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Epigenomes
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The Use of Epigenetic Biomarkers as Diagnostic and Therapeutic Options...
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The Use of Epigenetic Biomarkers as Diagnostic and Therapeutic Options 2.0

A special issue of Epigenomes (ISSN 2075-4655).

Deadline for manuscript submissions: closed (30 April 2022) | Viewed by 31854

Special Issue Editor

Dr. Yuen Yee Cheng

E-Mail Website
Guest Editor
Institute for Biomedical Materials and Devices, University of Technology Sydney, 15 Broadway, Ultimo, NSW 2007, Australia
Interests: biomedicine; nanotechnology; cancer treatment
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Epigenetic changes are key processes driving cellular aging, development, and carcinogenesis. Epigenetic dysregulation is a universal feature of neoplasms and is considered a hallmark of cancer. Subsequently, the study of the epigenome has attracted considerable attention for developing biomarker detection methods and therapeutic discovery for various malignancies for over a decade. Many drugs have been developed and have obtained FDA approval to be used in clinical practice. The distinctive signatures of which biomarkers can be used to identify patients who may potentially benefit from such treatment options are yet to be explored. Due to the current COVID-19 pandemic, many researchers are discussing the link between the COVID-19 SARS virus and epigenetic alterations in cancer patients. For example, the expression of angiotensin-converting enzyme 2 (ACE2), the receptor of COVID-19, is aberrantly expressed in many tumors. Some cancer drugs could also be repurposed as COVID-19 treatments.

We previous discussed that amongst all epigenetic alterations, DNA methylation is the most widely studied in cancer. This is because the status of DNA methylation changes during different stages of carcinogenesis can be readily detected using current technology. The advantage of using epigenetic changes as biomarkers is their stability and availability in many sample types. With modern technology, the detection of epigenetic changes can also be useful as a detection tool in non-invasive biospecimens such as blood plasma and serum.

Epigenetic changes are also useful for treatment discovery, as different malignancies present with different epigenetic signatures and therefore the reversal of this phenotype presents as a targetable therapy. For example, global DNA hypermethylation can be reversed with demethylation agents such as decitabine, while histone modification alterations can be attenuated with TSA or SAHA. Additionally, downregulated tumor-suppressor microRNA expression can be restored by synthetic microRNA replacement therapy. Epigenetic biomarkers including DNA methylation, histone modification, microRNA, circular RNA, non-coding RNA, etc. can all potentially be influenced by the COVID-19 virus RNA. The understanding of this complex relationship will facilitate not only treatment options for COVID-19 patients, but also cancer patients.

The present Special Issue aims to publish high-quality research articles as well as review contributions on a variety of topics related to epigenetic biomarkers, COVID-19, and therapeutic options.

Potential topics include, but are not limited to:

  • Types of epigenetic biomarkers used in clinical practice for different diseases:
    • DNA methylation of circulating or non-circulating DNA;
    • Histone modification (e.g., histone methylation and acetylation);
    • microRNA, circular RNA, and other non-coding RNA;
  • Methods of new epigenetic biomarker discovery;
  • The potential of liquid biopsy for epigenetic biomarker detection;
  • The process of developing of epigenetic biomarkers as treatment options for clinical practice.

Dr. Yuen Yee Cheng
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. Epigenomes is an international peer-reviewed open access quarterly 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 1500 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.

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Published Papers (7 papers)

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Editorial

Jump to: Research, Review

2 pages, 178 KiB  
Editorial
The Use of Epigenetic Biomarkers as Diagnostic and Therapeutic Options
by Le Zhang, Emma M. Rath and Yuen Yee Cheng
Epigenomes 2022, 6(4), 30; https://doi.org/10.3390/epigenomes6040030 - 27 Sep 2022
Cited by 1 | Viewed by 2220
Abstract
The last few decades have brought tremendous advances in the mechanisms of epigenetic regulation, with DNA methylation, histone methylation and acetylation, microRNAs and other noncoding RNAs being among the most prominent [...] Full article
(This article belongs to the Special Issue The Use of Epigenetic Biomarkers as Diagnostic and Therapeutic Options 2.0)

Research

Jump to: Editorial, Review

11 pages, 1728 KiB  
Communication
Global m6A RNA Methylation in SARS-CoV-2 Positive Nasopharyngeal Samples in a Mexican Population: A First Approximation Study
by Jorge Luis Batista-Roche, Bruno Gómez-Gil, Gertrud Lund, César Alejandro Berlanga-Robles and Alejandra García-Gasca
Epigenomes 2022, 6(3), 16; https://doi.org/10.3390/epigenomes6030016 - 29 Jun 2022
Cited by 5 | Viewed by 3450
Abstract
The Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) is the causal agent of COVID-19 (Coronavirus Disease-19). Both mutation and/or recombination events in the SARS-CoV-2 genome have resulted in variants that differ in transmissibility and severity. Furthermore, RNA methylation of the N6 position of adenosine (m6A) [...] Read more.
The Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) is the causal agent of COVID-19 (Coronavirus Disease-19). Both mutation and/or recombination events in the SARS-CoV-2 genome have resulted in variants that differ in transmissibility and severity. Furthermore, RNA methylation of the N6 position of adenosine (m6A) is known to be altered in cells infected with SARS-CoV-2. However, it is not known whether this epitranscriptomic modification differs across individuals dependent on the presence of infection with distinct SARS-CoV-2 variants, the viral load, or the vaccination status. To address this issue, we selected RNAs (n = 60) from SARS-CoV-2 sequenced nasopharyngeal samples (n = 404) of 30- to 60-year-old outpatients or hospitalized individuals from the city of Mazatlán (Mexico) between February 2021 and March 2022. Control samples were non-infected individuals (n = 10). SARS-CoV-2 was determined with real-time PCR, viral variants were determined with sequencing, and global m6A levels were determined by using a competitive immunoassay method. We identified variants of concern (VOC; alpha, gamma, delta, omicron), the variant of interest (VOI; epsilon), and the lineage B.1.1.519. Global m6A methylation differed significantly across viral variants (p = 3.2 × 10−7). In particular, we found that m6A levels were significantly lower in the VOC delta- and omicron-positive individuals compared to non-infected individuals (p = 2.541236 × 10−2 and 1.134411 × 10−4, respectively). However, we uncovered no significant correlation between global m6A levels and viral nucleocapsid (N) gene expression or age. Furthermore, individuals with complete vaccination schemes showed significantly lower m6A levels than unvaccinated individuals (p = 2.6 × 10−4), and differences in methylation levels across variants in unvaccinated individuals were significant (p = 3.068 × 10−3). These preliminary results suggest that SARS-CoV-2 variants show differences in global m6A levels. Full article
(This article belongs to the Special Issue The Use of Epigenetic Biomarkers as Diagnostic and Therapeutic Options 2.0)
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11 pages, 1778 KiB  
Article
Epigenetic Signatures of Centrosomes Are Novel Targets in Cancer Diagnosis: Insights from an Analysis of the Cancer Genome Atlas
by Zhou Zhang and Wei Zhang
Epigenomes 2022, 6(2), 14; https://doi.org/10.3390/epigenomes6020014 - 2 Jun 2022
Cited by 1 | Viewed by 2856
Abstract
The centrosome plays a central role for cellular signaling and is critical for several fundamental cellular processes in human cells. Centrosome abnormalities have been linked to multiple solid tumors and hematological malignancies. We sought to explore the potential role of the DNA methylation, [...] Read more.
The centrosome plays a central role for cellular signaling and is critical for several fundamental cellular processes in human cells. Centrosome abnormalities have been linked to multiple solid tumors and hematological malignancies. We sought to explore the potential role of the DNA methylation, a critical epigenetic modification, of centrosome-related genes in different cancers. The 450K array DNA methylation data and RNA-seq data were downloaded for ~4000 tumor samples and ~500 normal controls from The Cancer Genome Atlas (TCGA) project, covering 11 major cancer types. Cancers with more than 30 normal controls were retained for analysis. Differentially modified CpGs of centrosome genes were identified, and cancer-specific epigenetic models were developed using a machine-learning algorithm for each cancer type. The association between the methylation level of differential CpGs and the corresponding gene expression, as well as the co-localization of the differential CpGs and cis-regulatory elements were evaluated. In total, 2761 CpGs located on 160 centrosome genes for 6 cancers were included in the analysis. Cancer-specific models demonstrated a high accuracy in terms of the area under the receiver operating characteristic (ROC) curve (AUC > 0.9) in five cancers and showed tissue specificity. This study enhanced our understanding of the epigenetic mechanisms underlying the DNA methylation of centrosome-related genes in cancers, and showed the potential of these epigenetic modifications as novel cancer biomarkers. Full article
(This article belongs to the Special Issue The Use of Epigenetic Biomarkers as Diagnostic and Therapeutic Options 2.0)
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13 pages, 1452 KiB  
Article
Epigenetic Analyses of Alcohol Consumption in Combustible and Non-Combustible Nicotine Product Users
by Kelsey Dawes, Luke Sampson, Rachel Reimer, Shelly Miller, Robert Philibert and Allan Andersen
Epigenomes 2021, 5(3), 18; https://doi.org/10.3390/epigenomes5030018 - 1 Sep 2021
Cited by 6 | Viewed by 3952
Abstract
Alcohol and tobacco use are highly comorbid and exacerbate the associated morbidity and mortality of either substance alone. However, the relationship of alcohol consumption to the various forms of nicotine-containing products is not well understood. To improve this understanding, we examined the relationship [...] Read more.
Alcohol and tobacco use are highly comorbid and exacerbate the associated morbidity and mortality of either substance alone. However, the relationship of alcohol consumption to the various forms of nicotine-containing products is not well understood. To improve this understanding, we examined the relationship of alcohol consumption to nicotine product use using self-report, cotinine, and two epigenetic biomarkers specific for smoking (cg05575921) and drinking (Alcohol T Scores (ATS)) in n = 424 subjects. Cigarette users had significantly higher ATS values than the other groups (p < 2.2 × 10−16). Using the objective biomarkers, the intensity of nicotine and alcohol consumption was correlated in both the cigarette and smokeless users (R = −0.66, p = 3.1 × 10−14; R2 = 0.61, p = 1.97 × 10−4). Building upon this idea, we used the objective nicotine biomarkers and age to build and test a Balanced Random Forest classification model for heavy alcohol consumption (ATS > 2.35). The model performed well with an AUC of 0.962, 89.3% sensitivity, and 85% specificity. We conclude that those who use non-combustible nicotine products drink significantly less than smokers, and cigarette and smokeless users drink more with heavier nicotine use. These findings further highlight the lack of informativeness of self-reported alcohol consumption and suggest given the public and private health burden of alcoholism, further research into whether using non-combustible nicotine products as a mode of treatment for dual users should be considered. Full article
(This article belongs to the Special Issue The Use of Epigenetic Biomarkers as Diagnostic and Therapeutic Options 2.0)
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Review

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15 pages, 522 KiB  
Review
Epigenomic Approaches for the Diagnosis of Rare Diseases
by Beatriz Martinez-Delgado and Maria J. Barrero
Epigenomes 2022, 6(3), 21; https://doi.org/10.3390/epigenomes6030021 - 27 Jul 2022
Cited by 9 | Viewed by 4131
Abstract
Rare diseases affect more than 300 million people worldwide. Diagnosing rare diseases is a major challenge as they have different causes and etiologies. Careful assessment of clinical symptoms often leads to the testing of the most common genetic alterations that could explain the [...] Read more.
Rare diseases affect more than 300 million people worldwide. Diagnosing rare diseases is a major challenge as they have different causes and etiologies. Careful assessment of clinical symptoms often leads to the testing of the most common genetic alterations that could explain the disease. Patients with negative results for these tests frequently undergo whole exome or genome sequencing, leading to the identification of the molecular cause of the disease in 50% of patients at best. Therefore, a significant proportion of patients remain undiagnosed after sequencing their genome. Recently, approaches based on functional aspects of the genome, including transcriptomics and epigenomics, are beginning to emerge. Here, we will review these approaches, including studies that have successfully provided diagnoses for complex undiagnosed cases. Full article
(This article belongs to the Special Issue The Use of Epigenetic Biomarkers as Diagnostic and Therapeutic Options 2.0)
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21 pages, 2320 KiB  
Review
Insights into Cardiovascular Defects and Cardiac Epigenome in the Context of COVID-19
by Shreya Sarkar and Rwik Sen
Epigenomes 2022, 6(2), 13; https://doi.org/10.3390/epigenomes6020013 - 21 Apr 2022
Cited by 3 | Viewed by 4127
Abstract
Although few in number, studies on epigenome of the heart of COVID-19 patients show that epigenetic signatures such as DNA methylation are significantly altered, leading to changes in expression of several genes. It contributes to pathogenic cardiac phenotypes of COVID-19, e.g., low heart [...] Read more.
Although few in number, studies on epigenome of the heart of COVID-19 patients show that epigenetic signatures such as DNA methylation are significantly altered, leading to changes in expression of several genes. It contributes to pathogenic cardiac phenotypes of COVID-19, e.g., low heart rate, myocardial edema, and myofibrillar disarray. DNA methylation studies reveal changes which likely contribute to cardiac disease through unknown mechanisms. The incidence of severe COVID-19 disease, including hospitalization, requiring respiratory support, morbidity, and mortality, is disproportionately higher in individuals with co-morbidities. This poses unprecedented strains on the global healthcare system. While their underlying conditions make patients more susceptible to severe COVID-19 disease, strained healthcare systems, lack of adequate support, or sedentary lifestyles from ongoing lockdowns have proved detrimental to their underlying health conditions, thus pushing them to severe risk of congenital heart disease (CHD) itself. Prophylactic vaccines against COVID-19 have ushered new hope for CHD. A common connection between COVID-19 and CHD is SARS-CoV-2’s host receptor ACE2, because ACE2 regulates and protects organs, including the heart, in various ways. ACE2 is a common therapeutic target against cardiovascular disease and COVID-19 which damages organs. Hence, this review explores the above regarding CHDs, cardiovascular damage, and cardiac epigenetics, in COVID-19 patients. Full article
(This article belongs to the Special Issue The Use of Epigenetic Biomarkers as Diagnostic and Therapeutic Options 2.0)
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Graphical abstract

27 pages, 4243 KiB  
Review
Opportunities for Early Cancer Detection: The Rise of ctDNA Methylation-Based Pan-Cancer Screening Technologies
by Nicolas Constantin, Abu Ali Ibn Sina, Darren Korbie and Matt Trau
Epigenomes 2022, 6(1), 6; https://doi.org/10.3390/epigenomes6010006 - 4 Feb 2022
Cited by 18 | Viewed by 9617
Abstract
The efficiency of conventional screening programs to identify early-stage malignancies can be limited by the low number of cancers recommended for screening as well as the high cumulative false-positive rate, and associated iatrogenic burden, resulting from repeated multimodal testing. The opportunity to use [...] Read more.
The efficiency of conventional screening programs to identify early-stage malignancies can be limited by the low number of cancers recommended for screening as well as the high cumulative false-positive rate, and associated iatrogenic burden, resulting from repeated multimodal testing. The opportunity to use minimally invasive liquid biopsy testing to screen asymptomatic individuals at-risk for multiple cancers simultaneously could benefit from the aggregated diseases prevalence and a fixed specificity. Increasing both latter parameters is paramount to mediate high positive predictive value—a useful metric to evaluate a screening test accuracy and its potential harm-benefit. Thus, the use of a single test for multi-cancer early detection (stMCED) has emerged as an appealing strategy for increasing early cancer detection rate efficiency and benefit population health. A recent flurry of these stMCED technologies have been reported for clinical potential; however, their development is facing unique challenges to effectively improve clinical cost–benefit. One promising avenue is the analysis of circulating tumour DNA (ctDNA) for detecting DNA methylation biomarker fingerprints of malignancies—a hallmark of disease aetiology and progression holding the potential to be tissue- and cancer-type specific. Utilizing panels of epigenetic biomarkers could potentially help to detect earlier stages of malignancies as well as identify a tumour of origin from blood testing, useful information for follow-up clinical decision making and subsequent patient care improvement. Overall, this review collates the latest and most promising stMCED methodologies, summarizes their clinical performances, and discusses the specific requirements multi-cancer tests should meet to be successfully implemented into screening guidelines. Full article
(This article belongs to the Special Issue The Use of Epigenetic Biomarkers as Diagnostic and Therapeutic Options 2.0)
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