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Chowdhury B, Cho IH, Irudayaraj J. Technical advances in global DNA methylation analysis in human cancers. J Biol Eng. 2017;11:10doi: 10.1186/s13036-017-0052-9.
Chowdhury, B., Cho, I. H., & Irudayaraj, J. (2017). Technical advances in global DNA methylation analysis in human cancers. Journal of biological engineering, 1110. https://doi.org/10.1186/s13036-017-0052-9
Chowdhury, Basudev, et al. "Technical advances in global DNA methylation analysis in human cancers." Journal of biological engineering vol. 11 (2017): 10. doi: https://doi.org/10.1186/s13036-017-0052-9
Chowdhury B, Cho IH, Irudayaraj J. Technical advances in global DNA methylation analysis in human cancers. J Biol Eng. 2017 Mar 01;11:10. doi: 10.1186/s13036-017-0052-9. eCollection 2017. PMID: 28261325; PMCID: PMC5331624.
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J Biol Eng. 2017 Mar 01;11:10. doi: 10.1186/s13036-017-0052-9. eCollection 2017.

Technical advances in global DNA methylation analysis in human cancers.

Journal of biological engineering

Basudev Chowdhury, Il-Hoon Cho, Joseph Irudayaraj

Affiliations

  1. Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, 47907 IN USA.
  2. Department of Biomedical Laboratory Science, College of Health Science, Eulji University, Seongnam, 461-713 Republic of Korea.
  3. Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907 USA.

PMID: 28261325 PMCID: PMC5331624 DOI: 10.1186/s13036-017-0052-9

Abstract

Prototypical abnormalities of genome-wide DNA methylation constitute the most widely investigated epigenetic mechanism in human cancers. Errors in the cellular machinery to faithfully replicate the global 5-methylcytosine (5mC) patterns, commonly observed during tumorigenesis, give rise to misregulated biological pathways beneficial to the rapidly propagating tumor mass but deleterious to the healthy tissues of the affected individual. A growing body of evidence suggests that the global DNA methylation levels could serve as utilitarian biomarkers in certain cancer types. Important breakthroughs in the recent years have uncovered further oxidized derivatives of 5mC - 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), thereby expanding our understanding of the DNA methylation dynamics. While the biological roles of these epigenetic derivatives are being extensively characterized, this review presents a perspective on the opportunity of innovation in the global methylation analysis platforms. While multiple methods for global analysis of 5mC in clinical samples exist and have been reviewed elsewhere, two of the established methods - Liquid Chromatography coupled with mass spectrometry (LC-MS/MS) and Immunoquantification have successfully evolved to include the quantitation of 5hmC, 5fC and 5caC. Although the analytical performance of LC-MS/MS is superior, the simplicity afforded by the experimental procedure of immunoquantitation ensures it's near ubiquity in clinical applications. Recent developments in spectroscopy, nanotechnology and sequencing also provide immense promise for future evaluations and are discussed briefly. Finally, we provide a perspective on the current scenario of global DNA methylation analysis tools and present suggestions to develop the next generation toolset.

Keywords: 5-carboxylcytosine (5caC); 5-formylcytosine (5fC); 5-hydroxymethylcytosine (5hmC); 5-methylcytosine (5mC); Immunoquantitation; LC-MS/MS; Next generation toolset

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