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Edelmann S, Balaji J, Pasche S, Wiegand A, Nieratschker V. DNA Methylation of PXDN Is Associated with Early-Life Adversity in Adult Mental Disorders. Biomolecules 2024; 14:976. [PMID: 39199364 DOI: 10.3390/biom14080976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2024] [Revised: 08/01/2024] [Accepted: 08/06/2024] [Indexed: 09/01/2024] Open
Abstract
Early-life adversity (ELA) is characterized by exposure to traumatic events during early periods of life, particularly involving emotional, sexual and/or physical adversities during childhood. Mental disorders are strongly influenced by environmental and lifestyle-related risk factors including ELA. However, the molecular link between ELA and the risk of an adult mental disorder is still not fully understood. Evidence is emerging that long-lasting changes in the epigenetic processes regulating gene expression, such as DNA methylation, play an important role in the biological mechanisms linking ELA and mental disorders. Based on a recent study, we analyzed the DNA methylation of a specific CpG site within the gene PXDN-cg10888111-in blood in the context of ELA across a set of psychiatric disorders, namely Borderline Personality Disorder (BPD), Major Depressive Disorder (MDD) and Social Anxiety Disorder (SAD), and its potential contribution to their pathogenesis. We found significant hypermethylation in mentally ill patients with high levels of ELA compared to patients with low levels of ELA, whereas cg10888111 methylation in healthy control individuals was not affected by ELA. Further investigations revealed that this effect was driven by the MDD cohort. Providing a direct comparison of cg10888111 DNA methylation in blood in the context of ELA across three mental disorders, our results indicate the role of PXDN regulation in the response to ELA in the pathogenesis of mental disorders, especially MDD. Further studies will be needed to validate these results and decipher the corresponding biological network that is involved in the transmission of ELA to an adult mental disorder in general.
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Affiliation(s)
- Susanne Edelmann
- Department of Psychiatry and Psychotherapy, University Hospital of Tuebingen, Eberhard Karls University of Tuebingen, 72076 Tuebingen, Germany
- German Center for Mental Health (DZPG), Partner Site Tuebingen, 72076 Tuebingen, Germany
| | - Jeysri Balaji
- Department of Psychiatry and Psychotherapy, University Hospital of Tuebingen, Eberhard Karls University of Tuebingen, 72076 Tuebingen, Germany
| | - Sarah Pasche
- Department of Psychiatry and Psychotherapy, University Hospital of Tuebingen, Eberhard Karls University of Tuebingen, 72076 Tuebingen, Germany
| | - Ariane Wiegand
- Max Planck Fellow Group Precision Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany
- Department of Psychiatry and Psychotherapy, LMU University Hospital, LMU Munich, 80336 Munich, Germany
| | - Vanessa Nieratschker
- Department of Psychiatry and Psychotherapy, University Hospital of Tuebingen, Eberhard Karls University of Tuebingen, 72076 Tuebingen, Germany
- German Center for Mental Health (DZPG), Partner Site Tuebingen, 72076 Tuebingen, Germany
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2
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Trentin L, Basile D, Lazzari E, Fietta E, Rossi A, Graziani F, Cappetta A, Simionato F, D'Amore E, Perbellini O, Aprile G. Implementation of a MSRE ddPCR method for the detection of methylated WIF1 and NPY genes in colorectal cancer patients. TUMORI JOURNAL 2024:3008916241261675. [PMID: 39101541 DOI: 10.1177/03008916241261675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
BACKGROUND Colorectal cancer is a worldwide leading cause of death accounting for high-rate mortality. Mutations in the epidermal growth factor receptor and RAS/MAPK pathways, as well as altered methylation genes profiles, have been described as molecular mechanisms promoting and sustaining tumour development and progression. Aberrant methylation is a well-known epigenetic mechanism involved in gene regulation; particularly several genes were reported as hypermethylated in CRC. Recently, it was shown that epigenetic alterations in genes such as neuropeptide y, proenkephalin and Wnt inhibitory factor 1 can be used as promising disease biomarkers. Almost all methods developed for the DNA methylation analysis combined next generation sequencing, conventional qRT-PCR or ddPCR with the prior DNA modification with sodium bisulfite. METHODS AND RESULTS We implemented a ddPCR method to assess the methylation status of Wnt inhibitory factor 1 and neuropeptide y using the methylation sensitive restriction enzyme approach that does not impact on DNA quality and guarantees the discrimination of DNA methylation independent of bisulfite conversion. CONCLUSIONS We showed that this method is robust and sensitive also allowing the monitoring of CRC disease progression when applied to circulating free DNA samples from liquid biopsies, proving to be a fast and easy to implement assay to be used for the monitoring of the methylation pattern of clinically relevant target genes.
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Affiliation(s)
- Luca Trentin
- AULSS 8 Berica Ospedale San Bortolo, Laboratory of Haematology, Vicenza, Italy
- AULSS 2 Marca Trevigiana, Histocompatibility Laboratory, Treviso, Italy
| | - Debora Basile
- AULSS 8 Berica Ospedale San Bortolo, UOC Oncologia, Vicenza, Italy
- Unit of Medical Oncology, Ospedale San Giovanni di Dio, Crotone, Italy
| | - Elena Lazzari
- AULSS 8 Berica Ospedale San Bortolo, UOC Anatomia Patologica, Vicenza, Italy
| | - Elena Fietta
- AULSS 8 Berica Ospedale San Bortolo, Laboratory of Haematology, Vicenza, Italy
| | - Alice Rossi
- AULSS 8 Berica Ospedale San Bortolo, UOC Oncologia, Vicenza, Italy
| | | | | | | | - Emanuele D'Amore
- AULSS 8 Berica Ospedale San Bortolo, UOC Anatomia Patologica, Vicenza, Italy
| | - Omar Perbellini
- AULSS 8 Berica Ospedale San Bortolo, Laboratory of Haematology, Vicenza, Italy
| | - Giuseppe Aprile
- AULSS 8 Berica Ospedale San Bortolo, UOC Oncologia, Vicenza, Italy
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3
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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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4
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So MH, Lee JE, Lee HY. Strategies to deal with genetic analyzer-specific DNA methylation measurements. Electrophoresis 2024; 45:906-915. [PMID: 38488745 DOI: 10.1002/elps.202300185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 02/25/2024] [Accepted: 03/02/2024] [Indexed: 05/23/2024]
Abstract
Targeted bisulfite sequencing using single-base extension (SBE) can be used to measure DNA methylation via capillary electrophoresis on genetic analyzers in forensic labs. Several accurate age prediction models have been reported using this method. However, using different genetic analyzers with different software settings can generate different methylation values, leading to significant errors in age prediction. To address this issue, the study proposes and compares four methods as follows: (1) adjusting methylation values using numerous actual body fluid DNA samples, (2) adjusting methylation values using control DNAs with varying methylation ratios, (3) constructing new age prediction models for each genetic analyzer type, and (4) constructing new age prediction models that could be applied to all types of genetic analyzers. To test the methods for adjusting values using actual body fluid DNA samples, previously reported adjusting equations were used for blood/saliva DNA age prediction markers (ELOVL2, FHL2, KLF14, MIR29B2CHG/C1orf132, and TRIM59). New equations were generated for semen DNA age prediction markers (TTC7B, LOC401324/cg12837463, and LOC729960/NOX4) by drawing polynomial regression lines between the results of the three types of genetic analyzers (3130, 3500, and SeqStudio). The same method was applied to obtain adjustment equations using 11 control DNA samples. To develop new age prediction models for each genetic analyzer type, linear regression analysis was conducted using DNA methylation data from 150 blood, 150 saliva, and 62 semen samples. For the genetic analyzer-independent models, control DNAs were used to formulate equations for calibrating the bias of the data from each genetic analyzer, and linear regression analysis was performed using calibrated body fluid DNA data. In the comparison results, the genetic analyzer-specific models showed the highest accuracy. However, genetic analyzer-independent models through bias adjustment also provided accurate age prediction results, suggesting its use as an alternative in situations with multiple constraints.
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Affiliation(s)
- Moon Hyun So
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Ji Eun Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Hwan Young Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, South Korea
- Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, South Korea
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5
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Li Z, Liu N, Yuan F, Guan Z, Liu J, Liu F, Ren J, Yan J, Zhang G. Development of a novel panel for blood identification based on blood-specific CpG-linked SNP markers. Int J Legal Med 2024; 138:1205-1219. [PMID: 37853302 DOI: 10.1007/s00414-023-03105-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 09/27/2023] [Indexed: 10/20/2023]
Abstract
Blood-containing mixtures often appear in murder and robbery cases, and their identification plays a significant role in solving crimes. In recent years, the co-detection of DNA methylation markers (CpG) and single nucleotide polymorphism (SNP) markers has been shown to be a promising tool for the identification of semen and its donor. However, similar research on blood stains that are frequently found at crime scenes has not yet been reported. In this study, we employed blood-specific CpG-linked SNP markers (CpG-SNP) for blood-specific genotyping and the linking of blood and its donor. The tissue-specific CpG markers were screened from the literature and further verified by combining bisulfite conversion with amplification-refractory mutation system (ARMS) technology. Meanwhile, adjacent SNP markers with a minor allele frequency (MAF) greater than 0.1 were selected within 400 bp upstream and downstream of the CpG markers. SNP genotyping was performed using SNaPshot technology on a capillary electrophoresis (CE) platform. Finally, a multiplex panel, including 19 blood-specific CpG linked to 23 SNP markers, as well as 1 semen-specific CpG, 1 vaginal secretion-specific CpG, and 1 saliva-specific CpG marker, was constructed successfully. The panel showed good tissue specificity and blood stains stored at room temperature for up to nine months and moderately degraded (4 < DI < 10) could be effectively identified. Moreover, it could also be detected when blood content in the mixed stains was as low as 1%. In addition, 15 ng of DNA used for bisulfite conversion was required for obtaining a complete profile. The cumulative discrimination power of the panel among the Han population of northern China could reach 0.999983. This is the first investigation conducted for the simultaneous identification of blood and its donor regardless of other body fluids included in mixed stains. The successful construction of the panel will play a vital role in the comprehensive analysis of blood-containing mixtures in forensic practice.
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Affiliation(s)
- Zeqin Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, China
| | - Na Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, China
| | - Fang Yuan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, China
| | - Zimeng Guan
- Department of Biotechnology, Biomedical Sciences College, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250117, Shandong, China
| | - Jinding Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, China
| | - Feng Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, China
| | - Jianbo Ren
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, China.
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, China.
| | - Gengqian Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, China.
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, China.
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6
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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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7
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Davydova E, Perenkov A, Vedunova M. Building Minimized Epigenetic Clock by iPlex MassARRAY Platform. Genes (Basel) 2024; 15:425. [PMID: 38674360 PMCID: PMC11049545 DOI: 10.3390/genes15040425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Epigenetic clocks are valuable tools for estimating both chronological and biological age by assessing DNA methylation levels at specific CpG dinucleotides. While conventional epigenetic clocks rely on genome-wide methylation data, targeted approaches offer a more efficient alternative. In this study, we explored the feasibility of constructing a minimized epigenetic clock utilizing data acquired through the iPlex MassARRAY technology. The study enrolled a cohort of relatively healthy individuals, and their methylation levels of eight specific CpG dinucleotides in genes SLC12A5, LDB2, FIGN, ACSS3, FHL2, and EPHX3 were evaluated using the iPlex MassARRAY system and the Illumina EPIC array. The methylation level of five studied CpG sites demonstrated significant correlations with chronological age and an acceptable convergence of data obtained by the iPlex MassARRAY and Illumina EPIC array. At the same time, the methylation level of three CpG sites showed a weak relationship with age and exhibited a low concordance between the data obtained from the two technologies. The construction of the epigenetic clock involved the utilization of different machine-learning models, including linear models, deep neural networks (DNN), and gradient-boosted decision trees (GBDT). The results obtained from these models were compared with each other and with the outcomes generated by other well-established epigenetic clocks. In our study, the TabNet architecture (deep tabular data learning architecture) exhibited the best performance (best MAE = 5.99). Although our minimized epigenetic clock yielded slightly higher age prediction errors compared to other epigenetic clocks, it still represents a viable alternative to the genome-wide epigenotyping array.
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Affiliation(s)
- Ekaterina Davydova
- Institute of Biology and Biomedicine, Lobachevsky State University, 23 Gagarin Ave., Nizhny Novgorod 603022, Russia (M.V.)
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8
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Turiello R, Nouwairi RL, Keller J, Cunha LL, Dignan LM, Landers JP. A rotationally-driven dynamic solid phase sodium bisulfite conversion disc for forensic epigenetic sample preparation. LAB ON A CHIP 2023; 24:97-112. [PMID: 38019115 DOI: 10.1039/d3lc00867c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
The approaches to forensic human identification (HID) are largely comparative in nature, relying upon the comparison of short tandem repeat profiles to known reference materials and/or database profiles. However, many profiles are generated from evidence materials that either do not have a reference material for comparison or do not produce a database hit. As an alternative to individualizing analysis for HID, researchers of forensic DNA have demonstrated that the human epigenome can provide a wealth of information. However, epigenetic analysis requires sodium b̲is̲ulfite c̲onversion (BSC), a sample preparation method that is time-consuming, labor-intensive, prone to contamination, and characterized by DNA loss and fragmentation. To provide an alternative method for BSC that is more amenable to integration with the forensic DNA workflow, we describe a rotationally-driven, microfluidic method for dynamic solid phase-BSC (dSP-BSC) that streamlines the sample preparation process in an automated format, capable of preparing up to four samples in parallel. The method permitted decreased incubation intervals by ∼36% and was assessed for relative DNA recovery and conversion efficiency and compared to gold-standard and enzymatic approaches.
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Affiliation(s)
- R Turiello
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.
| | - R L Nouwairi
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.
| | - J Keller
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.
| | - L L Cunha
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.
| | - L M Dignan
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.
| | - J P Landers
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA.
- Department of Mechanical Engineering, University of Virginia, Charlottesville, VA, USA
- Department of Pathology, University of Virginia, Charlottesville, VA, USA
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9
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Xiao C, Li Y, Chen M, Yi S, Huang D. Improved age estimation from semen using sperm-specific age-related CpG markers. Forensic Sci Int Genet 2023; 67:102941. [PMID: 37820545 DOI: 10.1016/j.fsigen.2023.102941] [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: 05/10/2023] [Revised: 08/25/2023] [Accepted: 10/02/2023] [Indexed: 10/13/2023]
Abstract
Accurate age estimation from semen has the potential to greatly narrow the pool of unidentified suspects in sexual assault investigations. However, previous efforts utilizing semen age-related CpG (AR-CpG) markers have shown lower accuracy compared to blood AR-CpG-based methods. This discrepancy may be attributed to DNA methylation (DNAm) interferences from "round cells" such as leukocytes and immature sperm cells in semen. This study aimed to develop age calculators based on sperm-specific AR-CpG markers and to achieve performance-improved age estimates from sperm DNA. Through an analysis of publicly available MethylationEPIC microarray data from 90 sperm samples of healthy males aged 22-51 years, we identified 31 sperm-specific AR-CpG markers with absolute Pearson's R values > 0.5 and Benjamini-Hochberg adjusted p values < 0.013. The top 19 AR-CpG markers with the largest absolute R values and beta ranges > 0.10, along with 3 reported semen AR-CpG markers (cg06304190, cg06979108, and cg12837463), were integrated into two methylation SNaPshot panels (Ⅰ and Ⅱ), each containing 11 markers. The 21 qualified AR-CpG markers showed absolute R values ≥ 0.427 in an independent validation cohort of 253 sperm DNA samples (22-67 years), with cg21843517 exhibiting the strongest age correlation (R = 0.853). The optimal models, constructed using sperm DNAm data of the training set (n = 214, 22-67 years) and markers from panel Ⅰ (n = 11), panel Ⅱ (n = 10), or both panels, achieved mean absolute errors (MAEs) of 2.526-4.746, 3.890-5.715, and > 9.800 years on the test sets of sperm (n = 39, 23-64 years), semen (same donors as the sperm test set), and whole blood (n = 40, 22-65 years), respectively. The simplified models incorporating 3, 5, 9, or 14 AR-CpG markers (MAE = 2.918-4.139 years for sperm) still outperformed the Lee et al. original model (MAE = 6.444 years for semen) and the reconstructed panel Lee model (MAE = 6.011 years for sperm). The final models, utilizing all sperm DNAm data (n = 253) and markers from panel Ⅰ, panel Ⅱ, or both panels, yielded mean MAEs of 2.587, 2.766, and 2.200 years, respectively, on the 50 test sets generated by 5 repeats of 10-fold cross-validations. Additionally, multiple markers in both panels demonstrated the ability to discern sperm or semen from blood with 100% accuracy. In summary, our study substantiates the potential of sperm-specific AR-CpG markers for precise age estimation from sperm DNA, providing an improved toolset for forensic investigations.
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Affiliation(s)
- Chao Xiao
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China; Hubei Key Laboratory of the Forensic Science, Hubei University of Police, Wuhan, Hubei 430035, PR China.
| | - Ya Li
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Maomin Chen
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Shaohua Yi
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China
| | - Daixin Huang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, PR China.
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10
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Schall PZ, Winkler PA, Petersen-Jones SM, Yuzbasiyan-Gurkan V, Kidd JM. Genome-wide methylation patterns from canine nanopore assemblies. G3 (BETHESDA, MD.) 2023; 13:jkad203. [PMID: 37681359 PMCID: PMC10627269 DOI: 10.1093/g3journal/jkad203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/23/2023] [Accepted: 08/29/2023] [Indexed: 09/09/2023]
Abstract
Recent advances in long-read sequencing have enabled the creation of reference-quality genome assemblies for multiple individuals within a species. In particular, 8 long-read genome assemblies have recently been published for the canine model (dogs and wolves). These assemblies were created using a range of sequencing and computational approaches, with only limited comparisons described among subsets of the assemblies. Here we present 3 high-quality de novo reference assemblies based upon Oxford Nanopore long-read sequencing: 2 Bernese Mountain Dogs (BD & OD) and a Cairn terrier (CA611). These breeds are of particular interest due to the enrichment of unresolved genetic disorders. Leveraging advancement in software technologies, we utilized published data of Labrador Retriever (Yella) to generate a new assembly, resulting in a ∼280-fold increase in continuity (N50 size of 91 kbp vs 25.75 Mbp). In conjunction with these 4 new assemblies, we uniformly assessed 8 existing assemblies for generalized quality metrics, sequence divergence, and a detailed BUSCO assessment. We identified a set of ∼400 conserved genes during the BUSCO analysis missing in all assemblies. Genome-wide methylation profiles were generated from the nanopore sequencing, resulting in broad concordance with existing whole-genome and reduced-representation bisulfite sequencing, while highlighting superior overage of mobile elements. These analyses demonstrate the ability of Nanopore sequencing to resolve the sequence and epigenetic profile of canine genomes.
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Affiliation(s)
- Peter Z Schall
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Paige A Winkler
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Simon M Petersen-Jones
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Vilma Yuzbasiyan-Gurkan
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA
- Department of Microbiology and Molecular Genetics, College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
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11
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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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12
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Eagles NJ, Wilton R, Jaffe AE, Collado-Torres L. BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data. BMC Bioinformatics 2023; 24:340. [PMID: 37704947 PMCID: PMC10498615 DOI: 10.1186/s12859-023-05461-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 08/31/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND Bisulfite sequencing is a powerful tool for profiling genomic methylation, an epigenetic modification critical in the understanding of cancer, psychiatric disorders, and many other conditions. Raw data generated by whole genome bisulfite sequencing (WGBS) requires several computational steps before it is ready for statistical analysis, and particular care is required to process data in a timely and memory-efficient manner. Alignment to a reference genome is one of the most computationally demanding steps in a WGBS workflow, taking several hours or even days with commonly used WGBS-specific alignment software. This naturally motivates the creation of computational workflows that can utilize GPU-based alignment software to greatly speed up the bottleneck step. In addition, WGBS produces raw data that is large and often unwieldy; a lack of memory-efficient representation of data by existing pipelines renders WGBS impractical or impossible to many researchers. RESULTS We present BiocMAP, a Bioconductor-friendly methylation analysis pipeline consisting of two modules, to address the above concerns. The first module performs computationally-intensive read alignment using Arioc, a GPU-accelerated short-read aligner. Since GPUs are not always available on the same computing environments where traditional CPU-based analyses are convenient, the second module may be run in a GPU-free environment. This module extracts and merges DNA methylation proportions-the fractions of methylated cytosines across all cells in a sample at a given genomic site. Bioconductor-based output objects in R utilize an on-disk data representation to drastically reduce required main memory and make WGBS projects computationally feasible to more researchers. CONCLUSIONS BiocMAP is implemented using Nextflow and available at http://research.libd.org/BiocMAP/ . To enable reproducible analysis across a variety of typical computing environments, BiocMAP can be containerized with Docker or Singularity, and executed locally or with the SLURM or SGE scheduling engines. By providing Bioconductor objects, BiocMAP's output can be integrated with powerful analytical open source software for analyzing methylation data.
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Affiliation(s)
- Nicholas J Eagles
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, 21205, USA
| | - Richard Wilton
- Department of Physics and Astronomy, Johns Hopkins University, Baltimore, 21218, USA
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, 21205, USA
| | - Leonardo Collado-Torres
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, 21205, USA.
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13
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Bendixen KK, Mindegaard M, Epistolio S, Dazio G, Marchi F, Spina P, Arnspang EC, Soerensen M, Christensen UB, Frattini M, Petersen RK. A qPCR technology for direct quantification of methylation in untreated DNA. Nat Commun 2023; 14:5153. [PMID: 37620381 PMCID: PMC10449789 DOI: 10.1038/s41467-023-40873-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023] Open
Abstract
DNA methylation is important for gene expression and alterations in DNA methylation are involved in the development and progression of cancer and other major diseases. Analysis of DNA methylation patterns has until now been dependent on either a chemical or an enzymatic pre-treatment, which are both time consuming procedures and potentially biased due to incomplete treatment. We present a qPCR technology, EpiDirect®, that allows for direct PCR quantification of DNA methylations using untreated DNA. EpiDirect® is based on the ability of Intercalating Nucleic Acids (INA®) to differentiate between methylated and unmethylated cytosines in a special primer design. With this technology, we develop an assay to analyze the methylation status of a region of the MGMT promoter used in treatment selection and prognosis of glioblastoma patients. We compare the assay to two bisulfite-relying, methyl-specific PCR assays in a study involving 42 brain tumor FFPE samples, revealing high sensitivity, specificity, and the clinical utility of the method.
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Affiliation(s)
- Kamilla Kolding Bendixen
- PentaBase A/S, Odense, Denmark.
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark.
| | | | - Samantha Epistolio
- Laboratory of Molecular Pathology, Institute of Pathology, Ente Ospedaliero Cantonale (EOC), Locarno, Switzerland
| | - Giulia Dazio
- Laboratory of Molecular Pathology, Institute of Pathology, Ente Ospedaliero Cantonale (EOC), Locarno, Switzerland
| | - Francesco Marchi
- Service of Neurosurgery, Neurocenter of the Southern Switzerland, Regional Hospital of Lugano, Lugano, Switzerland
| | - Paolo Spina
- Laboratory of Molecular Pathology, Institute of Pathology, Ente Ospedaliero Cantonale (EOC), Locarno, Switzerland
- Department of Health Sciences, University of Eastern Piedmont, Novara, Italy
| | - Eva C Arnspang
- Department of Green Technology, University of Southern Denmark, Odense, Denmark
| | - Mette Soerensen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | | | - Milo Frattini
- Laboratory of Molecular Pathology, Institute of Pathology, Ente Ospedaliero Cantonale (EOC), Locarno, Switzerland
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14
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Mayne B, Espinoza T, Crook DA, Anderson C, Korbie D, Marshall JC, Kennard MJ, Harding DJ, Butler GL, Roberts B, Whiley J, Marshall S. Accurate, non-destructive, and high-throughput age estimation for Golden perch (Macquaria ambigua spp.) using DNA methylation. Sci Rep 2023; 13:9547. [PMID: 37308782 PMCID: PMC10260977 DOI: 10.1038/s41598-023-36773-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 06/09/2023] [Indexed: 06/14/2023] Open
Abstract
Age structure information of animal populations is fundamental to their conservation and management. In fisheries, age is routinely obtained by counting daily or annual increments in calcified structures (e.g., otoliths) which requires lethal sampling. Recently, DNA methylation has been shown to estimate age using DNA extracted from fin tissue without the need to kill the fish. In this study we used conserved known age-associated sites from the zebrafish (Danio rerio) genome to predict the age of golden perch (Macquaria ambigua), a large-bodied native fish from eastern Australia. Individuals aged using validated otolith techniques from across the species' distribution were used to calibrate three epigenetic clocks. One clock was calibrated using daily (daily clock) and another with annual (annual clock) otolith increment counts, respectively. A third used both daily and annual increments (universal clock). We found a high correlation between the otolith and epigenetic age (Pearson correlation > 0.94) across all clocks. The median absolute error was 2.4 days in the daily clock, 184.6 days in the annual clock, and 74.5 days in the universal clock. Our study demonstrates the emerging utility of epigenetic clocks as non-lethal and high-throughput tools for obtaining age estimates to support the management of fish populations and fisheries.
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Affiliation(s)
- Benjamin Mayne
- Environomics Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Indian Ocean Marine Research Centre, Crawley, WA, Australia.
| | - Tom Espinoza
- Department of Regional Development, Manufacturing and Water, Brisbane, QLD, Australia
| | - David A Crook
- Department of Primary Industries, Narrandera Fisheries Centre, Narrandera, NSW, Australia
| | - Chloe Anderson
- Environomics Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Indian Ocean Marine Research Centre, Crawley, WA, Australia
| | - Darren Korbie
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Jonathan C Marshall
- Queensland Department of Environment and Science, Brisbane, QLD, Australia
- Australian Rivers Institute and Griffith School of Environment and Science, Griffith University, Nathan, QLD, 4111, Australia
| | - Mark J Kennard
- Australian Rivers Institute and Griffith School of Environment and Science, Griffith University, Nathan, QLD, 4111, Australia
| | - Doug J Harding
- Department of Regional Development, Manufacturing and Water, Brisbane, QLD, Australia
| | - Gavin L Butler
- NSW Department of Primary Industries (Fisheries), Grafton, NSW, Australia
| | - Brien Roberts
- Fisheries Division, Department of Industry, Tourism and Trade, Darwin, NT, Australia
| | - Josh Whiley
- Australian Rivers Institute and Griffith School of Environment and Science, Griffith University, Nathan, QLD, 4111, Australia
| | - Sharon Marshall
- Department of Regional Development, Manufacturing and Water, Brisbane, QLD, Australia
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15
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Refn MR, Kampmann ML, Morling N, Tfelt-Hansen J, Børsting C, Pereira V. Prediction of chronological age and its applications in forensic casework: methods, current practices, and future perspectives. Forensic Sci Res 2023; 8:85-97. [PMID: 37621446 PMCID: PMC10445583 DOI: 10.1093/fsr/owad021] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/28/2023] [Indexed: 08/26/2023] Open
Abstract
Estimating an individual's age can be relevant in several areas primarily related to the clinical and forensic fields. In the latter, estimation of an individual's chronological age from biological material left by the perpetrator at a crime scene may provide helpful information for police investigation. Estimation of age is also beneficial in immigration cases, where age can affect the person's protection status under the law, or in disaster victim identification to narrow the list of potential missing persons. In the last decade, research has focused on establishing new approaches for age prediction in the forensic field. From the first forensic age estimations based on morphological inspections of macroscopic changes in bone and teeth, the focus has shifted to molecular methods for age estimation. These methods allow the use of samples from human biological material that does not contain morphological age features and can, in theory, be investigated in traces containing only small amounts of biological material. Molecular methods involving DNA analyses are the primary choice and estimation of DNA methylation levels at specific sites in the genome is the most promising tool. This review aims to provide an overview of the status of forensic age prediction using molecular methods, with particular focus in DNA methylation. The frequent challenges that impact forensic age prediction model development will be addressed, together with the importance of validation efforts within the forensic community.
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Affiliation(s)
- Mie Rath Refn
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marie-Louise Kampmann
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jacob Tfelt-Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen , Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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16
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Yu S, Cao S, He S, Zhang K. Locus-Specific Detection of DNA Methylation: The Advance, Challenge, and Perspective of CRISPR-Cas Assisted Biosensors. SMALL METHODS 2023; 7:e2201624. [PMID: 36609885 DOI: 10.1002/smtd.202201624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Indexed: 06/17/2023]
Abstract
Deoxyribonucleic acid (DNA) methylation is one of the epigenetic characteristics that result in heritable and revisable phenotype changes but without sequence changes in DNA. Aberrant methylation occurring at a specific locus was reported to be associated with cancers, insulin resistance, obesity, Alzheimer's disease, Parkinson's disease, etc. Therefore, locus-specific DNA methylation can serve as a valuable biomarker for disease diagnosis and therapy. Recently, Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems are applied to develop biosensors for DNA, ribonucleic acid, proteins, and small molecules detection. Because of their highly specific binding ability and signal amplification capacity, CRISPR-Cas assisted biosensor also serve as a potential tool for locus-specific detection of DNA methylation. In this perspective, based on the detection principle, a detailed classification and comprehensive discussion of recent works about the latest advances in locus-specific detection of DNA methylation using CRISPR-Cas systems are provided. Furthermore, current challenges and future perspectives of CRISPR-based locus-specific detection of DNA methylation are outlined.
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Affiliation(s)
- Songcheng Yu
- College of Public Health, Zhengzhou University, No.100 Science Avenue, Zhengzhou City, 450001, P. R. China
| | - Shengnan Cao
- College of Public Health, Zhengzhou University, No.100 Science Avenue, Zhengzhou City, 450001, P. R. China
| | - Sitian He
- College of Public Health, Zhengzhou University, No.100 Science Avenue, Zhengzhou City, 450001, P. R. China
| | - Kaixiang Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, No.100 Science Avenue, Zhengzhou City, 450001, P. R. China
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17
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Silva C, Machado M, Ferrão J, Sebastião Rodrigues A, Vieira L. Whole human genome 5'-mC methylation analysis using long read nanopore sequencing. Epigenetics 2022; 17:1961-1975. [PMID: 35856633 DOI: 10.1080/15592294.2022.2097473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Methylation microarray and bisulphite sequencing are often used to study 5'-methylcytosine (5'-mC) modification of CpG dinucleotides in the human genome. Although both technologies produce trustworthy results, the evaluation of the methylation status of CpG sites suffers from the potential side effects of DNA modification by bisulphite and/or the ambiguity of mapping short reads in repetitive and highly homologous genomic regions, respectively. Nanopore sequencing is an attractive alternative for the study of 5'-mC since it allows sequencing of native DNA molecules, whereas the long reads produced by this technology help to increase the resolution of those genomic regions. In this work, we show that nanopore sequencing with 10X coverage depth, using DNA from a human cell line, produces 5'-mC methylation frequencies consistent with those obtained by 450k microarray, digital restriction enzyme analysis of methylation, and reduced representation bisulphite sequencing. High correlation between methylation frequencies obtained by nanopore sequencing and the other methodologies was also noticeable in either low or high GC content regions, including CpG islands and transcription start sites. We also showed that a minimum of five reads per CpG yields strong correlations (>0.89) in replicate nanopore sequencing runs and an almost uniform linearity of the methylation frequency variation between zero and one. Furthermore, nanopore sequencing was able to correctly display methylation frequency patterns based on genomic annotations of CpG regions. These results demonstrate that nanopore sequencing is a fast, robust, and reliable approach to the study of 5'-mC in the human genome with low coverage depth.
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Affiliation(s)
- Catarina Silva
- Inovação, Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo JorgeUnidade de Tecnologia e , Lisboa, Portugal.,Saúde Humana (ToxOmics), NOVA Medical School
- Faculdade de Ciências Médicas, Universidade Nova de LisboaCentro de Toxicogenómica e , Lisboa, Portugal
| | - Miguel Machado
- Inovação, Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo JorgeUnidade de Tecnologia e , Lisboa, Portugal
| | - José Ferrão
- Inovação, Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo JorgeUnidade de Tecnologia e , Lisboa, Portugal
| | - António Sebastião Rodrigues
- Saúde Humana (ToxOmics), NOVA Medical School
- Faculdade de Ciências Médicas, Universidade Nova de LisboaCentro de Toxicogenómica e , Lisboa, Portugal
| | - Luís Vieira
- Inovação, Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo JorgeUnidade de Tecnologia e , Lisboa, Portugal.,Saúde Humana (ToxOmics), NOVA Medical School
- Faculdade de Ciências Médicas, Universidade Nova de LisboaCentro de Toxicogenómica e , Lisboa, Portugal
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18
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Yin Q, Qiao R, Xu T, Dai L, Han B, Gu W, Yang R. The influence of blood sample processing on blood-based DNA methylation signatures. Clin Biochem 2022; 115:116-125. [PMID: 35787405 DOI: 10.1016/j.clinbiochem.2022.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/07/2022] [Accepted: 06/29/2022] [Indexed: 11/03/2022]
Abstract
Stability is crucial for the clinical applicable biomarker such as DNA methylation profiles. However, the influence of various blood processing on the DNA methylation signatures have been barely studied. Here, we systematically evaluated the impact of temporary storage and frozen and thaw on the levels of DNA methylation. The methylation intensities of 13 CpG loci from 53 individuals (42 healthy participants and 11 lung cancer patients) whose blood samples were processed by up to 14 various protocols were quantitatively determined by the mass spectrometry, obtaining more than 8,000 quantitative data. We disclosed a trend of accumulatively increased DNA methylation along with time when the blood from healthy people were stored for up to 96 hours at room temperature (RT), whereas the storage at 4℃ had much weaker effects or no impact. On the contrary, the methylation patterns in the blood of lung cancer patients were more stable at both RT and 4℃ even for 96 hours. Multiple cycles of frozen and thaw could result in demethylation, but was more significant to the blood than to the extracted DNA. Our study indicated that the blood processing in vitro could influence the DNA methylation signatures and introduce unexpected biases.
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Affiliation(s)
- Qiming Yin
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Rong Qiao
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Tian Xu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Baohui Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, China
| | - Rongxi Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, China.
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19
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Harrison MC, Dohmen E, George S, Sillam-Dussès D, Séité S, Vasseur-Cognet M. Complex regulatory role of DNA methylation in caste- and age-specific expression of a termite. Open Biol 2022; 12:220047. [PMID: 35857972 PMCID: PMC9256085 DOI: 10.1098/rsob.220047] [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] [Indexed: 12/25/2022] Open
Abstract
The reproductive castes of eusocial insects are often characterized by extreme lifespans and reproductive output, indicating an absence of the fecundity/longevity trade-off. The role of DNA methylation in the regulation of caste- and age-specific gene expression in eusocial insects is controversial. While some studies find a clear link to caste formation in honeybees and ants, others find no correlation when replication is increased across independent colonies. Although recent studies have identified transcription patterns involved in the maintenance of high reproduction throughout the long lives of queens, the role of DNA methylation in the regulation of these genes is unknown. We carried out a comparative analysis of DNA methylation in the regulation of caste-specific transcription and its importance for the regulation of fertility and longevity in queens of the higher termite Macrotermes natalensis. We found evidence for significant, well-regulated changes in DNA methylation in mature compared to young queens, especially in several genes related to ageing and fecundity in mature queens. We also found a strong link between methylation and caste-specific alternative splicing. This study reveals a complex regulatory role of fat body DNA methylation both in the division of labour in termites, and during the reproductive maturation of queens.
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Affiliation(s)
- Mark C. Harrison
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Elias Dohmen
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | | | - David Sillam-Dussès
- University Sorbonne Paris Nord, Laboratory of Experimental and Comparative Ethology (LEEC), UR4443, Villetaneuse, France
| | - Sarah Séité
- UMR IRD 242, UPEC, CNRS 7618, UPMC 113, INRAE 1392, Institute of Ecology and Environmental Sciences of Paris, Paris 7 113, Bondy, France,University of Paris-Est, Créteil, France
| | - Mireille Vasseur-Cognet
- UMR IRD 242, UPEC, CNRS 7618, UPMC 113, INRAE 1392, Institute of Ecology and Environmental Sciences of Paris, Paris 7 113, Bondy, France,University of Paris-Est, Créteil, France,INSERM, Paris, France
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20
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Mpundu P, Muma JB, Mukumbuta N, Mukubesa AN, Muleya W, Kapila P, Hang'ombe BM, Munyeme M. Isolation, discrimination, and molecular detection of Listeria species from slaughtered cattle in Namwala District, Zambia. BMC Microbiol 2022; 22:160. [PMID: 35717165 PMCID: PMC9206240 DOI: 10.1186/s12866-022-02570-6] [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: 05/27/2021] [Accepted: 04/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The food industry is increasingly becoming more scrutinized, given the frequency and intensity with which zoonotic diseases are being reported. Pathogen tracking has become more applicable with regards food safety. It is in this regard that the present study was formulated to track Listeria species. in freshly slaughtered cattle carcasses by utilizing standard and molecular biological techniques. METHODS A cross-sectional study design was conducted from March to December 2020 with 200 samples being equally collected in the rainy and dry seasons. A total of 180 and 20 swabs were aseptically collected from carcasses and the environment respectively. Samples were first subjected to pre-enrichment in half-strength Fraser broth followed by enrichment in full strength Fraser broth and subsequent plating on Listeria agar. Listeria growth characteristics were identified up to species level based on their morphological and biochemical characteristics. Further, molecular detection and phylogenetic analysis was conducted. Quantitative proportionate survey data were analyzed using Stata Version 15 software to estimate crude prevalence taking into account complex design at abattoir level. Factors associated with contamination were characterized using logistic regression. Sequences were analyzed using, Genetyyx version 12 and phylogenetic Mega. RESULTS Of the 200 samples, 19 were positive for Listeria species identified as L.innocua 14/19 (73.7%) and L. monocytogenes 5/19 (26.3%). All isolates were from freshly slaughtered carcasses, and none from environment. Siginificant differences in contamination levels were observed based on season: rainy season yielded 14 (73.6%) whilst the dry season 5 (26.3%). The L. monocytogenes strains showed a high degree of homogeneity on phylogenetic analysis and clustered based on abattoir. Seasonality was identified as a major determinant influencing contamination based on the final logistic regression model. CONCLUSION This study found evidence of L. monocytogenes contamination on traditionally raised beef carcasses across various abattoirs surveyed. The failure to find Listeria contamination on the abattoir environment may to a greater extent intimate cattle carccases as primary sources of contamination. However, a more comprerehnsive study incorporating different geographical regions is needed to conclusively ascertain these present findings.
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Affiliation(s)
- Prudence Mpundu
- Department of Environmental and Occupational Health, Levy Mwanawasa Medical University, Lusaka, 33991, Zambia. .,Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, 10101, Zambia.
| | - John Bwalya Muma
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, 10101, Zambia
| | - Nawa Mukumbuta
- Department of Environmental and Occupational Health, Levy Mwanawasa Medical University, Lusaka, 33991, Zambia.,Department of Epidemiology and Biostatics, Levy Mwanawasa Medical University, Lusaka, 33991, Zambia
| | - Andrew Nalishuwa Mukubesa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, 10101, Zambia
| | - Walter Muleya
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Zambia, Lusaka, 10101, Zambia
| | - Penjaninge Kapila
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, 10101, Zambia
| | - Bernard Mudenda Hang'ombe
- Department of Para-Clinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka, 10101, Zambia
| | - Musso Munyeme
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, 10101, Zambia
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21
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Li Z, Li Y, Liu N, Yuan F, Liu F, Liu J, Yun K, Yan J, Zhang G. Typing of semen-containing mixtures using ARMS-based semen-specific CpG-InDel/STR markers. Int J Legal Med 2022; 136:1163-1176. [PMID: 35633397 DOI: 10.1007/s00414-022-02843-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/19/2022] [Indexed: 10/18/2022]
Abstract
Mixed traces are common biological materials found at crime scenes, and their identification remains a significant challenge in the field of forensic genetics. In recent years, DNA methylation has been considered as a promising approach for body fluid identification, and length polymorphic loci are still the preferred markers for personal identification. In this study, we used tissue-specific CpG sites with linked insertion or deletion (InDel) or short tandem repeat (STR) markers (CpG-InDel/STR) for both body fluid and individual identification. The tissue-specific CpG loci, which were all selected from the previous reports, were analyzed using a combination of bisulfite conversion and amplification refractory mutation system-multiprimer-PCR technology. InDels or STRs, which were selected within 400 bp upstream or downstream of the semen-specific CpG loci, were analyzed using a capillary electrophoresis platform. Eventually, we successfully constructed a panel containing 17 semen-specific CpG-InDel/STR compound markers compassing 21 InDels/STRs, 3 body-fluid positive controls (vaginal secretion-, saliva-, and blood-specific CpG), and 1 gender identification locus. Using this panel, full genotyping of individuals could be obtained successfully with 50 ng DNA input. Semen stains stored at room temperature for 7 months and degraded samples that were heat treated for up to 6 h were still identified efficiently. For semen containing mixed stains, it is also useful when the semen content is as low as 3.03%. Moreover, the cumulative discrimination power of this panel is 0.9999998. In conclusion, it is a robust panel enabling the validation of both the tissue source and individual identification of semen containing mixed stains and can be employed as an alternative solution for forensic case investigation.
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Affiliation(s)
- Zeqin Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China
| | - Yidan Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China
| | - Na Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China
| | - Fang Yuan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China
| | - Feng Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China
| | - Jinding Liu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China
| | - Keming Yun
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China.
| | - Gengqian Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030619, People's Republic of China.
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22
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Zhou XC, Chen QP, Yuan JJ, Zhou S, Li M, Zhou WP, Qin Y, Deng H, Zhang L. Kidney-Derived Methylated PAX2 Sequences in the Urine of Healthy Subjects as a Convenient Model for Optimizing Methylation-Based Liquid biopsy. Mol Biotechnol 2022; 64:1088-1094. [PMID: 35412261 DOI: 10.1007/s12033-022-00481-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 03/16/2022] [Indexed: 10/18/2022]
Abstract
Although urine-based liquid biopsy has received considerable attention, there is a lack of a simple model to optimize assay parameters, including cell-free DNA (cfDNA) extraction, bisulfite modification, and bis-DNA recovery after conversion for methylation analysis in urine. The primary aim of this work was to establish a practical model by developing a quantitative methylation-sensitive PCR (qMS-PCR) assay for PAX2 based on hypermethylated PAX2 cfDNA that could be detected in healthy human urine. We first studied the methylation status of PAX2 in kidney tissues and whole blood, followed by an assessment of commercial kits for bisulfite conversion and bis-DNA recovery. Furthermore, we investigated the influence of urine storage and collection conditions on the preservation of methylated PAX2 in urine samples by qMS-PCR. As expected, PAX2 methylation was identified in urine but not in blood. Two commercial kits (CellCook and Zymo Research) had similar conversion efficiency and bis-DNA recovery. Urine storage for up to 5 days did not change PAX2 methylation estimates. Overall, cold storage of urine samples and the CellCook urine container maintained higher levels of methylated PAX2 compared to urine kept at room temperature and the conventional tubes, respectively. These findings highlight the importance of using the correct approaches/kits and optimizing experimental conditions as a diagnostic tool in the clinical setting. Our study provides insights on the development of urine-based liquid biopsy with DNA methylation as a universal biomarker.
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Affiliation(s)
- Xiang-Cheng Zhou
- Maternal and Child Health Research Institute, Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, 511400, China
| | - Qiu-Ping Chen
- Maternal and Child Health Research Institute, Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, 511400, China
| | - Jia-Jia Yuan
- Maternal and Child Health Research Institute, Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, 511400, China
| | - Shuai Zhou
- Maternal and Child Health Research Institute, Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, 511400, China
| | - Mi Li
- Maternal and Child Health Research Institute, Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, 511400, China
| | - Wei-Ping Zhou
- Maternal and Child Health Research Institute, Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, 511400, China
| | - Yan Qin
- Department of Pathology, Guangdong Women and Children Hospital, Guangzhou, 511400, China
| | - Hua Deng
- Maternal and Child Health Research Institute, Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, 511400, China.
| | - Liang Zhang
- Maternal and Child Health Research Institute, Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, 511400, China.
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23
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Challenges in promoter methylation analysis in the new era of translational oncology: a focus on liquid biopsy. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166390. [PMID: 35296416 DOI: 10.1016/j.bbadis.2022.166390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 02/01/2022] [Accepted: 03/08/2022] [Indexed: 12/20/2022]
Abstract
Toward the discovery of novel reliable biomarkers, epigenetic alterations have been repeatedly proposed for the diagnosis and the development of therapeutic strategies against cancer. Indeed, for promoter methylation to actively become a tumor marker for clinical use, it must be combined with a highly informative technology evaluated in an appropriate biospecimen. Methodological standardization related to epigenetic research is, in fact, one of the most challenging tasks. Moreover, tissue-based biopsy is being complemented and, in some cases, replaced by liquid biopsy. This review will highlight the advancements made for both pre-analytical and analytical implementation for the prospective use of methylation biomarkers in clinical settings, with particular emphasis on liquid biopsy.
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24
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Dandapath I, Chakraborty R, Kaur K, Mahajan S, Singh J, Sharma MC, Sarkar C, Suri V. Molecular alterations of low-grade gliomas in young patients: Strategies and platforms for routine evaluation. Neurooncol Pract 2021; 8:652-661. [PMID: 34777834 PMCID: PMC8579091 DOI: 10.1093/nop/npab053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In recent years, it has been established that molecular biology of pediatric low-grade gliomas (PLGGs) is entirely distinct from adults. The majority of the circumscribed pediatric gliomas are driven by mitogen-activated protein kinase (MAPK) pathway, which has yielded important diagnostic, prognostic, and therapeutic biomarkers. Further, the Consortium to Inform Molecular and Practical Approaches to CNS Tumor Taxonomy (cIMPACT) Steering Committee in their fourth meeting, suggested including a panel of molecular markers for integrated diagnosis in "pediatric-type" diffuse gliomas. However, a designated set of platforms for the evaluation of these alterations has yet not been mentioned for easier implementation in routine molecular diagnostics. Herein, we have reviewed the relevance of analyzing these markers and discussed the strategies and platforms best apposite for clinical laboratories.
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Affiliation(s)
- Iman Dandapath
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | | | - Kavneet Kaur
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Swati Mahajan
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Jyotsna Singh
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Mehar C Sharma
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Chitra Sarkar
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Vaishali Suri
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
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25
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Aliferi A, Sundaram S, Ballard D, Freire-Aradas A, Phillips C, Lareu MV, Court DS. Combining current knowledge on DNA methylation-based age estimation towards the development of a superior forensic DNA intelligence tool. Forensic Sci Int Genet 2021; 57:102637. [PMID: 34852982 DOI: 10.1016/j.fsigen.2021.102637] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/19/2021] [Accepted: 11/17/2021] [Indexed: 01/09/2023]
Abstract
The estimation of chronological age from biological fluids has been an important quest for forensic scientists worldwide, with recent approaches exploiting the variability of DNA methylation patterns with age in order to develop the next generation of forensic 'DNA intelligence' tools for this application. Drawing from the conclusions of previous work utilising massively parallel sequencing (MPS) for this analysis, this work introduces a DNA methylation-based age estimation method for blood that exhibits the best combination of prediction accuracy and sensitivity reported to date. Statistical evaluation of markers from 51 studies using microarray data from over 4000 individuals, followed by validation using in-house generated MPS data, revealed a final set of 11 markers with the greatest potential for accurate age estimation from minimal DNA material. Utilising an algorithm based on support vector machines, the proposed model achieved an average error (MAE) of 3.3 years, with this level of accuracy retained down to 5 ng of starting DNA input (~ 1 ng PCR input). The accuracy of the model was retained (MAE = 3.8 years) in a separate test set of 88 samples of Spanish origin, while predictions for donors of greater forensic interest (< 55 years of age) displayed even higher accuracy (MAE = 2.6 years). Finally, no sex-related bias was observed for this model, while there were also no signs of variation observed between control and disease-associated populations for schizophrenia, rheumatoid arthritis, frontal temporal dementia and progressive supranuclear palsy in microarray data relating to the 11 markers.
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Affiliation(s)
- Anastasia Aliferi
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Sudha Sundaram
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - David Ballard
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom.
| | - Ana Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - Maria Victoria Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Galicia, Spain
| | - Denise Syndercombe Court
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
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26
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Heidegger A, Pisarek A, de la Puente M, Niederstätter H, Pośpiech E, Woźniak A, Schury N, Unterländer M, Sidstedt M, Junker K, Ventayol Garcia M, Laurent FX, Ulus A, Vannier J, Bastisch I, Hedman J, Sijen T, Branicki W, Xavier C, Parson W. Development and inter-laboratory validation of the VISAGE enhanced tool for age estimation from semen using quantitative DNA methylation analysis. Forensic Sci Int Genet 2021; 56:102596. [PMID: 34763164 DOI: 10.1016/j.fsigen.2021.102596] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 12/27/2022]
Abstract
The analysis of DNA methylation has become an established method for chronological age estimation. This has triggered interest in the forensic community to develop new methods for age estimation from biological crime scene material. Various assays are available for age estimation from somatic tissues, the majority from blood. Age prediction from semen requires different DNA methylation markers and the only assays currently developed for forensic analysis are based on SNaPshot or pyrosequencing. Here, we describe a new assay using massively parallel sequencing to analyse 13 candidate CpG sites targeted in two multiplex PCRs. The assay has been validated by five consortium laboratories of the VISible Attributes through GEnomics (VISAGE) project within a collaborative exercise and was tested for reproducible quantification of DNA methylation levels and sensitivity with DNA methylation controls. Furthermore, DNA extracts and stains on Whatman FTA cards from two semen samples were used to evaluate concordance and mimic casework samples. Overall, the assay yielded high read depths (> 1000 reads) at all 13 marker positions. The methylation values obtained indicated robust quantification with an average standard deviation of 2.8% at the expected methylation level of 50% across the 13 markers and a good performance with 50 ng DNA input into bisulfite conversion. The absolute difference of quantifications from one participating laboratory to the mean quantifications of concordance and semen stains of remaining laboratories was approximately 1%. These results demonstrated the assay to be robust and suitable for age estimation from semen in forensic investigations. In addition to the 13-marker assay, a more streamlined protocol combining only five age markers in one multiplex PCR was developed. Preliminary results showed no substantial differences in DNA methylation quantification between the two assays, indicating its applicability with the VISAGE age model for semen developed with data from the complete 13-marker tool.
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Affiliation(s)
- A Heidegger
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - A Pisarek
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - M de la Puente
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - H Niederstätter
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - E Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - A Woźniak
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - N Schury
- Federal Criminal Police Office, Wiesbaden, Germany
| | | | - M Sidstedt
- National Forensic Centre (NFC), Swedish Police Authority, Linköping, Sweden
| | - K Junker
- National Forensic Centre (NFC), Swedish Police Authority, Linköping, Sweden
| | - M Ventayol Garcia
- Biological Traces, Netherlands Forensic Institute, Laan van Ypenburg 6, 2497 GB The Hague, The Netherlands
| | - F X Laurent
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, Ecully Cedex, France
| | - A Ulus
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, Ecully Cedex, France
| | - J Vannier
- Institut National de Police Scientifique, Laboratoire de Police Scientifique de Lyon, Ecully Cedex, France
| | - I Bastisch
- Federal Criminal Police Office, Wiesbaden, Germany
| | - J Hedman
- National Forensic Centre (NFC), Swedish Police Authority, Linköping, Sweden; Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - T Sijen
- Biological Traces, Netherlands Forensic Institute, Laan van Ypenburg 6, 2497 GB The Hague, The Netherlands; University of Amsterdam, Swammerdam Institute of Life Sciences, Science Park 904, 1098XH Amsterdam, The Netherlands
| | - W Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland; Central Forensic Laboratory of the Police, Warsaw, Poland
| | - C Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.
| | - W Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, State College, PA, USA.
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27
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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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28
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Han DSC, Ni M, Chan RWY, Wong DKL, Hiraki LT, Volpi S, Jiang P, Lui KO, Chan KCA, Chiu RWK, Lo YMD. Nuclease deficiencies alter plasma cell-free DNA methylation profiles. Genome Res 2021; 31:2008-2021. [PMID: 34470801 PMCID: PMC8559716 DOI: 10.1101/gr.275426.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 07/23/2021] [Indexed: 11/24/2022]
Abstract
The effects of DNASE1L3 or DNASE1 deficiency on cell-free DNA (cfDNA) methylation were explored in plasma of mice deficient in these nucleases and in DNASE1L3-deficient humans. Compared to wild-type cfDNA, cfDNA in DNASE1L3-deficient mice was significantly hypomethylated, while cfDNA in DNASE1-deficient mice was hypermethylated. The cfDNA hypomethylation in DNASE1L3-deficient mice was due to increased fragmentation and representation from open chromatin regions (OCRs) and CpG islands (CGIs). These findings were absent in DNASE1-deficient mice, demonstrating the preference of DNASE1 to cleave in hypomethylated OCRs and CGIs. We also observed a substantial decrease of fragment ends at methylated CpGs in the absence of DNASE1L3, thereby demonstrating that DNASE1L3 prefers to cleave at methylated CpGs. Furthermore, we found that methylation levels of cfDNA varied by fragment size in a periodic pattern, with cfDNA of specific sizes being more hypomethylated and enriched for OCRs and CGIs. These findings were confirmed in DNASE1L3-deficient human cfDNA. Thus, we have found that nuclease-mediated cfDNA fragmentation markedly affects cfDNA methylation level on a genome-wide scale. This work provides a foundational understanding of the relationship between methylation, nuclease biology, and cfDNA fragmentation.
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Affiliation(s)
- Diana S C Han
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Meng Ni
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Rebecca W Y Chan
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Danny K L Wong
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Linda T Hiraki
- Division of Rheumatology, The Hospital for Sick Children, Toronto, Ontario M5G 1X5, Canada
| | - Stefano Volpi
- Clinica Pediatrica e Reumatologia, Centro per le malattie Autoinfiammatorie e Immunodeficienze, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Giannina Gaslini, 16147 Genova, Italy.,Dipartimento di Neuroscienze, Riabilitazione, Oftalmologia, Genetica e Scienze Materno-Infantili (DINOGMI), Università degli Studi di Genova, 16132 Genova, Italy
| | - Peiyong Jiang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Kathy O Lui
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - K C Allen Chan
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Rossa W K Chiu
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Y M Dennis Lo
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
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29
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Ahn J, Heo S, Lee J, Bang D. Introduction to Single-Cell DNA Methylation Profiling Methods. Biomolecules 2021; 11:1013. [PMID: 34356635 PMCID: PMC8301785 DOI: 10.3390/biom11071013] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 02/06/2023] Open
Abstract
DNA methylation is an epigenetic mechanism that is related to mammalian cellular differentiation, gene expression regulation, and disease. In several studies, DNA methylation has been identified as an effective marker to identify differences between cells. In this review, we introduce single-cell DNA-methylation profiling methods, including experimental strategies and approaches to computational data analysis. Furthermore, the blind spots of the basic analysis and recent alternatives are briefly described. In addition, we introduce well-known applications and discuss future development.
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Affiliation(s)
- Jongseong Ahn
- Department of Chemistry, Yonsei University, Seoul 03722, Korea; (J.A.); (S.H.)
| | - Sunghoon Heo
- Department of Chemistry, Yonsei University, Seoul 03722, Korea; (J.A.); (S.H.)
| | - Jihyun Lee
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul 02447, Korea
- Department of Biomedical Science and Technology, Kyung Hee University, Seoul 02447, Korea
| | - Duhee Bang
- Department of Chemistry, Yonsei University, Seoul 03722, Korea; (J.A.); (S.H.)
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30
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Woźniak A, Heidegger A, Piniewska-Róg D, Pośpiech E, Xavier C, Pisarek A, Kartasińska E, Boroń M, Freire-Aradas A, Wojtas M, de la Puente M, Niederstätter H, Płoski R, Spólnicka M, Kayser M, Phillips C, Parson W, Branicki W. Development of the VISAGE enhanced tool and statistical models for epigenetic age estimation in blood, buccal cells and bones. Aging (Albany NY) 2021; 13:6459-6484. [PMID: 33707346 PMCID: PMC7993733 DOI: 10.18632/aging.202783] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 02/16/2021] [Indexed: 01/07/2023]
Abstract
DNA methylation is known as a biomarker for age with applications in forensics. Here we describe the VISAGE (VISible Attributes through GEnomics) Consortium's enhanced tool for epigenetic age estimation in somatic tissues. The tool is based on eight DNA methylation markers (44 CpGs), bisulfite multiplex PCR followed by sequencing on the MiSeq FGx platform, and three statistical prediction models for blood, buccal cells and bones. The model for blood is based on six CpGs from ELOVL2, MIR29B2CHG, KLF14, FHL2, TRIM59 and PDE4C, and predicts age with a mean absolute error (MAE) of 3.2 years, while the model for buccal cells includes five CpGs from PDE4C, MIR29B2CHG, ELOVL2, KLF14 and EDARADD and predicts age with MAE of 3.7 years, and the model for bones has six CpGs from ELOVL2, KLF14, PDE4C and ASPA and predicts age with MAE of 3.4 years. The VISAGE enhanced tool for age estimation in somatic tissues enables reliable collection of DNA methylation data from small amounts of DNA using a sensitive multiplex MPS assay that provides accurate estimation of age in blood, buccal swabs, and bones using the statistical model tailored to each tissue.
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Affiliation(s)
- Anna Woźniak
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - Antonia Heidegger
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Danuta Piniewska-Róg
- Department of Forensic Medicine, Jagiellonian University Medical College, Krakow, Poland
| | - Ewelina Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Aleksandra Pisarek
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Michał Boroń
- Central Forensic Laboratory of the Police, Warsaw, Poland
| | - Ana Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Marta Wojtas
- Department of Forensic Medicine, Jagiellonian University Medical College, Krakow, Poland
| | - Maria de la Puente
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.,Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Harald Niederstätter
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Rafał Płoski
- Department Medical Genetics, Warsaw Medical University, Warsaw, Poland
| | | | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria.,Forensic Science Program, The Pennsylvania State University, University Park, PA 16802, USA
| | - Wojciech Branicki
- Central Forensic Laboratory of the Police, Warsaw, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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31
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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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32
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Eyvazi S, Khamaneh AM, Tarhriz V, Bandehpour M, Hejazi MS, Sadat ATE, Sepehri B. CpG Islands Methylation Analysis of CDH11, EphA5, and HS3ST2 Genes in Gastric Adenocarcinoma Patients. J Gastrointest Cancer 2021; 51:579-583. [PMID: 31407253 DOI: 10.1007/s12029-019-00290-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE Gastric cancer is an aggressive disease which is the fourth prevalent malignancy in the world. Beside the genetic factors, epigenetic alterations such as promoter CpG island hyper methylation are involved in the emergence of gastric cancer. Herein, we investigated the methylation status of CDH11, EphA5, and HS3ST2 genes in patients with and without gastric adenocarcinoma for the first time. METHODS In the study 40 paraffin-embedded tissue sections from gastric adenocarcinoma patients and 40 specimens from patients with functional dyspepsia were taken. DNA extraction was performed using a modified salting out method. Epizen DNA methylation kit was used to the bisulfite DNA conversion. The methylation status of CDH11, EphA5, and HS3ST2 genes were analyzed by methylation-specific PCR (MSP) technique. RESULTS Among the 80 specimens, 71 DNA samples were achieved (34 gastric adenocarcinoma patients and 37 control patients). The results showed that CDH11, EphA5, and HS3ST2 genes are methylated in 28 (82.45%), 19 (55.88%), and 26 (76.47%) of 34 DNA samples from gastric adenocarcinoma patients, respectively, whereas, these genes are methylated in 7 (18.91%), 9 (24.32%) and 7 (18.91%) of 37 samples from noncancerous patients, respectively. Statistical analyses using a chi-squared test showed that there is a statistically significant difference in methylation level of CDH11, EphA5, and HS3ST2 genes between gastric cancer and uncancerous patients (p < 0.05). CONCLUSION To the best of our knowledge, this is the first report on methylation of CDH11, EphA5, and HS3ST2 promoters' in gastric adenocarcinoma patients using MSP. Identification of novel cancer-related molecular mechanisms can be useful in detection of new treatment strategies.
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Affiliation(s)
- Shirin Eyvazi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Mahdi Khamaneh
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Vahideh Tarhriz
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mojgan Bandehpour
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Saeid Hejazi
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Bita Sepehri
- Liver and Gastrointestinal Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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33
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Sharma A, Sharma KL, Bansal C, Kumar A. Updates on "Cancer Genomics and Epigenomics". World J Clin Oncol 2020; 11:890-897. [PMID: 33312884 PMCID: PMC7701914 DOI: 10.5306/wjco.v11.i11.890] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 07/03/2020] [Accepted: 08/01/2020] [Indexed: 02/06/2023] Open
Abstract
The field of "Cancer Genomics and Epigenomes" has been widely investigated for their involvement in cancer to understand the basic processes of different malignancies. The aggregation of genetic and epigenetic alterations also displays a wide range of heterogeneity making it quite necessary to develop personalized treatment strategies. The complex interplay between DNA methylation and chromatin dynamics in malignant cells is one of the major epigenetic mechanisms that lead to gene activation and repression. Hence, each tumor needs to be fully characterized to satisfy the ideas of personalized treatment strategies. The present article addresses various aspects of genome characterization methods and their potential role in the field of cancer genomics and epigenomics.
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Affiliation(s)
- Aarti Sharma
- Department of Surgical Gastroenterology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226014, India
| | - Kiran Lata Sharma
- Department of Pathology, Baylor College of Medicine, Houston, TX 77030, United States
| | - Cherry Bansal
- Department of Pathology, Era’s Medical College and Hospital, Lucknow 226003, India
| | - Ashok Kumar
- Department of Surgical Gastroenterology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow 226014, India
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34
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Ha J, Kwon H, Cho KH, Yoon MY, Kim MY, Lee SH. Identification of epigenetic variation associated with synchronous pod maturity in mungbean (Vigna radiata L.). Sci Rep 2020; 10:17414. [PMID: 33060755 PMCID: PMC7562708 DOI: 10.1038/s41598-020-74520-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 09/22/2020] [Indexed: 12/20/2022] Open
Abstract
Cytosine methylation in genomic DNA affects gene expression, potentially causing phenotypic variation. Mungbean, an agronomically and nutritionally important legume species, is characterized by nonsynchronous pod maturity, resulting in multiple harvest which costs extra time and labor. To elucidate the epigenetic influences on synchronous pod maturity (SPM) in mungbean, we determined the genome-wide DNA methylation profiles of eight mungbean recombinant inbred lines (RILs) and their parental genotypes, and compared DNA methylation profiles between high SPM and low SPM RILs, thus revealing differentially methylated regions (DMRs). A total of 3, 18, and 28 pure DMRs, defined as regions showing no significant correlation between nucleotide sequence variation and methylation level, were identified in CpG, CHG, and CHH contexts, respectively. These DMRs were proximal to 20 genes. Among the 544 single nucleotide polymorphisms identified near the 20 genes, only one caused critical change in gene expression by early termination. Analysis of these genome-wide DNA methylation profiles suggests that epigenetic changes can influence the expression of proximal genes, regardless of nucleotide sequence variation, and that SPM is mediated through gibberellin-mediated hormone signaling pathways. These results provide insights into how epialleles contribute to phenotypic variation and improve SPM in mungbean cultivars.
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Affiliation(s)
- Jungmin Ha
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, Republic of Korea.,Department of Plant Science, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Hakyung Kwon
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kang-Heum Cho
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, Republic of Korea
| | - Min Young Yoon
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, Republic of Korea
| | - Moon Young Kim
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, Republic of Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea
| | - Suk-Ha Lee
- Department of Agriculture, Forestry and Bioresources, Seoul National University, Seoul, 08826, Republic of Korea. .,Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea.
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35
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Khan F, Hodjat M, Rahimifard M, Nigjeh MN, Azizi M, Baeeri M, Bayrami Z, Gholami M, Hassani S, Abdollahi M. Assessment of arsenic-induced modifications in the DNA methylation of insulin-related genes in rat pancreatic islets. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 201:110802. [PMID: 32531573 DOI: 10.1016/j.ecoenv.2020.110802] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/11/2020] [Accepted: 05/23/2020] [Indexed: 06/11/2023]
Abstract
Extended exposure to inorganic arsenic through contaminated drinking water has been linked with increased incidence of diabetes mellitus. The most common exposure occurs through the consumption of contaminated drinking water mainly through geogenic sources of inorganic arsenic. Epigenetic modifications are important mechanisms through which environmental pollutants could exert their toxic effects. Bisulfite sequencing polymerase chain reaction method followed by Sanger sequencing was performed for DNA methylation analysis. Our results showed that sodium arsenite treatment significantly reduced insulin secretion in pancreatic islets. It was revealed that the methylation of glucose transporter 2 (Glut2) gene was changed at two cytosine-phosphate-guanine (CpG) sites (-1743, -1734) in the promoter region of the sodium arsenite-treated group comparing to the control. No changes were observed in the methylation status of peroxisome proliferator-activated receptor-gamma (PPARγ), pancreatic and duodenal homeobox 1 (Pdx1) and insulin 2 (Ins2) CpG sites in the targeted regions. Measuring the gene expression level showed increase in Glut2 expression, while the expression of insulin (INS) and Pdx1 were significantly affected by sodium arsenite treatment. This study revealed that exposure to sodium arsenite changed the DNA methylation pattern of Glut2, a key transporter of glucose entry into the pancreatic beta cells (β-cells). Our data suggested possible epigenetic-mediated toxicity mechanism for arsenite-induced β-cells dysfunction. Further studies are needed to dissect the precise epigenetic modulatory activity of sodium arsenite that affect the biogenesis of insulin.
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Affiliation(s)
- Fazlullah Khan
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), The Institute of Pharmaceutical Sciences (TIPS), and Department of Toxicology and Pharmacology, School of Pharmacy, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Mahshid Hodjat
- Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahban Rahimifard
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), The Institute of Pharmaceutical Sciences (TIPS), and Department of Toxicology and Pharmacology, School of Pharmacy, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Mona Navaei Nigjeh
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), The Institute of Pharmaceutical Sciences (TIPS), and Department of Toxicology and Pharmacology, School of Pharmacy, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Masoumeh Azizi
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Maryam Baeeri
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), The Institute of Pharmaceutical Sciences (TIPS), and Department of Toxicology and Pharmacology, School of Pharmacy, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Zahra Bayrami
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), The Institute of Pharmaceutical Sciences (TIPS), and Department of Toxicology and Pharmacology, School of Pharmacy, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Mahdi Gholami
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), The Institute of Pharmaceutical Sciences (TIPS), and Department of Toxicology and Pharmacology, School of Pharmacy, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Shokoufeh Hassani
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), The Institute of Pharmaceutical Sciences (TIPS), and Department of Toxicology and Pharmacology, School of Pharmacy, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Mohammad Abdollahi
- Toxicology and Diseases Group (TDG), Pharmaceutical Sciences Research Center (PSRC), The Institute of Pharmaceutical Sciences (TIPS), and Department of Toxicology and Pharmacology, School of Pharmacy, Tehran University of Medical Sciences (TUMS), Tehran, Iran.
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36
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Erger F, Nörling D, Borchert D, Leenen E, Habbig S, Wiesener MS, Bartram MP, Wenzel A, Becker C, Toliat MR, Nürnberg P, Beck BB, Altmüller J. cfNOMe - A single assay for comprehensive epigenetic analyses of cell-free DNA. Genome Med 2020; 12:54. [PMID: 32580754 PMCID: PMC7315486 DOI: 10.1186/s13073-020-00750-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 06/02/2020] [Indexed: 02/07/2023] Open
Abstract
Cell-free DNA (cfDNA) analysis has become essential in cancer diagnostics and prenatal testing. We present cfNOMe, a two-in-one method of measuring cfDNA cytosine methylation and nucleosome occupancy in a single assay using non-disruptive enzymatic cytosine conversion and a custom bioinformatic pipeline. We show that enzymatic cytosine conversion better preserves cfDNA fragmentation information than does bisulfite conversion. Whereas previously separate experiments were required to study either epigenetic marking, cfNOMe delivers reliable results for both, enabling more comprehensive and inexpensive epigenetic cfDNA profiling. cfNOMe has the potential to advance biomarker discovery and diagnostic usage in diseases with systemic perturbations of cfDNA composition.
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Affiliation(s)
- Florian Erger
- Cologne Center for Genomics, University of Cologne, Cologne, Germany. .,Institute of Human Genetics, Faculty of Medicine and University Hospital Cologne, Cologne, Germany. .,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
| | - Deborah Nörling
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Domenica Borchert
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Esther Leenen
- Department of Nephrology, Transplantation and Medical Intensive Care, University Witten/Herdecke, Medical Center Cologne-Merheim, Cologne, Germany
| | - Sandra Habbig
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Michael S Wiesener
- Department of Nephrology and Hypertension, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Malte P Bartram
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,Department II of Internal Medicine, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Andrea Wenzel
- Institute of Human Genetics, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Christian Becker
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Mohammad R Toliat
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Bodo B Beck
- Institute of Human Genetics, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany. .,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
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37
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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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38
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Stastny I, Zubor P, Kajo K, Kubatka P, Golubnitschaja O, Dankova Z. Aberrantly Methylated cfDNA in Body Fluids as a Promising Diagnostic Tool for Early Detection of Breast Cancer. Clin Breast Cancer 2020; 20:e711-e722. [PMID: 32792225 DOI: 10.1016/j.clbc.2020.05.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/29/2020] [Accepted: 05/11/2020] [Indexed: 12/24/2022]
Abstract
Breast malignancies are the leading type of cancer among women. Its prevention and early detection, particularly in young women, remains challenging. To this end, cell-free DNA (cfDNA) detected in body fluids demonstrates great potential for early detection of tissue transformation and altered molecular setup, such as epigenetic profiles. Aberrantly methylated cfDNA in body fluids could therefore serve as a potential diagnostic and prognostic tool in breast cancer management. Abnormal methylation may lead to both an activation of oncogenes via hypomethylation and an inactivation of tumor suppressor genes by hypermethylation. We update the state of the art in the area of aberrant cfDNA methylation analyses as a diagnostic and prognostic tool in breast cancer, report on the main technological challenges, and provide an outlook for advancing the overall management of breast malignancies based on cfDNA as a target for diagnosis and tailored therapies.
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Affiliation(s)
- Igor Stastny
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic; Department of Obstetrics and Gynaecology, Martin University Hospital and Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic.
| | - Pavol Zubor
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic; Department of Gynecologic Oncology, The Norwegian Radium Hospital, Oslo University Hospital, 0379 Oslo, Norway
| | - Karol Kajo
- Department of Pathology, St Elizabeth Cancer Institute Hospital, Bratislava, Slovak Republic; Biomedical Research Centre, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Peter Kubatka
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic; Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Martin, Slovak Republic
| | - Olga Golubnitschaja
- Radiological Hospital, Rheinische, Excellence University of Bonn, Bonn, Germany; Breast Cancer Research Centre, Rheinische, Excellence University of Bonn, Bonn, Germany; Centre for Integrated Oncology, Cologne-Bonn, Excellence University of Bonn, Bonn, Germany
| | - Zuzana Dankova
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovak Republic
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39
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Crotti M, Adams CE, Elmer KR. Population genomic SNPs from epigenetic RADs: Gaining genetic and epigenetic data from a single established next‐generation sequencing approach. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13395] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marco Crotti
- Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow UK
| | - Colin E. Adams
- Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow UK
- Scottish Centre for Ecology and the Natural Environment University of Glasgow Rowardennan UK
| | - Kathryn R. Elmer
- Institute of Biodiversity, Animal Health & Comparative Medicine College of Medical, Veterinary & Life Sciences University of Glasgow Glasgow UK
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40
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Liu Y, Weyrich LS, Llamas B. More Arrows in the Ancient DNA Quiver: Use of Paleoepigenomes and Paleomicrobiomes to Investigate Animal Adaptation to Environment. Mol Biol Evol 2020; 37:307-319. [PMID: 31638147 DOI: 10.1093/molbev/msz231] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Whether and how epigenetic mechanisms and the microbiome play a role in mammalian adaptation raised considerable attention and controversy, mainly because they have the potential to add new insights into the Modern Synthesis. Recent attempts to reconcile neo-Darwinism and neo-Lamarckism in a unified theory of molecular evolution give epigenetic mechanisms and microbiome a prominent role. However, supporting empirical data are still largely missing. Because experimental studies using extant animals can hardly be done over evolutionary timescales, we propose that advances in ancient DNA techniques provide a valid alternative. In this piece, we evaluate 1) the possible roles of epigenomes and microbiomes in animal adaptation, 2) advances in the retrieval of paleoepigenome and paleomicrobiome data using ancient DNA techniques, and 3) the plasticity of either and interactions between the epigenome and the microbiome, while emphasizing that it is essential to take both into account, as well as the underlying genetic factors that may confound the findings. We propose that advanced ancient DNA techniques should be applied to a wide range of past animals, so novel dynamics in animal evolution and adaption can be revealed.
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Affiliation(s)
- Yichen Liu
- Australian Centre for Ancient DNA, School of Biological Sciences, Environment Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Laura S Weyrich
- Australian Centre for Ancient DNA, School of Biological Sciences, Environment Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, Environment Institute, University of Adelaide, Adelaide, South Australia, Australia
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41
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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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Liu Z, Wang Z, Jia E, Ouyang T, Pan M, Lu J, Ge Q, Bai Y. Analysis of genome-wide in cell free DNA methylation: progress and prospect. Analyst 2019; 144:5912-5922. [DOI: 10.1039/c9an00935c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In this work, we focus on the detection methods of cfDNA methylation based on NGS and the latest progress.
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Affiliation(s)
- Zhiyu Liu
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Zexin Wang
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Erteng Jia
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Tinglan Ouyang
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Min Pan
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Jiafeng Lu
- Center of Reproduction and Genetics
- Affiliated Suzhou Hospital of Nanjing Medical University
- Suzhou Municipal Hospital
- Suzhou 215002
- China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
| | - Yunfei Bai
- State Key Laboratory of Bioelectronics
- School of Biological Science and Medical Engineering
- Southeast University
- Nanjing
- China
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DNA methylation-based age prediction using massively parallel sequencing data and multiple machine learning models. Forensic Sci Int Genet 2018; 37:215-226. [DOI: 10.1016/j.fsigen.2018.09.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/23/2018] [Accepted: 09/06/2018] [Indexed: 01/09/2023]
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Li W, Li Q, Kang S, Same M, Zhou Y, Sun C, Liu CC, Matsuoka L, Sher L, Wong WH, Alber F, Zhou X. CancerDetector: ultrasensitive and non-invasive cancer detection at the resolution of individual reads using cell-free DNA methylation sequencing data. Nucleic Acids Res 2018; 46:e89. [PMID: 29897492 PMCID: PMC6125664 DOI: 10.1093/nar/gky423] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 05/01/2018] [Accepted: 05/29/2018] [Indexed: 12/13/2022] Open
Abstract
The detection of tumor-derived cell-free DNA in plasma is one of the most promising directions in cancer diagnosis. The major challenge in such an approach is how to identify the tiny amount of tumor DNAs out of total cell-free DNAs in blood. Here we propose an ultrasensitive cancer detection method, termed 'CancerDetector', using the DNA methylation profiles of cell-free DNAs. The key of our method is to probabilistically model the joint methylation states of multiple adjacent CpG sites on an individual sequencing read, in order to exploit the pervasive nature of DNA methylation for signal amplification. Therefore, CancerDetector can sensitively identify a trace amount of tumor cfDNAs in plasma, at the level of individual reads. We evaluated CancerDetector on the simulated data, and showed a high concordance of the predicted and true tumor fraction. Testing CancerDetector on real plasma data demonstrated its high sensitivity and specificity in detecting tumor cfDNAs. In addition, the predicted tumor fraction showed great consistency with tumor size and survival outcome. Note that all of those testing were performed on sequencing data at low to medium coverage (1× to 10×). Therefore, CancerDetector holds the great potential to detect cancer early and cost-effectively.
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Affiliation(s)
- Wenyuan Li
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Qingjiao Li
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Shuli Kang
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Mary Same
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Yonggang Zhou
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Carol Sun
- Oak Park High School, Oak Park, CA 91377, USA
| | - Chun-Chi Liu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taiwan 40227, Republic of China
| | - Lea Matsuoka
- Division of Hepatobiliary Surgery & Liver Transplantation, Department of Surgery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Linda Sher
- Department of Surgery, University of Southern California, Keck School of Medicine, Los Angeles, Los Angeles, CA 90033, USA
| | - Wing Hung Wong
- Department of Statistics, Stanford University, Stanford, CA 94305, USA
- Department of Health Research & Policy, Stanford University, Stanford, CA 94305, USA
| | - Frank Alber
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Xianghong Jasmine Zhou
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Institute for Quantitative and Computational Biosciences, University of California at Los Angeles, Los Angeles, CA 90095, USA
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Kint S, De Spiegelaere W, De Kesel J, Vandekerckhove L, Van Criekinge W. Evaluation of bisulfite kits for DNA methylation profiling in terms of DNA fragmentation and DNA recovery using digital PCR. PLoS One 2018; 13:e0199091. [PMID: 29902267 PMCID: PMC6002050 DOI: 10.1371/journal.pone.0199091] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 05/31/2018] [Indexed: 02/06/2023] Open
Abstract
DNA methylation is one of the most important epigenetic modifications in the regulation of gene transcription. The current gold standard to study this modification is bisulfite sequencing. Although multiple commercial bisulfite treatment kits provide good conversion efficiencies, DNA loss and especially DNA fragmentation remain troublesome. This hampers DNA methylation profiling of long DNA sequences. Here, we explored the performance of twelve commercial bisulfite kits by an in-depth comparison of DNA fragmentation using gel electrophoresis, qPCR and digital PCR, DNA recovery by spectroscopic measurements and digital PCR and conversion efficiency by next generation sequencing. The results show a clear performance difference between the bisulfite kits, and depending on the specific goal of the study, the most appropriate kit might differ. Moreover, we demonstrated that digital PCR is a valuable method to monitor both DNA fragmentation as well as DNA recovery after bisulfite treatment.
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Affiliation(s)
- Sam Kint
- Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Ghent, Belgium
- * E-mail:
| | - Ward De Spiegelaere
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Jonas De Kesel
- Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Wim Van Criekinge
- Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Taudt A, Roquis D, Vidalis A, Wardenaar R, Johannes F, Colomé-Tatché M. METHimpute: imputation-guided construction of complete methylomes from WGBS data. BMC Genomics 2018; 19:444. [PMID: 29879918 PMCID: PMC5992726 DOI: 10.1186/s12864-018-4641-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/03/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Whole-genome bisulfite sequencing (WGBS) has become the standard method for interrogating plant methylomes at base resolution. However, deep WGBS measurements remain cost prohibitive for large, complex genomes and for population-level studies. As a result, most published plant methylomes are sequenced far below saturation, with a large proportion of cytosines having either missing data or insufficient coverage. RESULTS Here we present METHimpute, a Hidden Markov Model (HMM) based imputation algorithm for the analysis of WGBS data. Unlike existing methods, METHimpute enables the construction of complete methylomes by inferring the methylation status and level of all cytosines in the genome regardless of coverage. Application of METHimpute to maize, rice and Arabidopsis shows that the algorithm infers cytosine-resolution methylomes with high accuracy from data as low as 6X, compared to data with 60X, thus making it a cost-effective solution for large-scale studies. CONCLUSIONS METHimpute provides methylation status calls and levels for all cytosines in the genome regardless of coverage, thus yielding complete methylomes even with low-coverage WGBS datasets. The method has been extensively tested in plants, but should also be applicable to other species. An implementation is available on Bioconductor.
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Affiliation(s)
- Aaron Taudt
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, Groningen, NL-9713 AV The Netherlands
- Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg, 85764 Germany
| | - David Roquis
- Department of Plant Sciences, Hans Eisenmann-Zentrum for Agricultural Sciences, Technical University Munich, Liesel-Beckmann-Str. 2, Freising, 85354 Germany
| | - Amaryllis Vidalis
- Department of Plant Sciences, Hans Eisenmann-Zentrum for Agricultural Sciences, Technical University Munich, Liesel-Beckmann-Str. 2, Freising, 85354 Germany
| | - René Wardenaar
- Department of Plant Sciences, Hans Eisenmann-Zentrum for Agricultural Sciences, Technical University Munich, Liesel-Beckmann-Str. 2, Freising, 85354 Germany
| | - Frank Johannes
- Department of Plant Sciences, Hans Eisenmann-Zentrum for Agricultural Sciences, Technical University Munich, Liesel-Beckmann-Str. 2, Freising, 85354 Germany
| | - Maria Colomé-Tatché
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, A. Deusinglaan 1, Groningen, NL-9713 AV The Netherlands
- Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, Neuherberg, 85764 Germany
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Emil-Erlenmeyer-Forum 2, Freising, 85354 Germany
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Abstract
Single-cell multiomics technologies typically measure multiple types of molecule from the same individual cell, enabling more profound biological insight than can be inferred by analyzing each molecular layer from separate cells. These single-cell multiomics technologies can reveal cellular heterogeneity at multiple molecular layers within a population of cells and reveal how this variation is coupled or uncoupled between the captured omic layers. The data sets generated by these techniques have the potential to enable a deeper understanding of the key biological processes and mechanisms driving cellular heterogeneity and how they are linked with normal development and aging as well as disease etiology. This review details both established and novel single-cell mono- and multiomics technologies and considers their limitations, applications, and likely future developments.
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Affiliation(s)
- Lia Chappell
- Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom; , ,
| | | | - Thierry Voet
- Wellcome Sanger Institute, Cambridge CB10 1SA, United Kingdom; , , .,Department of Human Genetics, KU Leuven, B-3000 Leuven, Belgium;
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Tierling S, Schmitt B, Walter J. Comprehensive Evaluation of Commercial Bisulfite-Based DNA Methylation Kits and Development of an Alternative Protocol With Improved Conversion Performance. GENETICS & EPIGENETICS 2018; 10:1179237X18766097. [PMID: 29636635 PMCID: PMC5888801 DOI: 10.1177/1179237x18766097] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 02/01/2018] [Indexed: 04/30/2023]
Abstract
DNA methylation is the most studied epigenetic modification with a wide range of regulatory functions in mammalian genomes. It almost exclusively resides on CpG dinucleotides and, among others, plays important roles in early embryo development, onset, and maintenance of cancer. During the past 3 decades, many approaches have been developed to discriminate methylated from unmethylated DNA including antibody-based enrichment of methylated DNA, restriction enzyme-based, or hybridization-based methods. The conversion of unmethylated cytosines to uracils by sodium or ammonium bisulfite is regarded as golden standard as this approach requires no enzymatic reaction and provides deep and reliable insight in methylation patterns at single-base resolution. Nowadays, there are many commercial kits for bisulfite conversion available but they perform differently and also vary in protocols and chemicals used. Here, we provide the first comprehensive and comparative evaluation of bisulfite conversion kits observing major differences in conversion efficiency and DNA degradation which greatly affect the performance of downstream applications, ie, polymerase chain reactions (PCRs). Moreover, deep sequencing of amplicons containing oxidized derivates of 5'-methylC shows that none of the tested kits efficiently converts 5'-formylC without substantial conversion of 5'-methylC or 5'-hydroxymethylC. Consequently, we developed a robust and easy-to-use protocol that allows maximal discrimination between 5'-formylC and 5'-methylC/5'-hydroxymethylC with low DNA degradation and high PCR efficiency on the bisulfite-treated DNA. We highly recommend to use our time- and cost-efficient protocol for any genome-wide or local high-resolution bisulfite sequencing application to minimize conversion-dependent error rates.
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Affiliation(s)
- Sascha Tierling
- Sascha Tierling, Faculty of Natural Sciences and Technology, Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany.
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Worm Ørntoft MB, Jensen SØ, Hansen TB, Bramsen JB, Andersen CL. Comparative analysis of 12 different kits for bisulfite conversion of circulating cell-free DNA. Epigenetics 2017; 12:626-636. [PMID: 28557629 PMCID: PMC5687322 DOI: 10.1080/15592294.2017.1334024] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Blood circulating cell-free DNA (cfDNA) is becoming popular in the search of promising predictive and prognostic biomarkers. Among these biomarkers, cfDNA methylation markers have especially gained considerable attention. A significant challenge in the utilization of cfDNA methylation markers is the limited amount of cfDNA available for analyses; reportedly, bisulfite conversion (BSC) reduce cfDNA amounts even further. Nevertheless, few efforts have focused on ensuring high cfDNA conversion efficiency and recovery after BSC. To compare cfDNA recovery of different BSC methods, we compared 12 different commercially available BSC kits. We tested whether DNA recovery was affected by the molecular weight and/or quantity of input DNA. We also tested BSC efficiency for each kit. We found that recovery varied for DNA fragments of different lengths: certain kits recovered short fragments better than others, and only 3 kits recovered DNA fragments of <100 bp well. In contrast, DNA input amount did not seem to affect DNA recovery: for quantities spanning between 820 and ∼25,000 genome equivalents per BSC, a linear relation was found between input and recovery amount. Overall, mean recovery ranged between 9 and 32%, with BSC efficiency of 97-99.9%. When plasma cfDNA was used as input for BSC, recovery varied from 22% for the poorest and 66% for the best performing kits, while conversion efficiency ranged from 96 to 100% among different kits. In conclusion, clear performance differences exist between commercially available BSC kits, both in terms of DNA recovery and conversion efficiency. The choice of BSC kit can substantially impact the amount of converted cfDNA available for downstream analysis, which is critical in a cfDNA methylation marker setting.
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Vincent M, Mundbjerg K, Skou Pedersen J, Liang G, Jones PA, Ørntoft TF, Dalsgaard Sørensen K, Wiuf C. epiG: statistical inference and profiling of DNA methylation from whole-genome bisulfite sequencing data. Genome Biol 2017; 18:38. [PMID: 28222791 PMCID: PMC5320668 DOI: 10.1186/s13059-017-1168-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 02/07/2017] [Indexed: 02/11/2023] Open
Abstract
The study of epigenetic heterogeneity at the level of individual cells and in whole populations is the key to understanding cellular differentiation, organismal development, and the evolution of cancer. We develop a statistical method, epiG, to infer and differentiate between different epi-allelic haplotypes, annotated with CpG methylation status and DNA polymorphisms, from whole-genome bisulfite sequencing data, and nucleosome occupancy from NOMe-seq data. We demonstrate the capabilities of the method by inferring allele-specific methylation and nucleosome occupancy in cell lines, and colon and tumor samples, and by benchmarking the method against independent experimental data.
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Affiliation(s)
- Martin Vincent
- Department of Mathematical Sciences, University of Copenhagen, Copenhagen, 2100, Denmark
| | - Kamilla Mundbjerg
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, Los Angeles, 90089-9176, CA, USA
| | - Jakob Skou Pedersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, 8200, Denmark
| | - Gangning Liang
- Department of Urology, Keck School of Medicine, University of Southern California, Los Angeles, 90089, CA, USA
| | - Peter A Jones
- Van Andel Research Institute, Grand Rapids, 49503, MI, USA
| | - Torben Falck Ørntoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, 8200, Denmark
| | | | - Carsten Wiuf
- Department of Mathematical Sciences, University of Copenhagen, Copenhagen, 2100, Denmark.
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