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Unraveling the Epigenetic Blueprint: Exploring DNA Methylation and Its Integration...
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Unraveling the Epigenetic Blueprint: Exploring DNA Methylation and Its Integration with Omics in Health and Disease

A special issue of Biomedicines (ISSN 2227-9059). This special issue belongs to the section "Molecular Genetics and Genetic Diseases".

Deadline for manuscript submissions: 31 May 2026 | Viewed by 1119

Special Issue Editors

Dr. Priyadarshini Kachroo

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Guest Editor
Department of Biomedical and Health Informatics, Rutgers School of Health Professions, Rutgers, The State University of New Jersey, Newark, NJ, USA
Interests: integrative omics; networks; metabolomics; epigenomics; exposomics; proteomics; microbiome; machine learning; causation; early-life exposures; lung diseases; complex and age-associated disease outcomes; translational therapeutics
Dr. Rinku Sharma

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Guest Editor
Channing Division of Network Medicine (CDNM), Medicine, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
Interests: multi-omics integration; mediation; biological networks; machine learning; microRNAs; metabolomics; epigenomics; transcriptomics

Special Issue Information

Dear Colleagues,

Epigenetic mechanisms are involved in development, inheritance, and disease. Over the last decade, the field of epigenetics research has grown tremendously, accelerating our understanding of human biology and its interaction with the environment. Several groundbreaking discoveries are continuing to grow in number and scope due to their appealing potential in gene regulation, editing, aging, and preventative interventions for complex diseases. We are now in an era of unprecedented omics data generation; therefore, a comprehensive view will enhance its interpretation as it relates to health, disease, and current medical practices, in addition to enhancing comprehension both on the side of researchers and clinicians. This Special Issue welcomes original research and methodical or review articles and aims to provide an opportunity to highlight studies involving and integrating epigenetics research, including, but not limited to, data generated through techniques such as ChIP-seq, ATAC-seq, whole-genome DNA methylation such as WGBS or RRBS, EPIC arrays, RNA sequencing, single-cell RNA-seq (scRNA-seq), single-cell epigenetics/epigenomics, metabolomics, proteomics, exposomics, therapeutics, aging, growth and developmental trajectories, multiomics, spatial transcriptomics/epigenomics, and techniques elucidating the role of micro-RNAs and non-coding RNAs in epigenetic modulation.

Dr. Priyadarshini Kachroo
Dr. Rinku Sharma
Guest Editors

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Keywords

  • multiomics
  • networks
  • epigenomics
  • machine learning
  • causation
  • early-life exposures
  • aging
  • translational therapeutics
  • metabolomics
  • epigenomics
  • exposomics
  • proteomics
  • microbiome

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Published Papers (2 papers)

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16 pages, 1243 KB  
Article
Interaction Between the VNTR of the DAT1 Gene and DAT1 Methylation in Relation to Impulsivity in Combat Sports Athletes
by Remigiusz Recław, Jolanta Chmielowiec, Krzysztof Chmielowiec, Dariusz Larysz, Agnieszka Pedrycz and Anna Grzywacz
Biomedicines 2025, 13(12), 2893; https://doi.org/10.3390/biomedicines13122893 - 26 Nov 2025
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Abstract
Background: Dopaminergic signaling is a key mechanism in behavioral regulation and impulse control. While DAT1 promoter methylation has been linked to behavioral dysregulation in clinical groups, its role in high-functioning populations such as elite athletes remains unclear. Objectives: To compare DAT1 [...] Read more.
Background: Dopaminergic signaling is a key mechanism in behavioral regulation and impulse control. While DAT1 promoter methylation has been linked to behavioral dysregulation in clinical groups, its role in high-functioning populations such as elite athletes remains unclear. Objectives: To compare DAT1 promoter methylation, DAT1 VNTR genotype, and impulsivity between elite combat sport athletes and matched controls, and to assess potential gene–environment interactions. Methods: The study included 209 male participants (100 elite combat athletes, 109 controls). Methylation of 33 CpG sites within the DAT1 promoter was quantified from peripheral blood DNA. DAT1 VNTR genotypes were determined via PCR and gel electrophoresis. Impulsivity was assessed using the Barratt Impulsiveness Scale (BIS-11). Group differences and interactions were analyzed using analysis of variance (ANOVA), non-parametric tests, and post hoc comparisons. Results: Athletes displayed significantly higher overall DAT1 promoter methylation and lower impulsivity scores across all BIS-11 subscales compared with controls. A significant group × genotype interaction for methylation indicated genotype-specific epigenetic differences by athletic status. No differences in VNTR genotype or allele frequencies were observed. Conclusions: Elevated DAT1 promoter methylation in elite athletes may be associated with enhanced behavioral control, potentially reflecting neurobiological adaptations to high-intensity training. These results highlight the need to integrate genetic and epigenetic perspectives in sports science. Longitudinal and multi-omics studies are warranted to determine causal links and evaluate the potential of epigenetic markers as indicators of performance-related traits. Full article
(This article belongs to the Special Issue Unraveling the Epigenetic Blueprint: Exploring DNA Methylation and Its Integration with Omics in Health and Disease)
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54 pages, 2248 KB  
Systematic Review
Analysis Methods for Diagnosing Rare Neurodevelopmental Diseases with Episignatures: A Systematic Review of the Literature
by Albert Alegret-García, Alejandro Cáceres, Marta Sevilla-Porras, Luís A. Pérez-Jurado and Juan R. González
Biomedicines 2025, 13(12), 3043; https://doi.org/10.3390/biomedicines13123043 - 11 Dec 2025
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Abstract
Background: Rare diseases (RDs) and neurodevelopmental disorders (NDDs) remain under-researched due to their low prevalence, leaving significant gaps in diagnostic strategies. Beyond next-generation sequencing, epigenetic profiling and particularly episignatures have emerged as a promising complementary diagnostic tool and for reclassifying variants of uncertain [...] Read more.
Background: Rare diseases (RDs) and neurodevelopmental disorders (NDDs) remain under-researched due to their low prevalence, leaving significant gaps in diagnostic strategies. Beyond next-generation sequencing, epigenetic profiling and particularly episignatures have emerged as a promising complementary diagnostic tool and for reclassifying variants of uncertain significance (VUS). However, clinical implementation remains limited, hindered by non-standardized methodologies and restricted data sharing that impede the development of sufficiently large datasets for robust episignature development. Methods: We conducted a systematic literature review following PRISMA 2020 guidelines to identify all studies reporting episignatures published between 2014 and 2025. The review summarizes methodological approaches used for episignature detection and implementation, as well as reports of epimutations. Results: A total of 108 studies met the inclusion criteria. All but three employed Illumina methylation arrays, mostly 450 K and EPIC versions for patient sample analysis. Three main methodological phases were identified: data quality control, episignature detection, and classification model training. Despite methodological variability across these stages, most studies demonstrated high predictive capabilities, often relying on methodologies developed by a small number of leading groups. Conclusions: Epigenetic screening has significant potential to improve diagnostic yield in RDs and NDDs. Continued methodological refinement and collaborative standardization efforts will be crucial for its successful integration into clinical practice. Nevertheless, key challenges persist, including the need for secure and ethical data-sharing frameworks, external validation, and methodological standardization. Full article
(This article belongs to the Special Issue Unraveling the Epigenetic Blueprint: Exploring DNA Methylation and Its Integration with Omics in Health and Disease)
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