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Pérez-Aliacar M, Ayensa-Jiménez J, Ranđelović T, Ochoa I, Doblaré M. Modelling glioblastoma resistance to temozolomide. A mathematical model to simulate cellular adaptation in vitro. Comput Biol Med 2024; 180:108866. [PMID: 39089107 DOI: 10.1016/j.compbiomed.2024.108866] [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: 02/14/2024] [Revised: 06/27/2024] [Accepted: 07/07/2024] [Indexed: 08/03/2024]
Abstract
Drug resistance is one of the biggest challenges in the fight against cancer. In particular, in the case of glioblastoma, the most lethal brain tumour, resistance to temozolomide (the standard of care drug for chemotherapy in this tumour) is one of the main reasons behind treatment failure and hence responsible for the poor prognosis of patients diagnosed with this disease. In this work, we combine the power of three-dimensional in vitro experiments of treated glioblastoma spheroids with mathematical models of tumour evolution and adaptation. We use a novel approach based on internal variables for modelling the acquisition of resistance to temozolomide that was observed in experiments for a group of treated spheroids. These internal variables describe the cell's phenotypic state, which depends on the history of drug exposure and affects cell behaviour. We use model selection to determine the most parsimonious model and calibrate it to reproduce the experimental data, obtaining a high level of agreement between the in vitro and in silico outcomes. A sensitivity analysis is carried out to investigate the impact of each model parameter in the predictions. More importantly, we show how the model is useful for answering biological questions, such as what is the intrinsic adaptation mechanism, or for separating the sensitive and resistant populations. We conclude that the proposed in silico framework, in combination with experiments, can be useful to improve our understanding of the mechanisms behind drug resistance in glioblastoma and to eventually set some guidelines for the design of new treatment schemes.
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Affiliation(s)
- Marina Pérez-Aliacar
- Mechanical Engineering Department, School of Engineering and Architecture, University of Zaragoza, C/ Maria de Luna, Zaragoza, 50018, Spain; Engineering Research Institute of Aragón (I3A), University of Zaragoza, C/ Mariano Esquillor, Zaragoza, 50018, Spain.
| | - Jacobo Ayensa-Jiménez
- Engineering Research Institute of Aragón (I3A), University of Zaragoza, C/ Mariano Esquillor, Zaragoza, 50018, Spain; Institute for Health Research Aragón (IIS Aragón), Avda. San Juan Bosco, Zaragoza, 50009, Spain.
| | - Teodora Ranđelović
- Institute for Health Research Aragón (IIS Aragón), Avda. San Juan Bosco, Zaragoza, 50009, Spain; Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Spain.
| | - Ignacio Ochoa
- Engineering Research Institute of Aragón (I3A), University of Zaragoza, C/ Mariano Esquillor, Zaragoza, 50018, Spain; Institute for Health Research Aragón (IIS Aragón), Avda. San Juan Bosco, Zaragoza, 50009, Spain; Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Spain.
| | - Manuel Doblaré
- Engineering Research Institute of Aragón (I3A), University of Zaragoza, C/ Mariano Esquillor, Zaragoza, 50018, Spain; Institute for Health Research Aragón (IIS Aragón), Avda. San Juan Bosco, Zaragoza, 50009, Spain; Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Spain; Nanjing Tech University, China.
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Yu Y, Fu W, Xie Y, Jiang X, Wang H, Yang X. A review on recent advances in assays for DNMT1: a promising diagnostic biomarker for multiple human cancers. Analyst 2024; 149:1002-1021. [PMID: 38204433 DOI: 10.1039/d3an01915b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
The abnormal expression of human DNA methyltransferases (DNMTs) is closely related with the occurrence and development of a wide range of human cancers. DNA (cytosine-5)-methyltransferase-1 (DNMT1) is the most abundant human DNA methyltransferase and is mainly responsible for genomic DNA methylation patterns. Abnormal expression of DNMT1 has been found in many kinds of tumors, and DNMT1 has become a valuable target for the diagnosis and drug therapy of diseases. Nowadays, DNMT1 has been found to be involved in multiple cancers such as pancreatic cancer, breast cancer, bladder cancer, lung cancer, gastric cancer and other cancers. In order to achieve early diagnosis and for scientific research, various analytical methods have been developed for qualitative or quantitative detection of low-abundance DNMT1 in biological samples and human tumor cells. Herein, we provide a brief explication of the research progress of DNMT1 involved in various cancer types. In addition, this review focuses on the types, principles, and applications of DNMT1 detection methods, and discusses the challenges and potential future directions of DNMT1 detection.
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Affiliation(s)
- Yang Yu
- Department of Laboratory Medicine, QianWei People's Hospital, Leshan 614400, China
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China.
| | - Wen Fu
- Department of Thoracic Surgery, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Yaxing Xie
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China.
| | - Xue Jiang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Hong Wang
- Department of Laboratory Medicine, QianWei People's Hospital, Leshan 614400, China
| | - Xiaolan Yang
- Key Laboratory of Medical Laboratory Diagnostics of the Education Ministry, College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China.
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Wen SWC, Borg M, Timm S, Hansen TF, Hilberg O, Andersen RF. Methylated Cell-Free Tumor DNA in Sputum as a Tool for Diagnosing Lung Cancer-A Systematic Review and Meta-Analysis. Cancers (Basel) 2024; 16:506. [PMID: 38339257 PMCID: PMC10854681 DOI: 10.3390/cancers16030506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Lung cancer is the leading cause of cancer-related mortality worldwide. Early diagnosis is pivotal for the prognosis. There is a notable overlap between lung cancer and chronic bronchitis, and the potential use of methylated tumor DNA in sputum as a biomarker for lung cancer detection is appealing. This systematic review and meta-analysis followed the PRISMA 2020 statement. A comprehensive search was conducted in Embase, Medline, Web of Science, and the Cochrane Library, using these search strings: Lung cancer, sputum, and methylated tumor DNA. A total of 15 studies met the eligibility criteria. Studies predominantly utilized a case-control design, with sensitivity ranging from 10 to 93% and specificity from 8 to 100%. A meta-analysis of all genes across studies resulted in a summary sensitivity of 54.3% (95% CI 49.4-59.2%) and specificity of 79.7% (95% CI 75.0-83.7%). Notably, two less explored genes (TAC1, SOX17) demonstrated sensitivity levels surpassing 85%. The study's findings highlight substantial variations in the sensitivity and specificity of methylated tumor DNA in sputum for lung cancer detection. Challenges in reproducibility could stem from differences in tumor site, sample acquisition, extraction methods, and methylation measurement techniques. This meta-analysis provides a foundation for prioritizing high-performing genes, calling for a standardization and refinement of methodologies before potential application in clinical trials.
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Affiliation(s)
- Sara Witting Christensen Wen
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
- Department of Regional Health Research, University of Southern Denmark, 5000 Odense, Denmark
| | - Morten Borg
- Department of Medicine, Vejle Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark;
| | - Signe Timm
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
- Department of Regional Health Research, University of Southern Denmark, 5000 Odense, Denmark
| | - Torben Frøstrup Hansen
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
- Department of Regional Health Research, University of Southern Denmark, 5000 Odense, Denmark
| | - Ole Hilberg
- Department of Regional Health Research, University of Southern Denmark, 5000 Odense, Denmark
- Department of Medicine, Vejle Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark;
| | - Rikke Fredslund Andersen
- Department of Biochemistry and Immunology, Vejle Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
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Borg M, Wen SWC, Andersen RF, Timm S, Hansen TF, Hilberg O. Methylated Circulating Tumor DNA in Blood as a Tool for Diagnosing Lung Cancer: A Systematic Review and Meta-Analysis. Cancers (Basel) 2023; 15:3959. [PMID: 37568774 PMCID: PMC10417522 DOI: 10.3390/cancers15153959] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/24/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths, and early detection is crucial for improving patient outcomes. Current screening methods using computed tomography have limitations, prompting interest in non-invasive diagnostic tools such as methylated circulating tumor DNA (ctDNA). The PRISMA guidelines for systematic reviews were followed. The electronic databases MEDLINE, Embase, Web of Science, and Cochrane Library were systematically searched for articles. The search string contained three main topics: Lung cancer, blood, and methylated ctDNA. The extraction of data and quality assessment were carried out independently by the reviewers. In total, 33 studies were eligible for inclusion in this systematic review and meta-analysis. The most frequently studied genes were SHOX2, RASSF1A, and APC. The sensitivity and specificity of methylated ctDNA varied across studies, with a summary sensitivity estimate of 46.9% and a summary specificity estimate of 92.9%. The area under the hierarchical summary receiver operating characteristics curve was 0.81. The included studies were generally of acceptable quality, although they lacked information in certain areas. The risk of publication bias was not significant. Based on the findings, methylated ctDNA in blood shows potential as a rule-in tool for lung cancer diagnosis but requires further research, possibly in combination with other biomarkers.
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Affiliation(s)
- Morten Borg
- Department of Medicine, Vejle Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark; (M.B.)
| | - Sara Witting Christensen Wen
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
- Department of Regional Health Research, University of Southern Denmark, 5000 Odense, Denmark
| | - Rikke Fredslund Andersen
- Department of Biochemistry and Immunology, Vejle Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
| | - Signe Timm
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
- Department of Regional Health Research, University of Southern Denmark, 5000 Odense, Denmark
| | - Torben Frøstrup Hansen
- Department of Oncology, Vejle Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark
- Department of Regional Health Research, University of Southern Denmark, 5000 Odense, Denmark
| | - Ole Hilberg
- Department of Medicine, Vejle Hospital, University Hospital of Southern Denmark, 7100 Vejle, Denmark; (M.B.)
- Department of Regional Health Research, University of Southern Denmark, 5000 Odense, Denmark
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Coppedè F, Bhaduri U, Stoccoro A, Nicolì V, Di Venere E, Merla G. DNA Methylation in the Fields of Prenatal Diagnosis and Early Detection of Cancers. Int J Mol Sci 2023; 24:11715. [PMID: 37511475 PMCID: PMC10380460 DOI: 10.3390/ijms241411715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
The central objective of the metamorphosis of discovery science into biomedical applications is to serve the purpose of patients and curtail the global disease burden. The journey from the discovery of DNA methylation (DNAm) as a biological process to its emergence as a diagnostic tool is one of the finest examples of such metamorphosis and has taken nearly a century. Particularly in the last decade, the application of DNA methylation studies in the clinic has been standardized more than ever before, with great potential to diagnose a multitude of diseases that are associated with a burgeoning number of genes with this epigenetic alteration. Fetal DNAm detection is becoming useful for noninvasive prenatal testing, whereas, in very preterm infants, DNAm is also shown to be a potential biological indicator of prenatal risk factors. In the context of cancer, liquid biopsy-based DNA-methylation profiling is offering valuable epigenetic biomarkers for noninvasive early-stage diagnosis. In this review, we focus on the applications of DNA methylation in prenatal diagnosis for delivering timely therapy before or after birth and in detecting early-stage cancers for better clinical outcomes. Furthermore, we also provide an up-to-date commercial landscape of DNAm biomarkers for cancer detection and screening of cancers of unknown origin.
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Affiliation(s)
- Fabio Coppedè
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy
- Interdepartmental Research Center of Biology and Pathology of Aging, University of Pisa, 56126 Pisa, Italy
| | - Utsa Bhaduri
- Laboratory of Regulatory & Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Andrea Stoccoro
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy
| | - Vanessa Nicolì
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, 56126 Pisa, Italy
| | - Eleonora Di Venere
- Department of Molecular Medicine & Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
| | - Giuseppe Merla
- Laboratory of Regulatory & Functional Genomics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, 71013 Foggia, Italy
- Department of Molecular Medicine & Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
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Mo S, Dai W, Wang H, Lan X, Ma C, Su Z, Xiang W, Han L, Luo W, Zhang L, Wang R, Zhang Y, Zhang W, Yang L, Lu R, Guo L, Zheng Y, Huang M, Xu Y, Liang L, Cai S, Cai G. Early detection and prognosis prediction for colorectal cancer by circulating tumour DNA methylation haplotypes: A multicentre cohort study. EClinicalMedicine 2023; 55:101717. [PMID: 36386039 PMCID: PMC9646872 DOI: 10.1016/j.eclinm.2022.101717] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Early detection and prognosis prediction of colorectal cancer (CRC) can significantly reduce CRC-related mortality. Recently, circulating tumour DNA (ctDNA) methylation has shown good application foreground in the early detection and prognosis prediction of multiple tumours. METHODS This multicentre cohort study evaluated ctDNA methylation haplotype patterns based on archived plasma samples (collected between 2010 and 2018) from 1138 individuals at two medical centres: Fudan University Shanghai Cancer Center (Shanghai, China) and Southern Medical University Nanfang Hospital (Guangzhou, Guangdong, China), including 366 healthy individuals, 182 patients with advanced adenoma (AA), and 590 patients with CRC. Samples were processed using the ColonES assay, a targeted bisulfite sequencing method that detects ctDNA methylation haplotype patterns in 191 genomic regions. Among these 1138 samples, 748 were used to develop a classification model, and 390 served as a blinded cohort for independent validation. The study is registered at https://register.clinicaltrials.gov with the unique identifier NCT03737591. RESULTS The model obtained from unblinded samples discriminated patients with CRC or AA from normal controls with high accuracy. In the blinded validation set, the ColonES assay achieved sensitivity values of 79.0% (95% confidence interval (CI), 66%-88%) in AA patients and 86.6% (95% CI, 81%-91%) in CRC patients with a specificity of 88.1% (95% CI, 81%-93%) in healthy individuals. The model area under the curve (AUC) for the blinded validation set was 0.903 for AA samples and 0.937 for CRC samples. Additionally, the prognosis of patients with high preoperative ctDNA methylation levels was worse than that of patients with low ctDNA methylation levels (p = 0.001 for relapse-free survival and p = 0.004 for overall survival). INTERPRETATION We successfully developed and validated an accurate, noninvasive detection method based on ctDNA methylation haplotype patterns that may enable early detection and prognosis prediction for CRC. FUNDING The Grant of National Natural Science Foundation of China (No.81871958), National Natural Science Foundation of China (No. 82203215), Shanghai Science and Technology Committee (No. 19140902100), Scientific Research Fund of Fudan University (No.IDF159052), Shanghai Municipal Health Commission (SHWJRS 2021-99), and Shanghai Sailing Program (22YF1408800).
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Affiliation(s)
- Shaobo Mo
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Weixing Dai
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hui Wang
- Singlera Genomics (Shanghai) Ltd, Shanghai, China
| | - Xiaoliang Lan
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | | | - Zhixi Su
- Singlera Genomics (Shanghai) Ltd, Shanghai, China
| | - Wenqiang Xiang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lingyu Han
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenqin Luo
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Long Zhang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Cancer Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Renjie Wang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yaodong Zhang
- Department of Intensive Care Unit, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Wenming Zhang
- Department of Endoscopy, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Lin Yang
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Renquan Lu
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Lin Guo
- Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Ying Zheng
- Department of Cancer Prevention, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Mingzhu Huang
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Ye Xu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Corresponding author. Department of Colorectal Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Li Liang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Southern Medical University, Guangzhou, China
- Corresponding author. Department of Pathology, Nanfang Hospital, Southern Medical University; Guangdong Province Key Laboratory of Molecular Tumor Pathology, Southern Medical University, Guangzhou, China.
| | - Sanjun Cai
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Cancer Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
- Corresponding author. Department of Colorectal Surgery, Fudan University Shanghai Cancer Center; Department of Cancer Institute, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Guoxiang Cai
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Corresponding author. Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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Challenges in promoter methylation analysis in the new era of translational oncology: a focus on liquid biopsy. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166390. [PMID: 35296416 DOI: 10.1016/j.bbadis.2022.166390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 02/01/2022] [Accepted: 03/08/2022] [Indexed: 12/20/2022]
Abstract
Toward the discovery of novel reliable biomarkers, epigenetic alterations have been repeatedly proposed for the diagnosis and the development of therapeutic strategies against cancer. Indeed, for promoter methylation to actively become a tumor marker for clinical use, it must be combined with a highly informative technology evaluated in an appropriate biospecimen. Methodological standardization related to epigenetic research is, in fact, one of the most challenging tasks. Moreover, tissue-based biopsy is being complemented and, in some cases, replaced by liquid biopsy. This review will highlight the advancements made for both pre-analytical and analytical implementation for the prospective use of methylation biomarkers in clinical settings, with particular emphasis on liquid biopsy.
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FTO and PLAG1 Genes Expression and FTO Methylation Predict Changes in Circulating Levels of Adipokines and Gastrointestinal Peptides in Children. Nutrients 2021; 13:nu13103585. [PMID: 34684585 PMCID: PMC8538237 DOI: 10.3390/nu13103585] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/03/2021] [Accepted: 10/06/2021] [Indexed: 12/19/2022] Open
Abstract
Adipokines and gastrointestinal tract hormones are important metabolic parameters, and both epigenetic factors and differential gene expression patterns may be associated with the alterations in their concentrations in children. The function of the FTO gene (FTO alpha-ketoglutarate dependent dioxygenase) in the regulation of the global metabolic rate is well described, whereas the influence of protooncogene PLAG1 (PLAG1 zinc finger) is still not fully understood. A cross-sectional study on a group of 26 children with various BMI values (15.3–41.7; median 28) was carried out. The aim was to evaluate the dependencies between the level of methylation and expression of aforementioned genes with the concentration of selected gastrointestinal tract hormones and adipokines in children. Expression and methylation were measured in peripheral blood mononuclear DNA by a microarray technique and a restriction enzyme method, respectively. All peptide concentrations were determined using the enzyme immunoassay method. The expression level of both FTO and PLAG1 genes was statistically significantly related to the concentration of adipokines: negatively for apelin and leptin receptor, and positively for leptin. Furthermore, both FTO methylation and expression negatively correlated with the concentration of resistin and visfatin. Cholecystokinin was negatively correlated, whereas fibroblast growth factor 21 positively correlated with methylation and expression of the FTO gene, while FTO and PLAG1 expression was negatively associated with the level of cholecystokinin and glucagon-like peptide-1. The PLAG1 gene expression predicts an increase in leptin and decrease in ghrelin levels. Our results indicate that the FTO gene correlates with the concentration of hormones produced by the adipose tissue and gastrointestinal tract, and PLAG1 gene may be involved in adiposity pathogenesis. However, the exact molecular mechanisms still need to be clarified.
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Faaborg L, Fredslund Andersen R, Waldstrøm M, Høgdall E, Høgdall C, Adimi P, Jakobsen A, Dahl Steffensen K. Analysis of HOXA9 methylated ctDNA in ovarian cancer using sense-antisense measurement. Clin Chim Acta 2021; 522:152-157. [PMID: 34419462 DOI: 10.1016/j.cca.2021.08.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/17/2021] [Accepted: 08/17/2021] [Indexed: 12/24/2022]
Abstract
DNA promoter methylation is an early event in tumorigenesis and holds promise as a valuable marker in ovarian cancer (OC). It can be measured using circulating tumor specific DNA (ctDNA) isolated from the bloodstream. Sensitivity, however, is a limiting factor of its diagnostic feasibility in OC. DNA methylation analyses are based on bisulfite conversion, resulting in two DNA strands that are no longer complementary. The current standard strategy would then target only one of the double stranded DNA strands, but the potential to increase the sensitivity by targeting both DNA strands is available. In this study, we aimed at evaluating the diagnostic potential of methylated HOXA9 ctDNA in OC by targeting both the DNA sense and antisense strand. Methylated HOXA9 was detected in the plasma of 47/79 (59.5%) patients with newly diagnosed OC using sense-antisense droplet digital PCR. Simultaneous sense-antisense measurement increased the sensitivity by 14.6% (51.9% to 59.5%) as compared to antisense only. In patients with FIGO stage I-II disease the sensitivity was increased by 25%. In conclusion, simultaneous measurement targeting both DNA strands can increase the sensitivity and the analytical approach appears valuable in the diagnostic setting of OC.
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Affiliation(s)
- Louise Faaborg
- Department of Oncology, Vejle Hospital, Lillebaelt Hospital - University Hospital of Southern Denmark, Beriderbakken 4, 7100 Vejle, Denmark; Institute of Regional Health Research, University of Southern Denmark, J.B. Winsløws Vej 19, 5000 Odense C, Denmark.
| | - Rikke Fredslund Andersen
- Department of Clinical Biochemistry, Vejle Hospital, Lillebaelt Hospital - University Hospital of Southern Denmark, Beriderbakken 4, 7100 Vejle, Denmark
| | - Marianne Waldstrøm
- Department of Oncology, Vejle Hospital, Lillebaelt Hospital - University Hospital of Southern Denmark, Beriderbakken 4, 7100 Vejle, Denmark; Department of Pathology, Vejle Hospital, Lillebaelt Hospital - University Hospital of Southern Denmark, Beriderbakken 4, 7100 Vejle, Denmark
| | - Estrid Høgdall
- Department of Pathology, Herlev Hospital, University of Copenhagen, Borgmester Ib Juuls Vej 1, 2730 Herlev, Denmark
| | - Claus Høgdall
- Department of Gynecology, The Juliane Marie Centre, Righospitalet, University of Copenhagen, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Parvin Adimi
- Department of Oncology, Vejle Hospital, Lillebaelt Hospital - University Hospital of Southern Denmark, Beriderbakken 4, 7100 Vejle, Denmark
| | - Anders Jakobsen
- Department of Oncology, Vejle Hospital, Lillebaelt Hospital - University Hospital of Southern Denmark, Beriderbakken 4, 7100 Vejle, Denmark; Institute of Regional Health Research, University of Southern Denmark, J.B. Winsløws Vej 19, 5000 Odense C, Denmark
| | - Karina Dahl Steffensen
- Department of Oncology, Vejle Hospital, Lillebaelt Hospital - University Hospital of Southern Denmark, Beriderbakken 4, 7100 Vejle, Denmark; Institute of Regional Health Research, University of Southern Denmark, J.B. Winsløws Vej 19, 5000 Odense C, Denmark
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10
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Czogała W, Czogała M, Strojny W, Wątor G, Wołkow P, Wójcik M, Bik Multanowski M, Tomasik P, Wędrychowicz A, Kowalczyk W, Miklusiak K, Łazarczyk A, Hałubiec P, Skoczeń S. Methylation and Expression of FTO and PLAG1 Genes in Childhood Obesity: Insight into Anthropometric Parameters and Glucose-Lipid Metabolism. Nutrients 2021; 13:1683. [PMID: 34063412 PMCID: PMC8155878 DOI: 10.3390/nu13051683] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 04/23/2021] [Accepted: 05/11/2021] [Indexed: 12/18/2022] Open
Abstract
The occurrence of childhood obesity is influenced by both genetic and epigenetic factors. FTO (FTO alpha-ketoglutarate dependent dioxygenase) is a gene of well-established connection with adiposity, while a protooncogene PLAG1 (PLAG1 zinc finger) has been only recently linked to this condition. We performed a cross-sectional study on a cohort of 16 obese (aged 6.6-17.7) and 10 healthy (aged 11.4-16.9) children. The aim was to evaluate the relationship between methylation and expression of the aforementioned genes and the presence of obesity as well as alterations in anthropometric measurements (including waist circumference (WC), body fat (BF_kg) and body fat percent (BF_%)), metabolic parameters (lipid profile, blood glucose and insulin levels, presence of insulin resistance) and blood pressure. Expression and methylation were measured in peripheral blood mononuclear cells using a microarray technique and a method based on restriction enzymes, respectively. Multiple regression models were constructed to adjust for the possible influence of age and sex on the investigated associations. We showed significantly increased expression of the FTO gene in obese children and in patients with documented insulin resistance. Higher FTO expression was also associated with an increase in WC, BF_kg, and BF_% as well as higher fasting concentration of free fatty acids (FFA). FTO methylation correlated positively with WC and BF_kg. Increase in PLAG1 expression was associated with higher BF%. Our results indicate that the FTO gene is likely to play an important role in the development of childhood adiposity together with coexisting impairment of glucose-lipid metabolism.
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Affiliation(s)
- Wojciech Czogała
- Department of Pediatric Oncology and Hematology, University Children’s Hospital of Krakow, 30-663 Krakow, Poland; (W.C.); (M.C.); (W.S.)
| | - Małgorzata Czogała
- Department of Pediatric Oncology and Hematology, University Children’s Hospital of Krakow, 30-663 Krakow, Poland; (W.C.); (M.C.); (W.S.)
- Department of Pediatric Oncology and Hematology, Faculty of Medicine, Jagiellonian University Medical College, 30-663 Krakow, Poland
| | - Wojciech Strojny
- Department of Pediatric Oncology and Hematology, University Children’s Hospital of Krakow, 30-663 Krakow, Poland; (W.C.); (M.C.); (W.S.)
| | - Gracjan Wątor
- Center for Medical Genomics—OMICRON, Jagiellonian University Medical College, 30-663 Krakow, Poland; (G.W.); (P.W.)
| | - Paweł Wołkow
- Center for Medical Genomics—OMICRON, Jagiellonian University Medical College, 30-663 Krakow, Poland; (G.W.); (P.W.)
| | - Małgorzata Wójcik
- Department of Pediatric and Adolescent Endocrinology, Faculty of Medicine, Jagiellonian University Medical College, 30-663 Krakow, Poland;
| | - Mirosław Bik Multanowski
- Department of Medical Genetics, Faculty of Medicine, Jagiellonian University Medical College, 30-663 Krakow, Poland;
| | - Przemysław Tomasik
- Department of Clinical Biochemistry, Faculty of Medicine, Jagiellonian University Medical College, 30-663 Krakow, Poland;
| | - Andrzej Wędrychowicz
- Department of Pediatrics, Gastroenterology and Nutrition, Faculty of Medicine, Jagiellonian University Medical College, 30-663 Krakow, Poland;
| | - Wojciech Kowalczyk
- Student Scientific Group of Pediatric Oncology and Hematology, Jagiellonian University Medical College, 30-663 Krakow, Poland; (W.K.); (K.M.); (A.Ł.); (P.H.)
| | - Karol Miklusiak
- Student Scientific Group of Pediatric Oncology and Hematology, Jagiellonian University Medical College, 30-663 Krakow, Poland; (W.K.); (K.M.); (A.Ł.); (P.H.)
| | - Agnieszka Łazarczyk
- Student Scientific Group of Pediatric Oncology and Hematology, Jagiellonian University Medical College, 30-663 Krakow, Poland; (W.K.); (K.M.); (A.Ł.); (P.H.)
| | - Przemysław Hałubiec
- Student Scientific Group of Pediatric Oncology and Hematology, Jagiellonian University Medical College, 30-663 Krakow, Poland; (W.K.); (K.M.); (A.Ł.); (P.H.)
| | - Szymon Skoczeń
- Department of Pediatric Oncology and Hematology, University Children’s Hospital of Krakow, 30-663 Krakow, Poland; (W.C.); (M.C.); (W.S.)
- Department of Pediatric Oncology and Hematology, Faculty of Medicine, Jagiellonian University Medical College, 30-663 Krakow, Poland
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Jensen SØ, Øgaard N, Nielsen HJ, Bramsen JB, Andersen CL. Enhanced Performance of DNA Methylation Markers by Simultaneous Measurement of Sense and Antisense DNA Strands after Cytosine Conversion. Clin Chem 2021; 66:925-933. [PMID: 32460325 DOI: 10.1093/clinchem/hvaa100] [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: 11/18/2019] [Accepted: 04/03/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND Most existing DNA methylation-based methods for detection of circulating tumor DNA (ctDNA) are based on conversion of unmethylated cytosines to uracil. After conversion, the 2 DNA strands are no longer complementary; therefore, targeting only 1 DNA strand merely utilizes half of the available input DNA. We investigated whether the sensitivity of methylation-based ctDNA detection strategies could be increased by targeting both DNA strands after bisulfite conversion. METHODS Dual-strand digital PCR assays were designed for the 3 colorectal cancer (CRC)-specific methylation markers KCNQ5, C9orf50, and CLIP4 and compared with previously reported single-strand assays. Performance was tested in tumor and leukocyte DNA, and the ability to detect ctDNA was investigated in plasma from 43 patients with CRC stages I to IV and 42 colonoscopy-confirmed healthy controls. RESULTS Dual-strand assays quantified close to 100% of methylated control DNA input, whereas single-strand assays quantified approximately 50%. Furthermore, dual-strand assays showed a 2-fold increase in the number of methylated DNA copies detected when applied to DNA purified from tumor tissue and plasma from CRC patients. When the results of the 3 DNA methylation markers were combined into a ctDNA detection test and applied to plasma, the dual-strand assay format detected 86% of the cancers compared with 74% for the single-strand assay format. The specificity was 100% for both the dual- and single-strand test formats. CONCLUSION Dual-strand assays enabled more sensitive detection of methylated ctDNA than single-strand assays.
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Affiliation(s)
- Sarah Ø Jensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Nadia Øgaard
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Hans Jørgen Nielsen
- Department of Surgical Gastroenterology, Center for Surgical Research, Hvidovre Hospital, Hvidovre, Denmark.,Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jesper B Bramsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Claus L Andersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
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12
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Young GP, Symonds EL, Nielsen HJ, Ferm L, Christensen IJ, Dekker E, van der Vlugt M, Mallant-Hent RC, Boulter N, Yu B, Chan M, Tevz G, LaPointe LC, Pedersen SK. Evaluation of a panel of tumor-specific differentially-methylated DNA regions in IRF4, IKZF1 and BCAT1 for blood-based detection of colorectal cancer. Clin Epigenetics 2021; 13:14. [PMID: 33478584 PMCID: PMC7818774 DOI: 10.1186/s13148-020-00999-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/22/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Differentially-methylated regions (DMRs) are characteristic of colorectal cancer (CRC) and some occur more frequently than common mutations. This study aimed to evaluate the clinical utility of assaying circulating cell-free DNA for methylation in BCAT1, IKZF1 and IRF4 for detection of CRC. METHODS A multiplexed real-time PCR assay targeting DMRs in each of the three genes was developed. Assay accuracy was explored in plasma specimens banked from observational cross-sectional trials or from volunteers scheduled for colonoscopy or prior to CRC surgery. RESULTS 1620 specimens were suitable for study inclusion including 184 and 616 cases with CRC and adenomas, respectively, and 820 cases without neoplasia (overall median age, 63.0 years; 56% males). Combining the PCR signals for all targeted DMRs returned the best sensitivity for CRC (136/184, 73.9%, 95% CI 67.1-79.7), advanced adenomas (53/337, 15.7%, 95% CI 12.0-20.1) and high-grade dysplastic (HGD) adenomas (9/35, 25.7%, 95% CI 14.0-42.3) with a 90.1%, specificity for neoplasia (739/820, 95% CI 87.9-92.0, p < 0.01). Detection of methylation in all three genes were more likely in CRC cases than those without it (OR 28.5, 95% CI 7.3-121.2, p < 0.0001). Of the 81 positive cases without neoplasia, 62 (76.5%) were positive by a single PCR replicate only and predominantly due to detection of methylated BCAT1 (53.2%). Single replicate positivity was significantly higher than that in CRC (26/136, 19.1%, p < 0.0001), and single BCAT1 replicate positivity was more likely in cases without neoplasia than in CRC (OR 17.7, 95% CI 6.6-43.3, p < 0.0001). When a positive result was limited to those with ≥ 1 PCR replicate positive for either IKZF1 or IRF4, or at least two replicates positive for BCAT1, the multi-panel test maintained a high sensitivity for CRC (131/184, 71.2%, 95% CI 64.3-77.3) and HGD adenomas (8/35, 22.9%, 95% CI 11.8-39.3, p = 0.029) but improved specificity significantly (772/820, 94.1%, 95% CI 92.3-95.6, p < 0.0001 vs. any PCR replicate positive). CONCLUSION The multi-panel methylation assay differentiates cases with CRC from those without it and does so with high specificity when criteria for BCAT1 detection are applied. The marker panel is flexible and studies in those at average risk for CRC are now warranted to determine which panel configuration best suits screening goals. TRIAL REGISTRATION ACTRN12611000318987. Registered 25 March 2011, https://www.anzctr.org.au/ ACTRN12611000318987.
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Affiliation(s)
- Graeme P Young
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, Australia
| | - Erin L Symonds
- Flinders Health and Medical Research Institute, Flinders University, Adelaide, Australia
- Bowel Health Service, Flinders Medical Centre, Bedford Park, South Australia, Australia
| | - Hans Jørgen Nielsen
- Department of Surgical Gastroenterology, Hvidovre Hospital, University of Copenhagen, Hvidovre, Denmark
| | - Linnea Ferm
- Department of Surgical Gastroenterology, Hvidovre Hospital, University of Copenhagen, Hvidovre, Denmark
| | - Ib J Christensen
- Department of Surgical Gastroenterology, Hvidovre Hospital, University of Copenhagen, Hvidovre, Denmark
| | - Evelien Dekker
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Manon van der Vlugt
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | | | - Nicky Boulter
- Clinical Genomics Pty Ltd, North Ryde, NSW, Australia
| | - Betty Yu
- Clinical Genomics Pty Ltd, North Ryde, NSW, Australia
| | - Michelle Chan
- Clinical Genomics Pty Ltd, North Ryde, NSW, Australia
| | - Gregor Tevz
- Clinical Genomics Pty Ltd, North Ryde, NSW, Australia
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De Chiara L, Leiro-Fernandez V, Rodríguez-Girondo M, Valverde D, Botana-Rial MI, Fernández-Villar A. Comparison of Bisulfite Pyrosequencing and Methylation-Specific qPCR for Methylation Assessment. Int J Mol Sci 2020; 21:ijms21239242. [PMID: 33287451 PMCID: PMC7730915 DOI: 10.3390/ijms21239242] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/18/2020] [Accepted: 12/01/2020] [Indexed: 12/18/2022] Open
Abstract
Different methodological approaches are available to assess DNA methylation biomarkers. In this study, we evaluated two sodium bisulfite conversion-dependent methods, namely pyrosequencing and methylation-specific qPCR (MS-qPCR), with the aim of measuring the closeness of agreement of methylation values between these two methods and its effect when setting a cut-off. Methylation of tumor suppressor gene p16/INK4A was evaluated in 80 lung cancer patients from which cytological lymph node samples were obtained. Cluster analyses were used to establish methylated and unmethylated groups for each method. Agreement and concordance between pyrosequencing and MS-qPCR was evaluated with Pearson’s correlation, Bland–Altman, Cohen’s kappa index and ROC curve analyses. Based on these analyses, cut-offs were derived for MS-qPCR. An acceptable correlation (Pearson’s R2 = 0.738) was found between pyrosequencing (PYRmean) and MS-qPCR (NMP; normalized methylation percentage), providing similar clinical results when categorizing data as binary using cluster analysis. Compared to pyrosequencing, MS-qPCR tended to underestimate methylation for values between 0 and 15%, while for methylation >30% overestimation was observed. The estimated cut-off for MS-qPCR data based on cluster analysis, kappa-index agreement and ROC curve analysis were much lower than that derived from pyrosequencing. In conclusion, our results indicate that independently of the approach used for estimating the cut-off, the methylation percentage obtained through MS-qPCR is lower than that calculated for pyrosequencing. These differences in data and therefore in the cut-off should be examined when using methylation biomarkers in the clinical practice.
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Affiliation(s)
- Loretta De Chiara
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain;
- Centro de Investigaciones Biomédicas (CINBIO), Centro Singular de Investigación de Galicia, Universidad de Vigo, 36310 Vigo, Spain
- Correspondence: ; Tel.: +34-986-813-841
| | - Virginia Leiro-Fernandez
- Pulmonary Department, Hospital Álvaro Cunqueiro, EOXI Vigo, 36213 Vigo, Spain; (V.L.-F.); (M.I.B.-R.); (A.F.-V.)
- PneumoVigo I +i Research Group, Sanitary Research Institute Galicia Sur (IIS Galicia Sur), 36213 Vigo, Spain
| | - Mar Rodríguez-Girondo
- Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, 2300RC Leiden, The Netherlands;
| | - Diana Valverde
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain;
- Centro de Investigaciones Biomédicas (CINBIO), Centro Singular de Investigación de Galicia, Universidad de Vigo, 36310 Vigo, Spain
| | - María Isabel Botana-Rial
- Pulmonary Department, Hospital Álvaro Cunqueiro, EOXI Vigo, 36213 Vigo, Spain; (V.L.-F.); (M.I.B.-R.); (A.F.-V.)
- PneumoVigo I +i Research Group, Sanitary Research Institute Galicia Sur (IIS Galicia Sur), 36213 Vigo, Spain
| | - Alberto Fernández-Villar
- Pulmonary Department, Hospital Álvaro Cunqueiro, EOXI Vigo, 36213 Vigo, Spain; (V.L.-F.); (M.I.B.-R.); (A.F.-V.)
- PneumoVigo I +i Research Group, Sanitary Research Institute Galicia Sur (IIS Galicia Sur), 36213 Vigo, Spain
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14
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Zhang X, Xiang Y, He D, Liang B, Wang C, Luo J, Zheng F. Identification of Potential Biomarkers for CAD Using Integrated Expression and Methylation Data. Front Genet 2020; 11:778. [PMID: 33033488 PMCID: PMC7509170 DOI: 10.3389/fgene.2020.00778] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 06/30/2020] [Indexed: 11/25/2022] Open
Abstract
DNA methylation plays an essential role in the pathogenesis of coronary artery disease (CAD) through regulating mRNA expressions. This study aimed to identify hub genes regulated by DNA methylation as biomarkers of CAD. Gene expression and methylation datasets of peripheral blood leukocytes (PBLs) of CAD were downloaded from the Gene Expression Omnibus (GEO) database. Subsequently, multiple computational approaches were performed to analyze the regulatory networks and to recognize hub genes. Finally, top hub genes were verified in a case-control study, based on their differential expressions and methylation levels between CAD cases and controls. In total, 535 differentially expressed-methylated genes (DEMGs) were identified and partitioned into 4 subgroups. TSS200 and 5′UTR were confirmed as high enrichment areas of differentially methylated CpGs sites (DMCs). The function of DEMGs is enriched in processes of histone H3-K27 methylation, regulation of post-transcription and DNA-directed RNA polymerase activity. Pathway enrichment showed DEMGs participated in the VEGF signaling pathway, adipocytokine signaling pathway, and PI3K-Akt signaling pathway. Besides, expressions of hub genes fibronectin 1 (FN1), phosphatase (PTEN), and tensin homolog and RNA polymerase III subunit A (POLR3A) were discordantly expressed between CAD patients and controls and related with DNA methylation levels. In conclusion, our study identified the potential biomarkers of PBLs for CAD, in which FN1, PTEN, and POLR3A were confirmed.
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Affiliation(s)
- Xiaokang Zhang
- Department of Clinical Laboratory Medicine and Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yang Xiang
- Department of Clinical Laboratory Medicine and Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Dingdong He
- Department of Clinical Laboratory Medicine and Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Bin Liang
- Department of Clinical Laboratory Medicine and Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Chen Wang
- Department of Clinical Laboratory Medicine and Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jing Luo
- Department of Clinical Laboratory Medicine and Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Fang Zheng
- Department of Clinical Laboratory Medicine and Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, China
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15
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Nell RJ, van Steenderen D, Menger NV, Weitering TJ, Versluis M, van der Velden PA. Quantification of DNA methylation independent of sodium bisulfite conversion using methylation-sensitive restriction enzymes and digital PCR. Hum Mutat 2020; 41:2205-2216. [PMID: 32906203 PMCID: PMC7756443 DOI: 10.1002/humu.24111] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/22/2020] [Accepted: 09/06/2020] [Indexed: 12/20/2022]
Abstract
Epigenetic regulation is important in human health and disease, but the exact mechanisms remain largely enigmatic. DNA methylation represents one epigenetic aspect but is challenging to quantify. In this study, we introduce a digital approach for the quantification of the amount and density of DNA methylation. We designed an experimental setup combining efficient methylation‐sensitive restriction enzymes with digital polymerase chain reaction (PCR) to quantify a targeted density of DNA methylation independent of bisulfite conversion. By using a stable reference and comparing experiments treated and untreated with these enzymes, copy number instability could be properly normalized. In silico simulations demonstrated the mathematical validity of the setup and showed that the measurement precision depends on the amount of input DNA and the fraction methylated alleles. This uncertainty could be successfully estimated by the confidence intervals. Quantification of RASSF1 promoter methylation in a variety of healthy and malignant samples and in a calibration curve confirmed the high accuracy of our approach, even in minute amounts of DNA. Overall, our results indicate the possibility of quantifying DNA methylation with digital PCR, independent of bisulfite conversion. Moreover, as the context‐density of methylation can also be determined, biological mechanisms can now be quantitatively assessed.
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Affiliation(s)
- Rogier J Nell
- Department of Ophthalmology, Leiden University Medical Center, Leiden, South Holland, The Netherlands
| | - Debby van Steenderen
- Department of Ophthalmology, Leiden University Medical Center, Leiden, South Holland, The Netherlands
| | - Nino V Menger
- Department of Ophthalmology, Leiden University Medical Center, Leiden, South Holland, The Netherlands
| | - Thomas J Weitering
- Department of Ophthalmology, Leiden University Medical Center, Leiden, South Holland, The Netherlands
| | - Mieke Versluis
- Department of Ophthalmology, Leiden University Medical Center, Leiden, South Holland, The Netherlands
| | - Pieter A van der Velden
- Department of Ophthalmology, Leiden University Medical Center, Leiden, South Holland, The Netherlands
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16
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Lin M, Qin Y, Zhou X, Chen N, Liu N, Xiao X. Thermodynamics-Guided Strand-Displacement-Based DNA Probe for Determination of the Average Methylation Levels of Multiple CpG Sites. Anal Chem 2019; 92:792-798. [PMID: 31763817 DOI: 10.1021/acs.analchem.9b03198] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Meng Lin
- Institute of Reproductive Health and Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P.R. China
| | - Yang Qin
- Institute of Reproductive Health and Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P.R. China
| | - Xing Zhou
- Institute of Reproductive Health and Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P.R. China
| | - Na Chen
- Institute of Reproductive Health and Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P.R. China
| | - Na Liu
- Institute of Reproductive Health and Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P.R. China
| | - Xianjin Xiao
- Institute of Reproductive Health and Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, P.R. China
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Chen Y, Zheng T, Li J, Cui J, Deng Z, You D, Yang L. Novel Iodine-induced Cleavage Real-time PCR Assay for Accurate Quantification of Phosphorothioate Modified Sites in Bacterial DNA. Sci Rep 2019; 9:7485. [PMID: 31097783 PMCID: PMC6522622 DOI: 10.1038/s41598-019-44011-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 04/17/2019] [Indexed: 12/16/2022] Open
Abstract
DNA Phosphorothioate (PT), replacing a non-bridging phosphate oxygen atom with a sulfur atom, is one kind of common DNA modification in bacteria. Whole genome scale description of the location and frequency of PT modification is the key to understand its biological function. Herein we developed a novel method, named with iodine-induced cleavage quantitative real-time PCR (IC-qPCR), to evaluate the frequency of PT modification at a given site in bacterial DNA. The efficiency, dynamic range, sensitivity, reproducibility and accuracy of IC-qPCR were well tested and verified employing an E. coli B7A strain as example. The amplification efficiency of IC-qPCR assay ranged from 91% to 99% with a high correlation coefficient ≥0.99. The limit of quantification was determined as low as 10 copies per reaction for the 607710 and 1818096 sites, and 5 copies for the 302695 and 4120753 sites. Based on the developed IC-qPCR method, the modification frequency of four PTs in E. coli B7A was determined with high accuracy, and the results showed that the PT modification was partial and that the modification frequency varied among investigated PT sites. All these results showed that IC-qPCR was suitable for evaluating the PT modification, which would be helpful to further understand the biological function of PT modification.
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Affiliation(s)
- Yi Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Tao Zheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jinli Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jinjie Cui
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Delin You
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Litao Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China.
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China.
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18
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Cui X, Cao L, Huang Y, Bai D, Huang S, Lin M, Yang Q, Lu TJ, Xu F, Li F. In vitro diagnosis of DNA methylation biomarkers with digital PCR in breast tumors. Analyst 2019; 143:3011-3020. [PMID: 29693662 DOI: 10.1039/c8an00205c] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Liquid biopsy of cancers using DNA methylation biomarkers has received significant interest, where the quantification of multiple biomarkers is generally needed for improving the sensitivity and specificity of cancer diagnosis. However, the inefficiency of the traditional quantitative polymerase chain reaction (qPCR)-based MethyLight assay for detecting the extremely low concentration of methylated DNA fragments in body fluids limits its clinical applications. Here, we developed an ultrasensitive microwell chip digital polymerase chain reaction (dPCR)-based MethyLight assay. Using the synthesized samples, the developed MethyLight assay can achieve 103-104-fold lower limit of detection and 1-16-fold lower limit of quantification than the traditional MethyLight assay. Four hypermethylated alleles (RARβ2, BRCA1, GSTP1 and RASSF1A) related to breast cancer in twenty-three clinical samples were tested using the microwell chip dPCR-based MethyLight assay. The results showed that the dPCR assay achieves ∼2 times enhancement in the cancer detection rate over the traditional quantitative PCR. Furthermore, the dPCR can detect the healthy and benign samples, which are undetectable using the traditional MethyLight assay. In multiple gene analysis, we achieved the highest detection rate of 93.3% (in the "OR" format of RARβ2 and GSTP1). Lastly, the estimated cut-off values in the dPCR assay were: <1, ∼1 to 100 and >100 (copies per μL) referring to the healthy, benign and malignant breast cancers, respectively. Therefore, the developed microwell chip dPCR-based MethyLight assay could provide a powerful tool for cancer biopsy diagnosis and disease monitoring.
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Affiliation(s)
- Xingye Cui
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China.
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Wang HQ, Yang CY, Wang SY, Wang T, Han JL, Wei K, Liu FC, Xu JD, Peng XZ, Wang JM. Cell-free plasma hypermethylated CASZ1, CDH13 and ING2 are promising biomarkers of esophageal cancer. J Biomed Res 2018; 32:424-433. [PMID: 30355852 PMCID: PMC6283827 DOI: 10.7555/jbr.32.20170065] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Identifying sensitive and specific biomarkers for early detection of cancer is immensely imperative for early diagnosis and treatment and better clinical outcome of cancer patients. This study aimed to construct a specific DNA methylation pattern of cancer suppressor genes and explore the feasibility of applying cell-free DNA based methylation as a biomarker for early diagnosis of esophageal squamous cell carcinoma (ESCC). We recruited early stage ESCC patients from Yangzhong County, China. The Illumina Infinium 450K Methylation BeadChip was used to construct a genome-wide DNA methylation profile. Then, differentiated genes were selected for the validation study using the Sequenom MassARRAY platform. The frequency of methylation was compared between cancer tissues, matched cell-free DNAs and normal controls. The specific methylation profiles were constructed, and the sensitivity and specificity were calculated. Seven CG sites in three genes CASZ1, CDH13 and ING2 were significantly hypermethylated in ESCC as compared with normal controls. A significant correlation was found between the methylation of DNA extracted from cancer tissues and matched plasma cell-free DNA, either for individual CG site or for cumulative methylation analysis. The sensitivity and specificity reached 100% at an appropriate cut-point using these specific methylation biomarkers. This study revealed that aberrant DNA methylation is a promising biomarker for molecular diagnosis of esophageal cancer. Hypermethylation of CASZ1, CDH13 and ING2 detected in plasma cell-free DNA can be applied as a potential noninvasive biomarker for diagnosis of esophageal cancer.
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Affiliation(s)
- Huan-Qiang Wang
- Department of Public Health and Preventive Medicine, Kangda College of Nanjing Medical University, Lianyungang, Jiangsu 222000, China
| | - Cong-Ying Yang
- Department of Social Medicine and Health Education,School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Si-Yuan Wang
- Department of Clinical Medicine, Kangda College of Nanjing Medical University, Lianyungang, Jiangsu 222000, China
| | - Tian Wang
- Department of Public Health and Preventive Medicine, Kangda College of Nanjing Medical University, Lianyungang, Jiangsu 222000, China
| | - Jing-Ling Han
- Department of Public Health and Preventive Medicine, Kangda College of Nanjing Medical University, Lianyungang, Jiangsu 222000, China
| | - Kai Wei
- Department of Public Health and Preventive Medicine, Kangda College of Nanjing Medical University, Lianyungang, Jiangsu 222000, China
| | - Fu-Cun Liu
- Department of Public Health and Preventive Medicine, Kangda College of Nanjing Medical University, Lianyungang, Jiangsu 222000, China
| | - Ji-da Xu
- Department of Public Health and Preventive Medicine, Kangda College of Nanjing Medical University, Lianyungang, Jiangsu 222000, China
| | - Xian-Zhen Peng
- Department of Public Health and Preventive Medicine, Kangda College of Nanjing Medical University, Lianyungang, Jiangsu 222000, China.,Department of Epidemiology,, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Jian-Ming Wang
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China
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20
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Feinsilber D, Ruiz M, Buga S, Hatch LA, Hatch AD, Mears KA. Integration of Next-generation Sequencing and Immune Checkpoint Inhibitors in Targeted Symptom Control and Palliative Care in Solid Tumor Malignancies: A Multidisciplinary Clinician Perspective. Cureus 2018; 10:e2909. [PMID: 30186714 PMCID: PMC6122684 DOI: 10.7759/cureus.2909] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The molecular characterization of solid tumor malignancies with respect to tumorgenesis, risk stratification, and prognostication of chemotherapeutic side effects is multi-faceted. Characterizing these mechanisms requires a detailed understanding of cytogenetics and pharmacology. In addition to the standard palliative care interventions that address issues such as fatigue, neuropathy, performance status, depression, nutrition, cachexia, anxiety, and medical ethics, we must also delve into individual chemotherapy side effects. Comprehending these symptoms is more complex with the advent of broader targeted therapies. With the advent and initiation of Foundation Medicine (FMI) testing, we have been able to tailor regimens to the individual genetics of the patient. Next-generation sequencing (NGS) is a bioinformatic analysis used in order to create a targeted effort to understand the complex genetics of a vast array of malignancies. Through the process known as high-throughput sequencing we, as clinicians, can obtain more real-time genetic data and incorporate the information into our reasoning process. The process involves a broad manner in which deoxyribonucleic acid (DNA) sequence data is obtained including genome sequencing and resequencing, protein-DNA or proteinomics, chromatin immunoprecipitation (ChIP)-sequencing, ribonucleic acid (RNA) sequencing, and epigenomic analysis. High-throughput sequencing techniques including single molecule real-time sequencing, ion semiconductor sequencing, pyrose sequencing, sequencing by synthesis, sequencing by ligation, nanopore sequencing, and chain termination (otherwise known as Sanger sequencing) have expanded the realm of NGS and clinicians options.
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Affiliation(s)
- Doron Feinsilber
- Hematology/Oncology, Medical College of Wisconsin/Froedert Cancer Center, Milwaukee, USA
| | - Marco Ruiz
- Memorial Cancer Institute, Memorial Healthcare System, Hollywood, USA
| | - Sorin Buga
- Supportive Care Medicine, City of Hope Medical Center, Duarte, USA
| | - Leigh A Hatch
- Morsani College of Medicine, University of South Florida, Tampa, USA
| | - Andrew D Hatch
- National Ophthalmic Research Institute, Retina Consultants of Southwest Florida, Tampa, USA
| | - Katrina A Mears
- Ophthalmology, Retina Consultants of Southwest Florida/National Ophthalmic Research Institute, Fort Myers, USA
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21
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Schröder C, Steimer W. gDNA extraction yield and methylation status of blood samples are affected by long-term storage conditions. PLoS One 2018; 13:e0192414. [PMID: 29415017 PMCID: PMC5802893 DOI: 10.1371/journal.pone.0192414] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 01/22/2018] [Indexed: 12/13/2022] Open
Abstract
Epigenetics is believed to provide great chances for a better understanding of the development and treatment of many diseases where the analysis of genomic DNA has so far failed to provide conclusive answers. Methylcytosine is a frequently used quantitative marker of epigenetic studies. Since immediate analysis of sampled material is in most cases not possible, storage time and conditions are critical aspects regarding the quality of genomic DNA and reliability of analysis. Blood is frequently used for such analyses. We, therefore, collected blood samples of ten volunteers and stored them under various conditions for ten months: -70°C, -20°C, 2-8°C and room temperature. An additional aliquot was frozen at -70°C and thawed once a week at room temperature. We then compared the DNA extraction yields and methylation status in relation to storage time and conditions. We found significantly lower DNA extraction yields (up to -97.45%; p ≤ 0.001) as well as significantly higher methylation levels after ten months of storage (up to +42.0%; p ≤ 0.001). These results suggest that storage time has an important influence on DNA analyses of blood samples for all storage conditions. This might be due to differences in stability of methylated and non-methylated DNA. Our study indicates that storage conditions and time may be a critical factor for epigenetic methylation studies and require rigorous validation. For reliable analyses we, therefore, recommend to perform epigenetic analysis directly after sample collection.
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Affiliation(s)
- Charlotte Schröder
- Institut für Klinische Chemie und Pathobiochemie, Klinikum rechts der Isar, Technische Universität München, München, Germany
| | - Werner Steimer
- Institut für Klinische Chemie und Pathobiochemie, Klinikum rechts der Isar, Technische Universität München, München, Germany
- * E-mail:
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22
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Nectoux J. Current, Emerging, and Future Applications of Digital PCR in Non-Invasive Prenatal Diagnosis. Mol Diagn Ther 2017; 22:139-148. [DOI: 10.1007/s40291-017-0312-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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23
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Zhang P, Wang H, Wang J, Liu Q, Wang Y, Feng F, Shi L. Association between protocadherin 8 promoter hypermethylation and the pathological status of prostate cancer. Oncol Lett 2017; 14:1657-1664. [PMID: 28789392 DOI: 10.3892/ol.2017.6282] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 10/26/2016] [Indexed: 11/06/2022] Open
Abstract
Promoter hypermethylation of tumor suppressor genes has been confirmed to serve a pivotal role in tumorigenesis. Protocadherin 8 (PCDH8), a novel tumor suppressor gene, has been reported to be inactivated by promoter hypermethylation a number of cancer types, including bladder cancer and renal cell carcinoma. The aim of the present study was to investigate the occurrence of PCDH8 hypermethylation in prostate cancer and its potential as a novel biomarker of prostate cancer. The transcriptional levels of PCDH8 were examined by quantitative polymerase chain reaction (PCR) in 82 prostate cancer tissues as well as 30 prostate hyperplasia tissues, and verified the protein level by western blot analysis of representative samples. PCDH8 expression levels were found to be reduced to 0.30±0.10 in 70.7% (58/82) of prostate cancer tissues. To identify the possible reason for mRNA downregulation, the methylation status of the PCDH8 promoter was assessed in prostate cancer tissues and prostate hyperplasia tissues by methylation-specific PCR (MSP). A total of 47 prostate cancer patients who exhibited reduced PCDH8 expression (57.3%; 47/82) also showed promoter hypermethylation (47/58). None of the samples (0/30) in the benign prostate hyperplasia group were positive on MSP. Furthermore, the associations between the methylation status of the PCDH8 promoter and various clinicopathological features of prostate cancer were analyzed, revealing that the methylation status of PCDH8 was closely associated with tumor size, tumor shape (papillary/non-papillary), tumor stage and tumor grade (all P<0.05), while there were no correlations with the age of the patients or the number of tumors (P>0.05). Additionally, patients with hypermethylation of the PCDH8 gene promoter had a relapse rate of 36.17% and a mortality rate of 29.79%, which were significantly higher than the hypermethylation-negative patients (P<0.05), indicating a poorer prognosis. Therefore, the methylation status of the PCDH8 gene in prostate cancer may be an important marker for use in the early diagnosis and prediction of prognosis in prostate cancer.
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Affiliation(s)
- Peng Zhang
- Department of Urology, Yantai Yuhuangding Hospital, Yantai, Shandong 264000, P.R. China
| | - Hui Wang
- Department of Urology, Yantai Yuhuangding Hospital, Yantai, Shandong 264000, P.R. China
| | - Jianming Wang
- Department of Urology, Yantai Yuhuangding Hospital, Yantai, Shandong 264000, P.R. China
| | - Qingzuo Liu
- Department of Urology, Yantai Yuhuangding Hospital, Yantai, Shandong 264000, P.R. China
| | - Yongqiang Wang
- Department of Urology, Yantai Yuhuangding Hospital, Yantai, Shandong 264000, P.R. China
| | - Fan Feng
- Department of Urology, Yantai Yuhuangding Hospital, Yantai, Shandong 264000, P.R. China
| | - Lei Shi
- Department of Urology, Yantai Yuhuangding Hospital, Yantai, Shandong 264000, P.R. China
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24
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Ye X, Zhang L, Chen B, Li J, Yang Q, Huang Q, Zhang J, Gao Y, Li Z, Cai C. A quantitative method for detecting DNA methylation over targeted genomic regions using isotope dilution liquid chromatography tandem mass spectrometry. Talanta 2017; 169:136-140. [PMID: 28411803 DOI: 10.1016/j.talanta.2017.03.082] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/20/2017] [Accepted: 03/26/2017] [Indexed: 12/16/2022]
Abstract
Aberrant DNA methylation is associated with various diseases. Quantitative analysis of regional DNA methylation levels of some specific genes would aid in diseases diagnosis and risk stratification. In this study, we developed a robust method for detecting DNA methylation level over targeted genomic regions using nucleobases quantification in bisulfite amplicons by isotope dilution liquid chromatography tandem mass spectrometry coupled with a simple equation. This method had wide detection range (from 0% to 100% methylation) and high accuracy while more time-saving compared to clonal bisulfite sequencing method. The application for clinical tissue samples showed good applicability and cost effectiveness. This analytical method is suitable for quantifying average DNA methylation level over targeted genomic regions and expected to be a useful tool for detecting DNA methylation biomarkers.
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Affiliation(s)
- Xiaoxia Ye
- Laboratory for Genetics, Nutrition and Health, Guangdong Medical University, Zhanjiang, Guangdong 524023, PR China
| | - Lijian Zhang
- Laboratory for Genetics, Nutrition and Health, Guangdong Medical University, Zhanjiang, Guangdong 524023, PR China; Guangdong Key Laboratory for Research and Development of Nature Drugs, Guangdong Medical University, Zhanjiang, Guangdong 524023, PR China
| | - Bin Chen
- Laboratory for Genetics, Nutrition and Health, Guangdong Medical University, Zhanjiang, Guangdong 524023, PR China; Guangdong Key Laboratory for Research and Development of Nature Drugs, Guangdong Medical University, Zhanjiang, Guangdong 524023, PR China
| | - Jian Li
- Laboratory for Genetics, Nutrition and Health, Guangdong Medical University, Zhanjiang, Guangdong 524023, PR China; Guangdong Key Laboratory for Research and Development of Nature Drugs, Guangdong Medical University, Zhanjiang, Guangdong 524023, PR China
| | - Qingjin Yang
- Laboratory for Genetics, Nutrition and Health, Guangdong Medical University, Zhanjiang, Guangdong 524023, PR China; Guangdong Key Laboratory for Research and Development of Nature Drugs, Guangdong Medical University, Zhanjiang, Guangdong 524023, PR China
| | - Qionglin Huang
- Laboratory for Genetics, Nutrition and Health, Guangdong Medical University, Zhanjiang, Guangdong 524023, PR China; Guangdong Key Laboratory for Research and Development of Nature Drugs, Guangdong Medical University, Zhanjiang, Guangdong 524023, PR China
| | - Junjie Zhang
- Laboratory for Genetics, Nutrition and Health, Guangdong Medical University, Zhanjiang, Guangdong 524023, PR China; Guangdong Key Laboratory for Research and Development of Nature Drugs, Guangdong Medical University, Zhanjiang, Guangdong 524023, PR China
| | - Yihua Gao
- Laboratory for Genetics, Nutrition and Health, Guangdong Medical University, Zhanjiang, Guangdong 524023, PR China; Guangdong Key Laboratory for Research and Development of Nature Drugs, Guangdong Medical University, Zhanjiang, Guangdong 524023, PR China
| | - Zhaojin Li
- Laboratory for Genetics, Nutrition and Health, Guangdong Medical University, Zhanjiang, Guangdong 524023, PR China; Guangdong Key Laboratory for Research and Development of Nature Drugs, Guangdong Medical University, Zhanjiang, Guangdong 524023, PR China
| | - Chun Cai
- Laboratory for Genetics, Nutrition and Health, Guangdong Medical University, Zhanjiang, Guangdong 524023, PR China; Guangdong Key Laboratory for Research and Development of Nature Drugs, Guangdong Medical University, Zhanjiang, Guangdong 524023, PR China.
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25
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Pharo HD, Honne H, Vedeld HM, Dahl C, Andresen K, Liestøl K, Jeanmougin M, Guldberg P, Lind GE. Experimental factors affecting the robustness of DNA methylation analysis. Sci Rep 2016; 6:33936. [PMID: 27671843 PMCID: PMC5037394 DOI: 10.1038/srep33936] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 08/31/2016] [Indexed: 01/03/2023] Open
Abstract
Diverging methylation frequencies are often reported for the same locus in the same disease, underscoring the need for limiting technical variability in DNA methylation analyses. We have investigated seven likely sources of variability at different steps of bisulfite PCR-based DNA methylation analyses using a fully automated quantitative methylation-specific PCR setup of six gene promoters across 20 colon cancer cell lines. Based on >15,000 individual PCRs, all tested parameters affected the normalized percent of methylated reference (PMR) differences, with a fourfold varying magnitude. Additionally, large variations were observed across the six genes analyzed. The highest variation was seen using single-copy genes as reference for normalization, followed by different amounts of template in the PCR, different amounts of DNA in the bisulfite reaction, and storage of bisulfite converted samples. Finally, when a highly standardized pipeline was repeated, the difference in PMR value for the same assay in the same cell line was on average limited to five (on a 0–100 scale). In conclusion, a standardized pipeline is essential for consistent methylation results, where parameters are kept constant for all samples. Nevertheless, a certain level of variation in methylation values must be expected, underscoring the need for careful interpretation of data.
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Affiliation(s)
- Heidi D Pharo
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, the Norwegian Radium Hospital, Oslo, Norway.,KG Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Biosciences, The Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Hilde Honne
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, the Norwegian Radium Hospital, Oslo, Norway.,KG Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Hege M Vedeld
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, the Norwegian Radium Hospital, Oslo, Norway.,KG Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Christina Dahl
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Kim Andresen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, the Norwegian Radium Hospital, Oslo, Norway.,KG Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Knut Liestøl
- Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Informatics, University of Oslo, Oslo, Norway
| | - Marine Jeanmougin
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, the Norwegian Radium Hospital, Oslo, Norway.,KG Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Per Guldberg
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Guro E Lind
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, the Norwegian Radium Hospital, Oslo, Norway.,KG Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, Oslo, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Department of Biosciences, The Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
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26
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Li Z, Guo X, Tang L, Peng L, Chen M, Luo X, Wang S, Xiao Z, Deng Z, Dai L, Xia K, Wang J. Methylation analysis of plasma cell-free DNA for breast cancer early detection using bisulfite next-generation sequencing. Tumour Biol 2016; 37:13111-13119. [PMID: 27449045 DOI: 10.1007/s13277-016-5190-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 07/13/2016] [Indexed: 12/15/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) has been considered as a potential biomarker for non-invasive cancer detection. To evaluate the methylation levels of six candidate genes (EGFR, GREM1, PDGFRB, PPM1E, SOX17, and WRN) in plasma cfDNA as biomarkers for breast cancer early detection, quantitative analysis of the promoter methylation of these genes from 86 breast cancer patients and 67 healthy controls was performed by using microfluidic-PCR-based target enrichment and next-generation bisulfite sequencing technology. The predictive performance of different logistic models based on methylation status of candidate genes was investigated by means of the area under the ROC curve (AUC) and odds ratio (OR) analysis. Results revealed that EGFR, PPM1E, and 8 gene-specific CpG sites showed significantly hypermethylation in cancer patients' plasma and significantly associated with breast cancer (OR ranging from 2.51 to 9.88). The AUC values for these biomarkers were ranging from 0.66 to 0.75. Combinations of multiple hypermethylated genes or CpG sites substantially improved the predictive performance for breast cancer detection. Our study demonstrated the feasibility of quantitative measurement of candidate gene methylation in cfDNA by using microfluidic-PCR-based target enrichment and bisulfite next-generation sequencing, which is worthy of further validation and potentially benefits a broad range of applications in clinical oncology practice. Quantitative analysis of methylation pattern of plasma cfDNA by next-generation sequencing might be a valuable non-invasive tool for early detection of breast cancer.
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Affiliation(s)
- Zibo Li
- The State Key Laboratory of Medical Genetics and School of Life Sciences, Central South University, 172 Tongzipo Road, Changsha, Hunan, 410013, China
| | - Xinwu Guo
- Sanway Gene Technology Inc., Changsha, Hunan, 410205, China
| | - Lili Tang
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Limin Peng
- Sanway Gene Technology Inc., Changsha, Hunan, 410205, China
| | - Ming Chen
- Sanway Gene Technology Inc., Changsha, Hunan, 410205, China
| | - Xipeng Luo
- Sanway Gene Technology Inc., Changsha, Hunan, 410205, China
| | - Shouman Wang
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Zhi Xiao
- Department of Breast Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Zhongping Deng
- Sanway Gene Technology Inc., Changsha, Hunan, 410205, China
- Research Center for Technologies in Nucleic Acid-Based Diagnostics, Changsha, Hunan, 410205, China
- Research Center for Technologies in Nucleic Acid-Based Diagnostics and Therapeutics, Changsha, Hunan, 410205, China
| | - Lizhong Dai
- Sanway Gene Technology Inc., Changsha, Hunan, 410205, China
- Research Center for Technologies in Nucleic Acid-Based Diagnostics, Changsha, Hunan, 410205, China
- Research Center for Technologies in Nucleic Acid-Based Diagnostics and Therapeutics, Changsha, Hunan, 410205, China
| | - Kun Xia
- The State Key Laboratory of Medical Genetics and School of Life Sciences, Central South University, 172 Tongzipo Road, Changsha, Hunan, 410013, China
| | - Jun Wang
- The State Key Laboratory of Medical Genetics and School of Life Sciences, Central South University, 172 Tongzipo Road, Changsha, Hunan, 410013, China.
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27
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Xu SY, Klein P, Degtyarev SK, Roberts RJ. Expression and purification of the modification-dependent restriction enzyme BisI and its homologous enzymes. Sci Rep 2016; 6:28579. [PMID: 27353146 PMCID: PMC4926085 DOI: 10.1038/srep28579] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/06/2016] [Indexed: 12/15/2022] Open
Abstract
The methylation-dependent restriction endonuclease (REase) BisI (G(m5)C ↓ NGC) is found in Bacillus subtilis T30. We expressed and purified the BisI endonuclease and 34 BisI homologs identified in bacterial genomes. 23 of these BisI homologs are active based on digestion of (m5)C-modified substrates. Two major specificities were found among these BisI family enzymes: Group I enzymes cut GCNGC containing two to four (m5)C in the two strands, or hemi-methylated sites containing two (m5)C in one strand; Group II enzymes only cut GCNGC sites containing three to four (m5)C, while one enzyme requires all four cytosines to be modified for cleavage. Another homolog, Esp638I cleaves GCS ↓ SGC (relaxed specificity RCN ↓ NGY, containing at least four (m5)C). Two BisI homologs show degenerate specificity cleaving unmodified DNA. Many homologs are small proteins ranging from 150 to 190 amino acid (aa) residues, but some homologs associated with mobile genetic elements are larger and contain an extra C-terminal domain. More than 156 BisI homologs are found in >60 bacterial genera, indicating that these enzymes are widespread in bacteria. They may play an important biological function in restricting pre-modified phage DNA.
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Affiliation(s)
- Shuang-yong Xu
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Pernelle Klein
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
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28
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Luchi N, Capretti P, Pazzagli M, Pinzani P. Powerful qPCR assays for the early detection of latent invaders: interdisciplinary approaches in clinical cancer research and plant pathology. Appl Microbiol Biotechnol 2016; 100:5189-204. [PMID: 27112348 DOI: 10.1007/s00253-016-7541-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/07/2016] [Accepted: 04/10/2016] [Indexed: 12/29/2022]
Abstract
Latent invaders represent the first step of disease before symptoms occur in the host. Based on recent findings, tumors are considered to be ecosystems in which cancer cells act as invasive species that interact with the native host cell species. Analogously, in plants latent fungal pathogens coevolve within symptomless host tissues. For these reasons, similar detection approaches can be used for an early diagnosis of the invasion process in both plants and humans to prevent or reduce the spread of the disease. Molecular tools based on the evaluation of nucleic acids have been developed for the specific, rapid, and early detection of human diseases. During the last decades, these techniques to assess and quantify the proliferation of latent invaders in host cells have been transferred from the medical field to different areas of scientific research, such as plant pathology. An improvement in molecular biology protocols (especially referring to qPCR assays) specifically designed and optimized for detection in host plants is therefore advisable. This work is a cross-disciplinary review discussing the use of a methodological approach that is employed within both medical and plant sciences. It provides an overview of the principal qPCR tools for the detection of latent invaders, focusing on comparisons between clinical cancer research and plant pathology, and recent advances in the early detection of latent invaders to improve prevention and control strategies.
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Affiliation(s)
- Nicola Luchi
- National Research Council (IPSP-CNR), Institute for Sustainable Plant Protection, Via Madonna del Piano 10, 50019, Sesto Fiorentino Firenze, Italy
| | - Paolo Capretti
- National Research Council (IPSP-CNR), Institute for Sustainable Plant Protection, Via Madonna del Piano 10, 50019, Sesto Fiorentino Firenze, Italy
- Department of Agri-Food Productions and Environmental Sciences (DiSPAA), University of Florence, Piazzale delle Cascine 28, Florence, Italy
| | - Mario Pazzagli
- Department of Clinical, Experimental and Biomedical Sciences, University of Florence, Viale Pieraccini, 6, 50139, Firenze, Italy
| | - Pamela Pinzani
- Department of Clinical, Experimental and Biomedical Sciences, University of Florence, Viale Pieraccini, 6, 50139, Firenze, Italy.
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29
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Soto J, Rodriguez-Antolin C, Vallespín E, de Castro Carpeño J, Ibanez de Caceres I. The impact of next-generation sequencing on the DNA methylation-based translational cancer research. Transl Res 2016; 169:1-18.e1. [PMID: 26687736 DOI: 10.1016/j.trsl.2015.11.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/29/2015] [Accepted: 11/14/2015] [Indexed: 01/08/2023]
Abstract
Epigenetics is currently in an exponential phase of growth, constituting one of the most promising fields in science, particularly in cancer research. Impaired epigenetic processes can lead to abnormal gene activity or inactivity, causing cellular disorders that are closely associated with tumor initiation and progression. Thus, there is a pivotal role of massive sequencing techniques for epigenetics, which aim to find novel biomarkers, factors of prognosis and prediction, and targets for achieving personalized treatments. We present a brief description of the evolution of next-generation sequencing technologies and its coupling with DNA methylation analysis techniques, highlighting its future in translational medicine and presenting significant findings in several malignancies. We also expose critical topics related to the implementation of these approaches, which is expected to be affordable for most research centers in the near future.
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Affiliation(s)
- Javier Soto
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Madrid, Spain; Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
| | - Carlos Rodriguez-Antolin
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Madrid, Spain; Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
| | - Elena Vallespín
- Structural and Functional Genomics, INGEMM-IdiPAZ-CIBERER, La Paz University Hospital, Madrid, Spain
| | | | - Inmaculada Ibanez de Caceres
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Madrid, Spain; Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain.
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Robust Detection of DNA Hypermethylation of ZNF154 as a Pan-Cancer Locus with in Silico Modeling for Blood-Based Diagnostic Development. J Mol Diagn 2016; 18:283-98. [PMID: 26857064 DOI: 10.1016/j.jmoldx.2015.11.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 10/19/2015] [Accepted: 11/19/2015] [Indexed: 12/30/2022] Open
Abstract
Sites that display recurrent, aberrant DNA methylation in cancer represent potential biomarkers for screening and diagnostics. Previously, we identified hypermethylation at the ZNF154 CpG island in 15 solid epithelial tumor types from 13 different organs. In this study, we measure the magnitude and pattern of differential methylation of this region across colon, lung, breast, stomach, and endometrial tumor samples using next-generation bisulfite amplicon sequencing. We found that all tumor types and subtypes are hypermethylated at this locus compared with normal tissue. To evaluate this site as a possible pan-cancer marker, we compare the ability of several sequence analysis methods to distinguish the five tumor types (184 tumor samples) from normal tissue samples (n = 34). The classification performance for the strongest method, measured by the area under (the receiver operating characteristic) curve (AUC), is 0.96, close to a perfect value of 1. Furthermore, in a computational simulation of circulating tumor DNA, we were able to detect limited amounts of tumor DNA diluted with normal DNA: 1% tumor DNA in 99% normal DNA yields AUCs of up to 0.79. Our findings suggest that hypermethylation of the ZNF154 CpG island is a relevant biomarker for identifying solid tumor DNA and may have utility as a generalizable biomarker for circulating tumor DNA.
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Establishment of the MethyLight Assay for Assessing Aging, Cigarette Smoking, and Alcohol Consumption. BIOMED RESEARCH INTERNATIONAL 2015; 2015:451981. [PMID: 26579533 PMCID: PMC4633697 DOI: 10.1155/2015/451981] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 08/13/2015] [Accepted: 10/05/2015] [Indexed: 12/22/2022]
Abstract
The environmental factors such as aging, smoking, and alcohol consumption have been reported to influence DNA methylation (DNAm). However, the versatility of DNAm measurement by DNAm array systems is low in clinical use. Thus, we developed the MethyLight assay as a simple method to measure DNAm. In the present study, we isolated peripheral blood DNA from 33 healthy volunteers and selected cg25809905, cg02228185, and cg17861230 as aging, cg23576855 as smoking, and cg02583484 as alcohol consumption biomarkers. The predicted age by methylation rates of cg25809905 and cg17861230 significantly correlated with chronological age. In immortalized B-cells, DNAm rates of two sites showed a younger status than the chronological age of donor. On the other hand, the predicted age of the patients with myocardial infarction (MI) was not accelerated. The methylation rate of cg23576855 was able to discriminate the groups based on the smoking status. The DNAm rate of cg02583484 was reduced in subjects with habitual alcohol consumption compared to that of subjects without habitual alcohol consumption. In conclusion, our MethyLight assay system reconfirms that aging, smoking, and alcohol consumption influenced DNAm in peripheral blood in the Japanese. This MethyLight system will facilitate DNAm measurement in epidemiological and clinical studies.
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Castegna A, Iacobazzi V, Infantino V. The mitochondrial side of epigenetics. Physiol Genomics 2015; 47:299-307. [PMID: 26038395 DOI: 10.1152/physiolgenomics.00096.2014] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 05/26/2015] [Indexed: 12/31/2022] Open
Abstract
The bidirectional cross talk between nuclear and mitochondrial DNA is essential for cellular homeostasis and proper functioning. Mitochondria depend on nuclear contribution for much of their functionality, but their activities have been recently recognized to control nuclear gene expression as well as cell function in many different ways. Epigenetic mechanisms, which tune gene expression in response to environmental stimuli, are key regulatory events at the interplay between mitochondrial and nuclear interactions. Emerging findings indicate that epigenetic factors can be targets or instruments of mitochondrial-nuclear cross talk. Additionally, the growing interest into mtDNA epigenetic modifications opens new avenues into the interaction mechanisms between mitochondria and nucleus. In this review we summarize the points of mitochondrial and nuclear reciprocal control involving epigenetic factors, focusing on the role of mitochondrial genome and metabolism in shaping epigenetic modulation of gene expression. The relevance of the new findings on the methylation of mtDNA is also highlighted as a new frontier in the complex scenario of mitochondrial-nuclear communication.
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Affiliation(s)
- Alessandra Castegna
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro," Bari, Italy; Center of Excellence in Comparative Genomics, University of Bari "Aldo Moro," Bari, Italy;
| | - Vito Iacobazzi
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro," Bari, Italy; Center of Excellence in Comparative Genomics, University of Bari "Aldo Moro," Bari, Italy; CNR Institute of Biomembranes and Bioenergetics, Bari, Italy; and
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Danese E, Minicozzi AM, Benati M, Montagnana M, Paviati E, Salvagno GL, Lima-Oliveira G, Gusella M, Pasini F, Lippi G, Guidi GC. Comparison of genetic and epigenetic alterations of primary tumors and matched plasma samples in patients with colorectal cancer. PLoS One 2015; 10:e0126417. [PMID: 25946211 PMCID: PMC4422441 DOI: 10.1371/journal.pone.0126417] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/01/2015] [Indexed: 02/06/2023] Open
Abstract
Background Although recent advances in circulating DNA analysis allow the prediction of tumor genomes by noninvasive means, some challenges remain, which limit the widespread introduction of cfDNA in cancer diagnostics. We analyzed the status of the two best characterized colorectal cancer (CRC) genetic and epigenetic alterations in a cohort of CRC patients, and then compared the degree to which the two patterns move from tissue to plasma in order to improve our understanding of biology modulating the concordance between tissues and plasma methylation and mutation profiles. Methods Plasma and tumor tissues were collected from 85 patients (69±14 years, 56 males). KRAS and SEPT9 status was assessed by allele refractory mutation system quantitative PCR and quantitative methylation-specific PCR, respectively. Six of the most common point mutations at codon 12 and 13 were investigated for KRAS analysis. Results KRAS mutations and SEPT9 promoter methylation were present in 34% (29/85) and in 82% (70/85) of primary tumor tissue samples. Both genetic and epigenetic analyses of cfDNA revealed a high overall concordance and specificity compared with tumor-tissue analyses. Patients presenting with both genetic and epigenetic alterations in tissue specimens (31.8%, 27/85) were considered for further analyses. The median methylation rates in tumour tissues and plasma samples were 64.5% (12.2–99.8%) and 14.5% (0–45.5%), respectively. The median KRAS mutation load (for matched mutations) was 33.6% (1.8–86.3%) in tissues and 2.9% (0–17.3) in plasma samples. The plasma/tissue (p/t) ratio of SEPT9 methylation rate was significantly higher than the p/t ratio of KRAS mutation load, especially in early stage cancers (p=0.0108). Conclusion The results of this study show a discrepant rate of epigenetic vs. genetic alterations moving from tissue to plasma. Many factors could affect mutation cfDNA analysis, including both presence of tumor clonal heterogeneity and strict compartmentalization of KRAS mutation profile. The present study highlights the importance of considering the nature of the alteration when analyzing tumor-derived cfDNA.
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Affiliation(s)
- Elisa Danese
- Laboratory of Clinical Biochemistry, Department of Life and Reproduction Sciences, University Hospital of Verona, Verona, Italy
- * E-mail:
| | - Anna Maria Minicozzi
- National Centre for Bowel Research and Surgical Innovation (NCBRSI), Academic Surgical Unit, Barts and The London NHS Trust, Queen Mary University of London, London, United Kingdom
| | - Marco Benati
- Laboratory of Clinical Biochemistry, Department of Life and Reproduction Sciences, University Hospital of Verona, Verona, Italy
| | - Martina Montagnana
- Laboratory of Clinical Biochemistry, Department of Life and Reproduction Sciences, University Hospital of Verona, Verona, Italy
| | - Elisa Paviati
- Laboratory of Clinical Biochemistry, Department of Life and Reproduction Sciences, University Hospital of Verona, Verona, Italy
| | - Gian Luca Salvagno
- Laboratory of Clinical Biochemistry, Department of Life and Reproduction Sciences, University Hospital of Verona, Verona, Italy
| | - Gabriel Lima-Oliveira
- Laboratory of Clinical Biochemistry, Department of Life and Reproduction Sciences, University Hospital of Verona, Verona, Italy
| | - Milena Gusella
- Oncology Department, Laboratory of Pharmacology and Molecular Biology, Rovigo General Hospital, Trecenta, Rovigo, Italy
| | - Felice Pasini
- Department of Medical Oncology, Rovigo Hospital, Rovigo, Italy
| | - Giuseppe Lippi
- Laboratory of Clinical Chemistry and Hematology, Academic Hospital of Parma, Parma, Italy
| | - Gian Cesare Guidi
- Laboratory of Clinical Biochemistry, Department of Life and Reproduction Sciences, University Hospital of Verona, Verona, Italy
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