Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
7.4
5.2
Journals
Cancers
Special Issues
Epigenetic Detection and Regulation of Cancer Biomarkers
share announcement

Epigenetic Detection and Regulation of Cancer Biomarkers

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

Deadline for manuscript submissions: closed (20 March 2023) | Viewed by 18515

Special Issue Editors

Dr. Eric Hervouet

E-Mail Website
Guest Editor
INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, University Bourgogne Franche-Comté F-25000 Besançon, France
Interests: epigenetics; cancer; immunology; autophagy
Dr. Paul Peixoto

E-Mail Website
Co-Guest Editor
INSERM, EFS BFC, UMR1098, RIGHT Institute, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, University Bourgogne Franche-Comté, 25000 Besançon, France
Interests: epigenetics; cancer; T lymphocytes plasticity; EMT

Special Issue Information

Dear Colleagues,

In the last several decades, epigenetics emerged as a major discipline leading to the dysregulation of genes in cancers and has also been involved in metastasis, immune escape, and metabolism regulation.

The disruption of DNA methylation machineries and the modulation of the contents or activities of epigenetic writers, readers, or erasers have been reported in cancers, but the origin of the epigenetic modifications observed in cancer cells frequently remains unknown. However, these epigenetic modifications are clearly involved in tumorigenesis by controlling the expression of genes involved in cancer hallmarks or by affecting chromosomal instability. Moreover, specific epigenetic modifications have been associated to cancer diagnosis, classification, and prognosis. This offers possibilities for personalized medicine.

Although it has historically been difficult to use epigenetics in patients, the accessibility to the genome of tumor cells using ctDNA and non-invasive approaches now offers incredible perspectives to discover and monitor cancer biomarkers and to improve patient sorting following epigenetic marks. These techniques allow an easy tracing for the evolution of tumor cells in treated or post-treated patients and may help to confirm an efficient therapy or in contrast may argue for a switch towards another treatment. 

Finally, the recent development of hundreds of epidrugs will make it possible to improve the therapeutic arsenal using new epigenetics therapies combined or not with conventional therapies and identify specific treatments which are more efficient and more specific in regards to patients and specific cancers.

Dr. Eric Hervouet
Dr. Paul Peixoto
Guest Editors

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. 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
  • cancer
  • biomarker
  • ctDNA
  • DNA methylation
  • prognosis

Published Papers (6 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

Jump to: Review

17 pages, 5925 KiB  
Article
Integrative Analysis Identifies Multi-Omics Signatures That Drive Molecular Classification of Uveal Melanoma
by Qianxing Mo, Lixin Wan, Michael J. Schell, Heather Jim, Shelley S. Tworoger and Guang Peng
Cancers 2021, 13(24), 6168; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers13246168 - 07 Dec 2021
Cited by 6 | Viewed by 3044
Abstract
By iCluster analysis, we found that the integrative molecular classification of the UM was primarily driven by DNA copy number variation on chromosomes 3, 6 and 8, differential methylation and expression of genes involved in the immune system, cell morphogenesis, movement and migration, [...] Read more.
By iCluster analysis, we found that the integrative molecular classification of the UM was primarily driven by DNA copy number variation on chromosomes 3, 6 and 8, differential methylation and expression of genes involved in the immune system, cell morphogenesis, movement and migration, and differential mutation of genes including GNA11, BAP1, EIF1AX, SF3B1 and GNAQ. Integrative analysis revealed that pathways including IL6/JAK/STAT3 signaling, angiogenesis, allograft rejection, inflammatory response and interferon gamma response were hypomethylated and up-regulated in the M3 iSubtype, which was associated with a worse overall survival, compared to the D3 iSubtype. Using two independent gene expression datasets, we demonstrated that the subtype-driving genes had an excellent prognostic power in classifying UM into high- or low-risk groups for metastasis. Integrative analysis of UM multi-omics data provided a comprehensive view of UM biology for understanding the underlying mechanism leading to UM metastasis. The concordant molecular alterations at multi-omics levels revealed by our integrative analysis could be used for patient stratification towards personalized management and surveillance. Full article
(This article belongs to the Special Issue Epigenetic Detection and Regulation of Cancer Biomarkers)
►▼ Show Figures

Figure 1

21 pages, 2894 KiB  
Article
Deciphering the Methylation Landscape in Breast Cancer: Diagnostic and Prognostic Biosignatures through Automated Machine Learning
by Maria Panagopoulou, Makrina Karaglani, Vangelis G. Manolopoulos, Ioannis Iliopoulos, Ioannis Tsamardinos and Ekaterini Chatzaki
Cancers 2021, 13(7), 1677; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers13071677 - 02 Apr 2021
Cited by 24 | Viewed by 3713
Abstract
DNA methylation plays an important role in breast cancer (BrCa) pathogenesis and could contribute to driving its personalized management. We performed a complete bioinformatic analysis in BrCa whole methylome datasets, analyzed using the Illumina methylation 450 bead-chip array. Differential methylation analysis vs. clinical [...] Read more.
DNA methylation plays an important role in breast cancer (BrCa) pathogenesis and could contribute to driving its personalized management. We performed a complete bioinformatic analysis in BrCa whole methylome datasets, analyzed using the Illumina methylation 450 bead-chip array. Differential methylation analysis vs. clinical end-points resulted in 11,176 to 27,786 differentially methylated genes (DMGs). Innovative automated machine learning (AutoML) was employed to construct signatures with translational value. Three highly performing and low-feature-number signatures were built: (1) A 5-gene signature discriminating BrCa patients from healthy individuals (area under the curve (AUC): 0.994 (0.982–1.000)). (2) A 3-gene signature identifying BrCa metastatic disease (AUC: 0.986 (0.921–1.000)). (3) Six equivalent 5-gene signatures diagnosing early disease (AUC: 0.973 (0.920–1.000)). Validation in independent patient groups verified performance. Bioinformatic tools for functional analysis and protein interaction prediction were also employed. All protein encoding features included in the signatures were associated with BrCa-related pathways. Functional analysis of DMGs highlighted the regulation of transcription as the main biological process, the nucleus as the main cellular component and transcription factor activity and sequence-specific DNA binding as the main molecular functions. Overall, three high-performance diagnostic/prognostic signatures were built and are readily available for improving BrCa precision management upon prospective clinical validation. Revisiting archived methylomes through novel bioinformatic approaches revealed significant clarifying knowledge for the contribution of gene methylation events in breast carcinogenesis. Full article
(This article belongs to the Special Issue Epigenetic Detection and Regulation of Cancer Biomarkers)
►▼ Show Figures

Graphical abstract

Review

Jump to: Research

15 pages, 289 KiB  
Review
Role of DNA Methylation Profiles as Potential Biomarkers and Novel Therapeutic Targets in Head and Neck Cancer
by Kyunghee Burkitt
Cancers 2023, 15(19), 4685; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers15194685 - 22 Sep 2023
Cited by 1 | Viewed by 1141
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide and is associated with high mortality. The main reasons for treatment failure are a low rate of early diagnosis, high relapse rates, and distant metastasis with poor outcomes. These [...] Read more.
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide and is associated with high mortality. The main reasons for treatment failure are a low rate of early diagnosis, high relapse rates, and distant metastasis with poor outcomes. These are largely due to a lack of diagnostic, prognostic, and predictive biomarkers in HNSCC. DNA methylation has been demonstrated to play an important role in the pathogenesis of HNSCC, and recent studies have also valued DNA methylation as a potential biomarker in HNSCC. This review summarizes the current knowledge on DNA methylation profiles in HPV-positive and HPV-negative HNSCC and how these may contribute to the pathogenesis of HNSCC. It also summarizes the potential value of DNA methylation as a biomarker in the diagnosis, prognosis, and prediction of the response to therapy. With the recent immunotherapy era in head and neck treatment, new strategies to improve immune responses by modulating TIMEs have been intensely investigated in early-phase trials. Therefore, this study additionally summarizes the role of DNA methylation in the regulation of TIMEs and potential predictive immunotherapy response biomarkers. Finally, this study reviews ongoing clinical trials using DNA methylation inhibitors in HNSCC. Full article
(This article belongs to the Special Issue Epigenetic Detection and Regulation of Cancer Biomarkers)
11 pages, 735 KiB  
Review
Meningioma Grading beyond Histopathology: Relevance of Epigenetic and Genetic Features to Predict Clinical Outcome
by Elena Marastoni and Valeria Barresi
Cancers 2023, 15(11), 2945; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers15112945 - 27 May 2023
Cited by 1 | Viewed by 2369
Abstract
Meningiomas are common tumors of the central nervous system. The grading system established by the World Health Organization (WHO) has recently included pTERT mutations and CDKN2A/B homozygous deletions as criteria for grade 3, owing to their association with increased recurrence risk. However, these [...] Read more.
Meningiomas are common tumors of the central nervous system. The grading system established by the World Health Organization (WHO) has recently included pTERT mutations and CDKN2A/B homozygous deletions as criteria for grade 3, owing to their association with increased recurrence risk. However, these alterations identify only a portion of meningiomas that are devoid of histopathological malignancy and are prone to recurrence. Over the last few years, the integration of epigenetic, genetic, transcriptomic, and proteomic profiling has led to the identification of three main groups of meningiomas with distinct clinical outcomes and peculiar genetic features. Meningiomas in the first group have the best prognosis, are distinguished by the lack of NF2 alterations and chromosomal instability, and may be responsive to cytotoxic drugs. Meningiomas in the second group have an intermediate prognosis and are characterized by NF2 alterations, mild chromosomal instability, and enrichment in immune cells. Meningiomas in the third group had the worst prognosis, displayed NF2 alterations coupled with high chromosomal instability, and were resistant to cytotoxic treatment. Classification into these three groups predicts the recurrence risk of meningiomas more accurately than WHO grading and could be applicable in routine practice, owing to the possibility of distinguishing the different groups by specific immunostaining. Full article
(This article belongs to the Special Issue Epigenetic Detection and Regulation of Cancer Biomarkers)
►▼ Show Figures

Figure 1

16 pages, 1064 KiB  
Review
Emerging Role of Epigenetic Alterations as Biomarkers and Novel Targets for Treatments in Pancreatic Ductal Adenocarcinoma
by Marcus T. T. Roalsø, Øyvind H. Hald, Marina Alexeeva and Kjetil Søreide
Cancers 2022, 14(3), 546; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers14030546 - 21 Jan 2022
Cited by 5 | Viewed by 2793
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with limited treatment options. Emerging evidence shows that epigenetic alterations are present in PDAC. The changes are potentially reversible and therefore promising therapeutic targets. Epigenetic aberrations also influence the tumor microenvironment with the potential to [...] Read more.
Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with limited treatment options. Emerging evidence shows that epigenetic alterations are present in PDAC. The changes are potentially reversible and therefore promising therapeutic targets. Epigenetic aberrations also influence the tumor microenvironment with the potential to modulate and possibly enhance immune-based treatments. Epigenetic marks can also serve as diagnostic screening tools, as epigenetic changes occur at early stages of the disease. Further, epigenetics can be used in prognostication. The field is evolving, and this review seeks to provide an updated overview of the emerging role of epigenetics in the diagnosis, treatment, and prognostication of PDAC. Full article
(This article belongs to the Special Issue Epigenetic Detection and Regulation of Cancer Biomarkers)
►▼ Show Figures

Figure 1

20 pages, 973 KiB  
Review
Epigenetic Therapies and Biomarkers in Breast Cancer
by Lauren Julia Brown, Joanna Achinger-Kawecka, Neil Portman, Susan Clark, Clare Stirzaker and Elgene Lim
Cancers 2022, 14(3), 474; https://0-doi-org.brum.beds.ac.uk/10.3390/cancers14030474 - 18 Jan 2022
Cited by 17 | Viewed by 4484
Abstract
Epigenetic therapies remain a promising, but still not widely used, approach in the management of patients with cancer. To date, the efficacy and use of epigenetic therapies has been demonstrated primarily in the management of haematological malignancies, with limited supportive data in solid [...] Read more.
Epigenetic therapies remain a promising, but still not widely used, approach in the management of patients with cancer. To date, the efficacy and use of epigenetic therapies has been demonstrated primarily in the management of haematological malignancies, with limited supportive data in solid malignancies. The most studied epigenetic therapies in breast cancer are those that target DNA methylation and histone modification; however, none have been approved for routine clinical use. The majority of pre-clinical and clinical studies have focused on triple negative breast cancer (TNBC) and hormone-receptor positive breast cancer. Even though the use of epigenetic therapies alone in the treatment of breast cancer has not shown significant clinical benefit, these therapies show most promise in use in combinations with other treatments. With improving technologies available to study the epigenetic landscape in cancer, novel epigenetic alterations are increasingly being identified as potential biomarkers of response to conventional and epigenetic therapies. In this review, we describe epigenetic targets and potential epigenetic biomarkers in breast cancer, with a focus on clinical trials of epigenetic therapies. We describe alterations to the epigenetic landscape in breast cancer and in treatment resistance, highlighting mechanisms and potential targets for epigenetic therapies. We provide an updated review on epigenetic therapies in the pre-clinical and clinical setting in breast cancer, with a focus on potential real-world applications. Finally, we report on the potential value of epigenetic biomarkers in diagnosis, prognosis and prediction of response to therapy, to guide and inform the clinical management of breast cancer patients. Full article
(This article belongs to the Special Issue Epigenetic Detection and Regulation of Cancer Biomarkers)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-6
Back to TopTop