Chemical Insights into Oxidative and Nitrative Modifications of DNA

Vitamin E nomenclature. Is RRR-α-tocopherol the only vitamin E?

It has generally been accepted that vitamin E refers to a group of tocochromanols, α-, β-, γ-, and δ-tocopherols and the corresponding four tocotrienols. Recently, Azzi and colleagues proposed to restrict the term vitamin E only to RRR-α-tocopherol, not to other tocopherols and tocotrienols (Azzi A et al. Free Radic Biol Med. 2023; 207:178-180. doi: 10.1016/j.freeradbiomed.2023.06.029). The aim of this paper is to express our opinion on the nomenclature of vitamin E based on available scientific data. In our opinion, it would be inappropriate to exclude all the tocochromanols other than RRR-α-tocopherol from the vitamin E group at this stage when the molecular mechanisms showing how vitamin E deficiency causes diseases such as ataxia and how vitamin E prevents/reverses such diseases are not elucidated. Understanding of whole functions of tocochromanols including underlying mechanisms and dynamics is essential before revision of currently accepted definition of vitamin E. The potential roles of γ-tocopherol and tocotrienols are discussed despite whether they are vitamin function should be clarified in the future studies.

Lycium ruthenicum water extract preserves retinal ganglion cells in chronic ocular hypertension mouse models

Lycium ruthenicum Murray (LR), known as "black goji berry" or "black wolfberry", is widely utilized in chinese herbal medicine. LR fruit showed its antioxidant and/or anti-inflammation activity in treating cardiac injury, experimental colitis, nonalcoholic fatty liver disease, fatigue, and aging. Glaucoma is the leading cause of irreversible blindness. Besides elevated intraocular pressure (IOP), oxidative stress and neuroinflammation were recognized to contribute to the pathogenesis of glaucoma. This study investigated the treatment effects of LR water extract (LRE) on retinal ganglion cells (RGCs) threatened by sustained IOP elevation in a laser-induced chronic ocular hypertension (COH) mouse model and the DBA/2J mouse strain. The antioxidation and anti-inflammation effects of LRE were further tested in the H2O2-challenged immortalized microglial (IMG) cell line in vitro. LRE oral feeding (2 g/kg) preserved the function of RGCs and promoted their survival in both models mimicking glaucoma. LRE decreased 8-hydroxyguanosine (oxidative stress marker) expression in the retina. LRE reduced the number of Iba-1+ microglia in the retina of COH mice, but not in the DBA/2J mice. At the mRNA level, LRE reversed the COH induced HO-1 and SOD-2 overexpressions in the retina of COH mice. Further in vitro study demonstrated that LRE pretreatment to IMG cells could significantly reduce H2O2 induced oxidative stress through upregulation of GPX-4, Prdx-5, HO-1, and SOD-2. Our work demonstrated that daily oral intake of LRE can be used as a preventative/treatment agent to protect RGCs under high IOP stress probably through reducing oxidative stress and inhibiting microglial activation in the retina.

Methods and applications of genome-wide profiling of DNA damage and rare mutations

DNA damage is a threat to genome integrity and can be a cause of many human diseases, owing to either changes in the chemical structure of DNA or conversion of the damage into a mutation, that is, a permanent change in DNA sequence. Determining the exact positions of DNA damage and ensuing mutations in the genome are important for identifying mechanisms of disease aetiology when characteristic mutations are prevalent and probably causative in a particular disease. However, this approach is challenging particularly when levels of DNA damage are low, for example, as a result of chronic exposure to environmental agents or certain endogenous processes, such as the generation of reactive oxygen species. Over the past few years, a comprehensive toolbox of genome-wide methods has been developed for the detection of DNA damage and rare mutations at single-nucleotide resolution in mammalian cells. Here, we review and compare these methods, describe their current applications and discuss future research questions that can now be addressed.

Epigenetic marks or not? The discovery of novel DNA modifications in eukaryotes

DNA modifications add another layer of complexity to the eukaryotic genome to regulate gene expression, playing critical roles as epigenetic marks. In eukaryotes, the study of DNA epigenetic modifications has been confined to 5mC and its derivatives for decades. However, rapid developing approaches have witnessed the expansion of DNA modification reservoirs during the past several years, including the identification of 6mA, 5gmC, 4mC, and 4acC in diverse organisms. However, whether these DNA modifications function as epigenetic marks requires careful consideration. In this review, we try to present a panorama of all the DNA epigenetic modifications in eukaryotes, emphasizing recent breakthroughs in the identification of novel DNA modifications. The characterization of their roles in transcriptional regulation as potential epigenetic marks is summarized. More importantly, the pathways for generating or eliminating these DNA modifications, as well as the proteins involved are comprehensively dissected. Furthermore, we briefly discuss the potential challenges and perspectives, which should be taken into account while investigating novel DNA modifications.

Effects of dietary methionine supplementation on the growth performance, immune responses, antioxidant capacity, and subsequent development of layer chicks

Deficiencies or excesses of dietary amino acids, and especially of methionine (Met), in laying hens can lead to abnormal protein anabolism and oxidative stress, which affect methylation and cause cellular dysfunction. This study investigated the effects of dietary methionine (Met) levels on growth performance, metabolism, immune response, antioxidant capacity, and the subsequent development of laying hens. A total of 384 healthy 1-day-old Hyline Grey chicks of similar body weight were randomly allocated to be fed diets containing 0.31%, 0.38%, 0.43% (control group), or 0.54% Met for 6 wk, with 6 replicates of 16 chicks in each. The growth performance of the chicks was then followed until 20 wk old. The results showed dietary supplementation with 0.43% or 0.54% Met significantly increased their mean daily body weight gain, final weight, and Met intake. However, the feed:gain (F/G) decreased linearly with increasing Met supplementation, from 0.31 to 0.54% Met. Met supplementation increased the serum albumin, IgM, and total glutathione concentrations of 14-day-old chicks. In contrast, the serum alkaline phosphatase activity and hydroxyl radical concentration tended to decrease with increasing Met supplementation. In addition, the highest serum concentrations of IL-10, T-SOD, and GSH-PX were in the 0.54% Met-fed group. At 42 d of age, the serum ALB, IL-10, T-SOD, GSH-PX, T-AOC, and T-GSH were correlated with dietary Met levels. Finally, Met supplementation reduced the serum concentrations of ALP, IL-1β, IgA, IgG, hydrogen peroxide, and hydroxyl radicals. Thus, the inclusion of 0.43% or 0.54% Met in the diet helps chicks achieve superior performance during the brooding period and subsequently. In conclusion, Met doses of 0.43 to 0.54% could enhance the growth performance, protein utilization efficiency, antioxidant capacity, and immune responses of layer chicks, and to promote more desirable subsequent development during the brooding period.