Ionizing radiation damage and repair from 3D-genomic perspective

Radioprotective Effects and Mechanisms of One-Year and Seven-Year White Tea Extracts Against 137Cs Radiation-Induced Cell Damage

Ionizing radiation (IR) is widely present in the environment, with 137Cesium (Cs) radiation having particularly severe impacts during nuclear accidents. The objective of our study was to assess the radiation protection or repair effect of one year (WT-1Y) or seven years (WT-7Y) of storage on white teas, as well as to investigate the mechanism of radioprotection. HGC-27 cells exposed to 137Cs γ-rays (30 Gy) exhibited significant changes in cell structure, apoptosis, ROS, LDH, and their expression of p53 and Caspase-3. The results showed that WT-1Y and WT-7Y acted as antioxidants, showed reduced ROS and LDH levels, and had increased CAT and SOD activities as well as cell survival rate. The WT treatments significantly inhibited apoptosis in both the pre- and post-radiation groups, with WT-1 showing stronger effects in pretreatment by reducing LDH, p53, and Caspase-3 levels and enhancing ROS scavenging and enzyme activities. Post-treatment analysis revealed WT-7 had greater effects on cell viability and SOD activity. Overall, both WT-1 and WT-7 mitigated radiation damage, likely by inhibiting the p53/Caspase-3 apoptosis pathway. A Spearman analysis of the differential metabolites in WT-1Y and WT-7Y with cellular radioprotective indicators revealed that metabolites, such as EGC, procyanidin B4, and phenolic acids (abundant in WT-1Y), quercetin-3-glucosylrutinoside, and caffeine (enriched in WT-7Y) contributed to their distinct effects in the pre- and post-treatment of 137Cs γ-rays.

Leveraging zebrafish models for advancing radiobiology: Mechanisms, applications, and future prospects in radiation exposure research

Ionizing radiation (IR) represents a significant risk to human health and societal stability. To effectively analyze the mechanisms of IR and enhance protective strategies, the development of more sophisticated animal models is imperative. The zebrafish, with its high degree of genomic homology to humans and the capacity for whole-body optical visualization and high-throughput screening, represents an invaluable model for the study of IR. This review examines the benefits of utilizing zebrafish as a model organism for research on IR, emphasizing recent advancements and applications. It presents a comprehensive overview of the methodologies for establishing IR models in zebrafish, addresses current challenges, and discusses future development trends. This paper provide theoretical support for elucidating the mechanisms of IR injury and developing effective treatment strategies.

The tardigrade Hypsibius exemplaris dramatically upregulates DNA repair pathway genes in response to ionizing radiation

Tardigrades can survive remarkable doses of ionizing radiation, up to about 1,000 times the lethal dose for humans. How they do so is incompletely understood. We found that the tardigrade Hypsibius exemplaris suffers DNA damage upon gamma irradiation, but the damage is repaired. We show that this species has a specific and robust response to ionizing radiation: irradiation induces a rapid upregulation of many DNA repair genes. This upregulation is unexpectedly extreme-making some DNA repair transcripts among the most abundant transcripts in the animal. By expressing tardigrade genes in bacteria, we validate that increased expression of some repair genes can suffice to increase radiation tolerance. We show that at least one such gene is important in vivo for tardigrade radiation tolerance. We hypothesize that the tardigrades' ability to sense ionizing radiation and massively upregulate specific DNA repair pathway genes may represent an evolved solution for maintaining DNA integrity.

Long-term, non-invasive FTIR detection of low-dose ionizing radiation exposure

Non-invasive methods of detecting radiation exposure show promise to improve upon current approaches to biological dosimetry in ease, speed, and accuracy. Here we developed a pipeline that employs Fourier transform infrared (FTIR) spectroscopy in the mid-infrared spectrum to identify a signature of low dose ionizing radiation exposure in mouse ear pinnae over time. Mice exposed to 0.1 to 2 Gy total body irradiation were repeatedly measured by FTIR at the stratum corneum of the ear pinnae. We found significant discriminative power for all doses and time-points out to 90 days after exposure. Classification accuracy was maximized when testing 14 days after exposure (specificity > 0.9 with a sensitivity threshold of 0.9) and dropped by roughly 30% sensitivity at 90 days. Infrared frequencies point towards biological changes in DNA conformation, lipid oxidation and accumulation and shifts in protein secondary structure. Since only hundreds of samples were used to learn the highly discriminative signature, developing human-relevant diagnostic capabilities is likely feasible and this non-invasive procedure points toward rapid, non-invasive, and reagent-free biodosimetry applications at population scales.

A graph neural network-based interpretable framework reveals a novel DNA fragility-associated chromatin structural unit

BACKGROUND

DNA double-strand breaks (DSBs) are among the most deleterious DNA lesions, and they can cause cancer if improperly repaired. Recent chromosome conformation capture techniques, such as Hi-C, have enabled the identification of relationships between the 3D chromatin structure and DSBs, but little is known about how to explain these relationships, especially from global contact maps, or their contributions to DSB formation.

RESULTS

Here, we propose a framework that integrates graph neural network (GNN) to unravel the relationship between 3D chromatin structure and DSBs using an advanced interpretable technique GNNExplainer. We identify a new chromatin structural unit named the DNA fragility-associated chromatin interaction network (FaCIN). FaCIN is a bottleneck-like structure, and it helps to reveal a universal form of how the fragility of a piece of DNA might be affected by the whole genome through chromatin interactions. Moreover, we demonstrate that neck interactions in FaCIN can serve as chromatin structural determinants of DSB formation.

CONCLUSIONS

Our study provides a more systematic and refined view enabling a better understanding of the mechanisms of DSB formation under the context of the 3D genome.