DNA Methylation Alterations in Fractionally Irradiated Rats and Breast Cancer Patients Receiving Radiotherapy

Effects of Ionizing Radiation on DNA Methylation Patterns and Their Potential as Biomarkers

DNA methylation is a common endogenous chemical modification in eukaryotic DNA, primarily involving the covalent attachment of a methyl group to the fifth carbon of cytosine residues, leading to the formation of 5-methylcytosine (5mC). This epigenetic modification plays a crucial role in gene expression regulation and genomic stability maintenance in eukaryotic systems. Ionizing radiation (IR) has been shown to induce changes in global DNA methylation patterns, which exhibit significant temporal stability. This stability makes DNA methylation profiles promising candidates for radiation-specific biomarkers. This review systematically examines the impact of IR on genome-wide DNA methylation landscapes and evaluates their potential as molecular indicators of radiation exposure. Advancing the knowledge of radiation-induced epigenetic modifications in radiobiology contributes to a deeper understanding of IR-driven epigenetic reprogramming and facilitates the development of novel molecular tools for the early detection and quantitative risk assessment of radiation exposure.

Discovery and confirmation of crucial genes associated with radiation-induced heart disease

Objective: Radiotherapy is an essential method for treating cancerous tumors, and the resultant radiation-induced heart disease (RIHD) has emerged as the leading non-cancerous cause of mortality among cancer survivors. However, the mechanisms of RIHD are still unknown, and specific biomarkers and effective treatment methods are needing to be found. Methods: Fourteen male C57BL/6J mice, each 8 weeks old, were randomly assigned into two groups: an experimental group (n = 7) and a control group (n = 7). The test group underwent irradiation with 30 Gy of 60Co γ-rays. To assess the acute and chronic damage to the myocardium caused by radiation, heart tissues were collected at one day and six weeks after irradiation for transcriptome sequencing, and H&E staining and immunohistochemical staining were done, respectively. Results: One day after radiation, the myocardial tissue showed a significant amount of inflammatory cell infiltration. Following a period of six weeks, there was an increase in hypertrophic cardiomyocytes and myocardial fibrosis. Additionally, we identified several genes (Cmpk2, Ifit3, Dhx58, Slc2a1, and Thbs1) that were strongly associated with RIHD. The expression of these genes in heart tissue was significantly upregulated after six weeks of radiation. Findings from the GO functional and KEGG pathway enrichment analysis, along with the hub gene function analysis, indicate that the mechanism behind RIHD might be linked to systemic inflammation and mitochondrial dysfunction. Conclusion: Acute radiation myocardial injury is characterized by inflammation, while chronic radiation myocardial injury is characterized by myocardial fibrosis. RIHD is linked to Cmpk2, Ifit3, Dhx58, Slc2a1, and Thbs1 genes through a mechanism that may cause systemic inflammation and mitochondrial dysfunction.

Implementation of the Methyl-Seq platform to identify tissue- and sex-specific DNA methylation differences in the rat epigenome

Epigenomic annotations for the rat lag far behind those of human and mouse, despite the rat's immense utility in pharmacological and behavioral studies and the need to understand their epigenetic mechanisms. We have designed a targeted-enrichment method followed by next-generation sequencing (Methyl-Seq) to identify DNA methylation (DNAm) signatures across the rat genome. The design reflected an attempt to create a more comprehensive investigation of the rat epigenome, as it included promoters, CpG islands, and island shores of all RefSeq genes. In this study, we implemented the rat Methyl-Seq platform and tested its ability to distinguish differentially methylated regions (DMRs) among three different tissue types, three distinct brain regions, and, in the hippocampus, between males and females. These comparisons yielded DNAm differences of differing magnitudes, many of which were independently validated by bisulfite pyrosequencing, including autosomal regions that were predicted to show the least degree of difference in DNAm between males and females. Quantitative reverse transcription PCR revealed that most genes associated with the DMRs showed tissue-, brain region-, and sex-specific differences in expression. In particular, we found evidence for sex-specific DNAm and expression differences at Tubb6, Lrrn2, Tex26, and Sox5l1, all of which play important roles in neurodevelopment and have been implicated in studies examining sex differences. Our results demonstrate the utility of the rat Methyl-Seq platform and suggest the presence of DNAm differences between the male and female hippocampus. The rat Methyl-Seq has the potential to provide epigenomic insights into pharmacological and behavioral studies performed in the rat.

Correction: Sallam et al. DNA Methylation Alterations in Fractionally Irradiated Rats and Breast Cancer Patients Receiving Radiotherapy. Int. J. Mol. Sci. 2022, 23, 16214

Radia Tamarat and Susana Constantino Rosa Santos were not included as authors in the original publication [...].

The Role of Selected Epigenetic Pathways in Cardiovascular Diseases as a Potential Therapeutic Target

Epigenetics is a rapidly developing science that has gained a lot of interest in recent years due to the correlation between characteristic epigenetic marks and cardiovascular diseases (CVDs). Epigenetic modifications contribute to a change in gene expression while maintaining the DNA sequence. The analysis of these modifications provides a thorough insight into the cardiovascular system from its development to its further functioning. Epigenetics is strongly influenced by environmental factors, including known cardiovascular risk factors such as smoking, obesity, and low physical activity. Similarly, conditions affecting the local microenvironment of cells, such as chronic inflammation, worsen the prognosis in cardiovascular diseases and additionally induce further epigenetic modifications leading to the consolidation of unfavorable cardiovascular changes. A deeper understanding of epigenetics may provide an answer to the continuing strong clinical impact of cardiovascular diseases by improving diagnostic capabilities, personalized medical approaches and the development of targeted therapeutic interventions. The aim of the study was to present selected epigenetic pathways, their significance in cardiovascular diseases, and their potential as a therapeutic target in specific medical conditions.

Postsynaptic density radiation signature following space irradiation

Introduction: The response of the brain to space radiation is an important concern for astronauts during space missions. Therefore, we assessed the response of the brain to ²⁸Si ion irradiation (600 MeV/n), a heavy ion present in the space environment, on cognitive performance and whether the response is associated with altered DNA methylation in the hippocampus, a brain area important for cognitive performance. Methods: We determined the effects of ²⁸Si ion irradiation on object recognition, 6-month-old mice irradiated with ²⁸Si ions (600 MeV/n, 0.3, 0.6, and 0.9 Gy) and cognitively tested two weeks later. In addition, we determined if those effects were associated with alterations in hippocampal networks and/or hippocampal DNA methylation. Results: At 0.3 Gy, but not at 0.6 Gy or 0.9 Gy, ²⁸Si ion irradiation impaired cognition that correlated with altered gene expression and 5 hmC profiles that mapped to specific gene ontology pathways. Comparing hippocampal DNA hydroxymethylation following proton, ⁵⁶Fe ion, and ²⁸Si ion irradiation revealed a general space radiation synaptic signature with 45 genes that are associated with profound phenotypes. The most significant categories were glutamatergic synapse and postsynaptic density. Discussion: The brain's response to space irradiation involves novel excitatory synapse and postsynaptic remodeling.