bims-rimeca Biomed News
on RNA methylation in cancer
Issue of 2022–10–02
38 papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics
  1. WTAP promotes oesophageal squamous cell carcinoma development by decreasing CPSF4 expression in an m6A-dependent manner.
  2. METTL3 suppresses anlotinib sensitivity by regulating m6A modification of FGFR3 in oral squamous cell carcinoma.
  3. Characterization of m6A methylation modifications and tumor microenvironment infiltration in thyroid cancer.
  4. The m6A methyltransferase METTL3 promotes trophoblast cell invasion by regulating MYLK expression.
  5. N6-methyladenosine reader YTHDF3 contributes to the aerobic glycolysis of osteosarcoma through stabilizing PGK1 stability.
  6. WTAP mediated the N6-methyladenosine modification of PDK4 to regulate the malignant behaviors of colorectal cancer cells in vitro and in vivo.
  7. Identification of clinical prognostic features of esophageal cancer based on m6A regulators.
  8. m6A RNA methylation in brain injury and neurodegenerative disease.
  9. m6A-induced lncDBET promotes the malignant progression of bladder cancer through FABP5-mediated lipid metabolism.
  10. N6-methyladenosine regulators are potential prognostic biomarkers for multiple myeloma.
  11. FTO promotes liver inflammation by suppressing m6A mRNA methylation of IL-17RA.
  12. The functions of N6-methyladenosine (m6A) RNA modifications in colorectal cancer.
  13. N6-methyladenosine modification on Hmbox1 is related to telomere dysfunction in DEHP-induced male reproductive injury.
  14. The role of RNA m6A methylation in lipid metabolism.
  15. A programmable system to methylate and demethylate N6-Methyladenosine (m6A) on specific RNA transcripts in mammalian cells.
  16. Significance of m6A regulatory factor in gene expression and immune function of osteoarthritis.
  17. METTL3 Attenuates Inflammation in Fusarium solani-Induced Keratitis via the PI3K/AKT Signaling Pathway.
  18. METTL16 predicts a favorable outcome and primes antitumor immunity in pancreatic ductal adenocarcinoma.
  19. Effects of writers, erasers and readers within miRNA-related m6A modification in cancers.
  20. The N6-methyladenosine-mediated lncRNA WEE2-AS1 promotes glioblastoma progression by stabilizing RPN2.
  21. WTAP mediates FOXP3 mRNA stability to promote SMARCE1 expression and augment glycolysis in colon adenocarcinoma.
  22. Identification of molecular patterns and diagnostic biomarkers in juvenile idiopathic arthritis based on the gene expression of m6A regulators.
  23. Modification of m6A mediates tissue immune microenvironment in calcific aortic valve disease.
  24. Analysis of N6-Methyladenosine RNA Methylation Regulators in Diagnosis and Distinct Molecular Subtypes of Ankylosing Spondylitis.
  25. Geographic encoding of transcripts enabled high-accuracy and isoform-aware deep learning of RNA methylation.
  26. m6A transferase METTL3 regulates endothelial-mesenchymal transition in diabetic retinopathy via lncRNA SNHG7/KHSRP/MKL1 axis.
  27. A bibliometric analysis of RNA methylation in diabetes mellitus and its complications from 2002 to 2022.
  28. m6A RNA methylation regulator-related signatures exhibit good prognosis prediction ability for head and neck squamous cell carcinoma.
  29. Comprehensive analysis about prognostic and immunological role of WTAP in pan-cancer.
  30. Positive epigenetic regulation loop between AR and NSUN2 promotes prostate cancer progression.
  31. Circ-CTNNB1 drives aerobic glycolysis and osteosarcoma progression via m6A modification through interacting with RBM15.
  32. Four types of RNA modification writers predict the prognosis of prostate cancer.
  33. Comprehensive analysis of the expression of N6-methyladenosine RNA methylation regulators in pulmonary artery hypertension.
  34. Interruption of aberrant chromatin looping is required for regenerating RB1 function and suppressing tumorigenesis.
  35. Long-term exercise training down-regulates m6A RNA demethylase FTO expression in the hippocampus and hypothalamus: an effective intervention for epigenetic modification.
  36. Histocompatibility Minor 13 (HM13), targeted by miR-760, exerts oncogenic role in breast cancer by suppressing autophagy and activating PI3K-AKT-mTOR pathway.
  37. Cryo-EM structures of human m6A writer complexes.
  38. M 6A RNA Methylation-Based Epitranscriptomic Modifications in Plasticity-Related Genes via miR-124-C/EBPα-FTO-Transcriptional Axis in the Hippocampus of Learned Helpless Rats.
  1. Med Oncol. 2022 Sep 29. 39(12): 231
    WTAP promotes oesophageal squamous cell carcinoma development by decreasing CPSF4 expression in an m6A-dependent manner.
    Qian Luo, Xuebing Zhan, Yunshu Kuang, Mingzhong Sun, Fangyuan Dong, Entao Sun, Bing Chen.
      m6A is a widespread RNA modification. However, the mechanism through which m6A regulated the progress of oesophageal squamous cell carcinoma (ESCC) remains undetermined. The levels and prognosis of WTAP were analysed using an ESCC tissue microarray (87 ESCC and 44 paracancerous tissues). TCGA and Oncolnc databases validate WTAP expression and prognosis. CCK8, colony formation (CF), wound healing, transwell cell invasion (CI), and migration (CM) assays were employed for the detection of the biological impacts of WTAP. Expression of tumour stemness-related genes was assessed via qRT-PCR and western blotting. The m6A RNA methylation (m6AMe) quantitative kit was employed for cellular methylation level detection. Arraystar m6A-mRNA and lncRNA epitranscriptomic microarray analyses were used to screen low methylation, high expression, and prognosis-related candidate gene CPSF4. KEGG enrichment analysis was used to screen the downstream signalling pathways of CPSF4. WTAP, a methyltransferase "writer", was markedly enhanced in ESCC and was strongly correlated with poor patient outcome. WTAP knockdown inhibited the cell proliferation (CP), CI, CM, and stemness of ESCC cells in vitro and reduced the overall m6A modification (m6AMo) percentage of ESCC cells. CPSF4 is a target of WTAP-based m6AMo. WTAP-based m6AMo of CPSF4 transcript reduced the stability of CPSF4 by relying on YTHDF2. We identified the significant role of WTAP-catalysed m6AMo in ESCC tumourigenesis, wherein it facilitates ESCC tumour growth and metastasis through decreasing CPSF4 expression in an m6A-dependent manner.
    Keywords:  CPSF4; N6-methyladenosine; Oesophageal squamous cell carcinoma; WTAP
    DOI:  https://doi.org/10.1007/s12032-022-01830-9
  2. Cancer Cell Int. 2022 Sep 27. 22(1): 295
    METTL3 suppresses anlotinib sensitivity by regulating m6A modification of FGFR3 in oral squamous cell carcinoma.
    Jie Chen, Shuai Li, Zhexun Huang, Congyuan Cao, Anxun Wang, Qianting He.
       BACKGROUND: N6-methyladenosine (m6A) is an abundant nucleotide modification in mRNA, but there were few studies on its role in cancer drug sensitivity and resistance. Anlotinib has been proved to have effective antitumor effects in oral squamous cell carcinoma (OSCC) in our previous study. Here, we sought to investigate the treatment target of anlotinib and the function and mechanisms of m6A modification in regulating anlotinib effect in OSCC.
    METHODS: Anlotinib treatment in a dose-dependent manner, western blotting, qRT-PCR and cell lost-of-function assays were used to study the treatment target of anlotinib in OSCC. RNA m6A dot blot assays, the m6A MeRIP-seq and MeRIP-qPCR, RNA and protein stability assays were used to explore the m6A modification of the treatment target of anlotinib. Cell lost-of-function assays after METTL3 depletion were conducted to investigate the effect of m6A modification level on the therapeutic effect of anlotinib in OSCC. Patient-derived tumor xenograft (PDX) models and immunohistochemistry staining were performed to study the relationship of METTL3 and antitumor sensitivity of anlotinib in vivo.
    RESULTS: Anlotinib targeted FGFR3 in the treatment of OSCC and inhibited tumor cell proliferation and promoted apoptosis by inactivating the FGFR3/AKT/mTOR signaling pathway. METTL3 was identified to target and modify FGFR3 m6A methylation and then decrease the stability of mRNA. METTL3 expression level was related to the anlotinib sensitivity in OSCC cells in vitro and METTL3 knockdown promoted anlotinib sensitivity of OSCC cells by inhibiting the FGFR3 expression. PDX models samples furthermore showed that METTL3 and FGFR3 levels were tightly correlated with the anlotinib efficacy in OSCC.
    CONCLUSIONS: In summary, our work revealed that FGFR3 was served as the treatment target of anlotinib and METTL3-mediated FGFR3 m6A modification played a critical function in the anlotinib sensitivity in OSCC.
    Keywords:  Anlotinib; FGFR3; METTL3; OSCC; TKI; m6A methylation
    DOI:  https://doi.org/10.1186/s12935-022-02715-7
  3. Clin Transl Oncol. 2022 Sep 26.
    Characterization of m6A methylation modifications and tumor microenvironment infiltration in thyroid cancer.
    Fei-Hong Ji, Zhen Yang, Chenyu Sun, Scott Lowe, Xin-Guang Qiu.
       BACKGROUND: Thyroid cancer (TC) is the most common endocrine malignancy worldwide, and immunotherapy is a new cancer treatment that stimulates and enhances the natural ability of the immune system to fight cancer cells. The role of RNA N6-methyladenosine (m6A) related genes in these challenges has recently become a research hotspot, but he potential role of m6A modifications in tumor microenvironment (TME) cell infiltration remains unknown.
    PURPOSE: There is growing evidence that m6A plays a critical role in the regulation of gene expression by participating in important biological processes. A comprehensive analysis of the m6A regulator-mediated infiltration characteristics of the TME will help advance the understanding of immune regulation in thyroid tumors.
    METHODS: This study assessed m6A modification modes in 510 thyroid cancer samples from the Cancer Genome Atlas (TCGA) databases according to a comprehensive set of 24 m6A regulators. In this study, we analyzed the biological characteristics and m6A methylation modification patterns. Based on this, we constructed m6A signatures and analyzed m6A modification features in tumor somatic mutations and TCGA molecular subtypes.
    RESULTS: These modification modes were systematically linked to TME cell infiltration signatures. m6A modification patterns were comprehensively assessed and correlated with immune cell infiltration features in the TME. An unsupervised clustering approach was applied and three distinct m6A modification subtypes and three m6A-associated gene subtypes were identified. Additionally, three distinct m6A methylation modification modes were identified in the thyroid cancer samples. The TME profiles of the identified genetic subtypes were strongly congruent with the immuno-heat and immuno-cold phenotypes.
    CONCLUSIONS: The results revealed that m6A modifications play an integral role in the diversity and complexity of thyroid carcinomas. Evaluating the m6A modification patterns of individual tumors will create more efficient immunotherapeutic strategies. A comprehensive analysis of the role of TME in thyroid cancer provides a research idea for studying the effect of m6A epigenetics on thyroid tumors and their immune microenvironment.
    Keywords:  Immunotherapy; Mutation burden; Thyroid cancer; Tumor microenvironment; m6A
    DOI:  https://doi.org/10.1007/s12094-022-02940-6
  4. Placenta. 2022 Sep 18. pii: S0143-4004(22)00405-2. [Epub ahead of print]129 1-6
    The m6A methyltransferase METTL3 promotes trophoblast cell invasion by regulating MYLK expression.
    Jian Zhao, Haigang Ding, Jinlong Ding, Xiaoliang Shi, Yao He, Hongdan Zhu, Hua Yuan, Tao Zhang, Juan Zhang.
       INTRODUCTION: The progression of placental diseases such as preeclampsia is closely related to trophoblast dysfunction. Recent studies indicated the dysregulation of N6-methyladenosine (m6A) RNA modification in trophoblast disorders, while the function of METTL3, a methyltransferase of m6A, in trophoblasts remains to be studied.
    METHODS: The expression of METTL3 was determined by real-time PCR and immunoblotting. METTL3 expression in trophoblast cell lines HTR-8/SVneo and JEG-3 was knocked down using shRNA. The invasion of trophoblast cells in Matrigel was determined using xCELLigence. The m6A-containing transcripts was determined by m6A-sequencing in HTR-8/SVneo cells. The myosin light chain kinase (MYLK) gene was transfected into HTR-8/SVneo cells.
    RESULTS: The expression of METTL3 was downregulated in preeclamptic placentae compared to normal placentae. Knockdown of METTL3 repressed the invasion of extravillous trophoblast cells. Mechanistically, METTL3 promoted the stability of MYLK mRNA through m6A modification. Overexpression of MYLK rescued retarded cell invasion by METTL3 depletion.
    DISCUSSION: Collectively, our results highlight an essential role of METTL3-MYLK axis in trophoblast invasion.
    Keywords:  Invasion; METTL3; MYLK; Preeclampsia; Trophoblast
    DOI:  https://doi.org/10.1016/j.placenta.2022.09.002
  5. J Cancer Res Clin Oncol. 2022 Sep 28.
    N6-methyladenosine reader YTHDF3 contributes to the aerobic glycolysis of osteosarcoma through stabilizing PGK1 stability.
    Deyin Liu, Zhong Li, Kun Zhang, Daigang Lu, Dawei Zhou, Yibin Meng.
       PURPOSE: N6-methyladenosine (m6A) modification is a pivotal transcript chemical modification of eukaryotics, which has been identified to play critical roles on tumor metabolic reprogramming. However, the functions of m6A-reading protein YTH N6-methyladenosine RNA-binding protein 3 (YTHDF3) in osteosarcoma is still unclear. This research planned to investigate the bio-functions and mechanism in osteosarcoma tumorigenesis.
    METHODS: The aerobic glycolysis of osteosarcoma cells were calculated by glucose uptake, lactate production analysis, ATP analysis and metabolic flux analysis for extracellular acidification rate (ECAR). Molecular binding was identified by RIP-qPCR, RNA decay analysis.
    RESULTS: Results indicated that YTHDF3 is upregulated in the osteosarcoma tissue samples and cells, and closely correlated to the poor prognosis of osteosarcoma patients. Functionally, gain and loss-of-functional assays illustrated that YTHDF3 promoted the proliferation and aerobic glycolysis of osteosarcoma cells in vitro, and accelerated the tumor growth in vivo. Mechanistically, a m6A-modified PGK1 mRNA functioned as the target of YTHDF3, and YTHDF3 enhanced the PGK1 mRNA stability via m6A-dependent manner.
    CONCLUSIONS: In conclusion, these findings indicated that YTHDF3 functioned as an oncogene in osteosarcoma tumorigenesis through m6A/PGK1 manner, providing a therapeutic strategy for human osteosarcoma.
    Keywords:  Aerobic glycolysis; N6-methyladenosine; Osteosarcoma; PGK1; YTHDF3
    DOI:  https://doi.org/10.1007/s00432-022-04337-y
  6. Curr Med Chem. 2022 Sep 22.
    WTAP mediated the N6-methyladenosine modification of PDK4 to regulate the malignant behaviors of colorectal cancer cells in vitro and in vivo.
    Xiaoyu Dai, Ke Chen, Yangyang Xie.
       BACKGROUND: The role of WT1-associated protein (WTAP) in mediating the N6-methyladenosine (m6A) modification of pyruvate dehydrogenase kinase 4 (PDK4) in colorectal cancer (CRC) has been previously reported.
    OBJECTIVE: This research manages to unveil the function and mechanism of WTAP mediating the m6A modification in CRC.
    METHODS: Expressions of PDK4 and WTAP in CRC were assessed by bioinformatics analysis and verified by Western blot. After the transfection with short hairpin RNAs (shRNAs) for WTAP (shWTAP) and PDK4 (shPDK4) to manipulate the expressions of PDK4 and WTAP, the viability, proliferation, migration, invasion, and levels of m6A, PDK4 and WTAP in CRC cells were determined by cell counting kit-8 (CCK-8), colony formation, transwell, Western blot, or M6A-RNA Immunoprecipitation (MeRIP)-qPCR assays. M6A binding sites in PDK4 were additionally predicted through bioinformatics analysis and the interaction of PDK4 and WTAP was confirmed using RNA pull-down assay. Tumor volume and weight in the constructed xenograft-tumor mouse model were recorded.
    RESULTS: PDK4 expression was lowyet WTAP and m6A expressions were high in CRC cells. WTAP bound with the m6A binding sites in PDK4. PDK4 silencing facilitated the viability, proliferation, migration and invasion, inhibited the expression of PDK4 in CRC cells, and accelerated the growth of xenografts in vivo. However, the depletion of WTAP4 exerted the opposite effects and further offset the impact of PDK4 silencing.
    CONCLUSION: WTAP mediates the m6A modification of PDK4 to regulate the malignant behaviors of CRC cells in vitro and in vivo.
    Keywords:  Colorectal cancer; N6-methyladenosine; PDK4; WTAP; Xenograft-tumor
    DOI:  https://doi.org/10.2174/0929867329666220922102949
  7. Front Immunol. 2022 ;13 950365
    Identification of clinical prognostic features of esophageal cancer based on m6A regulators.
    Huimei Wang, Yiping Zhang, Lin Chen, Yufeng Liu, Chen Xu, Dongxian Jiang, Qi Song, Haixing Wang, Liyan Wang, Yu Lin, Yuanmei Chen, Junqiang Chen, Yuanji Xu, Yingyong Hou.
       Background: Esophageal cancer (ESCA) is a common malignancy with high morbidity and mortality. n6-methyladenosine (m6A) regulators have been widely recognized as one of the major causes of cancer development and progression. However, for ESCA, the role of regulators is unclear. The aim of this study was to investigate the role of m6A RNA methylation regulators in the immune regulation and prognosis of ESCA.
    Methods: RNA-seq data were downloaded using the Cancer Genome Atlas (TCGA) database, and the expression differences of m6A RNA methylation regulators in ESCA were analyzed. Further m6A methylation regulator markers were constructed, and prognostic and predictive values were assessed using survival analysis and nomograms. Patients were divided into low-risk and high-risk groups. The signature was evaluated in terms of survival, single nucleotide polymorphism (SNP), copy number variation (CNV), tumor mutation burden (TMB), and functional enrichment analysis (TMB). The m6A expression of key genes in clinical specimens was validated using quantitative reverse transcription polymerase chain reaction (qRT-PCR).
    Results: In ESCA tissues, most of the 23 regulators were significantly differentially expressed. LASSO regression analysis included 7 m6A-related factors (FMR1, RBMX, IGFBP1, IGFBP2, ALKBH5, RBM15B, METTL14). In addition, this study also identified that the risk model is associated with biological functions, including base metabolism, DNA repair, and mismatch repair. In this study, a nomogram was created to predict the prognosis of ESCA patients. Bioinformatics analysis of human ESCA and normal tissues was performed using qRT-PCR. Finally. Seven genetic features were found to be associated with m6A in ESCA patients. The results of this study suggest that three different clusters of m6A modifications are involved in the immune microenvironment of ESCA, providing important clues for clinical diagnosis and treatment.
    Keywords:  esophageal cancer; m6A RNA methylation regulators; nomogram; prognosis; signature; the cancer genome atlas
    DOI:  https://doi.org/10.3389/fimmu.2022.950365
  8. Front Neurol. 2022 ;13 995747
    m6A RNA methylation in brain injury and neurodegenerative disease.
    Jianhui Deng, Xiaohui Chen, Andi Chen, Xiaochun Zheng.
      N6-methyladenosine (m6A), the most prevalent post-transcriptional RNA modification throughout the eukaryotic transcriptome, participates in diverse biophysiological processes including cell fates, embryonic development and stress responses. Accumulating evidence suggests that m6A modification in neural development and differentiation are highly regulated processes. As RNA m6A is crucial to protein translation and various bioprocesses, its modification dysregulation may also be associated with brain injury. This review highlights the biological significance of m6A modification in neurodegenerative disease and brain injury, including cerebrovascular disorders, is highlighted. Emphasis is placed on recent findings that elucidate the relevant molecular functional mechanism of m6A modification after brain injury and neurodegenerative disease. Finally, a neurobiological basis for further investigation of potential treatments is described.
    Keywords:  N6-methyladenosine; RNA; brain injury; neurodegenerative disease; post-transcriptional RNA modification
    DOI:  https://doi.org/10.3389/fneur.2022.995747
  9. Theranostics. 2022 ;12(14): 6291-6307
    m6A-induced lncDBET promotes the malignant progression of bladder cancer through FABP5-mediated lipid metabolism.
    Peihua Liu, Benyi Fan, Belaydi Othmane, Jiao Hu, Huihuang Li, Yu Cui, Zhenyu Ou, Jinbo Chen, Xiongbing Zu.
      The limited effect of adjuvant therapy for advanced bladder cancer (BCa) leads to a poor prognosis. Increasing evidence has shown that RNA N6-methyladenosine (m6A) modification plays important functional roles in tumorigenesis. Nevertheless, the role and mechanism of m6A-modified noncoding RNAs (ncRNAs) in BCa remain largely unknown. Methods: RT-PCR, western blotting and ONCOMINE dataset were used to determine the dominant m6A-related enzyme in BCa. M6A-lncRNA epitranscriptomic microarray was used to screen candidate targets of METTL14. RT-PCR, MeRIP and TCGA dataset were carried out to confirm the downstream target of METTL14. CHIRP/MS was conducted to identify the candidate proteins binding to lncDBET. RT-PCR, western blotting, RIP and KEGG analysis were used to confirm the target of lncDBET. The levels of METTL14, lncDBET and FABP5 were tested in vitro and in vivo. CCK-8, EdU, transwell and flow cytometry assays were performed to determine the oncogenic function of METTL14, lncDBET and FABP5, and their regulatory networks. Results: We identified that the m6A level of total RNA was elevated and that METTL14 was the dominant m6A-related enzyme in BCa. m6A modification mediated by METTL14 promoted the malignant progression of BCa by promoting the expression of lncDBET. Upregulated lncDBET activated the PPAR signalling pathway to promote the lipid metabolism of cancer cells through direct interaction with FABP5, thus promoting the malignant progression of BCa in vitro and in vivo. Conclusions: Our study establishes METTL14/lncDBET/FABP5 as a critical oncogenic axis in BCa.
    Keywords:  Bladder cancer; FABP5; METTL14; lncDBET; m6A
    DOI:  https://doi.org/10.7150/thno.71456
  10. IUBMB Life. 2022 Sep 30.
    N6-methyladenosine regulators are potential prognostic biomarkers for multiple myeloma.
    Jing Wang, Yifan Zuo, Chenglan Lv, Min Zhou, Yuan Wan.
      N6-methyladenosine (m6A) regulators play an important role in tumorigenesis; however, their role in multiple myeloma (MM) remains unknown. This study aimed to create an m6A RNA regulators prognostic signature for MM patients. We integrated data from the Multiple Myeloma Research Foundation CoMMpass Study and the Genotype-Tissue Expression database to analyze gene expression profiles of 21 m6A regulators. Consistent clustering analysis was used to identify the clusters of patients with MM having different clinical outcomes. Gene distribution was analyzed using principal component analysis. Next, we generated an mRNA gene signature of m6A regulators using a multivariate logistic regression model with least absolute shrinkage and selection operator. The expressions of m6A regulators, except FMR1, were significantly different in MM samples compared with those in normal samples. The KIAA1429, HNRNPC, FTO, and WTAP expression levels were dramatically downregulated in tumor samples, whereas those of other signatures were remarkably upregulated. Three clusters of patients with MM were identified, and significant differences were found in terms of overall survival (P = 0.024). A prognostic two-gene signature (KIAA1429 and HNRNPA2B1) was constructed, which had a good prognostic significance using ROC method (AUC= 0.792). Moreover, the risk score correlated with the infiltration immune cells. In addition, KEGG pathway analysis showed 16 pathways were dramatically enriched. The m6A signature might be an novel biomarker for predicting the prognosis of patients with MM (P = 0.002). Our study is the first to explore the potential application value of m6A in MM. These findings may enhance the understanding of the functional organization of m6A in MM and provide new insights into the treatment for MM patients.
    Keywords:  N6-methyladenosine; mRNA signature; multiple myeloma; prognostic signature; survival
    DOI:  https://doi.org/10.1002/iub.2678
  11. Front Oncol. 2022 ;12 989353
    FTO promotes liver inflammation by suppressing m6A mRNA methylation of IL-17RA.
    Xiaojie Gan, Zhihui Dai, Chunmei Ge, Haozan Yin, Yuefan Wang, Jian Tan, Shuhan Sun, Weiping Zhou, Shengxian Yuan, Fu Yang.
       Background: Previous studies have demonstrated that inflammation-related interleukin-17 (IL-17) signaling plays a pivotal role in the pathogenesis of non-alcoholic steatohepatitis (NASH)- and alcoholic liver disease (ALD)-induced hepatocellular carcinoma (HCC). However, rare efforts have been intended at implementing the analysis of N6-methyladenosine (m6A) mRNA methylation to elucidate the underpinning function of the IL-17 receptor A (IL-17RA) during the inflammation-carcinogenesis transformation of HCC.
    Methods: We performed methylated RNA immunoprecipitation sequencing (MeRIP-seq) using normal, HCC tumor and paired tumor adjacent tissues from patients to investigate the dynamic changes of m6A mRNA methylation in the process of HCC. Additionally, murine non-alcoholic fatty liver disease (NAFLD) model and murine chronic liver injury model were utilized to investigate the role of IL-17RA regulated by m6A mRNA modulator fat mass and obesity-associated (FTO) in chronic hepatic inflammation.
    Results: MeRIP-seq revealed the reduction of m6A mRNA methylation of IL-17RA in tumor adjacent tissues with chronic inflammation, suggesting the potential role of IL-17RA in the inflammation-carcinogenesis transformation of HCC. Besides, we demonstrated that FTO, rather than methyltransferase-like 3 (METTL3), methyltransferase-like 14 (METTL14), and alkB homolog 5 (ALKBH5) functions as a main modulator for the decrease of m6A mRNA methylation of IL-17RA via knockdown and overexpression of FTO in vitro and in vivo.
    Conclusions: Overall, we elaborated the underlying mechanisms of the increase of IL-17RA resulting in chronic inflammation via the demethylation of FTO in tumor adjacent tissues and demonstrated that targeting the specific m6A modulator FTO may provide an effective treatment for hepatitis patients to prevent the development of HCC.
    Keywords:  HCC; IL-17RA; RNA methylation; fto; liver inflammation; m6A
    DOI:  https://doi.org/10.3389/fonc.2022.989353
  12. Med Oncol. 2022 Sep 29. 39(12): 235
    The functions of N6-methyladenosine (m6A) RNA modifications in colorectal cancer.
    Haiyan Qiao, Linfeng Liu, Jun Chen, Bingbing Shang, Liang Wang.
      Colorectal cancers (CRC), which includes colon cancer (CC) and rectal cancer (RC), are some of the most common malignant tumors that are prone to distant metastasis. Its high incidence rate and high mortality rate have attracted much attention. In recent years, epigenetics has attracted increasing attention and has been the focus of many research studies. N6-methyladenosine(m6A) RNA modifications can modify eukaryotic mRNA to impact metabolism. The changes in the m6A regulatory genes are related to the occurrence and development of CRC and play an important role in the pathogenesis of CRC. The effect of m6A RNA modification is regulated by its related regulatory factors ("writer", "eraser", "reader"). In this review, we comprehensively analyzed the effect of m6A methylation on CRC and the relationship between the expression of related regulatory factors and the development and occurrence of CRC. Then, we summarized the roles of m6A and its regulatory factors in CRC and its potential clinical value, which provides a basis for further research on the mechanism of m6A methylation in CRC.
    Keywords:  Colon cancer; Colorectal cancer; Rectal cancer; m6A RNA modifications functions
    DOI:  https://doi.org/10.1007/s12032-022-01827-4
  13. Life Sci. 2022 Sep 26. pii: S0024-3205(22)00705-6. [Epub ahead of print] 121005
    N6-methyladenosine modification on Hmbox1 is related to telomere dysfunction in DEHP-induced male reproductive injury.
    Xiaofang Zhu, Haowei Fu, Jiahui Sun, Qiannan Di, Qian Xu.
       AIMS: Di (2-ethylhexyl) phthalate (DEHP), as an environmental endocrine-disrupting chemical (EDC), can induce male reproductive injury. N6-methyladenosine (m6A) plays a vital role in environmental exposure-induced diseases by regulating gene expression. Therefore, we aim to investigate the role of m6A in DEHP-induced reproductive injury.
    MAIN METHODS: We established an in vivo model of mice exposed to DEHP to explore the effect of DEHP on reproductive injury and m6A. To further explore the molecular mechanism of DEHP toxicity, we built a model of GC-2 cells exposed to mono-(2-ethylhexyl) phthalate (MEHP) in vitro and further silenced Mettl3 in GC-2cells. Besides, we also conducted MeRIP-qPCR and RIP assays to identify the target genes for m6A modification.
    KEY FINDINGS: DEHP induced testicular injury and senescence. And telomeres shortening, reduced levels of telomere repeat-binding factor 1 (TRF1), TRF2, protection of telomeres 1 (POT1), and telomerase reverse transcriptase (TERT) can be observed in DEHP-treated testes. MEHP also induced GC-2 cellular senescence and telomere dysfunction. Besides, increased m6A mediated by METTL3 stabilized homeobox containing 1 (Hmbox1) in an m6A-dependent manner in MEHP-exposed GC-2 cells. Mettl3 knockdown led to lower m6A modification and reduced Hmbox1 stability, resulting in further shortening of telomere length.
    SIGNIFICANCE: our work uncovered that DEHP led to male reproductive injury by telomere dysfunction and m6A modified Hmbox1 contributed to maintaining telomere homeostasis in this process, suggesting that accurate regulation of m6A modification level by drugs has potential value in the treatment of DEHP-induced male reproductive injury.
    Keywords:  Di-(2-ethylhexyl) phthalate (DEHP) N6-methyladenosine (m6A) modification telomere dysfunction male reproductive toxicity
    DOI:  https://doi.org/10.1016/j.lfs.2022.121005
  14. Front Endocrinol (Lausanne). 2022 ;13 866116
    The role of RNA m6A methylation in lipid metabolism.
    Yuting Wang, Yujie Wang, Jiarui Gu, Tianhong Su, Xiaosong Gu, Yu Feng.
      The m6A methylation is the most numerous modification of mRNA in mammals, coordinated by RNA m6A methyltransferases, RNA m6A demethylases, and RNA m6A binding proteins. They change the RNA m6A methylation level in their specific manner. RNA m6A modification has a significant impact on lipid metabolic regulation. The "writer" METTL3/METTL14 and the "eraser" FTO can promote the accumulation of lipids in various cells by affecting the decomposition and synthesis of lipids. The "reader" YTHDF recognizes m6A methylation sites of RNA and regulates the target genes' translation. Due to this function that regulates lipid metabolism, RNA m6A methylation plays a pivotal role in metabolic diseases and makes it a great potential target for therapy.
    Keywords:  FTO (fat mass and obesity-associated) gene; M6A; METTL3; lipid; obesity
    DOI:  https://doi.org/10.3389/fendo.2022.866116
  15. J Biol Chem. 2022 Sep 23. pii: S0021-9258(22)00968-1. [Epub ahead of print] 102525
    A programmable system to methylate and demethylate N6-Methyladenosine (m6A) on specific RNA transcripts in mammalian cells.
    Chen Chang, Gang Ma, Edwin Cheung, Andrew P Hutchins.
      RNA N6-Methyladenosine (m6A) is the most abundant internal mRNA modification and forms part of an epitranscriptomic system that modulates RNA function. m6A is reversibly catalyzed by specific enzymes, and those modifications can be recognized by RNA-binding proteins that in turn regulate biological processes. Although there are many reports demonstrating m6A participation in critical biological functions, this exploration has mainly been conducted through the global knockout or knockdown of the writers, erasers, or readers of m6A. Consequently, there is a lack of information about the role of m6A on single transcripts in biological processes, posing a challenge in understanding the biological functions of m6A. Here, we demonstrate a CRISPR/dCas13a-based RNA m6A-editors which can target RNAs using a single or multiple CRISPR RNA (crRNA) array to methylate or demethylate m6A in human 293T cells and mouse embryonic stem cells (mESCs). We systematically assay its capabilities to enable the targeted rewriting of m6A dynamics, including modulation of circular RNA translation and transcript half-life. Finally, we use the system to specifically modulate m6A levels on the non-coding XIST transcript to modulate X chromosome silencing and activation. The editors described here can be used to explore the roles of m6A in biological processes.
    Keywords:  CRISPR/Cas13a; Epitranscriptomics; X chromosome inactivation; m(6)A
    DOI:  https://doi.org/10.1016/j.jbc.2022.102525
  16. Front Physiol. 2022 ;13 918270
    Significance of m6A regulatory factor in gene expression and immune function of osteoarthritis.
    Xiaoyan Xie, Yun Zhang, Jian Yu, Feng Jiang, Chuyan Wu.
      One of the most prevalent posttranscriptional modifications of eukaryotic mRNA is the RNA N6-methyladenosine (m6A) regulator, which plays a significant role in various illnesses. The involvement of m6A regulators in osteoarthritis (OA) is not fully known. By comparing nonosteoarthritic and osteoarthritic patients, 26 important m6A regulators were identified from the gene expression omnibus GSE48556 dataset. Seven candidate m6A regulators (IGFBP3, WTAP, IGFBP1, HNRNPC, RBM15B, YTHDC1, and METTL3) were screened using a random forest model to assess the likelihood of OA. A column line graph model founded on seven m6A modulator candidates was created. According to decision curve analysis, patients might profit from the column line graph model. Based on chosen relevant m6A modifiers, a consensus clustering approach was utilized to categorize OA into two m6A categories (group A and group B). To measure the m6A pattern, a principal component analysis technique was created to generate the m6A score for every sample. Cluster A patients exhibited more excellent m6A scores than cluster B patients. Furthermore, we discovered that patients with lower and higher m6A scores had varied immunological responses using the m6A type. At last, m6A regulators contribute significantly to the progression of OA. Our research on m6A patterns might help to guide further OA immunotherapeutic techniques.
    Keywords:  immunity; m6A regulators; m6A score; osteoarthritis; random forest model
    DOI:  https://doi.org/10.3389/fphys.2022.918270
  17. Invest Ophthalmol Vis Sci. 2022 Sep 01. 63(10): 20
    METTL3 Attenuates Inflammation in Fusarium solani-Induced Keratitis via the PI3K/AKT Signaling Pathway.
    Liwei Huang, Hanfeng Tang, Jianzhang Hu.
       Purpose: Our previous investigations revealed a significant role of methyltransferase-like 3 (METTL3)-mediated N6-methyladenosine (m6A) modification in the development of corneal inflammation in Fusarium infection, but the exact mechanism is unknown. Therefore, this research aimed to explore how METTL3 affects the inflammatory process of fungal keratitis (FK) in mice.
    Methods: We established in vitro and in vivo models by inoculating mice and primary corneal stromal cells with F. solani. METTL3 expression was confirmed by real-time quantitative polymerase chain reaction, immunofluorescence, and western blotting. After that, siRNAMETTL3 and AAV-sh-METTL3 were transfected into cells and mice to explore the role of METTL3 in the PI3K/AKT signaling pathway and inflammation. PI3K, p-PI3K, AKT, and p-AKT expression was analyzed by western blotting. Viability of corneal stromal cells was measured using a Cell Counting Kit-8 (CCK-8). Additionally, we detected interleukin (IL)-6, IL-1β, and tumor necrosis factor alpha (TNF-α) levels in corneal tissues and analyzed the role of METTL3 in inflammation in FK using slit-lamp biomicroscopy and hematoxylin and eosin staining.
    Results: Here, our results show that METTL3 increased in mouse FK, and the expression of p-PI3K and p-AKT decreased when METTL3 was downregulated. We also found that knockdown of METTL3 expression attenuated the inflammatory response and decreased TNF-α, IL-1β, and IL-6 expression in corneal-infected mice. Furthermore, inhibition of the PI3K/AKT pathway attenuated the inflammatory response of FK, decreased the expression of the above inflammatory factors, and enhanced the viability of corneal stromal cells.
    Conclusions: Based on the study results, METTL3 downregulation attenuates Fusarium-induced corneal inflammation via the PI3K/AKT signaling pathway.
    DOI:  https://doi.org/10.1167/iovs.63.10.20
  18. Front Cell Dev Biol. 2022 ;10 759020
    METTL16 predicts a favorable outcome and primes antitumor immunity in pancreatic ductal adenocarcinoma.
    Liting Lu, Dandan Zheng, Junchi Qu, Yanyan Zhuang, Juanfei Peng, Sihua Lan, Shineng Zhang, Fengting Huang.
      Pancreatic carcinogenesis is a complicated and multi-step process. It is substantially assisted by N6-methyladenosine (m6A) RNA modification, especially when mutations of driver genes (KRAS, TP53, CDKN2A, and SMAD4) occur. However, the underlying mechanism remains obscure. In this research, we identified m6A regulators as potential biomarkers when mutations of driver genes occur, and investigated the role of these m6A candidates in pancreatic ductal adenocarcinoma (PDA). We first estimated the abnormal expression patterns of potential m6A regulators when all the driver genes are mutated, using The Cancer Genome Atlas and Gene Expression Omnibus databases. METTL16, an m6A"writer," was chosen as a unique candidate of PDA, owing to its markedly differential expression under mutations of all driver genes (KRAS, TP53, CDKN2A, and SMAD4) and its favorable prognostic value. Moreover, METTL16 was under-expressed in PDA tissues and cell lines. Consistently, gain- and loss-of-function experiments indicated that it had a tumor suppressor role in vitro and in vivo. Further, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed that METTL16 may have an effect on the tumor microenvironment. Notably, a markedly positive association between METTL16 expression and infiltration of B cells and CD8+ T cells was observed according to the CIBERSORT and TIMER databases. Enhanced expression of immune checkpoints and cytokines was elicited in patients with over-expression of METTL16. Notably, decreased expression of PD-L1 was observed when upregulation of METTL16 expression occurred in MIA PaCa-2 cells, while increased expression of PD-L1 existed when downregulation of METTL16 happened in HPAF-II cells. Collectively, these findings highlight the prognostic value of METTL16, and indicate that it is a potential immunotherapy target that could be used to regulate the tumor microenvironment and promote antitumor immunity in PDA.
    Keywords:  METTL16; N6-methyladenosine; pancreatic ductal adenocarcinoma; prognostic biomarker; tumor microenvironment
    DOI:  https://doi.org/10.3389/fcell.2022.759020
  19. Cell Prolif. 2022 Sep 26. e13340
    Effects of writers, erasers and readers within miRNA-related m6A modification in cancers.
    Huiru Feng, Xiaofei Yuan, Shuting Wu, Yue Yuan, Linchong Cui, Danfan Lin, Xiaohong Peng, Xiong Liu, Fan Wang.
       BACKGROUND: As one of the most abundant post-transcriptional mRNA modifications, N6-methyladenosine (m6A) has attracted extensive attention from scientists. Emerging evidence indicates that m6A modification plays a significant role in cancer-related signalling pathways. Existing research demonstrates that m6A modifications were also identified in miRNAs and contribute to cancer-related signalling pathways.
    METHODS: A literature retrieval has been performed to collect m6A-miRNA-related original articles published in recent years. Later, a systematic analysis has been conducted to abstract and classify the relationships between m6A modification and miRNAs, and their contributions to tumorigenesis and cancer development.
    RESULTS: Accumulating literature provides important insights into multiple relationships between m6A modifications and miRNAs. Mechanically, m6A writer and eraser alter pri-miRNAs m6A levels, and m6A readers could dually modulate pri-miRNAs processing and pri-miRNAs degradation. It is also been demonstrated that miRNAs impair m6A regulators' translation to influence m6A medication function in return. Aberrant expressions of m6A regulators and miRNAs could dysregulate proliferative, apoptosis, cell adhesion-related, and malignant transformation signalling pathways, and contribute to tumour occurrence and development.
    CONCLUSION: This review summarizes the interrelationship between m6A modification and miRNAs; highlights the combined effects of each type of m6A regulator and miRNAs in cancers. These findings enhance our understanding of m6A-miRNAs' multiple interactions and significant modulatory role in tumorigenesis and progression.
    DOI:  https://doi.org/10.1111/cpr.13340
  20. Theranostics. 2022 ;12(14): 6363-6379
    The N6-methyladenosine-mediated lncRNA WEE2-AS1 promotes glioblastoma progression by stabilizing RPN2.
    Boyan Li, Rongrong Zhao, Wei Qiu, Ziwen Pan, Shulin Zhao, Yanhua Qi, Jiawei Qiu, Shouji Zhang, Qindong Guo, Yang Fan, Hao Xu, Ming Li, Gang Li, Hao Xue.
      Background: Glioblastoma (GBM) is the most common primary brain malignancy and has high aggressiveness and a poor prognosis. N6-methyladenosine (m6A) represents the most prevalent methylation modification of lncRNAs and has been shown to play important roles in the pathophysiological processes of tumors. However, the distribution and function of m6A modifications in lncRNAs in GBM tissues have not been fully revealed. Methods: The global depiction of m6A-modified lncRNA expression patterns in GBM tumor tissues was screened via m6A high-throughput sequencing. Gain- and loss-of-function assays were performed to investigate the role of WEE2-AS1 in GBM. Mass spectrometry and RNA-pulldown, RNA immunoprecipitation (RIP), luciferase reporter and coimmunoprecipitation assays were performed to explore the mechanism of m6A-mediated upregulation of WEE2-AS1 expression and the downstream mechanism promoting the malignant progression of GBM. Results: Herein, we report the differential expression profile of m6A-modified lncRNAs in human GBM tissues for the first time. WEE2-AS1 was identified as a novel m6A-modified lncRNA that promotes GBM progression and was post-transcriptionally stabilized by IGF2BP3, an m6A reader. Moreover, we confirmed that WEE2-AS1 promoted RPN2 protein stabilization by preventing CUL2-mediated RPN2 K322 ubiquitination, thereby contributing to GBM malignant progression by activating the PI3K-Akt signaling pathway. In translational medicine, we found that blocking WEE2-AS1 expression improved the therapeutic sensitivity of dasatinib, a central nervous system penetrant that is FDA-approved in GBM. Conclusions: Overall, this work highlights that WEE2-AS1 may serve as a potential prognostic biomarker and therapeutic target in GBM, the knockdown of which significantly improves the efficacy of dasatinib, providing a promising strategy for improving targeted combination therapy for GBM patients.
    Keywords:  Glioblastoma; IGF2BP3; N6-methyladenosine; RPN2; ubiquitination
    DOI:  https://doi.org/10.7150/thno.74600
  21. Mamm Genome. 2022 Sep 29.
    WTAP mediates FOXP3 mRNA stability to promote SMARCE1 expression and augment glycolysis in colon adenocarcinoma.
    Yu Zhang, Xiaoxiao Tian, Yanli Bai, Xianmin Liu, Jingjing Zhu, Lamei Zhang, Jinliang Wang.
      N6-methyladenosine (m6A) is the most abundant mRNA internal modification and has reportedly been linked to aerobic glycolysis, a hallmark event in tumor development. This work focuses on the role of the m6A methyltransferase WT1-associated protein (WTAP) in metabolic reprogramming and development of colon adenocarcinoma (COAD) and the molecules involved. The WTAP expression in COAD tissues and cells was detected. WTAP was knocked down in two COAD cell lines to figure out its role in the glycolytic activity and malignant phenotype of cancer cells. Cancer cells were further injected into nude mice subcutaneously or via tail vein to evaluate tumor growth and metastasis. The downstream molecules involved were explored using bioinformatics tools, and the molecular interactions were confirmed by immunoprecipitation, luciferase assays, and rescue experiments. WTAP was abundantly expressed in COAD samples. Knockdown of WTAP suppressed glucose consumption, lactate production, and glycolysis, which consequently suppressed cancer cell growth and dissemination in vitro and in vivo. WTAP promoted m6A methylation and stabilized forkhead box P3 (FOXP3) mRNA with the participation of the m6A "reader" YTHDF1. FOXP3 could further bind to SMARCE1 promoter for transcriptional activation. Rescue experiments showed that upregulation of FOXP3 or SMARCE1 restored the glycolytic activity in COAD cells and augmented the growth and mobility of cells both in vitro and in vivo. This study demonstrates that WTAP grants glycolytic activity to COAD and promotes tumor malignant development via the m6A modification of FOXP3 mRNA and the upregulation of SMARCE1.
    DOI:  https://doi.org/10.1007/s00335-022-09962-z
  22. Front Pediatr. 2022 ;10 930119
    Identification of molecular patterns and diagnostic biomarkers in juvenile idiopathic arthritis based on the gene expression of m6A regulators.
    Shibo Zhang, Jing Qin, Yuechao Zhao, Jian Wang, Zhiliang Tian.
      The role of N 6-methyladenosine modification in immunity is increasingly being appreciated. However, the landscape of m6A regulators in juvenile idiopathic arthritis (JIA) is poorly understood. Thus, this study explored the impact of m6A modification and related lncRNAs in JIA immune microenvironment. Fourteen m6A regulators and eight lncRNAs were identified as potential diagnostic biomarkers for JIA. Two diagnostic models for JIA were also constructed. The putative molecular regulatory mechanism of FTO-mediated m6A modification in JIA was hypothesized. Three distinct m6A patterns mediated by 26 m6A regulators and three diverse lncRNA clusters mediated by 405 lncRNAs were thoroughly investigated. They exhibited dramatically diverse immune microenvironments and expression of HLA genes. The identification of two separate subtypes of enthesitis-related arthritis implies that our work may aid in the establishment of a more precise categorization system for JIA. m6A modification-related genes were obtained, and their underlying biological functions were explored. The m6Ascore system developed for individual JIA patients may be utilized to evaluate the immunological state or molecular pattern, thereby offering therapy recommendations. In short, through the investigation of the m6A regulators in JIA, the current work may contribute to our knowledge of the pathophysiology of JIA.
    Keywords:  diagnostic model; immune microenvironment; juvenile idiopathic arthritis; long non-coding RNA; m5C; m6A
    DOI:  https://doi.org/10.3389/fped.2022.930119
  23. Ann Transl Med. 2022 Sep;10(17): 931
    Modification of m6A mediates tissue immune microenvironment in calcific aortic valve disease.
    Jun-Yu Chen, Tao Xiong, Ya-Ru Sun, Juan Cong, Jing-Shuai Gong, Lei Peng, Yu-Wang Rong, Zi-Yao Wang, Qing Chang.
       Background: Several human diseases are associated with aberrant expression of regulators involved in N6-methyladenosine (m6A) RNA modification. However, their role in aortic valve calcification (AVC) is largely unknown. The aim of this study was to determine the general expression pattern and potential function of m6A regulators in AVC by bioinformatics methods.
    Methods: We obtained AVC datasets from the Gene Expression Omnibus (GEO). The identification of m6A-related differentially expressed genes (DEGs) and the Consensus Clustering method was performed to type AVC individuals based DEGs. Then, we quantified the effect of typing by principal component analysis (PCA). Next, we performed the weighted gene co-expression network analysis (WGCNA) and identified the main modules as well as functional analysis. Additionally, the key genes were screened by protein-protein interaction network (PPIN) analysis and identifying important genes of important modules. We again typed AVC individuals by the same method using key genes. Finally, we evaluated the link between key genes and immune infiltration.
    Results: We discovered that METTL14, ZC3H13, FTO, FMR1, HNRNPA2B1, HNRNPC, LRPPRC, YTHDC1, YTHDC2, and YTHDF1 expression levels decreased considerably in AVC tissues. Based on 10 genes, we typed 240 AVC samples as clusters A and B. We assessed the immune cell content in 240 samples using Cell-type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT) and found that B cell memory, CD8 T cells, T follicular helper cells, monocytes, M0 macrophages, resting dendritic cells (DCs), and interleukin-10 (IL-10) were concentrated in the cluster A group. Additionally, based on the important WGCNA modules, we identified 7 key genes. Next, 240 samples were retyped based on 7 key genes; we found that T cells CD8, T cells CD4 memory activated, T cells follicular helper, and macrophages M1 were significantly increased in gene cluster-1. Finally, we performed functional enrichment of gene cluster-typed samples, showing potential functional differences between different types.
    Conclusions: Our study provides a review of the m6A regulators' expression pattern and functional importance in human AVC. The data from this study might serve as a significant resource for future mechanistic and therapeutic investigations into the role of critical m6A regulators in AVC.
    Keywords:  Aortic valve calcification (AVC); N6-methyladenosine modification (m6A modification); immune infiltration; transcriptome classification
    DOI:  https://doi.org/10.21037/atm-22-3627
  24. Dis Markers. 2022 ;2022 4942599
    Analysis of N6-Methyladenosine RNA Methylation Regulators in Diagnosis and Distinct Molecular Subtypes of Ankylosing Spondylitis.
    Cheng Zhong, Jia-Hua Liang, Zhen Chen, Li-Ping Zhong, Guo-Dong Sun, Wei-Xing Xie, Dong-Ping Wang, Wen-de Zhuang, Hao-Hua Guo, Da-Xiang Jin, Yu-Ming Li.
      The most frequent internal modification in eukaryotic mRNA is N6-methyladenosine (m6A). However, what we know about the m6A regulators in Ankylosing spondylitis (AS) is still limited. In our study, eight distinct m6A regulators were selected utilizing Differentially Expressed Gene (DEG) analysis of the Gene Expression Omnibus GSE73754 dataset for making comparisons between AS (Ankylosing spondylitis) and non-AS patients. The random forest model and the nomogram model were used to screen the eight candidate m6A regulators and evaluate their prediction accuracy for the occurrence of AS. Furthermore, based on the selected m6A regulators, the AS patients were divided into two subgroups, and we applied principal component analysis algorithms to calculate their m6A score and evaluate the m6A patterns. Our findings revealed that patients in cluster A were linked to activated CD4 T cell immunity and activated CD8 T cell immunity. With its major contributions in the area of immunology, our research in m6A patterns may benefit the future diagnosis and treatment strategies of AS.
    DOI:  https://doi.org/10.1155/2022/4942599
  25. Nucleic Acids Res. 2022 Sep 26. pii: gkac830. [Epub ahead of print]
    Geographic encoding of transcripts enabled high-accuracy and isoform-aware deep learning of RNA methylation.
    Daiyun Huang, Kunqi Chen, Bowen Song, Zhen Wei, Jionglong Su, Frans Coenen, João Pedro de Magalhães, Daniel J Rigden, Jia Meng.
      As the most pervasive epigenetic mark present on mRNA and lncRNA, N6-methyladenosine (m6A) RNA methylation regulates all stages of RNA life in various biological processes and disease mechanisms. Computational methods for deciphering RNA modification have achieved great success in recent years; nevertheless, their potential remains underexploited. One reason for this is that existing models usually consider only the sequence of transcripts, ignoring the various regions (or geography) of transcripts such as 3'UTR and intron, where the epigenetic mark forms and functions. Here, we developed three simple yet powerful encoding schemes for transcripts to capture the submolecular geographic information of RNA, which is largely independent from sequences. We show that m6A prediction models based on geographic information alone can achieve comparable performances to classic sequence-based methods. Importantly, geographic information substantially enhances the accuracy of sequence-based models, enables isoform- and tissue-specific prediction of m6A sites, and improves m6A signal detection from direct RNA sequencing data. The geographic encoding schemes we developed have exhibited strong interpretability, and are applicable to not only m6A but also N1-methyladenosine (m1A), and can serve as a general and effective complement to the widely used sequence encoding schemes in deep learning applications concerning RNA transcripts.
    DOI:  https://doi.org/10.1093/nar/gkac830
  26. Genomics. 2022 Sep 26. pii: S0888-7543(22)00243-9. [Epub ahead of print] 110498
    m6A transferase METTL3 regulates endothelial-mesenchymal transition in diabetic retinopathy via lncRNA SNHG7/KHSRP/MKL1 axis.
    Xin Cao, Yu Song, Li-Li Huang, Ya-Jing Tian, Xiao-Le Wang, Ling-Yan Hua.
      Diabetic retinopathy is one of the microvascular complications in diabetic patients and the leading cause of blindness worldwide. The levels of METTL3, lncRNA SNHG7, KHSRP, MKL1, endothelial and mesenchymal markers were determined by RT-qPCR or western blot assays in vitro and in vivo. H&E staining was used to observe the retinal structure in a mouse model of DR. The expression levels of METTL3 and SNHG7 were significantly downregulated in DR patients, DR mice and high glucose-induced HRMECs cells. Notably, METTL3 installed the m6A modification and enhanced the stability of SNHG7. Besides, METTL3 inhibited HRMECs EndoMT by promoting the expression of SNHG7. Additionally, SNHG7 was found to weaken MKL1 mRNA stability by binding to the RNA-binding protein KHSRP. Furthermore, we verified that METTL3 regulated EndoMT in DR through the SNHG7/MKL1 axis. We conclude that METTL3 regulates endothelial-mesenchymal transition in DR via the SNHG7/KHSRP/MKL1 axis, providing a new target for DR treatment.
    Keywords:  Diabetic retinopathy; Endothelial-mesenchymal transition; KHSRP; METTL3; MKL1; SNHG7; m(6)A
    DOI:  https://doi.org/10.1016/j.ygeno.2022.110498
  27. Front Endocrinol (Lausanne). 2022 ;13 997034
    A bibliometric analysis of RNA methylation in diabetes mellitus and its complications from 2002 to 2022.
    Wenhua Zhang, Shuwen Zhang, Chenlu Dong, Shuaijie Guo, Weiyu Jia, Yijia Jiang, Churan Wang, Mingxue Zhou, Yanbing Gong.
       Background: RNA methylation has emerged as an active research field in diabetes mellitus (DM) and its complications, while few bibliometric analyses have been performed. We aimed to visualize the hotspots and trends using bibliometric analysis to provide a comprehensive and objective overview of the current search state in this field.
    Methods: The articles and reviews regarding RNA methylation in DM and its complications were from the Web of Science Core Collection. A retrospective bibliometric analysis and science mapping was performed using the CiteSpace software to plot the knowledge maps and predict the hotspots and trends.
    Results: Three hundred seventy-five qualified records were retrieved. The annual publications gradually increased over the past 20 years. These publications mainly came from 66 countries led by Canada and 423 institutions. Leiter and Sievenpiper were the most productive authors, and Jenkins ranked first in the cited authors. Diabetes Care was the most co-cited journal. The most common keywords were "Type 2 diabetes", "cardiovascular disease", "diabetes mellitus", and "n 6 methyladenosine". The extracted keywords mainly clustered in "beta-cell function", "type 2 diabetes", "diabetic nephropathy", "aging", and "n6-methyladenosine". N6-methyladenosine (m6A) in DM and its complications were the developing areas of study.
    Conclusion: Studies on RNA methylation, especially m6A modification, are the current hotspots and the future trends in type 2 diabetes (T2D) and diabetic nephropathy (DN), as well as a frontier field for other complications of DM. Strengthening future cooperation and exchange between countries and institutions is strongly advisable to promote research developments in this field.
    Keywords:  N6-methyladenosine (m 6 A); RNA methylation; bibliometric analysis; diabetes complications; diabetes mellitus
    DOI:  https://doi.org/10.3389/fendo.2022.997034
  28. Sci Rep. 2022 Sep 29. 12(1): 16358
    m6A RNA methylation regulator-related signatures exhibit good prognosis prediction ability for head and neck squamous cell carcinoma.
    Yujia Zhai, Lian Zheng.
      Head and neck squamous cell carcinoma (HNSCC) has become the sixth most common malignant disease worldwide and is associated with high mortality, with an overall 5-year survival rate of less than 50%. Recent studies have demonstrated that aberrantly expressed m6A regulators are involved in multiple biological and pathological processes, including cancers, but the specific mechanisms of m6A regulators in HNSCC are not well elucidated. In this study, we adopted The Cancer Genome Atlas (TCGA)-HNSCC database and performed a consensus clustering analysis to classify the HNSCC samples. Least absolute shrinkage and selection operator (LASSO) regression was applied to construct an m6A signature-based HNSCC risk prediction model. Cell type identification based on estimating relative subsets of RNA transcripts (CIBERSORT) algorithms was adopted to evaluate the immune cell infiltration level in the tumor microenvironment. Based on the expression of m6A regulators in HNSCC, we identified two clusters, cluster 1 (C1) and cluster 2 (C2). C2 showed a better prognosis than C1 and was mainly enriched in the HIPPO, MYC, NOTCH, and NRF signaling pathways. We constructed an m6A signature-based risk score model and classified patients into high- and low-risk score subgroups. The high-risk-score group showed poor clinical characteristics, higher immune infiltration levels, higher chemokine and chemokine receptor expression levels, and lower immune checkpoint gene expression than the low-risk-score subgroup. In conclusion, our comprehensive analysis suggests that the m6A signature-based risk score might function as a good prognostic predictor. Our study may provide novel therapeutic clues and help predict the prognosis of HNSCC.
    DOI:  https://doi.org/10.1038/s41598-022-20873-6
  29. Front Genet. 2022 ;13 1007696
    Comprehensive analysis about prognostic and immunological role of WTAP in pan-cancer.
    Jiangchu Lei, Yuzhi Fan, Chaobiao Yan, Yeernaer Jiamaliding, Yang Tang, Jiawei Zhou, Mengna Huang, Guomin Ju, Jian Wu, Chuanhui Peng.
      Background: Wilms tumor 1-associated protein (WTAP) plays a critical role in ribonucleic acid (RNA) methylation of N6 adenosine (m6A) modification, which is closely related with varieties of biological process. However, the role of WTAP in cancers remains to be determined. This study is designed to demonstrate the prognostic landscape of WTAP in pan-cancer and explore the relationship between WTAP expression and immune infiltration. Methods: Here, we investigated the expression level and prognostic role of WTAP in pan-cancer using multiple databases, including PrognoScan, GEPIA, and Kaplan-Meier Plotter. Then, applying the GEPIA and TIMER databases, we illustrated the correlations between WTAP expression and immune infiltration in tumors, especially liver hepatocellular carcinoma (LIHC), and esophageal carcinoma (ESCA). Results: WTAP had significant higher expression levels in tumor tissues of ESCA, LIHC, etc., while lower expression levels in those of bladder urothelial carcinoma (BLCA), breast invasive carcinoma (BRCA), etc. And WTAP demonstrated multifaceted prognostic value in cancers. Of our interests, WTAP exerted a harmful effect on LIHC patient for overall survival (OS) and progression free survival (PFS). WTAP expression also significantly associated with the infiltration levels of B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils, and dendritic cells (DC) in LIHC but not ESCA. Furthermore, combined analysis about WTAP expression level and immune cell specific gene markers implied WTAP correlates with regulatory cells (T reg) infiltration in LIHC and ESCA. Conclusion: The m6A regulator WTAP can serve as a prognostic biomarker for certain tumor types in pan-cancer and potentially result from immune cell infiltration.
    Keywords:  WTAP; database; immune infiltration; pan-cancer; survival analaysis
    DOI:  https://doi.org/10.3389/fgene.2022.1007696
  30. Clin Transl Med. 2022 Sep;12(9): e1028
    Positive epigenetic regulation loop between AR and NSUN2 promotes prostate cancer progression.
    Wenkai Zhu, Fangning Wan, Wenhao Xu, Zheng Liu, Junjie Wang, Hena Zhang, Shenglin Huang, Dingwei Ye.
       BACKGROUND: Prostate cancer (PCa) is a major type of cancer in man worldwide. Androgen deprivation therapy (ADT) and the next-generation androgen receptor (AR) pathway inhibitors have acquired great success in treating PCa. However, patients treated with ADT or AR targeted therapy are inevitably developing into castration-resistant prostate cancer (CRPC) or becoming drug resistance. The role of mRNA 5-methylcytosine (m5C) modification in cancers is largely unknown. This study aimed to explore the role of the m5C methyltransferase NSUN2 in Prostate cancer (PCa).
    METHODS: The expression of NSUN2 and its clinicopathological impact were evaluated in PCa cohorts. The effect of NSUN2 on the biological characteristics of PCa cells was investigated on the basis of gain-offunction and loss-of-function analyses. Subcutaneous models further uncovered the role of NSUN2 in tumor growth. Epi-transcriptome assays with RNA bisulfite sequencing (RNA-BisSeq) analysis and in vitro enzyme reaction assays were performed to validate the targeted effect of NSUN2 on AR. AR-binding sites in the NSUN2 promoter were investigated by ChIP and luciferase assays to uncover the interplay between NSUN2 and AR signaling. RIP-qPCR and EMSA methods were performed to confirm that YBX1 binds to AR m5 C sites.
    RESULTS: NSUN2 is highly expressed in PCa and predicts poor outcome. NSUN2 plays roles as a PCa oncogene both in vitro and in vivo. Depletion of NSUN2 results in decreased expression and activities of AR, including AR-V7. Mechanistically, NSUN2 posttranscriptionally stabilized AR by cluster m5 C modification in a m5CYBX1-dependent manner. Strikingly, treatment with enzalutamide, an effective AR inhibitor, reduces NSUN2 expression and decreases the m5C modification level in prostate cancer cells. Finally, we found that AR transcriptionally regulates NSUN2.
    CONCLUSION: NSUN2 stabilizes AR mRNA through cluster 5-methylcytosine modification and activates a positive feedback loop to promote prostate cancer.
    Keywords:  AR-V7; NSUN2; androgen receptor; castration-resistant prostate cancer; cluster; cytosine-5 methylation; prostate cancer
    DOI:  https://doi.org/10.1002/ctm2.1028
  31. Cell Prolif. 2022 Oct 01. e13344
    Circ-CTNNB1 drives aerobic glycolysis and osteosarcoma progression via m6A modification through interacting with RBM15.
    Feng Yang, Yangyang Liu, Jun Xiao, Bo Li, Yajun Chen, Anpei Hu, Jin Zeng, Zhili Liu, Hucheng Liu.
       OBJECTIVES: Circular RNAs (circRNAs) are a subclass of noncoding RNAs, playing essential roles in tumorigenesis and aggressiveness. Recent studies have revealed the pivotal functions of circ-CTNNB1 (a circular RNA derived from CTNNB1) in cancer progression. However, little is known about the role of circ-CTNNB1 in osteosarcoma (OS), a highly malignant bone tumour in children and adolescents.
    METHODS: Circ-CTNNB1 was analysed by qRT-PCR, and the results were confirmed by Sanger sequencing. The interaction and effects between circ-CTNNB1 and RNA binding motif protein 15 (RBM15) were analysed through biotin-labelled RNA pull-down and mass spectrometry, in vitro binding, and RNA electrophoretic mobility shift assays. In vitro and in vivo experiments were performed to evaluate the biological functions and underlying mechanisms of circ-CTNNB1 and RBM15 in OS cells.
    RESULTS: Circ-CTNNB1 was highly expressed in OS tissues and predominantly detected in the nucleus of OS cells. Ectopic expression of circ-CTNNB1 promoted the growth, invasion, and metastasis of OS cells in vitro and in vivo. Mechanistically, circ-CTNNB1 interacted with RBM15 and subsequently promoted the expression of hexokinase 2 (HK2), glucose-6-phosphate isomerase (GPI) and phosphoglycerate kinase 1 (PGK1) through N6-methyladenosine (m6A) modification to facilitate the glycolysis process and activate OS progression.
    CONCLUSIONS: Circ-CTNNB1 drives aerobic glycolysis and OS progression by facilitating RBM15-mediated m6A modification.
    DOI:  https://doi.org/10.1111/cpr.13344
  32. Andrologia. 2022 Aug 03. e14552
    Four types of RNA modification writers predict the prognosis of prostate cancer.
    Wei Fu, Jin Ding, Xujun You, Qixin Li, Xiaohua Pei, Guozheng Qin.
      RNA modification is an important part of epigenetic regulation. However, the relationship between RNA modification writers and prostate cancer (PCa) remains unclear. We obtained transcriptome data from The Cancer Genome Atlas; the expression of writers for four RNA modifications (N6-methyladenosine, N1-methyladenosine, alternative polyadenylation and adenosine-to-inosine RNA editing) was altered in PCa tissue when compared with normal tissue. RNA modification writers affect the expression of immune checkpoints. Gene ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that the RNA modification was related to the cell cycle. Hub genes were screened using machine learning, and a risk score model was established using multivariate Cox analysis. Univariate and multivariate Cox analyses showed that a risk score model based on RNA modification writers could be an independent prognostic factor for PCa. In conclusion, our study showed that RNA modification writers are differentially expressed in PCa and might influence the development of PCa by regulating immune checkpoints and the cell cycle. The risk score model of RNA modification writers is predicted to be an independent prognostic factor for PCa. Thus, RNA modification writers might be used as potential indicators for the clinical diagnosis of PCa.
    Keywords:  RNA modification writers; prognosis; prostate cancer
    DOI:  https://doi.org/10.1111/and.14552
  33. Front Genet. 2022 ;13 974740
    Comprehensive analysis of the expression of N6-methyladenosine RNA methylation regulators in pulmonary artery hypertension.
    Hao Zheng, Jing Hua, Hongpeng Li, Wenjuan He, Xiangyu Chen, Yingqun Ji, Qiang Li.
      Background: Pulmonary arterial hypertension (PAH) is a progressive disease characterized by pulmonary vascular remodeling. The development of PAH involves N6-methyladenosine (m6A) modification. However, the functional role of m6A regulators in PAH and the underlying regulatory mechanisms remain unknown so far. Methods: Microarray data (GSE149713) for monocrotaline induced PAH (MCT-PAH) rat models were downloaded and screened for differentially expressed genes (DEGs) and m6A regulators. Next, we screened for differentially expressed m6A regulators in endothelial cells (ECs), smooth muscle cells (SMCs), fibroblasts, interstitial macrophages, NK cells, B cells, T cells, regulatory T cells (Tregs) using scRNA sequencing data. The target DEGs of m6A regulators in ECs, SMCs, fibroblasts, and Tregs were functionally annotated using the Gene Ontology (GO) functional analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. In addition, the cellular interaction analysis was performed to reveal the receptor-ligand pairs regulated by m6A regulators. Pseudo-time trajectory analyses were performed and a ceRNA network of lncRNAs-miRNAs-mRNAs was constructed in SMCs. Furthermore, the RNA transcriptome sequencing data for the SMCs isolated from idiopathic PAH (IPAH) patients (GSE144274) were validated for differentially expressed m6A regulators. Moreover, the HNRNPA2B1 levels in the lung samples from PAH patients and MCT-PAH were determined using immunohistochemistry. Results: The m6A regulators were observed to be dysregulated in PAH. HNRNPA2B1expression level was increased in the PASMCs of scRNAs and IPAH patients. The target DEGs of HNRNPA2B1 were enriched in the regulation of muscle cell differentiation and vasculature development in PASMCs. The HNRNPA2B1 expression levels determined were consistent with the proliferation-related and collagen synthesis-related gene COL4A1. Moreover, the predicted transcription factors (TFs) foxd2/3 and NFκB could be involved in the regulation of HNRNPA2B1. HNRNPA2B1 might be regulating SMCs proliferation and phenotypic transition via rno-miR-330-3p/TGFβR3 and rno-miR-125a-3p/slc39a1. In addition, HNRNPA2B1 was observed to be highly expressed in the lung samples from MCT-PAH rat models and patients with PAH. Conclusion: In summary, the present study identified certain key functional m6A regulators that are involved in pulmonary vascular remodeling. The investigation of m6A patterns might be promising and provide biomarkers for diagnosis and treatment of PAH in the future.
    Keywords:  DEG analysis; RNA methylation; ceRNAs; m6A RNA modification; pulmonary hypertension
    DOI:  https://doi.org/10.3389/fgene.2022.974740
  34. Commun Biol. 2022 Sep 29. 5(1): 1036
    Interruption of aberrant chromatin looping is required for regenerating RB1 function and suppressing tumorigenesis.
    Xuyang Wen, Tianyi Ding, Fang Li, Jiayan Fan, Xianqun Fan, Renbing Jia, He Zhang.
      RB transcriptional corepressor 1 (RB1) is a critical regulatory gene in physiological and pathological processes. Genetic mutation is considered to be the main cause of RB1 inactivation. However, accumulating evidence has shown that not all RB1 dysfunction is triggered by gene mutations, and the additional mechanism underlying RB1 dysfunction remains unclear. Here, we firstly reveal that a CCCTC binding factor (CTCF) mediated intrachromosomal looping served as a regulatory inducer to inactivate RB1. Once the core genomic fragment was deleted by Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 (CRISPR/Cas9), this intrachromosomal looping was disrupted. After the open of chromatin, Enhancer of Zeste Homolog 2 (EZH2) was released and decreased the level of Tri-Methyl-Histone H3 Lys27 (H3K27me3) at the RB1 promoter, which substantially restored the expression of RB protein (pRB) and inhibited tumorigenesis. In addition, targeted correction of abnormal RB1 looping using the small-molecule compound GSK503 efficiently restored RB1 transcription and suppressed tumorigenesis. Our study reveals an alternative transcriptional mechanism underlying RB1 dysfunction independent of gene mutation, and advancing the discovery of potential therapeutic chemicals based on aberrant chromatin looping.
    DOI:  https://doi.org/10.1038/s42003-022-04007-2
  35. BMC Neurosci. 2022 Sep 26. 23(1): 54
    Long-term exercise training down-regulates m6A RNA demethylase FTO expression in the hippocampus and hypothalamus: an effective intervention for epigenetic modification.
    Shu-Jing Liu, Tong-Hui Cai, Chun-Lu Fang, Shao-Zhang Lin, Wen-Qi Yang, Yuan Wei, Fu Zhou, Ling Liu, Yuan Luo, Zi-Yi Guo, Ge Zhao, Ya-Ping Li, Liang-Ming Li.
       BACKGROUND: Exercise boosts the health of some brain parts, such as the hippocampus and hypothalamus. Several studies show that long-term exercise improves spatial learning and memory, enhances hypothalamic leptin sensitivity, and regulates energy balance. However, the effect of exercise on the hippocampus and hypothalamus is not fully understood. The study aimed to find epigenetic modifications or changes in gene expression of the hippocampus and hypothalamus due to exercise.
    METHODS: Male C57BL/6 mice were randomly divided into sedentary and exercise groups. All mice in the exercise group were subjected to treadmill exercise 5 days per week for 1 h each day. After the 12-week exercise intervention, the hippocampus and hypothalamus tissue were used for RNA-sequencing or molecular biology experiments.
    RESULTS: In both groups, numerous differentially expressed genes of the hippocampus (up-regulated: 53, down-regulated: 49) and hypothalamus (up-regulated: 24, down-regulated: 40) were observed. In the exercise group, increased level of N6-methyladenosine (m6A) was observed in the hippocampus and hypothalamus (p < 0.05). Furthermore, the fat mass and obesity-associated gene (FTO) of the hippocampus and hypothalamus were down-regulated in the exercise group (p < 0.001). In addition, the Fto co-expression genes of the mouse brain were studied and analyzed using database to determine the potential roles of exercise-downregulated FTO in the brain.
    CONCLUSION: The findings demonstrate that long-term exercise might elevates the levels of m6A-tagged transcripts in the hippocampus and hypothalamus via down-regulation of FTO. Hence, exercise might be an effective intervention for epigenetic modification.
    Keywords:  Exercise; FTO; Hippocampus; Hypothalamus; RNA-sequencing
    DOI:  https://doi.org/10.1186/s12868-022-00742-8
  36. Cell Death Dis. 2022 Sep 25. 13(8): 728
    Histocompatibility Minor 13 (HM13), targeted by miR-760, exerts oncogenic role in breast cancer by suppressing autophagy and activating PI3K-AKT-mTOR pathway.
    Haiyan Yang, Zhi Li, Zhangwei Wang, Xu Zhang, Xinyuan Dai, Guoren Zhou, Qiang Ding.
      Histocompatibility Minor 13 (HM13) is reported to participate in regulating multiple cancers. In the present study, we uncovered that HM13 was highly expressed in breast cancer and correlated with worse prognosis. Downregulation of HM13 could suppress breast cancer cell proliferation and metastasis abilities. Tumorigenicity mediated by HM13 was also observed in the xenograft model. Knockdown of HM13 could activate autophagy by inducing endoplasmic reticulum (ER) stress. Moreover, further experiments demonstrated that downregulated HM13 could inhibit PI3K-AKT-mTOR pathway. We then verified that HM13 was a direct target of miR-760 functioned as a tumor -suppressor in breast cancer. And the tumor suppressive effects of miR-760 could be partially reversed by HM13. Taken together, these findings elucidated that HM13, targeted by miR-760, could play an oncogenic role in breast cancer by inducing autophagic inhibition and facilitating PI3K-AKT-mTOR pathway. Our findings suggested HM13 could act as a novel therapeutic target candidate for breast cancer and supported the idea that autophagy inducers might represent a new approach to treat breast cancer.
    DOI:  https://doi.org/10.1038/s41419-022-05154-4
  37. Cell Res. 2022 Sep 27.
    Cryo-EM structures of human m6A writer complexes.
    Shichen Su, Shanshan Li, Ting Deng, Minsong Gao, Yue Yin, Baixing Wu, Chao Peng, Jianzhao Liu, Jinbiao Ma, Kaiming Zhang.
      N6-methyladenosine (m6A) is the most abundant ribonucleotide modification among eukaryotic messenger RNAs. The m6A "writer" consists of the catalytic subunit m6A-METTL complex (MAC) and the regulatory subunit m6A-METTL-associated complex (MACOM), the latter being essential for enzymatic activity. Here, we report the cryo-electron microscopy (cryo-EM) structures of MACOM at a 3.0-Å resolution, uncovering that WTAP and VIRMA form the core structure of MACOM and that ZC3H13 stretches the conformation by binding VIRMA. Furthermore, the 4.4-Å resolution cryo-EM map of the MACOM-MAC complex, combined with crosslinking mass spectrometry and GST pull-down analysis, elucidates a plausible model of the m6A writer complex, in which MACOM binds to MAC mainly through WTAP and METTL3 interactions. In combination with in vitro RNA substrate binding and m6A methyltransferase activity assays, our results illustrate the molecular basis of how MACOM assembles and interacts with MAC to form an active m6A writer complex.
    DOI:  https://doi.org/10.1038/s41422-022-00725-8
  38. Int J Neuropsychopharmacol. 2022 Sep 26. pii: pyac068. [Epub ahead of print]
    M 6A RNA Methylation-Based Epitranscriptomic Modifications in Plasticity-Related Genes via miR-124-C/EBPα-FTO-Transcriptional Axis in the Hippocampus of Learned Helpless Rats.
    Bhaskar Roy, Shinichiro Ochi, Yogesh Dwivedi.
       BACKGROUND: Impaired synaptic plasticity has been linked to dynamic gene regulatory network changes. Recently, gene regulation has been introduced with the emerging concept of unique m 6A-based reversible transcript methylation. In this study, we tested whether m 6A RNA methylation may potentially serve as a link between the stressful insults and altered expression of plasticity-related genes.
    METHODS: Expression of plasticity genes Nr3c1, Creb1, Ntrk2; m6A modifying enzymes Fto, Mettl3, Mettl14; DNA methylation enzymes Dnmt1, Dnmt3a; transcription factor C/ebp-α; and miRNA-124-3p were determined by qPCR in the hippocampus of rats who showed susceptibility to develop stress-induced depression (learned helplessness, LH). M 6A methylation of plasticity-related genes was determined following m 6A mRNA immunoprecipitation. Chromatin immunoprecipitation was used to examine the endogenous binding of C/EBP-αto the Fto promoter. MiR-124-mediated post-transcriptional inhibition of Fto via C/EBPα was determined using an in-vitro model.
    RESULTS: Hippocampus of LH rats showed downregulation of Nr3c1, Creb1, and Ntrk2 along with enrichment in their m 6A methylation. A downregulation in demethylating enzyme Fto and upregulation in methylating enzyme Mettl3 were also noted. The Fto promoter was hypomethylated due to the lower expression of Dnmt1 and Dnmt3a. At the same time, there was a lower occupancy of transcription factor C/EBPα on the Fto promoter. Conversely, C/ebp-α transcript was downregulated via induced miR-124-3p expression.
    CONCLUSIONS: Our study mechanistically linked defective C/EBP-α-FTO-axis, epigenetically influenced by induced expression of miR-124-3p, in modifying m 6A enrichment in plasticity-related genes. This could potentially be linked with abnormal neuronal plasticity in depression.
    Keywords:  C/EBPα; FTO; M 6A methylation; depression; hippocampus; miR-124-3p; plasticity
    DOI:  https://doi.org/10.1093/ijnp/pyac068
This page is being maintained by Thomas Krichel. It was last updated on 2024‒11‒22 at 4:28.