Context-Dependent Roles of RNA Modifications in Stress Responses and Diseases

Knockdown of cullin 3 inhibits progressive phenotypes and increases chemosensitivity in cholangiocarcinoma cells

Cholangiocarcinoma (CCA) is an extremely aggressive malignancy arising from the epithelial cells lining the bile ducts. It presents a substantial global health issue, with the highest incidence rates, ranging from 40‑100 cases/100,000 individuals, found in Southeast Asia, where liver fluke infection is endemic. In Europe and America, incidence rates range from 0.4‑2 cases/100,000 individuals. Globally, mortality rates range from 0.2‑2 deaths/100,000 person‑years and are increasing in most countries. Chemotherapy is the primary treatment for advanced CCA due to limited options from late‑stage diagnosis, but its efficacy is hindered by drug‑resistant phenotypes. In a previous study, proteomics analysis of drug‑resistant CCA cell lines (KKU‑213A‑FR and KKU‑213A‑GR) and the parental KKU‑213A line identified cullin 3 (Cul3) as markedly overexpressed in drug‑resistant cells. Cul3, a scaffold protein within CUL3‑RING ubiquitin ligase complexes, is crucial for ubiquitination and proteasome degradation, yet its role in drug‑resistant CCA remains to be elucidated. The present study aimed to elucidate the role of Cul3 in drug‑resistant CCA cell lines. Reverse transcription‑quantitative PCR and western blot analyses confirmed significantly elevated Cul3 mRNA and protein levels in drug‑resistant cell lines compared with the parental control. Short interfering RNA‑mediated Cul3 knockdown sensitized cells to 5‑fluorouracil and gemcitabine and inhibited cell proliferation, colony formation, migration and invasion. In addition, Cul3 knockdown induced G0/G1 cell cycle arrest and suppressed key cell cycle regulatory proteins, cyclin D, cyclin‑dependent kinase (CDK)4 and CDK6. Bioinformatics analysis of CCA patient samples using The Cancer Genome Atlas data revealed Cul3 upregulation in CCA tissues compared with normal bile duct tissues. STRING analysis of upregulated proteins in drug‑resistant CCA cell lines identified a highly interactive Cul3 network, including COMM Domain Containing 3, Ariadne RBR E3 ubiquitin protein ligase 1, Egl nine homolog 1, Proteasome 26S Subunit Non‑ATPase 13, DExH‑box helicase 9 and small nuclear ribonucleoprotein polypeptide G, which showed a positive correlation with Cul3 in CCA tissues. Knocking down Cul3 significantly suppressed the mRNA expression of these genes, suggesting that Cul3 may act as an upstream regulator of them. Gene Ontology analysis revealed that the majority of these genes were categorized under binding function, metabolic process, cellular anatomical entity, protein‑containing complex and protein‑modifying enzyme. Taken together, these findings highlighted the biological and clinical significance of Cul3 in drug resistance and progression of CCA.

Mutligenerational chronic exposure to near future ocean acidification in European sea bass (Dicentrarchus labrax): Insights into the regulation of the transcriptome in a sensory organ involved in feed intake, the tongue

In this study, we examined the effect of near future ocean acidification (OA) on the transcriptome of a sensory organ in contact with surrounding water, the tongue in adult European sea bass (Dicentrarchus labrax) by mean of RNAseq experiment. We acquired a total of 14.1 Mb quality-trimmed reads covering 18,703 expressed genes from the tongue of fish reared from two generations at actual (pH 8.0 condition) and predicted near-future seawater pH (pH 7.6 condition). Gene ontologies analyses of expressed genes support the evidence that the tongue exhibits biological processes related to the sensory system, tooth mineralization and immune defences among others. Our data revealed only 295 OA-induced regulated genes with 114 up- and 181 down-regulated by OA. Functions over-represented encompass processes involved in organic substance metabolic process, RNA metabolism and especially RNA methylation which, combined with the regulation of some hsp genes expression, suggest a molecular response to stress which might contribute to lingual cell homeostasis under OA. The immune system process is also found enriched within OA-induced regulated genes. With the exception of one fatty acid receptor, known taste perception effectors were not impacted by OA in the tongue. However, a complementary droplet digital PCR approach dedicated to genes involved in gustatory signal transduction revealed the down regulation by OA of pyrimidinergic receptor (p2ry4) transcript expression in the gills of the fish. Combined with scanning electron microscopy analysis, our RNAseq data revealed that OA has no impact on processes related to teeth development and mineralization. Altogether, our data reveal that multigenerational exposure to OA has not a substantially effect on the tongue transcriptome but emphasis should be placed on investigating the potential physiological consequences related to the regulation of genes related to cell stress, immune system and fatty acid sensitivity to conclude on species resilience in face of OA.

RNA modifications in physiology and pathology: Progressing towards application in clinical settings

The potential to modify individual nucleotides through chemical means in order to impact the electrostatic charge, hydrophobic properties, and base pairing of RNA molecules is harnessed in the medical application of stable synthetic RNAs like mRNA vaccines and synthetic small RNA molecules. These modifications are used to either increase or decrease the production of therapeutic proteins. Additionally, naturally occurring biochemical alterations of nucleotides play a role in regulating RNA metabolism and function, thereby modulating essential cellular processes. Research elucidating the mechanisms through which RNA modifications govern fundamental cellular functions in multicellular organisms has enhanced our comprehension of how irregular RNA modification profiles can lead to human diseases. Collectively, these fundamental scientific findings have unveiled the molecular and cellular functions of RNA modifications, offering new opportunities for therapeutic intervention and paving the way for a variety of innovative clinical strategies.

N6-Methyladenosine in Vascular Aging and Related Diseases: Clinical Perspectives

Aging leads to progressive deterioration of the structure and function of arteries, which eventually contributes to the development of vascular aging-related diseases. N6-methyladenosine (m6A) is the most prevalent modification in eukaryotic RNAs. This reversible m6A RNA modification is dynamically regulated by writers, erasers, and readers, playing a critical role in various physiological and pathological conditions by affecting almost all stages of the RNA life cycle. Recent studies have highlighted the involvement of m6A in vascular aging and related diseases, shedding light on its potential clinical significance. In this paper, we comprehensively discuss the current understanding of m6A in vascular aging and its clinical implications. We discuss the molecular insights into m6A and its association with clinical realities, emphasizing its significance in unraveling the mechanisms underlying vascular aging. Furthermore, we explore the possibility of m6A and its regulators as clinical indicators for early diagnosis and prognosis prediction and investigate the therapeutic potential of m6A-associated anti-aging approaches. We also examine the challenges and future directions in this field and highlight the necessity of integrating m6A knowledge into patient-centered care. Finally, we emphasize the need for multidisciplinary collaboration to advance the field of m6A research and its clinical application.

Transcriptional control of a metabolic switch regulating cellular methylation reactions is part of a common response to stress in divergent bee species

Recent global declines in bee health have elevated the need for a more complete understanding of the cellular stress mechanisms employed by diverse bee species. We recently uncovered the biomarker lethal (2) essential for life [l(2)efl] genes as part of a shared transcriptional program in response to a number of cell stressors in the western honey bee (Apis mellifera). Here, we describe another shared stress-responsive gene, glycine N-methyltransferase (Gnmt), which is known as a key metabolic switch controlling cellular methylation reactions. We observed Gnmt induction by both abiotic and biotic stressors. We also found increased levels of the GNMT reaction product sarcosine in the midgut after stress, linking metabolic changes with the observed changes in gene regulation. Prior to this study, Gnmt upregulation had not been associated with cellular stress responses in other organisms. To determine whether this novel stress-responsive gene would behave similarly in other bee species, we first characterized the cellular response to endoplasmic reticulum (ER) stress in lab-reared adults of the solitary alfalfa leafcutting bee (Megachile rotundata) and compared this with age-matched honey bees. The novel stress gene Gnmt was induced in addition to a number of canonical gene targets induced in both bee species upon unfolded protein response (UPR) activation, suggesting that stress-induced regulation of cellular methylation reactions is a common feature of bees. Therefore, this study suggests that the honey bee can serve as an important model for bee biology more broadly, although studies on diverse bee species will be required to fully understand global declines in bee populations.

N6-methyladenosine promotes aberrant redox homeostasis required for arsenic carcinogenesis by controlling the adaptation of key antioxidant enzymes

N6-methyladenosine (m6A), a high-profile RNA epigenetic modification, responds to oxidative stress and temporal-specifically mediates arsenic carcinogenesis. However, how m6A affects aberrant redox homeostasis required for arsenic carcinogenesis is poorly understood. Here, we established arsenic-carcinogenic models of different stages, including As-treated, As-transformed, and As-tumorigenic cell models. We found that arsenic-induced reactive oxygen species (ROS) elevated m6A levels, thus triggering m6A-dependent antioxidant defenses. During arsenic-induced cell transformation, METTL3-upregulated m6A on the mRNAs of SOD1, SOD2, CAT, TXN, and GPX1 promoted the mRNA translation and protein expressions of these antioxidant enzymes by increasing YTHDF1-mediated mRNA stability. Meanwhile, FTO-downregulated m6A on PRDX5 mRNA increased PRDX5 translation and expression by reducing YTHDF2-mediated mRNA decay. After upregulated antioxidant defenses balanced with high levels of ROS induced by arsenic, the m6A balance formed in mRNAs of six key antioxidant enzymes (SOD1, SOD2, CAT, TXN, GPX1, and PRDX5) and promoted high expressions of these antioxidant enzymes to maintain aberrant redox homeostasis. METTL3 inhibitor STM2457, FTO inhibitor FB23-2, or YTHDF1 knockdown disturbed the aberrant redox homeostasis by breaking the m6A balance, causing cell death in arsenic-induced tumors. Our results demonstrated that m6A promotes the formation and maintenance of aberrant redox homeostasis required for arsenic carcinogenesis by time-dependently orchestrating the adaptive expressions of six key m6A-targeted antioxidant enzymes. This study advances our understanding of arsenic carcinogenicity from the novel aspect of m6A-dependent adaptation to arsenic-induced oxidative stress.

The involvement of RNA N6-methyladenosine and histone methylation modification in decidualization and endometriosis-associated infertility

Defective decidualization of endometrial stromal cells (ESCs) in endometriosis (EM) patients leads to inadequate endometrial receptivity and EM-associated infertility. Hypoxia is an inevitable pathological process of EM and participates in deficient decidualization of the eutopic secretory endometrium. Enhancer of zeste homology 2 (EZH2) is a methyltransferase which catalyses H3K27Me3, leading to decreased expression levels of target genes. Although EZH2 expression is low under normal decidualization, it is abundantly increased in the eutopic secretory endometrium of EM and is induced by hypoxia. Chromatin immunoprecipitation-PCR results revealed that decidua marker IGFBP1 is a direct target of EZH2, partially explaining the increased levels of histone methylation modification in defected decidualization of EM. To mechanism controlling this, we examined the effects of hypoxia on EZH2 and decidualization. EZH2 mRNA showed decreased m6 A modification and increased expression levels under hypoxia and decidualization combined treatment. Increased EZH2 expression was due to the increased expression of m6 A demethylase ALKBH5 and decreased expression of the m6 A reader protein YTHDF2. YTHDF2 directly bind to the m6 A modification site of EZH2 to promote EZH2 mRNA degradation in ESCs. Moreover, selective Ezh2 depletion in mouse ESCs increased endometrial receptivity and improved mouse fertility by up-regulating decidua marker IGFBP1 expression. This is the first report showing that YTHDF2 can act as a m6 A reader to promote decidualization by decreasing the stability of EZH2 mRNA and further increasing the expression of IGFBP1 in ESCs. Taken together, our findings highlight the critical role of EZH2/H3K27Me3 in decidualization and reveal a novel epigenetic mechanism by which hypoxia can suppress EM decidualization by decreasing the m6 A modification of EZH2 mRNA.

RNA modifications in physiology and disease: towards clinical applications

The ability of chemical modifications of single nucleotides to alter the electrostatic charge, hydrophobic surface and base pairing of RNA molecules is exploited for the clinical use of stable artificial RNAs such as mRNA vaccines and synthetic small RNA molecules - to increase or decrease the expression of therapeutic proteins. Furthermore, naturally occurring biochemical modifications of nucleotides regulate RNA metabolism and function to modulate crucial cellular processes. Studies showing the mechanisms by which RNA modifications regulate basic cell functions in higher organisms have led to greater understanding of how aberrant RNA modification profiles can cause disease in humans. Together, these basic science discoveries have unravelled the molecular and cellular functions of RNA modifications, have provided new prospects for therapeutic manipulation and have led to a range of innovative clinical approaches.

Exploring N6-methyladenosine (m6A) modification in tree species: opportunities and challenges

N 6-methyladenosine (m6A) in eukaryotes is the most common and widespread internal modification in mRNA. The modification regulates mRNA stability, translation efficiency, and splicing, thereby fine-tuning gene regulation. In plants, m6A is dynamic and critical for various growth stages, embryonic development, morphogenesis, flowering, stress response, crop yield, and biomass. Although recent high-throughput sequencing approaches have enabled the rapid identification of m6A modification sites, the site-specific mechanism of this modification remains unclear in trees. In this review, we discuss the functional significance of m6A in trees under different stress conditions and discuss recent advancements in the quantification of m6A. Quantitative and functional insights into the dynamic aspect of m6A modification could assist researchers in engineering tree crops for better productivity and resistance to various stress conditions.

MODOMICS: a database of RNA modifications and related information. 2023 update

The MODOMICS database was updated with recent data and now includes new data types related to RNA modifications. Changes to the database include an expanded modification catalog, encompassing both natural and synthetic residues identified in RNA structures. This addition aids in representing RNA sequences from the RCSB PDB database more effectively. To manage the increased number of modifications, adjustments to the nomenclature system were made. Updates in the RNA sequences section include the addition of new sequences and the reintroduction of sequence alignments for tRNAs and rRNAs. The protein section was updated and connected to structures from the RCSB PDB database and predictions by AlphaFold. MODOMICS now includes a data annotation system, with 'Evidence' and 'Estimated Reliability' features, offering clarity on data support and accuracy. This system is open to all MODOMICS entries, enhancing the accuracy of RNA modification data representation. MODOMICS is available at https://iimcb.genesilico.pl/modomics/.

RNA N6-methyladenosine modification-based biomarkers for absorbed ionizing radiation dose estimation

Radiation triage and biological dosimetry are critical for the medical management of massive potentially exposed individuals following radiological accidents. Here, we performed a genome-wide screening of radiation-responding mRNAs, whose N6-methyladenosine (m6A) levels showed significant alteration after acute irradiation. The m6A levels of three genes, Ncoa4, Ate1 and Fgf22, in peripheral blood mononuclear cells (PBMCs) of mice showed excellent dose-response relationships and could serve as biomarkers of radiation exposure. Especially, the RNA m6A of Ncoa4 maintained a high level as long as 28 days after irradiation. We demonstrated its responsive specificity to radiation, conservation across the mice, monkeys and humans, and the dose-response relationship in PBMCs from cancer patients receiving radiation therapy. Finally, NOCA4 m6A-based biodosimetric models were constructed for estimating absorbed radiation doses in mice or humans. Collectively, this study demonstrated the potential feasibility of RNA m6A in radiation accidents management and clinical applications.

Pathogen-induced m6A dynamics affect plant immunity

Posttranscriptional regulation of mRNA mediated by methylation at the N6 position of adenine (N6-methyladenosine [m6A]) has profound effects on transcriptome regulation in plants. Focused studies across eukaryotes offer glimpses into the processes governed by m6A throughout developmental and disease states. However, we lack an understanding of the dynamics and the regulatory potential of m6A during biotic stress in plants. Here, we provide a comprehensive look into the effects of m6A on both the short-term and long-term responses to pathogen signaling in Arabidopsis (Arabidopsis thaliana). We demonstrate that m6A-deficient plants are more resistant to bacterial and fungal pathogen infections and have altered immune responses. Furthermore, m6A deposition is specifically coordinated on transcripts involved in defense and immunity prior to and proceeding the pathogen signal flagellin. Consequently, the dynamic modulation of m6A on specific stress-responsive transcripts is correlated with changes in abundance and cleavage of these transcripts. Overall, we show that the m6A methylome is regulated prior to and during simulated and active pathogen stress and functions in the coordination and balancing of normal growth and pathogen responses.

Epigenetic regulation in major depression and other stress-related disorders: molecular mechanisms, clinical relevance and therapeutic potential

Major depressive disorder (MDD) is a chronic, generally episodic and debilitating disease that affects an estimated 300 million people worldwide, but its pathogenesis is poorly understood. The heritability estimate of MDD is 30-40%, suggesting that genetics alone do not account for most of the risk of major depression. Another factor known to associate with MDD involves environmental stressors such as childhood adversity and recent life stress. Recent studies have emerged to show that the biological impact of environmental factors in MDD and other stress-related disorders is mediated by a variety of epigenetic modifications. These epigenetic modification alterations contribute to abnormal neuroendocrine responses, neuroplasticity impairment, neurotransmission and neuroglia dysfunction, which are involved in the pathophysiology of MDD. Furthermore, epigenetic marks have been associated with the diagnosis and treatment of MDD. The evaluation of epigenetic modifications holds promise for further understanding of the heterogeneous etiology and complex phenotypes of MDD, and may identify new therapeutic targets. Here, we review preclinical and clinical epigenetic findings, including DNA methylation, histone modification, noncoding RNA, RNA modification, and chromatin remodeling factor in MDD. In addition, we elaborate on the contribution of these epigenetic mechanisms to the pathological trait variability in depression and discuss how such mechanisms can be exploited for therapeutic purposes.

Targeting N7-methylguanosine tRNA modification blocks hepatocellular carcinoma metastasis after insufficient radiofrequency ablation

Radiofrequency heat ablation is an ideal radical treatment for hepatocellular carcinoma (HCC). However, insufficient radiofrequency ablation (IRFA) could lead to high recurrence of HCC. N7-methylguanosine (m7G) on tRNAs, an evolutionally conservative modification in mammals and yeast, modulates heat stress responses and tumor progression, while its function in HCC recurrence after IRFA remains unknown. Here, we found that IRFA significantly upregulates the level of m7G tRNA modification and its methyltransferase complex components METTL1/WDR4 in multiple systems including HCC patient-derived xenograft (PDX) mouse, patients' HCC tissues, sublethal-heat-treated models of HCC cell lines, and organoids. Functionally, gain-/loss-of-function assays showed that METTL1-mediated m7G tRNA modification promotes HCC metastasis under sublethal heat exposure both in vitro and in vivo. Mechanistically, we found that METTL1 and m7G tRNA modification enhance the translation of SLUG/SNAIL in a codon frequency-dependent manner under sublethal heat stress. Overexpression of SLUG/SNAIL rescued the malignant potency of METTL1 knockdown HCC cells after sublethal heat exposure. Our study uncovers the key functions of m7G tRNA modification in heat stress responses and HCC recurrence after IRFA, providing molecular basis for targeting METTL1-m7G-SLUG/SNAIL axis to prevent HCC metastasis after radiofrequency heat ablation treatment.

Study on the Correlation Between Regulatory Proteins of N6-methyladenosine and Oxidative Damage in Cadmium-induced Renal Injury

As a common environmental heavy metal pollutant, cadmium has been well evidenced to cause kidney damage; yet, the underlying mechanisms are still not fully clarified. In this study, cell viability of human renal tubular epithelial cell (HK-2) was determined by CCK-8 assay after treatment with CdSO₄. Then, apoptotic morphology of cells was observed by Hoechst staining and level of reactive oxygen species (ROS) was detected by fluorescent probes. Subsequently, mRNA levels of Nrf2, HO-1, m⁶A methyltransferases (METTL3, METTL14, METTL16, WATP), m⁶A demethylases (FTO, ALKBH5), m⁶A methyl-binding proteins (YTHDF1, YTHDF2, YTHDF3, YTHDC1, YTHDC2) were detected by real-time polymerase chain reaction (RT-PCR), closely followed by correlation analysis between Nrf2 mRNA levels and m⁶A methyltransferases and demethylases. Lastly, protein expressions of Nrf2, METTL3, and FTO were tested by western blotting assay. The detection results demonstrated that the treatment of CdSO₄ decreased viability while increased apoptosis rate. The Nrf2 mRNA level in CdSO₄-treated cells was significantly increased when compared with that in the control cells, and the HO-1 mRNA level elevated with the increasing of CdSO₄ concentrations. In addition, mRNA levels of METTL3, METTL14, METTL16, WTAP, FTO, and methyl-binding proteins in CdSO₄-treated cells were all higher than those in corresponding control cells. Further determination showed that protein expressions of Nrf2, METTL3, and FTO were also upregulation under the treatment of CdSO₄. Lastly, correlation analysis indicated that mRNA level of Nrf2 was positively correlated with mRNA levels of m⁶A methyltransferases and demethylases. In a word, our results demonstrated that the molecular changes of Nrf2 signaling pathway are correlated with the levels of m⁶A regulatory proteins, suggesting that there may be a regulatory relationship between Nrf2 signaling pathway and m⁶A regulatory proteins in the process of cadmium-induced renal cell cytotoxicity.

Post-transcriptional modification of m6A methylase METTL3 regulates ERK-induced androgen-deprived treatment resistance prostate cancer

As the most common modification of RNA, N⁶-methyladenosin (m⁶A) has been confirmed to be involved in the occurrence and development of various cancers. However, the relationship between m⁶A and castration resistance prostate cancer (CRPC), has not been fully studied. By m⁶A-sequencing of patient cancer tissues, we identified that the overall level of m⁶A in CRPC was up-regulated than castration sensitive prostate cancer (CSPC). Based on the analysis of m⁶A-sequencing data, we found m⁶A modification level of HRas proto-oncogene, GTPase (HRAS) and mitogen-activated protein kinase kinase 2 (MEK2 or MAP2K2) were enhanced in CRPC. Specifically, tissue microarray analysis and molecular biology experiments confirmed that METTL3, an m⁶A "writer" up-regulated after castration, activated the ERK pathway to contribute to malignant phenotype including ADT resistance, cell proliferation and invasion. We revealed that METTL3-mediated ERK phosphorylation by stabilizing the transcription of HRAS and positively regulating the translation of MEK2. In the Enzalutamide-resistant (Enz-R) C4-2 and LNCap cell line (C4-2^R, LNCap^R) established in the current study, the ERK pathway was confirmed to be regulated by METTL3. We also found that applying antisense oligonucleotides (ASOs) to target the METTL3/ERK axis can restore Enzalutamide resistance in vitro and in vivo. In conclusion, METTL3 activated the ERK pathway and induced the resistance to Enzalutamide by regulating the m⁶A level of critical gene transcription in the ERK pathway.

Role of m6A methylation in retinal diseases

Retinal diseases remain among the leading causes of visual impairment in developed countries, despite great efforts in prevention and early intervention. Due to the limited efficacy of current retinal therapies, novel therapeutic methods are urgently required. Over the past two decades, advances in next-generation sequencing technology have facilitated research on RNA modifications, which can elucidate the relevance of epigenetic mechanisms to disease. N6-methyladenosine (m6A), formed by methylation of adenosine at the N6-position, is the most widely studied RNA modification and plays an important role in RNA metabolism. It is dynamically regulated by writers (methyltransferases) and erasers (demethylases), and recognized by readers (m6A binding proteins). Although the discovery of m6A methylation can be traced back to the 1970s, its regulatory roles in retinal diseases are rarely appreciated. Here, we provide an overview of m6A methylation, and discuss its effects and possible mechanisms on retinal diseases, including diabetic retinopathy, age-related macular degeneration, retinoblastoma, retinitis pigmentosa, and proliferative vitreoretinopathy. Furthermore, we highlight potential agents targeting m6A methylation for retinal disease treatment and discuss the limitations and challenges of research in the field of m6A methylation.

RNA methylation and cellular response to oxidative stress-promoting anticancer agents

Disruption of the complex network that regulates redox homeostasis often underlies resistant phenotypes, which hinder effective and long-lasting cancer eradication. In addition, the RNA methylome-dependent control of gene expression also critically affects traits of cellular resistance to anti-cancer agents. However, few investigations aimed at establishing whether the epitranscriptome-directed adaptations underlying acquired and/or innate resistance traits in cancer could be implemented through the involvement of redox-dependent or -responsive signaling pathways. This is unexpected mainly because: i) the effectiveness of many anti-cancer approaches relies on their capacity to promote oxidative stress (OS); ii) altered redox milieu and reprogramming of mitochondrial function have been acknowledged as critical mediators of the RNA methylome-mediated response to OS. Here we summarize the current state of understanding on this topic, as well as we offer new perspectives that might lead to original approaches and strategies to delay or prevent the problem of refractory cancer and tumor recurrence.

Current and potential roles of RNA modification-mediated autophagy dysregulation in cancer

Autophagy, a cellular lysosomal degradation and survival pathway, supports nutrient recycling and adaptation to metabolic stress and participates in various stages of tumor development, including tumorigenesis, metastasis, and malignant state maintenance. Among the various factors contributing to the dysregulation of autophagy in cancer, RNA modification can regulate autophagy by directly affecting the expression of core autophagy proteins. We propose that autophagy disorder mediated by RNA modification is an important mechanism for cancer development. Therefore, this review mainly discusses the role of RNA modification-mediated autophagy regulation in tumorigenesis. We summarize the molecular basis of autophagy and the core proteins and complexes at different stages of autophagy, especially those involved in cancer development. Moreover, we describe the crosstalk of RNA modification and autophagy and review the recent advances and potential role of the RNA modification/autophagy axis in the development of multiple cancers. Furthermore, the dual role of the RNA modification/autophagy axis in cancer drug resistance is discussed. A comprehensive understanding and extensive exploration of the molecular crosstalk of RNA modifications with autophagy will provide important insights into tumor pathophysiology and provide more options for cancer therapeutic strategies.

Interaction between N6-methyladenosine (m6A) modification and environmental chemical-induced diseases in various organ systems

A wide variety of chemicals are ubiquitous in the environment and thus exposure to these environmental chemicals poses a serious threat to public health. Particularly, environmental factors such as air pollution, heavy metals, and endocrine-disrupting chemicals (EDCs) can lead to diseases in various organ systems. Recent research in environmental epigenetics has demonstrated that N6-methyladenosine (m6A) modification is a key mechanism of environment-related diseases. m6A modification is the most abundant chemical modification in mRNAs, which can specifically regulate gene expression by affecting RNA translation, stability, processing, and nuclear export. In this review, we discussed how environmental chemicals affected m6A modification and mediated environment-related disease occurrence by classifying the diseases of various systems. Here, we conclude that environmental chemicals alter the levels of m6A and its modulators, which then participate in the occurrence of diseases in various systems by regulating gene expression and downstream signaling pathways such as METTL3/m6A ZBTB4/YTHDF2/EZH2, Foxo3a/FTO/m6A ephrin-B2/YTHDF2, and HIF1A/METTL3/m6A BIRC5/IGF2BP3/VEGFA. Considering the significant role of m6A and its modulators in response to environmental chemicals, they are expected to be used as biomarkers of environment-related diseases. Additionally, targeting m6A modulators using small molecule inhibitors and activators is expected to be a new method for the treatment of environment-related diseases. This review systematically and comprehensively clarifies the important role of m6A in diseases caused by environmental chemicals, thus establishing a scientific basis for the treatment of diseases in various organ systems.

Up-Regulation of SH3TC2 Induced by YTHDF1 Predicts Poor Outcome and Facilitates Cell-Cycle Progress in Colorectal Cancer

N6-methyladenosine (m6A) modification plays a crucial role in determining the fate and function of RNA transcripts in tumor cells. Nevertheless, how m6A regulates the expression of key molecules and coordinates its involvement in the development of colorectal cancer (CRC) remains largely unclear. Here, we report that the m6A reading protein YTHDF1-mediated up-regulation of SH3TC2 promotes CRC growth both in vitro and in vivo. In a pan-cancer analysis across more than thirty types of cancer, we found that SH3TC2 was dysregulated in nine cancers, including BLCA, CHOL, COAD, LAML, PAAD, READ, SKCM, BRCA, and TGCT, and was closely associated with patient prognosis in four cancers, including COAD, MESO, PAAD, and READ. In particular, SH3TC2 was overexpressed in CRC as confirmed by six independent study cohorts. Clinically, high expression of SH3TC2 predicted worse disease-free survival (DFS) in CRC patients. SH3TC2 showed fascinating diagnostic value and was correlated with immunosuppression in CRC. Functionally, RNA-sequencing combined with experiments revealed that knockdown of SH3TC3 significantly inhibited cell-cycle progress of CRC, impairing cell growth. Mechanistically, YTHDF1 protein directly binds with SH3TC2 mRNA and promotes its elevation in an m6A-dependent manner. Thus, our findings provide a mechanism to target the YTHDF1/SH3TC2 axis for CRC therapy.

The alteration of N6-methyladenosine (m6A) modification at the transcriptome-wide level in response of heat stress in bovine mammary epithelial cells

Background

Heat stress has a substantial negative economic impact on the dairy industry. N6-methyladenosine (m6A) is the most common internal RNA modification in eukaryotes and plays a key role in regulating heat stress response in animals. In dairy cows, however, this modification remains largely unexplored. Therefore, we examined the effects of heat stress on the m6A modification and gene expression in bovine mammary epithelial cells to elucidate the mechanism of heat stress response. In this study, Mammary alveolar cells-large T antigen (MAC-T) cells were incubated at 37 °C (non-heat stress group, NH) and 40 °C (heat stress group, H) for 2 hours, respectively. HSP70, HSF1, BAX and CASP3 were up regulated in H group compared with those in the NH group.

Results

Methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) were conducted to identify m6A peaks and to produce gene expression data of MAC-T cells in the H and NH groups. In total, we identified 17,927 m6A peaks within 9355 genes in the H group, and 18,974 peaks within 9660 genes in the NH groups using MeRIP-seq. Compared with the NH group, 3005 significantly differentially enriched m6A peaks were identified, among which 1131 were up-regulated and 1874 were down-regulated. In addition, 1502 significantly differentially expressed genes were identified using RNA-seq, among which 796 were up-regulated and 706 were down-regulated in the H group compared to the NH group. Furthermore, 199 differentially expressed and synchronously differentially methylated genes were identified by conjoint analysis of the MeRIP-seq and RNA-seq data, which were subsequently divided into four groups: 47 hyper-up, 53 hyper-down, 59 hypo-up and 40 hypo-down genes. In addition, GO enrichment and KEGG analyses were used to analyzed the potential functions of the genes in each section.

Conclusion

The comparisons of m6A modification patterns and conjoint analyses of m6A modification and gene expression profiles suggest that m6A modification plays a critical role in the heat stress response by regulating gene expression.

Epitranscriptomic mRNA modifications governing plant stress responses: underlying mechanism and potential application

Plants inevitably encounter environmental adversities, including abiotic and biotic stresses, which significantly impede plant growth and reduce crop yield. Thus, fine-tuning the fate and function of stress-responsive RNAs is indispensable for plant survival under such adverse conditions. Recently, post-transcriptional RNA modifications have been studied as a potent route to regulate plant gene expression under stress. Among over 160 mRNA modifications identified to date, N⁶ -methyladenosine (m⁶ A) in mRNAs is notable because of its multifaceted roles in plant development and stress response. Recent transcriptome-wide mapping has revealed the distribution and patterns of m⁶ A in diverse stress-responsive mRNAs in plants, building a foundation for elucidating the molecular link between m⁶ A and stress response. Moreover, the identification and characterization of m⁶ A writers, readers and erasers in Arabidopsis and other model crops have offered insights into the biological roles of m⁶ A in plant abiotic stress responses. Here, we review the recent progress of research on mRNA modifications, particularly m⁶ A, and their dynamics, distribution, regulation and biological functions in plant stress responses. Further, we posit potential strategies for breeding stress-tolerant crops by engineering mRNA modifications and propose the future direction of research on RNA modifications to gain a much deeper understanding of plant stress biology.

Emerging roles of the RNA modifications N6-methyladenosine and adenosine-to-inosine in cardiovascular diseases

Cardiovascular diseases lead the mortality and morbidity disease metrics worldwide. A multitude of chemical base modifications in ribonucleic acids (RNAs) have been linked with key events of cardiovascular diseases and metabolic disorders. Named either RNA epigenetics or epitranscriptomics, the post-transcriptional RNA modifications, their regulatory pathways, components, and downstream effects substantially contribute to the ways our genetic code is interpreted. Here we review the accumulated discoveries to date regarding the roles of the two most common epitranscriptomic modifications, N6-methyl-adenosine (m6A) and adenosine-to-inosine (A-to-I) editing, in cardiovascular disease.

Transcriptional expression of m6A and m5C RNA methyltransferase genes in the brain and fat body of honey bee adult workers

Honey bee (Apis mellifera) adult workers change behaviors and nutrition according to age progression. Young workers, such as nurses, perform in-hive tasks and consume protein-rich pollen, while older workers (foragers) leave the colony to search for food, and consume carbohydrate-rich nectar. These environmentally stimulated events involve transcriptional and DNA epigenetic marks alterations in worker tissues. However, post-transcriptional RNA modifications (epitranscriptomics) are still poorly explored in bees. We investigated the transcriptional profiles of m6A and m5C RNA methyltransferases in the brain and fat body of adult workers of 1) different ages and performing different tasks [nurses of 8 days-old (N-8D) and foragers of 29 days-old (F-29D), sampled from wild-type colonies], and 2) same-aged young workers caged in an incubator and treated with a pollen-rich [PR] or a pollen-deprived [PD] diet for 8 days. In the brain, METTL3, DNMT2, NOP2, NSUN2, NSUN5, and NSUN7 genes increased expression during adulthood (from N-8D to F-29D), while the opposite pattern was observed in the fat body for METTL3, DNMT2, and NSUN2 genes. Regarding diet treatments, high expression levels were observed in the brains of the pollen-deprived group (DNMT2, NOP2, and NSUN2 genes) and the fat bodies of the pollen-rich group (NOP2, NSUN4, and NSUN5 genes) compared to the brains of the PR group and the fat bodies of the PD group, respectively. Our data indicate that RNA epigenetics may be an important regulatory layer in the development of adult workers, presenting tissue-specific signatures of RNA methyltransferases expression in response to age, behavior, and diet content.

Melatonin: Regulation of Viral Phase Separation and Epitranscriptomics in Post-Acute Sequelae of COVID-19

The relentless, protracted evolution of the SARS-CoV-2 virus imposes tremendous pressure on herd immunity and demands versatile adaptations by the human host genome to counter transcriptomic and epitranscriptomic alterations associated with a wide range of short- and long-term manifestations during acute infection and post-acute recovery, respectively. To promote viral replication during active infection and viral persistence, the SARS-CoV-2 envelope protein regulates host cell microenvironment including pH and ion concentrations to maintain a high oxidative environment that supports template switching, causing extensive mitochondrial damage and activation of pro-inflammatory cytokine signaling cascades. Oxidative stress and mitochondrial distress induce dynamic changes to both the host and viral RNA m6A methylome, and can trigger the derepression of long interspersed nuclear element 1 (LINE1), resulting in global hypomethylation, epigenetic changes, and genomic instability. The timely application of melatonin during early infection enhances host innate antiviral immune responses by preventing the formation of "viral factories" by nucleocapsid liquid-liquid phase separation that effectively blockades viral genome transcription and packaging, the disassembly of stress granules, and the sequestration of DEAD-box RNA helicases, including DDX3X, vital to immune signaling. Melatonin prevents membrane depolarization and protects cristae morphology to suppress glycolysis via antioxidant-dependent and -independent mechanisms. By restraining the derepression of LINE1 via multifaceted strategies, and maintaining the balance in m6A RNA modifications, melatonin could be the quintessential ancient molecule that significantly influences the outcome of the constant struggle between virus and host to gain transcriptomic and epitranscriptomic dominance over the host genome during acute infection and PASC.

The Methylation Game: Epigenetic and Epitranscriptomic Dynamics of 5-Methylcytosine

DNA and RNA methylation dynamics have been linked to a variety of cellular processes such as development, differentiation, and the maintenance of genome integrity. The correct deposition and removal of methylated cytosine and its oxidized analogues is pivotal for cellular homeostasis, rapid responses to exogenous stimuli, and regulated gene expression. Uncoordinated expression of DNA/RNA methyltransferases and demethylase enzymes has been linked to genome instability and consequently to cancer progression. Furthermore, accumulating evidence indicates that post-transcriptional DNA/RNA modifications are important features in DNA/RNA function, regulating the timely recruitment of modification-specific reader proteins. Understanding the biological processes that lead to tumorigenesis or somatic reprogramming has attracted a lot of attention from the scientific community. This work has revealed extensive crosstalk between epigenetic and epitranscriptomic pathways, adding a new layer of complexity to our understanding of cellular programming and responses to environmental cues. One of the key modifications, m5C, has been identified as a contributor to regulation of the DNA damage response (DDR). However, the various mechanisms of dynamic m5C deposition and removal, and the role m5C plays within the cell, remains to be fully understood.

Challenges with Simulating Modified RNA: Insights into Role and Reciprocity of Experimental and Computational Approaches

RNA is critical to a broad spectrum of biological and viral processes. This functional diversity is a result of their dynamic nature; the variety of three-dimensional structures that they can fold into; and a host of post-transcriptional chemical modifications. While there are many experimental techniques to study the structural dynamics of biomolecules, molecular dynamics simulations (MDS) play a significant role in complementing experimental data and providing mechanistic insights. The accuracy of the results obtained from MDS is determined by the underlying physical models i.e., the force-fields, that steer the simulations. Though RNA force-fields have received a lot of attention in the last decade, they still lag compared to their protein counterparts. The chemical diversity imparted by the RNA modifications adds another layer of complexity to an already challenging problem. Insight into the effect of RNA modifications upon RNA folding and dynamics is lacking due to the insufficiency or absence of relevant experimental data. This review provides an overview of the state of MDS of modified RNA, focusing on the challenges in parameterization of RNA modifications as well as insights into relevant reference experiments necessary for their calibration.

Roles of RNA Modifications in Diverse Cellular Functions

Chemical modifications of RNA molecules regulate both RNA metabolism and fate. The deposition and function of these modifications are mediated by the actions of writer, reader, and eraser proteins. At the cellular level, RNA modifications regulate several cellular processes including cell death, proliferation, senescence, differentiation, migration, metabolism, autophagy, the DNA damage response, and liquid-liquid phase separation. Emerging evidence demonstrates that RNA modifications play active roles in the physiology and etiology of multiple diseases due to their pervasive roles in cellular functions. Here, we will summarize recent advances in the regulatory and functional role of RNA modifications in these cellular functions, emphasizing the context-specific roles of RNA modifications in mammalian systems. As m6A is the best studied RNA modification in biological processes, this review will summarize the emerging advances on the diverse roles of m6A in cellular functions. In addition, we will also provide an overview for the cellular functions of other RNA modifications, including m5C and m1A. Furthermore, we will also discuss the roles of RNA modifications within the context of disease etiologies and highlight recent advances in the development of therapeutics that target RNA modifications. Elucidating these context-specific functions will increase our understanding of how these modifications become dysregulated during disease pathogenesis and may provide new opportunities for improving disease prevention and therapy by targeting these pathways.

Epitranscriptomic Reprogramming Is Required to Prevent Stress and Damage from Acetaminophen

Epitranscriptomic marks, in the form of enzyme catalyzed RNA modifications, play important gene regulatory roles in response to environmental and physiological conditions. However, little is known with respect to how acute toxic doses of pharmaceuticals influence the epitranscriptome. Here we define how acetaminophen (APAP) induces epitranscriptomic reprogramming and how the writer Alkylation Repair Homolog 8 (Alkbh8) plays a key gene regulatory role in the response. Alkbh8 modifies tRNA selenocysteine (tRNA^Sec) to translationally regulate the production of glutathione peroxidases (Gpx’s) and other selenoproteins, with Gpx enzymes known to play protective roles during APAP toxicity. We demonstrate that APAP increases toxicity and markers of damage, and decreases selenoprotein levels in Alkbh8 deficient mouse livers, when compared to wildtype. APAP also promotes large scale reprogramming of many RNA marks comprising the liver tRNA epitranscriptome including: 5-methoxycarbonylmethyluridine (mcm⁵U), isopentenyladenosine (i⁶A), pseudouridine (Ψ), and 1-methyladenosine (m¹A) modifications linked to tRNA^Sec and many other tRNA’s. Alkbh8 deficiency also leads to wide-spread epitranscriptomic dysregulation in response to APAP, demonstrating that a single writer defect can promote downstream changes to a large spectrum of RNA modifications. Our study highlights the importance of RNA modifications and translational responses to APAP, identifies writers as key modulators of stress responses in vivo and supports the idea that the epitranscriptome may play important roles in responses to pharmaceuticals.

METTL3-m6A-Rubicon axis inhibits autophagy in nonalcoholic fatty liver disease

N6-methyladenosine (m⁶A) mRNA modification plays critical roles in various biological events and is involved in multiple complex diseases. However, the role of m⁶A modification in autophagy in nonalcoholic fatty liver disease (NAFLD) remains largely unknown. Here, we report that m⁶A modification was increased in livers of NAFLD mouse models and in free fatty acid (FFA)-treated hepatocytes, and the abnormal m⁶A modification was attributed to the upregulation of methyltransferase like 3 (METTL3) induced by lipotoxicity. Knockdown of METTL3 promoted hepatic autophagic flux and clearance of lipid droplets (LDs), while overexpression of METTL3 inhibited these processes. Mechanistically, METTL3 directly bound to Rubicon mRNA and mediated the m⁶A modification, while YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), as a partner of METTL3, interacted with the m⁶A-marked Rubicon mRNA and promoted its stability. Subsequently, RUBICON inhibited autophagosome-lysosome fusion and further blocked clearance of LDs. Taken together, our results showed a critical role of METTL3 and YTHDF1 in regulating lipid metabolism via the autophagy pathway and provided a novel insight into m⁶A mRNA methylation in NAFLD.

The Identification of Two RNA Modification Patterns and Tumor Microenvironment Infiltration Characterization of Lung Adenocarcinoma

Background: RNA modification plays an important role in many diseases. A comprehensive study of tumor microenvironment (TME) characteristics mediated by RNA modification regulators will improve the understanding of TME immune regulation.

Methods: We selected 26 RNA modification “writers” of lung adenocarcinoma (LUAD) samples and performed unsupervised clustering analysis to explore RNA modification patterns in LUAD. Differentially expressed genes (DEGs) with RNA modification patterns were screened to develop a “writers” of RNA modification score (WM score) system. The infiltration ratio of TME cell subsets was analyzed by CIBERSORT.

Results: We identified two RNA modification modes showing different characteristics of overall survival (OS) and TME cell infiltration. According to WM score, LUAD patients were divided into a high-WM score group and a low-WM score group. High-scored patients had a poor prognosis and higher tumor mutation burden (TMB), they were more sensitive to four LUAD therapies (erlotinib, XA V939, gefitinib, and KU-55933) and more clinically responsive to PD-L1 treatment. Those with a low WM score showed higher stromal scores, ESTIMATE scores, and survival chance.

Conclusion: Our work revealed the potential role of RNA modification patterns in TME, genetic variation, targeted inhibitor therapy, and immunotherapy. Identifying RNA modification pattern of LUAD patients help understand the characteristics of TME and may promote the development of immunotherapy strategies.

Nanoparticle-Induced m6A RNA Modification: Detection Methods, Mechanisms and Applications

With the increasing application of nanoparticles (NPs) in medical and consumer applications, it is necessary to ensure their safety. As m⁶A (N⁶-methyladenosine) RNA modification is one of the most prevalent RNA modifications involved in many diseases and essential biological processes, the relationship between nanoparticles and m⁶A RNA modification for the modulation of these events has attracted substantial research interest. However, there is limited knowledge regarding the relationship between nanoparticles and m⁶A RNA modification, but evidence is beginning to emerge. Therefore, a summary of these aspects from current research on nanoparticle-induced m⁶A RNA modification is timely and significant. In this review, we highlight the roles of m⁶A RNA modification in the bioimpacts of nanoparticles and thus elaborate on the mechanisms of nanoparticle-induced m⁶A RNA modification. We also summarize the dynamic regulation and biofunctions of m⁶A RNA modification. Moreover, we emphasize recent advances in the application perspective of nanoparticle-induced m⁶A RNA modification in medication and toxicity of nanoparticles to provide a potential method to facilitate the design of nanoparticles by deliberately tuning m⁶A RNA modification.

Epitranscriptomic regulation of cognitive development and decline

Functional genomics and systems biology have opened new doors to previously inaccessible genomic information and holistic approaches to study complex networks of genes and proteins in the central nervous system. The advances are revolutionizing our understanding of the genetic underpinning of cognitive development and decline by facilitating identifications of novel molecular regulators and physiological pathways underlying brain function, and by associating polymorphism and mutations to cognitive dysfunction and neurological diseases. However, our current understanding of these complex gene regulatory mechanisms has yet lacked sufficient mechanistic resolution for further translational breakthroughs. Here we review recent findings from the burgeoning field of epitranscriptomics in association of cognitive functions with a special focus on the epitranscritomic regulation in subcellular locations such as chromosome, synapse, and mitochondria. Although there are important gaps in knowledge, current evidence is suggesting that this layer of RNA regulation may be of particular interest for the spatiotemporally coordinated regulation of gene networks in developing and maintaining brain function that underlie cognitive changes.