Genomics and Epitranscriptomics Regulation in Cancer

A special issue of Biomedicines (ISSN 2227-9059). This special issue belongs to the section "Cancer Biology and Oncology".

Deadline for manuscript submissions: 30 June 2026 | Viewed by 688

Special Issue Editors


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Guest Editor
Division of Pharmacology and Toxicology, Dell Paediatric Research Institute, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
Interests: cancer genomics; bioinformatics; algorithms; machine learning; genomic instability

E-Mail Website
Guest Editor
Division of Pharmacology and Toxicology, Dell Paediatric Research Institute, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
Interests: cancer genomics; alternative splicing; bioinformatics

Special Issue Information

Dear Colleagues,

Cancer pathogenesis involves not only genetic alterations but also sophisticated layers of post-transcriptional regulation that collectively dictate malignant phenotypes. The emergence of epitranscriptomics, the study of post-transcriptional RNA modifications, has unveiled a dynamic regulatory dimension in cancer biology, complementing established genomic and transcriptomic perspectives.

This Special Issue aims to compile advanced research and reviews that elucidate the roles of genomic and epitranscriptomic mechanisms in cancer development, progression, and treatment. Research areas may include (but are not limited to) the following:

  • Mutations, copy number variations, and structural variations in cancer genomes;
  • The role of RNA modifications in tumorigenesis, metastasis, and therapy response;
  • Regulatory roles of microRNAs, long non‑coding RNAs, and circular RNAs in cancer;
  • Genetic and epitranscriptomic alterations contributing to resistance against therapeutic strategies;
  • Epitranscriptomic regulators as therapeutic targets.

We look forward to receiving your contributions.

Dr. Ilias Georgakopoulos-Soares
Dr. Candace S. Y. Chan
Guest Editors

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Keywords

  • cancer genomics
  • epitranscriptomics
  • RNA modifications
  • non-coding RNAs
  • gene expression regulation
  • RNA splicing

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Published Papers (1 paper)

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Research

18 pages, 2399 KB  
Article
Integrative Whole-Genome and Epigenome Profiling of cfDNA in Familial Prostate Cancer: Insights from a Pilot Study
by Anna Truda, Angela Cordella, Ilenia De Leo, Armando Di Palo, Roberta Iorio, Simona Marino, Roberto La Rocca, Claudia Collà Ruvolo, Nicoletta Potenza, Maria Ravo and Giovanna Marchese
Biomedicines 2026, 14(4), 818; https://doi.org/10.3390/biomedicines14040818 - 3 Apr 2026
Viewed by 467
Abstract
Background: Familial prostate cancer (PCa) accounts for nearly 20% of all PCa cases and is associated with increased genetic susceptibility and earlier disease onset. However, early detection and risk stratification in genetically predisposed individuals remain challenging. Circulating cell-free DNA (cfDNA) provides a minimally [...] Read more.
Background: Familial prostate cancer (PCa) accounts for nearly 20% of all PCa cases and is associated with increased genetic susceptibility and earlier disease onset. However, early detection and risk stratification in genetically predisposed individuals remain challenging. Circulating cell-free DNA (cfDNA) provides a minimally invasive source of tumor-derived genomic and epigenomic information. Integrating multi-omic cfDNA analyses may enhance the discovery of biomarkers relevant to familial PCa biology. Methods: We conducted a pilot feasibility study employing whole-genome, strand-specific sequencing of cfDNA from eight patients with familial PCa. A unified analytical pipeline was used to jointly profile genomic alterations and epigenomic features. Variant calling, methylation mapping, and allele-specific methylation (ASM) analysis were performed to identify somatic mutations, characterize epigenetic dysregulation, and explore potential interactions between genetic and epigenetic mechanisms. Results: Sequencing revealed 18,878 genetic variants, including 2276 potentially pathogenic alterations. We identified 26 recurrent high-impact mutations, such as stop-gain and start-loss variants, in genes including MUC4, MCM9, and SKA3. Epigenomic profiling demonstrated widespread gene-specific hypermethylation, consistent with transcriptional repression in these loci. ASM events were detected in TTC22, TEX51, WDR89, LAIR2, and SKA3, suggesting coordinated interactions between somatic variation and epigenetic regulation in familial PCa. Conclusions: This proof-of-concept study highlights the feasibility and potential of integrating whole-genome and epigenome profiling of cfDNA to decode the molecular architecture of familial prostate cancer. By jointly capturing genomic alterations and epigenetic signatures, including allele-specific methylation, this multi-omic liquid biopsy approach supports a high-resolution exploration of biologically relevant molecular features. Moreover, this integrated profiling strategy provides a minimally invasive and clinically scalable tool that may substantially improve risk assessment. These findings offer a promising foundation for future validation studies in larger cohorts, with the aim of advancing multi-omic cfDNA analysis as a next-generation technology in the field of precision oncologic epigenetics. Full article
(This article belongs to the Special Issue Genomics and Epitranscriptomics Regulation in Cancer)
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