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Gu Y, Jin CX, Tong ZH, Jiang T, Yao FC, Zhang Y, Huang J, Song FB, Sun JL, Luo J. Expression of genes related to gonadal development and construction of gonadal DNA methylation maps of Trachinotus blochii under hypoxia. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 935:173172. [PMID: 38740210 DOI: 10.1016/j.scitotenv.2024.173172] [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: 01/03/2024] [Revised: 04/12/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Abstract
Chronic hypoxia can affect the growth and metabolism of fish and potentially impact gonadal development through epigenetic regulation. Trachinotus blochii (Golden pompano) is widely cultured near the coast and is sensitive to low oxygen conditions. We found that hypoxia and reoxygenation processes acted on multiple targets on the HPG axis, leading to endocrine disorders. Changes in the expression of key genes in the brain (gnrh), pituitary (fsh and lh), ovaries (cyp19a1a, foxl2, and er), and testes (dmrt1, ar, sox9, and gsdf) were associated with significant decreases in estrogen and testosterone levels. Hypoxia and reoxygenation lead to changes in DNA methylation levels in the gonads. Hypoxia upregulated the expression of dnmt1, dnmt3a, dnmt3b, tet1, and tet2 in females and dnmt3a and dnmt3b in males, while reoxygenation down-regulated the expression of dnmt1, dnmt3a, dnmt3b, tet1, and tet2 in males. Whole genome methylation sequencing showed that the number of differentially methylated regions was highest on chromosome 10 (5192) and lowest on chromosome 24 (275). Differentially methylated genes in females and males, as well as between males and females, were enriched in the oxytocin signaling pathway, fatty acid metabolism pathway, and HIF-1a pathway. In summary, hypoxia and reoxygenation can induce endocrine disorders, affect the expression of HPG axis genes, change the methylation pattern and modification pattern of gonad DNA, and then have potential effects on gonad development.
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Affiliation(s)
- Yue Gu
- School of Marine Biology and Fisheries, Sanya Nanfan Research Institute of Hainan University, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China
| | - Chun Xiu Jin
- School of Marine Biology and Fisheries, Sanya Nanfan Research Institute of Hainan University, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China
| | - Zai Hui Tong
- School of Marine Biology and Fisheries, Sanya Nanfan Research Institute of Hainan University, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China
| | - Tian Jiang
- School of Marine Biology and Fisheries, Sanya Nanfan Research Institute of Hainan University, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China
| | - Fu Cheng Yao
- School of Marine Biology and Fisheries, Sanya Nanfan Research Institute of Hainan University, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China
| | - Yu Zhang
- School of Marine Biology and Fisheries, Sanya Nanfan Research Institute of Hainan University, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China
| | - Jie Huang
- School of Marine Biology and Fisheries, Sanya Nanfan Research Institute of Hainan University, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China
| | - Fei Biao Song
- School of Marine Biology and Fisheries, Sanya Nanfan Research Institute of Hainan University, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China
| | - Jun Long Sun
- School of Marine Biology and Fisheries, Sanya Nanfan Research Institute of Hainan University, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China.
| | - Jian Luo
- School of Marine Biology and Fisheries, Sanya Nanfan Research Institute of Hainan University, Hainan Aquaculture Breeding Engineering Research Center, Hainan Academician Team Innovation Center, Hainan University, Haikou 570228, China.
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2
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Derbala D, Garnier A, Bonnet E, Deleuze JF, Tost J. Whole-Genome Bisulfite Sequencing Protocol for the Analysis of Genome-Wide DNA Methylation and Hydroxymethylation Patterns at Single-Nucleotide Resolution. Methods Mol Biol 2024; 2842:353-382. [PMID: 39012605 DOI: 10.1007/978-1-0716-4051-7_18] [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] [Indexed: 07/17/2024]
Abstract
The analysis of genome-wide epigenomic alterations including DNA methylation and hydroxymethylation has become a subject of intensive research for many biological and clinical questions. DNA methylation analysis bears the particular promise to supplement or replace biochemical and imaging-based tests for the next generation of personalized medicine. Whole-genome bisulfite sequencing (WGBS) using next-generation sequencing technologies is currently considered the gold standard for a comprehensive and quantitative analysis of DNA methylation throughout the genome. However, bisulfite conversion does not allow distinguishing between cytosine methylation and hydroxymethylation requiring an additional chemical or enzymatic step to identify hydroxymethylated cytosines. Here, we provide a detailed protocol based on a commercial kit for the preparation of sequencing libraries for the comprehensive whole-genome analysis of DNA methylation and/or hydroxymethylation. The protocol is based on the construction of sequencing libraries from limited amounts of input DNA by ligation of methylated adaptors to the fragmented DNA prior to bisulfite conversion. For analyses requiring a quantitative distinction between 5-methylcytosine and 5-hydroxymethylcytosines levels, an oxidation step is included in the same workflow to perform oxidative bisulfite sequencing (OxBs-Seq). In this case, two sequencing libraries will be generated and sequenced: a classic methylome following bisulfite conversion and analyzing modified cytosines (not distinguishing between methylated and hydroxymethylated cytosines) and a methylome analyzing only methylated cytosines, respectively. Hydroxymethylation levels are deduced from the differences between the two reactions. We also provide a step-by-step description of the data analysis using publicly available bioinformatic tools. The described protocol has been successfully applied to different human and plant samples and yields robust and reproducible results.
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Affiliation(s)
- David Derbala
- Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie François Jacob, Université Paris -Saclay, Evry, France
| | - Abel Garnier
- Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie François Jacob, Université Paris -Saclay, Evry, France
| | - Eric Bonnet
- Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie François Jacob, Université Paris -Saclay, Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie François Jacob, Université Paris -Saclay, Evry, France
| | - Jörg Tost
- Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie François Jacob, Université Paris -Saclay, Evry, France.
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3
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Gentien D, Saberi-Ansari E, Servant N, Jolly A, de la Grange P, Némati F, Liot G, Saule S, Teissandier A, Bourc'his D, Girard E, Wong J, Masliah-Planchon J, Narmanli E, Liu Y, Torun E, Goulancourt R, Rodrigues M, Gaudé LV, Reyes C, Bazire M, Chenegros T, Henry E, Rapinat A, Bohec M, Baulande S, M'kacher R, Jeandidier E, Nicolas A, Ciriello G, Margueron R, Decaudin D, Cassoux N, Piperno-Neumann S, Stern MH, Gibcus JH, Dekker J, Heard E, Roman-Roman S, Waterfall JJ. Multi-omics comparison of malignant and normal uveal melanocytes reveals molecular features of uveal melanoma. Cell Rep 2023; 42:113132. [PMID: 37708024 PMCID: PMC10598242 DOI: 10.1016/j.celrep.2023.113132] [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: 01/12/2023] [Revised: 07/10/2023] [Accepted: 08/30/2023] [Indexed: 09/16/2023] Open
Abstract
Uveal melanoma (UM) is a rare cancer resulting from the transformation of melanocytes in the uveal tract. Integrative analysis has identified four molecular and clinical subsets of UM. To improve our molecular understanding of UM, we performed extensive multi-omics characterization comparing two aggressive UM patient-derived xenograft models with normal choroidal melanocytes, including DNA optical mapping, specific histone modifications, and DNA topology analysis using Hi-C. Our gene expression and cytogenetic analyses suggest that genomic instability is a hallmark of UM. We also identified a recurrent deletion in the BAP1 promoter resulting in loss of expression and associated with high risk of metastases in UM patients. Hi-C revealed chromatin topology changes associated with the upregulation of PRAME, an independent prognostic biomarker in UM, and a potential therapeutic target. Our findings illustrate how multi-omics approaches can improve our understanding of tumorigenesis and reveal two distinct mechanisms of gene expression dysregulation in UM.
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Affiliation(s)
- David Gentien
- Translational Research Department, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France; Genomics Platform, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France.
| | - Elnaz Saberi-Ansari
- Translational Research Department, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France; INSERM U830, Research Center, Institut Curie, PSL Research University, 75005 Paris, France
| | | | | | | | - Fariba Némati
- Translational Research Department, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France; Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL Research University, 75248 Paris, France
| | - Géraldine Liot
- Institut Curie, PSL Research University, CNRS, INSERM, UMR3347, U1021, Orsay, France
| | - Simon Saule
- Institut Curie, PSL Research University, CNRS, INSERM, UMR3347, U1021, Orsay, France; Université Paris-Saclay Centre National de La Recherche Scientifique, UMR 3347, Unité 1021, Orsay, France
| | - Aurélie Teissandier
- Institut Curie, PSL Research University, Sorbonne University, INSERM U934, CNRS UMR 3215, 75005 Paris, France
| | - Deborah Bourc'his
- Institut Curie, PSL Research University, Sorbonne University, INSERM U934, CNRS UMR 3215, 75005 Paris, France
| | | | - Jennifer Wong
- Department of Diagnostic and Theranostic Molecular Pathology, Unit of Somatic Genetic, Hospital, Institut Curie, Paris, France
| | - Julien Masliah-Planchon
- Department of Diagnostic and Theranostic Molecular Pathology, Unit of Somatic Genetic, Hospital, Institut Curie, Paris, France
| | - Erkan Narmanli
- Translational Research Department, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France; INSERM U830, Research Center, Institut Curie, PSL Research University, 75005 Paris, France
| | - Yuanlong Liu
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Cancer Center Leman, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Emma Torun
- Institut Curie, PSL Research University, Sorbonne University, INSERM U934, CNRS UMR 3215, 75005 Paris, France
| | | | - Manuel Rodrigues
- Department of Medical Oncology, Institut Curie, PSL Research University, 75005 Paris, France; INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée par la Ligue Nationale Contre le Cancer, Department of Genetics, Institut Curie, PSL Research University, 75005 Paris, France
| | - Laure Villoing Gaudé
- Translational Research Department, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France; Genomics Platform, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France
| | - Cécile Reyes
- Translational Research Department, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France; Genomics Platform, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France
| | - Matéo Bazire
- Translational Research Department, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France; Genomics Platform, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France
| | - Thomas Chenegros
- Translational Research Department, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France; Genomics Platform, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France
| | - Emilie Henry
- Translational Research Department, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France; Genomics Platform, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France
| | - Audrey Rapinat
- Translational Research Department, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France; Genomics Platform, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France
| | - Mylene Bohec
- Institut Curie Genomics of Excellence (ICGex) Platform, Institut Curie Research Center, PSL Research University, Paris, France
| | - Sylvain Baulande
- Institut Curie Genomics of Excellence (ICGex) Platform, Institut Curie Research Center, PSL Research University, Paris, France
| | | | - Eric Jeandidier
- Laboratoire de Génétique, Groupe Hospitalier de la Région de Mulhouse Sud-Alsace, Mulhouse, France
| | - André Nicolas
- Pathex, Institut Curie, PSL Research University, Paris, France
| | - Giovanni Ciriello
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland; Swiss Cancer Center Leman, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Raphael Margueron
- Institut Curie, PSL Research University, Sorbonne University, INSERM U934, CNRS UMR 3215, 75005 Paris, France
| | - Didier Decaudin
- Translational Research Department, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France; Laboratory of Preclinical Investigation, Translational Research Department, Institut Curie, PSL Research University, 75248 Paris, France
| | - Nathalie Cassoux
- Department of Medical Oncology, Institut Curie, PSL Research University, 75005 Paris, France; Department of Ocular Oncology, Faculty of Medicine, Institut Curie, Université de Paris Descartes, 75005 Paris, France
| | - Sophie Piperno-Neumann
- Department of Medical Oncology, Institut Curie, PSL Research University, 75005 Paris, France
| | - Marc-Henri Stern
- INSERM U830, DNA Repair and Uveal Melanoma (D.R.U.M.), Equipe Labellisée par la Ligue Nationale Contre le Cancer, Department of Genetics, Institut Curie, PSL Research University, 75005 Paris, France
| | - Johan Harmen Gibcus
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Job Dekker
- Howard Hughes Medical Institute, Department of Systems Biology, Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Edith Heard
- Director's Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Sergio Roman-Roman
- Translational Research Department, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France.
| | - Joshua J Waterfall
- Translational Research Department, Research Center, Institut Curie, Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France; INSERM U830, Research Center, Institut Curie, PSL Research University, 75005 Paris, France.
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4
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Wang Z, Xiang S, Zhou C, Xu Q. DeepMethylation: a deep learning based framework with GloVe and Transformer encoder for DNA methylation prediction. PeerJ 2023; 11:e16125. [PMID: 37780374 PMCID: PMC10538282 DOI: 10.7717/peerj.16125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/27/2023] [Indexed: 10/03/2023] Open
Abstract
DNA methylation is a crucial topic in bioinformatics research. Traditional wet experiments are usually time-consuming and expensive. In contrast, machine learning offers an efficient and novel approach. In this study, we propose DeepMethylation, a novel methylation predictor with deep learning. Specifically, the DNA sequence is encoded with word embedding and GloVe in the first step. After that, dilated convolution and Transformer encoder are utilized to extract the features. Finally, full connection and softmax operators are applied to predict the methylation sites. The proposed model achieves an accuracy of 97.8% on the 5mC dataset, which outperforms state-of-the-art methods. Furthermore, our predictor exhibits good generalization ability as it achieves an accuracy of 95.8% on the m1A dataset. To ease access for other researchers, our code is publicly available at https://github.com/sb111169/tf-5mc.
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Affiliation(s)
- Zhe Wang
- Wuhan University of Science and Technology, Wuhan, Hubei, China
| | - Sen Xiang
- Wuhan University of Science and Technology, Wuhan, Hubei, China
| | - Chao Zhou
- China Three Gorges University, Yichang, Hubei, China
| | - Qing Xu
- China Three Gorges University, Yichang, Hubei, China
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5
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Yu JCY, Zeng Y, Zhao K, Lu T, Oros Klein K, Colmegna I, Lora M, Bhatnagar SR, Leask A, Greenwood CMT, Hudson M. Novel insights into systemic sclerosis using a sensitive computational method to analyze whole-genome bisulfite sequencing data. Clin Epigenetics 2023; 15:96. [PMID: 37270501 DOI: 10.1186/s13148-023-01513-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 05/28/2023] [Indexed: 06/05/2023] Open
Abstract
BACKGROUND Abnormal DNA methylation is thought to contribute to the onset and progression of systemic sclerosis. Currently, the most comprehensive assay for profiling DNA methylation is whole-genome bisulfite sequencing (WGBS), but its precision depends on read depth and it may be subject to sequencing errors. SOMNiBUS, a method for regional analysis, attempts to overcome some of these limitations. Using SOMNiBUS, we re-analyzed WGBS data previously analyzed using bumphunter, an approach that initially fits single CpG associations, to contrast DNA methylation estimates by both methods. METHODS Purified CD4+ T lymphocytes of 9 SSc and 4 control females were sequenced using WGBS. We separated the resulting sequencing data into regions with dense CpG data, and differentially methylated regions (DMRs) were inferred with the SOMNiBUS region-level test, adjusted for age. Pathway enrichment analysis was performed with ingenuity pathway analysis (IPA). We compared the results obtained by SOMNiBUS and bumphunter. RESULTS Of 8268 CpG regions of ≥ 60 CpGs eligible for analysis with SOMNiBUS, we identified 131 DMRs and 125 differentially methylated genes (DMGs; p-values less than Bonferroni-corrected threshold of 6.05-06 controlling family-wise error rate at 0.05; 1.6% of the regions). In comparison, bumphunter identified 821,929 CpG regions, 599 DMRs (of which none had ≥ 60 CpGs) and 340 DMGs (q-value of 0.05; 0.04% of all regions). The top ranked gene identified by SOMNiBUS was FLT4, a lymphangiogenic orchestrator, and the top ranked gene on chromosome X was CHST7, known to catalyze the sulfation of glycosaminoglycans in the extracellular matrix. The top networks identified by IPA included connective tissue disorders. CONCLUSIONS SOMNiBUS is a complementary method of analyzing WGBS data that enhances biological insights into SSc and provides novel avenues of investigation into its pathogenesis.
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Affiliation(s)
- Jeffrey C Y Yu
- McGill University, 845 Sherbrooke St W, Montreal, H3A 0G4, Canada
| | - Yixiao Zeng
- McGill University, 845 Sherbrooke St W, Montreal, H3A 0G4, Canada
| | - Kaiqiong Zhao
- McGill University, 845 Sherbrooke St W, Montreal, H3A 0G4, Canada
| | - Tianyuan Lu
- McGill University, 845 Sherbrooke St W, Montreal, H3A 0G4, Canada
| | - Kathleen Oros Klein
- Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Côte Sainte Catherine, Montreal, H3T 1E2, Canada
| | - Inés Colmegna
- McGill University, 845 Sherbrooke St W, Montreal, H3A 0G4, Canada
- Research Institute of the McGill University Health Center, Montreal, Canada
| | - Maximilien Lora
- Research Institute of the McGill University Health Center, Montreal, Canada
| | | | | | - Celia M T Greenwood
- McGill University, 845 Sherbrooke St W, Montreal, H3A 0G4, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Côte Sainte Catherine, Montreal, H3T 1E2, Canada
| | - Marie Hudson
- McGill University, 845 Sherbrooke St W, Montreal, H3A 0G4, Canada.
- Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Côte Sainte Catherine, Montreal, H3T 1E2, Canada.
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Russell SK, Harrison JK, Olson BS, Lee HJ, O'Brien VP, Xing X, Livny J, Yu L, Roberson EDO, Bomjan R, Fan C, Sha M, Estfanous S, Amer AO, Colonna M, Stappenbeck TS, Wang T, Hannan TJ, Hultgren SJ. Uropathogenic Escherichia coli infection-induced epithelial trained immunity impacts urinary tract disease outcome. Nat Microbiol 2023; 8:875-888. [PMID: 37037942 PMCID: PMC10159856 DOI: 10.1038/s41564-023-01346-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/20/2023] [Indexed: 04/12/2023]
Abstract
Previous urinary tract infections (UTIs) can predispose one to future infections; however, the underlying mechanisms affecting recurrence are poorly understood. We previously found that UTIs in mice cause differential bladder epithelial (urothelial) remodelling, depending on disease outcome, that impacts susceptibility to recurrent UTI. Here we compared urothelial stem cell (USC) lines isolated from mice with a history of either resolved or chronic uropathogenic Escherichia coli (UPEC) infection, elucidating evidence of molecular imprinting that involved epigenetic changes, including differences in chromatin accessibility, DNA methylation and histone modification. Epigenetic marks in USCs from chronically infected mice enhanced caspase-1-mediated cell death upon UPEC infection, promoting bacterial clearance. Increased Ptgs2os2 expression also occurred, potentially contributing to sustained cyclooxygenase-2 expression, bladder inflammation and mucosal wounding-responses associated with severe recurrent cystitis. Thus, UPEC infection acts as an epi-mutagen reprogramming the urothelial epigenome, leading to urothelial-intrinsic remodelling and training of the innate response to subsequent infection.
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Affiliation(s)
- Seongmi K Russell
- Department of Molecular Microbiology and Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, MO, USA
| | - Jessica K Harrison
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Benjamin S Olson
- Department of Molecular Microbiology and Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, MO, USA
| | - Hyung Joo Lee
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Valerie P O'Brien
- Department of Molecular Microbiology and Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, MO, USA
- Fred Hutchinson Cancer Center, Human Biology Division, Seattle, WA, USA
| | - Xiaoyun Xing
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Jonathan Livny
- Infectious Disease and Microbiome Program, The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Lu Yu
- Department of Molecular Microbiology and Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, MO, USA
| | - Elisha D O Roberson
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Department of Medicine, Division of Rheumatology, Washington University School of Medicine, St Louis, MO, USA
| | - Rajdeep Bomjan
- Department of Molecular Microbiology and Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, MO, USA
| | - Changxu Fan
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Marina Sha
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Shady Estfanous
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy Helwan University, Cairo, Egypt
| | - Amal O Amer
- Department of Microbial Infection and Immunity, Infectious Diseases Institute, Ohio State University, Columbus, OH, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Thaddeus S Stappenbeck
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA.
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA.
| | - Thomas J Hannan
- Department of Molecular Microbiology and Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
| | - Scott J Hultgren
- Department of Molecular Microbiology and Center for Women's Infectious Disease Research, Washington University School of Medicine, St Louis, MO, USA.
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7
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Singh A, Pajni K, Panigrahi I, Khetarpal P. Clinical and Molecular Heterogeneity of Silver-Russell Syndrome and Therapeutic Challenges: A Systematic Review. Curr Pediatr Rev 2023; 19:157-168. [PMID: 35293298 DOI: 10.2174/1573396318666220315142542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/26/2021] [Accepted: 01/06/2022] [Indexed: 02/08/2023]
Abstract
BACKGROUND Silver-Russell syndrome (SRS) is a developmental disorder involving extreme growth failure, characteristic facial features and underlying genetic heterogeneity. As the clinical heterogeneity of SRS makes diagnosis a challenging task, the worldwide incidence of SRS could vary from 1:30,000 to 1:100,000. Although various chromosomal, genetic, and epigenetic mutations have been linked with SRS, the cause had only been identified in half of the cases. MATERIAL AND METHODS To have a better understanding of the SRS clinical presentation and mutation/ epimutation responsible for SRS, a systematic review of the literature was carried out using appropriate keywords in various scientific databases (PROSPERO protocol registration CRD42021273211). Clinical features of SRS have been compiled and presented corresponding to the specific genetic subtype. An attempt has been made to understand the recurrence risk and the role of model organisms in understanding the molecular mechanisms of SRS pathology, treatment, and management strategies of the affected patients through the analysis of selected literature. RESULTS 156 articles were selected to understand the clinical and molecular heterogeneity of SRS. Information about detailed clinical features was available for 228 patients only, and it was observed that body asymmetry and relative macrocephaly were most prevalent in cases with methylation defects of the 11p15 region. In about 38% of cases, methylation defects in ICRs or genomic mutations at the 11p15 region have been implicated. Maternal uniparental disomy of chromosome 7 (mUPD7) accounts for about 7% of SRS cases, and rarely, uniparental disomy of other autosomes (11, 14, 16, and 20 chromosomes) has been documented. Mutation in half of the cases is yet to be identified. Studies involving mice as experimental animals have been helpful in understanding the underlying molecular mechanism. As the clinical presentation of the syndrome varies a lot, treatment needs to be individualized with multidisciplinary effort. CONCLUSION SRS is a clinically and genetically heterogeneous disorder, with most of the cases being implicated with a mutation in the 11p15 region and maternal disomy of chromosome 7. Recurrence risk varies according to the molecular subtype. Studies with mice as a model organism have been useful in understanding the underlying molecular mechanism leading to the characteristic clinical presentation of the syndrome. Management strategies often need to be individualized due to varied clinical presentations.
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Affiliation(s)
- Amit Singh
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, 151401, India
| | - Ketan Pajni
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, 151401, India
| | - Inusha Panigrahi
- Department of Paediatric Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Preeti Khetarpal
- Department of Human Genetics and Molecular Medicine, School of Health Sciences, Central University of Punjab, Bathinda, 151401, India
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8
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Omar M, Alexiou M, Rekhi UR, Lehmann K, Bhardwaj A, Delyea C, Elahi S, Febbraio M. DNA methylation changes underlie the long-term association between periodontitis and atherosclerotic cardiovascular disease. Front Cardiovasc Med 2023; 10:1164499. [PMID: 37153468 PMCID: PMC10160482 DOI: 10.3389/fcvm.2023.1164499] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 03/22/2023] [Indexed: 05/09/2023] Open
Abstract
Periodontitis, the leading cause of adult tooth loss, has been identified as an independent risk factor for cardiovascular disease (CVD). Studies suggest that periodontitis, like other CVD risk factors, shows the persistence of increased CVD risk even after mitigation. We hypothesized that periodontitis induces epigenetic changes in hematopoietic stem cells in the bone marrow (BM), and such changes persist after the clinical elimination of the disease and underlie the increased CVD risk. We used a BM transplant approach to simulate the clinical elimination of periodontitis and the persistence of the hypothesized epigenetic reprogramming. Using the low-density lipoprotein receptor knockout (LDLRo ) atherosclerosis mouse model, BM donor mice were fed a high-fat diet to induce atherosclerosis and orally inoculated with Porphyromonas gingivalis (Pg), a keystone periodontal pathogen; the second group was sham-inoculated. Naïve LDLR o mice were irradiated and transplanted with BM from one of the two donor groups. Recipients of BM from Pg-inoculated donors developed significantly more atherosclerosis, accompanied by cytokine/chemokines that suggested BM progenitor cell mobilization and were associated with atherosclerosis and/or PD. Using whole-genome bisulfite sequencing, 375 differentially methylated regions (DMRs) and global hypomethylation in recipients of BM from Pg-inoculated donors were observed. Some DMRs pointed to the involvement of enzymes with major roles in DNA methylation and demethylation. In validation assays, we found a significant increase in the activity of ten-eleven translocase-2 and a decrease in the activity of DNA methyltransferases. Plasma S-adenosylhomocysteine levels were significantly higher, and the S-adenosylmethionine to S-adenosylhomocysteine ratio was decreased, both of which have been associated with CVD. These changes may be related to increased oxidative stress as a result of Pg infection. These data suggest a novel and paradigm-shifting mechanism in the long-term association between periodontitis and atherosclerotic CVD.
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9
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Vogt G. Environmental Adaptation of Genetically Uniform Organisms with the Help of Epigenetic Mechanisms-An Insightful Perspective on Ecoepigenetics. EPIGENOMES 2022; 7:1. [PMID: 36648862 PMCID: PMC9844400 DOI: 10.3390/epigenomes7010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/11/2022] [Accepted: 12/15/2022] [Indexed: 12/28/2022] Open
Abstract
Organisms adapt to different environments by selection of the most suitable phenotypes from the standing genetic variation or by phenotypic plasticity, the ability of single genotypes to produce different phenotypes in different environments. Because of near genetic identity, asexually reproducing populations are particularly suitable for the investigation of the potential and molecular underpinning of the latter alternative in depth. Recent analyses on the whole-genome scale of differently adapted clonal animals and plants demonstrated that epigenetic mechanisms such as DNA methylation, histone modifications and non-coding RNAs are among the molecular pathways supporting phenotypic plasticity and that epigenetic variation is used to stably adapt to different environments. Case studies revealed habitat-specific epigenetic fingerprints that were maintained over subsequent years pointing at the existence of epigenetic ecotypes. Environmentally induced epimutations and corresponding gene expression changes provide an ideal means for fast and directional adaptation to changing or new conditions, because they can synchronously alter phenotypes in many population members. Because microorganisms inclusive of human pathogens also exploit epigenetically mediated phenotypic variation for environmental adaptation, this phenomenon is considered a universal biological principle. The production of different phenotypes from the same DNA sequence in response to environmental cues by epigenetic mechanisms also provides a mechanistic explanation for the "general-purpose genotype hypothesis" and the "genetic paradox of invasions".
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Affiliation(s)
- Günter Vogt
- Faculty of Biosciences, University of Heidelberg, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany
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10
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Schaffner SL, Kobor MS. DNA methylation as a mediator of genetic and environmental influences on Parkinson's disease susceptibility: Impacts of alpha-Synuclein, physical activity, and pesticide exposure on the epigenome. Front Genet 2022; 13:971298. [PMID: 36061205 PMCID: PMC9437223 DOI: 10.3389/fgene.2022.971298] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/25/2022] [Indexed: 12/15/2022] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder with a complex etiology and increasing prevalence worldwide. As PD is influenced by a combination of genetic and environment/lifestyle factors in approximately 90% of cases, there is increasing interest in identification of the interindividual mechanisms underlying the development of PD as well as actionable lifestyle factors that can influence risk. This narrative review presents an outline of the genetic and environmental factors contributing to PD risk and explores the possible roles of cytosine methylation and hydroxymethylation in the etiology and/or as early-stage biomarkers of PD, with an emphasis on epigenome-wide association studies (EWAS) of PD conducted over the past decade. Specifically, we focused on variants in the SNCA gene, exposure to pesticides, and physical activity as key contributors to PD risk. Current research indicates that these factors individually impact the epigenome, particularly at the level of CpG methylation. There is also emerging evidence for interaction effects between genetic and environmental contributions to PD risk, possibly acting across multiple omics layers. We speculated that this may be one reason for the poor replicability of the results of EWAS for PD reported to date. Our goal is to provide direction for future epigenetics studies of PD to build upon existing foundations and leverage large datasets, new technologies, and relevant statistical approaches to further elucidate the etiology of this disease.
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Affiliation(s)
- Samantha L. Schaffner
- Edwin S. H. Leong Healthy Aging Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Genetics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Michael S. Kobor
- Edwin S. H. Leong Healthy Aging Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Genetics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
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11
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Dugé de Bernonville T, Daviaud C, Chaparro C, Tost J, Maury S. From Methylome to Integrative Analysis of Tissue Specificity. Methods Mol Biol 2022; 2505:223-240. [PMID: 35732948 DOI: 10.1007/978-1-0716-2349-7_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
DNA methylation is the most studied epigenetic mark in both plants and animals. The gold standard for assaying genome-wide DNA methylation at single-base resolution is whole-genome bisulfite sequencing (WGBS). Here, we describe an improved procedure for WGBS and original bioinformatic workflows applied to unravel tissue-specific variations of the methylome in relation to gene expression and accumulation of secondary metabolites in the medicinal plant Catharanthus roseus.
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Affiliation(s)
- Thomas Dugé de Bernonville
- EA2106 Biomolécules et Biotechnologies Végétales, Université de Tours, Tours, France
- Limagrain, Centre de Recherches de Chappes, Route d'Ennezat, Chappes, France
| | - Christian Daviaud
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Université Paris Saclay, Evry, France
| | - Cristian Chaparro
- UMR5244 IHPE, Université Montpellier, CNRS, IFREMER, Université Perpignan, Perpignan, France
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Université Paris Saclay, Evry, France
| | - Stéphane Maury
- EA1207 USC1328 Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAe, Université d'Orléans, Orléans, France.
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12
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Wilson ER, Helton NM, Heath SE, Fulton RS, Payton JE, Welch JS, Walter MJ, Westervelt P, DiPersio JF, Link DC, Miller CA, Ley TJ, Spencer DH. Focal disruption of DNA methylation dynamics at enhancers in IDH-mutant AML cells. Leukemia 2022; 36:935-945. [PMID: 34873300 PMCID: PMC8979817 DOI: 10.1038/s41375-021-01476-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 11/01/2021] [Accepted: 11/15/2021] [Indexed: 12/17/2022]
Abstract
Recurrent mutations in IDH1 or IDH2 in acute myeloid leukemia (AML) are associated with increased DNA methylation, but the genome-wide patterns of this hypermethylation phenotype have not been comprehensively studied in AML samples. We analyzed whole-genome bisulfite sequencing data from 15 primary AML samples with IDH1 or IDH2 mutations, which identified ~4000 focal regions that were uniquely hypermethylated in IDHmut samples vs. normal CD34+ cells and other AMLs. These regions had modest hypermethylation in AMLs with biallelic TET2 mutations, and levels of 5-hydroxymethylation that were diminished in IDH and TET-mutant samples, indicating that this hypermethylation results from inhibition of TET-mediated demethylation. Focal hypermethylation in IDHmut AMLs occurred at regions with low methylation in CD34+ cells, implying that DNA methylation and demethylation are active at these loci. AML samples containing IDH and DNMT3AR882 mutations were significantly less hypermethylated, suggesting that IDHmut-associated hypermethylation is mediated by DNMT3A. IDHmut-specific hypermethylation was highly enriched for enhancers that form direct interactions with genes involved in normal hematopoiesis and AML, including MYC and ETV6. These results suggest that focal hypermethylation in IDH-mutant AML occurs by altering the balance between DNA methylation and demethylation, and that disruption of these pathways at enhancers may contribute to AML pathogenesis.
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Affiliation(s)
- Elisabeth R. Wilson
- grid.4367.60000 0001 2355 7002Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University, St. Louis, MO USA
| | - Nichole M. Helton
- grid.4367.60000 0001 2355 7002Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University, St. Louis, MO USA
| | - Sharon E. Heath
- grid.4367.60000 0001 2355 7002Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University, St. Louis, MO USA
| | - Robert S. Fulton
- grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University, St. Louis, MO USA
| | - Jacqueline E. Payton
- grid.4367.60000 0001 2355 7002Department of Pathology and Immunology, Washington University, St. Louis, MO USA
| | - John S. Welch
- grid.4367.60000 0001 2355 7002Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University, St. Louis, MO USA
| | - Matthew J. Walter
- grid.4367.60000 0001 2355 7002Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University, St. Louis, MO USA
| | - Peter Westervelt
- grid.4367.60000 0001 2355 7002Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University, St. Louis, MO USA
| | - John F. DiPersio
- grid.4367.60000 0001 2355 7002Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University, St. Louis, MO USA
| | - Daniel C. Link
- grid.4367.60000 0001 2355 7002Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University, St. Louis, MO USA
| | - Christopher A. Miller
- grid.4367.60000 0001 2355 7002Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University, St. Louis, MO USA
| | - Timothy J. Ley
- grid.4367.60000 0001 2355 7002Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University, St. Louis, MO USA
| | - David H. Spencer
- grid.4367.60000 0001 2355 7002Department of Medicine, Division of Oncology, Section of Stem Cell Biology, Washington University, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002Department of Pathology and Immunology, Washington University, St. Louis, MO USA ,grid.4367.60000 0001 2355 7002McDonnell Genome Institute, Washington University, St. Louis, MO USA
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13
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Zhang J, Xie S, Xu J, Liu H, Wan S. Cancer Biomarkers Discovery of Methylation Modification With Direct High-Throughput Nanopore Sequencing. Front Genet 2021; 12:672804. [PMID: 34122526 PMCID: PMC8188482 DOI: 10.3389/fgene.2021.672804] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/07/2021] [Indexed: 01/12/2023] Open
Abstract
Cancer is a complex disease, driven by a combination of genetic and epigenetic alterations. DNA and RNA methylation modifications are the most common epigenetic events that play critical roles in cancer development and progression. Bisulfite converted sequencing is a widely used technique to detect base modifications in DNA methylation, but its main drawbacks lie in DNA degradation, lack of specificity, or short reads with low sequence diversity. The nanopore sequencing technology can directly detect base modifications in native DNA as well as RNA without harsh chemical treatment, compared to bisulfite sequencing. Furthermore, CRISPR/Cas9-targeted enrichment nanopore sequencing techniques are straightforward and cost-effective when targeting genomic regions are of interest. In this review, we mainly focus on DNA and RNA methylation modification detection in cancer with the current nanopore sequencing approaches. We also present the respective strengths, weaknesses of nanopore sequencing techniques, and their future translational applications in identification of epigenetic biomarkers for cancer detection and prognosis.
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Affiliation(s)
- Junjie Zhang
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou, China
| | - Shuilian Xie
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou, China
| | - Jingxiang Xu
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou, China
| | - Hui Liu
- Institute of Hepatology, The Affiliated Fifth People’s Hospital of Ganzhou, Gannan Medical University, Ganzhou, China
| | - Shaogui Wan
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou, China
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14
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Vandenbussche I, Sass A, Van Nieuwerburgh F, Pinto-Carbó M, Mannweiler O, Eberl L, Coenye T. Detection of cytosine methylation in Burkholderia cenocepacia by single-molecule real-time sequencing and whole-genome bisulfite sequencing. MICROBIOLOGY-SGM 2021; 167. [PMID: 33565960 DOI: 10.1099/mic.0.001027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Research on prokaryotic epigenetics, the study of heritable changes in gene expression independent of sequence changes, led to the identification of DNA methylation as a versatile regulator of diverse cellular processes. Methylation of adenine bases is often linked to regulation of gene expression in bacteria, but cytosine methylation is also frequently observed. In this study, we present a complete overview of the cytosine methylome in Burkholderia cenocepacia, an opportunistic respiratory pathogen in cystic fibrosis patients. Single-molecule real-time (SMRT) sequencing was used to map all 4mC-modified cytosines, as analysis of the predicted MTases in the B. cenocepacia genome revealed the presence of a 4mC-specific phage MTase, M.BceJII, targeting GGCC sequences. Methylation motif GCGGCCGC was identified, and out of 6850 motifs detected across the genome, 2051 (29.9 %) were methylated at the fifth position. Whole-genome bisulfite sequencing (WGBS) was performed to map 5mC methylation and 1635 5mC-modified cytosines were identified in CpG motifs. A comparison of the genomic positions of the modified bases called by each method revealed no overlap, which confirmed the authenticity of the detected 4mC and 5mC methylation by SMRT sequencing and WGBS, respectively. Large inter-strain variation of the 4mC-methylated cytosines was observed when B. cenocepacia strains J2315 and K56-2 were compared, which suggests that GGCC methylation patterns in B. cenocepacia are strain-specific. It seems likely that 4mC methylation of GGCC is not involved in regulation of gene expression but rather is a remnant of bacteriophage invasion, in which methylation of the phage genome was crucial for protection against restriction-modification systems of B. cenocepacia.
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Affiliation(s)
- Ian Vandenbussche
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Andrea Sass
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | | | - Marta Pinto-Carbó
- Department of Plant and Microbial Microbiology, University of Zurich, Zurich, Switzerland
| | - Olga Mannweiler
- Department of Plant and Microbial Microbiology, University of Zurich, Zurich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Microbiology, University of Zurich, Zurich, Switzerland
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
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15
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Ali A, Han K, Liang P. Role of Transposable Elements in Gene Regulation in the Human Genome. Life (Basel) 2021; 11:118. [PMID: 33557056 PMCID: PMC7913837 DOI: 10.3390/life11020118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 01/28/2021] [Accepted: 02/02/2021] [Indexed: 02/07/2023] Open
Abstract
Transposable elements (TEs), also known as mobile elements (MEs), are interspersed repeats that constitute a major fraction of the genomes of higher organisms. As one of their important functional impacts on gene function and genome evolution, TEs participate in regulating the expression of genes nearby and even far away at transcriptional and post-transcriptional levels. There are two known principal ways by which TEs regulate the expression of genes. First, TEs provide cis-regulatory sequences in the genome with their intrinsic regulatory properties for their own expression, making them potential factors for regulating the expression of the host genes. TE-derived cis-regulatory sites are found in promoter and enhancer elements, providing binding sites for a wide range of trans-acting factors. Second, TEs encode for regulatory RNAs with their sequences showed to be present in a substantial fraction of miRNAs and long non-coding RNAs (lncRNAs), indicating the TE origin of these RNAs. Furthermore, TEs sequences were found to be critical for regulatory functions of these RNAs, including binding to the target mRNA. TEs thus provide crucial regulatory roles by being part of cis-regulatory and regulatory RNA sequences. Moreover, both TE-derived cis-regulatory sequences and TE-derived regulatory RNAs have been implicated in providing evolutionary novelty to gene regulation. These TE-derived regulatory mechanisms also tend to function in a tissue-specific fashion. In this review, we aim to comprehensively cover the studies regarding these two aspects of TE-mediated gene regulation, mainly focusing on the mechanisms, contribution of different types of TEs, differential roles among tissue types, and lineage-specificity, based on data mostly in humans.
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Affiliation(s)
- Arsala Ali
- Department of Biological Sciences, Brock University, St. Catharines, ON L2S 3A1, Canada;
| | - Kyudong Han
- Department of Microbiology, Dankook University, Cheonan 31116, Korea;
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea
| | - Ping Liang
- Department of Biological Sciences, Brock University, St. Catharines, ON L2S 3A1, Canada;
- Centre of Biotechnologies, Brock University, St. Catharines, ON L2S 3A1, Canada
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16
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Li S, Tollefsbol TO. DNA methylation methods: Global DNA methylation and methylomic analyses. Methods 2020; 187:28-43. [PMID: 33039572 DOI: 10.1016/j.ymeth.2020.10.002] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022] Open
Abstract
DNA methylation provides a pivotal layer of epigenetic regulation in eukaryotes that has significant involvement for numerous biological processes in health and disease. The function of methylation of cytosine bases in DNA was originally proposed as a "silencing" epigenetic marker and focused on promoter regions of genes for decades. Improved technologies and accumulating studies have been extending our understanding of the roles of DNA methylation to various genomic contexts including gene bodies, repeat sequences and transcriptional start sites. The demand for comprehensively describing DNA methylation patterns spawns a diversity of DNA methylation profiling technologies that target its genomic distribution. These approaches have enabled the measurement of cytosine methylation from specific loci at restricted regions to single-base-pair resolution on a genome-scale level. In this review, we discuss the different DNA methylation analysis technologies primarily based on the initial treatments of DNA samples: bisulfite conversion, endonuclease digestion and affinity enrichment, involving methodology evolution, principles, applications, and their relative merits. This review may offer referable information for the selection of various platforms for genome-wide analysis of DNA methylation.
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Affiliation(s)
- Shizhao Li
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States.
| | - Trygve O Tollefsbol
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States; Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Center for Healthy Aging, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, United States.
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17
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Li Y, Wei Z, Huang S, Yang B. mRNA expression and DNA methylation analysis of the inhibitory mechanism of H 2O 2 on the proliferation of A549 cells. Oncol Lett 2020; 20:288. [PMID: 33014166 PMCID: PMC7520746 DOI: 10.3892/ol.2020.12151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 08/18/2020] [Indexed: 01/29/2023] Open
Abstract
Reactive oxygen species, particularly hydrogen peroxide (H2O2), can induce proliferation inhibition and death of A549 cells via oxidative stress. Oxidative stress has effect on DNA methylation. Oxidative stress and DNA methylation feature a common denominator: The one carbon cycle. To explore the inhibitory mechanism of H2O2 on the proliferation of lung cancer cells, the present study analysed the mRNA expression and methylation profiles in A549 cells treated with H2O2 for 24 h, as adenocarcinoma is the most common pathological type of lung cancer. The DNA methylation profile was constructed using reduced representation bisulphite sequencing, which identified 29,755 differentially methylated sites (15,365 upregulated and 14,390 downregulated), and 1,575 differentially methylated regions located in the gene promoters were identified using the methylKit. Analysis of the assocaition between gene expression and methylation levels revealed that several genes were downregulated and hypermethylated, including cyclin-dependent kinase inhibitor 3, denticleless E3 ubiquitin protein ligase homolog, centromere protein (CENP)F, kinesin family member (KIF)20A, CENPA, KIF11, PCNA clamp-associated factor and GINS complex subunit 2, which may be involved in the inhibitory process of H2O2 on the proliferation of A549 cells.
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Affiliation(s)
- Yepeng Li
- Department of Oncology, Biomedical Research Center, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi Zhuang Autonomous Region 533000, P.R. China
| | - Zhongheng Wei
- Department of Oncology, Biomedical Research Center, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi Zhuang Autonomous Region 533000, P.R. China
| | - Shiqing Huang
- Department of Oncology, Biomedical Research Center, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi Zhuang Autonomous Region 533000, P.R. China
| | - Bo Yang
- Key Laboratory of Guangxi College and Universities, Biomedical Research Center, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi Zhuang Autonomous Region 533000, P.R. China
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18
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Oxidative Bisulfite Sequencing: An Experimental and Computational Protocol. Methods Mol Biol 2020. [PMID: 32822043 DOI: 10.1007/978-1-0716-0876-0_26] [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: 08/31/2023]
Abstract
Bisulfite sequencing (BS-seq) remains the gold standard technique to quantitively map DNA methylation at a single-base resolution. However, BS-seq cannot discriminate between 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Oxidative bisulfite sequencing (oxBS-seq) was one of the first techniques that enabled absolute quantification of 5mC and 5hmC at single-base resolution. OxBS-seq uses chemical oxidation of 5hmC prior to bisulfite treatment to provide a direct readout of 5mC; comparison with BS-seq data can then be used to infer 5hmC levels. Here we describe in detail an updated version of our laboratory's oxBS-seq protocol, which uses potassium perruthenate (KRuO4) as an oxidant. We also describe a bioinformatics pipeline designed to handle Illumina short read sequencing data from whole-genome oxBS-seq.
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19
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Li Y. Modern epigenetics methods in biological research. Methods 2020; 187:104-113. [PMID: 32645449 DOI: 10.1016/j.ymeth.2020.06.022] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/23/2020] [Accepted: 06/29/2020] [Indexed: 01/09/2023] Open
Abstract
The definition of epigenetics refers that molecular modifications on DNA that can regulate gene activity are independent of DNA sequence and mitotically stable. Notably, epigenetics studies have grown exponentially in the past few years. Recent progresses that lead to exciting discoveries and groundbreaking nature of this area demand thorough methodologies and advanced technologies to move epigenetics to the forefront of molecular biology. The most recognized epigenetic regulations are DNA methylation, histone modifications, and non-coding RNAs (ncRNAs). This review will discuss the modern techniques that are available to detect locus-specific and genome-wide changes for all epigenetic codes. Furthermore, updated analysis of technologies, newly developed methods, recent breakthroughs and bioinformatics pipelines in epigenetic analysis will be presented. These methods, as well as many others presented in this specific issue, provide comprehensive guidelines in the area of epigenetics that facilitate further developments in this promising and rapidly developing field.
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Affiliation(s)
- Yuanyuan Li
- Department of Obstetrics, Gynecology & Women's Heath, University of Missouri, Columbia, MO 65212, USA; Department of Surgery, University of Missouri, Columbia, MO 65212, USA.
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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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Analysis of DNA methylation differences in gonads of the large yellow croaker. Gene 2020; 749:144754. [PMID: 32376450 DOI: 10.1016/j.gene.2020.144754] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 11/20/2022]
Abstract
DNA methylation is an essential epigenetic modification that significantly regulates gene expression during development and differentiation. In this study, genome-wide methylation analysis of different gonads of the large yellow croaker was performed using whole-genome bisulfite sequencing (WGBS), which has characterized DNA methylation patterns in gonad tissue and identified candidate regions for future studies. Clustering analysis revealed that male and neomale methylation patterns were close compared to female. Based on KEGG pathway analysis of differentially methylated genes, we obtained signaling pathways related to gonadal development. We further investigated the methylation status of previously reported sex determination genes, and found that these genes showed different methylation status in three types of gonads, which may provide important clues to reveal the sex determination genes in the large yellow croaker. Furthermore, combined with transcriptome analysis, we found 7 sex-related genes in three comparison groups where expression negatively correlated with methylation.
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Comparison of commercially available whole-genome sequencing kits for variant detection in circulating cell-free DNA. Sci Rep 2020; 10:6190. [PMID: 32277101 PMCID: PMC7148341 DOI: 10.1038/s41598-020-63102-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 03/19/2020] [Indexed: 12/13/2022] Open
Abstract
Circulating cell-free DNA (ccfDNA) has great potential for non-invasive diagnosis, prognosis and monitoring treatment of disease. However, a sensitive and specific whole-genome sequencing (WGS) method is required to identify novel genetic variations (i.e., SNVs, CNVs and INDELS) on ccfDNA that can be used as clinical biomarkers. In this article, five WGS methods were compared: ThruPLEX Plasma-seq, QIAseq cfDNA All-in-One, NEXTFLEX Cell Free DNA-seq, Accel-NGS 2 S PCR FREE DNA and Accel-NGS 2 S PLUS DNA. The Accel PCR-free kit did not produce enough material for sequencing. The other kits had significant common number of SNVs, INDELs and CNVs and showed similar results for SNVs and CNVs. The detection of variants and genomic signatures depends more upon the type of plasma sample rather than the WGS method used. Accel detected several variants not observed by the other kits. ThruPLEX seemed to identify more low-abundant SNVs and SNV signatures were similar to signatures observed with the QIAseq kit. Accel and NEXTFLEX had similar CNV and SNV signatures. These results demonstrate the importance of establishing a standardized workflow for identifying non-invasive candidate biomarkers. Moreover, the combination of variants discovered in ccfDNA using WGS has the potential to identify enrichment pathways, while the analysis of signatures could identify new subgroups of patients.
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Martins C, Dreij K, Costa PM. The State-of-the Art of Environmental Toxicogenomics: Challenges and Perspectives of "Omics" Approaches Directed to Toxicant Mixtures. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16234718. [PMID: 31779274 PMCID: PMC6926496 DOI: 10.3390/ijerph16234718] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/23/2019] [Accepted: 11/25/2019] [Indexed: 12/17/2022]
Abstract
The last decade witnessed extraordinary advances in “omics” methods, particularly transcriptomics, proteomics and metabolomics, enabling toxicologists to integrate toxicokinetics and toxicodynamics with mechanistic insights on the mode-of-action of noxious chemicals, single or combined. The toxicology of mixtures is, nonetheless, a most challenging enterprise, especially for environmental toxicologists and ecotoxicologists, who invariably deal with chemical mixtures, many of which contain unknowns. Despite costs and demanding computations, the systems toxicology framework, of which “omics” is a major component, endeavors extracting adverse outcome pathways for complex mixtures. Still, the interplay between the multiple components of gene expression and cell metabolism tends to be overlooked. As an example, the proteome allocates DNA methyltransferases whose altered transcription or loss of function by action of chemicals can have a global impact on gene expression in the cell. On the other hand, chemical insult can produce reactive metabolites and radicals that can intercalate or bind to DNA as well as to enzymes and structural proteins, compromising their activity. These examples illustrate the importance of exploring multiple “omes” and the purpose of “omics” and multi-“omics” for building truly predictive models of hazard and risk. Here we will review the state-of-the-art of toxicogenomics highlighting successes, shortcomings and perspectives for next-generation environmental toxicologists.
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Affiliation(s)
- Carla Martins
- UCIBIO—Applied Molecular Biosciences Unit, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Unit of Biochemical Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Box 210, SE-171 77 Stockholm, Sweden;
- Correspondence: (C.M.); (P.M.C.); Tel.: +351-212-948-300 (ext. 11103) (P.M.C.)
| | - Kristian Dreij
- Unit of Biochemical Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Box 210, SE-171 77 Stockholm, Sweden;
| | - Pedro M. Costa
- UCIBIO—Applied Molecular Biosciences Unit, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
- Correspondence: (C.M.); (P.M.C.); Tel.: +351-212-948-300 (ext. 11103) (P.M.C.)
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Mardis ER. The Impact of Next-Generation Sequencing on Cancer Genomics: From Discovery to Clinic. Cold Spring Harb Perspect Med 2019; 9:cshperspect.a036269. [PMID: 30397020 DOI: 10.1101/cshperspect.a036269] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The application of next-generation sequencing (NGS) technology to the study of cancer genomes has been transformational. Not only has this technology revealed the genetic and epigenetic underpinnings of disease onset and progression, but also has redefined our clinical diagnosis and treatment paradigms. This rapid translation from discovery to clinical platform has occurred in the context of new pharmaceutical paradigms, enabling the use of NGS for the diagnosis and definition of therapeutic vulnerabilities of cancer. This review explores this transformation and identifies cutting-edge applications of NGS that will result in its additional utility in cancer care.
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Affiliation(s)
- Elaine R Mardis
- The Ohio State University College of Medicine, Columbus, Ohio 43205
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Xu SJ, Heller EA. Recent advances in neuroepigenetic editing. Curr Opin Neurobiol 2019; 59:26-33. [PMID: 31015104 DOI: 10.1016/j.conb.2019.03.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/28/2019] [Accepted: 03/18/2019] [Indexed: 02/09/2023]
Abstract
A wealth of studies in the mammalian nervous system indicate the role of epigenetic gene regulation in both basic neurobiological function and disease. However, the relationship between epigenetic regulation and neuropathology is largely correlational due to the presence of mixed cell populations within brain regions and the genome-wide effects of classical approaches to manipulate the epigenome. Locus-specific epigenetic editing allows direct epigenetic regulation of specific genes to elucidate the direct causal relationship between epigenetic modifications and transcription. This review discusses some of the latest innovations in the efficacy and flexibility in this approach that hold promise for neurobiological application.
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Affiliation(s)
- Song-Jun Xu
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth A Heller
- Department of Systems Pharmacology and Translational Therapeutics and Penn Epigenetics Institute, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA, USA.
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26
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Highly sensitive detection of DNA hypermethylation in melanoma cancer cells. Biosens Bioelectron 2018; 124-125:136-142. [PMID: 30366258 DOI: 10.1016/j.bios.2018.10.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 10/02/2018] [Accepted: 10/10/2018] [Indexed: 12/31/2022]
Abstract
Aberrant hypermethylation of CpG islands in the promoter region of tumor suppressor genes is a promising biomarker for early cancer detection. This methylation status is reflected in the methylation pattern of ctDNA shed from the primary tumor; however, to realize the full clinical utility of ctDNA methylation detection via liquid biopsy for early cancer diagnosis, improvements in the sensitivity and multiplexability of existing technologies must be improved. Additionally, the assay must be cheap and easy to perform in a clinical setting. We report the integration of methylation specific PCR (MSP) to melt curve analysis on giant magnetoresistive (GMR) biosensors to greatly enhance the sensitivity of our DNA hybridization assay for methylation detection. Our GMR sensor is functionalized with synthetic DNA probes that target methylated or unmethylated CpG sites in the MSP amplicon, and measures the difference in melting temperature (Tm) between the two probes (ΔTm), giving an analytical limit of detection down to 0.1% methylated DNA in solution. Additionally, linear regression of ΔTm's for serial dilutions of methylated:unmethylated mixtures allows for quantification of methylation percentage, which could have diagnostic and prognostic utility. Lastly, we performed multiplexed MSP on two different genes, and show the ability of our GMR assay to resolve this mixture, despite their amplicons' overlapping Tm's in standard EvaGreen melt analysis. The multiplexing ability of our assay and its enhanced sensitivity, without necessitating deep sequencing, represent important steps toward realizing an assay for the detection of methylated ctDNA in plasma for early cancer detection in a clinical setting.
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