Cancer Epigenomics: New Clinical Opportunities and Challenges

A special issue of Cancers (ISSN 2072-6694). This special issue belongs to the section "Molecular Cancer Biology".

Deadline for manuscript submissions: closed (30 June 2021) | Viewed by 6864

Special Issue Editors


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Guest Editor
Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, 33011 Oviedo, Spain
Interests: epigenetics; DNA methylation; histones; cancer; aging

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Guest Editor
1. University Institute of Oncology of Asturias (IUOPA), University of Oviedo, 33006 Oviedo, Spain
2. Health Research Institute of Asturias (ISPA), 33011 Oviedo, Spain
Interests: epigenomics; cancer; aging; proteomics; chromatin signatures; biomarkers; precision medicine
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Special Issue Information

Dear colleagues,

Genome-wide epigenetic alterations are now a well-established hallmark of cancer, and recent years have witnessed the advent of high-throughput technologies applied to epigenomics. In particular, the development of WG-BS sequencing, ChIP-seq, FAIRE-seq, ATAC-inspired methodologies (ATAC-seq, ATAC-me) and RNA-seq, among others, has enabled a growing body of research aimed at characterizing epigenetic changes at the global scale. These such studies have begun to generate useful datasets along with new tools and strategies for cancer research. Furthermore, the reversible nature of epigenetic changes opens up the possibility of partially restoring the abnormal cancer epigenome to its healthy state, thus representing an attractive strategy for cancer therapy.

In this Special Issue dedicated to cancer epigenomics, we invite original experimental and clinical studies as well as reviews of the plethora of altered epigenetic mechanisms during tumorigenesis as seen through the -omics prism. We will address epigenomic studies and integrative analysis of epigenomic data across different tumor types, with a special focus on clinical translation under the form of novel diagnostic biomarkers as well as new opportunities for cancer patient screening, stratification, and follow-up. We will also discuss challenges that need to be overcome in future to expedite translation of these findings into clinical oncology.

Prof. Dr. Mario Fdez. Fraga
Dr. Virginia López Martínez
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Cancers is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 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

  • epigenetics
  • epigenome
  • DNA methylation
  • chromatin
  • histone posttranslational modifications
  • microRNAs
  • bioinformatics
  • omics analyses

Published Papers (2 papers)

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Research

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15 pages, 2257 KiB  
Article
Comparison of Global DNA Methylation Patterns in Human Melanoma Tissues and Their Derivative Cell Lines
by Euan J. Rodger, Suzan N. Almomani, Jackie L. Ludgate, Peter A. Stockwell, Bruce C. Baguley, Michael R. Eccles and Aniruddha Chatterjee
Cancers 2021, 13(9), 2123; https://doi.org/10.3390/cancers13092123 - 28 Apr 2021
Cited by 11 | Viewed by 3071
Abstract
DNA methylation is a heritable epigenetic mark that is fundamental to mammalian development. Aberrant DNA methylation is an epigenetic hallmark of cancer cells. Cell lines are a critical in vitro model and very widely used to unravel mechanisms of cancer cell biology. However, [...] Read more.
DNA methylation is a heritable epigenetic mark that is fundamental to mammalian development. Aberrant DNA methylation is an epigenetic hallmark of cancer cells. Cell lines are a critical in vitro model and very widely used to unravel mechanisms of cancer cell biology. However, limited data are available to assess whether DNA methylation patterns in tissues are retained when cell lines are established. Here, we provide the first genome-scale sequencing-based methylation map of metastatic melanoma tumour tissues and their derivative cell lines. We show that DNA methylation profiles are globally conserved in vitro compared to the tumour tissue of origin. However, we identify sites that are consistently hypermethylated in cell lines compared to their tumour tissue of origin. The genes associated with these common differentially methylated regions are involved in cell metabolism, cell cycle and apoptosis and are also strongly enriched for the H3K27me3 histone mark and PRC2 complex-related genes. Our data indicate that although global methylation patterns are similar between tissues and cell lines, there are site-specific epigenomic differences that could potentially impact gene expression. Our work provides a valuable resource for identifying false positives due to cell culture and for better interpretation of cancer epigenetics studies in the future. Full article
(This article belongs to the Special Issue Cancer Epigenomics: New Clinical Opportunities and Challenges)
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Review

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18 pages, 2398 KiB  
Review
Lysine Acetylation, Cancer Hallmarks and Emerging Onco-Therapeutic Opportunities
by Meilan Hu, Fule He, Erik W. Thompson, Kostya (Ken) Ostrikov and Xiaofeng Dai
Cancers 2022, 14(2), 346; https://doi.org/10.3390/cancers14020346 - 11 Jan 2022
Cited by 15 | Viewed by 3176
Abstract
Acetylation, a reversible epigenetic process, is implicated in many critical cellular regulatory systems including transcriptional regulation, protein structure, activity, stability, and localization. Lysine acetylation is the most prevalent and intensively investigated among the diverse acetylation forms. Owing to the intrinsic connections of acetylation [...] Read more.
Acetylation, a reversible epigenetic process, is implicated in many critical cellular regulatory systems including transcriptional regulation, protein structure, activity, stability, and localization. Lysine acetylation is the most prevalent and intensively investigated among the diverse acetylation forms. Owing to the intrinsic connections of acetylation with cell metabolism, acetylation has been associated with metabolic disorders including cancers. Yet, relatively little has been reported on the features of acetylation against the cancer hallmarks, even though this knowledge may help identify appropriate therapeutic strategies or combinatorial modalities for the effective treatment and resolution of malignancies. By examining the available data related to the efficacy of lysine acetylation against tumor cells and elaborating the primary cancer hallmarks and the associated mechanisms to target the specific hallmarks, this review identifies the intrinsic connections between lysine acetylation and cancer hallmarks and proposes novel modalities that can be combined with HDAC inhibitors for cancer treatment with higher efficacy and minimum adverse effects. Full article
(This article belongs to the Special Issue Cancer Epigenomics: New Clinical Opportunities and Challenges)
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