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Epigenetic Biomarkers
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Epigenetic Biomarkers

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Human Genomics and Genetic Diseases".

Deadline for manuscript submissions: closed (30 June 2015) | Viewed by 58797

Special Issue Editors

Dr. Jeffrey Craig

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Guest Editor
1. Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia
2. Department of Paediatrics, The University of Melbourne, Parkville, VIC 3052, Australia
Interests: epigenetics, methylation, twins, developmental origins of disease, gene regulation, nature or nurture, cardiovascular disease, neurodevelopment
Dr. Thomas Mikeska

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Guest Editor
Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia
Interests: cancer epigenetics; DNA methylation; cancer genetics; translational cancer research; personalized medicine; methodologies for genetic and DNA methylation analysis

Special Issue Information

Dear Colleagues,

Writing our 2014 review in Genes on DNA methylation biomarkers made us both realize that this was a fast-moving field. It stretches from biomarker discovery, through development through to clinical implementation. The vast majority of epigenetic biomarkers, in particular DNA methylation biomarkers, come from the fast progressing area of cancer research. However, there are also advances being made in the field of environmental epigenomics and epigenomics of chronic diseases such as cardiovascular disease and type 2 diabetes. We would like to summarize, in a single issue of Genes, the state of the epigenetic biomarkers field in late 2015 by showcasing the best research from around the world. We are flexible about the length and format of articles (original research or review) and flexible about the particular stage of epigenetic biomarker development, from discovery to the clinic. This also includes applications of innovative and clinical relevant methodologies for epigenetic biomarker detection and measurement. We hope you share our interest in this fascinating area and can join us in this exciting undertaking.

Prof. Dr. Jeffrey Craig
Dr. Thomas Mikeska
Guest Editors

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.


Keywords

  • biomarkers
  • epigenetics
  • DNA methylation
  • histone modifications
  • cancer
  • chronic disease
  • predisposition
  • risk prediction
  • diagnosis
  • prognosis
  • methods

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Published Papers (7 papers)

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Research

Jump to: Review

24 pages, 3014 KiB  
Article
COBRA-Seq: Sensitive and Quantitative Methylome Profiling
by Hilal Varinli, Aaron L. Statham, Susan J. Clark, Peter L. Molloy and Jason P. Ross
Genes 2015, 6(4), 1140-1163; https://doi.org/10.3390/genes6041140 - 23 Oct 2015
Cited by 10 | Viewed by 8062
Abstract
Combined Bisulfite Restriction Analysis (COBRA) quantifies DNA methylation at a specific locus. It does so via digestion of PCR amplicons produced from bisulfite-treated DNA, using a restriction enzyme that contains a cytosine within its recognition sequence, such as TaqI. Here, we introduce [...] Read more.
Combined Bisulfite Restriction Analysis (COBRA) quantifies DNA methylation at a specific locus. It does so via digestion of PCR amplicons produced from bisulfite-treated DNA, using a restriction enzyme that contains a cytosine within its recognition sequence, such as TaqI. Here, we introduce COBRA-seq, a genome wide reduced methylome method that requires minimal DNA input (0.1–1.0 mg) and can either use PCR or linear amplification to amplify the sequencing library. Variants of COBRA-seq can be used to explore CpG-depleted as well as CpG-rich regions in vertebrate DNA. The choice of enzyme influences enrichment for specific genomic features, such as CpG-rich promoters and CpG islands, or enrichment for less CpG dense regions such as enhancers. COBRA-seq coupled with linear amplification has the additional advantage of reduced PCR bias by producing full length fragments at high abundance. Unlike other reduced representative methylome methods, COBRA-seq has great flexibility in the choice of enzyme and can be multiplexed and tuned, to reduce sequencing costs and to interrogate different numbers of sites. Moreover, COBRA-seq is applicable to non-model organisms without the reference genome and compatible with the investigation of non-CpG methylation by using restriction enzymes containing CpA, CpT, and CpC in their recognition site. Full article
(This article belongs to the Special Issue Epigenetic Biomarkers)
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14 pages, 1347 KiB  
Article
Hypermethylation of the VTRNA1-3 Promoter is Associated with Poor Outcome in Lower Risk Myelodysplastic Syndrome Patients
by Alexandra Søgaard Helbo, Marianne Treppendahl, Derya Aslan, Konstantinos Dimopoulos, Cecilie Nandrup-Bus, Mette Skov Holm, Mette Klarskov Andersen, Gangning Liang, Lasse Sommer Kristensen and Kirsten Grønbæk
Genes 2015, 6(4), 977-990; https://doi.org/10.3390/genes6040977 - 14 Oct 2015
Cited by 19 | Viewed by 7493
Abstract
Myelodysplastic syndrome (MDS) is a heterogeneous group of clonal hematopoietic disorders. MDS is frequently associated with deletions on chromosome 5q as well as aberrant DNA methylation patterns including hypermethylation of key tumor suppressors. We have previously shown that hypermethylation and silencing of the [...] Read more.
Myelodysplastic syndrome (MDS) is a heterogeneous group of clonal hematopoietic disorders. MDS is frequently associated with deletions on chromosome 5q as well as aberrant DNA methylation patterns including hypermethylation of key tumor suppressors. We have previously shown that hypermethylation and silencing of the non-coding RNA VTRNA2-1 are correlated with poor outcomes in acute myeloid leukemia patients. In this study, we find that VTRNA1-2 and VTRNA1-3, both located on chromosome 5q, can be regulated and silenced by promoter DNA methylation, and that the hypomethylating agent 5-aza-2-deoxycytidine causes reactivation these genes. In normal hematopoiesis, we find that vault RNAs (vtRNAs) show differential methylation between various hematopoietic cell populations, indicating that allele-specific methylation events may occur during hematopoiesis. In addition, we show that VTRNA1-3 promoter hypermethylation is frequent in lower risk MDS patients and is associated with a decreased overall survival. Full article
(This article belongs to the Special Issue Epigenetic Biomarkers)
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23 pages, 1567 KiB  
Article
Heterogeneous DNA Methylation Patterns in the GSTP1 Promoter Lead to Discordant Results between Assay Technologies and Impede Its Implementation as Epigenetic Biomarkers in Breast Cancer
by Grethe I. Grenaker Alnaes, Jo Anders Ronneberg, Vessela N. Kristensen and Jörg Tost
Genes 2015, 6(3), 878-900; https://doi.org/10.3390/genes6030878 - 17 Sep 2015
Cited by 18 | Viewed by 6763
Abstract
Altered DNA methylation patterns are found in many diseases, particularly in cancer, where the analysis of DNA methylation holds the promise to provide diagnostic, prognostic and predictive information of great clinical value. Methylation of the promoter-associated CpG island of GSTP1 occurs in many [...] Read more.
Altered DNA methylation patterns are found in many diseases, particularly in cancer, where the analysis of DNA methylation holds the promise to provide diagnostic, prognostic and predictive information of great clinical value. Methylation of the promoter-associated CpG island of GSTP1 occurs in many hormone-sensitive cancers, has been shown to be a biomarker for the early detection of cancerous lesions and has been associated with important clinical parameters, such as survival and response to treatment. In the current manuscript, we assessed the performance of several widely-used sodium bisulfite conversion-dependent methods (methylation-specific PCR, MethyLight, pyrosequencing and MALDI mass-spectrometry) for the analysis of DNA methylation patterns in the GSTP1 promoter. We observed large discordances between the results obtained by the different technologies. Cloning and sequencing of the investigated region resolved single-molecule DNA methylation patterns and identified heterogeneous DNA methylation patterns as the underlying cause of the differences. Heterogeneous DNA methylation patterns in the GSTP1 promoter constitute a major obstacle to the implementation of DNA methylation-based analysis of GSTP1 and might explain some of the contradictory findings in the analysis of the significance of GSTP1 promoter methylation in breast cancer. Full article
(This article belongs to the Special Issue Epigenetic Biomarkers)
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Review

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19 pages, 249 KiB  
Review
Cord Blood DNA Methylation Biomarkers for Predicting Neurodevelopmental Outcomes
by Nicolette A. Hodyl, Claire T. Roberts and Tina Bianco-Miotto
Genes 2016, 7(12), 117; https://doi.org/10.3390/genes7120117 - 3 Dec 2016
Cited by 26 | Viewed by 6754
Abstract
Adverse environmental exposures in pregnancy can significantly alter the development of the fetus resulting in impaired child neurodevelopment. Such exposures can lead to epigenetic alterations like DNA methylation, which may be a marker of poor cognitive, motor and behavioral outcomes in the infant. [...] Read more.
Adverse environmental exposures in pregnancy can significantly alter the development of the fetus resulting in impaired child neurodevelopment. Such exposures can lead to epigenetic alterations like DNA methylation, which may be a marker of poor cognitive, motor and behavioral outcomes in the infant. Here we review studies that have assessed DNA methylation in cord blood following maternal exposures that may impact neurodevelopment of the child. We also highlight some key studies to illustrate the potential for DNA methylation to successfully identify infants at risk for poor outcomes. While the current evidence is limited, in that observations to date are largely correlational, in time and with larger cohorts analyzed and longer term follow-up completed, we may be able to develop epigenetic biomarkers that not only indicate adverse early life exposures but can also be used to identify individuals likely to be at an increased risk of impaired neurodevelopment even in the absence of detailed information regarding prenatal environment. Full article
(This article belongs to the Special Issue Epigenetic Biomarkers)
26 pages, 725 KiB  
Review
Epigenetic Biomarkers of Preterm Birth and Its Risk Factors
by Anna K. Knight and Alicia K. Smith
Genes 2016, 7(4), 15; https://doi.org/10.3390/genes7040015 - 13 Apr 2016
Cited by 32 | Viewed by 9398
Abstract
A biomarker is a biological measure predictive of a normal or pathogenic process or response. Biomarkers are often useful for making clinical decisions and determining treatment course. One area where such biomarkers would be particularly useful is in identifying women at risk for [...] Read more.
A biomarker is a biological measure predictive of a normal or pathogenic process or response. Biomarkers are often useful for making clinical decisions and determining treatment course. One area where such biomarkers would be particularly useful is in identifying women at risk for preterm delivery and related pregnancy complications. Neonates born preterm have significant morbidity and mortality, both in the perinatal period and throughout the life course, and identifying women at risk of delivering preterm may allow for targeted interventions to prevent or delay preterm birth (PTB). In addition to identifying those at increased risk for preterm birth, biomarkers may be able to distinguish neonates at particular risk for future complications due to modifiable environmental factors, such as maternal smoking or alcohol use during pregnancy. Currently, there are no such biomarkers available, though candidate gene and epigenome-wide association studies have identified DNA methylation differences associated with PTB, its risk factors and its long-term outcomes. Further biomarker development is crucial to reducing the health burden associated with adverse intrauterine conditions and preterm birth, and the results of recent DNA methylation studies may advance that goal. Full article
(This article belongs to the Special Issue Epigenetic Biomarkers)
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23 pages, 1499 KiB  
Review
Characterization of DNA Methylation in Circulating Tumor Cells
by Constantin F. Pixberg, Wolfgang A. Schulz, Nikolas H. Stoecklein and Rui P. L. Neves
Genes 2015, 6(4), 1053-1075; https://doi.org/10.3390/genes6041053 - 21 Oct 2015
Cited by 48 | Viewed by 10031
Abstract
Epigenetics contributes to molecular mechanisms leading to tumor cell transformation and systemic progression of cancer. However, the dynamics of epigenetic remodeling during metastasis remains unexplored. In this context, circulating tumor cells (CTCs) might enable a direct insight into epigenetic mechanisms relevant for metastasis [...] Read more.
Epigenetics contributes to molecular mechanisms leading to tumor cell transformation and systemic progression of cancer. However, the dynamics of epigenetic remodeling during metastasis remains unexplored. In this context, circulating tumor cells (CTCs) might enable a direct insight into epigenetic mechanisms relevant for metastasis by providing direct access to systemic cancer. CTCs can be used as prognostic markers in cancer patients and are regarded as potential metastatic precursor cells. However, despite substantial technical progress, the detection and molecular characterization of CTCs remain challenging, in particular the analysis of DNA methylation. As recent studies have started to address the epigenetic state of CTCs, we discuss here the potential of such investigations to elucidate mechanisms of metastasis and to develop tumor biomarkers. Full article
(This article belongs to the Special Issue Epigenetic Biomarkers)
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32 pages, 1194 KiB  
Review
Current and Future Prospects for Epigenetic Biomarkers of Substance Use Disorders
by Allan M. Andersen, Meeshanthini V. Dogan, Steven R.H. Beach and Robert A. Philibert
Genes 2015, 6(4), 991-1022; https://doi.org/10.3390/genes6040991 - 14 Oct 2015
Cited by 65 | Viewed by 9491
Abstract
Substance abuse has an enormous impact on economic and quality of life measures throughout the world. In more developed countries, overutilization of the most common forms of substances of abuse, alcohol and tobacco, is addressed primarily through prevention of substance use initiation and [...] Read more.
Substance abuse has an enormous impact on economic and quality of life measures throughout the world. In more developed countries, overutilization of the most common forms of substances of abuse, alcohol and tobacco, is addressed primarily through prevention of substance use initiation and secondarily through the treatment of those with substance abuse or dependence. In general, these therapeutic approaches to substance abuse are deemed effective. However, there is a broad consensus that the development of additional tools to aid diagnosis, prioritize treatment selection and monitor treatment response could have substantial impact on the effectiveness of both substance use prevention and treatment. The recent demonstrations by a number of groups that substance use exposure is associated with robust changes in DNA methylation signatures of peripheral blood cells suggests the possibility that methylation assessments of blood or saliva could find broad clinical applications. In this article, we review recent progress in epigenetic approaches to substance use assessment with a particular emphasis on smoking (and alcohol) related applications. In addition, we highlight areas, such as the epigenetics of psychostimulant, opioid and cannabis abuse, which are markedly understudied and could benefit from intensified collaborative efforts to define epigenetic biomarkers of abuse and dependence. Full article
(This article belongs to the Special Issue Epigenetic Biomarkers)
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