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Cancer Epigenetics-Recent Developments in Epigenetic Diagnostics and Therapy

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

Deadline for manuscript submissions: closed (15 August 2021) | Viewed by 13358

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Special Issue Editor

Dr. Jarosław Paluszczak

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Guest Editor

Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, Święcicki 4 Str., 60-781 Poznań, Poland
Interests: head and neck cancer; epigenetics; CNS cancer; colorectal cancer; targeted therapy; Wnt signaling pathway; metabolism of cancer cells; metronomic therapy; biomarkers
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Special Issue Information

Dear Colleagues,

The field of cancer epigenetics has flourished in the past twenty years, and our knowledge and understanding of epigenetic abnormalities has expanded enormously. This has resulted in the introduction of therapeutics targeting epigenetic aberrations in patients with hematological cancers and solid tumors. Additionally, DNA methylation-based cancer biomarkers were successfully developed and introduced into clinical practice.

On the other hand, the complexity of epigenetic phenomena, which emerges from epigenomic studies, leads to new questions about the basic mechanisms of action of the epigenetic machinery and the mechanisms of its dysregulation in cancer. The picture of epigenetic modifications in various physiological and pathological conditions becomes much more detailed, drawing attention to the many interactions between epigenetic writers, readers and erasers, and the cross-talk between epigenetics and, e.g., metabolic pathways. The accumulating knowledge allows its translational implementation in oncological diagnostics and therapy.

I hope that this Special Issue on Cancer Epigenetics will be a creative space for presenting the results of novel studies and exchanging ideas about the significance of DNA methylation and histone modifications in cancer. What is needed is in-depth synthesis of current knowledge, but also marking the unknown terrain in the field, in order to be able to ask the right questions in the future. Therefore, you are invited to contribute to this discussion.

Dr. Jarosław Paluszczak
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

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. Genes is an international peer-reviewed open access monthly 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 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

Cancer epigenetics
DNA methylation
Histone modifications
Chromatin
Epigenetic biomarkers
Epigenetic readers, writers, and erasers as therapeutic targets
Epigenetic therapy

Published Papers (3 papers)

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Research

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23 pages, 714 KiB

Open AccessArticle

Tensor-Decomposition-Based Unsupervised Feature Extraction Applied to Prostate Cancer Multiomics Data

by Y-h. Taguchi and Turki Turki

Genes 2020, 11(12), 1493; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11121493 - 11 Dec 2020

Cited by 2 | Viewed by 3125

Abstract

The large p small n problem is a challenge without a de facto standard method available to it. In this study, we propose a tensor-decomposition (TD)-based unsupervised feature extraction (FE) formalism applied to multiomics datasets, in which the number of features is more than 100,000 whereas the number of samples is as small as about 100, hence constituting a typical large p small n problem. The proposed TD-based unsupervised FE outperformed other conventional supervised feature selection methods, random forest, categorical regression (also known as analysis of variance, or ANOVA), penalized linear discriminant analysis, and two unsupervised methods, multiple non-negative matrix factorization and principal component analysis (PCA) based unsupervised FE when applied to synthetic datasets and four methods other than PCA based unsupervised FE when applied to multiomics datasets. The genes selected by TD-based unsupervised FE were enriched in genes known to be related to tissues and transcription factors measured. TD-based unsupervised FE was demonstrated to be not only the superior feature selection method but also the method that can select biologically reliable genes. To our knowledge, this is the first study in which TD-based unsupervised FE has been successfully applied to the integration of this variety of multiomics measurements. Full article

(This article belongs to the Special Issue Cancer Epigenetics-Recent Developments in Epigenetic Diagnostics and Therapy)

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Review

Jump to: Research

20 pages, 2090 KiB

Open AccessReview

Thymoquinone Is a Multitarget Single Epidrug That Inhibits the UHRF1 Protein Complex

by Omeima Abdullah, Ziad Omran, Salman Hosawi, Ali Hamiche, Christian Bronner and Mahmoud Alhosin

Genes 2021, 12(5), 622; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12050622 - 22 Apr 2021

Cited by 14 | Viewed by 3564

Abstract

Silencing of tumor suppressor genes (TSGs) through epigenetic mechanisms, mainly via abnormal promoter DNA methylation, is considered a main mechanism of tumorigenesis. The abnormal DNA methylation profiles are transmitted from the cancer mother cell to the daughter cells through the involvement of a macromolecular complex in which the ubiquitin-like containing plant homeodomain (PHD), and an interesting new gene (RING) finger domains 1 (UHRF1), play the role of conductor. Indeed, UHRF1 interacts with epigenetic writers, such as DNA methyltransferase 1 (DNMT1), histone methyltransferase G9a, erasers like histone deacetylase 1 (HDAC1), and functions as a hub protein. Thus, targeting UHRF1 and/or its partners is a promising strategy for epigenetic cancer therapy. The natural compound thymoquinone (TQ) exhibits anticancer activities by targeting several cellular signaling pathways, including those involving UHRF1. In this review, we highlight TQ as a potential multitarget single epidrug that functions by targeting the UHRF1/DNMT1/HDAC1/G9a complex. We also speculate on the possibility that TQ might specifically target UHRF1, with subsequent regulatory effects on other partners. Full article

(This article belongs to the Special Issue Cancer Epigenetics-Recent Developments in Epigenetic Diagnostics and Therapy)

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21 pages, 696 KiB

Open AccessEditor’s ChoiceReview

Novel Approaches to Epigenetic Therapies: From Drug Combinations to Epigenetic Editing

by Aleksandra Majchrzak-Celińska, Anna Warych and Mikołaj Szoszkiewicz

Genes 2021, 12(2), 208; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12020208 - 31 Jan 2021

Cited by 60 | Viewed by 5996

Abstract

Cancer development involves both genetic and epigenetic alterations. Aberrant epigenetic modifications are reversible, allowing excellent opportunities for therapeutic intervention. Nowadays, several epigenetic drugs are used worldwide to treat, e.g., myelodysplastic syndromes and leukemias. However, overcoming resistance and widening the therapeutic profiles are the most important challenges faced by traditional epigenetic drugs. Recently, novel approaches to epigenetic therapies have been proposed. Next-generation epigenetic drugs, with longer half-life and better bioavailability, are being developed and tested. Since epigenetic phenomena are interdependent, treatment modalities include co-administration of two different epigenetic drugs. In order to sensitize cancer cells to chemotherapy, epigenetic drugs are administered prior to chemotherapy, or both epigenetic drug and chemotherapy are used together to achieve synergistic effects and maximize treatment efficacy. The combinations of epigenetic drug with immunotherapy are being tested, because they have proved to enhance antitumor immune responses. The next approach involves targeting the metabolic causes of epigenetic changes, i.e., enzymes which, when mutated, produce oncometabolites. Finally, epigenome editing makes it possible to modify individual chromatin marks at a defined region with unprecedented specificity and efficiency. This review summarizes the above attempts in fulfilling the promise of epigenetic drugs in the effective cancer treatment. Full article

(This article belongs to the Special Issue Cancer Epigenetics-Recent Developments in Epigenetic Diagnostics and Therapy)

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