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Ye C, Zhao Z, Lai P, Chen C, Jian F, Liang H, Guo Q. Strategies for the detection of site-specific DNA methylation and its application, opportunities and challenges in the field of electrochemical biosensors. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:5496-5508. [PMID: 39051422 DOI: 10.1039/d4ay00779d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
DNA methylation is an epigenetic modification that plays a crucial role in various biological processes. Aberrant DNA methylation is closely associated with the onset of diseases, and the specific localization of methylation sites in the genome offers further insight into the connection between methylation and diseases. Currently, there are numerous methods available for site-specific methylation detection. Electrochemical biosensors have garnered significant attention due to their distinct advantages, such as rapidity, simplicity, high sensitivity, low cost, and the potential for miniaturization. In this paper, we present a systematic review of the primary sensing strategies utilized in the past decade for analyzing site-specific methylation and their applications in electrochemical sensors, from a novel perspective focusing on the localization analysis of site-specific methylation. These strategies include bisulfite treatment, restriction endonuclease treatment, other sensing strategies, and deamination without direct bisulfite treatment. We hope that this paper can offer ideas and references for establishing site-specific methylation electrochemical analysis in clinical practice.
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Affiliation(s)
- Chenliu Ye
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Zhibin Zhao
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Penghui Lai
- The Second Hospital of Longyan, Longyan 364000, China
| | - Chunmei Chen
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Fumei Jian
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Haiying Liang
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
| | - Qiongying Guo
- Department of Pharmacy, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan 364000, China.
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2
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Zamuner FT, Ramos-López A, García-Negrón A, Purcell-Wiltz A, Cortés-Ortiz A, Cuevas AR, Gosala K, Winkler E, Sidransky D, Guerrero-Preston R. Evaluation of silica spin‑column and magnetic bead formats for rapid DNA methylation analysis in clinical and point‑of‑care settings. Biomed Rep 2024; 21:112. [PMID: 38912171 PMCID: PMC11190640 DOI: 10.3892/br.2024.1800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/20/2024] [Indexed: 06/25/2024] Open
Abstract
Late-stage cancers lack effective treatment, underscoring the need for early diagnosis to improve prognosis and decrease mortality rates. Molecular markers, such as DNA methylation, offer promise in early cancer detection. The present study compared commercial kits for analyzing DNA from cervical liquid cytology samples in cancer screening. Rapid bisulfite conversion kits using silica spin-columns and magnetic beads were assessed against standard DNA extraction and bisulfite conversion methods for profiling DNA methylation using quantitative methylation-specific PCR. β-actin amplification indicated the suitability of small sample volumes for methylation studies using either the pellet or supernatant (cell-free DNA) parts. Comparison of Bisulfite Conversion Kit-Whole Cell (Abcam), Methylamp Bisulfite Modification (Epigentek), EpiTect Fast LyseAll Bisulfite Kit (Qiagen GmbH) and EZ DNA Methylation-Direct Kit (Zymo Research Corp.) showed no significant differences in β-actin cycle threshold values. EZ-96 DNA Methylation-Lightning MagPrep (Zymo Research Corp.), a hybrid kit in a 96-well plate format, exhibited swift turnaround time and similar amplification efficiency. Automation with magnetic bead kits increased throughput without compromising amplification efficiency in open PCR systems. Cost analysis favored direct kits over the gold standard manual protocol. This comparison aids in selecting cost-effective DNA methylation diagnostic tests. The present study confirmed comparable kit performance in methylation-based analysis, highlighting the adequacy of cytology samples and the potential of bodily fluids as alternatives for liquid biopsy.
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Affiliation(s)
- Fernando T. Zamuner
- Department of Otolaryngology and Head and Neck Surgery, Head and Neck Cancer Research Laboratory, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Ashley Ramos-López
- LifeGene-Biomarks, Research and Development Unit, Toa Baja 00949, Puerto Rico
| | | | - Ana Purcell-Wiltz
- LifeGene-Biomarks, Research and Development Unit, Toa Baja 00949, Puerto Rico
- Department of Medicine, San Juan Bautista School of Medicine, Caguas 00725, Puerto Rico
| | - Andrea Cortés-Ortiz
- LifeGene-Biomarks, Research and Development Unit, Toa Baja 00949, Puerto Rico
- Department of Medicine, San Juan Bautista School of Medicine, Caguas 00725, Puerto Rico
| | - Aniris Román Cuevas
- LifeGene-Biomarks, Research and Development Unit, Toa Baja 00949, Puerto Rico
- Department of Biology, University of Puerto Rico, Río Piedras 00931, Puerto Rico
| | - Keerthana Gosala
- Department of Otolaryngology and Head and Neck Surgery, Head and Neck Cancer Research Laboratory, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Eli Winkler
- Department of Otolaryngology and Head and Neck Surgery, Head and Neck Cancer Research Laboratory, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- New York University Langone Health, New York, NY 10016, USA
| | - David Sidransky
- Department of Otolaryngology and Head and Neck Surgery, Head and Neck Cancer Research Laboratory, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Rafael Guerrero-Preston
- LifeGene-Biomarks, Research and Development Unit, Toa Baja 00949, Puerto Rico
- LifeGene-Biomarks, FastForward Innovation Hub, Baltimore, MD 21205, USA
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3
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Castagnola MJ, Medina-Paz F, Zapico SC. Uncovering Forensic Evidence: A Path to Age Estimation through DNA Methylation. Int J Mol Sci 2024; 25:4917. [PMID: 38732129 PMCID: PMC11084977 DOI: 10.3390/ijms25094917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/27/2024] [Accepted: 04/28/2024] [Indexed: 05/13/2024] Open
Abstract
Age estimation is a critical aspect of reconstructing a biological profile in forensic sciences. Diverse biochemical processes have been studied in their correlation with age, and the results have driven DNA methylation to the forefront as a promising biomarker. DNA methylation, an epigenetic modification, has been extensively studied in recent years for developing age estimation models in criminalistics and forensic anthropology. Epigenetic clocks, which analyze DNA sites undergoing hypermethylation or hypomethylation as individuals age, have paved the way for improved prediction models. A wide range of biomarkers and methods for DNA methylation analysis have been proposed, achieving different accuracies across samples and cell types. This review extensively explores literature from the past 5 years, showing scientific efforts toward the ultimate goal: applying age prediction models to assist in human identification.
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Affiliation(s)
- María Josefina Castagnola
- Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Tiernan Hall 365, Newark, NJ 07102, USA; (M.J.C.); (F.M.-P.)
| | - Francisco Medina-Paz
- Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Tiernan Hall 365, Newark, NJ 07102, USA; (M.J.C.); (F.M.-P.)
| | - Sara C. Zapico
- Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Tiernan Hall 365, Newark, NJ 07102, USA; (M.J.C.); (F.M.-P.)
- Department of Anthropology and Laboratories of Analytical Biology, National Museum of Natural History, MRC 112, Smithsonian Institution, Washington, DC 20560, USA
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Kresse SH, Brandt-Winge S, Pharo H, Flatin BTB, Jeanmougin M, Vedeld HM, Lind GE. Evaluation of commercial kits for isolation and bisulfite conversion of circulating cell-free tumor DNA from blood. Clin Epigenetics 2023; 15:151. [PMID: 37710283 PMCID: PMC10503171 DOI: 10.1186/s13148-023-01563-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/05/2023] [Indexed: 09/16/2023] Open
Abstract
BACKGROUND DNA methylation biomarkers in circulating cell-free DNA (cfDNA) have great clinical potential for cancer management. Most methods for DNA methylation analysis require bisulfite conversion, causing DNA degradation and loss. This is particularly challenging for cfDNA, which is naturally fragmented and normally present in low amounts. The aim of the present study was to identify an optimal combination of cfDNA isolation and bisulfite conversion kits for downstream analysis of DNA methylation biomarkers in plasma. RESULTS Of the five tested bisulfite conversion kits (EpiJET Bisulfite Conversion Kit, EpiTect Plus DNA Bisulfite Kit (EpiTect), EZ DNA Methylation-Direct Kit, Imprint DNA Modification Kit (Imprint) and Premium Bisulfite Kit), the highest and lowest DNA yield and recovery were achieved using the EpiTect kit and the Imprint kit, respectively, with more than double the amount of DNA for the EpiTect kit. Of the three tested cfDNA isolation kits (Maxwell RSC ccfDNA Plasma Kit, QIAamp Circulating Nucleic Acid Kit (CNA) and QIAamp MinElute ccfDNA Mini Kit), the CNA kit yielded around twice as much cfDNA compared to the two others kits, although with more high molecular weight DNA present. When comparing various combinations of cfDNA isolation kits and bisulfite conversion kits, the CNA kit and the EpiTect kit were identified as the best-performing combination, resulting in the highest yield of bisulfite converted cfDNA from normal plasma, as measured by droplet digital PCR (ddPCR). As a proof of principle, this kit combination was used to process plasma samples from 13 colorectal cancer patients for subsequent ddPCR methylation analysis of BCAT1 and IKZF1. Methylation of BCAT1 and/or IKZF1 was identified in 6/10 (60%) stage IV patients and 1/3 (33%) stage III patients. CONCLUSIONS Based on a thorough evaluation of five bisulfite conversion kits and three cfDNA isolation kits, both individually and in combination, the CNA kit and the EpiTect kit were identified as the best-performing kit combination, with highest DNA yield and recovery across a range of DNA input amounts. The combination was successfully used for detection of clinically relevant DNA methylation biomarkers in plasma from cancer patients.
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Affiliation(s)
- Stine H Kresse
- Department of Molecular Oncology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Montebello, 0379, Oslo, Norway
| | - Sara Brandt-Winge
- Department of Molecular Oncology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Montebello, 0379, Oslo, Norway
| | - Heidi Pharo
- Department of Molecular Oncology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Montebello, 0379, Oslo, Norway
| | - Bjørnar T B Flatin
- Department of Molecular Oncology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Montebello, 0379, Oslo, Norway
| | - Marine Jeanmougin
- Department of Molecular Oncology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Montebello, 0379, Oslo, Norway
| | - Hege Marie Vedeld
- Department of Molecular Oncology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Montebello, 0379, Oslo, Norway
| | - Guro E Lind
- Department of Molecular Oncology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Montebello, 0379, Oslo, Norway.
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.
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Pourasghariazar M, Zarredar H, Asadi M, Caner A, Akhgari A, Valizadeh H, Bornehdeli S, Hashemzadeh S, Raeisi M. Comparative evaluation of ZMYND-8 and RARβ2 genes promoters’ methylation changes in tumor and tumor margin tissues of patients with lung cancer. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2023. [DOI: 10.1186/s43042-023-00399-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023] Open
Abstract
Abstract
Background
Lung cancer remains one of the most lethal carcinomas worldwide because of its late diagnosis. One of the DNA modifications is methylation, one of the primary alterations of tumor development, consisting of fascinating indicators for cancer diagnosis. This study investigated ZMYND-8 and RARβ2 gene methylation in NSCLC as a new epigenetic tool.
Methods
First, to find out the potential diagnostic capability of ZMYND-8 and RARβ2 genes methylation, we entirely surfed DNA methylation microarrays from the Cancer Genome Atlas (TCGA) data of NSCLC samples. Additionally, we took advantage of using q-MSP in several pieces comprising NSCLC tumors and neighboring normal tissues; ZMYND-8 and RARβ2 genes methylation grades were acquired.
Results
Our finding displayed significant hypomethylation of ZMYND-8 and hypermethylation of RARβ2 in NSCLC samples compared to neighboring standard specimens, which significantly correlated with the clinical stage of malignancy. In addition, the incredible precision of ZMYND-8 and RARβ2 methylations as reliable cancer diagnosis indicators in NSCLC was confirmed, drawing the ROC curve analysis with an AUC value of 0.751 and 0.8676, respectively, for ZMYND-8 and RARβ2. Additional studies of other dominant cancer entities in TCGA displayed that RARβ2’s higher methylation degree and ZMYND-8 lower methylation degree are prevalent changes in tumor evolution which could be possibly considered as a potential diagnostic biomarkers for lung cancer.
Conclusion
Based on this study, ZMYND-8 and RARβ2 methylation are reliable biomarkers for lung cancer.
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Johnston AD, Lu J, Korbie D, Trau M. Modelling clinical DNA fragmentation in the development of universal PCR-based assays for bisulfite-converted, formalin-fixed and cell-free DNA sample analysis. Sci Rep 2022; 12:16051. [PMID: 36163372 PMCID: PMC9512909 DOI: 10.1038/s41598-022-18196-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/08/2022] [Indexed: 11/09/2022] Open
Abstract
In fragmented DNA, PCR-based methods quantify the number of intact regions at a specific amplicon length. However, the relationship between the population of DNA fragments within a sample and the likelihood they will amplify has not been fully described. To address this, we have derived a mathematical equation that relates the distribution profile of a stochastically fragmented DNA sample to the probability that a DNA fragment within that sample can be amplified by any PCR assay of arbitrary length. Two panels of multiplex PCR assays for quantifying fragmented DNA were then developed: a four-plex panel that can be applied to any human DNA sample and used to estimate the percentage of regions that are intact at any length; and a two-plex panel optimized for quantifying circulating cell-free DNA (cfDNA). For these assays, regions of the human genome least affected by copy number aberration were identified and selected; within these copy-neutral regions, each PCR assay was designed to amplify both genomic and bisulfite-converted DNA; and all assays were validated for use in both conventional qPCR and droplet-digital PCR. Finally, using the cfDNA-optimized assays we find evidence of universally conserved nucleosome positioning among individuals.
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Affiliation(s)
- Andrew D Johnston
- Centre for Personalized NanoMedicine, The University of Queensland, St Lucia, QLD, 4072, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, Westmead, NSW, Australia
| | - Jennifer Lu
- Centre for Personalized NanoMedicine, The University of Queensland, St Lucia, QLD, 4072, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Darren Korbie
- Centre for Personalized NanoMedicine, The University of Queensland, St Lucia, QLD, 4072, Australia.
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia.
| | - Matt Trau
- Centre for Personalized NanoMedicine, The University of Queensland, St Lucia, QLD, 4072, Australia.
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia.
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia.
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Fatemi N, Tierling S, Es HA, Varkiani M, Nazemalhosseini Mojarad E, Asadzadeh Aghdaei H, Walter J, Totonchi M. DNA Methylation Biomarkers in Colorectal Cancer: Clinical Applications for Precision Medicine. Int J Cancer 2022; 151:2068-2081. [PMID: 35730647 DOI: 10.1002/ijc.34186] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/29/2022] [Accepted: 06/08/2022] [Indexed: 11/06/2022]
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer death worldwide that is attributed to gradual long-term accumulation of both genetic and epigenetic changes. To reduce the mortality rate of CRC and to improve treatment efficacy, it will be important to develop accurate noninvasive diagnostic tests for screening, acute, and personalized diagnosis. Epigenetic changes such as DNA methylation play an important role in the development and progression of CRC. Over the last decade, a panel of DNA methylation markers has been reported showing a high accuracy and reproducibility in various semi-invasive or noninvasive biosamples. Research to obtain comprehensive panels of markers allowing a highly sensitive and differentiating diagnosis of CRC is ongoing. Moreover, the epigenetic alterations for cancer therapy, as a precision medicine strategy will increase their therapeutic potential over time. Here, we discuss the current state of DNA methylation-based biomarkers and their impact on CRC diagnosis. We emphasize the need to further identify and stratify methylation-biomarkers and to develop robust and effective detection methods that are applicable for a routine clinical setting of CRC diagnostics particularly at the early stage of the disease.
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Affiliation(s)
- Nayeralsadat Fatemi
- Basic & Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology & Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sascha Tierling
- Department of Genetics/Epigenetics, Faculty NT, Life Sciences, Saarland University, Saarbrücken, Germany
| | | | - Maryam Varkiani
- Department of Molecular Genetics, Faculty of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
| | - Ehsan Nazemalhosseini Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic & Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology & Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jörn Walter
- Department of Genetics/Epigenetics, Faculty NT, Life Sciences, Saarland University, Saarbrücken, Germany
| | - Mehdi Totonchi
- Basic & Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology & Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
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8
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Guerin LN, Barnett KR, Hodges E. Dual detection of chromatin accessibility and DNA methylation using ATAC-Me. Nat Protoc 2021; 16:5377-5397. [PMID: 34663963 PMCID: PMC11057009 DOI: 10.1038/s41596-021-00608-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 08/02/2021] [Indexed: 01/05/2023]
Abstract
The epigenome is multidimensional, with individual molecular components operating on different levels to control transcriptional output. Techniques that combine measurements of these features can reveal their precise correspondence in genomic space, or temporal connectivity, to better understand how they jointly regulate genes. ATAC-Me is an integrated method to probe DNA methylation and chromatin accessibility from a single DNA fragment library. Intact nuclei undergo Tn5 transposition to isolate DNA fragments within nucleosome-free regions. Isolated fragments are exposed to sodium bisulfite before library amplification and sequencing. A typical ATAC-Me experiment detects ~60,000-75,000 peak regions (P < 0.05), covering ~3-4 million CpG sites with at least 5× coverage. These sites display a range of methylation values depending on the cellular and genomic context. The approach is well suited for time course studies that aim to capture chromatin and DNA methylation dynamics in tandem during cellular differentiation. The protocol is completed in 2 d with standard molecular biology equipment and expertise. Analysis of resulting data uses publicly available software requiring basic bioinformatics skills to interpret results.
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Affiliation(s)
- Lindsey N. Guerin
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Kelly R. Barnett
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Emily Hodges
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
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9
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Kerachian MA, Azghandi M, Mozaffari-Jovin S, Thierry AR. Guidelines for pre-analytical conditions for assessing the methylation of circulating cell-free DNA. Clin Epigenetics 2021; 13:193. [PMID: 34663458 PMCID: PMC8525023 DOI: 10.1186/s13148-021-01182-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/04/2021] [Indexed: 02/06/2023] Open
Abstract
Methylation analysis of circulating cell-free DNA (cirDNA), as a liquid biopsy, has a significant potential to advance the detection, prognosis, and treatment of cancer, as well as many genetic disorders. The role of epigenetics in disease development has been reported in several hereditary disorders, and epigenetic modifications are regarded as one of the earliest and most significant genomic aberrations that arise during carcinogenesis. Liquid biopsy can be employed for the detection of these epigenetic biomarkers. It consists of isolation (pre-analytical) and detection (analytical) phases. The choice of pre-analytical variables comprising cirDNA extraction and bisulfite conversion methods can affect the identification of cirDNA methylation. Indeed, different techniques give a different return of cirDNA, which confirms the importance of pre-analytical procedures in clinical diagnostics. Although novel techniques have been developed for the simplification of methylation analysis, the process remains complex, as the steps of DNA extraction, bisulfite treatment, and methylation detection are each carried out separately. Recent studies have noted the absence of any standard method for the pre-analytical processing of methylated cirDNA. We have therefore conducted a comprehensive and systematic review of the important pre-analytical and analytical variables and the patient-related factors which form the basis of our guidelines for analyzing methylated cirDNA in liquid biopsy.
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Affiliation(s)
- Mohammad Amin Kerachian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran.
| | - Marjan Azghandi
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Sina Mozaffari-Jovin
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alain R Thierry
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier, France.
- INSERM, U1194, Montpellier, France.
- University of Montpellier, Montpellier, France.
- ICM, Regional Institute of Cancer of Montpellier, Montpellier, France.
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10
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Desaulniers D, Vasseur P, Jacobs A, Aguila MC, Ertych N, Jacobs MN. Integration of Epigenetic Mechanisms into Non-Genotoxic Carcinogenicity Hazard Assessment: Focus on DNA Methylation and Histone Modifications. Int J Mol Sci 2021; 22:10969. [PMID: 34681626 PMCID: PMC8535778 DOI: 10.3390/ijms222010969] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetics involves a series of mechanisms that entail histone and DNA covalent modifications and non-coding RNAs, and that collectively contribute to programing cell functions and differentiation. Epigenetic anomalies and DNA mutations are co-drivers of cellular dysfunctions, including carcinogenesis. Alterations of the epigenetic system occur in cancers whether the initial carcinogenic events are from genotoxic (GTxC) or non-genotoxic (NGTxC) carcinogens. NGTxC are not inherently DNA reactive, they do not have a unifying mode of action and as yet there are no regulatory test guidelines addressing mechanisms of NGTxC. To fil this gap, the Test Guideline Programme of the Organisation for Economic Cooperation and Development is developing a framework for an integrated approach for the testing and assessment (IATA) of NGTxC and is considering assays that address key events of cancer hallmarks. Here, with the intent of better understanding the applicability of epigenetic assays in chemical carcinogenicity assessment, we focus on DNA methylation and histone modifications and review: (1) epigenetic mechanisms contributing to carcinogenesis, (2) epigenetic mechanisms altered following exposure to arsenic, nickel, or phenobarbital in order to identify common carcinogen-specific mechanisms, (3) characteristics of a series of epigenetic assay types, and (4) epigenetic assay validation needs in the context of chemical hazard assessment. As a key component of numerous NGTxC mechanisms of action, epigenetic assays included in IATA assay combinations can contribute to improved chemical carcinogen identification for the better protection of public health.
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Affiliation(s)
- Daniel Desaulniers
- Environmental Health Sciences and Research Bureau, Hazard Identification Division, Health Canada, AL:2203B, Ottawa, ON K1A 0K9, Canada
| | - Paule Vasseur
- CNRS, LIEC, Université de Lorraine, 57070 Metz, France;
| | - Abigail Jacobs
- Independent at the Time of Publication, Previously US Food and Drug Administration, Rockville, MD 20852, USA;
| | - M. Cecilia Aguila
- Toxicology Team, Division of Human Food Safety, Center for Veterinary Medicine, US Food and Drug Administration, Department of Health and Human Services, Rockville, MD 20852, USA;
| | - Norman Ertych
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany;
| | - Miriam N. Jacobs
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton OX11 0RQ, UK;
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11
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Pham DAT, Le SD, Doan TM, Luu PT, Nguyen UQ, Ho SV, Vo LTT. Standardization of DNA amount for bisulfite conversion for analyzing the methylation status of LINE-1 in lung cancer. PLoS One 2021; 16:e0256254. [PMID: 34403448 PMCID: PMC8370637 DOI: 10.1371/journal.pone.0256254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 08/04/2021] [Indexed: 11/18/2022] Open
Abstract
Highly methylated Long Interspersed Nucleotide Elements 1 (LINE-1) constitute approximately 20% of the human genome, thus serving as a surrogate marker of global genomic DNA methylation. To date, there is still lacking a consensus about the precise location in LINE-1 promoter and its methylation threshold value, making challenging the use of LINE-1 methylation as a diagnostic, prognostic markers in cancer. This study reports on a technical standardization of bisulfite-based DNA methylation analysis, which ensures the complete bisulfite conversion of repeated LINE-1 sequences, thus allowing accurate LINE-1 methylation value. In addition, the study also indicated the precise location in LINE-1 promoter of which significant variance in methylation level makes LINE-1 methylation as a potential diagnostic biomarker for lung cancer. A serial concentration of 5-50-500 ng of DNA from 275 formalin-fixed paraffin-embedded lung tissues were converted by bisulfite; methylation level of two local regions (at nucleotide position 300–368 as LINE-1.1 and 368–460 as LINE-1.2) in LINE-1 promoter was measured by real time PCR. The use of 5 ng of genomic DNA but no more allowed to detect LINE-1 hypomethylation in lung cancer tissue (14.34% versus 16.69% in non-cancerous lung diseases for LINE-1.1, p < 0.0001, and 30.28% versus 32.35% for LINE-1.2, p < 0.05). Our study thus highlighted the optimal and primordial concentration less than 5 ng of genomic DNA guarantees the complete LINE-1 bisulfite conversion, and significant variance in methylation level of the LINE-1 sequence position from 300 to 368 allowed to discriminate lung cancer from non-cancer samples.
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Affiliation(s)
| | - Son Duc Le
- Faculty of Biology, University of Science, Vietnam National University, Hanoi, Vietnam
| | - Trang Mai Doan
- Faculty of Biology, University of Science, Vietnam National University, Hanoi, Vietnam
| | - Phuong Thu Luu
- Faculty of Biology, University of Science, Vietnam National University, Hanoi, Vietnam
| | - Uyen Quynh Nguyen
- Department of Biology, VNU Institute of Microbiology and Biotechnology, Hanoi, Vietnam
| | - Son Van Ho
- Department of Biochemistry, 175 Hospital, Ho Chi Minh City, Vietnam
| | - Lan Thi Thuong Vo
- Faculty of Biology, University of Science, Vietnam National University, Hanoi, Vietnam
- * E-mail:
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12
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Martisova A, Holcakova J, Izadi N, Sebuyoya R, Hrstka R, Bartosik M. DNA Methylation in Solid Tumors: Functions and Methods of Detection. Int J Mol Sci 2021; 22:ijms22084247. [PMID: 33921911 PMCID: PMC8073724 DOI: 10.3390/ijms22084247] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 02/06/2023] Open
Abstract
DNA methylation, i.e., addition of methyl group to 5′-carbon of cytosine residues in CpG dinucleotides, is an important epigenetic modification regulating gene expression, and thus implied in many cellular processes. Deregulation of DNA methylation is strongly associated with onset of various diseases, including cancer. Here, we review how DNA methylation affects carcinogenesis process and give examples of solid tumors where aberrant DNA methylation is often present. We explain principles of methods developed for DNA methylation analysis at both single gene and whole genome level, based on (i) sodium bisulfite conversion, (ii) methylation-sensitive restriction enzymes, and (iii) interactions of 5-methylcytosine (5mC) with methyl-binding proteins or antibodies against 5mC. In addition to standard methods, we describe recent advances in next generation sequencing technologies applied to DNA methylation analysis, as well as in development of biosensors that represent their cheaper and faster alternatives. Most importantly, we highlight not only advantages, but also disadvantages and challenges of each method.
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13
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AlAbdi L, Saha D, He M, Dar MS, Utturkar SM, Sudyanti PA, McCune S, Spears BH, Breedlove JA, Lanman NA, Gowher H. Oct4-Mediated Inhibition of Lsd1 Activity Promotes the Active and Primed State of Pluripotency Enhancers. Cell Rep 2021; 30:1478-1490.e6. [PMID: 32023463 DOI: 10.1016/j.celrep.2019.11.040] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/30/2019] [Accepted: 12/19/2019] [Indexed: 12/16/2022] Open
Abstract
An aberrant increase in pluripotency gene (PpG) expression due to enhancer reactivation could induce stemness and enhance the tumorigenicity of cancer stem cells. Silencing of PpG enhancers (PpGe) during embryonic stem cell differentiation involves Lsd1-mediated H3K4me1 demethylation and DNA methylation. Here, we observed retention of H3K4me1 and DNA hypomethylation at PpGe associated with a partial repression of PpGs in F9 embryonal carcinoma cells (ECCs) post-differentiation. H3K4me1 demethylation in F9 ECCs could not be rescued by Lsd1 overexpression. Given our observation that H3K4me1 demethylation is accompanied by strong Oct4 repression in P19 ECCs, we tested if Oct4 interaction with Lsd1 affects its catalytic activity. Our data show a dose-dependent inhibition of Lsd1 activity by Oct4 and retention of H3K4me1 at PpGe in Oct4-overexpressing P19 ECCs. These data suggest that Lsd1-Oct4 interaction in cancer stem cells could establish a "primed" enhancer state that is susceptible to reactivation, leading to aberrant PpG expression.
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Affiliation(s)
- Lama AlAbdi
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Debapriya Saha
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Ming He
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Mohd Saleem Dar
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Sagar M Utturkar
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Putu Ayu Sudyanti
- Department of Statistics, Purdue University, West Lafayette, IN 47907, USA
| | - Stephen McCune
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Brice H Spears
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - James A Breedlove
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Nadia A Lanman
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA; Department of Comparative Pathobiology, Purdue University, West Lafayette, IN 47907, USA
| | - Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
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14
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Hong SR, Shin KJ. Bisulfite-Converted DNA Quantity Evaluation: A Multiplex Quantitative Real-Time PCR System for Evaluation of Bisulfite Conversion. Front Genet 2021; 12:618955. [PMID: 33719336 PMCID: PMC7947210 DOI: 10.3389/fgene.2021.618955] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/27/2021] [Indexed: 11/13/2022] Open
Abstract
Bisulfite (BS) conversion, which includes a series of chemical reactions using bisulfite, is a prerequisite to most DNA methylation analysis methods, and thus is an essential step in the associated research process. Unfortunately, BS conversion leads to the degradation or loss of DNA, which can hinder further downstream analysis. In addition, it is well known that incomplete BS conversion is crucial, as it causes an exaggeration of the DNA methylation level, which can adversely affect the results. Therefore, there have been many attempts to measure three key features of BS conversion: BS conversion efficiency, recovery, and degradation level. In this study, a multiplex quantitative real-time PCR system named BisQuE was suggested to simultaneously analyze three important aspects of the conversion step. By adopting cytosine-free PCR primers for two differently sized multicopy regions, the short amplicon and long amplicon were obtained from both the genomic and BS-converted DNA, thus enabling the obtaining of reliable and sensitive results and the calculation of the degradation level of the conversion step. Also, probes for detecting converted/unconverted templates and C-T indicators for inducing the formula were included in this assay to quantify BS-converted DNA in order to compute the conversion efficiency and recovery. Six BS conversion kits (EZ DNA Methylation-Lightning Kit, Premium Bisulfite kit, MethylEdge® Bisulfite Conversion System, EpiJET Bisulfite Conversion Kit, EpiTect Fast DNA Bisulfite Kit, and NEBNext® Enzymatic Methyl-seq Conversion Module) were tested in 20 samples using 50 ng of genomic DNA as an input with the BisQuE. The conversion efficiency, degradation levels, as well as recovery rates of the kits were investigated. A total of 99.61-99.90% conversion efficiency was perceived for five of the kits, while the NEBNext kit showed about 94%. The lowest degradation level was shown by the NEBNext kit, whereas the other kits were quite similar. The recovery rates of the kits were found to be within the range of 18-50%. A Qubit assay was also used to compare the recovery rate of BisQuE.
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Affiliation(s)
- Sae Rom Hong
- Department of Forensic Medicine and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - Kyoung-Jin Shin
- Department of Forensic Medicine and Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
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15
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Vandenbussche I, Sass A, Van Nieuwerburgh F, Pinto-Carbó M, Mannweiler O, Eberl L, Coenye T. Detection of cytosine methylation in Burkholderia cenocepacia by single-molecule real-time sequencing and whole-genome bisulfite sequencing. MICROBIOLOGY-SGM 2021; 167. [PMID: 33565960 DOI: 10.1099/mic.0.001027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Research on prokaryotic epigenetics, the study of heritable changes in gene expression independent of sequence changes, led to the identification of DNA methylation as a versatile regulator of diverse cellular processes. Methylation of adenine bases is often linked to regulation of gene expression in bacteria, but cytosine methylation is also frequently observed. In this study, we present a complete overview of the cytosine methylome in Burkholderia cenocepacia, an opportunistic respiratory pathogen in cystic fibrosis patients. Single-molecule real-time (SMRT) sequencing was used to map all 4mC-modified cytosines, as analysis of the predicted MTases in the B. cenocepacia genome revealed the presence of a 4mC-specific phage MTase, M.BceJII, targeting GGCC sequences. Methylation motif GCGGCCGC was identified, and out of 6850 motifs detected across the genome, 2051 (29.9 %) were methylated at the fifth position. Whole-genome bisulfite sequencing (WGBS) was performed to map 5mC methylation and 1635 5mC-modified cytosines were identified in CpG motifs. A comparison of the genomic positions of the modified bases called by each method revealed no overlap, which confirmed the authenticity of the detected 4mC and 5mC methylation by SMRT sequencing and WGBS, respectively. Large inter-strain variation of the 4mC-methylated cytosines was observed when B. cenocepacia strains J2315 and K56-2 were compared, which suggests that GGCC methylation patterns in B. cenocepacia are strain-specific. It seems likely that 4mC methylation of GGCC is not involved in regulation of gene expression but rather is a remnant of bacteriophage invasion, in which methylation of the phage genome was crucial for protection against restriction-modification systems of B. cenocepacia.
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Affiliation(s)
- Ian Vandenbussche
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Andrea Sass
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | | | - Marta Pinto-Carbó
- Department of Plant and Microbial Microbiology, University of Zurich, Zurich, Switzerland
| | - Olga Mannweiler
- Department of Plant and Microbial Microbiology, University of Zurich, Zurich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Microbiology, University of Zurich, Zurich, Switzerland
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
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16
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Kressler C, Gasparoni G, Nordström K, Hamo D, Salhab A, Dimitropoulos C, Tierling S, Reinke P, Volk HD, Walter J, Hamann A, Polansky JK. Targeted De-Methylation of the FOXP3-TSDR Is Sufficient to Induce Physiological FOXP3 Expression but Not a Functional Treg Phenotype. Front Immunol 2021; 11:609891. [PMID: 33488615 PMCID: PMC7817622 DOI: 10.3389/fimmu.2020.609891] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/20/2020] [Indexed: 12/22/2022] Open
Abstract
CD4+ regulatory T cells (Tregs) are key mediators of immunological tolerance and promising effector cells for immuno-suppressive adoptive cellular therapy to fight autoimmunity and chronic inflammation. Their functional stability is critical for their clinical utility and has been correlated to the demethylated state of the TSDR/CNS2 enhancer element in the Treg lineage transcription factor FOXP3. However, proof for a causal contribution of the TSDR de-methylation to FOXP3 stability and Treg induction is so far lacking. We here established a powerful transient-transfection CRISPR-Cas9-based epigenetic editing method for the selective de-methylation of the TSDR within the endogenous chromatin environment of a living cell. The induced de-methylated state was stable over weeks in clonal T cell proliferation cultures even after expression of the editing complex had ceased. Epigenetic editing of the TSDR resulted in FOXP3 expression, even in its physiological isoform distribution, proving a causal role for the de-methylated TSDR in FOXP3 regulation. However, successful FOXP3 induction was not associated with a switch towards a functional Treg phenotype, in contrast to what has been reported from FOXP3 overexpression approaches. Thus, TSDR de-methylation is required, but not sufficient for a stable Treg phenotype induction. Therefore, targeted demethylation of the TSDR may be a critical addition to published in vitro Treg induction protocols which so far lack FOXP3 stability.
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Affiliation(s)
- Christopher Kressler
- Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Berlin, Germany.,Immuno-Epigenetics, German Rheumatism Research Centre (DRFZ), Berlin, Germany
| | | | - Karl Nordström
- Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Dania Hamo
- Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Berlin, Germany.,Immuno-Epigenetics, German Rheumatism Research Centre (DRFZ), Berlin, Germany
| | | | | | - Sascha Tierling
- Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Petra Reinke
- Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Hans-Dieter Volk
- Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Jörn Walter
- Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Alf Hamann
- Immuno-Epigenetics, German Rheumatism Research Centre (DRFZ), Berlin, Germany
| | - Julia K Polansky
- Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Berlin, Germany.,Immuno-Epigenetics, German Rheumatism Research Centre (DRFZ), Berlin, Germany.,Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, Berlin, Germany
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17
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Moser DA, Müller S, Hummel EM, Limberg AS, Dieckmann L, Frach L, Pakusch J, Flasbeck V, Brüne M, Beygo J, Klein-Hitpass L, Kumsta R. Targeted bisulfite sequencing: A novel tool for the assessment of DNA methylation with high sensitivity and increased coverage. Psychoneuroendocrinology 2020; 120:104784. [PMID: 32673938 DOI: 10.1016/j.psyneuen.2020.104784] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 05/28/2020] [Accepted: 06/22/2020] [Indexed: 02/06/2023]
Abstract
DNA methylation analysis is increasingly used in stress research. Available methods are expensive, laborious and often limited by either the analysis of short CpG stretches or low assay sensitivity. Here, we present a cost-efficient next generation sequencing-based strategy for the simultaneous investigation of multiple candidate genes in large cohorts. To illustrate the method, we present analysis of four candidate genes commonly assessed in psychoneuroendocrine research: Glucocorticoid receptor (NR3C1), Serotonin transporter (SLC6A4), FKBP Prolyl isomerase 5 (FKBP5), and the Oxytocin receptor (OXTR). DNA methylation standards (100 %; 75 %; 50 %; 25 % and 0 %) and DNA of a female and male donor were bisulfite treated in three independent trials and were used to generate sequencing libraries for 42 CpGs from the NR3C1 1 F promoter region, 84 CpGs of the SLC6A4 5' regulatory region, 5 CpGs located in FKBP5 intron 7, and additional 12 CpGs located in a potential enhancer element in intron 3 of the OXTR. In addition, DNA of 45 patients with borderline personality disorder (BPD) and 45 healthy controls was assayed. Multiplex libraries of all samples were sequenced on a MiSeq system and analyzed for mean methylation values of all CpG sites using amplikyzer2 software. Results indicated excellent accuracy of the assays when investigating replicates generated from the same bisulfite converted DNA, and very high linearity (R2 > 0.9) of the assays shown by the analysis of differentially methylated DNA standards. Comparing DNA methylation between BPD and healthy controls revealed no biologically relevant differences. The technical approach as described here facilitates targeted DNA methylation analysis and represents a highly sensitive, cost-efficient and high throughput tool to close the gap between coverage and precision in epigenetic research of stress-associated phenotypes.
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Affiliation(s)
- D A Moser
- Department of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany.
| | - S Müller
- Department of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany
| | - E M Hummel
- Department of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany
| | - A S Limberg
- Department of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany
| | - L Dieckmann
- Department of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany
| | - L Frach
- Department of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany
| | - J Pakusch
- Department of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany
| | - V Flasbeck
- LWL University Hospital Department of Psychiatry, Psychotherapy and Preventive Medicine, Division of Social Neuropsychiatry and Evolutionary Medicine, Ruhr-University Bochum, Bochum, Germany
| | - M Brüne
- LWL University Hospital Department of Psychiatry, Psychotherapy and Preventive Medicine, Division of Social Neuropsychiatry and Evolutionary Medicine, Ruhr-University Bochum, Bochum, Germany
| | - J Beygo
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - L Klein-Hitpass
- Institute of Cell Biology (Tumor Research), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - R Kumsta
- Department of Genetic Psychology, Faculty of Psychology, Ruhr-University Bochum, Bochum, Germany
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18
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Development and optimization of the VISAGE basic prototype tool for forensic age estimation. Forensic Sci Int Genet 2020; 48:102322. [PMID: 32574993 DOI: 10.1016/j.fsigen.2020.102322] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 04/22/2020] [Accepted: 06/03/2020] [Indexed: 01/03/2023]
Abstract
The VISAGE (VISible Attributes through GEnomics) consortium aims to develop, optimize and validate prototype tools to broaden the use of DNA intelligence methods in forensic routine laboratories. This includes age estimation based on the quantification of DNA methylation at specific CpG sites. Here, we present the VISAGE basic prototype tool for age estimation targeting 32 CpGs from five genes ELOVL2, MIR29B2CHG (herein, MIR29B2C), FHL2, TRIM59 and KLF14. The assay interrogates these well described age markers by multiplex PCR for bisulfite converted DNA and massively parallel sequencing on a MiSeq FGx instrument. We describe protocol optimizations including tests on five bisulfite conversion kits and an evaluation of the assay's reproducibility and sensitivity with artificially methylated DNA standards. We observed robust quantification of methylation levels with a mean standard deviation of 1.4 % across ratios. Sensitivity tests showed no increase of variability down to 20 ng DNA input into bisulfite conversion with a median difference below 1.6 % between technical replicates.
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19
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Lan VTT, Trang VL, Ngan NT, Son HV, Toan NL. An Internal Control for Evaluating Bisulfite Conversion in the Analysis of Short Stature Homeobox 2 Methylation in Lung Cancer. Asian Pac J Cancer Prev 2019; 20:2435-2443. [PMID: 31450918 PMCID: PMC6852808 DOI: 10.31557/apjcp.2019.20.8.2435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 08/01/2019] [Indexed: 12/17/2022] Open
Abstract
Objective: The methylation status is considered as powerful diagnostic, prognostic, and predictive biomarkers. However, the limited DNA amount and conversion efficiency after bisulfite treatment are considerable hindrances in quantitative methylation analysis. In this study, we designed an artificial internal control (IC) system that contained the cytosine-free fragment (CFF) following CpG sequences of the SHOX2 promoter whose methylation status has been described as a valuable biomarker of lung cancer. Its performance in quantifying DNA recovery and bisulfite conversion efficiency as well as in detecting false-positive SHOX2 methylation was determined on samples from lung cancer patients. Material and Methods: The IC system is composed of two pConIC and pUnIC plasmids that both contain a cytosine-free (CF) sequence derived from the CFF and the CpG containing SHOX2 sequences. They are identical in sequence, except that in the ConIC insert, all cytosines have been converted into thymines. Thus, the ConIC can be used as calibrator of 100% bisulfite conversion efficiency, while the UnIC is the indicator in order to evaluate the DNA recovery, bisulfite conversion efficiency of the SHOX2 promoter sequence by quantitative real time PCR. Results: The copy number of the target sequences impacted on both DNA recovery rates and bisulfite conversion efficiency. An amount of 0.005 ng pUnIC (106 copies) showed recovery rate of 18%, similar to that of pConIC, and a bisulfite conversion efficiency of the SHOX2 reaching 98.7%. On the contrary, higher copy number of pUnIC showed incomplete conversion (<85%) and over recovery (~42%). Using this calibrator/indicator couple, we were able to detect false-positive SHOX2 methylation (3.77% instead of 0.03%) due to incomplete bisulfite conversion.Conclusion: Our results proposed a customizable internal control using the ConIC/UnIC as calibrator/indicator to quantify simultaneously and accurately the DNA recovery and bisulfite conversion efficiencies of individual sequence as well as whole genome in methylation assays, thus promoting the validation of standardized clinical DNA methylation biomarker values to progress toward clinical applications
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Affiliation(s)
| | - Vu Lan Trang
- Sorbonne Universités, UPMC Univ. Paris 06, École normale supérieure, PSL Research University, CNRS, INSERM, APHP, Laboratoire des Biomolécules (LBM), Paris, France
| | | | | | - Nguyen Linh Toan
- Department of Pathophysiology, Medical University, Ha Dong, Vietnam
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