to 0.856.
In the validation cohort, the AUC of SHOX2, PTGER4 and TM was also much
higher than traditional serum markers. Conclusions: Our results indicated that the DT model calculated from the TM and CYFRA21 -1
can accurately classify LC and benign diseases, which showed better
diagnostic performance than traditional serum parameter.
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Affiliation(s)
- Wenhai Huang
- Department of Thoracic Surgery, Jiangmen Centre Hospital, Jiangmen, Guangdong, China
| | - Hao Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shuishen Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xueping Wang
- Department of Laboratory Medicine, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Juan Ouyang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhichao Lin
- Department of Thoracic Surgery, Jiangmen Centre Hospital, Jiangmen, Guangdong, China
| | - Peisong Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
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13
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Li N, Zeng Y, Tai M, Lin B, Zhu D, Luo Y, Ren X, Zhu X, Li L, Wu H, Huang J. Analysis of the Prognostic Value and Gene Expression Mechanism of SHOX2 in Lung Adenocarcinoma. Front Mol Biosci 2021; 8:688274. [PMID: 34262939 PMCID: PMC8273341 DOI: 10.3389/fmolb.2021.688274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/26/2021] [Indexed: 01/15/2023] Open
Abstract
Background: Detection of SHOX2 methylation has been used to assist in the early diagnosis of lung cancer in many hospitals as SHOX2 may be important in the tumorigenesis of lung cancer. However, there are few studies on the mRNA expression, methylation, and molecular mechanism of SHOX2 in lung cancer. We aimed to explore the role of SHOX2 in lung adenocarcinoma (LUAD). Methods: First, we examined the differential expression of SHOX2 mRNA and methylation in cancerous and normal tissues using databases. Second, we analyzed the relationship between SHOX2 expression and common clinical parameters in LUAD patients. Third, we further explored the methylated level and its specific location of SHOX2 and the mainly factors of SHOX2 gene expression. Finally, we screened the correlatively expressed genes to analyze the pathways from the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes using DAVID. Results: We found that the mRNA expression of SHOX2 was higher in multiple cancers, including LUAD and lung squamous cell carcinoma (LUSC), than in normal tissues. Among LUAD patients, SHOX2 expression was higher in patients of middle–young age, with smoking history, in advanced stages, and with nodal distant metastasis. In addition, our results showed that patients with high expression of SHOX2 are prone to recurrence, poor differentiation, and poor prognosis. Thus, we identified that SHOX2 might be an oncogene for LUAD progression. The main factor influencing the high expression of SHOX2 mRNA may be DNA methylation, followed by copy number variation (CNV), but not by gene mutations in LUAD. Unexpectedly, we found that SHOX2 undergoes hypomethylation in the gene body instead of hypermethylation in the promoter. Additionally, SHOX2 has cross talk in the PI3K–Akt signaling pathway and ECM–receptor interaction. Conclusion:SHOX2 is highly expressed in most cancers. SHOX2 gene expression might be mainly regulated by methylation of its gene body in LUAD, and its high expression or hypomethylation indicates poor differentiation and poor prognosis. SHOX2 could be involved in PI3K–Akt and other important cancer-related signaling pathways to promote tumorigenesis.
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Affiliation(s)
- Nanhong Li
- Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China.,The Center of Pathological Diagnosis and Research, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Yu Zeng
- Department of Respiration, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Min Tai
- Department of Pathology, Guangdong Medical University, Zhanjiang, China
| | - Biyun Lin
- The Center of Pathological Diagnosis and Research, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Di Zhu
- Department of Pathology, Guangdong Medical University, Zhanjiang, China
| | - Yi Luo
- Department of Pathology, Guangdong Medical University, Zhanjiang, China
| | - Xinle Ren
- Department of Pathology, Guangdong Medical University, Zhanjiang, China
| | - Xiaoying Zhu
- Department of Pathology, Guangdong Medical University, Zhanjiang, China
| | - Lanlan Li
- Department of Pathology, Guangdong Medical University, Zhanjiang, China
| | - Hongrong Wu
- The Center of Pathological Diagnosis and Research, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Jian Huang
- The Center of Pathological Diagnosis and Research, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China.,Department of Pathology, Guangdong Medical University, Zhanjiang, China
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14
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DNA methylation of PTGER4 in peripheral blood plasma helps to distinguish between lung cancer, benign pulmonary nodules and chronic obstructive pulmonary disease patients. Eur J Cancer 2021; 147:142-150. [PMID: 33662689 DOI: 10.1016/j.ejca.2021.01.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/23/2021] [Accepted: 01/28/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND/INTRODUCTION In contrast to patients who present with advanced stage lung cancer and associated poor prognosis, patients with early-stage lung cancer may be candidates for curative treatments. The results of the NELSON lung cancer screening trial are expected to stimulate the development and implementation of a lung cancer screening strategy in most countries. Widespread use of chest computed tomography scans will also result in the detection of solitary pulmonary nodules. Because reliable biomarkers to distinguish between malignant and benign lesions are lacking, tissue-based histopathological diagnostics remain the gold standard. In this study, we aimed to establish a test to assess the predictive ability of DNA hypermethylation of SHOX2 and PTGER4 in plasma to discriminate between patients with 1.) lung cancer, 2.) benign lesions, and 3.) patients with chronic obstructive pulmonary disease (COPD). PATIENTS AND METHODS We retrospectively analysed SHOX2 and PTGER4 methylation in 121 prospectively collected plasma samples of patients with lung cancer (group 1A), benign lesions (group 1B), and COPD without nodules (group 2). RESULTS PTGER4 DNA hypermethylation was more frequently observed in patients with lung cancer than in controls (p = 0.0004). Results remained significant after correction for tumour volume, smoking status, age, and eligibility for the NELSON trial. CONCLUSIONS Detection of methylated PTGER4 in plasma DNA may serve as a biomarker to support clinical decision-making in patients with pulmonary lesions at lung cancer screening in high-risk populations. Further exploration in prospective studies is warranted.
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15
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Rizk MMMA, Helal SMF, Gad AYS, Younan DNA, Moemen SAEMMR. SHOX2 gene methylation in Egyptians having lung cancer. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2020. [DOI: 10.1186/s43042-020-00069-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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16
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Xu Z, Wang Y, Wang L, Xiong J, Wang H, Cui F, Peng H. The performance of the SHOX2/ PTGER4 methylation assay is influenced by cancer stage, age, type and differentiation. Biomark Med 2020; 14:341-351. [PMID: 32250153 DOI: 10.2217/bmm-2019-0325] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Aim: To investigate the clinicopathological factors affecting the mSHOX2/mPTGER4 assay performance and its application in lung cancer detection in Chinese population. Materials & methods: A total of 455 subjects were recruited in this case-control study (302 untreated lung cancer patients, 153 normal subjects). Blood samples were collected before therapy and the mSHOX2/mPTGER4 level was measured with Epi proLung assay. Results: The mSHOX2/mPTGER4 sensitivity was 75.6% at 84.8% specificity. Both markers showed stage-dependent sensitivity. mSHOX2 was more sensitive to small-cell lung cancer and mPTGER4 was more sensitive to poorly differentiated lung cancer. Sensitivity increased with age but was not affected by sex. The mPRGER4/mSHOX2 sensitivity was significantly higher than that of protein markers. Conclusion: The mSHOX2/mPTGER4 assay showed some values with more limitations in lung cancer early detection.
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Affiliation(s)
- Zheyuan Xu
- Department of Thoracic Surgery, The First People's Hospital of Yunnan Province, Kunming, Yunnan, China.,Department of Thoracic Surgery, The Affiliated Hospital of Kunming University of Science & Technology, Kunming, Yunnan, China
| | - Yang Wang
- Department of Thoracic Surgery, The First People's Hospital of Yunnan Province, Kunming, Yunnan, China.,Department of Thoracic Surgery, The Affiliated Hospital of Kunming University of Science & Technology, Kunming, Yunnan, China
| | - Lan Wang
- Department of Thoracic Surgery, The First People's Hospital of Yunnan Province, Kunming, Yunnan, China.,Department of Thoracic Surgery, The Affiliated Hospital of Kunming University of Science & Technology, Kunming, Yunnan, China
| | - Jian Xiong
- Department of Thoracic Surgery, The First People's Hospital of Yunnan Province, Kunming, Yunnan, China.,Department of Thoracic Surgery, The Affiliated Hospital of Kunming University of Science & Technology, Kunming, Yunnan, China
| | - Han Wang
- Department of Thoracic Surgery, The First People's Hospital of Yunnan Province, Kunming, Yunnan, China.,Department of Thoracic Surgery, The Affiliated Hospital of Kunming University of Science & Technology, Kunming, Yunnan, China
| | - Fengxian Cui
- Department of Thoracic Surgery, The First People's Hospital of Yunnan Province, Kunming, Yunnan, China.,Department of Thoracic Surgery, The Affiliated Hospital of Kunming University of Science & Technology, Kunming, Yunnan, China
| | - Hao Peng
- Department of Thoracic Surgery, The First People's Hospital of Yunnan Province, Kunming, Yunnan, China.,Department of Thoracic Surgery, The Affiliated Hospital of Kunming University of Science & Technology, Kunming, Yunnan, China
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17
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Zang R, Wang X, Jin R, Lei Y, Huang J, Liu C, Zheng S, Zhou F, Wu Q, Sun N, Gao S, He J. Translational value of IDH1 and DNA methylation biomarkers in diagnosing lung cancers: a novel diagnostic panel of stage and histology-specificity. J Transl Med 2019; 17:430. [PMID: 31888670 PMCID: PMC6936123 DOI: 10.1186/s12967-019-2117-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 10/26/2019] [Indexed: 12/24/2022] Open
Abstract
Background Lung cancer is the leading cause of cancer-related death worldwide, and the timely and serial assessment of low-dose computed tomography (LDCT) in high-risk populations remains a challenge. Furthermore, testing a single biomarker for the diagnosis of lung cancers is of relatively low effectiveness. Thus, a stronger diagnostic combination of blood biomarkers is needed to improve the diagnosis of non-small cell lung cancer (NSCLC). Methods The blood levels of individual biomarkers [IDH1, DNA methylation of short stature homeobox 2 gene (SHOX2), and prostaglandin E receptor 4 gene (PTGER4)] were measured and statistically analyzed in samples from healthy controls and patients with lung cancer. In total, 221 candidates were enrolled and randomly assigned into two groups for the training and validation of a diagnostic panel. Additionally, a subgroup analysis was performed in the whole cohort. Results A newly combined 3-marker diagnostic model for lung cancers was established and validated with area under the receiver operating characteristic (ROC) curve (AUC) values ranging from 0.835 to 0.905 in independent groups showing significantly stronger diagnostic value compared with a single tested biomarker. The sensitivity of the diagnostic model was as high as 86.1% and 80.0% in the training and validation sets, respectively. Although no apparent differences were found between the 3-marker and 2-marker models, the high clinical T-stage and histological type specificity of IDH1 and two other methylated DNA biomarkers were demonstrated in the subgroup analysis. Conclusions The combination of single biomarkers with high stage-specificity and histological type specificity (SHOX2 and PTGER4 DNA methylation and IDH1) showed better diagnostic performance in the detection of lung cancers compared with single marker assessment. A greater clinical utility of the panel may be developed by adding demographic/epidemiologic characteristics.
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Affiliation(s)
- Ruochuan Zang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xinfeng Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Runsen Jin
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yuanyuan Lei
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jianbing Huang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Chengming Liu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Sufei Zheng
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Fang Zhou
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Qian Wu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Nan Sun
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Shugeng Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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18
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Peng X, Liu X, Xu L, Li Y, Wang H, Song L, Xiao W. The mSHOX2 is capable of assessing the therapeutic effect and predicting the prognosis of stage IV lung cancer. J Thorac Dis 2019; 11:2458-2469. [PMID: 31372283 DOI: 10.21037/jtd.2019.05.81] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Background Instant monitoring of the therapeutic effect of systematic therapy in late-stage lung cancer is crucial for response assessment and strategy adjustment. Previous study found that specific plasma methylation markers may be applied to therapeutic effect assessment. In order to investigate the performance of plasma mSHOX2 in assessing the therapeutic effect and predicting the prognosis of stage IV lung cancer, we performed the study focusing on patients underwent chemotherapy or tyrosine kinase inhibitor (TKI)-based targeted therapy. Methods Blood samples from 163 subjects, including 30 stage I, 29 stage II, 26 stage III and 68 stage IV lung cancer patients, were recruited in this study. Quantitative relationship between primary tumor size and the plasma mSHOX2 level was established. Blood samples before therapy and two cycles after therapy were obtained from 68 stage IV patients, and the mSHOX2 level was quantified as ΔΔCt. Results Sharp decrease of plasma mSHOX2 level was seen in patients with partial response (PR) while not in those with stable disease (SD). The plasma mSHOX2 level change reflected the degree of response and correlated with the maximal diameter of primary tumors in linear relationship. The mSHOX2 levels before and two cycles after therapy were predictors of the overall survival, while the mSHOX2 level change or the tumor size change were not predictors of the overall survival. Furthermore, univariable and multivariable Cox regression revealed that mSHOX2 level before therapy was the only independent predictor of the overall survival with a hazard ratio of 1.414. Conclusions mSHOX2 is effective for therapeutic effect assessment and prognosis prediction of stage IV lung cancer patients underwent systematic therapy.
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Affiliation(s)
- Xiumei Peng
- The Chinese PLA Medical College and the Chinese PLA General Hospital, Beijing 100853, China.,Department of Oncology, the Fourth Medical Center of the Chinese PLA General Hospital, Beijing 100037, China
| | - Xiaoliang Liu
- Department of Radiotherapy, the Chinese PLA General Hospital, Beijing 100853, China
| | - Long Xu
- Department of Oncology, the General Hospital of the Chinese PLA Northern Theater Command, Shenyang 110016, China
| | - Yuemin Li
- The Chinese PLA Medical College and the Chinese PLA General Hospital, Beijing 100853, China.,Department of Radiotherapy, the Eighth Medical Center of the Chinese PLA General Hospital, Beijing 100091, China
| | - Huaiqing Wang
- Department of Radiotherapy, the Eighth Medical Center of the Chinese PLA General Hospital, Beijing 100091, China.,Department of Graduate, Hebei North University, Zhangjiakou 075000, China
| | - Lele Song
- The Chinese PLA Medical College and the Chinese PLA General Hospital, Beijing 100853, China.,Department of Radiotherapy, the Eighth Medical Center of the Chinese PLA General Hospital, Beijing 100091, China.,BioChain (Beijing) Science and Technology, Inc., Beijing 100176, China
| | - Wenhua Xiao
- The Chinese PLA Medical College and the Chinese PLA General Hospital, Beijing 100853, China.,Department of Oncology, the Fourth Medical Center of the Chinese PLA General Hospital, Beijing 100037, China
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19
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Li L, Fu K, Zhou W, Snyder M. Applying circulating tumor DNA methylation in the diagnosis of lung cancer. PRECISION CLINICAL MEDICINE 2019; 2:45-56. [PMID: 35694699 PMCID: PMC8985769 DOI: 10.1093/pcmedi/pbz003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/17/2019] [Accepted: 03/14/2019] [Indexed: 02/05/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide. Low dose computed tomography (LDCT) is commonly used for disease screening, with identified candidate cancerous regions further diagnosed using tissue biopsy. However, existing techniques are all invasive and unavoidably cause multiple complications. In contrast, liquid biopsy is a noninvasive, ideal surrogate for tissue biopsy that can identify circulating tumor DNA (ctDNA) containing tumorigenic signatures. It has been successfully implemented to assist treatment decisions and disease outcome prediction. ctDNA methylation, a type of lipid biopsy that profiles critical epigenetic alterations occurring during carcinogenesis, has gained increasing attention. Indeed, aberrant ctDNA methylation occurs at early stages in lung malignancy and therefore can be used as an alternative for the early diagnosis of lung cancer. In this review, we give a brief synopsis of the biological basis and detecting techniques of ctDNA methylation. We then summarize the latest progress in use of ctDNA methylation as a diagnosis biomarker. Lastly, we discuss the major issues that limit application of ctDNA methylation in the clinic, and propose possible solutions to enhance its usage.
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Affiliation(s)
- Lei Li
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, USA
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, 37 Guoxuexiang, Chengdu, China
| | - Kai Fu
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, USA
| | - Wenyu Zhou
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, USA
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, USA
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20
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Genome-wide DNA methylation analysis reveals molecular subtypes of pancreatic cancer. Oncotarget 2018; 8:28990-29012. [PMID: 28423671 PMCID: PMC5438707 DOI: 10.18632/oncotarget.15993] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 02/12/2017] [Indexed: 12/13/2022] Open
Abstract
Pancreatic cancer (PC) is the fourth leading cause of cancer deaths in the United States with a five-year patient survival rate of only 6%. Early detection and treatment of this disease is hampered due to lack of reliable diagnostic and prognostic markers. Recent studies have shown that dynamic changes in the global DNA methylation and gene expression patterns play key roles in the PC development; hence, provide valuable insights for better understanding the initiation and progression of PC. In the current study, we used DNA methylation, gene expression, copy number, mutational and clinical data from pancreatic patients. We independently investigated the DNA methylation and differential gene expression profiles between normal and tumor samples and correlated methylation levels with gene expression patterns. We observed a total of ~23-thousand differentially methylated CpG sites (Δβ≥0.1) between normal and tumor samples, where majority of the CpG sites are hypermethylated in PC, and this phenomenon is more prominent in the 5′UTRs and promoter regions compared to the gene bodies. Differential methylation is observed in genes associated with the homeobox domain, cell division and differentiation, cytoskeleton, epigenetic regulation and development, pancreatic development and pancreatic signaling and pancreatic cancer core signaling pathways. Correlation analysis suggests that methylation in the promoter region and 5′UTR has mostly negative correlations with gene expression while gene body and 3′UTR associated methylation has positive correlations. Regulatory element analysis suggests that HOX cluster and histone core proteins are upstream regulators of hypomethylation, while SMAD4, STAT4, STAT5B and zinc finger proteins (ZNF) are upstream regulators of hypermethylation. Non-negative matrix factorization (NMF) clustering of differentially methylated sites generated three clusters in PCs suggesting the existence of distinct molecular subtypes. Cluster 1 and cluster 2 showed samples enriched with clinical phenotypes like neoplasm histological grade and pathologic T-stage T3, respectively, while cluster 3 showed the enrichment of samples with neoplasm histological grade G1. To the best of our knowledge, this is the first genome-scale methylome analysis of PC data from TCGA. Our clustering analysis provides a strong basis for future work on the molecular subtyping of epigenetic regulation in pancreatic cancer.
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Abstract
Lung cancer is the leading cause of cancer-related deaths in the world. Despite significant advances in the early detection and treatment of the disease, the prognosis remains poor, with an overall 5-year survival rate ranging from 15% to 20%. This poor prognosis results largely from early micrometastatic spread of cancer cells to nearby lymph nodes or tissues and partially from early recurrence after curative surgical resection. Recently, precision medicines that target potential oncogenic driver mutations have been approved to treat lung cancer. However, some lung cancer patients do not have targetable mutations, and many patients develop resistance to targeted therapy. Tumor heterogeneity and mutational density are also challenges in treating lung cancer, which underscores the need for developing alternative therapeutic strategies for treating lung cancer. Epigenetic therapy may circumvent the problems of tumor heterogeneity and drug resistance by affecting the expression of several hundred target genes. This review highlights precision medicine using an innovative approach of epigenetic priming prior to conventional standard therapy or targeted cancer therapy in lung cancer.
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Affiliation(s)
- Dongho Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Duk-Hwan Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea. .,Samsung Medical Center, Research Institute for Future Medicine, Seoul, South Korea.
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Schröck A, Leisse A, de Vos L, Gevensleben H, Dröge F, Franzen A, Wachendörfer M, Schröck F, Ellinger J, Teschke M, Wilhelm-Buchstab T, Landsberg J, Holdenrieder S, Hartmann G, Field JK, Bootz F, Kristiansen G, Dietrich D. Free-Circulating Methylated DNA in Blood for Diagnosis, Staging, Prognosis, and Monitoring of Head and Neck Squamous Cell Carcinoma Patients: An Observational Prospective Cohort Study. Clin Chem 2017; 63:1288-1296. [PMID: 28515105 DOI: 10.1373/clinchem.2016.270207] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 03/21/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND Circulating cell-free DNA methylation testing in blood has recently received regulatory approval for screening of colorectal cancer. Its application in other clinical settings, including staging, prognosis, prediction, and recurrence monitoring is highly promising, and of particular interest in head and neck squamous cell carcinomas (HNSCCs) that represent a heterogeneous group of cancers with unsatisfactory treatment guidelines. METHODS Short stature homeobox 2 (SHOX2) and septin 9 (SEPT9) DNA methylation in plasma from 649 prospectively enrolled patients (training study: 284 HNSCC/122 control patients; testing study: 141 HNSCC/102 control patients) was quantified before treatment and longitudinally during surveillance. RESULTS In the training study, 59% of HNSCC patients were methylation-positive at 96% specificity. Methylation levels correlated with tumor and nodal category (P < 0.001). Initially increased methylation levels were associated with a higher risk of death [SEPT9: hazard ratio (HR) = 5.27, P = 0.001; SHOX2: HR = 2.32, P = 0.024]. Disease recurrence/metastases were detected in 47% of patients up to 377 days earlier compared to current clinical practice. The onset of second cancers was detected up to 343 days earlier. In the testing study, sensitivity (52%), specificity (95%), prediction of overall survival (SEPT9: HR = 2.78, P = 0.022; SHOX2: HR = 2.50, P = 0.026), and correlation with tumor and nodal category (P <0.001) were successfully validated. CONCLUSIONS Methylation testing in plasma is a powerful diagnostic tool for molecular disease staging, risk stratification, and disease monitoring. Patients with initially high biomarker levels might benefit from intensified treatment and posttherapeutic surveillance. The early detection of a recurrent/metastatic disease or a second malignancy could lead to an earlier consecutive treatment, thereby improving patients' outcomes.
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Affiliation(s)
- Andreas Schröck
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Annette Leisse
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany.,Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - Luka de Vos
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | | | - Freya Dröge
- Ear, Nose and Throat Clinic, University Hospital Essen, Essen, Germany
| | - Alina Franzen
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Malin Wachendörfer
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany.,Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - Friederike Schröck
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Joerg Ellinger
- Department of Urology, University Hospital Bonn, Bonn, Germany
| | - Marcus Teschke
- Department of Oral and Maxillofacial Surgery, University Hospital Bonn, Bonn, Germany
| | | | | | | | - Gunther Hartmann
- Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - John K Field
- University of Liverpool Cancer Research Center, Liverpool, UK
| | - Friedrich Bootz
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | | | - Dimo Dietrich
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany;
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Sailer V, Holmes EE, Gevensleben H, Goltz D, Dröge F, Franzen A, Dietrich J, Kristiansen G, Bootz F, Schröck A, Dietrich D. PITX3 DNA methylation is an independent predictor of overall survival in patients with head and neck squamous cell carcinoma. Clin Epigenetics 2017; 9:12. [PMID: 28174607 PMCID: PMC5290668 DOI: 10.1186/s13148-017-0317-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Accepted: 01/20/2017] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Molecular biomarkers assisting risk-group assignment and subsequent treatment stratification are urgently needed for patients with squamous cell cancer of the head and neck region (HNSCC). Aberrant methylation is a frequent event in cancer and, therefore, a promising source for potential biomarkers. Here, the methylation status of the paired-like homeodomain transcription factor 3 (PITX3) was evaluated in HNSCC. METHODS Using a quantitative real-time PCR, PITX3 methylation was assessed in a cohort of 326 HNSCC patients treated for localized or locally advanced disease (training cohort). The results were validated with Infinium HumanMethylation450 BeadChip data from a 528 HNSCC patient cohort (validation cohort) generated by The Cancer Genome Atlas (TCGA) Research Network. RESULTS PITX3 methylation was significantly higher methylated in tumor compared to normal adjacent tissue (NAT; training cohort: median methylation NAT 32.3%, tumor 71.8%, p < 0.001; validation cohort: median methylation NAT 16.9%, tumor 35.9%, p < 0.001). PITX3 methylation was also significantly correlated with lymph node status both in the training (p = 0.006) and validation (p < 0.001) cohort. PITX3 methylation was significantly higher in HPV-associated (p16-positive) tumors compared to p16-negative tumors (training cohort: 73.7 vs. 66.2%, p = 0.013; validation cohort: 40.0 vs. 33.1%, p = 0.015). Hypermethylation was significantly associated with the risk of death (training cohort: hazard ratio (HR) = 1.80, [95% confidence interval (CI) 1.20-2.69], p = 0.005; validation cohort: HR = 1.43, [95% CI 1.05-1.95], p = 0.022). In multivariate Cox analyses, PITX3 added independent prognostic information. Messenger RNA (mRNA) expression analysis revealed an inverse correlation with PITX3 methylation in the TCGA cohort. CONCLUSIONS PITX3 DNA methylation is an independent prognostic biomarker for overall survival in patients with HNSCC and might aid in the process of risk stratification for individualized treatment.
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Affiliation(s)
- Verena Sailer
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY USA.,Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY USA
| | | | | | - Diane Goltz
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Freya Dröge
- Department of Otorhinolaryngology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Alina Franzen
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany
| | - Jörn Dietrich
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany
| | | | - Friedrich Bootz
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany
| | - Andreas Schröck
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany
| | - Dimo Dietrich
- Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany
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Genome-wide DNA Methylation Profiling Reveals Methylation Markers Associated with 3q Gain for Detection of Cervical Precancer and Cancer. Clin Cancer Res 2017; 23:3813-3822. [DOI: 10.1158/1078-0432.ccr-16-2641] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/15/2016] [Accepted: 01/04/2017] [Indexed: 11/16/2022]
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ThE uSE of AbErrAnT METhylATEd gEnES SEPT9 And VIM for clInIcAl dIAgnoSIS of colorEcTAl cAncEr. КЛИНИЧЕСКАЯ ПРАКТИКА 2016. [DOI: 10.17816/clinpract7415-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Definition of epigenetic disorders is important for early diagnosis of colorectal cancer. To obtain a model of diagnostic test system with high sensitivity and specificity, we determined the frequency of methylation in SEPT9 and VIM genes. Epigenetic events also were compared with mutations in the RAS family genes. It was confirmed the presence of aberrant methylation in SEPT9 and VIM genes in tumor cells. DNA of tumor samples was significantly more methylated than samples with DNA from adjacent tissue (P = 8,67E-19 for SEPT9 gene and P=8,68E-19 for VIM gene). In the group of patients carried mutations in KRAS or NRAS genes tumor DNA significantly more methylated in gene SEPT9 (P = 0.0018), in contrast to the tumor DNA from patients not carried mutations. We have demonstrated that the combined use of methylation markers can improve the sensitivity of the test systems used in the diagnostics of colon cancer.
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Branchi V, Schaefer P, Semaan A, Kania A, Lingohr P, Kalff JC, Schäfer N, Kristiansen G, Dietrich D, Matthaei H. Promoter hypermethylation of SHOX2 and SEPT9 is a potential biomarker for minimally invasive diagnosis in adenocarcinomas of the biliary tract. Clin Epigenetics 2016; 8:133. [PMID: 27999621 PMCID: PMC5153824 DOI: 10.1186/s13148-016-0299-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 11/29/2016] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Biliary tract carcinoma (BTC) is a fatal malignancy which aggressiveness contrasts sharply with its relatively mild and late clinical presentation. Novel molecular markers for early diagnosis and precise treatment are urgently needed. The purpose of this study was to evaluate the diagnostic and prognostic value of promoter hypermethylation of the SHOX2 and SEPT9 gene loci in BTC. METHODS Relative DNA methylation of SHOX2 and SEPT9 was quantified in tumor specimens and matched normal adjacent tissue (NAT) from 71 BTC patients, as well as in plasma samples from an independent prospective cohort of 20 cholangiocarcinoma patients and 100 control patients. Receiver operating characteristic (ROC) curve analyses were performed to probe the diagnostic ability of both methylation markers. DNA methylation was correlated to clinicopathological data and to overall survival. RESULTS SHOX2 methylation was significantly higher in tumor tissue than in NAT irrespective of tumor localization (p < 0.001) and correctly identified 71% of BTC specimens with 100% specificity (AUC = 0.918; 95% CI 0.865-0.971). SEPT9 hypermethylation was significantly more frequent in gallbladder carcinomas compared to cholangiocarcinomas (p = 0.01) and was associated with large primary tumors (p = 0.01) as well as age (p = 0.03). Cox proportional hazard analysis confirmed microscopic residual tumor at the surgical margin (R1-resection) as an independent prognostic factor, while SHOX2 and SEPT9 methylation showed no correlation with overall survival. Elevated DNA methylation levels were also found in plasma derived from cholangiocarcinoma patients. SHOX2 and SEPT9 methylation as a marker panel achieved a sensitivity of 45% and a specificity of 99% in differentiating between samples from patients with and without cholangiocarcinoma (AUC = 0.752; 95% CI 0.631-0.873). CONCLUSIONS SHOX2 and SEPT9 are frequently methylated in biliary tract cancers. Promoter hypermethylation of SHOX2 and SEPT9 may therefore serve as a minimally invasive biomarker supporting diagnosis finding and therapy monitoring in clinical specimens.
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Affiliation(s)
- V Branchi
- Department of General, Visceral, Thoracic and Vascular Surgery University Hospital Bonn, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - P Schaefer
- Department of General, Visceral, Thoracic and Vascular Surgery University Hospital Bonn, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - A Semaan
- Department of General, Visceral, Thoracic and Vascular Surgery University Hospital Bonn, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - A Kania
- Department of General, Visceral, Thoracic and Vascular Surgery University Hospital Bonn, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - P Lingohr
- Department of General, Visceral, Thoracic and Vascular Surgery University Hospital Bonn, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - J C Kalff
- Department of General, Visceral, Thoracic and Vascular Surgery University Hospital Bonn, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - N Schäfer
- Department of General, Visceral, Thoracic and Vascular Surgery University Hospital Bonn, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
| | - G Kristiansen
- Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | - D Dietrich
- Institute of Pathology, University Hospital Bonn, Bonn, Germany.,Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - H Matthaei
- Department of General, Visceral, Thoracic and Vascular Surgery University Hospital Bonn, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany
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Semaan A, van Ellen A, Meller S, Bergheim D, Branchi V, Lingohr P, Goltz D, Kalff JC, Kristiansen G, Matthaei H, Pantelis D, Dietrich D. SEPT9 and SHOX2 DNA methylation status and its utility in the diagnosis of colonic adenomas and colorectal adenocarcinomas. Clin Epigenetics 2016; 8:100. [PMID: 27660666 PMCID: PMC5028994 DOI: 10.1186/s13148-016-0267-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/13/2016] [Indexed: 02/06/2023] Open
Abstract
Background Colorectal cancer (CRC) appear to arise from precursor lesions in a well-characterized adenoma-carcinoma sequence. Significant efforts have been invested to develop biomarkers that identify early adenocarcinomas and adenomas with high-grade dysplasia, since these are believed to harbor a particularly high risk for malignant transition and thus require resection. Promoter methylation of SEPT9 and SHOX2 has been suggested as a biomarker for various solid malignant tumors. Hence, the present study aimed to test their biomarker potential in CRC and precursor lesions. Results Assessment of promoter methylation of SEPT9 distinguished adenomas and CRC from controls as well as advanced from non-advanced adenomas (all p < 0.001). Correspondingly, SHOX2 methylation levels in adenomas and colorectal carcinomas were significantly higher compared to those in normal control tissues (p < 0.001). Histologic transition from adenomas to CRC was paralleled by amplification of the SEPT9 gene locus. Conclusions SEPT9/SHOX2 methylation assays may help to distinguish colorectal cancer and adenomas from normal and inflammatory colonic tissue, as well as advanced from non-advanced adenomas. Further studies need to validate these findings before introduction in clinical routine.
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Affiliation(s)
- Alexander Semaan
- Department of General, Visceral, Thoracic and Vascular Surgery, University of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Anne van Ellen
- Institute of Pathology, University of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Sebastian Meller
- Institute of Pathology, University of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Dominik Bergheim
- Institute of Pathology, University of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Vittorio Branchi
- Department of General, Visceral, Thoracic and Vascular Surgery, University of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Philipp Lingohr
- Department of General, Visceral, Thoracic and Vascular Surgery, University of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Diane Goltz
- Institute of Pathology, University of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Jörg C Kalff
- Department of General, Visceral, Thoracic and Vascular Surgery, University of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Glen Kristiansen
- Institute of Pathology, University of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Hanno Matthaei
- Department of General, Visceral, Thoracic and Vascular Surgery, University of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Dimitrios Pantelis
- Department of General, Visceral, Thoracic and Vascular Surgery, University of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
| | - Dimo Dietrich
- Institute of Pathology, University of Bonn, Sigmund-Freud-Straße 25, 53127 Bonn, Germany
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Song L, Yu H, Li Y. Diagnosis of Lung Cancer by SHOX2 Gene Methylation Assay. Mol Diagn Ther 2016; 19:159-67. [PMID: 26014676 DOI: 10.1007/s40291-015-0144-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Lung cancer is the most prevalent cancer in the world. Few effective and cheap methods are available so far for early detection and screening of lung cancer. Although histological and cytological examinations are gold standards in lung cancer diagnosis, patients are always at late stages when diagnosis is confirmed. Therefore, new diagnostic methods are needed urgently to increase the early diagnostic rate, enhance the confirmed diagnostic rate, and reduce mortality. The SHOX2 gene methylation assay has become a promising option for the above purposes. It has been shown to enhance the confirmed diagnostic rate of lung cancer in several clinical trials when combined with histological or cytological assays, and has the potential to become an early diagnostic tool. This article reviews the outcome of clinical trials using the SHOX2 gene methylation assay alone or in combination with other examinations, and suggests its future applications and research directions.
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Affiliation(s)
- Lele Song
- The Chinese PLA 309 Hospital, No. 17, Heishanhu Road, HaiDian District, Beijing, 100091, People's Republic of China,
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Jung M, Pützer S, Gevensleben H, Meller S, Kristiansen G, Dietrich D. Diagnostic and prognostic value of SHOX2 and SEPT9 DNA methylation and cytology in benign, paramalignant, and malignant ascites. Clin Epigenetics 2016; 8:24. [PMID: 26937257 PMCID: PMC4774089 DOI: 10.1186/s13148-016-0192-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/25/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Cytology remains the gold standard for the detection of malignant cells in ascites. However, its sensitivity is limited. The aim of this study was to evaluate DNA methylation biomarkers for the differential diagnosis of benign (ascites in patients without malignancy), malignant (ascites in cancer patients directly caused by malignancy), and paramalignant (ascites in cancer patients caused by comorbidities but not by malignancy) ascites. METHODS A cohort of 283 patients (134 cancer patients, 149 patients with benign diseases) presenting with ascites was prospectively enrolled. Ascites was evaluated by means of cytopathological investigation and DNA methylation of SHOX2 and SEPT9 in the cell-free and cellular fraction. DNA methylation in bisulfite-converted DNA was determined using quantitative methylation specific real-time PCR. Cytopathological and DNA methylation results were evaluated with regard to diagnosis and overall survival (OS). RESULTS Patients with positive DNA methylation had a poor overall survival compared to methylation-negative patients (hazard ratio: HR = 1.97, p = 0.001). In multivariate survival analysis, DNA methylation was an independent prognostic parameter (p = 0.003) together with age (HR = 1.03, p < 0.001) and the presence of malignant disease (HR = 1.87, p < 0.001). The combination of methylation with cytopathological analyses led to a 42 % increase in the detection rate of malignant ascites, resulting in 37 % positively diagnosed cancer patients and a specificity of 97 %. Among cancer patients, patients with DNA methylation-positive ascites showed an adverse clinical course (HR = 1.63, p = 0.039). CONCLUSIONS DNA methylation testing adds diagnostic and prognostic information and might constitute an effective ancillary method for the differential diagnosis of malignant, paramalignant, and benign ascites.
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Affiliation(s)
- Maria Jung
- Institute of Pathology, University Hospital Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany
| | - Svenja Pützer
- Institute of Pathology, University Hospital Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany
| | - Heidrun Gevensleben
- Institute of Pathology, University Hospital Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany
| | - Sebastian Meller
- Institute of Pathology, University Hospital Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany
| | - Glen Kristiansen
- Institute of Pathology, University Hospital Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany
| | - Dimo Dietrich
- Institute of Pathology, University Hospital Bonn, Sigmund-Freud-Str. 25, 53127 Bonn, Germany.,Department of Otolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
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Zhang YA, Ma X, Sathe A, Fujimoto J, Wistuba I, Lam S, Yatabe Y, Wang YW, Stastny V, Gao B, Larsen JE, Girard L, Liu X, Song K, Behrens C, Kalhor N, Xie Y, Zhang MQ, Minna JD, Gazdar AF. Validation of SCT Methylation as a Hallmark Biomarker for Lung Cancers. J Thorac Oncol 2015; 11:346-360. [PMID: 26725182 DOI: 10.1016/j.jtho.2015.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/02/2015] [Accepted: 11/04/2015] [Indexed: 12/14/2022]
Abstract
INTRODUCTION The human secretin gene (SCT) encodes secretin, a hormone with limited tissue distribution. Analysis of the 450k methylation array data in The Cancer Genome Atlas (TCGA) indicated that the SCT promoter region is differentially hypermethylated in lung cancer. Our purpose was to validate SCT methylation as a potential biomarker for lung cancer. METHODS We analyzed data from TCGA and developed and applied SCT-specific bisulfite DNA sequencing and quantitative methylation-specific polymerase chain reaction assays. RESULTS The analyses of TCGA 450K data for 801 samples showed that SCT hypermethylation has an area under the curve (AUC) value greater than 0.98 that can be used to distinguish lung adenocarcinomas or squamous cell carcinomas from nonmalignant lung tissue. Bisulfite sequencing of lung cancer cell lines and normal blood cells allowed us to confirm that SCT methylation is highly discriminative. By applying a quantitative methylation-specific polymerase chain reaction assay, we found that SCT hypermethylation is frequently detected in all major subtypes of malignant non-small cell lung cancer (AUC = 0.92, n = 108) and small cell lung cancer (AUC = 0.93, n = 40) but is less frequent in lung carcinoids (AUC = 0.54, n = 20). SCT hypermethylation appeared in samples of lung carcinoma in situ during multistage pathogenesis and increased in invasive samples. Further analyses of TCGA 450k data showed that SCT hypermethylation is highly discriminative in most other types of malignant tumors but less frequent in low-grade malignant tumors. The only normal tissue with a high level of methylation was the placenta. CONCLUSIONS Our findings demonstrated that SCT methylation is a highly discriminative biomarker for lung and other malignant tumors, is less frequent in low-grade malignant tumors (including lung carcinoids), and appears at the carcinoma in situ stage.
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Zhao QT, Guo T, Wang HE, Zhang XP, Zhang H, Wang ZK, Yuan Z, Duan GC. Diagnostic value of SHOX2 DNA methylation in lung cancer: a meta-analysis. Onco Targets Ther 2015; 8:3433-9. [PMID: 26640383 PMCID: PMC4657794 DOI: 10.2147/ott.s94300] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The diagnostic value of SHOX2 DNA methylation in patients with lung cancer remains controversial. Thus, we performed a systematic review and meta-analysis to assess diagnostic accuracy of SHOX2 DNA methylation in the lymph node, bronchial aspirates, pleural effusion, plasma, and tumor tissue for lung cancer. We conducted a comprehensive literature search in PubMed, Ovid, the Cochrane library, and Web of Science databases in May 2015. The diagnostic sensitivity (SEN), specificity (SPE), positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and summary receiver operating characteristic (SROC) curve were pooled using STATA 12.0 software. A total of 2,296 subjects included 1,129 lung cancer patients in eight studies were recruited in this meta-analysis. The summary estimates for SHOX2 DNA methylation in the diagnosis of lung cancer in these studies were pooled SEN =0.70 (95% confidence interval [CI]: 0.46–0.87), SPE =0.96 (95% CI: 0.91–0.99), PLR 20.01 (95% CI: 6.96–57.52), NLR 0.31 (95% CI: 0.15–0.64), and DOR 65.11 (95% CI: 13.10–323.61), and the area under the curve (AUC) was 0.96 (95% CI: 0.94–0.97). SHOX2 DNA methylation has greater diagnostic value in detecting lung cancer. In addition, considering the potential publication bias and high heterogeneity, further research studies with more well-designed and large sample sizes are needed in the future.
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Affiliation(s)
- Qing-Tao Zhao
- Department of Thoracic Surgery, Hebei General Hospital, Shijiazhuang, Hebei, People's Republic of China
| | - Tao Guo
- Department of Thoracic Surgery, Hebei General Hospital, Shijiazhuang, Hebei, People's Republic of China
| | - Hui-En Wang
- Department of Thoracic Surgery, Hebei General Hospital, Shijiazhuang, Hebei, People's Republic of China
| | - Xiao-Peng Zhang
- Department of Thoracic Surgery, Hebei General Hospital, Shijiazhuang, Hebei, People's Republic of China
| | - Hua Zhang
- Department of Thoracic Surgery, Hebei General Hospital, Shijiazhuang, Hebei, People's Republic of China
| | - Zhi-Kang Wang
- Department of Thoracic Surgery, Hebei General Hospital, Shijiazhuang, Hebei, People's Republic of China
| | - Zheng Yuan
- Department of Thoracic Surgery, Hebei General Hospital, Shijiazhuang, Hebei, People's Republic of China
| | - Guo-Chen Duan
- Department of Thoracic Surgery, Hebei General Hospital, Shijiazhuang, Hebei, People's Republic of China
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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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Erives AJ. Genes conserved in bilaterians but jointly lost with Myc during nematode evolution are enriched in cell proliferation and cell migration functions. Dev Genes Evol 2015; 225:259-73. [PMID: 26173873 PMCID: PMC4568025 DOI: 10.1007/s00427-015-0508-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 06/24/2015] [Indexed: 12/11/2022]
Abstract
Animals use a stereotypical set of developmental genes to build body architectures of varying sizes and organizational complexity. Some genes are critical to developmental patterning, while other genes are important to physiological control of growth. However, growth regulator genes may not be as important in small-bodied “micro-metazoans” such as nematodes. Nematodes use a simplified developmental strategy of lineage-based cell fate specifications to produce an adult bilaterian body composed of a few hundreds of cells. Nematodes also lost the MYC proto-oncogenic regulator of cell proliferation. To identify additional regulators of cell proliferation that were lost with MYC, we computationally screened and determined 839 high-confidence genes that are conserved in bilaterians/lost in nematodes (CIBLIN genes). We find that 30 % of all CIBLIN genes encode transcriptional regulators of cell proliferation, epithelial-to-mesenchyme transitions, and other processes. Over 50 % of CIBLIN genes are unnamed genes in Drosophila, suggesting that there are many understudied genes. Interestingly, CIBLIN genes include many Myc synthetic lethal (MycSL) hits from recent screens. CIBLIN genes include key regulators of heparan sulfate proteoglycan (HSPG) sulfation patterns, and lysyl oxidases involved in cross-linking and modification of the extracellular matrix (ECM). These genes and others suggest the CIBLIN repertoire services critical functions in ECM remodeling and cell migration in large-bodied bilaterians. Correspondingly, CIBLIN genes are co-expressed with Myc in cancer transcriptomes, and include a preponderance of known determinants of cancer progression and tumor aggression. We propose that CIBLIN gene research can improve our understanding of regulatory control of cellular growth in metazoans.
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Affiliation(s)
- Albert J Erives
- Department of Biology, University of Iowa, Iowa City, IA, 52242-1324, USA.
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Singh S, Rajput YS, Barui AK, Sharma R, Grover S. Expression of developmental genes in brown fat cells grown in vitro is linked with lipid accumulation. In Vitro Cell Dev Biol Anim 2015; 51:1003-11. [DOI: 10.1007/s11626-015-9930-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Accepted: 06/08/2015] [Indexed: 01/19/2023]
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Langevin SM, Kratzke RA, Kelsey KT. Epigenetics of lung cancer. Transl Res 2015; 165:74-90. [PMID: 24686037 PMCID: PMC4162853 DOI: 10.1016/j.trsl.2014.03.001] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 02/25/2014] [Accepted: 03/06/2014] [Indexed: 12/20/2022]
Abstract
Lung cancer is the leading cause of cancer-related mortality in the United States. Epigenetic alterations, including DNA methylation, histone modifications, and noncoding RNA expression, have been reported widely in the literature to play a major role in the genesis of lung cancer. The goal of this review is to summarize the common epigenetic changes associated with lung cancer to give some clarity to its etiology, and to provide an overview of the potential translational applications of these changes, including applications for early detection, diagnosis, prognostication, and therapeutics.
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Affiliation(s)
- Scott M Langevin
- Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Robert A Kratzke
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota Medical School, Minneapolis, Minn
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, RI; Department of Pathology and Laboratory Medicine, Brown University, Providence, RI.
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Hatzimichael E, Lagos K, Sim VR, Briasoulis E, Crook T. Epigenetics in diagnosis, prognostic assessment and treatment of cancer: an update. EXCLI JOURNAL 2014; 13:954-76. [PMID: 26417314 PMCID: PMC4464089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 07/29/2014] [Indexed: 11/06/2022]
Abstract
Cancer cells contain multiple genetic and epigenetic changes. The relative specificity of many epigenetic changes for neoplastic cells has allowed the identification of diagnostic, prognostic and predictive biomarkers for a number of solid tumors and hematological malignancies. Moreover, epigenetically-acting drugs are already in routine use for cancer and numerous additional agents are in clinical trials. Here, we review recent progress in the development and application of epigenetic strategies for the diagnosis, risk stratification and treatment of cancer.
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Affiliation(s)
| | - Konstantinos Lagos
- Department of Haematology, University Hospital of Ioannina, Ioannina, Greece
| | - Van Ren Sim
- Dundee Cancer Center, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | | | - Tim Crook
- Dundee Cancer Center, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
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DNA methylation ratio variability may impede clinical application of cancer diagnostic markers. Anal Bioanal Chem 2014; 406:6529-37. [DOI: 10.1007/s00216-014-7914-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 05/16/2014] [Accepted: 05/19/2014] [Indexed: 01/22/2023]
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Dietrich D, Meller S, Uhl B, Ralla B, Stephan C, Jung K, Ellinger J, Kristiansen G. Nucleic acid-based tissue biomarkers of urologic malignancies. Crit Rev Clin Lab Sci 2014; 51:173-99. [DOI: 10.3109/10408363.2014.906130] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Fleischhacker M, Dietrich D, Liebenberg V, Field JK, Schmidt B. The role of DNA methylation as biomarkers in the clinical management of lung cancer. Expert Rev Respir Med 2014; 7:363-83. [DOI: 10.1586/17476348.2013.814397] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Dietrich D, Jung M, Puetzer S, Leisse A, Holmes EE, Meller S, Uhl B, Schatz P, Ivascu C, Kristiansen G. Diagnostic and prognostic value of SHOX2 and SEPT9 DNA methylation and cytology in benign, paramalignant and malignant pleural effusions. PLoS One 2013; 8:e84225. [PMID: 24386354 PMCID: PMC3874014 DOI: 10.1371/journal.pone.0084225] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 11/20/2013] [Indexed: 02/06/2023] Open
Abstract
Pleural effusions (PE) are a common clinical problem. The discrimination between benign (BPE), malignant (MPE) and paramalignant (PPE) pleural effusions is highly important to ensure appropriate patient treatment. Today, cytology is the gold standard for diagnosing malignant pleural effusions. However, its sensitivity is limited due to the sometimes low abundance of tumor cells and the challenging assessment of cell morphology in cytological samples. This study aimed to develop and validate a diagnostic test, which allows for the highly specific detection of malignant cells in pleural effusions based on the DNA methylation biomarkers SHOX2 and SEPT9. A quantitative real-time PCR assay was developed which enabled the accurate and sensitive detection of SHOX2 and SEPT9 in PEs. Cytological and DNA methylation analyses were conducted in a case control study comprised of PEs from 114 patients (58 cases, 56 controls). Cytological analysis as well as SHOX2 and SEPT9 methylation resulted in 100% specificity. 21% of the cases were cytologically positive and 26% were SHOX2 or SEPT9 methylation positive. The combined analysis of cytology and DNA methylation resulted in an increase of 71% positively classified PEs from cancer patients as compared to cytological analysis alone. The absolute sensitivity of cytology and DNA methylation was not determinable due to the lack of an appropriate gold standard diagnostic for distinguishing between MPEs and PPEs. Therefore, it was unclear which PEs from cancer patients were malignant (containing tumor cells) and which PEs were paramalignant and resulted from benign conditions in cancer patients, respectively. Furthermore, DNA methylation analysis in PEs allowed the prognosis of the overall survival in cancer patients (Kaplan-Meier analysis, log rank test, p = 0.02 (SHOX2), p = 0.02 (SEPT9)). The developed test may be used as a diagnostic and prognostic adjunct to existing clinical and cytopathological investigations in patients with PEs of unclear etiology.
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Affiliation(s)
- Dimo Dietrich
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
- * E-mail:
| | - Maria Jung
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
| | - Svenja Puetzer
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
| | - Annette Leisse
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
| | - Emily Eva Holmes
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
| | - Sebastian Meller
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
| | - Barbara Uhl
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
| | | | - Claudia Ivascu
- Roche Pharma AG, Hematology/Oncology, Grenzach-Wyhlen, Germany
| | - Glen Kristiansen
- University Hospital Bonn (UKB), Institute of Pathology, Bonn, Germany
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Darwiche K, Zarogoulidis P, Baehner K, Welter S, Tetzner R, Wohlschlaeger J, Theegarten D, Nakajima T, Freitag L. Assessment of SHOX2 methylation in EBUS-TBNA specimen improves accuracy in lung cancer staging. Ann Oncol 2013; 24:2866-70. [PMID: 24026539 DOI: 10.1093/annonc/mdt365] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Endobronchial ultrasound with transbronchial needle aspiration (EBUS-TBNA) is a well-established method to assess mediastinal lymph nodes for lung cancer. However, a proportion of patients require further investigation, due to the low negative predictive value (NPV). The objective of this study was to determine whether the assessment of short stature homeobox 2 (SHOX2) DNA methylation level in lymph node tissue obtained by EBUS-TBNA improves the accuracy of mediastinal staging. PATIENTS AND METHODS EBUS-TBNA was carried out for suspicious lymph nodes of 154 patients. Negative or ambiguous histological results were confirmed by surgical means and clinical follow-up over 6 months. EBUS-TBNA was assessed on 80 positive and 85 negative classified lymph nodes and compared with the result of the SHOX2 DNA methylation real-time PCR analysis. Relative methylation measured by delta-delta cycle threshold (ΔΔCt) was used to classify the samples. Clinical performance of the EBUS-TBNA procedure with and without the additional SHOX2 assessment was calculated against the final classification according to the gold standard. RESULTS Based on data from 105 patients, an average 80-fold increase in the SHOX2 methylation level was measured for positive compared with negative lymph nodes. SHOX2 results with a ΔΔCt value of <6.5 indicate positive lymph nodes. Applying this molecular analysis to EBUS-TBNA cases, not diagnosed by pathologic assessment, the sensitivity of staging was improved by 17%-99%. The NPV increased from 80% to 99%. CONCLUSIONS The combination of EBUS-TBNA and SHOX2 methylation level strongly improves the assessment of the nodal status by identifying additional malignant lesions and confirming benign nodes and therefore avoiding invasive follow-up procedures.
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Affiliation(s)
- K Darwiche
- Department of Interventional Pneumology, Ruhrlandklinik, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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Mengxi D, Qian W, Nan W, Xiaoguang X, Shijun L. Effect of DNA methylation inhibitor on RASSF1A genes expression in non-small cell lung cancer cell line A549 and A549DDP. Cancer Cell Int 2013; 13:91. [PMID: 24011511 PMCID: PMC3846638 DOI: 10.1186/1475-2867-13-91] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 09/03/2013] [Indexed: 12/16/2022] Open
Abstract
Background Ras association domain family 1A gene (RASSFlA) is a candidate suppressor gene, Lack of RASSF1A expression was found in lung cancer. High DNA methylation at the promoter region is the main reason for inactivating RASSF1A transcription. Methods In this study, we examined RASSF1A’s methylation status and its mRNA expression level between non-small cell lung cancer cell line A549 and anti-Cisplatin cell strain A549DDP, Furthermore, methylation of A549DDP was reversed by treatment of 5-Aza-2′ - deoxycytidine (5-Aza-cdR),a DNA methyltransferase inhibitor. Results We found that RASSF1A’s methylation status and its mRNA expression were obvious differences between A549 and A549DDP. 5-Aza-CdR treatment remarkablly reduced cell vability of A549DDP. Moreover, 5-Aza-CdR treatment induced A549DDP cell apoptosis in a dose dependent manner with declining cell percentage in S and G2/M stage, and increasing proportion in G0/G1 stage. Cell motility was blocked in G0/G1 stage. All of A549DDP cells showed unmethylated expression, its high methylation status was reversed in a dose-dependent manner within a certain range. Conclusions The abnormal gene methylation status of RASSF1A is a molecular biomarker in lung cancer diagnosis, treatment and prognosis.
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Affiliation(s)
- Duan Mengxi
- Department of Clinical Laboratory, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China.
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Yang T, Zhang H, Cai SY, Shen YN, Yuan SX, Yang GS, Wu MC, Lu JH, Shen F. Elevated SHOX2 Expression is Associated with Tumor Recurrence of Hepatocellular Carcinoma. Ann Surg Oncol 2013; 20 Suppl 3:S644-9. [DOI: 10.1245/s10434-013-3132-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Indexed: 02/06/2023]
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Nagel S, Meyer C, Quentmeier H, Kaufmann M, Drexler HG, MacLeod RAF. Chromothripsis in Hodgkin lymphoma. Genes Chromosomes Cancer 2013; 52:741-7. [PMID: 23630094 DOI: 10.1002/gcc.22069] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 03/27/2013] [Indexed: 01/15/2023] Open
Abstract
Chromosomal rearrangements are common features of most cancers, where they contribute to deregulated gene expression. Chromothripsis is a recently described oncogenic mechanism whereby small genomic pieces originating from one chromosomal region undergo massive rearrangements in a single step. Here, we document chromothripsis in Hodgkin lymphoma (HL) cell lines by genomic profiling, showing alternating amplicons of defined chromosomal regions. In L-1236 cells, fluorescent in situ hybridization analyses identified aberrations affecting amplified chromosomal segments that derived from the long arm regions of chromosomes 3 and 9 and that colocalized to a derivative chromosome 6, indicating the cataclysmic origin of this mutation. The ABL1 gene at 9q34 was targeted by these rearrangements leading to its overexpression in L-1236 cells, correlating with pharmacological resistance to treatment with the kinase inhibitor dasatinib. Collectively, we identified and characterized chromothriptic rearrangements in HL cell lines to serve as models for analyzing this novel oncogenomic mechanism.
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Affiliation(s)
- Stefan Nagel
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ--German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
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Abstract
This chapter summarizes the current knowledge on gene copy number changes found in lung tumors, and their application in the diagnosis, prognostication, and prediction of response to chemotherapy. Examples of the identification of specific "driver" oncogenes within amplified DNA segments are described. A model of how array-CGH could be integrated clinically into the routine workup of lung cancers in clinical laboratory is proposed.
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Affiliation(s)
- Kenneth J Craddock
- Department of Pathology, Toronto General Hospital University Health Network, Toronto, ON, Canada.
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Mikeska T, Bock C, Do H, Dobrovic A. DNA methylation biomarkers in cancer: progress towards clinical implementation. Expert Rev Mol Diagn 2012; 12:473-87. [PMID: 22702364 DOI: 10.1586/erm.12.45] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Altered DNA methylation is ubiquitous in human cancers and specific methylation changes are often correlated with clinical features. DNA methylation biomarkers, which use those specific methylation changes, provide a range of opportunities for early detection, diagnosis, prognosis, therapeutic stratification and post-therapeutic monitoring. Here we review current approaches to developing and applying DNA methylation biomarkers in cancer therapy. We discuss the obstacles that have so far limited the routine use of DNA methylation biomarkers in clinical settings and describe ways in which these obstacles can be overcome. Finally, we summarize the current state of clinical implementation for some of the most widely studied and well-validated DNA methylation biomarkers, including SEPT9, VIM, SHOX2, PITX2 and MGMT.
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Affiliation(s)
- Thomas Mikeska
- Molecular Pathology Research & Development Laboratory, Department of Pathology, Peter MacCallum Cancer Centre, Locked Bag 1, A'Beckett Street, Melbourne, Victoria 8006, Australia
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Nikolaidis G, Raji OY, Markopoulou S, Gosney JR, Bryan J, Warburton C, Walshaw M, Sheard J, Field JK, Liloglou T. DNA methylation biomarkers offer improved diagnostic efficiency in lung cancer. Cancer Res 2012; 72:5692-701. [PMID: 22962272 DOI: 10.1158/0008-5472.can-12-2309] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The exceptional high mortality of lung cancer can be instigated to a high degree by late diagnosis. Despite the plethora of studies on potential molecular biomarkers for lung cancer diagnosis, very few have reached clinical implementation. In this study, we developed a panel of DNA methylation biomarkers and validated their diagnostic efficiency in bronchial washings from a large retrospective cohort. Candidate targets from previous high-throughput approaches were examined by pyrosequencing in an independent set of 48 lung tumor/normal paired. Ten promoters were selected and quantitative methylation-specific PCR (qMSP) assays were developed and used to screen 655 bronchial washings from the Liverpool Lung Project (LLP) subjects divided into training (194 cases and 214 controls) and validation (139 cases and 109 controls) sets. Three statistical models were used to select the optimal panel of markers and to evaluate the performance of the discriminatory algorithms. The final logit regression model incorporated hypermethylation at p16, TERT, WT1, and RASSF1. The performance of this 4-gene methylation signature in the validation set showed 82% sensitivity and 91% specificity. In comparison, cytology alone in this set provided 43% sensitivity at 100% specificity. The diagnostic efficiency of the panel did not show any biases with age, gender, smoking, and the presence of a nonlung neoplasm. However, sensitivity was predictably higher in central (squamous and small cell) than peripheral (adenocarcinomas) tumors, as well as in stage 2 or greater tumors. These findings clearly show the impact of DNA methylation-based assays in the diagnosis of cytologically occult lung neoplasms. A prospective trial is currently imminent in the LLP study to provide data on the enhancement of diagnostic accuracy in a clinical setting, including by additional markers.
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Affiliation(s)
- Georgios Nikolaidis
- Department of Molecular & Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
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Jantus-Lewintre E, Usó M, Sanmartín E, Camps C. Update on biomarkers for the detection of lung cancer. LUNG CANCER-TARGETS AND THERAPY 2012; 3:21-29. [PMID: 28210122 DOI: 10.2147/lctt.s23424] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Patients at risk for lung cancer may have subclinical disease for years before presentation. The diagnosis of this disease is primarily based on symptoms, and detection often occurs after curative intervention is no longer possible. At present, no lung cancer early-detection biomarker is clinically available. This study reviews the most recent advances in early detection and molecular diagnostic biomarkers for the detection of lung cancer. This review includes an overview of the various biological specimens and matrices in which these biomarkers could be analyzed, as well as the diverse strategies and approaches for identifying new biomarkers that are currently being explored. Several novel and attractive biomarker candidates for the early detection of lung cancer exist. A remarkable shift is taking place from research based on single markers to analyzing signatures that are more complex in order to take advantage of new high-throughput technologies. However, it is still necessary to validate the most promising markers and the standardization of procedures that will lead to specific clinical applications.
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Affiliation(s)
- Eloisa Jantus-Lewintre
- Molecular Oncology Laboratory, Fundación para la Investigación del Hospital General Universitario, Valencia, Spain
| | - Marta Usó
- Molecular Oncology Laboratory, Fundación para la Investigación del Hospital General Universitario, Valencia, Spain
| | - Elena Sanmartín
- Molecular Oncology Laboratory, Fundación para la Investigación del Hospital General Universitario, Valencia, Spain
| | - Carlos Camps
- Molecular Oncology Laboratory, Fundación para la Investigación del Hospital General Universitario, Valencia, Spain; Deparment of Medical Oncology, Consorcio Hospital General Universitario, Valencia, Spain; Department of Medicine, Universitat de València, Valencia, Spain
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Dietrich D, Hasinger O, Liebenberg V, Field JK, Kristiansen G, Soltermann A. DNA methylation of the homeobox genes PITX2 and SHOX2 predicts outcome in non-small-cell lung cancer patients. DIAGNOSTIC MOLECULAR PATHOLOGY : THE AMERICAN JOURNAL OF SURGICAL PATHOLOGY, PART B 2012; 21:93-104. [PMID: 22555092 DOI: 10.1097/pdm.0b013e318240503b] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Biomarkers that facilitate prediction of disease progression in lung cancer patients might be clinically valuable in optimizing individualized therapy. In this study, the ability of the DNA methylation biomarkers PITX2 and SHOX2 to predict disease outcome in lung cancer patients has been evaluated. Quantitative, methylation-specific (HeavyMethyl), real-time polymerase chain reaction assays were used to measure DNA methylation of PITX2 and SHOX2 in bisulfite-converted DNA from formalin-fixed, paraffin-embedded tissues from 474 non-small-cell lung cancer patients. In univariate Cox Proportional Hazard analysis, high methylation of SHOX2 and PITX2 was a significant predictor of progression-free survival [SHOX2: n=465, hazard ratio (HR)=1.395 (1.130 to 1.721), P=0.002; PITX2: n=445, HR=1.312 (1.059 to 1.625), P=0.013]. Patients with low methylation of either PITX2 and/or SHOX2 (n=319) showed a significantly higher risk of disease progression as compared with patients with higher methylation of both genes [n=126; HR=1.555 (1.210 to 1.999), P=0.001]. This was particularly true for the subgroup of patients receiving no adjuvant radiotherapy or chemotherapy [n=258, HR=1.838 (1.252 to 2.698), P=0.002]. In multivariate analysis, both biomarkers added significant independent prognostic information to pT, pN, pM, and grade. Another interesting finding of this study was that SHOX2 and PITX2 DNA methylation was shown to be inversely correlated with TTF1 (also known as NKX2-1) expression (PITX2: P=0.018, SHOX2: P<0.001). TFF1 expression was previously found to be associated with improved survival in the same patient cohort. DNA methylation of PITX2 and SHOX2 is an independent prognostic biomarker for disease progression in non-small-cell lung cancer patients.
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Affiliation(s)
- Dimo Dietrich
- Institute of Pathology, University Hospital Bonn, Bonn, Germany.
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Abstract
INTRODUCTION Recently, analysis of DNA methylation of the SHOX2 locus was shown to reliably identify lung cancer in bronchial aspirates of patients with disease. As a plasma-based assay would expand the possible applications of the SHOX2 biomarker, this study aimed to develop a modified SHOX2 assay for use in a blood-based test and to analyze the performance of this optimized SHOX2 methylation assay in plasma. METHODS Quantitative real-time polymerase chain reaction was used to analyze DNA methylation of SHOX2 in plasma samples from 411 individuals. A training study (20 stage IV patients with lung cancer and 20 controls) was performed to show the feasibility of detecting the SHOX2 biomarker in blood and to determine a methylation cutoff for patient classification. The resulting cutoff was verified in a testing study composed of 371 plasma samples from patients with lung cancer and controls. RESULTS DNA methylation of SHOX2 could be used as a biomarker to distinguish between malignant lung disease and controls at a sensitivity of 60% (95% confidence interval: 53-67%) and a specificity of 90% (95% confidence interval: 84-94%). Cancer in patients with stages II (72%), III (55%), and IV (83%) was detected at a higher sensitivity when compared with stage I patients. Small cell lung cancer (80%) and squamous cell carcinoma (63%) were detected at the highest sensitivity when compared with adenocarcinomas. CONCLUSIONS SHOX2 DNA methylation is a biomarker for detecting the presence of malignant lung disease in blood plasma from patients with lung cancer.
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