Transient Focal Ischemia Significantly Alters the m6A Epitranscriptomic Tagging of RNAs in the Brain

Fusarium infection alters the m6A-modified transcript landscape in the cornea

N6-methyladenosine (m⁶A) is the most common post-transcriptional modification of RNA in eukaryotes that regulates the post-transcriptional expression level of genes without changing the base sequence. The role of m⁶A in fungal keratitis has not yet been elucidated. Here, we aimed to identify m⁶A modification changes and their potential roles in fungal keratitis. The murine model of fungal keratitis was established by inoculating mice with Fusarium solani (F. solani). The overall m⁶A level was detected via an m⁶A RNA methylation assay kit. The expression levels of key m⁶A modification-related genes were estimated by quantitative real-time polymerase chain reaction (PCR). The expression and localization of METTL (methyltransferase like)3, the key component of the m⁶A methyltransferase complex, was determined by immunostaining and Western blotting (WB). Immunoprecipitation methylation microarray was used to describe the changes in m⁶A modification in F. solani-infected corneal tissue. The overall m⁶A level in corneal tissue on the 5th day in the F. solani-treated group was upregulated compared with that in the control group. The demethylase levels were unaltered, but the level of the methylase METTL3 was increased significantly after fungal infection. Additionally, differences were found in m⁶A modifications in 1137 mRNAs, of which 780 were hypermethylated and 357 were hypomethylated. To the best of our knowledge, the present work is the first investigation on the m⁶A modification profiles in experimental fungal keratitis, and it may provide a potential therapeutic target.

microRNA-421-3p prevents inflammatory response in cerebral ischemia/reperfusion injury through targeting m6A Reader YTHDF1 to inhibit p65 mRNA translation

OBJECTIVE

Ischemic stroke is one of the leading causes of death globally, and inflammation is considered as a vital contributor to the pathophysiology of ischemic stroke. Recently, microRNA-421-3p-derived macrophages is found to promote motor function recovery in spinal cord injury. Here, we explored whether microRNA-421-3p is involved in inflammation responses during cerebral ischemia/reperfusion (I/R) injury and its molecular mechanism.

METHODS

An in vivo experimental animal model of intraluminal middle cerebral artery occlusion/reperfusion (MCAO/R) and in vitro model of microglial subjected to oxygen-glucose deprivation and reoxygenation (OGD/R) were used. The effects of microRNA-421-3p on cerebral I/R injury and its underlying mechanism were detected by quantitative real-time PCR, western blotting, immunofluorescence staining, RNA immunoprecipitation, flow cytometry, luciferase reporter assay, and bioinformatics analysis.

RESULTS

We find that microRNA-421-3p is significantly decreased in cerebral I/R injury in vitro and in vivo. Furthermore, overexpression of microRNA-421-3p evidently suppresses pro-inflammatory factor expressions and inhibits NF-κB p65 protein expression and nuclear translocation in BV2 microglia cells treated with OGD/R. However, microRNA-421-3p neither promotes p65 mRNA expression, nor affects p65 mRNA or protein stability. Moreover, we find the m6A 'reader' protein YTH domain family protein 1 (YTHDF1) is the specific target of microRNA-421-3p, and YTHDF1 specifically binds to the m6a site of p65 mRNA to promote its translation.

CONCLUSION

microRNA-421-3p prevents inflammatory response in cerebral ischemia/reperfusion injury through targeting YTHDF1 to inhibit p65 mRNA translation. These findings provide novel insights into understanding the molecular pathogenesis of cerebral I/R injury.

m6A RNA Methylation in Cardiovascular Diseases

Cardiovascular diseases (CVDs) remain the leading cause of death and disability worldwide, despite marked improvements in prevention, diagnosis, and early intervention. There is an urgent need to discover more effective therapeutic strategies, which would be facilitated by a more in-depth understanding of CVDs and their underlying molecular mechanisms. Recent advances in knowledge about epigenetic mechanisms, especially RNA methylation, have revealed a close relationship between epigenetic modifications and CVDs and have brought to potential novel targets for diagnosis and treatment. Here, we provide a review of recent studies exploring RNA N⁶-methyladenosine (m⁶A) modification, with particular emphasis on its role in CVDs, such as coronary heart disease, hypertension, cardiac hypertrophy, and heart failure. We also introduce the "life cycle" of m⁶A and its dominant function in several biological processes. Finally, we highlight the prospects of treatment based on interfering with m⁶A, which could have a transformative effect on clinical medicine.

N6-methyladenosine as a Novel Regulator of Brain Physiology and Diseases

N⁶-methyladenosine (m⁶A) is identified as the most widespread and abundant internal chemical modification of RNA in eukaryotes. A series of proteins including methyltransferases (also known as "writers"), demethylases (also known as "erasers"), and m⁶A-binding proteins (also known as "readers") were indicated to participate in the m⁶A methylation. m⁶A has emerged as a regulator of various cellular, developmental, and disease processes. Notably, there is highest abundance of m⁶A methylation in brain than in other organs, which indicates that m⁶A plays an essential role in brain functions. Here, we describe the general features, mechanisms, and functions of m⁶A in the brain, and discuss the emerging roles of m⁶A in brain physiology and diseases.

Bioinformatics analysis integrating metabolomics of m6A RNA microarray in intervertebral disc degeneration

Aim: To explore the potential functions and mechanism of N⁶.methyladenosine (m⁶A) abnormality of RNAs in nucleus pulposus from the intervertebral disc degeneration (IDD). Materials & methods: We performed rat model, m⁶A epitranscriptomic microarray, bioinformatics analysis and metabolomics. Results: In IDD, most of the differentially methylated RNAs showed a significant demethylation situation. The competing endogenous RNA network LOC102555094/miR-431/GSK-3β combining downstream Wnt pathway were identified in bioinformatics analysis. For metabolomics, activation of Wnt pathway led to reprogramming of glucose metabolism and enzyme activation of PKM2. Finally, quantitative real-time PCR and methylated RNA immunoprecipitation coupled with quantitative real-time PCR revealed the positive correlation between demethylation of LOC102555094 and expression of both FTO and ZFP217. Conclusion: LOC102555094 might be demethylated by ZFP217, activating FTO and LOC102555094/miR-431/GSK-3β/Wnt played a crucial role in IDD.

N6-methyladenosine (m6A) methylation in ischemia-reperfusion injury

Ischemia-reperfusion (I/R) injury is common during surgery and often results in organ dysfunction. The mechanisms of I/R injury are complex, diverse, and not well understood. RNA methylation is a novel epigenetic modification that is involved in the regulation of various biological processes, such as immunity, response to DNA damage, tumorigenesis, metastasis, stem cell renewal, fat differentiation, circadian rhythms, cell development and differentiation, and cell division. Research on RNA modifications, specifically N6-methyladenosine (m6A), have confirmed that they are involved in the regulation of organ I/R injury. In this review, we summarized current understanding of the regulatory roles and significance of m6A RNA methylation in I/R injury in different organs.

Research Progress of N6-Methyladenosine in the Cardiovascular System

According to the World Health Organization cardiovascular disease risk charts, the mortality rate of cardiovascular diseases in people is still high. The medical expenses caused by cardiovascular diseases are increasing daily, and the medical burden is becoming heavier; as such, it is imperative to prevent and cure cardiovascular diseases. A large number of scholars are analyzing the pathogenesis of cardiovascular diseases from various perspectives. Recent findings suggest that N6-methyladenosine (m6A) plays a multifaceted role in the cardiovascular system. m6A is a methylated modification product on RNA molecules and exists on various RNA molecules. It is one of the most common epigenetic modifications discovered to date. It regulates the expression of genes and subsequent responses. The amount of m6A is determined by methylases (writers) and demethylases (erasers). The third type of proteins, readers, selectively bind to m6A to regulate RNA stability and gene expression. In this paper, the relationship between m6A and related enzymes and cardiovascular structure and function was reviewed based on recent research results regarding the cardiovascular system.

Hypothermia protects neurons against ischemia/reperfusion-induced pyroptosis via m6A-mediated activation of PTEN and the PI3K/Akt/GSK-3β signaling pathway

Cerebral ischemia/reperfusion (I/R) injury often leads to irreversible neuronal injury and even death, and hypothermia is the only therapeutic method that has been proven to be effective. However, the molecular mechanisms underlying the effect of hypothermia treatment on I/R injury have not been fully elucidated. In the present study, we aimed to evaluate the neuroprotective effects and mechanisms of hypothermia against hypoxia/reoxygenation (H/R)-induced neuronal damage. Primary hippocampal neurons were exposed to H/R and were then treated with hypothermia. We observed that hypothermia significantly increased cellular viability, downregulated the expression of pyroptosis-related proteins-including NLR pyrin domain containing 3 (NLRP3), apoptotic speck-like protein containing CARD (ASC), cleaved Caspase-1, and Gasdermin-D (GsdmD) p30-and reduced secretion of the pro-inflammatory cytokines, IL-1β and IL-18. Additionally, pretreatment with MCC950, a specific small-molecule inhibitor of the NLRP3 inflammasome, yielded a protective effect on cellular viability that was comparable to that of hypothermia treatment. Furthermore, hypothermia also significantly elevated the expression level of phosphatase and tensin homologous protein (PTEN) and activated the phosphorylation levels of protein kinase B (Akt) and glycogen synthase kinase-3β (GSK-3β). These protective effects of hypothermia on pyroptosis-related proteins and pro-inflammatory cytokines were partially reversed by the specific PI3K/Akt inhibitor, LY294002. Moreover, the methylated level of PTEN mRNA was elevated in hippocampal neurons upon H/R, whereas this level remained stable in the hypothermia group. Therefore, our findings suggest that hypothermia protects neurons against neuronal H/R-induced pyroptosis, and that m6A-mediated activation of PTEN and the phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K)/Akt/GSK-3β signaling pathway may play crucial roles during this process.

Ischemia-related changes of fat-mass and obesity-associated protein expression in the gerbil hippocampus

Fat-mass and obesity-associated protein (Fto) plays important roles in energy metabolism. It also acts as a demethylase and is most abundantly found in the brain. In the present study, we examined the spatial and temporal changes of Fto immunoreactivity after five minutes of transient forebrain ischemia in the hippocampus. In the control group, Fto immunoreactivity was mainly observed in the nucleus of pyramidal cells in the CA1 and CA3 regions as well as the polymorphic layer, granule cell layer, and subgranular zone of the dentate gyrus. Fto immunoreactivity was transiently, but not significantly, increased in the hippocampal CA3 region and the dentate gyrus two days after ischemia compared to mice without ischemia in the sham-operated group. Four days after ischemia, low Fto immunoreactivity was observed in the stratum pyramidale of the CA1 region because of neuronal death, but Fto immunoreactive cells were abundantly detected in the stratum pyramidale of the CA3 region, which is relatively resistant to ischemic damage. Thereafter, Fto immunoreactivity progressively decreased in the hippocampal CA1 and CA3 regions and the dentate gyrus until ten days after ischemia. At this time-point, Fto immunoreactivity was significantly lower in the hippocampal CA1 and CA3 regions and the dentate gyrus compared to that in the sham-operated group. The reduction of Fto immunoreactive structures in the hippocampus may be associated with impairments in Fto-related hippocampal function.

Invited Review: Epigenetics in neurodevelopment

Neural development requires the orchestration of dynamic changes in gene expression to regulate cell fate decisions. This regulation is heavily influenced by epigenetics, heritable changes in gene expression not directly explained by genomic information alone. An understanding of the complexity of epigenetic regulation is rapidly emerging through the development of novel technologies that can assay various features of epigenetics and gene regulation. Here, we provide a broad overview of several commonly investigated modes of epigenetic regulation, including DNA methylation, histone modifications, noncoding RNAs, as well as epitranscriptomics that describe modifications of RNA, in neurodevelopment and diseases. Rather than functioning in isolation, it is being increasingly appreciated that these various modes of gene regulation are dynamically interactive and coordinate the complex nature of neurodevelopment along multiple axes. Future work investigating these interactions will likely utilize 'multi-omic' strategies that assay cell fate dynamics in a high-dimensional and high-throughput fashion. Novel human neurodevelopmental models including iPSC and cerebral organoid systems may provide further insight into human-specific features of neurodevelopment and diseases.