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Li B, Jiang C, Xu Y, Fan X, Yang L, Zou B, Fan B, Wang L. Genome-wide DNA methylation signature predict clinical benefit of bevacizumab in non-small cell lung cancer. BMC Cancer 2022; 22:828. [PMID: 35906610 PMCID: PMC9338664 DOI: 10.1186/s12885-022-09918-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 07/19/2022] [Indexed: 11/17/2022] Open
Abstract
Background The efficacy of bevacizumab in non-small cell lung cancer (NSCLC) patients is unsatisfactory, and the selection of suitable patients is still challenging. Given the epigenetic modifications can contribute to an aberrant regulation of angiogenesis and microenvironment, we investigated DNA methylation profiles to determine clinical benefit of bevacizumab in NSCLC patients. Methods Genome-wide DNA methylation profiling was performed in NSCLC patients treated with chemotherapy in combination with bevacizumab. Patients were divided into better prognosis group (A group) and inferior prognosis group (B group) based on their survival. The difference of methylation patterns and respective functional enrichment analysis were performed between two groups. Prognostic DNA methylation signature for bevacizumab was established with the least absolute shrinkage and selection operator regression analyses. TISIDB database was further used to infer immunological relationship for prognostic related DNA methylation. Results Twenty patients were included in this study, and significantly distinct methylation patterns were observed between patients with different prognosis. Related genes of different methylation regions were significantly enriched in the biological process of cell projection assembly, neutrophil mediated immunity, and pathway of VEGFA-VEGFR2 signaling pathway, neutrophil degranulation. A 10-gene DNA methylation signature for prognosis prediction was established with the C-index of 0.76. And host genes of signature were found to be related to the abundance of ActCD4, Th1, ActCD8, NKT and neutrophil cells. Conclusion The 10-gene DNA methylation signature could serve as a novel biomarker to predict the clinical benefit of bevacizumab therapy and improve this anti-tumor approach for NSCLC patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09918-1.
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Affiliation(s)
- Butuo Li
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, Shandong, China
| | - Chao Jiang
- Department of Otorhinolaryngology Head and Neck Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Yiyue Xu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, Shandong, China
| | - Xinyu Fan
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, Shandong, China
| | - Linlin Yang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, Shandong, China
| | - Bing Zou
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, Shandong, China
| | - Bingjie Fan
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, Shandong, China
| | - Linlin Wang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, 250117, Shandong, China.
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2
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Rossnerova A, Honkova K, Pelclova D, Zdimal V, Hubacek JA, Chvojkova I, Vrbova K, Rossner P, Topinka J, Vlckova S, Fenclova Z, Lischkova L, Klusackova P, Schwarz J, Ondracek J, Ondrackova L, Kostejn M, Klema J, Dvorackova S. DNA Methylation Profiles in a Group of Workers Occupationally Exposed to Nanoparticles. Int J Mol Sci 2020; 21:E2420. [PMID: 32244494 PMCID: PMC7177382 DOI: 10.3390/ijms21072420] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 03/27/2020] [Accepted: 03/30/2020] [Indexed: 02/07/2023] Open
Abstract
The risk of exposure to nanoparticles (NPs) has rapidly increased during the last decade due to the vast use of nanomaterials (NMs) in many areas of human life. Despite this fact, human biomonitoring studies focused on the effect of NP exposure on DNA alterations are still rare. Furthermore, there are virtually no epigenetic data available. In this study, we investigated global and gene-specific DNA methylation profiles in a group of 20 long-term (mean 14.5 years) exposed, nanocomposite, research workers and in 20 controls. Both groups were sampled twice/day (pre-shift and post-shift) in September 2018. We applied Infinium Methylation Assay, using the Infinium MethylationEPIC BeadChips with more than 850,000 CpG loci, for identification of the DNA methylation pattern in the studied groups. Aerosol exposure monitoring, including two nanosized fractions, was also performed as proof of acute NP exposure. The obtained array data showed significant differences in methylation between the exposed and control groups related to long-term exposure, specifically 341 CpG loci were hypomethylated and 364 hypermethylated. The most significant CpG differences were mainly detected in genes involved in lipid metabolism, the immune system, lung functions, signaling pathways, cancer development and xenobiotic detoxification. In contrast, short-term acute NP exposure was not accompanied by DNA methylation changes. In summary, long-term (years) exposure to NP is associated with DNA epigenetic alterations.
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Affiliation(s)
- Andrea Rossnerova
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague 4, Czech Republic; (K.H.); (I.C.); (J.T.)
| | - Katerina Honkova
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague 4, Czech Republic; (K.H.); (I.C.); (J.T.)
| | - Daniela Pelclova
- Department of Occupational Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Na Bojisti 1, 120 00 Prague 2, Czech Republic; (D.P.); (S.V.); (Z.F.); (L.L.); (P.K.)
| | - Vladimir Zdimal
- Laboratory of Aerosol Chemistry and Physics, Institute of Chemical Process Fundamentals CAS, Rozvojova 1, 165 02 Prague 6, Czech Republic; (V.Z.); (J.S.); (J.O.); (L.O.); (M.K.)
| | - Jaroslav A. Hubacek
- Center for Experimental Medicine, Institute for Clinical and Experimental Medicine, Videnska 1958/9, 140 21 Prague 4, Czech Republic;
| | - Irena Chvojkova
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague 4, Czech Republic; (K.H.); (I.C.); (J.T.)
| | - Kristyna Vrbova
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague 4, Czech Republic; (K.V.); (P.R.)
| | - Pavel Rossner
- Department of Nanotoxicology and Molecular Epidemiology, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague 4, Czech Republic; (K.V.); (P.R.)
| | - Jan Topinka
- Department of Genetic Toxicology and Epigenetics, Institute of Experimental Medicine CAS, Videnska 1083, 142 20 Prague 4, Czech Republic; (K.H.); (I.C.); (J.T.)
| | - Stepanka Vlckova
- Department of Occupational Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Na Bojisti 1, 120 00 Prague 2, Czech Republic; (D.P.); (S.V.); (Z.F.); (L.L.); (P.K.)
| | - Zdenka Fenclova
- Department of Occupational Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Na Bojisti 1, 120 00 Prague 2, Czech Republic; (D.P.); (S.V.); (Z.F.); (L.L.); (P.K.)
| | - Lucie Lischkova
- Department of Occupational Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Na Bojisti 1, 120 00 Prague 2, Czech Republic; (D.P.); (S.V.); (Z.F.); (L.L.); (P.K.)
| | - Pavlina Klusackova
- Department of Occupational Medicine, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Na Bojisti 1, 120 00 Prague 2, Czech Republic; (D.P.); (S.V.); (Z.F.); (L.L.); (P.K.)
| | - Jaroslav Schwarz
- Laboratory of Aerosol Chemistry and Physics, Institute of Chemical Process Fundamentals CAS, Rozvojova 1, 165 02 Prague 6, Czech Republic; (V.Z.); (J.S.); (J.O.); (L.O.); (M.K.)
| | - Jakub Ondracek
- Laboratory of Aerosol Chemistry and Physics, Institute of Chemical Process Fundamentals CAS, Rozvojova 1, 165 02 Prague 6, Czech Republic; (V.Z.); (J.S.); (J.O.); (L.O.); (M.K.)
| | - Lucie Ondrackova
- Laboratory of Aerosol Chemistry and Physics, Institute of Chemical Process Fundamentals CAS, Rozvojova 1, 165 02 Prague 6, Czech Republic; (V.Z.); (J.S.); (J.O.); (L.O.); (M.K.)
| | - Martin Kostejn
- Laboratory of Aerosol Chemistry and Physics, Institute of Chemical Process Fundamentals CAS, Rozvojova 1, 165 02 Prague 6, Czech Republic; (V.Z.); (J.S.); (J.O.); (L.O.); (M.K.)
| | - Jiri Klema
- Department of Computer Science, Czech Technical University in Prague, Karlovo namesti 13, 121 35 Prague 2, Czech Republic;
| | - Stepanka Dvorackova
- Department of Machining and Assembly, Department of Engineering Technology, Department of Material Science, Faculty of Mechanical Engineering, Technical University in Liberec, Studentska 1402/2 Liberec, Czech Republic;
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3
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An overview of omics approaches to characterize the effect of perfluoroalkyl substances in environmental health. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.12.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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4
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Hu J, Yu Y. Epigenetic response profiles into environmental epigenotoxicant screening and health risk assessment: A critical review. CHEMOSPHERE 2019; 226:259-272. [PMID: 30933735 DOI: 10.1016/j.chemosphere.2019.03.096] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/06/2019] [Accepted: 03/14/2019] [Indexed: 06/09/2023]
Abstract
The epigenome may be an important interface between exposure to environmental contaminants and adverse outcome on human health. Many environmental pollutants deregulate gene expression and promote diseases by modulating the epigenome. Adverse epigenetic responses have been widely used for risk assessment of chemical substances. Various pollutants, including trace elements and persistent organic pollutants, have been detected frequently in the environment. Epigenetic toxicity of environmental matrices including water, air, soil, and food cannot be ignored. This review provides a comprehensive overview of epigenetic effects of pollutants and environmental matrices. We start with an overview of the mechanisms of epigenetic regulation and the effects of several types of environmental pollutants (trace elements, persistent organic pollutants, endocrine disrupting chemicals, and volatile organic pollutants) on epigenetic modulation. We then discuss the epigenetic responses to environmental water, air, and soil based on in vivo and in vitro assays. Finally, we discuss recommendations to promote the incorporation of epigenotoxicity into contamination screening and health risk assessment.
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Affiliation(s)
- Junjie Hu
- School of Environment and Civil Engineering, Dongguan University of Technology, Dongguan, 523808, Guangdong, PR China
| | - Yingxin Yu
- Guangzhou Key Laboratory Environmental Catalysis and Pollution Control, Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, Guangdong, PR China.
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5
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Moinova HR, LaFramboise T, Lutterbaugh JD, Chandar AK, Dumot J, Faulx A, Brock W, De la Cruz Cabrera O, Guda K, Barnholtz-Sloan JS, Iyer PG, Canto MI, Wang JS, Shaheen NJ, Thota PN, Willis JE, Chak A, Markowitz SD. Identifying DNA methylation biomarkers for non-endoscopic detection of Barrett's esophagus. Sci Transl Med 2019; 10:10/424/eaao5848. [PMID: 29343623 DOI: 10.1126/scitranslmed.aao5848] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 11/08/2017] [Indexed: 12/17/2022]
Abstract
We report a biomarker-based non-endoscopic method for detecting Barrett's esophagus (BE) based on detecting methylated DNAs retrieved via a swallowable balloon-based esophageal sampling device. BE is the precursor of, and a major recognized risk factor for, developing esophageal adenocarcinoma. Endoscopy, the current standard for BE detection, is not cost-effective for population screening. We performed genome-wide screening to ascertain regions targeted for recurrent aberrant cytosine methylation in BE, identifying high-frequency methylation within the CCNA1 locus. We tested CCNA1 DNA methylation as a BE biomarker in cytology brushings of the distal esophagus from 173 individuals with or without BE. CCNA1 DNA methylation demonstrated an area under the curve of 0.95 for discriminating BE-related metaplasia and neoplasia cases versus normal individuals, performing identically to methylation of VIM DNA, an established BE biomarker. When combined, the resulting two biomarker panel was 95% sensitive and 91% specific. These results were replicated in an independent validation cohort of 149 individuals who were assayed using the same cutoff values for test positivity established in the training population. To progress toward non-endoscopic esophageal screening, we engineered a well-tolerated, swallowable, encapsulated balloon device able to selectively sample the distal esophagus within 5 min. In balloon samples from 86 individuals, tests of CCNA1 plus VIM DNA methylation detected BE metaplasia with 90.3% sensitivity and 91.7% specificity. Combining the balloon sampling device with molecular assays of CCNA1 plus VIM DNA methylation enables an efficient, well-tolerated, sensitive, and specific method of screening at-risk populations for BE.
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Affiliation(s)
- Helen R Moinova
- Department of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Thomas LaFramboise
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - James D Lutterbaugh
- Department of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Apoorva Krishna Chandar
- Department of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - John Dumot
- Department of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Ashley Faulx
- Department of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Wendy Brock
- Department of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | | | - Kishore Guda
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Prasad G Iyer
- Barrett's Esophagus Unit, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Marcia I Canto
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA
| | - Jean S Wang
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicholas J Shaheen
- Center for Esophageal Diseases and Swallowing, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Prashanti N Thota
- Digestive Disease and Surgery Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Joseph E Willis
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA. .,Department of Pathology, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA.,University Hospitals Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Amitabh Chak
- Department of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA. .,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA.,University Hospitals Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Sanford D Markowitz
- Department of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA. .,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA.,University Hospitals Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
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6
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Sadikovic B, Aref-Eshghi E, Levy MA, Rodenhiser D. DNA methylation signatures in mendelian developmental disorders as a diagnostic bridge between genotype and phenotype. Epigenomics 2019; 11:563-575. [PMID: 30875234 DOI: 10.2217/epi-2018-0192] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Epigenetic and genetic mechanisms regulate the establishment and maintenance of gene expression in its proper context. Recent genome-wide mapping approaches have identified DNA methylation (DNAm) signatures in patients clinically diagnosed with syndromes manifesting as developmental disabilities with intellectual impairments. Here, we review recent studies in which these DNA methylation signatures have enabled highly sensitive and specific screening of such individuals and have clarified ambiguous cases where subjects present with genetic sequence variants of unknown clinical significance (VUS). We propose that these episignatures be considered as echoes and/or legacies of the initiating mutational events within proteins of the so-called epigenetic machinery. As well, we discuss approaches to directly confirm the functional consequences and the implications of these episignatures to patient management and treatment.
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Affiliation(s)
- Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology & Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Erfan Aref-Eshghi
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology & Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - Michael A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, N6A 5W9, Canada.,Department of Pathology & Laboratory Medicine, Western University, London, ON, N6A 3K7, Canada
| | - David Rodenhiser
- Departments of Pediatrics, Biochemistry & Oncology, Western University, London, ON, N6A 3K7, Canada.,Children's Health Research Institute & Lawson Health Research Institute, London, ON, N6C 2V5, Canada.,London Regional Cancer Program, Lawson Health Research Institute, London, ON, N6A 5W9, Canada
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7
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Guan Z, Yu H, Cuk K, Zhang Y, Brenner H. Whole-Blood DNA Methylation Markers in Early Detection of Breast Cancer: A Systematic Literature Review. Cancer Epidemiol Biomarkers Prev 2018; 28:496-505. [DOI: 10.1158/1055-9965.epi-18-0378] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/09/2018] [Accepted: 11/20/2018] [Indexed: 11/16/2022] Open
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8
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Syedmoradi L, Esmaeili F, Norton ML. Towards DNA methylation detection using biosensors. Analyst 2018; 141:5922-5943. [PMID: 27704092 DOI: 10.1039/c6an01649a] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA methylation, a stable and heritable covalent modification which mostly occurs in the context of a CpG dinucleotide, has great potential as a biomarker to detect disease, provide prognoses and predict therapeutic responses. It can be detected in a quantitative manner by many different approaches both genome-wide and at specific gene loci, in various biological fluids such as urine, plasma, and serum, which can be obtained without invasive procedures. The current, classical methods are effective in studying DNA methylation patterns, however, for the most part; they have major drawbacks such as expensive instruments, complicated and time consuming protocols as well as relatively low sensitivity, and high false positive rates. To overcome these obstacles, great efforts have been made toward the development of reliable sensor devices to solve these limitations, providing sensitive, fast and cost-effective measurements. The use of biosensors for DNA methylation biomarkers has increased in recent years, because they are portable, simple, rapid, and inexpensive which offers a straightforward way to detect methylated biomarkers. In this review, we give an overview of the conventional techniques for the detection of DNA methylation and then will focus on recent advances in biosensor based methylation detection that eliminate bisulfite conversion and PCR amplification.
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Affiliation(s)
- Leila Syedmoradi
- Department of Medical Nanotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Fariba Esmaeili
- Department of Medical Nanotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Michael L Norton
- Department of Chemistry, Marshall University, One John Marshall Drive, Huntington, WV 25755, USA.
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Van Wesenbeeck L, Janssens L, Meeuws H, Lagatie O, Stuyver L. Droplet digital PCR is an accurate method to assess methylation status on FFPE samples. Epigenetics 2018. [PMID: 29527977 PMCID: PMC5997148 DOI: 10.1080/15592294.2018.1448679] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Most tissue samples available for cancer research are archived as formalin-fixed paraffin-embedded (FFPE) samples. However, the fixation process and the long storage duration lead to DNA fragmentation and hinder epigenome analysis. The use of droplet digital PCR (ddPCR) to detect DNA methylation has recently emerged. In this study, we compare an optimized ddPCR assay with a conventional qPCR assay by targeting a dilution series of control DNA. In addition, we compare the ddPCR technology with results from Infinium arrays targeting two separate CpG sites on a set of colon adenoma FFPE samples. Our data demonstrate that qPCR and ddPCR assess methylation status equally well on dilution controls with a high DNA input. However, the methylation detection on low-input samples is more accurate using ddPCR. The proposed primer design (methylation-independent primers with amplification of solely the converted DNA target) will allow for methylation detection, independent of bisulfite conversion efficiency. Those data show that ddPCR can be used for methylation analysis on FFPE samples with a wide range of DNA input and that the precision of the assay depends largely on the total amount of amplifiable DNA fragments. Due to accessibility of the ddPCR technology and its accuracy on high- as well as low-DNA input samples, we propose the use of this approach for studies involving degraded FFPE samples.
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Affiliation(s)
| | - Leen Janssens
- a Janssen Diagnostics, A Division of Janssen Pharmaceutica , Beerse , Belgium
| | - Hanne Meeuws
- a Janssen Diagnostics, A Division of Janssen Pharmaceutica , Beerse , Belgium
| | - Ole Lagatie
- a Janssen Diagnostics, A Division of Janssen Pharmaceutica , Beerse , Belgium
| | - Lieven Stuyver
- a Janssen Diagnostics, A Division of Janssen Pharmaceutica , Beerse , Belgium
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10
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Gampenrieder SP, Rinnerthaler G, Hackl H, Pulverer W, Weinhaeusel A, Ilic S, Hufnagl C, Hauser-Kronberger C, Egle A, Risch A, Greil R. DNA Methylation Signatures Predicting Bevacizumab Efficacy in Metastatic Breast Cancer. Am J Cancer Res 2018; 8:2278-2288. [PMID: 29721079 PMCID: PMC5928889 DOI: 10.7150/thno.23544] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 12/08/2017] [Indexed: 02/01/2023] Open
Abstract
Background: Biomarkers predicting response to bevacizumab in breast cancer are still missing. Since epigenetic modifications can contribute to an aberrant regulation of angiogenesis and treatment resistance, we investigated the influence of DNA methylation patterns on bevacizumab efficacy. Methods: Genome-wide methylation profiling using the Illumina Infinium HumanMethylation450 BeadChip was performed in archival FFPE specimens of 36 patients with HER2-negative metastatic breast cancer treated with chemotherapy in combination with bevacizumab as first-line therapy (learning set). Based on objective response and progression-free survival (PFS) and considering ER expression, patients were divided in responders (R) and non-responders (NR). Significantly differentially methylated gene loci (CpGs) with a strong change in methylation levels (Δβ>0.15 or Δβ<-0.15) between R and NR were identified and further investigated in 80 bevacizumab-treated breast cancer patients (optimization set) and in 15 patients treated with chemotherapy alone (control set) using targeted deep amplicon bisulfite sequencing. Methylated gene loci were considered predictive if there was a significant association with outcome (PFS) in the optimization set but not in the control set using Spearman rank correlation, Cox regression, and logrank test. Results: Differentially methylated loci in 48 genes were identified, allowing a good separation between R and NR (odds ratio (OR) 101, p<0.0001). Methylation of at least one cytosine in 26 gene-regions was significantly associated with progression-free survival (PFS) in the optimization set, but not in the control set. Using information from the optimization set, the panel was reduced to a 9-gene signature, which could divide patients from the learning set into 2 clusters, thereby predicting response with an OR of 40 (p<0.001) and an AUC of 0.91 (LOOCV). A further restricted 3-gene methylation model showed a significant association of predicted responders with longer PFS in the learning and optimization set even in multivariate analysis with an excellent and good separation of R and NR with AUC=0.94 and AUC=0.86, respectively. Conclusion: Both a 9-gene and 3-gene methylation signature can discriminate between R and NR to a bevacizumab-based therapy in MBC and could help identify patients deriving greater benefit from bevacizumab.
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Multiplexed and Sensitive DNA Methylation Testing Using Methylation-Sensitive Restriction Enzymes "MSRE-qPCR". Methods Mol Biol 2018; 1708:407-424. [PMID: 29224156 DOI: 10.1007/978-1-4939-7481-8_21] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
DNA methylation is a chemically stable key-player in epigenetics. In the vertebrate genome the 5-methyl cytosine (5mC) has been found almost exclusively in the CpG dinucleotide context. CpG dinucleotides are enriched in CpG islands very frequently located within or close to gene promoters. Analyses of DNA methylation changes in human diagnostics have been conducted classically using methylation-sensitive restriction enzymes (MSRE). Since the discovery of bisulfite conversion-based sequencing and PCR assays, MSRE-based PCR assays have been less frequently used, although especially in the field of cancer epigenetics MSRE-based genome-wide discovery and targeted screening applications have been and are still performed successfully. Even though epigenome-wide discovery of altered DNA methylation patterns has found its way into various fields of human disease and molecular genetics research, the validation of findings upon discovery is still a bottleneck. Usually several multiples of 10 up to 100 candidate biomarkers from discovery have to be confirmed or are of interest for further work. In particular, bisulfite PCR assays are often limited in the number of candidates which can be analyzed, due to their low multiplexing capability, especially, if only small amounts of DNA are available from for example clinical specimens. In clinical research and diagnostics a similar situation arises for the analyses of cell-free DNA (cfDNA) in body fluids or circulating tumor cells (CTCs). Although tissue- or disease- (e.g., cancer) specific DNA methylation patterns can be deduced very efficiently in a genome-wide manner if around 100 ng of DNA are available, confirming these candidates and selecting target-sequences for studying methylation changes in liquid biopsies using cfDNA or CTCs remains a big challenge. Along these lines we have developed MSRE-qPCR and introduce here method details, which have been found very suitable for the efficient confirmation and testing of DNA methylation in a quantitative multiplexed manner (e.g., 48-96 plex) from ng amounts of DNA. The method is applicable in a standard qPCR setting as well for nanoliter scaled high-throughput qPCR, enabling detection of <10 copies of targets, thus suitable to pick up 0.1-1% of specific methylated DNA in an unmethylated background.
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12
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Xue G, Lu CJ, Pan SJ, Zhang YL, Miao H, Shan S, Zhu XT, Zhang Y. DNA hypomethylation of CBS promoter induced by folate deficiency is a potential noninvasive circulating biomarker for colorectal adenocarcinomas. Oncotarget 2017; 8:51387-51401. [PMID: 28881655 PMCID: PMC5584256 DOI: 10.18632/oncotarget.17988] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 05/06/2017] [Indexed: 02/06/2023] Open
Abstract
Aberrant DNA methylation patterns, which induced by folate deficiency, play important roles in tumorigenesis of colorectal cancer (CRC). Some DNA methylation alterations can also be detected in cell-free DNA (cfDNA) of patients’ plasma, making cfDNA an ideal noninvasive circulating biomarker. However, exact DNA methylation alterations induced by folate deficiency in tumorigenesis of CRC and exact potential circulating cfDNA methylation biomarker are still unclear. Therefore, DNA methylation patterns of the normal human colon mucosal epithelial cell line (NCM460), cultured with normal or low folate content, were screened and the DNA hypomethylation of cystathionine-beta-synthase (CBS) promoter was further validated in vitro and vivo. Then, the correlation analysis between folate level, DNA methylation alteration in promoter and expression of CBS was carried out in vitro and vivo. Further, the methylation patterns of CBS promoter in plasma cfDNA were detected and statistically correlated with pathological parameters and clinical outcome. Our study showed that DNA hypomethylation in CBS promoter, induced by folate deficiency, would lead to up-regulation of CBS both in vitro and vivo. Patients with cfDNA hypomethylation of CBS promoter in plasma were correlated with high tumor stage and poor clinical outcome. In addition, cfDNA hypomethylation of CBS promoter in plasma was shown to be an independent prognostic factor for recurrence and cancer-related death in CRC. Our results indicated that DNA hypomethylation of CBS promoter induced by folate deficiency could serve as a potential noninvasive circulating biomarker and may be helpful in developing more effective prognostic markers for CRC.
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Affiliation(s)
- Geng Xue
- Department of Medical Genetics, College of Basic Medical Sciences, Second Military Medical University, Shanghai 200433, China
| | - Chao-Jing Lu
- Department of Thoracic Surgery, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Shu-Jun Pan
- Department of Medical Administration, Hangzhou Sanatorium of People's Liberation Army, Hangzhou 310007, China
| | - Yin-Ling Zhang
- Department of Medical Genetics, College of Basic Medical Sciences, Second Military Medical University, Shanghai 200433, China
| | - Hui Miao
- Department of Medical Genetics, College of Basic Medical Sciences, Second Military Medical University, Shanghai 200433, China
| | - Shi Shan
- Department of Medical Genetics, College of Basic Medical Sciences, Second Military Medical University, Shanghai 200433, China
| | - Xiao-Ting Zhu
- Department of Medical Genetics, College of Basic Medical Sciences, Second Military Medical University, Shanghai 200433, China
| | - Yi Zhang
- Department of Medical Genetics, College of Basic Medical Sciences, Second Military Medical University, Shanghai 200433, China
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13
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Martín-Sánchez E, Mendaza S, Ulazia-Garmendia A, Monreal-Santesteban I, Blanco-Luquin I, Córdoba A, Vicente-García F, Pérez-Janices N, Escors D, Megías D, López-Serra P, Esteller M, Illarramendi JJ, Guerrero-Setas D. CHL1 hypermethylation as a potential biomarker of poor prognosis in breast cancer. Oncotarget 2017; 8:15789-15801. [PMID: 28178655 PMCID: PMC5362523 DOI: 10.18632/oncotarget.15004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 01/03/2017] [Indexed: 02/06/2023] Open
Abstract
The CHL1 gene encodes a cell-adhesion molecule proposed as being a putative tumour-suppressor gene in breast cancer (BC). However, neither the underlying molecular mechanisms nor the clinical value of CHL1 downregulation in BC has been explored. The methylation status of three CpG sites in the CHL1 promoter was analysed by pyrosequencing in neoplastic biopsies from 142 patients with invasive BC and compared with that of non-neoplastic tissues. We found higher CHL1 methylation levels in breast tumours than in non-neoplastic tissues, either from mammoplasties or adjacent-to-tumour, which correlated with lower levels of protein expression in tumours measured by immunohistochemistry. A panel of five BC cell lines was treated with two epigenetic drugs, and restoration of CHL1 expression was observed, indicating in vitro dynamic epigenetic regulation. CHL1 was silenced by shRNA in immortalized but non-neoplastic mammary cells, and enhanced cell proliferation and migration, but not invasion, were found by real-time cell analysis. The prognostic value of CHL1 hypermethylation was assessed by the log-rank test and fitted in a Cox regression model. Importantly, CHL1 hypermethylation was very significantly associated with shorter progression-free survival in our BC patient series, independent of age and stage (p = 0.001). In conclusion, our results indicate that CHL1 is downregulated by hypermethylation and that this epigenetic alteration is an independent prognostic factor in BC.
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Affiliation(s)
| | - Saioa Mendaza
- Cancer Epigenetics Group, Navarrabiomed. Departmento de Salud-UPNA. IdiSNA, Pamplona, Spain
| | - Ane Ulazia-Garmendia
- Cancer Epigenetics Group, Navarrabiomed. Departmento de Salud-UPNA. IdiSNA, Pamplona, Spain
| | | | - Idoia Blanco-Luquin
- Immunomodulation Group, Navarrabiomed. Departmento de Salud-UPNA. IdiSNA, Pamplona, Spain
| | - Alicia Córdoba
- Department of Pathology, Complejo Hospitalario de Navarra, Servicio Navarro de Salud-Osasunbidea, Pamplona, Spain
| | - Francisco Vicente-García
- Department of Surgery, Complejo Hospitalario de Navarra, Servicio Navarro de Salud-Osasunbidea, Pamplona, Spain
| | - Noemí Pérez-Janices
- Cancer Epigenetics Group, Navarrabiomed. Departmento de Salud-UPNA. IdiSNA, Pamplona, Spain
| | - David Escors
- Immunomodulation Group, Navarrabiomed. Departmento de Salud-UPNA. IdiSNA, Pamplona, Spain
| | - Diego Megías
- Confocal Microscopy Unit, Spanish National Cancer Research Centre, Madrid, Spain
| | - Paula López-Serra
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute - IDIBELL, Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute - IDIBELL, Barcelona, Spain
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - José Juan Illarramendi
- Department of Oncology, Complejo Hospitalario de Navarra, Servicio Navarro de Salud-Osasunbidea, Pamplona, Spain
| | - David Guerrero-Setas
- Cancer Epigenetics Group, Navarrabiomed. Departmento de Salud-UPNA. IdiSNA, Pamplona, Spain
- Department of Pathology, Complejo Hospitalario de Navarra, Servicio Navarro de Salud-Osasunbidea, Pamplona, Spain
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14
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Tarn BE, Sung KJ, Sikes HD. Engineering affinity agents for the detection of hemi-methylated CpG sites in DNA. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2016; 1:273-277. [PMID: 28580176 PMCID: PMC5450655 DOI: 10.1039/c6me00073h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Wild-type methyl-CpG-binding domain (MBD) proteins specifically bind symmetrically methylated DNA sequences, and assays have been developed that use these proteins for profiling DNA methylation. Here, we use directed evolution in the yeast surface display format to identify a new protein variant that binds hemi-methylated CpG dinucleotides.
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Affiliation(s)
- B E Tarn
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - K-J Sung
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - H D Sikes
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
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15
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Pabinger S, Ernst K, Pulverer W, Kallmeyer R, Valdes AM, Metrustry S, Katic D, Nuzzo A, Kriegner A, Vierlinger K, Weinhaeusel A. Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers. PLoS One 2016; 11:e0160227. [PMID: 27467908 PMCID: PMC4965138 DOI: 10.1371/journal.pone.0160227] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/16/2016] [Indexed: 11/18/2022] Open
Abstract
Targeted sequencing of PCR amplicons generated from bisulfite deaminated DNA is a flexible, cost-effective way to study methylation of a sample at single CpG resolution and perform subsequent multi-target, multi-sample comparisons. Currently, no platform specific protocol, support, or analysis solution is provided to perform targeted bisulfite sequencing on a Personal Genome Machine (PGM). Here, we present a novel tool, called TABSAT, for analyzing targeted bisulfite sequencing data generated on Ion Torrent sequencers. The workflow starts with raw sequencing data, performs quality assessment, and uses a tailored version of Bismark to map the reads to a reference genome. The pipeline visualizes results as lollipop plots and is able to deduce specific methylation-patterns present in a sample. The obtained profiles are then summarized and compared between samples. In order to assess the performance of the targeted bisulfite sequencing workflow, 48 samples were used to generate 53 different Bisulfite-Sequencing PCR amplicons from each sample, resulting in 2,544 amplicon targets. We obtained a mean coverage of 282X using 1,196,822 aligned reads. Next, we compared the sequencing results of these targets to the methylation level of the corresponding sites on an Illumina 450k methylation chip. The calculated average Pearson correlation coefficient of 0.91 confirms the sequencing results with one of the industry-leading CpG methylation platforms and shows that targeted amplicon bisulfite sequencing provides an accurate and cost-efficient method for DNA methylation studies, e.g., to provide platform-independent confirmation of Illumina Infinium 450k methylation data. TABSAT offers a novel way to analyze data generated by Ion Torrent instruments and can also be used with data from the Illumina MiSeq platform. It can be easily accessed via the Platomics platform, which offers a web-based graphical user interface along with sample and parameter storage. TABSAT is freely available under a GNU General Public License version 3.0 (GPLv3) at https://github.com/tadkeys/tabsat/ and http://demo.platomics.com/.
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Affiliation(s)
- Stephan Pabinger
- Health & Environment Department, Molecular Diagnostics, AIT–Austrian Institute of Technology, Vienna, Austria
- * E-mail:
| | - Karina Ernst
- Health & Environment Department, Molecular Diagnostics, AIT–Austrian Institute of Technology, Vienna, Austria
| | - Walter Pulverer
- Health & Environment Department, Molecular Diagnostics, AIT–Austrian Institute of Technology, Vienna, Austria
| | - Rainer Kallmeyer
- Health & Environment Department, Molecular Diagnostics, AIT–Austrian Institute of Technology, Vienna, Austria
| | - Ana M. Valdes
- The Department of Twin Research & Genetic Epidemiology, King’s College London, St Thomas’ Campus, London, United Kingdom
| | - Sarah Metrustry
- The Department of Twin Research & Genetic Epidemiology, King’s College London, St Thomas’ Campus, London, United Kingdom
| | | | | | | | - Klemens Vierlinger
- Health & Environment Department, Molecular Diagnostics, AIT–Austrian Institute of Technology, Vienna, Austria
| | - Andreas Weinhaeusel
- Health & Environment Department, Molecular Diagnostics, AIT–Austrian Institute of Technology, Vienna, Austria
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16
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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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17
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McCarthy D, Pulverer W, Weinhaeusel A, Diago OR, Hogan DJ, Ostertag D, Hanna MM. MethylMeter(®): bisulfite-free quantitative and sensitive DNA methylation profiling and mutation detection in FFPE samples. Epigenomics 2016; 8:747-65. [PMID: 27337298 DOI: 10.2217/epi-2016-0004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM Development of a sensitive method for DNA methylation profiling and associated mutation detection in clinical samples. MATERIALS & METHODS Formalin-fixed and paraffin-embedded tumors received by clinical laboratories often contain insufficient DNA for analysis with bisulfite or methylation sensitive restriction enzymes-based methods. To increase sensitivity, methyl-CpG DNA capture and Coupled Abscription PCR Signaling detection were combined in a new assay, MethylMeter(®). Gliomas were analyzed for MGMT methylation, glioma CpG island methylator phenotype and IDH1 R132H. RESULTS MethylMeter had 100% assay success rate measuring all five biomarkers in formalin-fixed and paraffin-embedded tissue. MGMT methylation results were supported by survival and mRNA expression data. CONCLUSION MethylMeter is a sensitive and quantitative method for multitarget DNA methylation profiling and associated mutation detection. The MethylMeter-based GliomaSTRAT assay measures methylation of four targets and one mutation to simultaneously grade gliomas and predict their response to temozolomide. This information is clinically valuable in management of gliomas.
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Affiliation(s)
- David McCarthy
- Ribomed Biotechnologies Inc., 3469 Kurtz St., San Diego, CA 92110, USA
| | - Walter Pulverer
- Molecular Diagnostics, Health & Environment Department, Austrian Institute of Technology, Muthgasse 11, 1190 Vienna, Austria
| | - Andreas Weinhaeusel
- Molecular Diagnostics, Health & Environment Department, Austrian Institute of Technology, Muthgasse 11, 1190 Vienna, Austria
| | - Oscar R Diago
- Tocagen Inc., 3030 Bunker Hill Street, Suite 230; San Diego, CA 92109, USA
| | - Daniel J Hogan
- Tocagen Inc., 3030 Bunker Hill Street, Suite 230; San Diego, CA 92109, USA
| | - Derek Ostertag
- Tocagen Inc., 3030 Bunker Hill Street, Suite 230; San Diego, CA 92109, USA
| | - Michelle M Hanna
- Ribomed Biotechnologies Inc., 3469 Kurtz St., San Diego, CA 92110, USA
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18
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Heimer BW, Tam BE, Minkovsky A, Sikes HD. Using nanobiotechnology to increase the prevalence of epigenotyping assays in precision medicine. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2016; 9. [PMID: 27126368 DOI: 10.1002/wnan.1407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/07/2016] [Accepted: 03/17/2016] [Indexed: 12/31/2022]
Abstract
Epigenetic silencing of genes that are important for DNA repair, cell cycle control, apoptosis, and cellular interactions with the extracellular matrix has been causally linked to several subtypes of cancer. Translating this knowledge of the implications of promoter methylation to wide and routine use in clinical pathology laboratories has been more challenging than the case of genetic analyses because epigenetic modifications do not change the underlying sequence of the affected nucleic acid, rendering polymerase chain reaction analysis alone uninformative. Two epigenotyping assays that detect promoter methylation are currently standard of care in treatment of two distinct tumor types in only a few top hospitals across the United States. Both rely on a harsh chemical step that degrades over 90% of tumor DNA samples, which are often available in limited quantities, and imparts the potential for false-negative or false-positive results if the reaction conditions are not exactly correct. Using nanotechnology and biotechnology to devise practical new analysis techniques that avoid the drawbacks of current techniques represents a powerful approach that is likely to significantly increase the clinical use of this class of biomarkers in the coming years. WIREs Nanomed Nanobiotechnol 2017, 9:e1407. doi: 10.1002/wnan.1407 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Brandon W Heimer
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brooke E Tam
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alissa Minkovsky
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Hadley D Sikes
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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