bims-rimeca 2023-01-08 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2023‒01‒08
sixteen papers selected by
Sk Ramiz Islam
Saha Institute of Nuclear Physics

BTG2 suppresses renal cell carcinoma progression through N6-methyladenosine.
N6-methyladenosine (m6A) RNA modification in the pathophysiology of heart failure: a narrative review.
Transcriptome-wide profiling and quantification of N6-methyladenosine by enzyme-assisted adenosine deamination.
Prognostic and therapeutic implication of m6A methylation in Crohn disease.
Integrated Clinical and Prognostic Analysis of the m6A RNA Methylation Regulator YTHDF3 in Pan-Cancer and its Correlation with Cancer Cell Proliferation.
WTAP-mediated m6A modification on circCMTM3 inhibits hepatocellular carcinoma ferroptosis by recruiting IGF2BP1 to increase PARK7 stability.
METTL3 protects METTL14 from STUB1-mediated degradation to maintain m6 A homeostasis.
Exclusion of m6A from splice-site proximal regions by the exon junction complex dictates m6A topologies and mRNA stability.
Joint analysis of m6A and mRNA expression profiles in the testes of idiopathic nonobstructive azoospermia patients.
KDM1A-mediated upregulation of METTL3 ameliorates Alzheimer's disease via enhancing autophagic clearance of p-Tau through m6A-dependent regulation of STUB1.
m6A regulators featured by tumor immune microenvironment landscapes and correlated with immunotherapy in non-small cell lung cancer (NSCLC).
N6-methyladenosine in macrophage function: a novel target for metabolic diseases.
Dynamic regulation and key roles of ribonucleic acid methylation.
METTL5 stabilizes c-Myc by facilitating USP5 translation to reprogram glucose metabolism and promote hepatocellular carcinoma progression.
Transcriptome-wide analysis of mRNA N6 -methyladenosine modification in the embryonic development of Spodoptera frugiperda.
Identification and comparison of m6A modifications in glioblastoma non-coding RNAs with MeRIP-seq and Nanopore dRNA-seq.

Front Oncol. 2022 ;12 1049928

BTG2 suppresses renal cell carcinoma progression through N6-methyladenosine.

Fuming Qi, Wenlong Liu, Bo Tan, Juan Zhang, Yan Ma, Congcong Cao, Fujun Ma, Bo Zhu, Jinhui Yang, Xiaoyun Liu.

  The biological functions of N6-methyladenosine (m6A) modification of mRNA have recently received a great deal of attention. In previous studies, m6A methylation modification has been shown to regulate mRNA fate and to be crucial for the progression and development of tumors. BTG2 (B-cell translocation gene 2) is a member of BTG/TOB anti-proliferative protein family. BTG2 could inhibit cell proliferation and migration and regulate the cell cycle progression. In this study, we confirm that BTG2 is frequently down-regulated in renal cell carcinoma (RCC) tissues and its low expression is associated with unfavorable prognosis and decreased m6A level. Moreover, we found that m6A methylation modifies the 5'UTR of BTG2 to promote its mRNA stability by binding to IGF2BP2. It has been shown that CRISPR/dCas13b-METLL3 can specifically increase BTG2 m6A modification to significantly increase its m6A and expression levels. Then m6A hypermethylation in BTG2 mRNA could dramatically inhibit RCC cells proliferation and migration, and induce cells apoptosis. Taken together, our data show that BTG2 functions as a tumor suppressor and is frequently silenced via m6A modification in RCC.

Keywords:  BTG2; Mettl3; RCC; dCas13b; m6A

DOI:  https://doi.org/10.3389/fonc.2022.1049928
Cardiovasc Diagn Ther. 2022 Dec;12(6): 908-925

N6-methyladenosine (m6A) RNA modification in the pathophysiology of heart failure: a narrative review.

Sihan Liu, Tongyu Wang, Zeyi Cheng, Jing Liu.

  Background and Objective: Heart failure is the end-stage of various cardiovascular diseases. Recent progress in molecular biology has facilitated the understanding of the mechanisms of heart failure development at the molecular level. N6-adenosine methylation (m6A) is a post-transcriptional modification of RNA. Recent research work reported that m6A regulates gene expression and subsequently affects the activation of cell signaling pathways related to heart failure. Moreover, m6A regulators like methyltransferase-like 3 (METTL3) were reported to participate in myocardium hypertrophy. However, the current research work related to the role of m6A participating in the occurrence of heart failure is rare in some aspects like immune cell infiltration and diabetic heart diseases. Thus, it is reasonable to review the current achievements and provide further study orientation.Methods: We searched related literature using the keywords: m6A AND heart failure in PubMed, Web of Science and Medline. The language was confined to English. The published year of searched literature ranged from 2012 to 2022. The searched results were put into Endnote software for management. Two authors investigated the searching terms and reviewed the full text of selected terms.
Key Content and Findings: m6A and its regulators are involved in the metabolism of various types of RNAs. m6A modification can regulate various types of cell signaling pathways related to the heart failure via interaction with m6A regulators. m6A and its regulators broadly participate in the myocardium fibrosis, myocardium hypertrophy, myocardial cell apoptosis, and ischemic reperfusion injury. Specifically, m6A participates in the cell apoptosis via regulation of autophagy flux. However, the current research work does not have enough evidence to prove that m6A regulator played its specific effect on the target transcript via regulating the m6A level.
Conclusions: m6A and its regulators participates in the progression of heart failure via modifying the RNA level. Future investigation of m6A should focus on the interaction between the m6A regulators and targeted transcript. Besides, the regulation role of m6A in immune cell infiltration and diabetic heart diseases should also be focused.

Keywords:  Heart failure (HF); N6-adenosine methylation (m6A); cell apoptosis; myocardial fibrosis; myocardial hypertrophy; narrative review

DOI:  https://doi.org/10.21037/cdt-22-277
Nat Biotechnol. 2023 Jan 02.

Transcriptome-wide profiling and quantification of N6-methyladenosine by enzyme-assisted adenosine deamination.

Yu-Lan Xiao, Shun Liu, Ruiqi Ge, Yuan Wu, Chuan He, Mengjie Chen, Weixin Tang.

N6-methyladenosine (m6A), the most abundant internal messenger RNA modification in higher eukaryotes, serves myriad roles in regulating cellular processes. Functional dissection of m6A is, however, hampered in part by the lack of high-resolution and quantitative detection methods. Here we present evolved TadA-assisted N6-methyladenosine sequencing (eTAM-seq), an enzyme-assisted sequencing technology that detects and quantifies m6A by global adenosine deamination. With eTAM-seq, we analyze the transcriptome-wide distribution of m6A in HeLa and mouse embryonic stem cells. The enzymatic deamination route employed by eTAM-seq preserves RNA integrity, facilitating m6A detection from limited input samples. In addition to transcriptome-wide m6A profiling, we demonstrate site-specific, deep-sequencing-free m6A quantification with as few as ten cells, an input demand orders of magnitude lower than existing quantitative profiling methods. We envision that eTAM-seq will enable researchers to not only survey the m6A landscape at unprecedented resolution, but also detect m6A at user-specified loci with a simple workflow.

DOI: https://doi.org/10.1038/s41587-022-01587-6
Medicine (Baltimore). 2022 Dec 23. 101(51): e32399

Prognostic and therapeutic implication of m6A methylation in Crohn disease.

Yujin He, Yonghui Hu, Mei Yuan, Weiwei Xu, Yaqin Du, Jinguo Liu.

BACKGROUND: N6-methyladenosine (m6A) methylation has been reported to participate in inflammatory bowel disease (including Crohn disease [CD]). However, the prognostic and therapeutic implication of m6A methylation modification in CD is still unclear.METHODS: Genomic information of CD patients was integrated to assess disease-related m6A regulators, and difference and correlation analyses of m6A regulators were explored by using the R packages. Next, CD patients were classified by the expression of differential and intersecting genes in m6A regulators, and difference and correlation analyses were conducted among immune infiltration and therapeutic responses. Finally, colon tissue resected from patients with CD were assessed to verify expression of Wilms tumor 1-associated protein (WTAP) and METTL14 from these m6A regulators.
RESULTS: We identified 23 m6A regulators in CD patients. Difference analysis of these regulators showed that expression of METTL14, WTAP, RBM15 and YTHDF2/3 was upregulated in the treatment group compared with the control group, with expression of METTL3, YTHDF1, leucine-rich pentatricopeptide repeat motif-containing protein, HNRNPA2B1, IGF2BP1 and fat mass and obesity-associated protein downregulated. Moreover, RBM15, WTAP, leucine-rich pentatricopeptide repeat motif-containing protein, YTHDF1 and YTHDF3 were considered the characteristic genes of CD in m6A regulators. In addition, we identified 4 intersection genes of 3 m6A cluster patterns. Based on the expression of these intersection genes, difference analysis among m6A regulators indicated that the expression of 8 m6A regulators had statistical differences among the 3 geneCluster patterns. Assays of colon tissues from CD patients showed that expression of WTAP and METTL14 were higher in areas of stenosis than non-stenosis.
CONCLUSION: m6A methylation modification might affect disease risk, immune infiltration and therapeutic responses in CD. Evaluating the expression of m6A regulators might provide insight into the prediction of disease prognosis and therapeutic responses.

DOI: https://doi.org/10.1097/MD.0000000000032399
J Cancer. 2022 ;13(15): 3623-3639

Integrated Clinical and Prognostic Analysis of the m6A RNA Methylation Regulator YTHDF3 in Pan-Cancer and its Correlation with Cancer Cell Proliferation.

Leiqun Cao, Bingjie Zeng, Yulan Wang, Xianzhao Wang, Yueyang Qin, Congcong Zhang, Mengyi Wu, Jiayi Wang, Xiao Zhang, Lifang Ma.

  Background: N6-methyladenosine (m6A) is the most abundant and extensive chemical modification of mammalian RNA molecules. Although numerous studies have investigated m6A methylation-related genes, to the best of our knowledge, none have examined the expression patterns of YTH N6-methyladenosine RNA binding protein 3 (YTHDF3) across cancers. Methods: Using various publicly available datasets, we searched for a potential carcinogenic role of YTHDF3 in 33 tumor types. Furthermore, the clinicopathological parameters, clinical prognostic value, enrichment analysis, mutations, microsatellite instability (MSI), tumor mutation burden (TMB), levels of infiltrating cells, and related immune checkpoint genes were included. Finally, we performed a validation analysis using existing clinical samples and proliferation-related functional experiments. Results: YTHDF3 is highly expressed in most cancer types and associated with patient prognosis in certain tumors. The ROC analysis suggested that YTHDF3 has high diagnostic value in 13 types of cancer. Furthermore, we found that the genes associated with YTHDF3 were enriched for translation initiation and mRNA metabolic processes. The results of the GSEA enrichment suggest that YTHDF3 may be associated with different pathways in cells in various tumor types. We further analyzed the correlations between YTHDF3 expression and MSI, TMB, and immune checkpoint genes. YTHDF3 also possibly exerts important antitumor immunotherapy effects. Additionally, the results of the immune analysis using TIMER showed that high YTHDF3 expression levels in pan-cancer tissues were related to an immunosuppressive microenvironment. Finally, we experimentally demonstrated that both overexpression and downregulation of YTHDF3 can affect cancer cell proliferation rates. Conclusion: YTHDF3 is a promising biomarker for cancer diagnosis. This study provides the first comprehensive pan-cancer report on YTHDF3 and increases our understanding of its oncogenic role in different tumors.

Keywords:  Cancer; Immunosuppressive microenvironment; Methylation; Prognosis; YTHDF3

DOI:  https://doi.org/10.7150/jca.78403
Dig Liver Dis. 2022 Dec 29. pii: S1590-8658(22)00827-1. [Epub ahead of print]

WTAP-mediated m6A modification on circCMTM3 inhibits hepatocellular carcinoma ferroptosis by recruiting IGF2BP1 to increase PARK7 stability.

Shuwei Chen, Hongxiang Xia, Langqing Sheng.

  BACKGROUND: Hepatocellular carcinoma (HCC) has poor prognosis and high mortality. CircCMTM3 was significantly up-regulated in HCC. However, the mechanism of circCMTM3 in HCC is not full elucidated.METHODS: The expression level of circCMTM3, PARK7, GPX4, and Ki67 in HCC cells and tissues were quantified by qRT-PCR, IHC, and Western blotting. The level of GSH, total iron, Fe2+, and MDA were detected by their kits. CCK-8 and flow cytometry analysis were used to evaluated cell proliferation and lipid ROS level, respectively. m6A level of circCMTM3 was assessed by MeRIP-PCR. RNA pulldown, RIP, and FISH detected the interaction between circCMTM3, WTAP, and PARK7. Tumor xenograft model was constructed to validate the function of cicrCMTM3 and WTAP.
RESULTS: CircCMTM3 and WTAP were enhanced in HCC tissues and cells. Knockdown of WTAP inhibited m6A modification of circCMTM3, which promoted HCC ferroptosis. circCMTM3 silencing suppressed the expression and stability of PARK7 through binding with IGF2BP1 in HCC cells, which finally induced ferroptosis. In vivo studies demonstrated that silencing WTAP and circCMTM3 suppressed tumor growth and promoted HCC ferroptosis in nude mice by regulating PARK7 signaling.
CONCLUSION: CircCMTM3 promoted the carcinogenesis through inhibiting ferroptosis by recruiting IGF2BP1 to increase PARK7 stability in HCC, suggesting that cicrCMTM3 may be an important marker for HCC treatment.

Keywords:  CircCMTM3; Ferroptosis; Hepatocellular carcinoma; M(6)A modification; PARK7 signaling

DOI:  https://doi.org/10.1016/j.dld.2022.12.005
EMBO Rep. 2023 Jan 04. e55762

METTL3 protects METTL14 from STUB1-mediated degradation to maintain m6 A homeostasis.

Zhan-Cheng Zeng, Qi Pan, Yu-Meng Sun, Heng-Jing Huang, Xiao-Tong Chen, Tian-Qi Chen, Bo He, Hua Ye, Shun-Xin Zhu, Ke-Jia Pu, Ke Fang, Wei Huang, Yue-Qin Chen, Wen-Tao Wang.

  N6 -Methyladenosine (m6 A) is an important RNA modification catalyzed by methyltransferase-like 3 (METTL3) and METTL14. m6 A homeostasis mediated by the methyltransferase (MTase) complex plays key roles in various biological processes. However, the mechanism underlying METTL14 protein stability and its role in m6 A homeostasis remain elusive. Here, we show that METTL14 stability is regulated by the competitive interaction of METTL3 with the E3 ligase STUB1. STUB1 directly interacts with METTL14 to mediate its ubiquitination at lysine residues K148, K156, and K162 for subsequent degradation, resulting in a significant decrease in total m6 A levels. The amino acid regions 450-454 and 464-480 of METTL3 are essential to promote METTL14 stabilization. Changes in STUB1 expression affect METTL14 protein levels, m6 A modification and tumorigenesis. Collectively, our findings uncover an ubiquitination mechanism controlling METTL14 protein levels to fine-tune m6 A homeostasis. Finally, we present evidence that modulating STUB1 expression to degrade METTL14 could represent a promising therapeutic strategy against cancer.

Keywords:  METTL14; METTL3; STUB1; m6A homeostasis; ubiquitination-mediated degradation

DOI:  https://doi.org/10.15252/embr.202255762
Mol Cell. 2022 Dec 30. pii: S1097-2765(22)01205-9. [Epub ahead of print]

Exclusion of m6A from splice-site proximal regions by the exon junction complex dictates m6A topologies and mRNA stability.

Anna Uzonyi, David Dierks, Ronit Nir, Oh Sung Kwon, Ursula Toth, Isabelle Barbosa, Cindy Burel, Alexander Brandis, Walter Rossmanith, Hervé Le Hir, Boris Slobodin, Schraga Schwartz.

  N6-methyladenosine (m6A), a widespread destabilizing mark on mRNA, is non-uniformly distributed across the transcriptome, yet the basis for its selective deposition is unknown. Here, we propose that m6A deposition is not selective. Instead, it is exclusion based: m6A consensus motifs are methylated by default, unless they are within a window of ∼100 nt from a splice junction. A simple model which we extensively validate, relying exclusively on presence of m6A motifs and exon-intron architecture, allows in silico recapitulation of experimentally measured m6A profiles. We provide evidence that exclusion from splice junctions is mediated by the exon junction complex (EJC), potentially via physical occlusion, and that previously observed associations between exon-intron architecture and mRNA decay are mechanistically mediated via m6A. Our findings establish a mechanism coupling nuclear mRNA splicing and packaging with the covalent installation of m6A, in turn controlling cytoplasmic decay.

Keywords:  N6-methyladenosine; RNA degradation; RNA modifications; exon junction complex; exon-intron architecture; gene regulation; m6A; posttranscriptional modification; splicing

DOI:  https://doi.org/10.1016/j.molcel.2022.12.026
Front Endocrinol (Lausanne). 2022 ;13 1063929

Joint analysis of m6A and mRNA expression profiles in the testes of idiopathic nonobstructive azoospermia patients.

Qiuqin Tang, Wei Wu, Yiwen Lu, Yijie Zhou, Wangfei Wu, Jinhui Li, Lianjun Pan, Xiufeng Ling, Feng Pan.

  Background: Growing evidence has indicated that epigenetic factors might be associated with the pathophysiology of idiopathic nonobstructive azoospermia (iNOA). As the most common RNA modification, N6-methyladenosine (m6A) methylation has recently attracted more attention in the regulation of spermatogenesis; however, its role in the mechanisms of iNOA is still unclear.Objective: To determine the differential expression of mRNA and m6A methylation status in the testes of iNOA patients.
Methods: Testes tissues from diagnosed iNOA and controlled obstructive azoospermia (OA) patients were collected and grouped according to the histological examinations. Total RNA was isolated and quantified by an m6A RNA Methylation Quantification Kit. The expression level of mRNAs was detected by qRT-PCR analysis. Differentially expressed m6A genes were analyzed using the human ArrayStar m6A epitranscriptomic microarray, and bioinformatics analyses were applied.
Results: A total of 36 iNOA and 8 controlled patients were included. The global expression of m6A in the iNOA group was significantly decreased. A dosage relationship was observed between the m6A decline and the degree of impaired spermatogenesis, with the successive process of normal spermatogeneis, hypospermatogenesis (HP), maturation arrest (MA), and Sertoli cell-only syndrome (SO). Four down-expressed genes (BDNF, TMEM38B, RPL3L, and C22orf42) displayed significantly lower expression of m6A methylation. Additionally, they also showed a gradually down-expressed tendency in the three groups (OA, HP, SO/MA groups). Moreover, m6A reader EIF3A was approved to have differential expression through microarrays analysis, which was consistent with the result from the qRT-PCR test.
Conclusions: The m6A expression was gradually downregulated in the testes tissue from iNOA patients in accordance with the degree of spermatogenic dysfunction. The determined differential expression of mRNA and m6A methylation status may represent potentially novel molecular targets for the mechanism study of iNOA in the epigenetic level, which could benefit the understanding of the pathophysiology of iNOA.

Keywords:  azoospermia; m6A; male infertility; methylation; spermatogenesis

DOI:  https://doi.org/10.3389/fendo.2022.1063929
Free Radic Biol Med. 2022 Dec 29. pii: S0891-5849(22)01133-9. [Epub ahead of print]

KDM1A-mediated upregulation of METTL3 ameliorates Alzheimer's disease via enhancing autophagic clearance of p-Tau through m6A-dependent regulation of STUB1.

Zhanbin Tang, Jingwei Cao, Jialin Yao, Xuehui Fan, Jingkun Zhao, Mianqiao Zhao, Qiong Duan, Baichao Han, Shurong Duan.

  BACKGROUND: Alzheimer's disease (AD) is a severe neurodegenerative disorder that progressively destroys cognitive skills. Exploring the mechanism underlying autophagic clearance of phosphorylated tau (p-Tau) contributes to developing novel therapeutic strategies for AD.METHODS: SH-SY5Y and HT22 cells were treated with Aβ1-42 to establish an in vitro model of AD. Cell viability was examined using CCK8. TUNEL staining was applied to evaluate cell apoptosis. LC3 puncta was examined by IF staining. m6A modification level was evaluated through MeRIP. RNA pull-down and RIP assays were used for analyzing the interaction between IGF2BP1 and STUB1 transcripts. The binding of KDM1A to the promoter of METTL3 was confirmed by ChIP assays. APP/PS1 transgenic mice were used as an in vivo model of AD. Cognitive skills of mice were evaluated with the Morris water maze. Hippocampal damage and Aβ deposition were detected through H&E and IHC staining.
RESULTS: Dysregulated levels of autophagy, p-Tau and m6A was observed in an in vitro model of AD. Overexpression of METTL3 or STUB1 enhanced autophagy but reduced p-Tau level in Aβ1-42-treated cells. METTL3 stabilized STUB1 mRNA through the m6A-IGF2BP1-dependent mechanism and naturally promoted STUB1 expression, thereby enhancing autophagic p-Tau clearance in Aβ1-42-treated cells. Overexpression of KDM1A enhanced autophagy, m6A modification and autophagic p-Tau clearance in Aβ1-42-treated cells. KDM1A-mediated upregulation of METTL3 promoted autophagic p-Tau clearance and ameliorated Alzheimer's disease both in vitro and in vivo.
CONCLUSION: KDM1A-mediated upregulation of METTL3 enhances autophagic clearance of p-Tau through m6A-dependent regulation of STUB1, thus ameliorating Alzheimer's disease. Our study provides novel mechanistic insights into AD pathogenesis and potential drug targets for AD.

Keywords:  Alzheimer's disease; Autophagic p-Tau clearance; KDM1A; METTL3; STUB1; m6A modification

DOI:  https://doi.org/10.1016/j.freeradbiomed.2022.12.099
Front Oncol. 2022 ;12 1087753

m6A regulators featured by tumor immune microenvironment landscapes and correlated with immunotherapy in non-small cell lung cancer (NSCLC).

Baowen Yuan, Hao Qin, Jingyao Zhang, Min Zhang, Yunkai Yang, Xu Teng, Hefen Yu, Wei Huang, Yan Wang.

  Introduction: Recent research has confirmed the critical role that epigenetic factors play in regulating the immune response. Nonetheless, what role m6A methylation modification might play in the immune response of non-small cell lung cancer (NSCLC) remains vague.Methods: Herein, the gene expression, copy number variations (CNVs), and somatic mutations of 31 m6A regulators in NSCLC and adjacent control samples from the GEO and TCGA databases were comprehensively explored. Using consensus clustering, m6A modification patterns were identified. Correlations between m6A modification patterns and immune cell infiltration traits in the tumor immune microenvironment (TME) were systematically analyzed. Differentially expressed genes were verified and screened by random forest and cox regression analysis by comparing different m6A modification patterns. Based on the retained gene panel, a risk model was built, and m6Ascore for each sample was calculated. The function of m6Ascore in NSCLC prognosis, tumor somatic mutations, and chemotherapy/immunotherapy response prediction were evaluated.
Results: Consensus clustering classified all NSCLC samples into two m6A clusters (m6A_clusterA and m6A_clusterB) according to the expression levels of 25 m6A regulator genes. Hierarchical clustering further divides the NSCLC samples into two m6A gene clusters: m6AgeneclusterA and m6AgeneclusterB. A panel of 83 genes was screened from the 194 differentially expressed genes between m6A gene clusters. Based on this, a risk score model was established. m6A modification clusters, m6A gene clusters, and m6Ascore calculated from the risk model were able to predict tumor stages, immune cell infiltration, clinical prognosis, and tumor somatic mutations. NSCLC patients with high m6Ascore have poor drug resistance to chemotherapy drugs (Cisplatin and Gemcitabine) and exhibit considerable therapeutic benefits and favorable clinical responses to anti-PD1 or anti-CTLA4 immunotherapy.
Discussion: In conclusion, methylation modification patterns mediated by the m6A regulators in individuals play a non-negligible role in prognosis prediction and immunotherapy response, which will facilitate personalized treatment and immunotherapeutic strategies for NSCLC patients in the future.

Keywords:  immunotherapy; m6A modification; m6A regulators; non-small cell lung cancer (NSCLC); tumor immune microenvironment (TME)

DOI:  https://doi.org/10.3389/fonc.2022.1087753
Trends Endocrinol Metab. 2022 Dec 29. pii: S1043-2760(22)00217-X. [Epub ahead of print]

N6-methyladenosine in macrophage function: a novel target for metabolic diseases.

Xiao Zhu, HaoJun Tang, Min Yang, Kai Yin.

  N6-methyladenosine (m6A) is one of the most prevalent internal transcriptional modifications. Evidence has highlighted changes in m6A in metabolic disorders and various metabolic diseases. However, the precise mechanisms of these m6A changes in such conditions are not understood. Macrophages are crucial for the innate immune system and exert either beneficial or harmful roles in metabolic disease. Notably, m6A was found to be closely related to macrophage phenotype and dysfunction. In this review, we summarize m6A in macrophage function from the perspective of macrophage development, activation, and polarization, pyroptosis, and metabolic disorders. Furthermore, we discuss how m6A-mediated macrophage function affects metabolic diseases, including atherosclerosis and nonalcoholic fatty liver disease (NAFLD). Finally, we discuss challenges and prospects for m6A in macrophage and metabolic diseases with the aim of providing guidance for the treatment of metabolic diseases.

Keywords:  N6-methyladenosine; macrophage; metabolic diseases

DOI:  https://doi.org/10.1016/j.tem.2022.12.006
Front Cell Neurosci. 2022 ;16 1058083

Dynamic regulation and key roles of ribonucleic acid methylation.

Jia Zou, Hui Liu, Wei Tan, Yi-Qi Chen, Jing Dong, Shu-Yuan Bai, Zhao-Xia Wu, Yan Zeng.

  Ribonucleic acid (RNA) methylation is the most abundant modification in biological systems, accounting for 60% of all RNA modifications, and affects multiple aspects of RNA (including mRNAs, tRNAs, rRNAs, microRNAs, and long non-coding RNAs). Dysregulation of RNA methylation causes many developmental diseases through various mechanisms mediated by N 6-methyladenosine (m6A), 5-methylcytosine (m5C), N 1-methyladenosine (m1A), 5-hydroxymethylcytosine (hm5C), and pseudouridine (Ψ). The emerging tools of RNA methylation can be used as diagnostic, preventive, and therapeutic markers. Here, we review the accumulated discoveries to date regarding the biological function and dynamic regulation of RNA methylation/modification, as well as the most popularly used techniques applied for profiling RNA epitranscriptome, to provide new ideas for growth and development.

Keywords:  5-hydroxymethylcytosine; 5-methylcytosine; N1-methyladenosine; N6-methyladenosine; RNA methylation; pseudouridine

DOI:  https://doi.org/10.3389/fncel.2022.1058083
Cancer Commun (Lond). 2023 Jan 05.

METTL5 stabilizes c-Myc by facilitating USP5 translation to reprogram glucose metabolism and promote hepatocellular carcinoma progression.

Peng Xia, Hao Zhang, Haofeng Lu, Kequan Xu, Xiang Jiang, Yuke Jiang, Xiangdong Gongye, Zhang Chen, Jie Liu, Xi Chen, Weijie Ma, Zhonglin Zhang, Yufeng Yuan.

  BACKGROUND: Hepatocellular carcinoma (HCC) is one of the most prevalent cancers in the world, with a high likelihood of metastasis and a dismal prognosis. The reprogramming of glucose metabolism is critical in the development of HCC. The Warburg effect has recently been confirmed to occur in a variety of cancers, including HCC. However, little is known about the molecular biological mechanisms underlying the Warburg effect in HCC cells. In this study, we sought to better understand how methyltransferase 5, N6-adenosine (METTL5) controls the development of HCC and the Warburg effect.METHODS: In the current study, quantitative real-time polymerase chain reaction and Western blotting were used to detect the expression of METTL5 in HCC tissues and cell lines. Several different cell models and animal models were established to determine the role of METTL5 in glucose metabolism reprogramming and the underlying molecular mechanism of HCC. Glutathione-S-transferase pulldown, coimmunoprecipitation, RNA sequencing, non-targeted metabolomics, polysome profiling, and luciferase reporter assays were performed to investigate the molecular mechanisms of METTL5 in HCC cells.
RESULTS: We discovered that METTL5 drove glucose metabolic reprogramming to promote the proliferation and metastasis of HCC. Mechanistically, upregulation of METTL5 promoted c-Myc stability and thus activated its downstream glycolytic genes lactate dehydrogenase A (LDHA), enolase 1 (ENO1), triosephosphate isomerase 1 (TPI1), solute carrier family 2 member 1 (SLC2A1), and pyruvate kinase M2 (PKM2). The c-Box and ubiquitin binding domain (UBA) regions of ubiquitin specific peptidase 5 (USP5) binded to c-Myc protein and inhibited K48-linked polyubiquitination of c-Myc. Further study revealed that METTL5 controled the USP5 translation process, which in turn regulated the ubiquitination of c-Myc. Furthermore, we identified cAMP responsive element binding protein 1 (CREB1)/P300 as a critical transcriptional regulator of METTL5 that promoted the transcription of METTL5 in HCC. In patient-derived tumor xenograft (PDX) models, adenovirus-mediated knockout of METTL5 had a good antitumor effect and prolonged the survival of PDX-bearing mice.
CONCLUSIONS: These findings point to a novel mechanism by which CREB1/P300-METTL5-USP5-c-Myc controls abnormal glucose metabolism and promotes tumor growth, suggesting that METTL5 is a potential therapeutic target and prognostic biomarker for HCC.

Keywords:  CREB1; METTL5; P300; USP5; c-Myc; deubiquitination; glucose metabolism; hepatocellular carcinoma

DOI:  https://doi.org/10.1002/cac2.12403
Insect Sci. 2023 Jan 06.

Transcriptome-wide analysis of mRNA N6 -methyladenosine modification in the embryonic development of Spodoptera frugiperda.

Yaqing Chen, Yushan Lai, Runzhou Liu, Lin Yao, Xiao-Qiang Yu, Xiaoyun Wang.

  N6 -methyladenosine RNA (m6 A) is the most abundant modification of messenger RNA (mRNA), which has been demonstrated in regulating various post-transcriptional processes. Many studies have shown that m6 A methylation play key roles in sex determination, neuronal functions, and embryonic development in Drosophila and mammals. Here, we analyzed transcriptome-wide profile of m6 A modification in the embryonic development of the destructive agricultural pest Spodoptera frugiperda. We found that the two key mRNA m6 A methyltransferases SfrMETTL3 and SfrMETTL14 have high homologies with other insects and mammals, suggesting that SfrMETTL3 and SfrMETTL14 may have conserved function among different species. From MeRIP sequencing analysis, we obtained 46 869 m6 A peaks representing 8 587 transcripts in the 2 h embryos after oviposition, and 41 389 m6 A peaks representing 9 230 transcripts in the 24 h embryos, respectively. In addition, 5 995 m6 A peaks were differentially expressed including 3 752 up-regulated and 2 243 down-regulated peaks. Functional analysis with GO and KEGG suggested that differentially expressed m6 A peak-modified genes were enriched in cell and organ development between the 2 h and 24 embryos. By conjoint analysis of MeRIP-seq and RNA-seq data, we found that RNA m6 A methylation may regulate the transcriptional levels of genes related to tissue and organ development from 2 h to 24 h embryos. Our study reveals the role of RNA m6 A epigenetic regulation in the embryonic development of S. frugiperda, and provides new insights for the embryonic development of insects. This article is protected by copyright. All rights reserved.

Keywords:  N6-methyladenosine; RNA methylation; Spodoptera frugiperda; embryonic development

DOI:  https://doi.org/10.1111/1744-7917.13172
Epigenetics. 2023 Jan 03. 1-14

Identification and comparison of m6A modifications in glioblastoma non-coding RNAs with MeRIP-seq and Nanopore dRNA-seq.

Raulas Krusnauskas, Rytis Stakaitis, Giedrius Steponaitis, Kristian Almstrup, Paulina Vaitkiene.

  The most prominent RNA modification - N6-methyladenosine (m6A) - affects gene regulation and cancer progression. The extent and effect of m6A on long non-coding RNAs (lncRNAs) is, however, still not clear. The most established method for m6A detection is methylated RNA immunoprecipitation and sequencing (MeRIP-seq). However, Oxford Nanopore Technologies recently developed direct RNA-seq (dRNA-seq) method, allowing m6A identification at higher resolution and in its native form. We performed whole transcriptome sequencing of the glioblastoma cell line U87-MG with both MeRIP-seq and dRNA-seq. For MeRIP-seq, m6A peaks were identified using nf-core/chipseq, and for dRNA-seq - EpiNano pipeline. MeRIP-seq analysis revealed 5086 lncRNAs transcripts, while dRNA-seq identified 336 lncRNAs transcripts from which 556 and 198 were found to be m6A modified, respectively. While 24 lncRNAs with m6A overlapped between two methods. Gliovis database analysis revealed that the expression of the major part of identified overlapping lncRNAs was associated with glioma grade or patient survival prognosis. We found that the frequency of m6A occurrence in lncRNAs varied more than 9-fold throughout the provided list of 24 modified lncRNAs. The highest m6A frequency was detected in MIR1915HG, THAP9-AS1, MALAT1, NORAD1, and NEAT1 (49-88nt), while MIR99AHG, SNHG3, LOXL1-AS1, ILF3-DT showed the lowest m6A frequency (445-261nt). Taken together, (1) we provide a high accuracy list of 24 m6A modified lncRNAs of U87-MG cells; (2) we conclude that MeRIP-seq is more suitable for an initial m6A screening study, due to its higher lncRNA coverage, whereas dRNA-seq is most useful when more in-depth analysis of m6A quantity and precise location is of interest.Abbreviations: (dRNA-seq) direct RNA-seq, (GBM) glioblastoma, (LGG) low-grade glioma, (lncRNAs) long non-coding RNAs, (m6A) N6-methyladenosine, (MeRIP-seq) methylated RNA immunoprecipitation and sequencing, (ncRNA) non-coding RNA, (ONT) Oxford Nanopore Technologi; Lietuvos Mokslo Taryba.

Keywords:  MeRIP-seq; epi-transcriptome; glioblastoma; lncRNA; m6A; nanopore dRNA-seq

DOI:  https://doi.org/10.1080/15592294.2022.2163365