bims-rimeca Biomed News
on RNA methylation in cancer
Issue of 2022–09–18
forty-nine papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics
  1. METTL3 mediated m6 A mRNA contributes to the resistance of carbon-ion radiotherapy in non-small cell lung cancer.
  2. IGF2BP2 promotes the progression of ovarian endometriosis by regulating m6A-modified MEIS2 and GATA6.
  3. Mettl3-dependent m6A modification attenuates the brain stress response in Drosophila.
  4. Detection of m6A RNA modifications at single-nucleotide resolution using m6A-selective allyl chemical labeling and sequencing.
  5. Adenosine N6-methylation upregulates the expression of human CYP2B6 by altering the chromatin status.
  6. Comprehensive characterization of tumor microenvironment and m6A RNA methylation regulators and its effects on PD-L1 and immune infiltrates in cervical cancer.
  7. m6A RNA, FTO, ALKBH5 Expression in Type 2 Diabetic and Obesity Patients.
  8. METTL3 upregulates COPS5 expression in osteosarcoma in an m6A-related manner to promote osteosarcoma progression.
  9. m6A-TSHub: Unveiling the Context-specific m6A Methylation and m6A-affecting Mutations in 23 Human Tissues.
  10. The Critical Role of RNA m6A Methylation in Gliomas: Targeting the Hallmarks of Cancer.
  11. Transcriptome-wide analyses of RNA m6A methylation in hexaploid wheat reveal its roles in mRNA translation regulation.
  12. m6A modification of mRNA in skin diseases.
  13. The prognostic value and multiomic features of m6A-related risk signature in lung adenocarcinoma.
  14. Molecular characterization, clinical relevance and immune feature of m7G regulator genes across 33 cancer types.
  15. Unravelling the Complex Interactions Between the FTO Gene, Lifestyle, and Cancer.
  16. METTL3 dual regulation of the stability of LINC00662 and VEGFA RNAs promotes colorectal cancer angiogenesis.
  17. YTHDF1 Protects Auditory Hair Cells from Cisplatin-Induced Damage by Activating Autophagy via the Promotion of ATG14 Translation.
  18. Formation and removal of 1,N6-dimethyladenosine in mammalian transfer RNA.
  19. m6A regulator-mediated RNA methylation modification patterns are involved in immune microenvironment regulation of coronary heart disease.
  20. Role of the N6-methyladenosine regulatory factor in reducing the risk of cardiovascular disease: subtype diagnosis following aerobic exercise-assisted weight loss.
  21. Prognostic value of comprehensive typing based on m6A and gene cluster in TNBC.
  22. Exploring the epitranscriptome by native RNA sequencing.
  23. Analysis of m6A-related signatures associated with the tumor immune microenvironment and predict survival in acute myeloid leukemia.
  24. Identification of m6A modification patterns and development of m6A-hypoxia prognostic signature to characterize tumor microenvironment in triple-negative breast cancer.
  25. N6-Methyladenosine Methylome Profiling of Muscle and Adipose Tissues Reveals Methylase-mRNA Metabolic Regulatory Networks in Fat Deposition of Rex Rabbits.
  26. N6-Methyladenine Modification of Hepatitis Delta Virus Regulates Its Virion Assembly by Recruiting YTHDF1.
  27. The effects of RNA methylation on immune cells development and function.
  28. Transcriptional expression of m6A and m5C RNA methyltransferase genes in the brain and fat body of honey bee adult workers.
  29. DNA methylation regulators-related molecular patterns and tumor immune landscape in hepatocellular carcinoma.
  30. METTLing in Stem Cell and Cancer Biology.
  31. METTL1-mediated m7G tRNA modification promotes lenvatinib resistance in hepatocellular carcinoma.
  32. The Role of N6-Methyladenosine-Associated lncRNAs in the Immune Microenvironment and Prognosis of Colorectal Cancer.
  33. A potential biomarker of esophageal squamous cell carcinoma WTAP promotes the proliferation and migration of ESCC.
  34. AKG induces cell apoptosis by inducing reactive oxygen species-mediated endoplasmic reticulum stress and by suppressing PI3K/AKT/mTOR-mediated autophagy in renal cell carcinoma.
  35. m5C Regulator-mediated methylation modification clusters contribute to the immune microenvironment regulation of multiple myeloma.
  36. LncRNA ALKBH3-AS1 enhances ALKBH3 mRNA stability to promote hepatocellular carcinoma cell proliferation and invasion.
  37. Inhibition of METTL5 improves preimplantation development of mouse somatic cell nuclear transfer embryos.
  38. m6A modification-mediated lncRNA TP53TG1 inhibits gastric cancer progression by regulating CIP2A stability.
  39. Changes in the m6A RNA methylome accompany the promotion of soybean root growth by rhizobia under cadmium stress.
  40. Prognostic model based on m6A-associated lncRNAs in esophageal cancer.
  41. Prognostic value of JAK3 promoter methylation and mRNA expression in clear cell renal cell carcinoma.
  42. Identification and construction of a prognostic risk model based on multi-RNA methylation regulators in cervical cancer.
  43. Histone H1 regulates non-coding RNA turnover on chromatin in a m6A-dependent manner.
  44. ROS inhibits RORα degradation by decreasing its arginine methylation in liver cancer.
  45. Cancer-associated fibroblasts-derived FMO2 as a biomarker of macrophage infiltration and prognosis in epithelial ovarian cancer.
  46. MEX3C-mediated decay of SOCS3 mRNA promotes JAK2/STAT3 signaling to facilitate metastasis in hepatocellular carcinoma.
  47. HMGA2 drives the IGFBP1/AKT pathway to counteract the increase in P27KIP1 protein levels in mtDNA/RNA-less cancer cells.
  48. Neuronal Depolarization Induced RNA m5C Methylation Changes in Mouse Cortical Neurons.
  49. N6-Methyladenosine (m6A)-Related lncRNAs Are Potential Signatures for Predicting Prognosis and Immune Response in Lung Squamous Cell Carcinoma.
  1. Cancer Sci. 2022 Sep 17.
    METTL3 mediated m6 A mRNA contributes to the resistance of carbon-ion radiotherapy in non-small cell lung cancer.
    Xiaofeng Xu, Peiru Zhang, Yangle Huang, Weizhong Shi, Jingfang Mao, Ningyi Ma, Lin Kong, Lin Guo, Jinlong Liu, Jian Chen, Renquan Lu.
      Lung cancer is one of the leading causes of death among cancer patients worldwide. Carbo-ion radiotherapy is a radical non-surgical treatment with high local control rates and no serious adverse events. N6-methyladenosine (m6A) modification is one of the most common chemical modifications in eukaryotic messenger RNAs (mRNAs), which has important effects on the stability, splicing and translation of mRNAs. Recently, the regulatory role of m6A in tumorigenesis has been recognized more and more. However, the dysregulation of m6A and its role in carbo-ion radiotherapy of non-small cell lung cancer (NSCLC) remains unclear. In this study, we found that the level of Methyltransferase-like 3 (METTL3) and its mediated m6A modification were elevated in the NSCLC cells with carbo-ion radiotherapy. Knockdown of METTL3 in NSCLC cells impaired the proliferation, migration, and invasion in vitro and in vivo. Moreover, we found that METTL3 mediated m6A modification mRNA inhibit the decay of H2AX mRNA and enhance its expression, which lead to the enhanced DNA damage repair and cell survival.
    Keywords:  H2AX; Methyltransferase-like 3; N6-methyladenosine; carbon-ion radiotherapy; non-small cell lung cancer
    DOI:  https://doi.org/10.1111/cas.15590
  2. Int J Biochem Cell Biol. 2022 Sep 13. pii: S1357-2725(22)00141-8. [Epub ahead of print] 106296
    IGF2BP2 promotes the progression of ovarian endometriosis by regulating m6A-modified MEIS2 and GATA6.
    Shaojie Zhao, Bing Zhang, Hua Yuan, Yongxiang Yin, Suwan Qi, Wenjuan Li, Xiadi Wu, Feng Yaling.
       BACKGROUND: m6A-RNA modification mediated by the N6-methyladenosine RNA methylation-related molecule methyltransferase-like 3 has been implicated in the progression of endometriosis. However, the functions of other m6A regulators, especially in ovarian endometriosis, remain unknown.
    METHODS: Three datasets (GSE7305, GSE7307, and GSE37837) with diagnosed ovarian endometriosis were extracted from the Gene Expression Omnibus database. Using bioinformatics methods such as Weighted Gene Co-expression Network Analysis, Gene Ontology analysis, protein-protein interaction, and correlation, hub genes were identified. Using dot blot and N6-methyladenosine-IP-qPCR, the total and individual N6-methyladenosine gene levels were quantified. On clinical ovarian ectopic and eutopic endometrium tissues, N6-methyladenosine RNA methylation sequencing was performed. To authenticate protein localization and expression level, immunohistochemical staining and western blot were conducted, respectively. The database Connectivity Map was used to predict small molecules with potential therapeutic effects.
    RESULTS: In ovarian endometriosis, the N6-methyladenosine "reader" molecule IGF2BP2 and related target genes MEIS2 and GATA6 were highly expressed. IGF2BP2 promoted the proliferation, migration, and invasion of ectopic endometrial stromal cells by stabilizing the mRNA of MEIS2 and GATA6. Synergistically, METTL3 and IGF2BP2 increased the N6-methyladenosine methylation of MEIS2 and GATA6. We developed five molecules (Mercaptopurine, MK-886, CP-863187, Canadine, and Securinine) that could be used to treat ovarian endometriosis based on IGF2BP2.
    CONCLUSION: Our findings provided additional support for a systematized understanding of the role of N6-methyladenosine RNA methylation in endometriosis and confirmed for the first time the mechanism of IGF2BP2 in promoting ovarian endometriosis. This provides the molecular foundation for potential future therapies for ovarian endometriosis.
    DATA AVAILABILITY: The data used to support the findings of this study are available from the corresponding author upon request.
    Keywords:  GATA Binding Protein 6; IGF2BP2; MEIS2; N 6-methyladenosine; Ovarian endometriosis
    DOI:  https://doi.org/10.1016/j.biocel.2022.106296
  3. Nat Commun. 2022 Sep 14. 13(1): 5387
    Mettl3-dependent m6A modification attenuates the brain stress response in Drosophila.
    Alexandra E Perlegos, Emily J Shields, Hui Shen, Kathy Fange Liu, Nancy M Bonini.
      N6-methyladenosine (m6A), the most prevalent internal modification on eukaryotic mRNA, plays an essential role in various stress responses. The brain is uniquely vulnerable to cellular stress, thus defining how m6A sculpts the brain's susceptibility may provide insight to brain aging and disease-related stress. Here we investigate the impact of m6A mRNA methylation in the adult Drosophila brain with stress. We show that m6A is enriched in the adult brain and increases with heat stress. Through m6A-immunoprecipitation sequencing, we show 5'UTR Mettl3-dependent m6A is enriched in transcripts of neuronal processes and signaling pathways that increase upon stress. Mettl3 knockdown results in increased levels of m6A targets and confers resilience to stress. We find loss of Mettl3 results in decreased levels of nuclear m6A reader Ythdc1, and knockdown of Ythdc1 also leads to stress resilience. Overall, our data suggest that m6A modification in Drosophila dampens the brain's biological response to stress.
    DOI:  https://doi.org/10.1038/s41467-022-33085-3
  4. STAR Protoc. 2022 Sep 14. pii: S2666-1667(22)00557-3. [Epub ahead of print]3(4): 101677
    Detection of m6A RNA modifications at single-nucleotide resolution using m6A-selective allyl chemical labeling and sequencing.
    Yong Peng, Hanzhe Meng, Ruiqi Ge, Shun Liu, Mengjie Chen, Chuan He, Lulu Hu.
      As the most abundant internal mRNA modification, N6-methyladenosine (m6A) was involved in almost all the aspects of RNA metabolism. Here, we introduce our protocol for m6A-SAC-seq, which enables the whole transcriptome-wide mapping of m6A RNA modification at single-nucleotide resolution with stoichiometry information. m6A-SAC-seq relies on selective allyl labeling of m6A by specific methyltransferase and chemical treatment that introduce mutation upon reverse transcription. The technique only requires ∼30 ng of input RNA. For complete details on the use and execution of this protocol, please refer to Hu et al. (2022).
    Keywords:  Bioinformatics; Biotechnology and bioengineering; Chemistry; Genomics; Molecular biology; Molecular/Chemical probes; Protein biochemistry; Protein expression and purification; Sequence analysis
    DOI:  https://doi.org/10.1016/j.xpro.2022.101677
  5. Biochem Pharmacol. 2022 Sep 13. pii: S0006-2952(22)00341-0. [Epub ahead of print] 115247
    Adenosine N6-methylation upregulates the expression of human CYP2B6 by altering the chromatin status.
    Motoki Isono, Masataka Nakano, Tatsuki Fukami, Miki Nakajima.
      N6-Methyladenosine (m6A) modification is the most prevalent RNA modification in mammals. We have recently demonstrated that inhibition of m6A modification by 3-deazaadenosine results in an increase in the expression of the cytochrome P450 (CYP) isoforms CYP1A2, CYP2B6, and CYP2C8 in human liver-derived cells. In the present study, we aimed to clarify the mechanism of m6A-mediated regulation of CYP2B6 expression. RNA immunoprecipitation using an anti-m6A antibody revealed that CYP2B6 mRNA in human liver and hepatocarcinoma-derived HepaRG cells was m6A-modified around the stop codon. In contrast to the treatment with 3-deazaadenosine, double knockdown of methyltransferase like (METTL) 3 and METTL14 (METTL3/14) resulted in a decrease in the levels of CYP2B6 mRNA in Huh-7 and HepaRG cells and a decrease in bupropion hydroxylase activity, a marker activity of CYP2B6, in HepaRG cells. The stability of CYP2B6 mRNA was not influenced by siMETTL3/14. Reporter assays using the plasmids containing the last exon or 5'-flanking region of CYP2B6 indicated that reporter activities were not influenced by knockdown of METTL3/14. The expression levels of the constitutive androstane receptor, pregnane X receptor, and retinoid X receptor, which are the nuclear receptors regulating the transcription of CYP2B6, were not influenced by siMETTL3/14. The chromatin immunoprecipitation and formaldehyde-assisted enrichment of regulatory elements assays revealed that H3K9me2, a repressive histone marker, was enriched in the vicinity of the upstream region of CYP2B6, and knockdown of METTL3/14 induced the condensation of the chromatin structure in this region. In conclusion, we demonstrated that METTL3/14 upregulated CYP2B6 expression by altering the chromatin status.
    Keywords:  CYP2B6; Chromatin status; Drug metabolism; Histone modification; P450; RNA methylation
    DOI:  https://doi.org/10.1016/j.bcp.2022.115247
  6. Front Immunol. 2022 ;13 976107
    Comprehensive characterization of tumor microenvironment and m6A RNA methylation regulators and its effects on PD-L1 and immune infiltrates in cervical cancer.
    Huihui Ji, Jian-An Zhang, Hejing Liu, Kehan Li, Zhi-Wei Wang, Xueqiong Zhu.
      Understanding the role of N6-adenosine methylation (m6A) in the tumor microenvironment (TME) is important since it can contribute to tumor development. However, the research investigating the association between m6A and TME and cervical cancer is still in its early stages. The aim of this study was to discover the possible relationship between m6A RNA methylation regulators, TME, PD-L1 expression levels, and immune infiltration in cervical cancer. We gathered RNA-seq transcriptome data and clinical information from cervical cancer patients using The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases. To begin, researchers assessed the differences in m6A regulatory factor expression levels between cervical cancer and normal tissues. Clustering analysis was adapted to assess PD-L1 expression, immunological score, immune cell infiltration, TME, and probable pathways in cervical cancer samples. The majority of m6A regulators were found to be considerably overexpressed in cervical cancer tissues. Using consensus clustering of 21 m6A regulators, we identified two subtypes (clusters 1/2) of cervical cancer, and we found that WHO stage and grade were associated with the subtypes. PD-L1 expression increased dramatically in cervical cancer tissues and was significantly linked to ALKBH5, FTO, METTL3, RBM15B, YTHDF1, YTHDF3, and ZC3H13 expression levels. Plasma cells and regulatory T cells (Tregs) were considerably elevated in cluster 2. Cluster 1 is involved in numerous signature pathways, including basal transcription factors, cell cycle, RNA degradation, and the spliceosome. The prognostic signature-based riskscore (METTL16, YTHDF1, and ZC3H13) was found to be an independent prognostic indicator of cervical cancer. The tumor immune microenvironment (TIME) was linked to m6A methylation regulators, and changes in their copy number will affect the quantity of tumor-infiltrating immune cells dynamically. Overall, our research discovered a powerful predictive signature based on m6A RNA methylation regulators. This signature correctly predicted the prognosis of cervical cancer patients. The m6A methylation regulator could be a critical mediator of PD-L1 expression and immune cell infiltration, and it could have a significant impact on the TIME of cervical cancer.
    Keywords:  M6A; PD-1; PD-L1; TIME; TME; cervical cancer
    DOI:  https://doi.org/10.3389/fimmu.2022.976107
  7. J Coll Physicians Surg Pak. 2022 Sep;32(9): 1143-1148
    m6A RNA, FTO, ALKBH5 Expression in Type 2 Diabetic and Obesity Patients.
    Erhan Onalan, Burkay Yakar, Ebru Etem Onalan, Koray Karakulak, Tugce Kaymaz, Emir Donder.
       OBJECTIVE: To investigate whether m6A content changes in type 2 diabetes mellitus (T2DM) and obese individuals and whether the relationship of m6A content with the mRNA expression levels of FTO and ALKBH5 genes.
    STUDY DESIGN: Cross-sectional study.
    PLACE AND DURATION OF STUDY: Department of Internal Medicine, Firat University, Medical School, Elazig, Turkey, between January 2019 and January 2022.
    METHODOLOGY: The study included 34 newly diagnosed patients with type 2 diabetes mellitus, 34 obese individuals, and 33 healthy individuals without any chronic and metabolic disease matched for age and gender. The global m6A RNA methylation, FTO, and ALKBH5 gene analyses of all the participants were performed. Total cholesterol, triglyceride, LDL, HDL, HbA1c, and insulin and glucose levels were measured.
    RESULTS: The median percentages of m6A RNA methylation in the control group, obese, and T2DM participants were 5.62%, 4.20%, and 5.21% respectively (p=0.004). The m6A RNA methylation percentage of the obese participants was significantly lower than controls (p=0.021). The FTO and ALKBH5 mRNA levels were significantly lower in obese and T2DM participants than in controls. There was a negative significant correlation between m6A RNA level and FTO i.e. (r=-0.291, p=0.003) and ALKBH5 (r=-0.321. p=0.001) levels.
    CONCLUSION: m6A RNA expression levels of obese individuals were lower than healthy controls. The FTO and ALKBH5 mRNA expressions were lower in both obese and T2DM participants compared to the healthy controls. There was no significant difference between obese and T2DM individuals in terms of m6A RNA expression, FTO and ALKBH5 mRNA expression. m6A RNA expression, FTO, and ALKBH5 levels have a potential role in obesity and diabetes mellitus.
    KEY WORDS: m6A RNA methylation, Epigenesis, Genetic, FTO, ALKBH5.
    DOI:  https://doi.org/10.29271/jcpsp.2022.09.1143
  8. Exp Cell Res. 2022 Sep 10. pii: S0014-4827(22)00346-9. [Epub ahead of print] 113353
    METTL3 upregulates COPS5 expression in osteosarcoma in an m6A-related manner to promote osteosarcoma progression.
    Can Zhang, Jun Wan, Qing Liu, Feng Long, Zhongchi Wen, Yupeng Liu.
      N6-methyladenosine (m6A) is the most abundant and well-studied internal modification of messenger RNAs (mRNAs). Although m6A mRNA modification has been frequently observed in osteosarcoma, the roles and underlying mechanisms of m6A modification are not yet fully elucidated. In this study, an m6A regulator, METTL3, showed to be dramatically up-regulated within osteosarcoma tissues and cells than non-cancerous healthy samples and human normal osteoblasts, respectively. In vitro, knockdown of METTL3 suppressed the viability of osteosarcomas, and their abilities to migrate and invade; in vivo, knockdown of METTL3 repressed tumor growth within xenotransplant tumor model. METTL3 upregulates COPS5 expression may be through promoting COPS5 methylation to stabilize COPS5 mRNA. The expression level of COPS5 also showed to be up-regulated within osteosarcoma tissue samples and cells. COPS5 knockdown caused no changes in METTL3 effects on METTL3 expression but partially eliminated METTL3 effects on COPS5 expression. METTL3 overexpression promoted, whereas COPS5 knockdown inhibited the malignant behaviors of osteosarcoma cells; COPS5 knockdown partially eliminated the effects of METTL3 overexpression on osteosarcoma cells. Conclusively, METTL3 and COPS5 serve as oncogenic regulators in osteosarcoma. METTL3 upregulates COPS5 expression in osteosarcoma in an m6A-related manner.
    Keywords:  COPS5; METTL3; N6-methyladenosine (m(6)A) regulators; Osteosarcoma; mRNA stability
    DOI:  https://doi.org/10.1016/j.yexcr.2022.113353
  9. Genomics Proteomics Bioinformatics. 2022 Sep 09. pii: S1672-0229(22)00114-0. [Epub ahead of print]
    m6A-TSHub: Unveiling the Context-specific m6A Methylation and m6A-affecting Mutations in 23 Human Tissues.
    Bowen Song, Daiyun Huang, Yuxin Zhang, Zhen Wei, Jionglong Su, João Pedro de Magalhães, Daniel J Rigden, Jia Meng, Kunqi Chen.
      As the most pervasive epigenetic marker present on mRNA and lncRNA, N6-methyladenosine (m6A) RNA methylation has been shown to participate in essential biological processes. Recent studies revealed the distinct patterns of m6A methylome across human tissues, and a major challenge remains in elucidating the tissue-specific presence and circuitry of m6A methylation. We present here a comprehensive online platform m6A-TSHub for unveiling the context-specific m6A methylation and genetic mutations that potentially regulate m6A epigenetic mark. m6A-TSHub consists of four core components, including (1) m6A-TSDB: a comprehensive database of 184,554 functionally annotated m6A sites derived from 23 human tissues and 499,369 m6A sites from 25 tumor conditions, respectively; (2) m6A-TSFinder: a web server for high-accuracy prediction of m6A methylation sites within a specific tissue from RNA sequences, which was constructed using multi-instance deep neural networks with gated attention; (3) m6A-TSVar: a web server for assessing the impact of genetic variants on tissue-specific m6A RNA modification; and (4) m6A-CAVar: a database of 587,983 TCGA cancer mutations (derived from 27 cancer types) that were predicted to affect m6A modifications in the primary tissue of cancers. The database should make a useful resource for studying the m6A methylome and genetic factor of epitranscriptome disturbance in a specific tissue (or cancer type). m6A-TSHub is accessible at: www.xjtlu.edu.cn/biologicalsciences/m6ats.
    Keywords:  Cancer mutations; Context-specific analysis; Functional annotation; Genome analysis; N(6)-methyladenosine (m(6)A)
    DOI:  https://doi.org/10.1016/j.gpb.2022.09.001
  10. Cell Mol Neurobiol. 2022 Sep 15.
    The Critical Role of RNA m6A Methylation in Gliomas: Targeting the Hallmarks of Cancer.
    Zhouhan Xu, Jun Jiang, Shun Wang.
      Gliomas are the most common central cancer with high aggressive-capacity and poor prognosis, remaining to be the threat of most patients. With the blood-brain barrier and highly malignant progression, the efficacy of high-intensity treatment is limited. The N6-methyladenine (m6A) modification is found in rRNA, snRNA, miRNA, lncRNA, and mRNA, influencing the metabolism and translation of these RNAs and consequently regulating the proliferation, metastasis, apoptosis, etc. of glioma cells. The key role that m6A modification in gliomas has played makes it a prospective target for diagnosis and treatment. However, with studying deeper in m6A modification and gliomas, the conclusion and mechanism are abundant and complex. This review focused on the dysregulation of m6A regulators and m6A modification of key genes and pathways in Hallmarks of gliomas. Furthermore, the potential of exploiting m6A modification for gliomas diagnosis and therapeutics was also discussed. This review will summarize the recent studies about m6A modification, revealing that m6A modification plays an important role in the malignant progression, angiogenesis, microenvironment, and genome instability in gliomas by exploring the interaction and network between m6A modification-related regulators and classical tumor-related genes. And it might provide some clue for the molecular mechanism, diagnosis, and treatment of gliomas.
    Keywords:  Glioma; Malignant progression; Metabolism reprogramming; Phenotypic plasticity; Tumor microenvironment; m6A modification
    DOI:  https://doi.org/10.1007/s10571-022-01283-8
  11. Front Plant Sci. 2022 ;13 917335
    Transcriptome-wide analyses of RNA m6A methylation in hexaploid wheat reveal its roles in mRNA translation regulation.
    Tao Huang, Wei-Jie He, Cheng Li, Jing-Bo Zhang, Yu-Cai Liao, Bo Song, Peng Yang.
      N6-methyladenosine (m6A) is the most abundant RNA modification in eukaryotic messenger RNAs. m6A was discovered in wheat about 40 years ago; however, its potential roles in wheat remain unknown. In this study, we profiled m6As in spikelets transcriptome at the flowering stage of hexaploid wheat and found that m6As are evenly distributed across the A, B, and D subgenomes but their extents and locations vary across homeologous genes. m6As are enriched in homeologous genes with close expression levels and the m6A methylated genes are more conserved. The extent of m6A methylation is negatively correlated with mRNA expression levels and its presence on mRNAs has profound impacts on mRNA translation in a location-dependent manner. Specifically, m6As within coding sequences and 3'UTRs repress the translation of mRNAs while the m6As within 5'UTRs and start codons could promote it. The m6A-containing mRNAs are significantly enriched in processes and pathways of "translation" and "RNA transport," suggesting the potential role of m6As in regulating the translation of genes involved in translation regulation. Our data also show a stronger translation inhibition by small RNAs (miRNA and phasiRNA) than by m6A methylation, and no synergistical effect between the two was observed. We propose a secondary amplification machinery of translation regulation triggered by the changes in m6A methylation status. Taken together, our results suggest translation regulation as a key role played by m6As in hexaploid wheat.
    Keywords:  N6-methyladenosine; RNA modification; m6A; small RNA; translation; wheat
    DOI:  https://doi.org/10.3389/fpls.2022.917335
  12. Zhong Nan Da Xue Xue Bao Yi Xue Ban. 2022 Aug 28. pii: 1672-7347(2022)08-1154-09. [Epub ahead of print]47(8): 1154-1162
    m6A modification of mRNA in skin diseases.
    Zhuoxian Yan, Pengfei Liang.
      N6-methyladenosine (m6A) is the predominant post-transcriptional modification for eukaryotic mRNA. It's regulated by methyltransferases, demethylases, and m6A binding proteins, and plays an important role in regulating splicing, translation, and degradation of mRNA. Skin diseases, especially immune skin diseases and skin tumors, have a complicated pathogenesis and are refractory to treatment, seriously affecting the patient quality of life. Recent studies have revealed that m6A and its regulatory proteins can affect the development of numerous skin diseases. The m6A modification was found to be involved in skin accessory development, including hair follicle and sweat gland formation. The level of m6A modification was significantly altered in a variety of skin diseases including melanoma, cutaneous squamous cell carcinoma, Merkel cell carcinoma, and psoriasis, and affected a variety of biological processes including cell proliferation and differentiation migration. The m6A and its regulatory proteins may become potential molecular markers or therapeutic targets for skin diseases, and have promising clinical applications in early diagnosis, efficacy determination, prognosis prediction, and gene therapy of skin diseases.
    Keywords:  N6-methyladenosine; RNA methylation; skin disease; skin stem cell; wound repair
    DOI:  https://doi.org/10.11817/j.issn.1672-7347.2022.210332
  13. Am J Transl Res. 2022 ;14(8): 5379-5393
    The prognostic value and multiomic features of m6A-related risk signature in lung adenocarcinoma.
    Xiangcheng Wang, Qin Yu, Hongfang Yu, Yuzhe Wang, Liping Sun, Lei Yu, Hongwei Cui, Hao Yang.
       OBJECTIVES: N6-methyladenosine (m6A), a predominant RNA modification, has been recently linked to messenger RNA splicing, stability and expression, and its dysregulation may be important in the initiation as well as development of human cancers. The current study was proposed to investigate the clinico-pathological value and multiomic characteristics of m6A-linked genes in the diagnosis and prognosis of lung adenocarcinoma (LUAD).
    METHODS: The expression levels and mutation types of 21 previously identified m6A regulators were analyzed using the TCGA (The Cancer Genome Atlas) database. The patients were categorized into two groups, a training group (n=392) and a testing group (n=98). Next, the prognostic score of m6A regulators was determined by the Cox survival analysis and a regression model of LASSO to develop a risk profile for patients with LUAD. Moreover, features of risk signature, including chemosensitivity, tumor immune microenvironment and genetic mutation, were also explored.
    RESULTS: In total, 18 of 21 m6A regulators showed significantly differential expression in LUAD (P<0.05). Among them, 6 genes were observed to be associated with the Overall Survival (OS) of patients with LUAD. Three genes (IGF2BP1 and 2, and HNRNPC) were further evaluated as a prognostic signature in LUAD. Patients, grouped as high risk based on the median of risk score, had poorer OS in comparison with those in low-risk group (P<0.05). The accuracy of our prognostic signatures was high: the AUC were 0.67, 0.59, 0.64 (training set), and 0.65, 0.69, 0.64 (testing set) at survival of 1- , 3- and 5-year, respectively. The prognostic performance of IGF2BP1, IGF2BP2 and HNRNPC was successfully validated in two independent external cohorts. High-risk score was an indicator of chemoresistance, TP53 mutation and increased infiltration of immune cells, and in vitro assessment of the cellular function of HNRNPC confirmed that the gene is involved in cell proliferation and invasion.
    CONCLUSION: The prognostic signature based on m6A regulators might provide novel insights into prognostic assessment and individualized treatment for patients with LUAD.
    Keywords:  HNRNPC; Lung adenocarcinoma (LUAD); N6-methyladenosine (m6A); TCGA; prognostic signature
  14. Front Genet. 2022 ;13 981567
    Molecular characterization, clinical relevance and immune feature of m7G regulator genes across 33 cancer types.
    Zhanzhan Li, Yanyan Li, Lin Shen, Liangfang Shen, Na Li.
      Over 170 RNA modifications have been identified after transcriptions, involving in regulation of RNA splicing, processing, translation and decay. Growing evidence has unmasked the crucial role of N6-methyladenosine (m6A) in cancer development and progression, while, as a relative newly found RNA modification, N7-methylguanosine (m7G) is also certified to participate in tumorigenesis via different catalytic machinery from that of m6A. However, system analysis on m7G RNA modification-related regulator genes is lack. In this study, we first investigated the genetic alteration of m7G related regulator genes in 33 cancers, and found mRNA expression levels of most regulator genes were positively correlated with copy number variation (CNV) and negatively correlated with methylation in most cancers. We built a m7G RNA modification model based on the enrichment of the regulator gene scores to evaluate the m7G modification levels in 33 cancers, and investigated the connections of m7G scores to clinical outcomes. Furthermore, we paid close attention to the role of m7G in immunology due to the widely used immune checkpoint blockade therapy. Our results showed the higher m7G scores related to immunosuppression of tumor cells. Further confirmation with phase 3 clinical data with application of anti-PDL1/PDL indicated the impact of m7G modification level on immunotherapy effect. Relevance of m7G regulator genes and drug sensitivity was also evaluated to provide a better treatment choice when treating cancers. In summary, our study uncovered the profile of m7G RNA modification through various cancers, and figured out the connection of m7G modification levels with therapeutical outcomes, providing potential better options of cancer treatment.
    Keywords:  N7 -methylguanosine (m7G); RNA modification; cancer; immunotherapy; methylation
    DOI:  https://doi.org/10.3389/fgene.2022.981567
  15. Adv Nutr. 2022 Sep 14. pii: nmac101. [Epub ahead of print]
    Unravelling the Complex Interactions Between the FTO Gene, Lifestyle, and Cancer.
    Sepideh Abdollahi, Naeemeh Hasanpour Ardekanizadeh, Seyed Mohammad Poorhosseini, Maryam Gholamalizadeh, Zahra Roumi, Mark O Goodarzi, Saeid Doaei.
      Carcinogenesis as a complicated process originates from genetic, epigenetic, and environmental factors. Recent studies have reported a potential critical role for the fat mass and obesity-associated (FTO) gene in carcinogenesis through different signaling pathways such as mRNA N6-methyladenosine (m6-A) demethylation. The most common internal modification in mammalian mRNAs is the m6-A RNA methylation that has a significant biological functioning through regulation of cancer-related cellular processes. Some environmental factors, like physical activity and dietary intake, may influence signaling pathways engaged in carcinogenesis, through regulating FTO gene expression. Also, people with FTO gene polymorphisms may be differently influenced by cancer risk factors. For example, FTO risk allele carriers may need higher intake of nutrients to prevent cancer than others. In order to obtain a deeper viewpoint of the FTO, lifestyle, and cancer-related pathway interactions, this review aims to discuss upstream and downstream pathways associated with the FTO gene and cancer.
    Keywords:   FTO ; carcinogenesis; lifestyle; m6-a; signal transduction
    DOI:  https://doi.org/10.1093/advances/nmac101
  16. Discov Oncol. 2022 Sep 17. 13(1): 89
    METTL3 dual regulation of the stability of LINC00662 and VEGFA RNAs promotes colorectal cancer angiogenesis.
    Guoying Zhang, Tianjun Wang, Zihui Huang, Yuanyuan Chen, Li Sun, Xia Xia, Fang He, Chenying Fan, Shukui Wang, Wanli Liu.
       PURPOSE: The angiogenesis is among the primary factors that affect tumor recurrence and distant organ metastasis in colorectal cancer (CRC). N6-methyladenosine (m6A) modification is one of the most common chemical modifications in eukaryotic mRNA, especially at the post-transcriptional level. Methyltransferase-like 3 (METTL3) promoting angiogenesis in a variety of tumors has been reported. However, the mechanism of how METTL3 dual-regulates the stability of long non-coding RNAs (lncRNAs) and vascular-related factor RNAs to affect angiogenesis in CRC is unclear.
    METHODS: 64 paired CRC and adjacent normal tissues were collected. In vitro, quantitative real-time polymerase chain reaction (qRT-PCR), immunohistochemistry (IHC), actinomycin assay, methylated RNA immunoprecipitation (MeRIP) experiment,3-(4,5)-dimethylthiahiazo(-z-y1)-3,5-di-phenytetrazoliumromide (MTT) and colony formation assay were performed. The functions were also studied in zebrafish model animals in vivo.
    RESULTS: We found that the vascular endothelial growth factor A(VEGFA), METTL3 and LINC00662 RNAs were highly expressed in CRC, and that METTL3 was significantly positively correlated with LINC00662 and VEGFA. The protein expression levels of CD31, CD34, VEGFA, m6A and METTL3 were all significantly increased in the CRC tissues. The angiogenesis experiments both in vivo and in vitro found that METTL3 and LINC00662 promoted angiogenesis in CRC. The actinomycin assay indicated that METTL3 maintained the stability of LINC00662 and VEGFA RNAs. In addition, the MeRIP experiment confirmed that the LINC00662 and VEGFA RNAs had METTL3-enriched sites.
    CONCLUSION: These findings suggest that METTL3 and LINC00662 may both serve as diagnostic and prognostic predictive biomarkers for CRC and potential targets for anti-vascular therapy.
    Keywords:  Colorectal cancer angiogenesis; LINC00662; METTL3; N6-methyladenosine (m6A); VEGFA
    DOI:  https://doi.org/10.1007/s12672-022-00557-3
  17. Mol Neurobiol. 2022 Sep 13.
    YTHDF1 Protects Auditory Hair Cells from Cisplatin-Induced Damage by Activating Autophagy via the Promotion of ATG14 Translation.
    Yuyu Huang, Dekun Gao, Yan Wu, Lianhua Sun, Jianyong Chen, Junmin Chen, Xingxu Huang, Jun Yang, Shuna Li.
      N6-methyladenosine (m6A) has been recognized as a common type of post-transcriptional epigenetic modification. m6A modification and YTHDF1, one of its reader proteins, have been documented to play a pivotal role in numerous human diseases via regulating mRNA splicing, translation, stability, and subcellular localization. The chemotherapeutic drug cisplatin (CDP) can damage sensory hair cells (HCs) and result in permanent sensorineural hearing loss. However, whether YTHDF1-mediated modification of mRNA is potentially involved in CDP-induced injury in sensory hair cells was not fully clarified. This study investigated the potential mechanisms for the modification of YTHDF1 in CDP-induced damage in HCs. Here, we discovered that YTHDF1's expression level statistically increased significantly after treating with CDP. Apoptosis and cell death of HCs induced by CDP were exacerbated after the knockdown of YTHDF1, while overexpression of YTHDF1 in HCs alleviated their injury induced by CDP. Moreover, YTHDF1 expression correlated with cisplatin-induced autophagy with statistical significance in HCs; namely, YTHDF1's overexpression enhanced the activation of autophagy, while its deficiency suppressed autophagy and, at the same time, increased the loss of HCs after CDP damage. WB analysis and qRT-PCR results of autophagy-related genes indicated that YTHDF1 promoted the translation of autophagy-related genes ATG14, thus boosting autophagy. Therefore, CDP-induced YTHDF1 expression protected HCs against CDP-induced apoptosis by upregulating the translation of autophagy-related genes ATG14, along with enhancing autophagy. Based on these findings, it can be inferred that YTHDF1 is potentially a target for ameliorating drug-induced HCs damage through m6A modification.
    Keywords:  ATG proteins; YTHDF1; autophagy; cisplatin; ototoxicity
    DOI:  https://doi.org/10.1007/s12035-022-03021-z
  18. Nucleic Acids Res. 2022 Sep 12. pii: gkac770. [Epub ahead of print]
    Formation and removal of 1,N6-dimethyladenosine in mammalian transfer RNA.
    Xue-Jiao You, Shan Zhang, Juan-Juan Chen, Feng Tang, Jingang He, Jie Wang, Chu-Bo Qi, Yu-Qi Feng, Bi-Feng Yuan.
      RNA molecules harbor diverse modifications that play important regulatory roles in a variety of biological processes. Over 150 modifications have been identified in RNA molecules. N6-methyladenosine (m6A) and 1-methyladenosine (m1A) are prevalent modifications occurring in various RNA species of mammals. Apart from the single methylation of adenosine (m6A and m1A), dual methylation modification occurring in the nucleobase of adenosine, such as N6,N6-dimethyladenosine (m6,6A), also has been reported to be present in RNA of mammals. Whether there are other forms of dual methylation modification occurring in the nucleobase of adenosine other than m6,6A remains elusive. Here, we reported the existence of a novel adenosine dual methylation modification, i.e. 1,N6-dimethyladenosine (m1,6A), in tRNAs of living organisms. We confirmed that m1,6A is located at position 58 of tRNAs and is prevalent in mammalian cells and tissues. The measured level of m1,6A ranged from 0.0049% to 0.047% in tRNAs. Furthermore, we demonstrated that TRMT6/61A could catalyze the formation of m1,6A in tRNAs and m1,6A could be demethylated by ALKBH3. Collectively, the discovery of m1,6A expands the diversity of RNA modifications and may elicit a new tRNA modification-mediated gene regulation pathway.
    DOI:  https://doi.org/10.1093/nar/gkac770
  19. Front Cardiovasc Med. 2022 ;9 905737
    m6A regulator-mediated RNA methylation modification patterns are involved in immune microenvironment regulation of coronary heart disease.
    Zhaoshui Li, Yanjie Song, Meng Wang, Ruxin Shen, Kun Qin, Yu Zhang, Ting Jiang, Yifan Chi.
       Background: Although the roles of m6A modification in the immune responses to human diseases have been increasingly revealed, their roles in immune microenvironment regulation in coronary heart disease (CHD) are poorly understood.
    Methods: The GSE20680 and GSE20681 datasets related to CHD were acquired from the Gene Expression Omnibus (GEO) database. A total of 30 m6A regulators were used to perform LASSO regression to identify the significant genes involved in CHD. Unsupervised clustering analysis was conducted using the m6A regulators to distinguish the m6A RNA methylation patterns in patients with CHD. The differentially expressed genes (DEGs) and biological characteristics, including GO and KEGG enrichment results, were assessed for the different m6A patterns to analyse the impacts of m6A regulators on CHD. Hub genes were identified, and subsequent microRNAs-mRNAs (miRNAs-mRNAs) and mRNAs-transcriptional factors (mRNA-TFs) interaction networks were constructed by the protein and protein interaction (PPI) network method using Cytoscape software. The infiltrating proportion of immune cells was assessed by ssGSEA and the CIBERSORT algorithm. Quantitative real-time PCR (qRT-PCR) was performed to detect the expression of the significant m6A regulators and hub genes.
    Results: Four of 30 m6A regulators (HNRNPC, YTHDC2, YTHDF3, and ZC3H13) were identified to be significant in the development of CHD. Two m6A RNA methylation clusters were distinguished by unsupervised clustering analysis based on the expression of the 30 m6A regulators. A total of 491 genes were identified as DEGs between the two clusters. A PPI network including 308 mRNAs corresponding to proteins was constructed, and 30 genes were identified as hub genes that were enriched in the bioprocesses of peptide cross-linking, keratinocyte differentiation. Twenty-seven hub genes were found to be related to miRNAs, and seven hub genes were found to be related to TFs. Moreover, among the 30 hub genes, eight genes were found to be upregulated in CHD, and three were found to be downregulated in CHD compared to the normal people. The high m6A modification pattern was associated with a higher infiltrated abundance of immune cells.
    Conclusion: Our findings demonstrated that m6A modification plays crucial roles in the diversity and complexity of the immune microenvironment in CHD.
    Keywords:  LASSO regression; coronary heart disease; immune microenvironment; m6A RNA methylation; unsupervised clustering
    DOI:  https://doi.org/10.3389/fcvm.2022.905737
  20. Am J Transl Res. 2022 ;14(8): 5363-5378
    Role of the N6-methyladenosine regulatory factor in reducing the risk of cardiovascular disease: subtype diagnosis following aerobic exercise-assisted weight loss.
    Xiaoya Hao, Yukun Li, Guo Huang, Ying Zeng.
       OBJECTIVES: This study aimed to construct a model based on different N6-methyladenosine (m6A) regulatory factors involved in reducing the risk of the development of cardiovascular diseases under conditions of aerobic exercise.
    METHODS: We screened for significantly different expressions of m6A regulators from the GSE66175 dataset. Five candidate m6A regulators were identified using the random forest model to predict aerobic exercise-mediated fat loss and reduction of the risk of cardiovascular disease. A nomogram model was established for analysis, and the consensus clustering method was used to distinguish between the two m6A clusters (clusters A and B). The single-sample gene set-enrichment analysis method was used to assess the abundance of immune cells in the samples related to cardiovascular anomalies. We determined the relationship between the functions of 29 immune cells and m6A clusters.
    RESULTS: Twelve significantly and differentially expressed m6A regulators in the control and aerobic exercise groups were screened out, and it was observed that METTL13 correlated positively with the expression levels of the YTH domain containing 1 (YTHDC1), YTH N (6)-methyl adenosine RNA binding protein 1, and leucine-rich pentatricopeptide repeat-containing. The fat mass and obesity-associated gene negatively correlated with YTHDC1 and the fragile X mental retardation 1 protein. The random forest and support vector machine models were used to screen the ELAV-like RNA binding protein 1 (ELAVL1), RNA binding motif protein 15B (RBM15B), insulin-like growth factor binding protein 1 (IGFBP1), Wilms tumor 1-associated protein (WTAP), and zinc finger CCCH-type containing 13 (ZC3H13) genes. Analysis of the line graph model and the results obtained using decision curve analysis revealed the efficiency of the model. Gene ontology enrichment analysis was used to analyze the m6A regulatory gene model, and the results suggested that it was associated with RNA splicing. The results obtained using the Kyoto Encyclopedia of Genes and Genomes enrichment analysis method suggests that the genes were associated with Alzheimer's disease and neurodegeneration pathways associated with multiple diseases. The m6A regulatory gene model was associated with most of the immune cells infiltrating tumors and was also closely related to genes associated with lipid metabolism.
    CONCLUSIONS: The m6A regulatory factor plays an important role in reducing the risk of cardiovascular disease under conditions of aerobic exercise-assisted weight loss. It is also associated with the metabolic pathways of low-density lipoprotein, high-density lipoprotein, and triglyceride.
    Keywords:  Cardiovascular disease; N6-methyladenosine (m6A); cluster subtypes
  21. J Cancer Res Clin Oncol. 2022 Sep 15.
    Prognostic value of comprehensive typing based on m6A and gene cluster in TNBC.
    Haoming Wu, Jikun Feng, Jundong Wu, Wenjing Zhong, Xiazi Zouxu, Weiling Huang, Xinjian Huang, Jiarong Yi, Xi Wang.
       BACKGROUND: Triple-negative breast cancer (TNBC) is resistant to targeted therapy with HER2 monoclonal antibodies and endocrine therapy, because it lacks the estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2). TNBC is a subtype of breast cancer with the worst prognosis and the highest mortality rate compared to other subtypes. N6-methyladenosine (m6A) modification is significant in cancer and metastasis, because it can alter gene expression and function at numerous levels, such as RNA splicing, stability, translocation, and translation. There are limited investigations into the connection between TNBC and m6A.
    MATERIALS AND METHODS: Breast cancer-related data were retrieved from the Cancer Genome Atlas (TCGA) database, and 116 triple-negative breast cancer cases were identified from the data. The GSE31519 data set, which included 68 cases of TNBC, was obtained from the Gene Expression Omnibus (GEO) database. Survival analysis was used to determine the prognosis of distinct m6A types based on their m6A group, gene group, and m6A score. To investigate the potential mechanism, GO and KEGG analyses were performed on the differentially expressed genes.
    RESULTS: The expression of m6A-related genes and their impact on prognosis in TNBC patients were studied. According to the findings, m6A was crucial in determining the prognosis of TNBC patients, and the major m6A-linked genes in this process were YTHDF2, RBM15B, IGFBP3, and WTAP. YTHDF2, RBM15B and IGFBP3 are associated with poor prognosis, while WTAP is associated with good prognosis. By cluster analysis, the gene cluster and the m6A cluster were beneficial in predicting the prognosis of TNBC patients. The m6A score based on m6A and gene clusters was more effective in predicting the prognosis of TNBC patients. Furthermore, the tumor microenvironment may play an important role in the process of m6A, influencing TNBC prognosis.
    CONCLUSIONS: N6-adenylic acid methylation (m6A) was important in altering the prognosis of TNBC patients, and the key m6A-associated genes in this process were YTHDF2, RBM15B, IGFBP3, and WTAP. Furthermore, the comprehensive typing based on m6A and gene clusters was useful in predicting TNBC patients' prognosis, showing potential as valuable evaluating tools for TNBC.
    Keywords:  GEO; M6A; Prognosis; TCGA; TNBC; Typing
    DOI:  https://doi.org/10.1007/s00432-022-04345-y
  22. RNA. 2022 Sep 14. pii: rna.079404.122. [Epub ahead of print]
    Exploring the epitranscriptome by native RNA sequencing.
    Oguzhan Begik, John S Mattick, Eva Maria Novoa.
      Chemical RNA modifications, collectively referred to as the 'epitranscriptome', are essential players in fine-tuning gene expression. Our ability to analyze RNA modifications has improved rapidly in recent years, largely due to the advent of high throughput sequencing methodologies, which typically consist of coupling modification-specific reagents, such as antibodies or enzymes, to next-generation sequencing. Recently, it also became possible to map RNA modifications directly by sequencing native RNAs using nanopore technologies, which has been applied for the detection of a number of RNA modifications, such as N6-methyladenosine (m6A), pseudouridine (Ψ) and inosine (I). However, the signal modulations caused by most RNA modifications have yet to be determined. A global effort is needed to determine the signatures of the full range of RNA modifications to avoid the technical biases that have so far limited our understanding of the epitranscriptome.
    Keywords:  Epitranscriptomics; Nanopore sequencin; Native RNA sequencing; RNA modifications
    DOI:  https://doi.org/10.1261/rna.079404.122
  23. Ann Transl Med. 2022 Aug;10(16): 902
    Analysis of m6A-related signatures associated with the tumor immune microenvironment and predict survival in acute myeloid leukemia.
    Shushu Yuan, Zhirong Cong, Jiali Ji, Li Zhu, Qi Jiang, Ying Zhou, Qian Shen, Daniela Damiani, Xiaohong Xu, Bingzong Li.
       Background: Most previous studies have focused on the intrinsic carcinogenic pathways of tumors; however, little is known about the potential role of N6-methyladenosine (m6A) methylation in the tumor immune microenvironment (TIME). To better diagnose and treat acute myeloid leukemia (AML), we sought to examine the correlation between m6A regulatory factors and immune infiltration in cases of AML. At the same time, a prognostic model was constructed to predict the survival of AML.
    Methods: We extracted data from The Cancer Genome Atlas (TCGA) database, including ribonucleic acid sequencing (RNA-seq) transcriptome data and data on the corresponding clinical characteristics of AML patients. We identified two m6A modification patterns with distinct clinical outcomes and found a significant relationship between them. Simultaneous discovery of distinct m6A clusters associated with the tumor immune microenvironment [immune cell types and Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data (ESTIMATE) algorithm] are closely related. Next, we implemented Lasso (Least Absolute Shrinkage and Selection Operator) Cox regression to build a predictive model in the 2-m6A regulator TCGA dataset to further explore m6A prognostic features in AML, and perform correlation validation.
    Results: We identified 2 molecular subtypes (Clusters 1 and 2) by the consistent clustering of significant m6A regulators in AML. Cluster 2 was associated with a higher immune score and obvious immune cell infiltration, and thus patients in Cluster 2 had a poorer prognosis than those in Cluster 1 (P<0.05). Additionally, the 2 m6A-related signatures representing the independent prognostic factors in AML were screened to construct a prognostic risk-score model. We found that patients with low-risk scores had higher immune scores than those with high-risk scores (P<0.05).
    Conclusions: Our research confirmed that m6A methylation plays an important role in AML. Further provide new directions for the prognosis and treatment of AML.
    Keywords:  Tumor immune microenvironment (TIME); acute myeloid leukemia (AML); m6A; survival
    DOI:  https://doi.org/10.21037/atm-22-3858
  24. Front Immunol. 2022 ;13 978092
    Identification of m6A modification patterns and development of m6A-hypoxia prognostic signature to characterize tumor microenvironment in triple-negative breast cancer.
    Xi Shen, Jianxin Zhong, Jinlan He, Jiaqi Han, Nianyong Chen.
       Background: N6-methylation (m6A) modification of RNA has been found to have essential effects on aspects of the tumor microenvironment (TME) including hypoxia status and mobilization of immune cells. However, there are no studies to explore the combined effect of m6A modification and hypoxia on molecular heterogeneity and TME of triple-negative breast cancer (TNBC).
    Methods: We collected The Cancer Genome Atlas (TCGA-TNBC, N=139), the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC-TNBC, N=297), the GSE103091, GSE21653, and GSE135565 series from the Gene Expression Omnibus (GEO-TNBC, N=247), and FUSCCTNBC (N=245) for our study. The non-negative matrix factorization algorithm was used to cluster TNBC samples. Immune cell infiltration was analyzed by the CIBERSORT algorithm. The enrichment scores were calculated by single-sample gene set enrichment analysis(ssGSEA) to characterize TME in TNBC samples. Immunohistochemistry (IHC) and qRT-PCR were performed to detect the gene expression.
    Results: Based on the expression of m6A-related genes, we identified three distinct m6A clusters (denoted A, B, and C) in TNBC samples. Comparing the TME characteristics among the three clusters, we observed that cluster C was strongly related to hypoxia status and immune suppression, whereas clusters A and B displayed more immune cell infiltration. Therefore, we combine m6A and hypoxia related genes to classify two m6A-hypoxia clusters of TNBC and screened six prognostic genes by LASSO-Cox regression to construct a m6A-hypoxia signature(MHPS), which divided TNBC samples into high- and low-risk groups. We identified different TME features, immune cell infiltration between the two groups, and a better immunotherapy response was observed in the low-risk group. A nomogram was constructed with tumor size, lymph node, and risk score to improve clinical application of MHPS.
    Conclusion: We identified distinct TME characteristics of TNBC based on three different m6A modification patterns. Then, we constructed a specific m6A-hypoxia signature for TNBC to evaluate risk and predict immunotherapy response of patients, to enable more accurate treatment in the future.
    Keywords:  Triple-negative breast cancer; immune cell infiltration; m6A RNA methylation; m6A-hypoxia signature; tumor microenvironment
    DOI:  https://doi.org/10.3389/fimmu.2022.978092
  25. Biology (Basel). 2022 Jun 21. pii: 944. [Epub ahead of print]11(7):
    N6-Methyladenosine Methylome Profiling of Muscle and Adipose Tissues Reveals Methylase-mRNA Metabolic Regulatory Networks in Fat Deposition of Rex Rabbits.
    Gang Luo, Shuhui Wang, Yaotian Ai, Jiapeng Li, Zhanjun Ren.
      N6-methyladenosine (m6A) is the most prevalent internal form of modification in messenger RNA in higher eukaryotes and plays an important role in cancer, immunity, reproduction, development, and fat deposition. Intramuscular fat is the main factor used to measure the meat quality of an animal. The deposition of intramuscular fat and perirenal fat increases with age. However, there is no data on m6A modification of Rex rabbits and its potential biological roles in adipose deposition and muscle growth. Here, we performed two high-throughput sequencing methods, m6A-modified RNA immunoprecipitation sequence (MeRIP-seq) and RNA sequence (RNA-seq), to identify key genes with m6A modification on fat deposition in the muscle and adipose tissues of Rex rabbits. Then, qRT-PCR was used to identify the differently methylated genes related to fat deposition. Our findings showed that there were 12,876 and 10,973 m6A peaks in the rabbit muscle and adipose tissue transcriptomes, respectively. Stop codons, 3'-untranslated regions, and coding regions were found to be mainly enriched for m6A peaks. In addition, we found 5 differential methylases and 12 key genes of methylation modification related to fat deposition between muscle and adipose tissues samples. The expression levels of six random key genes were significantly higher in the fat than that in the muscle of Rex rabbits at different stages (p &lt; 0.01). Finally, five differential methylases were found to regulate adipogenesis by affecting the expression of screened genes in different ways. These findings provided a theoretical basis for our future research on the function of m6A modification during the growth of fat deposits.
    Keywords:  Rex rabbits; fat deposition; m6A modification; metabolic regulatory; methylation
    DOI:  https://doi.org/10.3390/biology11070944
  26. J Virol. 2022 Sep 14. e0112422
    N6-Methyladenine Modification of Hepatitis Delta Virus Regulates Its Virion Assembly by Recruiting YTHDF1.
    Geon-Woo Kim, Jae-Su Moon, Severin O Gudima, Aleem Siddiqui.
      Hepatitis delta virus (HDV) is a defective satellite virus that uses hepatitis B virus (HBV) envelope proteins to form its virions and infect hepatocytes via the HBV receptors. Concomitant HDV/HBV infection continues to be a major health problem, with at least 25 million people chronically infected worldwide. N6-methyladenine (m6A) modification of cellular and viral RNAs is the most prevalent internal modification that occurs cotranscriptionally, and this modification regulates various biological processes. We have previously described a wider range of functional roles of m6A methylation of HBV RNAs, including its imminent regulatory role in the encapsidation of pregenomic RNA. In this study, we present evidence that m6A methylation also plays an important role in the HDV life cycle. Using the methylated RNA immunoprecipitation (MeRIP) assay, we identified that the intracellular HDV genome and antigenome are m6A methylated in HDV- and HBV-coinfected primary human hepatocytes and HepG2 cell expressing sodium taurocholate cotransporting polypeptide (NTCP), while the extracellular HDV genome is not m6A methylated. We observed that HDV genome and delta antigen levels are significantly decreased in the absence of METTL3/14, while the extracellular HDV genome levels are increased by depletion of METTL3/14. Importantly, YTHDF1, an m6A reader protein, interacts with the m6A-methylated HDV genome and inhibits the interaction between the HDV genome and antigens. Thus, m6A of the HDV genome negatively regulates virion production by inhibiting the interaction of the HDV genome with delta antigens through the recruitment of YTHDF1. This is the first study that provides insight into the functional roles of m6A in the HDV life cycle. IMPORTANCE The functional roles of N6-methyladenine (m6A) modifications in the HBV life cycle have been recently highlighted. Here, we investigated the functional role of m6A modification in the HDV life cycle. HDV is a subviral agent of HBV, as it uses HBV envelope proteins to form its virions. We found that m6A methylation also occurs in the intracellular HDV genome and antigenome but not in the extracellular HDV genome. The m6A modification of the HDV genome recruits m6A reader protein (YTHDF1) onto the viral genome. The association of YTHDF1 with the HDV genome abrogates the interaction of delta antigens with the HDV genome and inhibits virion assembly. This study describes the unique effects of m6A on regulation of the HDV life cycle.
    Keywords:  HDV life cycle; N6-methyladenine modification; hepatitis delta virus; virion assembly
    DOI:  https://doi.org/10.1128/jvi.01124-22
  27. FASEB J. 2022 Oct;36(10): e22552
    The effects of RNA methylation on immune cells development and function.
    Ling-Feng Zha, Jing-Lin Wang, Xiang Cheng.
      Among the more than 170 known RNA modifications, methylation modification is the most frequent and well-studied. Depending on where the methylation occurs, RNA methylation can be classified as N6 -methyladenosine, N1 -methyladenosine, 5-methylcytosine, N7 -methylguanosine, and others. The methylation of RNA is constantly and dynamically modified in the complex microenvironment by methyltransferases, demethylases, and methylation reading proteins. These changes affect the proliferation and differentiation of immune cells as well as their effector activities by affecting RNA location, activity, stability, and translation efficiency. This review outlines how diverse RNA methylation alterations affect immune cell development and biological activity, as well as the role of RNA methylation in health and disease, to provide a molecular basis for future immunotherapies.
    Keywords:  RNA; epigenetics; immune cells; methylation; modification
    DOI:  https://doi.org/10.1096/fj.202200716R
  28. Front Cell Dev Biol. 2022 ;10 921503
    Transcriptional expression of m6A and m5C RNA methyltransferase genes in the brain and fat body of honey bee adult workers.
    Luana Bataglia, Zilá Luz Paulino Simões, Francis Morais Franco Nunes.
      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.
    Keywords:  RNA methylation; aging; bee; behavior; epitranscriptomics; m5C; m6A; nutrition
    DOI:  https://doi.org/10.3389/fcell.2022.921503
  29. Front Oncol. 2022 ;12 877817
    DNA methylation regulators-related molecular patterns and tumor immune landscape in hepatocellular carcinoma.
    Dingli Song, Zhenyu Zhou, Jie Wu, Tao Wei, Guang Zhao, Hong Ren, Boxiang Zhang.
      Increasing evidence showed that the dysregulation of DNA methylation regulators is a decisive feature of almost all cancer types and affects tumor progressions. However, few studies focused on the underlying influences of DNA methylation regulators-related genes (DMRegs) in immune cell-infiltration characteristics, tumor microenvironment (TME) and immunotherapy in HCC patients. In our study, the alterations of DNA methylation regulators modification patterns (DMRPs) were clustered from hepatocellular carcinoma (HCC) samples based on the expression of DNA methylation regulators as well as genetic and transcriptional features. In addition, based on molecular identification of three distinct molecular subtypes, we found that different DMRPs alterations were related to different clinicopathological characteristics, prognosis, and immune cells infiltration features. Moreover, we constructed and validated a DNA methylation regulators-related genes score (DMRegs_score) to predict the survival of HCC patients. A high DMRegs _score, which was characterized by more TP53 wild mutation, high expression of PD-1, CTLA-4, and remarkable immunity activation, was indicative of poor prognosis. Furthermore, we validated the expression of eight genes which were used for the prognostic signature in this risk score by RT-qPCR using tissues from our center. More importantly, DMRegs_score was highly correlated with targeted drug sensitivity. Additionally, we developed a highly accurate scoring system that could be used to improve the clinical applicability of DMRegs _score. In conclusion, these findings may contribute to a better understanding of DNA methylation regulators and provide new strategies for evaluating prognosis and developing more effective combination therapy for HCC patients.
    Keywords:  DNA methylation regulators; classification; hepatocellular cancer; immune infiltration; signature
    DOI:  https://doi.org/10.3389/fonc.2022.877817
  30. Stem Cell Rev Rep. 2022 Sep 12.
    METTLing in Stem Cell and Cancer Biology.
    John G Tooley, James P Catlin, Christine E Schaner Tooley.
      The methyltransferase-like (METTL) family is a diverse group of methyltransferases that can methylate nucleotides, proteins, and small molecules. Despite this diverse array of substrates, they all share a characteristic seven-beta-strand catalytic domain, and recent evidence suggests many also share an important role in stem cell biology. The most well characterized family members METTL3 and METTL14 dimerize to form an N6-methyladenosine (m6A) RNA methyltransferase with established roles in cancer progression. However, new mouse models indicate that METTL3/METTL14 are also important for embryonic stem cell (ESC) development and postnatal hematopoietic and neural stem cell self-renewal and differentiation. METTL1, METTL5, METTL6, METTL8, and METTL17 also have recently identified roles in ESC pluripotency and differentiation, while METTL11A/11B, METTL4, METTL7A, and METTL22 have been shown to play roles in neural, mesenchymal, bone, and hematopoietic stem cell development, respectively. Additionally, a variety of other METTL family members are translational regulators, a role that could place them as important players in the transition from stem cell quiescence to differentiation. Here we will summarize what is known about the role of METTL proteins in stem cell differentiation and highlight the connection between their growing importance in development and their established roles in oncogenesis.
    Keywords:  Cancer; METTL; Metabolism; Methyltransferase; Stem cell; Transcription; Translation
    DOI:  https://doi.org/10.1007/s12015-022-10444-7
  31. Cancer Res. 2022 Sep 14. pii: CAN-22-0963. [Epub ahead of print]
    METTL1-mediated m7G tRNA modification promotes lenvatinib resistance in hepatocellular carcinoma.
    Manling Huang, Jianting Long, Zhijia Yao, Yi Zhao, Yutong Zhao, Junbin Liao, Kai Lei, Han Xiao, Zihao Dai, Sui Peng, Shuibin Lin, Lixia Xu, Ming Kuang.
      The tyrosine kinase inhibitor lenvatinib is a first-line drug for treating patients with advanced hepatocellular carcinoma (HCC). However, its efficacy is severely hampered by drug resistance. Insights into the molecular mechanisms underlying lenvatinib resistance could provide new strategies to improve and prolong responses. Here, we performed unbiased proteomic screening of parental and lenvatinib-resistant HCC cells and discovered that METTL1 and WDR4, the two key components of the tRNA m7G methyltransferase complex, were dramatically upregulated in lenvatinib-resistant cells. METTL1 knockdown overrode resistance by impairing the proliferation capacity of HCC cells and promoting apoptosis under lenvatinib treatment. In addition, overexpression of wild-type METTL1 but not its catalytic dead mutant induced lenvatinib resistance. Animal experiments including hydrodynamic injection, subcutaneous implantation, and orthotopic xenograft mouse models further demonstrated the critical function of METTL1/WDR4-mediated m7G tRNA modification in promoting lenvatinib resistance in vivo. Mechanistically, METTL1 promoted translation of EGFR pathway genes to trigger drug resistance. This work reveals the important role of METTL1-mediated m7G tRNA modification in promoting lenvatinib resistance and provides a promising prediction marker and intervention target for resistance.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-22-0963
  32. J Oncol. 2022 ;2022 4689396
    The Role of N6-Methyladenosine-Associated lncRNAs in the Immune Microenvironment and Prognosis of Colorectal Cancer.
    Congfei Yuan, Caidong Liu, Shuli Zhao, Xishan Zhang, Haifeng Jia, Baiyu Chen, Maojin Zhang, Yuan Zheng, Jin Zhou, Yanzhi Bo.
       Background: The role of N6-methyladenosine long noncoding RNAs (lncRNAs) in colorectal cancer (CRC) is elusive.
    Materials and Methods: We identified m6A-associated lncRNAs by using the data gathered from The Cancer Genome Atlas (TCGA) and stratified CRC patients into different subgroups. Cox regression analysis was performed to construct an m6A-associated lncRNA signature. The role of this signature in the immune microenvironment and prognosis was dissected subsequently. Finally, a gene set enrichment analysis (GSEA) was conducted to predict the possible mechanisms based on the signature.
    Results: Three m6A-associated clusters were constructed from 866 differentially expressed lncRNAs. Cluster 2 had poor prognosis and low immune cell infiltration. An m6A-associated lncRNA signature consisting of 14 lncRNAs was constructed and recognized as an independent prognostic indicator of CRC by using survival analysis and receiver operating characteristic (ROC) curves. The clinical features and immune cell infiltration status were significantly different in patients stratified by the risk score. Furthermore, GSEA showed that the P53 pathway and natural killer cell-mediated cytotoxicity were more enriched in the low-risk group.
    Conclusion: Our data revealed that m6A-associated lncRNAs could be potential prognostic indicators of immunogenicity in CRC.
    DOI:  https://doi.org/10.1155/2022/4689396
  33. Pathol Res Pract. 2022 Sep 06. pii: S0344-0338(22)00358-2. [Epub ahead of print]238 154114
    A potential biomarker of esophageal squamous cell carcinoma WTAP promotes the proliferation and migration of ESCC.
    GaoMeng Luo, Yao Qi, ZhengYao Lei, XiaoYing Shen, MingMin Chen, LiLi Du, CaiXia Wu, JiaQi Bo, ShunLi Wang, Jun Zhao, XiangHua Yi.
      This study focuses on the function of WTAP in esophageal squamous cell carcinoma (ESCC) samples and cell lines. The results showed that WTAP expression in ESCC tissues was significantly upregulated in 78.1% (57 of 73) of the ESCC tissues at the protein level compared with adjacent non-cancerous tissues via immunohistochemical staining. The WTAP protein expression level was positively correlated with the lymph node metastasis and TNM stage, and patients with higher WTAP protein expression level exhibited a shorter overall survival interval. Knocking down WTAP significantly reduced cell proliferation and migration but promoted cell apoptosis of TE-1and KYSE150 cells. Moreover, WTAP inhibition reduced the expression of ki67 and Snail related to cell proliferation and migration but increased the expression of Bax and Caspase-3 which were involved in cell apoptosis. In conclusion, our results suggest that the WTAP, a potential biomarker of ESCC, maybe play an important role in ESCC-genesis through regulating expression of genes related to cell proliferation, migration and apoptosis.
    Keywords:  ESCC; Esophageal squamous cell carcinoma; IHC; Immunohistochemistry; M6A methylation; N6-methyladenosine (m6A) RNA modification; QPCR; Real-time quantitative PCR; TMA; Tissue microarray; WTAP; Wilms' tumor 1-associated protein
    DOI:  https://doi.org/10.1016/j.prp.2022.154114
  34. Environ Toxicol. 2022 Sep 16.
    AKG induces cell apoptosis by inducing reactive oxygen species-mediated endoplasmic reticulum stress and by suppressing PI3K/AKT/mTOR-mediated autophagy in renal cell carcinoma.
    Fan Wu, Xuexia Xie, Guoliang Li, Dongping Bao, Haomin Li, Guohao Wu, Yiqi Lai, Yaping Xing, Peng Ouyang, Guo Chen, Zhifeng Wang, Caiyong Lai.
       BACKGROUND: Alpha-ketoglutarate (AKG) or 2-oxoglutarate is a key substance in the tricarboxylic acid cycle (TCA) and has been known to play an important role in cancerogenesis and tumor progression. Renal cell carcinoma (RCC) is the most common type of kidney cancer, and it has a high mortality rate. Autophagy is a phenomenon of self-digestion, and its significance in tumor genesis and progression remains debatable. However, the mechanisms underlying how AKG regulates autophagy in RCC remain unknown. Thus, the purpose of this study was to assess the therapeutic efficacy of AKG and its molecular mechanisms.
    METHODS: RCC cell lines 786O and ACHN were treated with varying doses of AKG for 24 h. CCK-8, Transwell, and scratch wound healing assays were utilized to evaluate the role of AKG in RCC cells. Autophagy protein and PI3K/AKT/mTOR pathway protein levels were analyzed by Western blot.
    RESULTS: AKG inhibited the proliferation of RCC cells 786O and ACHN in a dose-dependent manner according to the CCK-8 assay. In addition, flow cytometry and Western blot analysis revealed that AKG dose-dependently triggered apoptosis and autophagy in RCC cells. By promoting cell apoptosis and autophagy, AKG dramatically suppressed tumor growth. Mechanistically, AKG induces autophagy by promoting ROS generation and inhibiting the PI3K/AKT/mTOR pathway.
    CONCLUSIONS: The anti-tumor effect of AKG promotes autophagy in renal cancer cells via mediating ROS-PI3K/Akt/mTOR, and may be used as a potential anticancer drug for kidney cancer.
    Keywords:  PI3K/AKT/mTOR; ROS; alpha-ketoglutarate; kidney cancer
    DOI:  https://doi.org/10.1002/tox.23658
  35. Front Genet. 2022 ;13 920164
    m5C Regulator-mediated methylation modification clusters contribute to the immune microenvironment regulation of multiple myeloma.
    Hefei Ren, Chang Liu, Hongkun Wu, Zhenhua Wang, Sai Chen, Xiaomin Zhang, Jigang Ren, Huiying Qiu, Lin Zhou.
      Background: Multiple myeloma (MM) is a hematological malignancy in which plasma cells proliferate abnormally. 5-methylcytosine (m5C) methylation modification is the primary epigenetic modification and is involved in regulating the occurrence, development, invasion, and metastasis of various tumors; however, its immunological functions have not been systematically described in MM. Thus, this study aimed to clarify the significance of m5C modifications and how the immune microenvironment is linked to m5C methylation in MM. Method: A total of 483 samples (60 healthy samples, 423 MM samples) from the Gene Expression Omnibus dataset were acquired to assess the expression of m5C regulators. A nomogram model was established to predict the occurrence of MM. We investigated the impact of m5C modification on immune microenvironment characteristics, such as the infiltration of immunocytes and immune response reactions. We then systematically evaluated three different m5C expression patterns to assess immune characteristics and metabolic functional pathways and established m5C-related differentially expressed genes (DEGs). In addition, biological process analysis was performed and an m5C score was constructed to identify potentially significant immunological functions in MM. Result: Differential expressions of m5C regulators were identified between healthy and MM samples. The nomogram revealed that m5C regulators could predict higher disease occurrence of MM. We identified three distinct m5C clusters with unique immunological and metabolic characteristics. Among the three different m5C clusters, cluster C had more immune characteristics and more metabolism-related pathways than clusters A and B. We analyzed 256 m5C-related DEGs and classified the samples into three different m5C gene clusters. Based on the m5C and m5C gene clusters, we calculated m5C scores and classified each patient into high- and low-m5C score groups. Conclusion: Our study demonstrated that m5C modification is involved in and contributes to the diversity and complexity of the immune microenvironment, which offers promise for the development of accurate therapeutic strategies.
    Keywords:  5-methylcytosine; biological function; immune microenvironment; immune therapy; multiple myeloma
    DOI:  https://doi.org/10.3389/fgene.2022.920164
  36. J Cell Mol Med. 2022 Sep 13.
    LncRNA ALKBH3-AS1 enhances ALKBH3 mRNA stability to promote hepatocellular carcinoma cell proliferation and invasion.
    Qiliang Lu, Hao Wang, Xiangxiang Lei, Qiancheng Ma, Jie Zhao, Wen Sun, Cheng Guo, Dongsheng Huang, Qiuran Xu.
      Long noncoding RNAs (lncRNAs) are confirmed as the key regulators of hepatocellular carcinoma (HCC) occurrence and progression, but the role of AlkB homologue 3 antisense RNA 1 (ALKBH3-AS1) in HCC is unclear. We revealed the overexpression of ALKBH3-AS1 in HCC tissues. The upregulated levels of ALKBH3-AS1 were observed in HCC cells. ALKBH3-AS1 was expressed in the nucleus and cytoplasm of HCC cells. The high ALKBH3-AS1 expression was markedly associated with a decreased survival rate of HCC patients. ALKBH3-AS1 knockdown repressed and ALKBH3-AS1 overexpression enhanced HCC cell invasion and proliferation. ALKBH3-AS1 silencing restricted HCC growth in vivo. A significant positive correlation between ALKBH3-AS1 and ALKBH3 mRNA levels was confirmed in HCC specimens. ALKBH3-AS1 silencing reduced ALKBH3 expression by stabilizing its mRNA stability in HCC cells. Notably, the impact of ALKBH3 silencing on HCC cells was similar to that of ALKBH3-AS1 knockdown. ALKBH3 restoration prominently attenuated the suppressive effects resulting from ALKBH3-AS1 silencing in HCCLM3 cells. Hypoxia-inducible factor-1α (HIF-1α) transcriptionally activated ALKBH3-AS1 expression in hypoxic HCC cells. ALKBH3-AS1 knockdown markedly attenuated cell proliferation and invasion in hypoxic Huh7 cells. Collectively, HIF-1α-activated ALKBH3-AS1 exerted an oncogenic role by enhancing ALKBH3 mRNA stability in HCC cells.
    Keywords:  ALKBH3; ALKBH3-AS1; hepatocellular carcinoma; hypoxia; mRNA stability
    DOI:  https://doi.org/10.1111/jcmm.17558
  37. Reproduction. 2022 Sep 01. pii: REP-22-0169. [Epub ahead of print]
    Inhibition of METTL5 improves preimplantation development of mouse somatic cell nuclear transfer embryos.
    Luchun Zhang, Meng Yuan, Xingwei Huang, Qianzi Cao, Shaogang Huang, Ruizhen Sun, Lei Lei.
      N6-methyladenosine (m6A) is one of the most important epigenetic modifications in eukaryotic RNAs that regulates development and diseases. It is identified by several proteins. Methyltransferase-like 5 (METTL5), an enzyme that methylates 18S rRNA m6A, controls the translation of proteins and regulates pluripotency in embryonic stem cells (ESC). However, the functions of METTL5 in embryonic development have not been explored. Here, we found that Mettl5 was upregulated in somatic cell nuclear transfer (SCNT) embryos compared with normal fertilized embryos. Therefore, we hypothesized that METTL5 knockdown during the early stage of SCNT would improve the developmental rate of SCNT embryos. Notably, injection of Mettl5 small interfering RNA (si-Mettl5) into enucleated oocytes during nuclear transfer increased the rate of development and the number of cells in blastocysts. Moreover, inhibition of METTL5 reduced the activity of phosphorylated ribosomal protein S6, decreased the levels of the repressive histone modification H3K27me3, and increased the expression of activating histone modifications H3K27ac and H3K4me3 and mRNA levels of some 2-cell-specific genes. These results expand our understanding of the role of METTL5 in early embryonic development, and provide a novel idea for improving the efficiency of nuclear transfer cloning.
    DOI:  https://doi.org/10.1530/REP-22-0169
  38. Cancer Sci. 2022 Sep 17.
    m6A modification-mediated lncRNA TP53TG1 inhibits gastric cancer progression by regulating CIP2A stability.
    Deliang Fang, Xinde Ou, Kaiyu Sun, Xingyu Zhou, Youpei Li, Peng Shi, Zirui Zhao, Yulong He, Jianjun Peng, Jianbo Xu.
      Long noncoding RNAs (lncRNAs) are associated with various types of cancer. However, the precise roles of many lncRNAs in tumor progression remain unclear. In this study, we found that the expression of the lncRNA TP53TG1 was downregulated in gastric cancer (GC) and it functioned as a tumor suppressor. In addition, low TP53TG1 expression was significantly associated with poor survival in patients with GC. TP53TG1 inhibited the proliferation, metastasis, and cell cycle progression, while promoted the apoptosis of GC cells. m6A modification sites are highly abundant on TP53TG1, and demethylase ALKBH5 reduces TP53TG1 stability and downregulates its expression. TP53TG1 interacts with cancerous inhibitor of protein phosphatase 2A (CIP2A) and triggers its ubiquitination-mediated degradation, resulting in the inhibition of PI3K/AKT pathway. These results suggest that TP53TG1 plays an important role in inhibiting the progression of GC and provides a crucial target for GC treatment.
    Keywords:  ALKBH5; CIP2A; PI3K/AKT; TP53TG1; gastric cancer
    DOI:  https://doi.org/10.1111/cas.15581
  39. J Hazard Mater. 2022 Aug 31. pii: S0304-3894(22)01636-3. [Epub ahead of print]441 129843
    Changes in the m6A RNA methylome accompany the promotion of soybean root growth by rhizobia under cadmium stress.
    Xue Han, Jialin Wang, Yu Zhang, Youlin Kong, Huiying Dong, Xuezhen Feng, Tianshu Li, Changjun Zhou, Jidong Yu, Dawei Xin, Qingshan Chen, Zhaoming Qi.
      Cadmium (Cd) is the most widely distributed heavy metal pollutant in soil and has significant negative effects on crop yields and human health. Rhizobia can enhance soybean growth in the presence of heavy metals, and the legume-rhizobia symbiosis has been used to promote heavy-metal phytoremediation, but much remains to be learned about the molecular networks that underlie these effects. Here, we demonstrated that soybean root growth was strongly suppressed after seven days of Cd exposure but that the presence of rhizobia largely eliminated this effect, even prior to nodule development. Moreover, rhizobia did not appear to promote root growth by limiting plant Cd uptake: seedlings with and without rhizobia had similar root Cd concentrations. Previous studies have demonstrated a role for m6A RNA methylation in the response of rice and barley to Cd stress. We therefore performed transcriptome-wide m6A methylation profiling to investigate changes in the soybean RNA methylome in response to Cd with and without rhizobia. Here, we provide some of the first data on transcriptome-wide m6a RNA methylation patterns in soybean; m6A modifications were concentrated at the 3' UTR of transcripts and showed a positive relationship with transcript abundance. Transcriptome-wide m6A RNA methylation peaks increased in the presence of Cd, and the integration of m6A methylome and transcriptome results enabled us to identify 154 genes whose transcripts were both differentially methylated and differentially expressed in response to Cd stress. Annotation results suggested that these genes were associated with Ca2+ homeostasis, ROS pathways, polyamine metabolism, MAPK signaling, hormones, and biotic stress responses. There were 176 differentially methylated and expressed transcripts under Cd stress in the presence of rhizobia. In contrast to the Cd-only gene set, they were also enriched in genes related to auxin, jasmonic acid, and brassinosteroids, as well as abiotic stress tolerance. They contained fewer genes related to Ca2+ homeostasis and also included candidates with known functions in the legume-rhizobia symbiosis. These findings offer new insights into how rhizobia promote soybean root growth under Cd stress; they provide candidate genes for research on plant heavy metal responses and for the use of legumes in phytoremediation.
    Keywords:  Cd stress; N6-methyladenosine (m6A) modification; Rhizobia; Soybean root
    DOI:  https://doi.org/10.1016/j.jhazmat.2022.129843
  40. Front Endocrinol (Lausanne). 2022 ;13 947708
    Prognostic model based on m6A-associated lncRNAs in esophageal cancer.
    Weidong Wang, Danhong Dong, Pengfei Yu, Tong Chen, Ruiqi Gao, Jiangpeng Wei, Zhenchang Mo, Haikun Zhou, Qinchuan Yang, Chao Yue, Xisheng Yang, Xiaohua Li, Gang Ji.
       Background: This research aimed to build an m6A-associated lncRNA prognostic model of esophageal cancer that can be used to predict outcome in esophageal cancer patients.
    Methods: RNA sequencing transcriptome data and clinical information about patients with esophageal cancer were obtained according to TCGA. Twenty-four m6A-associated genes were selected based on previous studies. m6A-associated lncRNAs were determined through Pearson correlation analysis. Three m6A-associated lncRNA prognostic signatures were built through analysis of the training set using univariate, LASSO, and multivariate Cox regression. To validate the stabilization of the risk signature, Kaplan-Meier and ROC curve analyses were performed on the testing and complete sets. The prognoses of EC patients were predicted quantitatively by building a nomogram. GSEA was conducted to analyze the underlying signaling pathways and biological processes. To identify the underlying mechanisms through which the lncRNAs act, we constructed a PPI network and a ceRNA network and conducted GO and KEGG pathway analyses. EC samples were evaluated using the ESTIMATE algorithm to compute stromal, immune, and estimate scores. The ssGSEA algorithm was used to quantitatively infer immune cell infiltration and immune functions. The TIDE algorithm was performed to simulate immune evasion and predict the response to immunotherapy.
    Results: We identified and validated an m6A-associated lncRNA risk model in EC that could correctly and reliably predict the OS of EC patients. The ceRNA network, PPI network, and GO and KEGG pathway analyses confirmed and the underlying mechanisms and functions provided enlightenment regarding therapeutic strategies for EC. Immunotherapy responses were better in the low-risk subgroup, and PD-1 and CTLA4 checkpoint immunotherapy benefited the patients in the low-risk subgroup.
    Conclusions: We constructed a new m6A-related lncRNA prognostic risk model of EC, based on three m6A-related lncRNAs: LINC01612, AC025166.1 and AC016876.2, that can predict the prognoses of EC patients.
    Keywords:  bioinformatics; esophageal cancer; lncRNA; m6A; prognostic signature
    DOI:  https://doi.org/10.3389/fendo.2022.947708
  41. J Adv Res. 2022 09;pii: S2090-1232(21)00235-6. [Epub ahead of print]40 153-166
    Prognostic value of JAK3 promoter methylation and mRNA expression in clear cell renal cell carcinoma.
    Qian Long, Chunyu Huang, Jinsheng Huang, Qi Meng, Yanjun Cheng, Yilin Li, Liru He, Miao Chen, Changlin Zhang, Xiaonan Wang, Wancui Zhu, Jin Peng, Dingbo Shi, Fufu Zheng, Pei Dong, Wuguo Deng.
       INTRODUCTION: Janus kinase 3 (JAK3) is a well-established oncogene in clear cell renal cell carcinoma (ccRCC). The methylation status of oncogene promoters has emerged as biomarkers for cancer diagnosis and prognosis.
    OBJECTIVE: This study aims to investigate the biological and clinical significance of JAK3 promoter methylation in ccRCC.
    METHODS: We analyzed the relationship of JAK3 promoter methylation with its mRNA expression, overall survival, and immune cell infiltration in a cohort obtained from The Cancer Genome Atlas (TCGA), which was further validated by another independent cohort. We further validated correlations of JAK3 promoter methylation with JAK3 expression, overall survival, and immune cell infiltration in an independent ccRCC cohort (Sun Yat-sen University Cancer Center (SYSUCC) cohort) by methods of immunohistochemistry (IHC) and pyrosequencing.
    RESULTS: We found JAK3 promoter was significantly hypomethylated in tumor tissues compared to normal adjacent tissues in ccRCC, and JAK3 promoter hypomethylation was strongly correlated with high JAK3 mRNA expression in all three ccRCC cohorts we examined. JAK3 promoter hypomethylation predicted advanced clinicopathological characteristics and shorter overall survival (TCGA cohort and SYSUCC cohort). Furthermore, we found that JAK3 promoter methylation was significantly associated with immune cell infiltration and expression of immune checkpoint molecules (TCGA cohort and CPTAC cohort). Finally, our SYSUCC cohort validated that JAK3 promoter methylation was correlated with CD4+ and CD8+ T cell infiltration in ccRCC tumor tissues.
    CONCLUSION: Our data demonstrated that the crucial role of JAK3 promoter methylation in its expression regulation and tumor microenvironment. JAK3 promoter methylation and expression are associated with clinicopathological characteristics, overall survival, and immune cell infiltration in ccRCC. We propose a rationale for further validation of JAK3 promoter methylation as a molecular biomarker for predicting responses to immune checkpoint inhibitors in ccRCC.
    Keywords:  Epigenetic biomarker; Janus kinase 3; Renal cell carcinoma; Tumor immune cell infiltration; Tumor immune microenvironment
    DOI:  https://doi.org/10.1016/j.jare.2021.11.016
  42. J Obstet Gynaecol Res. 2022 Sep 13.
    Identification and construction of a prognostic risk model based on multi-RNA methylation regulators in cervical cancer.
    Xiaoling Yan, Yuan Qu, Wenxuan Huang, Hao Zhang, Lei Zhu, Liying Zhang.
       AIM: Cervical cancer is one of the most aggressive female cancers. RNA methylation is a necessary epigenetic modification in biological process. This study aimed to construct an RNA methylation regulator-based risk model for predicting the prognosis of cervical cancer patients.
    METHODS: The transcriptome profiles of cervical cancer data were obtained from The Cancer Genome Atlas (TCGA) and GSE44001. An RNA methylation-related risk model was constructed and assessed by the Least absolute shrinkage and selection operator (Lasso)-penalized Cox regression model and receiver operating characteristic (ROC). Kaplan-Meier and Cox regression analyses were used to evaluate the prognostic effect of the risk model and calculated scores. The immune infiltration difference was further analyzed between the subgroups with a single-sample gene set enrichment analysis (ssGSEA).
    RESULTS: A total of 63 methylation modulators were included in this study, and 618 cervical cancer patients were identified from TCGA and GSE44001. Differential expression genes profiling RNA methylation regulators between normal and tumor samples were distinct. A four-gene signature panel was constructed to predict the prognostic risk. The predictive ability was satisfactory. Cervical cancer patients were classified into high- or low-risk subgroups according to the median risk score. Moreover, the immune infiltration patterns between them differed.
    CONCLUSIONS: A risk model including four RNA methylation regulators was constructed, which will provide new perspectives for further investigation of the relationship between RNA methylation and cervical cancer.
    Keywords:  RNA methylation; cervical cancer; immune infiltration; prognosis; risk model
    DOI:  https://doi.org/10.1111/jog.15421
  43. Cell Rep. 2022 Sep 13. pii: S2211-1247(22)01157-3. [Epub ahead of print]40(11): 111329
    Histone H1 regulates non-coding RNA turnover on chromatin in a m6A-dependent manner.
    José Miguel Fernández-Justel, Cristina Santa-María, Sara Martín-Vírgala, Shreya Ramesh, Alberto Ferrera-Lagoa, Mónica Salinas-Pena, Javier Isoler-Alcaraz, Magdalena M Maslon, Albert Jordan, Javier F Cáceres, María Gómez.
      Linker histones are highly abundant chromatin-associated proteins with well-established structural roles in chromatin and as general transcriptional repressors. In addition, it has been long proposed that histone H1 exerts context-specific effects on gene expression. Here, we identify a function of histone H1 in chromatin structure and transcription using a range of genomic approaches. In the absence of histone H1, there is an increase in the transcription of non-coding RNAs, together with reduced levels of m6A modification leading to their accumulation on chromatin and causing replication-transcription conflicts. This strongly suggests that histone H1 prevents non-coding RNA transcription and regulates non-coding transcript turnover on chromatin. Accordingly, altering the m6A RNA methylation pathway rescues the replicative phenotype of H1 loss. This work unveils unexpected regulatory roles of histone H1 on non-coding RNA turnover and m6A deposition, highlighting the intimate relationship between chromatin conformation, RNA metabolism, and DNA replication to maintain genome performance.
    Keywords:  CP: Molecular biology; R-loops; chromatin RNAs; chromatin conformation; histone H1; lncRNAs; m6A; mESCs; replication-transcription conflicts; replicative stress
    DOI:  https://doi.org/10.1016/j.celrep.2022.111329
  44. Cancer Sci. 2022 Sep 17.
    ROS inhibits RORα degradation by decreasing its arginine methylation in liver cancer.
    Hyuntae Im, Hee-Ji Baek, Eunbi Yang, Kyeongkyu Kim, Se Kyu Oh, Jung-Shin Lee, Hyunkyung Kim, Ji Min Lee.
      Retinoic acid receptor-related orphan receptor α (RORα) is a transcription factor involved in nuclear gene expression and a known tumor suppressor. RORα was the first identified substrate of lysine methylation-dependent degradation. However, the mechanisms of other post-translational modifications (PTMs) that cause RORα remain largely unknown, especially in liver cancer. Arginine methylation is a common PTM in arginine residues of non- and histone proteins and affects substrate protein function and fate. We found a conserved amino acid sequence, including R37 in the RORα N-terminus compared to histone H3. Here, we provide evidence that R37 methylation-dependent degradation is carried out by protein arginine methyltransferase 5 (PRMT5). Further, we discovered that PRMT5 regulated the interaction between the E3 ubiquitin ligase ITCH and RORα through RORα arginine methylation. Arginine methylation-dependent ubiquitination-mediated RORα degradation reduced downstream target gene activation. H2 O2 -induced reactive oxygen species (ROS) decreased PRMT5 protein levels, consequently increasing RORα protein levels in HepG2 liver cancer cells. In addition, ROS inhibited liver cancer progression by inducing apoptosis via PRMT5-mediated RORα methylation and the ITCH axis. Our results potentiate PRMT5 as an elimination target in cancer therapy, and this additional regulatory level within ROS signaling may help identify new targets for therapeutic intervention in liver cancer.
    Keywords:  Arginine methylation; RORα-PRMT5-ITCH; ROS; liver cancer; methyl-degron
    DOI:  https://doi.org/10.1111/cas.15595
  45. Gynecol Oncol. 2022 Sep 13. pii: S0090-8258(22)00589-3. [Epub ahead of print]
    Cancer-associated fibroblasts-derived FMO2 as a biomarker of macrophage infiltration and prognosis in epithelial ovarian cancer.
    Sihui Yu, Rui Yang, Tianhan Xu, Xi Li, Sufang Wu, Jiawen Zhang.
       OBJECTIVE: Recent molecular profiling revealed that cancer-associated fibroblasts (CAFs) are essential for matrix remodeling and tumor progression. Our study aimed to investigate the role of flavin-containing monooxygenase 2 (FMO2) in epithelial ovarian cancer (EOC) as a novel CAF-derived prognostic biomarker.
    METHODS: Primary fibroblasts were isolated from EOC samples. Microdissection and single-cell RNA sequencing (scRNA-seq) datasets (including TCGA, GSE9891, GSE63885, GSE118828 and GSE178913) were retrieved to determine the expression profiles. Gene set enrichment analysis (GSEA) was used to explore the correlation between FMO2 and stromal activation as well as immune infiltration. The predictive value of FMO2 and combined macrophage infiltration level was verified in an independent EOC cohort (n = 113).
    RESULTS: We demonstrated that FMO2 was upregulated in tumor stroma and correlated with fibroblast activation. Besides, FMO2 had the predictive power for worse clinical outcome of EOC patients. In the mesenchymal subtype of EOC, the FMO2-defined signature revealed that FMO2 contributed to infiltration of tumor-infiltrating lymphocytes. Moreover, we confirmed the positive correlation between FMO2 and CD163+ cell infiltration level in EOC tissues, and showed that combination of FMO2 expression with CD163+ cell infiltration level in the tumor stroma could predict poor overall survival (HR = 3.63, 95% CI = 1.93-6.84, p = 0.0008). Additionally, FMO2 also predicted the prognosis of patients with ovarian cancer based on the expression of immune checkpoints (such as PD-L1 and PD1).
    CONCLUSION: Our results address the tumor-supporting role of FMO2 in EOC and its association with immune components, and it might be a prospective target for stroma-oriented therapies against EOC.
    Keywords:  Cancer-associated fibroblasts; Epithelial ovarian cancer; FMO2; Macrophage; Tumor microenvironment
    DOI:  https://doi.org/10.1016/j.ygyno.2022.09.003
  46. Cancer Res. 2022 Sep 16. pii: CAN-22-1203. [Epub ahead of print]
    MEX3C-mediated decay of SOCS3 mRNA promotes JAK2/STAT3 signaling to facilitate metastasis in hepatocellular carcinoma.
    Yunyun Xiao, Yue Li, Dongni Shi, Xiaoqing Wang, Shuqin Dai, Muwen Yang, Lingzhi Kong, Boyu Chen, Xinjian Huang, Chuyong Lin, Wenting Liao, Benke Xu, Xin Chen, Lishuai Wang, Xiangfu Chen, Ying Ouyang, Guozhen Liu, Heping Li, Libing Song.
      Tumor metastasis is one of the major causes of high mortality in patients with hepatocellular carcinoma (HCC). Sustained activation of STAT3 signaling plays a critical role in HCC metastasis. RNA binding protein (RBP)-mediated post-transcriptional regulation is involved in the precise control of signal transduction, including STAT3 signaling. In this study, we investigated whether RBPs are important regulators of HCC metastasis. The RBP MEX3C was found to be significantly upregulated in highly metastatic HCC and correlated with poor prognosis in HCC. Mechanistically, MEX3C increased JAK2/STAT3 pathway activity by downregulating SOCS3, a major negative regulator of JAK2/STAT3 signaling. MEX3C interacted with the 3'UTR of SOCS3 and recruited CNOT7 to ubiquitinate and accelerate decay of SOCS3 mRNA. Treatment with MEX3C-specific antisense oligonucleotide (ASO) significantly inhibited JAK2/STAT3 pathway activation, suppressing HCC migration in vitro and metastasis in vivo. These findings highlight a novel mRNA decay-mediated mechanism for the disruption of SOCS3-driven negative regulation of JAK2/STAT3 signaling, suggesting MEX3C may be a potential prognostic biomarker and promising therapeutic target in HCC.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-22-1203
  47. Cancer Sci. 2022 Sep 14.
    HMGA2 drives the IGFBP1/AKT pathway to counteract the increase in P27KIP1 protein levels in mtDNA/RNA-less cancer cells.
    Tsuyoshi Maruyama, Koji Saito, Masato Higurashi, Fumihiro Ishikawa, Yohko Kohno, Kazunori Mori, Motoko Shibanuma.
      Recent comprehensive analyses of mtDNA and orthogonal RNA-sequencing data revealed that in numerous human cancers, mtDNA copy numbers and mtRNA amounts are significantly reduced, followed by low respiratory gene expression. Under such conditions (called mt-Low), cells encounter severe cell proliferation defects; thus, they must acquire countermeasures against this fatal disadvantage during malignant transformation. This study elucidated a countermeasure against the mt-Low condition-induced antiproliferative effects in hepatocellular carcinoma (HCC) cells. The mechanism relied on the architectural transcriptional regulator HMGA2, which was preferably expressed in HCC cells of the mt-Low type in vitro and in vivo. Detailed in vitro analyses suggest that HMGA2 regulates insulin-like growth factor binding protein 1 (IGFBP1) expression, leading to AKT activation, which then phosphorylates the cyclin-dependent kinase inhibitor (CKI), P27KIP1, and facilitates its ubiquitin-mediated degradation. Accordingly, intervention in the HMGA2 function by RNAi resulted in an increase in P27KIP1 levels and an induction of senescence-like cell proliferation inhibition in mt-Low-type HCC cells. Conclusively, the HMGA2/IGFBP1/AKT axis has emerged as a countermeasure against P27KIP1 CKI upregulation under mt-Low conditions, thereby circumventing cell proliferation inhibition and supporting the tumorigenic state. Notably, similar to in vitro cell lines, HMGA2 was likely to regulate IGFBP1 expression in HCC in vivo, thereby contributing to poor patient prognosis. Considering the significant number of cases under mt-Low or the threat of CKI upregulation cancer-wide, the axis is noteworthy as a vulnerability of cancer cells or target for tumor-agnostic therapy inducing irreversible cell proliferation inhibition via CKI upregulation in a large population with cancer.
    Keywords:  HMGA2; IGFBP1; P27KIP1; hepatocellular carcinoma; mitochondria-deficiency
    DOI:  https://doi.org/10.1111/cas.15582
  48. Biology (Basel). 2022 Jun 29. pii: 988. [Epub ahead of print]11(7):
    Neuronal Depolarization Induced RNA m5C Methylation Changes in Mouse Cortical Neurons.
    Xiguang Xu, Zachary Johnson, Hehuang Xie.
      Neuronal activity is accomplished via substantial changes in gene expression, which may be accompanied by post-transcriptional modifications including RNA cytosine-5 methylation (m5C). Despite several reports on the transcriptome profiling of activated neurons, the dynamics of neuronal mRNA m5C modification in response to environmental stimuli has not been explored. Here, we provide transcriptome-wide maps of m5C modification, together with gene expression profiles, for mouse cortical neurons at 0 h, 2 h, and 6 h upon membrane depolarization. Thousands of differentially expressed genes (DEGs) were identified during the neuronal depolarization process. In stimulated neurons, the majority of early response genes were found to serve as expression regulators of late response genes, which are involved in signaling pathways and diverse synaptic functions. With RNA bisulfite sequencing data, a union set of 439 m5C sites was identified with high confidence, and approximately 30% of them were shared by neurons at all three time points. Interestingly, over 41% of the m5C sites showed increased methylation upon neuronal activation and were enriched in transcripts coding for proteins with synaptic functions. In addition, a modest negative correlation was observed between RNA expression and methylation. In summary, our study provided dynamic transcriptome-wide landscapes of RNA m5C methylation in neurons, and revealed that mRNA m5C methylation is associated with the regulation of gene expression.
    Keywords:  RNA bisulfite sequencing; RNA cytosine-5 methylation; RNA-seq; gene expression; neuronal depolarization
    DOI:  https://doi.org/10.3390/biology11070988
  49. J Oncol. 2022 ;2022 5240611
    N6-Methyladenosine (m6A)-Related lncRNAs Are Potential Signatures for Predicting Prognosis and Immune Response in Lung Squamous Cell Carcinoma.
    Yang Zhou, Xuhui Guan, Shuncong Wang, Huanhuan Sun, Haiqing Ma.
       Background: Despite increasing understanding of m6A-related lncRNAs in lung cancer, the role of m6A-related lncRNAs in the prognosis and treatment of lung squamous cell carcinoma is poorly understood to date. Thus, the current study aims to elucidate its role and build a model to predict the prognosis of LUSC patients.
    Materials and Methods: The data of the current study were accessed from the TCGA database. Pearson correlation analysis was performed to identify lncRNAs correlated to m6A. Next, an m6A-related lncRNAs risk model was built using a single factor, least absolute association, selection operator, and multivariate Cox regression analysis.
    Results: The relevance between 23 m6A genes and 14,056 lncRNAs is shown by Pearson correlation analysis by Sankey diagram. Multivariate Cox regression analysis determined that 11 m6A-lncRNAs show predictive potential in prognosis, which is confirmed by the consistency index, Kaplan-Meier analysis, principal component analysis, and ROC curve. Additionally, the immune analysis showed that the enrichment of immune cells, major histocompatibility complex molecules, and immune checkpoints in the high and low-risk subgroups were markedly disparate, with the high-risk group showing a stronger immune escape ability and a worse response to immunotherapy.
    Conclusion: In conclusion, the risk model based on m6A-related lncRNAs showed great promise in predicting the prognosis and the efficacy of immunotherapy.
    DOI:  https://doi.org/10.1155/2022/5240611
This page is being maintained by Thomas Krichel. It was last updated on 2024‒11‒22 at 4:28.