bims-rimeca 2021-03-21 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2021–03–21
25 papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics

m6A RNA methylation regulators play an important role in the prognosis of patients with testicular germ cell tumor.
Gene Expression Profile and Prognostic Value of m6A RNA Methylation Regulators in Hepatocellular Carcinoma.
Comprehensive Analysis of Expression Regulation for RNA m6A Regulators With Clinical Significance in Human Cancers.
Role of m6A methyltransferase component VIRMA in multiple human cancers (Review).
m6A regulator-mediated RNA methylation modification patterns are involved in immune microenvironment regulation of periodontitis.
m6A Modifications Play Crucial Roles in Glial Cell Development and Brain Tumorigenesis.
The m6A methyltransferase METTL3 promotes hypoxic pulmonary arterial hypertension.
RNA N6-Methyladenosine Regulator-Mediated Methylation Modifications Pattern and Immune Infiltration Features in Glioblastoma.
Identification of an N6-methyladenosine-mediated positive feedback loop that promotes Epstein-Barr virus infection.
N6 -methyladenosine modification of lncRNA Pvt1 governs epidermal stemness.
Expression patterns and prognostic value of m6A RNA methylation regulators in adrenocortical carcinoma.
The role of N6-methyladenosine modification in the life cycle and disease pathogenesis of hepatitis B and C viruses.
METTL3 regulates skeletal muscle specific miRNAs at both transcriptional and post-transcriptional levels.
The Impact of m6A RNA Modification in Therapy Resistance of Cancer: Implication in Chemotherapy, Radiotherapy, and Immunotherapy.
Prognostic and Predictive Value of m6A "Eraser" Related Gene Signature in Gastric Cancer.
An integrated model of N6-methyladenosine regulators to predict tumor aggressiveness and immune evasion in pancreatic cancer.
N6-methyladenosine modification of circCUX1 confers radioresistance of hypopharyngeal squamous cell carcinoma through caspase1 pathway.
Identification of m6A-Associated RNA Binding Proteins Using an Integrative Computational Framework.
METTL3 regulates PM2.5-induced cell injury by targeting OSGIN1 in human airway epithelial cells.
Histone lactylation drives oncogenesis by facilitating m6A reader protein YTHDF2 expression in ocular melanoma.
Emerging role of RNA modification N6-methyladenosine in immune evasion.
FTO-mediated cytoplasmic m6Am demethylation adjusts stem-like properties in colorectal cancer cell.
Low expression of TRAF3IP2-AS1 promotes progression of NONO-TFE3 translocation renal cell carcinoma by stimulating N6-methyladenosine of PARP1 mRNA and downregulating PTEN.
Dual effects of N6-methyladenosine on cancer progression and immunotherapy.
m6A methylation potentiates cytosolic dsDNA recognition in a sequence-specific manner.

Transl Androl Urol. 2021 Feb;10(2): 662-679

m6A RNA methylation regulators play an important role in the prognosis of patients with testicular germ cell tumor.

Rong Cong, Chengjian Ji, Jiayi Zhang, Qijie Zhang, Xiang Zhou, Liangyu Yao, Jiaochen Luan, Xianghu Meng, Ninghong Song.

   Background: N6-methyladenosine (m6A) is found to be associated with promoting tumorigenesis in different types of cancers, however, the function of m6A-related genes in testicular germ cell tumors (TGCT) development remains to be illuminated. This study aimed to investigated the prognostic value of m6A RNA methylation regulators in TGCT.
Methods: We collected TGCT patients' information about clinicopathologic parameters and twenty-two m6A regulatory genes expression from The Cancer Genome Atlas (TCGA) database and Genotype-Tissue Expression (GTEx). We analyzed the differentially expressed m6A RNA methylation regulators between tumor tissues and normal tissues, as well as the correlation of m6A RNA methylation regulators. By using Cox univariate analysis, last absolute shrinkage and selection operator (LASSO) Cox regression algorithm and Cox multivariate proportional hazards regression analysis, a risk score was constructed based on a TCGA training cohort, and further verified in the TCGA testing cohort. Then, univariate and multivariate Cox regression analyses were used to evaluate the relationship between risk score and progression-free survival (PFS) in TGCT. Finally, the six-gene risk score was further verified by two gene expression profiles (GSE3218 and GSE10783) as an independent external validation cohort.
Results: Distinct expression patterns of m6A regulatory genes were identified between TGCT tissues and normal tissues in TCGA and GTEx datasets. To predict prognosis of TGCT patients, a risk score was calculated based on six selected m6A RNA methylation regulators (YTHDF1, RBM15, IGF2BP1, ZC3H13, METTL3, and FMR1). Additionally, we found significant differences between the high-risk and low-risk groups in serum marker study levels and histologic subtype. Univariate and multivariate analysis indicated that high risk score was associated with unfavorable PFS. Ultimately, the risk score was further verified by two gene expression profiles (GSE3218 and GSE10783).
Conclusions: Based on six selected m6A RNA methylation regulators, we developed a m6A methylation related risk score that can independently predict the prognosis of TGCT patients, and verify the prediction efficiency in TCGA and GEO datasets. Patients in high-risk group were associated with serum tumor marker study levels beyond the normal limits, non-seminoma, and unfavorable survival time. However, further prospective experiments should be carried out to verify our results.

Keywords:  N6-methyladenosine (m6A); Testicular germ cell tumors (TGCT); m6A RNA methylation; prognosis; risk score

DOI:  https://doi.org/10.21037/tau-20-963
J Hepatocell Carcinoma. 2021 ;8 85-101

Gene Expression Profile and Prognostic Value of m6A RNA Methylation Regulators in Hepatocellular Carcinoma.

Xian Chang, Yang-Fan Lv, Jing He, Ya Cao, Chang-Qing Li, Qiao-Nan Guo.

   Background: N6-methyladenosine (m6A) RNA methylation is the most prevalent modification of mammalian RNA, and it is associated with tumorigenesis and cancer progression. Its regulation is mediated via m6A-related regulators, including "erasers," "readers," and "writers". The present study evaluated the expression profile, risk signature and prognostic value of 13 m6A regulators in hepatocellular carcinoma (HCC) using different datasets, including The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) and clinical samples.
Methods: We used 374 HCC samples derived from the TCGA database, 569 HCC samples from 2 GEO datasets, and clinical tumour and nontumour tissues derived from 60 patients with HCC who underwent surgery in Xinqiao Hospital Chongqing to assess the gene expression profiles and prognostic values of m6A-related regulators in HCC.
Results: Eight of 13 core m6A-related regulators were overexpressed in all databases, including TCGA, GSE, clinical tumour and nontumour tissues of HCC. Two clusters (Cluster 1 and Cluster 2) were identified via consensus clustering. Cluster 2 was associated with poorer prognosis, higher tumour grade, higher AFP levels, and worse outcome compared to Cluster 1, which indicates that these m6A-related regulators are highly correlated with HCC malignancy. We performed survival analyses using the Log rank tests and a Cox regression model. Gene enrichment analysis was used to detect the related KEGG and GO pathways. We derived a prognostic risk signature using five selected m6A-related regulators.
Conclusion: Our work suggested that m6A-related regulators might be key participants in the tumour progression of HCC and potential biomarkers with prognostic value.

Keywords:  N6-methyladenosine; RNA methylation regulators; RNA modification; hepatocellular carcinoma; m6A; prognosis

DOI:  https://doi.org/10.2147/JHC.S296438
Front Oncol. 2021 ;11 624395

Comprehensive Analysis of Expression Regulation for RNA m6A Regulators With Clinical Significance in Human Cancers.

Xiaonan Liu, Pei Wang, Xufei Teng, Zhang Zhang, Shuhui Song.

   Background: N6-methyladenosine (m6A), the most abundant chemical modification on eukaryotic messenger RNA (mRNA), is modulated by three class of regulators namely "writers," "erasers," and "readers." Increasing studies have shown that aberrant expression of m6A regulators plays broad roles in tumorigenesis and progression. However, it is largely unknown regarding the expression regulation for RNA m6A regulators in human cancers.
Results: Here we characterized the expression profiles of RNA m6A regulators in 13 cancer types with The Cancer Genome Atlas (TCGA) data. We showed that METTL14, FTO, and ALKBH5 were down-regulated in most cancers, whereas YTHDF1 and IGF2BP3 were up-regulated in 12 cancer types except for thyroid carcinoma (THCA). Survival analysis further revealed that low expression of several m6A regulators displayed longer overall survival times. Then, we analyzed microRNA (miRNA)-regulated and DNA methylation-regulated expression changes of m6A regulators in pan-cancer. In total, we identified 158 miRNAs and 58 DNA methylation probes (DMPs) involved in expression regulation for RNA m6A regulators. Furthermore, we assessed the survival significance of those regulatory pairs. Among them, 10 miRNAs and 7 DMPs may promote cancer initiation and progression; conversely, 3 miRNA/mRNA pairs in kidney renal clear cell carcinoma (KIRC) may exert tumor-suppressor function. These findings are indicative of their potential prognostic values. Finally, we validated two of those miRNA/mRNA pairs (hsa-miR-1307-3p/METTL14 and hsa-miR-204-5p/IGF2BP3) that could serve a critical role for potential clinical application in KIRC patients.
Conclusions: Our findings highlighted the importance of upstream regulation (miRNA and DNA methylation) governing m6A regulators' expression in pan-cancer. As a result, we identified several informative regulatory pairs for prognostic stratification. Thus, our study provides new insights into molecular mechanisms of m6A modification in human cancers.

Keywords:  DNA methylation; N6-methyladenosine; The Cancer Genome Atlas; microRNA; prognosis

DOI:  https://doi.org/10.3389/fonc.2021.624395
Cancer Cell Int. 2021 Mar 17. 21(1): 172

Role of m6A methyltransferase component VIRMA in multiple human cancers (Review).

Wei Zhu, Jing-Zi Wang, Ji-Fu Wei, Chen Lu.

  N6-Methyladenosine (m6A) modification is one of the most widely distributed RNA modifications in eukaryotes. It participates in various RNA functions and plays vital roles in tissue development, stem cell formation and differentiation, heat shock response control, and circadian clock controlling, particularly during tumor development. The reversible regulation of m6A modification is affected by the so-called 'reader', 'writer' and 'eraser'. As a required component and the largest methyltransferase, vir-like m6A methyltransferase associated (VIRMA) can promote the progression of cancer and is associated with poor survival in multiple types of cancer. The present review investigated the role of VIRMA in various types of cancer. In an m6A-dependent or -independent manner, VIRMA can play an oncogenic role by regulating cancer cell proliferation, migration and invasion, metastasis, apoptosis resistance and tumor growth in different pathways by targeting stem factors, CCAT1/2, ID2, GATA3, CDK1, c-Jun, etc. VIRMA can also predict better prognosis in kidney renal clear cell carcinoma (KIRC), kidney renal papillary cell carcinoma (KIRP) and papillary thyroid carcinoma by TCGA analysis. The obvious oncogenic roles of VIRMA observed in different types of cancer and the mechanisms of VIRMA promoting cancers provided the basis for potential therapeutic targeting for cancer treatments.

Keywords:  Cancer; KIAA1429; M6A; Therapy; VIRMA

DOI:  https://doi.org/10.1186/s12935-021-01868-1
J Cell Mol Med. 2021 Mar 16.

m6A regulator-mediated RNA methylation modification patterns are involved in immune microenvironment regulation of periodontitis.

Xiaoqi Zhang, Shizhen Zhang, Xinyu Yan, Yue Shan, Lu Liu, Jing Zhou, Qianyun Kuang, Minqi Li, Hu Long, Wenli Lai.

  The role of epigenetic regulation in immunity is emerging, especially for RNA N6-methyladenosine (m6A) modification. However, little is known about the role of m6A in the regulation of the immune microenvironment of periodontitis. Thus, we aim to investigate the impact of m6A modification in periodontitis immune microenvironment. The RNA modification patterns mediated by 23 m6A-regulators were systematically evaluated in 310 periodontitis samples. The impact of m6A modification on immune microenvironment characteristics was explored, including infiltrating immunocytes, immune reaction gene-sets and HLAs (human leukocyte antigen) gene. m6A phenotype-related immune genes were also identified. 17 m6A regulators were dysregulated and a 15-m6A regulator signature can well distinguish periodontitis and control samples. ALKBH5 and FMR1 are closely related to infiltrating monocyte abundance. ELAVL1 and CBLL1 are significant regulators in immune reaction of TNF_Family_Members_Receptors and Cytokine. The expression of HLA-B and HLA-DOA is affected by ALKBH5 and LRPPRC. 3 distinct RNA modification patterns mediated by 23 m6A regulators were identified. They differ from immunocyte abundance, immune reaction and HLA gene. 1631 m6A phenotype-related genes and 70 m6A-mediated immune genes were identified, and the biological functions of these were explored. Our finding demonstrated the m6A modification plays a crucial role in the diversity and complexity of the immune microenvironment of periodontitis.

Keywords:  RNA modification; epigenetics; immune microenvironment; immunity; m6A; periodontitis

DOI:  https://doi.org/10.1111/jcmm.16469
Front Oncol. 2021 ;11 611660

m6A Modifications Play Crucial Roles in Glial Cell Development and Brain Tumorigenesis.

Jing Wang, Yongqiang Sha, Tao Sun.

  RNA methylation is a reversible post-transcriptional modification to RNA and has a significant impact on numerous biological processes. N 6-methyladenosine (m6A) is known as one of the most common types of eukaryotic mRNA methylation modifications, and exists in a wide variety of organisms, including viruses, yeast, plants, mice, and humans. Widespread and dynamic m6A methylation is identified in distinct developmental stages in the brain, and controls development of neural stem cells and their differentiation into neurons, glial cells such as oligodendrocytes and astrocytes. Here we summarize recent advances in our understanding of RNA methylation regulation in brain development, neurogenesis, gliogenesis, and its dysregulation in brain tumors. This review will highlight biological roles of RNA methylation in development and function of neurons and glial cells, and provide insights into brain tumor formation, and diagnostic and treatment strategies.

Keywords:  N6-methyladenosine (m6A); brain development; brain tumor; glial cell; glioma; neural stem cell

DOI:  https://doi.org/10.3389/fonc.2021.611660
Life Sci. 2021 Mar 16. pii: S0024-3205(21)00351-9. [Epub ahead of print] 119366

The m6A methyltransferase METTL3 promotes hypoxic pulmonary arterial hypertension.

Yuhan Qin, Yong Qiao, Linqing Li, Erfei Luo, Dong Wang, Yuyu Yao, Chengchun Tang, Gaoliang Yan.

   AIMS: N6-methyladenosine (m6A) is the most prevalent internal chemical RNA modification in mammal mRNAs. Accumulating evidence has shown the critical role of m6A in cardiovascular diseases including cardiac hypertrophy, heart failure, ischemic heart disease, vascular calcification, restenosis, and aortic aneurysm. However, whether m6A participates in the occurrence and development of hypoxic pulmonary hypertension (HPH) remains largely unknown. The present study aims to explore the role of key transferase METTL3, in the development of HPH.
MATERIALS AND METHODS: Pulmonary artery smooth muscle cells (PASMCs) and hypoxic rat models were used to research the METTL3-mediated m6A in HPH. EdU, transwell and TUNEL were performed to evaluate the proliferation, migration and apoptosis rates. m6A RNA Methylation Quantification Kit and m6A-qPCR were utilized to measure the total m6A level and m6A level of PTEN mRNA. RNA immunoprecipitation was used to detect the interaction between METTL3 and PTEN mRNA.
KEY FINDINGS: Both METTL3 mRNA and protein were found abnormally upregulated in vivo and in vitro. Furthermore, downregulation of METTL3 attenuated PASMCs proliferation and migration. In addition, m6A binding protein YTHDF2 was found significantly increased in PASMCs under hypoxia. YTHDF2 recognized METTL3 mediated m6A modified PTEN mRNA and promoted the degradation of PTEN. Decreased PTEN led to over-proliferation of PASMCs through activation of PI3K/Akt signaling pathway.
SIGNIFICANCE: METTL3/YTHDF2/PTEN axis exerts a significant role in hypoxia induced PASMCs proliferation, providing a novel therapeutic target for HPH.

Keywords:  Hypoxic pulmonary hypertension; METTL3; PTEN; YTHDF2; m(6)A methylation

DOI:  https://doi.org/10.1016/j.lfs.2021.119366
Front Oncol. 2021 ;11 632934

RNA N6-Methyladenosine Regulator-Mediated Methylation Modifications Pattern and Immune Infiltration Features in Glioblastoma.

Yimin Pan, Kai Xiao, Yue Li, Yuzhe Li, Qing Liu.

  Glioblastoma (GBM) is a group of intracranial neoplasms with intra-tumoral heterogeneity. RNA N6-methyladenosine (m6A) methylation modification reportedly plays roles in immune response. The relationship between the m6A modification pattern and immune cell infiltration in GBM remains unknown. Utilizing expression data of GBM patients, we thoroughly explored the potential m6A modification pattern and m6A-related signatures based on 21 regulators. Thereafter, the m6A methylation modification-based prognostic assessment pipeline (MPAP) was constructed to quantitatively assess GBM patients' clinical prognosis combining the Robustness and LASSO regression. Single-sample gene-set enrichment analysis (ssGSEA) was used to estimate the specific immune cell infiltration level. We identified two diverse clusters with diverse m6A modification characteristics. Based on differentially expressed genes (DEGs) within two clusters, m6A-related signatures were identified to establish the MPAP, which can be used to quantitatively forecast the prognosis of GBM patients. In addition, the relationship between 21 m6A regulators and specific immune cell infiltration was demonstrated in our study and the m6A regulator ELAVL1 was determined to play an important role in the anticancer response to PD-L1 therapy. Our findings indicated the relationship between m6A methylation modification patterns and tumor microenvironment immune cell infiltration, through which we could comprehensively understand resistance to multiple therapies in GBM, as well as accomplish precise risk stratification according to m6A-related signatures.

Keywords:  glioblastoma; immune infiltration; immunotherapy; m6A; prognosis

DOI:  https://doi.org/10.3389/fonc.2021.632934
J Biol Chem. 2021 Mar 16. pii: S0021-9258(21)00325-2. [Epub ahead of print] 100547

Identification of an N6-methyladenosine-mediated positive feedback loop that promotes Epstein-Barr virus infection.

Dan-Ling Dai, Xingyang Li, Lin Wang, Chu Xie, Yanan Jin, Mu-Sheng Zeng, Zhixiang Zuo, Tian-Liang Xia.

  N6-methyladenosine (m6A) is among the most abundant mRNA modifications, particularly in eukaryotes, and is found in mammals, plants and even some viruses. Although essential for the regulation of many biological processes, the exact role of m6A modification in virus-host interactions remains largely unknown. Here, using m6A -immunoprecipitation and sequencing, we find that Epstein-Barr virus (EBV) infection decreases the m6A modification of transcriptional factor KLF4 mRNA and subsequently increases its protein level. Mechanistically, EBV immediate-early protein BZLF1 interacts with the promoter of m6A methyltransferase METTL3, inhibiting its expression. Subsequently, the decrease of METTL3 reduces the level of KLF4 mRNA m6A modification, preventing its decay by the m6A reader protein YTHDF2. As a result, KLF4 protein level is upregulated and, in turn, promotes EBV infection of nasopharyngeal epithelial cells. Thus, our results suggest the existence of a positive feedback loop formed between EBV and host molecules via cellular mRNA m6A levels, and this feedback loop acts to facilitate viral infection. This mechanism contains multiple potential targets for controlling viral infectious diseases.

Keywords:  BZLF1; Epstein-Barr virus (EBV); KLF4; METTL3; RNA methylation; RNA methyltransferase; herpesvirus; m(6)A modification; mRNA decay

DOI:  https://doi.org/10.1016/j.jbc.2021.100547
EMBO J. 2021 Mar 17. e106276

N6 -methyladenosine modification of lncRNA Pvt1 governs epidermal stemness.

Jimmy Lee, Yuchen Wu, Bryan T Harada, Yuanyuan Li, Jing Zhao, Chuan He, Yanlei Ma, Xiaoyang Wu.

  Dynamic chemical modifications of RNA represent novel and fundamental mechanisms that regulate stemness and tissue homeostasis. Rejuvenation and wound repair of mammalian skin are sustained by epidermal progenitor cells, which are localized within the basal layer of the skin epidermis. N6 -methyladenosine (m6 A) is one of the most abundant modifications found in eukaryotic mRNA and lncRNA (long noncoding RNA). In this report, we survey changes of m6 A RNA methylomes upon epidermal differentiation and identify Pvt1, a lncRNA whose m6 A modification is critically involved in sustaining stemness of epidermal progenitor cells. With genome-editing and a mouse genetics approach, we show that ablation of m6 A methyltransferase or Pvt1 impairs the self-renewal and wound healing capability of skin. Mechanistically, methylation of Pvt1 transcripts enhances its interaction with MYC and stabilizes the MYC protein in epidermal progenitor cells. Our study presents a global view of epitranscriptomic dynamics that occur during epidermal differentiation and identifies the m6 A modification of Pvt1 as a key signaling event involved in skin tissue homeostasis and wound repair.

Keywords:  Pvt1 signaling; epidermal progenitor cell; lncRNA; m6A modification

DOI:  https://doi.org/10.15252/embj.2020106276
Medicine (Baltimore). 2021 Mar 12. 100(10): e25031

Expression patterns and prognostic value of m6A RNA methylation regulators in adrenocortical carcinoma.

Yang Fu, Shanshan Sun, Jianbin Bi, Chuize Kong, Lei Yin.

ABSTRACT: Adrenocortical carcinoma (ACC) is considered a rare cancer with poor prognosis. We used public datasets from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases to assess the relationships between N6-methyladenosine (m6A)-related genes and ACC.We used the Wilcoxon signed-rank test to compare m6A-related gene expression in ACC tissues with that in normal tissues. Then, ACC patients were grouped based on a cluster analysis of m6A-related gene expression. m6A-related genes that were significantly associated with survival were incorporated into a risk signature, and 2 groups were divided according to median risk score. Fisher exact tests were utilized to analyze differences in clinical variables between groups. We compared the overall survival (OS) rates of the groups by means of Kaplan-Meier curves and Cox regression analyses.We found that RBM15, ZC3H3, YTDHF1, YTDHF2, and ALBH5 were overexpressed in ACC and that KIAA1429, YTHDC1, HNRNPC, WTAP, METTL3, and FTO were down regulated in ACC. In addition, membership in cluster 2 or the high-risk group was associated with advanced clinical factors and poor prognosis. The univariable and multivariable Cox regression analyses showed that risk score can be considered an independent prognostic factor for ACC.We found that the expression of m6A-related genes could be used as an independent prognostic factor in ACC. However, the current study has some limitations, and further studies of m6A-related genes in ACC are needed.

DOI: https://doi.org/10.1097/MD.0000000000025031
Exp Mol Med. 2021 Mar 19.

The role of N6-methyladenosine modification in the life cycle and disease pathogenesis of hepatitis B and C viruses.

Geon-Woo Kim, Aleem Siddiqui.

N6-methyladenosine (m6A) is the most prevalent modification of mammalian cellular RNAs. m6A methylation is linked to epigenetic regulation of several aspects of gene expression, including RNA stability, splicing, nuclear export, RNA folding, and translational activity. m6A modification is reversibly catalyzed by methyltransferases (m6A writers) and demethylases (m6A erasers), and the dynamics of m6A-modified RNA are regulated by m6A-binding proteins (m6A readers). Recently, several studies have shown that m6A methylation sites have been identified in hepatitis B virus (HBV) transcripts and the hepatitis C virus (HCV) RNA genome. Here, we review the role of m6A modification in HBV/HCV replication and its contribution to liver disease pathogenesis. A better understanding of the functions of m6A methylation in the life cycles of HBV and HCV is required to establish the role of these modifications in liver diseases associated with these viral infections.

DOI: https://doi.org/10.1038/s12276-021-00581-3
Biochem Biophys Res Commun. 2021 Mar 16. pii: S0006-291X(21)00418-6. [Epub ahead of print]552 52-58

METTL3 regulates skeletal muscle specific miRNAs at both transcriptional and post-transcriptional levels.

Li-Ting Diao, Shu-Juan Xie, Hang Lei, Xiu-Sheng Qiu, Meng-Chun Huang, Shuang Tao, Ya-Rui Hou, Yan-Xia Hu, Yu-Jia Sun, Qi Zhang, Zhen-Dong Xiao.

  METTL3 increasing the mature miRNA levels via N6-Methyladenosine (m6A) modification of primary miRNA (pri-miRNA) transcripts has emerged as an important post-transcriptional regulation of miRNA biogenesis. Our previous studies and others have showed that muscle specific miRNAs are essential for skeletal muscle differentiation. Whether these miRNAs are also regulated by METTL3 is still unclear. Here, we found that m6A motifs were present around most of these miRNAs, which were indeed m6A modified as confirmed by m6A-modified RNA immunoprecipitation (m6A RIP). However, we surprisingly found that these muscle specific miRNAs were repressed instead of increased by METTL3 in C2C12 in vitro differentiation and mouse skeletal muscle regeneration after injury in vivo model. To elucidate the underlined mechanism, we performed reporter assays in 293T cells and validated METTL3 increasing these miRNAs at post-transcriptional level as expected. Furthermore, in myogenic C2C12 cells, we found that METTL3 not only repressed the expression of myogenic transcription factors (TFs) which can enhance the muscle specific miRNAs, but also increased the expression of epigenetic regulators which can repress these miRNAs. Thus, METTL3 could repress the muscle specific miRNAs at transcriptional level indirectly. Taken together, our results demonstrated that skeletal muscle specific miRNAs were repressed by METTL3 and such repression is likely synthesized transcriptional and post-transcriptional regulations.

Keywords:  HDAC; MEF2C; METTL3; Skeletal muscle differentiation; m6A; miRNA

DOI:  https://doi.org/10.1016/j.bbrc.2021.03.035
Front Oncol. 2020 ;10 612337

The Impact of m6A RNA Modification in Therapy Resistance of Cancer: Implication in Chemotherapy, Radiotherapy, and Immunotherapy.

Omprakash Shriwas, Pallavi Mohapatra, Sibasish Mohanty, Rupesh Dash.

  m6A RNA methylation, which serves as a critical regulator of transcript expression, has gathered tremendous scientific interest in recent years. From RNA processing to nuclear export, RNA translation to decay, m6A modification has been studied to affect various aspects of RNA metabolism, and it is now considered as one of the most abundant epitranscriptomic modification. RNA methyltransferases (writer), m6A-binding proteins (readers), and demethylases (erasers) proteins are frequently upregulated in several neoplasms, thereby regulating oncoprotein expression, augmenting tumor initiation, enhancing cancer cell proliferation, progression, and metastasis. Though the potential role of m6A methylation in growth and proliferation of cancer cells has been well documented, its potential role in development of therapy resistance in cancer is not clear. In this review, we focus on m6A-associated regulation, mechanisms, and functions in acquired chemoresistance, radioresistance, and resistance to immunotherapy in cancer.

Keywords:  ALKBH5; METTL3; PD-1; YTHDF1; cisplatin; m6A methylation

DOI:  https://doi.org/10.3389/fonc.2020.612337
Front Oncol. 2021 ;11 631803

Prognostic and Predictive Value of m6A "Eraser" Related Gene Signature in Gastric Cancer.

Xin Xu, En Zhou, Jun Zheng, Chihao Zhang, Yinghua Zou, Jiayun Lin, Jiwei Yu.

   Background: N6-methyladenosine (m6A) RNA modification plays a critical role in gastric cancer (GC). However, the relationship between the m6A "eraser", FTO, and ALKBH5, and the prognosis of GC still remains unclear. This study aimed to evaluate the effect of FTO and ALKBH5 on the prognosis of patients and their potential roles in GC.
Materials and Methods: A total of 738 GC samples with clinical information obtained from two independent datasets were included and divided into training set and testing set. Differential expression analysis of the m6A "eraser" related genes was performed. The LASSO Cox regression model was constructed to analyze the m6A "eraser" related risk genes. The univariate and multivariate Cox regression model were employed to identify the independent prognostic factors. Kaplan-Meier method was used for survival analysis. A nomogram model was then carried out to predict the prognosis of GC patients. Additionally, GO and KEGG analyses were conducted to identify the potential role of the m6A "eraser" related genes in GC. The relative proportion of 22 different genotypes in immune infiltrating cells was calculated by CIBERSORT algorithm.
Results: In total, nine m6A "eraser" related risk genes and risk scores were obtained and calculated. Patients in high-risk group demonstrated significantly worse prognosis than those in low-risk group. Age, stage, and risk score were considered as independent prognostic factors. The nomogram model constructed accurately predicted the 3-year and 5-year overall survival (OS) of patients. Furthermore, m6A "eraser" might play a functional role in GC. The expression of m6A "eraser" leads to changes in tumor immune microenvironment.
Conclusions: FTO and ALKBH5 showed association with the prognosis of GC. The m6A "eraser" related genes, which is considered as a reliable prognostic and predictive tool, assists in predicting the OS in GC patients.

Keywords:  ALKBH5; FTO; gastric cancer; immune infiltrating cells; prognosis

DOI:  https://doi.org/10.3389/fonc.2021.631803
EBioMedicine. 2021 Mar 10. pii: S2352-3964(21)00064-5. [Epub ahead of print]65 103271

An integrated model of N6-methyladenosine regulators to predict tumor aggressiveness and immune evasion in pancreatic cancer.

Zhijun Zhou, Junxia Zhang, Chao Xu, Jingxuan Yang, Yuqing Zhang, Mingyang Liu, Xiuhui Shi, Xiaoping Li, Hanxiang Zhan, Wei Chen, Lacey R McNally, Kar-Ming Fung, Wenyi Luo, Courtney W Houchen, Yulong He, Changhua Zhang, Min Li.

   BACKGROUND: N6-methyladenosine (m6A) is the most abundant mRNA modification. Whether m6A regulators can determine tumor aggressiveness and risk of immune evasion in pancreatic ductal adenocarcinoma (PDAC) remains unknown.
METHODS: An integrated model named "m6Ascore" is constructed based on RNA-seq data of m6A regulators in PDAC. Association of m6Ascore and overall survival is validated across several different datasets. Overlaps of m6Ascore and established molecular classifications of PDAC is examined. Immune infiltration, enriched pathways, somatic copy number alterations (SCNAs), mutation profiles and response to immune checkpoint inhibitors are compared between m6Ascore-high and m6Ascore-low tumors.
FINDINGS: m6Ascore is associated with dismal overall survival and increased tumor recurrence in PDAC as well as several other solid tumors including colorectal cancer and breast cancer. Basal-like (Squamous) PDAC has higher m6Ascore than that in the classical PDAC. Mechanism study showed m6Ascore-high tumors are characterized with reduced immune infiltration and T cells exhaustion. Meanwhile, m6Ascore is associated with genes regulating cachexia and chemoresistance in PDAC. Furthermore, distinct SCNAs patterns and mutation profiles of KRAS and TP53 are present in m6Ascore-high tumors, indicating immune evasion. m6Ascore-low tumors have higher response rates to immune checkpoint inhibitors (ICIs).
INTERPRETATION: These findings indicate m6Ascore can predict aggressiveness and immune evasion in pancreatic cancer. This model has implications for pancreatic cancer prognosis and treatment response to ICIs.
FUNDING: This work was supported in part by National Institutes of Health (NIH) grants to M. Li (R01 CA186338, R01 CA203108, R01 CA247234 and the William and Ella Owens Medical Research Foundation) and NIH/National Cancer Institute Q39 award P30CA225520 to Stephenson Cancer Center.

Keywords:  Immune evasion; Immunotherapy; Pancreatic cancer, m6A regulators; RNA modification

DOI:  https://doi.org/10.1016/j.ebiom.2021.103271
Cell Death Dis. 2021 Mar 19. 12(4): 298

N6-methyladenosine modification of circCUX1 confers radioresistance of hypopharyngeal squamous cell carcinoma through caspase1 pathway.

Ping Wu, Xing Fang, Yalan Liu, Yaoyun Tang, Wei Wang, Xin Li, Yuhua Fan.

Hypopharyngeal squamous cell carcinoma (HPSCC) is one of the most common malignant tumors in otolaryngology head and neck surgery and is one of the worst prognostic malignant tumors. Endogenous circular RNA (circRNA) is more stable than mRNA, microRNA (miRNA), and long non-coding RNA (LncRNA) in exosomes, plasma, and urine, and participates in gene expression regulation to perform different functions. Therefore, circRNA is expected to become a biomarker and therapy target for many tumors. However, the expression and function of circRNA regulated by N6-methyladenosine (m6A) are still unclear in HNSCC. In this study, we demonstrated that a specific circRNA, circCUX1, was upregulated in HPSCC patients who are resistant to radiotherapy and predicts poor survival outcome. We further found that methyltransferase like 3 (METTL3) mediated the m6A methylation of circCUX1 and stabilizes its expression. Knockdown circCUX1 promotes the sensitivity of hypopharyngeal cancer cells to radiotherapy. In addition, circCUX1 binds to Caspase1 and inhibits its expression, resulting in a decrease in the release of inflammatory factors, thereby developing tolerance to radiotherapy. Our findings indicate that circCUX1 is a potential therapeutic target for radiotherapy tolerance in HPSCC patients.

DOI: https://doi.org/10.1038/s41419-021-03558-2
Front Genet. 2021 ;12 625797

Identification of m6A-Associated RNA Binding Proteins Using an Integrative Computational Framework.

Yiqian Zhang, Michiaki Hamada.

  N6-methyladenosine (m6A) is an abundant modification on mRNA that plays an important role in regulating essential RNA activities. Several wet lab studies have identified some RNA binding proteins (RBPs) that are related to m6A's regulation. The objective of this study was to identify potential m6A-associated RBPs using an integrative computational framework. The framework was composed of an enrichment analysis and a classification model. Utilizing RBPs' binding data, we analyzed reproducible m6A regions from independent studies using this framework. The enrichment analysis identified known m6A-associated RBPs including YTH domain-containing proteins; it also identified RBM3 as a potential m6A-associated RBP for mouse. Furthermore, a significant correlation for the identified m6A-associated RBPs is observed at the protein expression level rather than the gene expression level. On the other hand, a Random Forest classification model was built for the reproducible m6A regions using RBPs' binding data. The RBP-based predictor demonstrated not only competitive performance when compared with sequence-based predictions but also reflected m6A's action of repelling against RBPs, which suggested that our framework can infer interaction between m6A and m6A-associated RBPs beyond sequence level when utilizing RBPs' binding data. In conclusion, we designed an integrative computational framework for the identification of known and potential m6A-associated RBPs. We hope the analysis will provide more insights on the studies of m6A and RNA modifications.

Keywords:  N6-methyladenosine; RNA binding proteins; RNA modification; enrichment analysis; random forest

DOI:  https://doi.org/10.3389/fgene.2021.625797
J Hazard Mater. 2021 Mar 03. pii: S0304-3894(21)00536-7. [Epub ahead of print]415 125573

METTL3 regulates PM2.5-induced cell injury by targeting OSGIN1 in human airway epithelial cells.

Qi Yuan, Huanhuan Zhu, Hanting Liu, Meilin Wang, Haiyan Chu, Zhengdong Zhang.

  N6-methyladenosine (m6A) is implicated in alteration of cellular biological processes caused by exogenous environmental factors. However, little is known about the role of m6A in airborne fine particulate matter (PM2.5)-induced adverse effects. Thus, we investigated the role of m6A modification in PM2.5-induced airway epithelial cell injury. We observed a methyltransferase-like 3 (METTL3)-dependent induction of m6A modification after PM2.5 treatment in HBE and A549 cells. METTL3 knockdown attenuated PM2.5-induced apoptosis and arrest of cell cycle. mRNA sequencing and RNA N6-methyladenosine binding protein immunoprecipitation (Me-RIP) assay identified m6A-modified oxidative stress induced growth inhibitor 1 (OSGIN1) as the target gene of METTL3. Knockdown of METTL3 resulted a shorter mRNA half-life of OSGIN1 by catalyzing its m6A modification. Knockdown of METTL3 or OSGIN1 attenuated cell apoptosis, arrest of cell cycle and autophagy induced by PM2.5. In conclusion, METTL3 may mediate PM2.5-induced cell injury by targeting OSGIN1 in human airway epithelial cells. Our work uncovered a critical role of METTL3 in PM2.5-induced airway epithelial cell injury and provided insight into the vital role of m6A modification in PM2.5-induced human hazards.

Keywords:  Cell injury; METTL3; N(6)-methyladenosine; OSGIN1; PM(2.5)

DOI:  https://doi.org/10.1016/j.jhazmat.2021.125573
Genome Biol. 2021 Mar 16. 22(1): 85

Histone lactylation drives oncogenesis by facilitating m6A reader protein YTHDF2 expression in ocular melanoma.

Jie Yu, Peiwei Chai, Minyue Xie, Shengfang Ge, Jing Ruan, Xianqun Fan, Renbing Jia.

   BACKGROUND: Histone lactylation, a metabolic stress-related histone modification, plays an important role in the regulation of gene expression during M1 macrophage polarization. However, the role of histone lactylation in tumorigenesis remains unclear.
RESULTS: Here, we show histone lactylation is elevated in tumors and is associated with poor prognosis of ocular melanoma. Target correction of aberrant histone lactylation triggers therapeutic efficacy both in vitro and in vivo. Mechanistically, histone lactylation contributes to tumorigenesis by facilitating YTHDF2 expression. Moreover, YTHDF2 recognizes the m6A modified PER1 and TP53 mRNAs and promotes their degradation, which accelerates tumorigenesis of ocular melanoma.
CONCLUSION: We reveal the oncogenic role of histone lactylation, thereby providing novel therapeutic targets for ocular melanoma therapy. We also bridge histone modifications with RNA modifications, which provides novel understanding of epigenetic regulation in tumorigenesis.

Keywords:  Histone lactylation; Ocular melanoma; Transcriptional activation; YTHDF2; m6A

DOI:  https://doi.org/10.1186/s13059-021-02308-z
Cell Death Dis. 2021 Mar 19. 12(4): 300

Emerging role of RNA modification N6-methyladenosine in immune evasion.

Xin Lou, Juan-Juan Wang, Ya-Qing Wei, Jin-Jin Sun.

The innate and adaptive immune cells have complex signaling pathways for sensing and initiating immune responses against disease. These pathways are interrupted at different levels to occur immune evasion, including by N6-methyladenosine (m6A) modification. In this review, we discuss studies revealing the immune evasion mechanism by m6A modification, which underlies the retouching of these signaling networks and the rapid tolerance of innate and adaptive immune molecules during disease. We also focus on the functions of m6A in main chemokines regulation, and their roles in promotive and suppressive immune cell recruitment. We then discuss some of the current challenges in the field and describe future directions for the immunological mechanisms of m6A modification.

DOI: https://doi.org/10.1038/s41419-021-03585-z
Nat Commun. 2021 Mar 19. 12(1): 1716

FTO-mediated cytoplasmic m6Am demethylation adjusts stem-like properties in colorectal cancer cell.

Sébastien Relier, Julie Ripoll, Hélène Guillorit, Amandine Amalric, Cyrinne Achour, Florence Boissière, Jérôme Vialaret, Aurore Attina, Françoise Debart, Armelle Choquet, Françoise Macari, Virginie Marchand, Yuri Motorin, Emmanuelle Samalin, Jean-Jacques Vasseur, Julie Pannequin, Francesca Aguilo, Evelyne Lopez-Crapez, Christophe Hirtz, Eric Rivals, Amandine Bastide, Alexandre David.

Cancer stem cells (CSCs) are a small but critical cell population for cancer biology since they display inherent resistance to standard therapies and give rise to metastases. Despite accruing evidence establishing a link between deregulation of epitranscriptome-related players and tumorigenic process, the role of messenger RNA (mRNA) modifications in the regulation of CSC properties remains poorly understood. Here, we show that the cytoplasmic pool of fat mass and obesity-associated protein (FTO) impedes CSC abilities in colorectal cancer through its N6,2'-O-dimethyladenosine (m6Am) demethylase activity. While m6Am is strategically located next to the m7G-mRNA cap, its biological function is not well understood and has not been addressed in cancer. Low FTO expression in patient-derived cell lines elevates m6Am level in mRNA which results in enhanced in vivo tumorigenicity and chemoresistance. Inhibition of the nuclear m6Am methyltransferase, PCIF1/CAPAM, fully reverses this phenotype, stressing the role of m6Am modification in stem-like properties acquisition. FTO-mediated regulation of m6Am marking constitutes a reversible pathway controlling CSC abilities. Altogether, our findings bring to light the first biological function of the m6Am modification and its potential adverse consequences for colorectal cancer management.

DOI: https://doi.org/10.1038/s41467-021-21758-4
J Hematol Oncol. 2021 Mar 19. 14(1): 46

Low expression of TRAF3IP2-AS1 promotes progression of NONO-TFE3 translocation renal cell carcinoma by stimulating N6-methyladenosine of PARP1 mRNA and downregulating PTEN.

Lei Yang, Yi Chen, Ning Liu, QianCheng Shi, Xiaodong Han, Weidong Gan, Dongmei Li.

   BACKGROUND: NONO-TFE3 translocation renal cell carcinoma (NONO-TFE3 tRCC) is one subtype of RCCs associated with Xp11.2 translocation/TFE3 gene fusions RCC (Xp11.2 tRCCs). Long non-coding RNA (lncRNA) has attracted great attention in cancer research. The function and mechanisms of TRAF3IP2 antisense RNA 1 (TRAF3IP2-AS1), a natural antisense lncRNA, in NONO-TFE3 tRCC remain poorly understood.
METHODS: FISH and qRT-PCR were undertaken to study the expression, localization and clinical significance of TRAF3IP2-AS1 in Xp11.2 tRCC tissues and cells. The functions of TRAF3IP2-AS1 in tRCC were investigated by proliferation analysis, EdU staining, colony and sphere formation assay, Transwell assay and apoptosis analysis. The regulatory mechanisms among TRAF3IP2-AS1, PARP1, PTEN and miR-200a-3p/153-3p/141-3p were investigated by luciferase assay, RNA immunoprecipitation, Western blot and immunohistochemistry.
RESULTS: The expression of TRAF3IP2-AS1 was suppressed by NONO-TFE3 fusion in NONO-TFE3 tRCC tissues and cells. Overexpression of TRAF3IP2-AS1 inhibited the proliferation, migration and invasion of UOK109 cells which were derived from cancer tissue of patient with NONO-TFE3 tRCC. Mechanistic studies revealed that TRAF3IP2-AS1 accelerated the decay of PARP1 mRNA by direct binding and recruitment of N6-methyladenosie methyltransferase complex. Meanwhile, TRAF3IP2-AS1 competitively bound to miR-200a-3p/153-3p/141-3p and prevented those from decreasing the level of PTEN.
CONCLUSIONS: TRAF3IP2-AS1 functions as a tumor suppressor in NONO-TFE3 tRCC progression and may serve as a novel target for NONO-TFE3 tRCC therapy. TRAF3IP2-AS1 expression has the potential to serve as a novel diagnostic and prognostic biomarker for NONO-TFE3 tRCC detection.

Keywords:  M6A modification; NONO-TFE3; PARP1; PTEN; TRAF3IP2-AS1

DOI:  https://doi.org/10.1186/s13045-021-01059-5
Mol Ther Nucleic Acids. 2021 Jun 04. 24 25-39

Dual effects of N6-methyladenosine on cancer progression and immunotherapy.

Hui Li, Hao Wu, Qin Wang, Shipeng Ning, Shouping Xu, Da Pang.

  According to the latest global cancer statistics, cancer has become a major threat to human health, but cancer treatment has encountered many bottlenecks. As an emerging topic in epigenetics, N6-methyladenosine (m6A) is the most common internal modification on eukaryotic mRNA, which has attracted increasing attention in recent years. Accumulating studies have shown that aberrant m6A modifications have profound effects on the characteristics of tumors, which undoubtedly led to a significant breakthrough in cancer treatment. Although m6A function as an oncogene or tumor suppressor is not fully revealed, determining its precise function in the development and evolution of malignant tumors is crucial in improving clinical decisions involving targeted therapies. In this review, we briefly introduce the composition of the m6A methylation machinery and mainly summarize the biological mechanism of m6A in cancer cell death, angiogenesis, epithelial-mesenchymal transition (EMT), and therapeutic resistance. Subsequently, we present the exogenous regulatory factors of m6A and highlight the role of m6A on immune cells and cancer immunotherapy. The potential therapeutic strategies of m6A in human cancer are also discussed, considering research gaps and future applications.

Keywords:  N6-methyladenine; angiogenesis; cell death; epithelial-mesenchymal transition; therapeutic resistance; treatment

DOI:  https://doi.org/10.1016/j.omtn.2021.02.001
Open Biol. 2021 Mar;11(3): 210030

m6A methylation potentiates cytosolic dsDNA recognition in a sequence-specific manner.

Melania Balzarolo, Sander Engels, Anja J de Jong, Katka Franke, Timo K van den Berg, Muhammet F Gulen, Andrea Ablasser, Edith M Janssen, Bas van Steensel, Monika C Wolkers.

  Nucleic acid sensing through pattern recognition receptors is critical for immune recognition of microbial infections. Microbial DNA is frequently methylated at the N6 position of adenines (m6A), a modification that is rare in mammalian host DNA. We show here how that m6A methylation of 5'-GATC-3' motifs augments the immunogenicity of synthetic double-stranded (ds)DNA in murine macrophages and dendritic cells. Transfection with m6A-methylated DNA increased the expression of the activation markers CD69 and CD86, and of Ifnβ, iNos and Cxcl10 mRNA. Similar to unmethylated cytosolic dsDNA, recognition of m6A DNA occurs independently of TLR and RIG-I signalling, but requires the two key mediators of cytosolic DNA sensing, STING and cGAS. Intriguingly, the response to m6A DNA is sequence-specific. m6A is immunostimulatory in some motifs, but immunosuppressive in others, a feature that is conserved between mouse and human macrophages. In conclusion, epigenetic alterations of DNA depend on the context of the sequence and are differentially perceived by innate cells, a feature that could potentially be used for the design of immune-modulating therapeutics.

Keywords:  5′-GATC-3′ motifs; N6-methyl-adenine (m6a); cGAS–STING; dendritic cells; double-stranded (ds)DNA; macrophages

DOI:  https://doi.org/10.1098/rsob.210030