4 Conclusions
The potential reversibility of epigenetic modifications is a stimulating prospect for
the development and improvement of technologies and methods to enable their
characterization and, above all, to test the ability of new drugs to revert their
pathological alterations, primarily in cancer. This chapter provides an overview of
the current status of epigenetic assays based on epigenetic enzymatic activity and
binding, genome-wide modifications and miRNAs and discusses the advantages,
disadvantages and practical applications of each technique.
The growing amount of achievable information provided by innovative epigenetic approaches has prompted the parallel growth of so-called “computational
epigenetics”. A considerable number of computational approaches and tools are
used in epigenetic studies for (1) epigenetic data repositories (e.g. International
Human Epigenome Consortium Data Portal, Epigenome Atlas, Chromatin:
4DGenome, NIH Roadmap Epigenomics, miRbase, UCSC MethBase) and (2) statistical data analysis, prediction and visualization (e.g. Bioconductor (R) packages,
epiGbs, MethPipe, MOABS, DaVIE, miRSystem) and data annotation, visualization
and integration (e.g. DAVID, STRING, oPOSSUM, GeneMANIA, IPA).
Despite the plethora of accurate experimental and computational approaches,
more efficient assays, bioinformatics methods and tools are still required to evaluate
the complexity of epigenetic mechanisms and the sophisticated interaction networks
governing gene expression in physiological and pathological conditions. Translating
epigenetics into the clinic is undoubtedly a fundamental research perspective and the
future direction of personalized medicine.
Compliance with Ethical Standards
Funding: The authors acknowledge AIRC17217; PON_0101227; VALERE: Vanvitelli per la
Ricerca; Regione Campania lotta alle patologie oncologiche: iCURE (CUP B21C17000030007);
and Regione Campania FASE2: IDEAL (CUP B53D18000080007). We thank C. Fisher for
linguistic editing.
Conflict of Interest: The authors declare no competing interests.
Ethical Statement: This article does not contain any studies with human participants or animals
performed by any of the authors.
References
1. Bernstein BE, Meissner A, Lander ES (2007) The mammalian epigenome. Cell 128
(4):669–681. https://doi.org/10.1016/j.cell.2007.01.033
2. Baylin SB, Jones PA (2011) A decade of exploring the cancer epigenome – biological and
translational implications. Nat Rev Cancer 11(10):726–734. https://doi.org/10.1038/nrc3130
3. Cheuk IW, Shin VY, Kwong A (2017) Detection of methylated circulating DNA as noninvasive
biomarkers for breast cancer diagnosis. J Breast Cancer 20(1):12–19. https://doi.org/10.4048/
jbc.2017.20.1.12
554
C. Dell’Aversana et al.
The potential reversibility of epigenetic modifications is a stimulating prospect for
the development and improvement of technologies and methods to enable their
characterization and, above all, to test the ability of new drugs to revert their
pathological alterations, primarily in cancer. This chapter provides an overview of
the current status of epigenetic assays based on epigenetic enzymatic activity and
binding, genome-wide modifications and miRNAs and discusses the advantages,
disadvantages and practical applications of each technique.
The growing amount of achievable information provided by innovative epigenetic approaches has prompted the parallel growth of so-called “computational
epigenetics”. A considerable number of computational approaches and tools are
used in epigenetic studies for (1) epigenetic data repositories (e.g. International
Human Epigenome Consortium Data Portal, Epigenome Atlas, Chromatin:
4DGenome, NIH Roadmap Epigenomics, miRbase, UCSC MethBase) and (2) statistical data analysis, prediction and visualization (e.g. Bioconductor (R) packages,
epiGbs, MethPipe, MOABS, DaVIE, miRSystem) and data annotation, visualization
and integration (e.g. DAVID, STRING, oPOSSUM, GeneMANIA, IPA).
Despite the plethora of accurate experimental and computational approaches,
more efficient assays, bioinformatics methods and tools are still required to evaluate
the complexity of epigenetic mechanisms and the sophisticated interaction networks
governing gene expression in physiological and pathological conditions. Translating
epigenetics into the clinic is undoubtedly a fundamental research perspective and the
future direction of personalized medicine.
Compliance with Ethical Standards
Funding: The authors acknowledge AIRC17217; PON_0101227; VALERE: Vanvitelli per la
Ricerca; Regione Campania lotta alle patologie oncologiche: iCURE (CUP B21C17000030007);
and Regione Campania FASE2: IDEAL (CUP B53D18000080007). We thank C. Fisher for
linguistic editing.
Conflict of Interest: The authors declare no competing interests.
Ethical Statement: This article does not contain any studies with human participants or animals
performed by any of the authors.
References
1. Bernstein BE, Meissner A, Lander ES (2007) The mammalian epigenome. Cell 128
(4):669–681. https://doi.org/10.1016/j.cell.2007.01.033
2. Baylin SB, Jones PA (2011) A decade of exploring the cancer epigenome – biological and
translational implications. Nat Rev Cancer 11(10):726–734. https://doi.org/10.1038/nrc3130
3. Cheuk IW, Shin VY, Kwong A (2017) Detection of methylated circulating DNA as noninvasive
biomarkers for breast cancer diagnosis. J Breast Cancer 20(1):12–19. https://doi.org/10.4048/
jbc.2017.20.1.12
554
C. Dell’Aversana et al.