bims-rimeca 2022-02-27 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2022‒02‒27
24 papers selected by
Sk Ramiz Islam
Saha Institute of Nuclear Physics

The Combined Effects of circRNA Methylation Promote Pulmonary Fibrosis.
Recent advances in crosstalk between N6-methyladenosine (m6A) modification and circular RNAs in cancer.
Chronic Hexavalent Chromium Exposure Up-regulates the RNA Methyltransferase METTL3 Expression to Promote Cell Transformation, Cancer Stem Cell-like Property and Tumorigenesis.
Integrative Analysis of m6A RNA Methylation Regulators and the Tumor Immune Microenvironment in Non-Small-Cell Lung Cancer.
Molecular Characterization of m6A Modifications in Non-Clear Cell Renal Cell Carcinoma and Potential Relationship with Pathological Types.
The m6A reader IGF2BP3 promotes acute myeloid leukemia progression by enhancing RCC2 stability.
Interplay Between m6A RNA Methylation and Regulation of Metabolism in Cancer.
METTL3/IGF2BP3 axis inhibits tumor immune surveillance by upregulating N6-methyladenosine modification of PD-L1 mRNA in breast cancer.
Mutant NPM1-Regulated FTO-Mediated m6A Demethylation Promotes Leukemic Cell Survival via PDGFRB/ERK Signaling Axis.
m6A methyltransferase KIAA1429 acts as an oncogenic factor in colorectal cancer by regulating SIRT1 in an m6A-dependent manner.
Dysregulated m6A Modification Promotes Lipogenesis and Development of Non-alcoholic Fatty Liver Disease and Hepatocellular Carcinoma.
YTHDF1 promotes breast cancer progression by facilitating FOXM1 translation in an m6A-dependent manner.
Classification of Hepatocellular Carcinoma Based on N6-Methylandenosine-Related lncRNAs Profiling.
Gene Signatures and Prognostic Value of m6A RNA Methylation Regulators in Uterine Corpus Endometrial Carcinoma.
N7-methylguanosine tRNA modification promotes tumorigenesis and chemoresistance through WNT/β-catenin pathway in nasopharyngeal carcinoma.
A reciprocal feedback between N6-methyladenosine reader YTHDF3 and lncRNA DICER1-AS1 promotes glycolysis of pancreatic cancer through inhibiting maturation of miR-5586-5p.
MiR-451a promotes cell growth, migration and EMT in osteosarcoma by regulating YTHDC1-mediated m6A methylation to activate the AKT/mTOR signaling pathway.
29 m6A-RNA Methylation (Epitranscriptomic) Regulators Are Regulated in 41 Diseases including Atherosclerosis and Tumors Potentially via ROS Regulation - 102 Transcriptomic Dataset Analyses.
YTHDF2 Inhibits the Migration and Invasion of Lung Adenocarcinoma by Negatively Regulating the FAM83D-TGFβ1-SMAD2/3 Pathway.
Role of m5 C RNA methylation regulators in colorectal cancer prognosis and immune microenvironment.
Chemical Method to Sequence 5-Formylcytosine on RNA.
5-Methylcytosine profiles in mouse transcriptomes suggest the randomness of m5C formation catalyzed by RNA methyltransferase.
5-methylcytosine modification by Plasmodium NSUN2 stabilizes mRNA and mediates the development of gametocytes.
EZH2 suppresses insulinoma development by epigenetically reducing KIF4A expression via H3K27me3 modification.

Am J Respir Cell Mol Biol. 2022 Feb 25.

The Combined Effects of circRNA Methylation Promote Pulmonary Fibrosis.

Sha Wang, Wei Luo, Jie Huang, Menglin Chen, Jiawei Ding, Yusi Cheng, Wei Zhang, Shencun Fang, Jing Wang, Jie Chao.

  N6-methyladenosine (m6A) is the most common type of RNA methylation modification, mainly occurring on mRNA. Whether m6A-modified circRNAs are involved in pulmonary fibrosis in different settings remains unclear. Using an m6A-circRNA epitranscriptomic chip, candidate circRNAs were selected, among which hsa_circ_0000672 and hsa_circ_0005654 were specifically involved in SiO2-induced pulmonary fibrosis by targeting the same protein, eIF4A3, indicating that the m6A modification of these two circRNAs has a synergistic effect on fibroblast dysfunction induced by SiO2. A mechanistic study revealed that the m6A modification of circRNAs was mainly mediated by the methyltransferase METTL3. Furthermore, METTL3 promoted the activation, migration and activity of pulmonary fibroblasts and participated in SiO2-induced pulmonary fibrosis via the circRNA m6A modification. m6A methylation of circRNAs mediates silica-induced fibrosis, enriching the understanding of circRNAs and uncovering a potential new target for treating fibrosis-related diseases.

Keywords:  METTL3; m6A; noncoding RNA; pulmonary fibrosis

DOI:  https://doi.org/10.1165/rcmb.2021-0379OC
Mol Ther Nucleic Acids. 2022 Mar 08. 27 947-955

Recent advances in crosstalk between N6-methyladenosine (m6A) modification and circular RNAs in cancer.

Xin Huang, Haoyu Guo, Lutong Wang, Lingkai Yang, Zengwu Shao, Weiyue Zhang.

  N6-methyladenosine (m6A), as the most common RNA modification, plays a vital role in the development of cancers. Circular RNAs (circRNAs) are a class of single-stranded covalently closed RNA molecules. Recently, m6A modification has been identified as performing biological functions for regulating circRNAs. Increasing evidence also shows that circRNAs are involved in cancer progression by targeting m6A regulators. In this review, we describe the functional crosstalk between m6A and circRNAs, and illustrate their roles in cancer development. m6A methylation mediates the biogenesis, stability, and cytoplasmic export of circRNAs in different cancer types. Moreover, circRNAs regulate the expression of m6A regulators, participate in the degradation of m6A regulators, and regulate the m6A modification of target mRNAs. Finally, we discuss the potential applications and future research directions of m6A modification and circRNAs in cancer. Further understanding of the biological roles of m6A and circRNAs will provide new insight into the diagnosis and treatment of cancer patients.

Keywords:  N6-methyladenosine modification; circular RNAs; drug resistance; metastasis; radiotherapy tolerance; tumorigenesis

DOI:  https://doi.org/10.1016/j.omtn.2022.01.013
Toxicol Sci. 2022 Feb 24. pii: kfac023. [Epub ahead of print]

Chronic Hexavalent Chromium Exposure Up-regulates the RNA Methyltransferase METTL3 Expression to Promote Cell Transformation, Cancer Stem Cell-like Property and Tumorigenesis.

Zhishan Wang, Mohammad Burhan Uddin, Jie Xie, Hua Tao, Patti C Zeidler-Erdely, Kazuya Kondo, Chengfeng Yang.

  Hexavalent chromium [Cr(VI)] is a common environmental carcinogen causing lung cancer in humans. This study investigates the mechanism of Cr(VI) carcinogenesis focusing on the role of the epitranscriptomic dysregulation. The epitranscriptomic effect of Cr(VI) was determined in Cr(VI)-transformed human bronchial epithelial cells, chromate-exposed mouse and human lungs. The epitranscriptomic effect and its role in Cr(VI)-induced cell transformation, cancer stem cell (CSC)-like property and tumorigenesis were determined by microarray analysis, soft agar colony formation, suspension spheroid formation and mouse xenograft tumorigenesis assays. It was found that chronic Cr(VI) exposure causes epitranscriptomic dysregulations as evidenced by the increased levels of total RNA N6-methyladenosine (m6A) modification and the RNA m6A methyltransferase METTL3 in Cr(VI)-transformed cells and chromate exposure-caused mouse and human lung tumors. Knockdown of METTL3 expression in Cr(VI)-transformed cells significantly reduces their m6A levels and transformed phenotypes and tumorigenicity in mice. Moreover, knockdown of METTL3 expression in parental non-transformed cells significantly reduces the capability of chronic Cr(VI) exposure to induce cell transformation and CSC-like property. Together, this study reveals that chronic Cr(VI) exposure is capable of altering cellular epitranscriptome by increasing the m6A RNA modification via upregulating the RNA methyltransferase METTL3 expression, which plays an important role in Cr(VI)-induced cell transformation, CSC-like property and tumorigenesis.

Keywords:  Cancer stem cell (CSC)-like property; Epitranscriptome; Hexavalent chromium; METTL3; RNA modification; m6A

DOI:  https://doi.org/10.1093/toxsci/kfac023
Dis Markers. 2022 ;2022 2989200

Integrative Analysis of m6A RNA Methylation Regulators and the Tumor Immune Microenvironment in Non-Small-Cell Lung Cancer.

Jiaqi Zhu, Yun Jiang, Tianyi Wang, Anqi Wu, Tingting Zhou, Anping Zhang, Yijie Tang, Zihao Shen, Jinjie Wang, Hao Zhou, Jiahai Shi, Jianle Chen.

Background: Non-small-cell lung cancer (NSCLC) is a major component of lung cancer and is significantly correlated with poor prognosis. N6-methyladenosine (m6A) RNA methylation is closely related to the occurrence, progression, and prognosis of cancer. The potential biological functions and mechanisms of m6A RNA methylation in the immune microenvironment are still unclear.Methods: We assessed m6A RNA methylation modification patterns in 1326 NSCLC patient samples based on 20 m6A regulators, linking these clusters to the tumor microenvironment and immune cell infiltration. The m6Ascore was created to quantify the m6A modification patterns of individual tumors. We then assessed the value of NSCLC patients in terms of clinical prognosis and immunotherapy response.
Results: According to different mRNA expression levels, two different m6A clusters were identified. m6A aggregation was significantly associated with clinical prognostic characteristics, the tumor microenvironment, and immune-related biological processes. Fifteen differential genes were screened based on these two m6A clusters, and to further investigate the mechanisms of action of these differential genes, they were subjected to unsupervised clustering analysis, which classified them into four different genomic isoforms. Prognostic analysis indicated that the survival advantage of the m6A gene cluster A modification mode was significantly prominent. We continued to construct the m6Ascore, which was used as a scoring tool to evaluate tumor typing, immunity, and prognosis. Patients with a low m6Ascore showed a significant survival advantage, and the group with a low m6Ascore had a better prognosis predicted by immunotherapy. The anti-PD-1/L1 immunotherapy cohort showed that a lower m6Ascore was associated with higher efficacy of immunotherapy.
Conclusions: The results suggest that m6A RNA methylation regulators make an important difference in the tumor immune microenvironment of patients with NSCLC. m6A gene characterization and the construction of the m6Ascore provide us with a richer understanding of m6A RNA methylation modification patterns in NSCLC patients and help to predict clinical prognosis and immunotherapeutic response.

DOI: https://doi.org/10.1155/2022/2989200
Int J Gen Med. 2022 ;15 1595-1608

Molecular Characterization of m6A Modifications in Non-Clear Cell Renal Cell Carcinoma and Potential Relationship with Pathological Types.

Xuebao Xiang, Yi Guo, Zhongyuan Chen, Zengnan Mo.

  Background: N6-Methyladenosine (m6A) modification is a eukaryotic mRNA modification that modulates the fate of modified RNA and, therefore, the expression of proteins. m6A modifications are associated with important roles in several cancers. Most studies related to m6A modification are based on clear cell renal cell carcinoma (ccRCC) and little is known about its role in non-ccRCC.Methods: We summarized the molecular features of different m6A modification patterns in non-ccRCC based on The Cancer Genome Atlas database and correlated them with phenotypes such as immune patterns and prognosis. We also computed the m6Ascore and assessed its prognostic value using multivariate Cox regression analysis.
Results: We found the immune-excluded phenotype to be predominant in non-ccRCC patients. We also found that in non-clear cell carcinoma, different m6A modification profiles determine different immune patterns and are associated with different prognosis. m6AgeneCluser typing strongly associated with pathological status. Based on our findings, we suggest that the m6Ascore can be used as an independent prognostic value for prognostic assessment in non-ccRCC.
Conclusion: This study confirms the important role of m6A modifications in non-ccRCC, reveals the heterogeneity of tumor immunity, and highlights the promise of non-ccRCC therapy.

Keywords:  N6-methyladenosine; RNA modification; immune patterns; m6A score; non-clear cell renal cell carcinoma; renal cell carcinoma

DOI:  https://doi.org/10.2147/IJGM.S348343
Exp Mol Med. 2022 Feb 25.

The m6A reader IGF2BP3 promotes acute myeloid leukemia progression by enhancing RCC2 stability.

Nan Zhang, Yan Shen, Huan Li, Ying Chen, Ping Zhang, Shifeng Lou, Jianchuan Deng.

N6-methyladenosine (m6A) is the most abundant posttranscriptional modification of mRNA in eukaryotes. Recent evidence suggests that dysregulated m6A-associated proteins and m6A modifications play a pivotal role in the initiation and progression of diseases such as cancer. Here, we identified that IGF2BP3 is specifically overexpressed in acute myeloid leukemia (AML), a subtype of leukemia associated with poor prognosis and high genetic risk. IGF2BP3 is required for maintaining AML cell survival in an m6A-dependent manner, and knockdown of IGF2BP3 dramatically suppresses the apoptosis, reduces the proliferation, and impairs the leukemic capacity of AML cells in vitro and in vivo. Mechanistically, IGF2BP3 interacts with RCC2 mRNA and stabilizes the expression of m6A-modified RNA. Thus, we provided compelling evidence demonstrating that the m6A reader IGF2BP3 contributes to tumorigenesis and poor prognosis in AML and can serve as a target for the development of cancer therapeutics.

DOI: https://doi.org/10.1038/s12276-022-00735-x
Front Cell Dev Biol. 2022 ;10 813581

Interplay Between m6A RNA Methylation and Regulation of Metabolism in Cancer.

Youchaou Mobet, Xiaoyi Liu, Tao Liu, Jianhua Yu, Ping Yi.

  Methylation of adenosine in RNA to N6-methyladenosine (m6A) is widespread in eukaryotic cells with his integral RNA regulation. This dynamic process is regulated by methylases (editors/writers), demethylases (remover/erasers), and proteins that recognize methylation (effectors/readers). It is now evident that m6A is involved in the proliferation and metastasis of cancer cells, for instance, altering cancer cell metabolism. Thus, determining how m6A dysregulates metabolic pathways could provide potential targets for cancer therapy or early diagnosis. This review focuses on the link between the m6A modification and the reprogramming of metabolism in cancer. We hypothesize that m6A modification could dysregulate the expression of glucose, lipid, amino acid metabolism, and other metabolites or building blocks of cells by adaptation to the hypoxic tumor microenvironment, an increase in glycolysis, mitochondrial dysfunction, and abnormal expression of metabolic enzymes, metabolic receptors, transcription factors as well as oncogenic signaling pathways in both hematological malignancies and solid tumors. These metabolism abnormalities caused by m6A's modification may affect the metabolic reprogramming of cancer cells and then increase cell proliferation, tumor initiation, and metastasis. We conclude that focusing on m6A could provide new directions in searching for novel therapeutic and diagnostic targets for the early detection and treatment of many cancers.

Keywords:  M6A; cancer; metabolism; metabolite; methylation; oncogenic; reprogramming

DOI:  https://doi.org/10.3389/fcell.2022.813581
Mol Cancer. 2022 Feb 23. 21(1): 60

METTL3/IGF2BP3 axis inhibits tumor immune surveillance by upregulating N6-methyladenosine modification of PD-L1 mRNA in breast cancer.

Weijun Wan, Xiang Ao, Quan Chen, Yang Yu, Luoquan Ao, Wei Xing, Wei Guo, Xiaofeng Wu, Chengxiu Pu, Xueting Hu, Zhan Li, Mengwei Yao, Donglin Luo, Xiang Xu.

  BACKGROUND: Continual expression of PD-L1 in tumor cells is critical for tumor immune escape and host T cell exhaustion, however, knowledge on its clinical benefits through inhibition is limited in breast cancer. N6-methyladenosine (m6A) plays a crucial role in multiple biological activities. Our study aimed to investigate the regulatory role of the m6A modification in PD-L1 expression and immune surveillance in breast cancer.METHODS: MeRIP-seq and epitranscriptomic microarray identified that PD-L1 is the downstream target of METTL3. MeRIP-qPCR, absolute quantification of m6A modification assay, and RIP-qPCR were used to examine the molecular mechanism underlying METTL3/m6A/IGF2BP3 signaling axis in PD-L1 expression. B-NDG and BALB/c mice were used to construct xenograft tumor models to verify the phenotypes upon METTL3 and IGF2BP3 silencing. In addition, breast cancer tissue microarray was used to analyze the correlation between PD-L1 and METTL3 or IGF2BP3 expression.
RESULTS: We identified that PD-L1 was a downstream target of METTL3-mediated m6A modification in breast cancer cells. METTL3 knockdown significantly abolished m6A modification and reduced stabilization of PD-L1 mRNA. Additionally, METTL3-mediated PD-L1 mRNA activation was m6A-IGF2BP3-dependent. Moreover, inhibition of METTL3 or IGF2BP3 enhanced anti-tumor immunity through PD-L1-mediated T cell activation, exhaustion, and infiltration both in vitro and in vivo. PD-L1 expression was also positively correlated with METTL3 and IGF2BP3 expression in breast cancer tissues.
CONCLUSION: Our study suggested that METTL3 could post-transcriptionally upregulate PD-L1 expression in an m6A-IGF2BP3-dependent manner to further promote stabilization of PD-L1 mRNA, which may have important implications for new and efficient therapeutic strategies in the tumor immunotherapy.

Keywords:  Breast cancer; Immune surveillance; METTL3; PD-L1; m6A

DOI:  https://doi.org/10.1186/s12943-021-01447-y
Front Oncol. 2022 ;12 817584

Mutant NPM1-Regulated FTO-Mediated m6A Demethylation Promotes Leukemic Cell Survival via PDGFRB/ERK Signaling Axis.

Qiaoling Xiao, Li Lei, Jun Ren, Meixi Peng, Yipei Jing, Xueke Jiang, Junpeng Huang, Yonghong Tao, Can Lin, Jing Yang, Minghui Sun, Lisha Tang, Xingyu Wei, Zailin Yang, Ling Zhang.

  Acute myeloid leukemia (AML) with nucleophosmin 1 (NPM1) mutations exhibits distinct biological and clinical features, accounting for approximately one-third of AML. Recently, the N 6-methyladenosine (m6A) RNA modification has emerged as a new epigenetic modification to contribute to tumorigenesis and development. However, there is limited knowledge on the role of m6A modifications in NPM1-mutated AML. In this study, the decreased m6A level was first detected and high expression of fat mass and obesity-associated protein (FTO) was responsible for the m6A suppression in NPM1-mutated AML. FTO upregulation was partially induced by NPM1 mutation type A (NPM1-mA) through impeding the proteasome pathway. Importantly, FTO promoted leukemic cell survival by facilitating cell cycle and inhibiting cell apoptosis. Mechanistic investigations demonstrated that FTO depended on its m6A RNA demethylase activity to activate PDGFRB/ERK signaling axis. Our findings indicate that FTO-mediated m6A demethylation plays an oncogenic role in NPM1-mutated AML and provide a new layer of epigenetic insight for future treatments of this distinctly leukemic entity.

Keywords:  ERK cascade; FTO; N6-methyladenosine; PDGFRB; acute myeloid leukemia; nucleophosmin 1

DOI:  https://doi.org/10.3389/fonc.2022.817584
Cell Death Discov. 2022 Feb 25. 8(1): 83

m6A methyltransferase KIAA1429 acts as an oncogenic factor in colorectal cancer by regulating SIRT1 in an m6A-dependent manner.

Yuan Zhou, Zhengda Pei, Aizezi Maimaiti, Linyi Zheng, Zhongcheng Zhu, Mengxiang Tian, Zhongyi Zhou, Fengbo Tan, Qian Pei, Yuqiang Li, Wenxue Liu.

N6-methyladenosine (m6A) modifications of RNAs are involved in various aspects of colorectal carcinogenesis via regulation of mRNA stability, splicing, and translation. KIAA1429, an m6A methyltransferase, was found deregulated in multiple cancer types. However, its role in colorectal cancer remains elusive. By analyzing TCGA and GEPIA database, we found that KIAA1429 in colorectal cancer was highly expressed. In addition, we used immunohistochemistry, western blotting, and QRT-PCR to detect the expression of KIAA1429 in colorectal cancer samples and cell lines, and we found that KIAA1429 was overexpressed in colorectal cancer sample and cell line. Functionally, silencing of KIAA1429 by shRNA in colorectal cancer cell lines resulted in decreased cell proliferation, colony formation, and migration. On the contrary, overexpression of KIAA1429 increased cell proliferation, colony formation, and migration. Further mechanism analysis demonstrated that KIAA1429 increased the expression of SIRT1 via regulating its mRNA stability in an m6A-dependent manner. More importantly, in vivo experiment showed that depletion of KIAA1429 significantly inhibited colorectal tumor growth. In conclusion, our results suggested that the m6A methyltransferase KIAA1429 promotes the growth and motility of colorectal cancer and could be a potent therapeutic target.

DOI: https://doi.org/10.1038/s41420-022-00878-w
Mol Ther. 2022 Feb 19. pii: S1525-0016(22)00105-8. [Epub ahead of print]

Dysregulated m6A Modification Promotes Lipogenesis and Development of Non-alcoholic Fatty Liver Disease and Hepatocellular Carcinoma.

Yeming Yang, Jingshu Cai, Xue Yang, Kaifang Wang, Kuanxiang Sun, Zhenglin Yang, Lin Zhang, Lu Yang, Chun Gu, Xiang Huang, Ziyan Wang, Xianjun Zhu.

Type 2 diabetes mellitus (DM2) is associated closely with Non-alcoholic fatty liver disease (NAFLD) through affecting lipid metabolism, which may lead to non-alcoholic steatohepatitis (NASH), fibrosis and Hepatocellular carcinoma (HCC). N6-methyladenosine (m6A) RNA methylation is an important epigenetic regulation for gene expression, and related to HCC development. We developed a new NAFLD model oriented from DM2 mouse, which spontaneously progressed to histological features of NASH, fibrosis and HCC with high incidence. By RNA sequencing, protein expression and MeRIP-qPCR analysis, we found that enhanced expression of ACLY and SCD1 in this NAFLD model and human HCC samples were due to excessive m6A modification, but not elevation of mature SREBP1. Moreover, targeting METTL3/14 in vitro increases protein level of ACLY and SCD1, as well as triglyceride and cholesterol production and accumulation of lipid droplets. m6A sequencing analysis revealed that, overexpressed METTL14 bind to mRNA of ACLY and SCD1 and alter their expression pattern. Our findings demonstrate a new NAFLD mouse model, which provide a study platform for DM2-related NAFLD; and reveal a unique epitranscriptional regulating mechanism for lipid metabolism via m6A-modified protein expression of ACLY and SCD1.

DOI: https://doi.org/10.1016/j.ymthe.2022.02.021
Cell Biosci. 2022 Feb 23. 12(1): 19

YTHDF1 promotes breast cancer progression by facilitating FOXM1 translation in an m6A-dependent manner.

Hengyu Chen, Yuanhang Yu, Ming Yang, Haohao Huang, Shenghui Ma, Jin Hu, Zihan Xi, Hui Guo, Guojie Yao, Liu Yang, Xiaoqing Huang, Feng Zhang, Guanghong Tan, Huangfu Wu, Wuping Zheng, Lei Li.

  BACKGROUND: N6-methyladenosine (m6A) is the most common post-transcriptional modification at the RNA level. However, the exact molecular mechanisms of m6A epigenetic regulation in breast cancer remain largely unknown and need to be fully elucidated.METHODS: The integrating bioinformatics analyses were used to screen clinical relevance and dysregulated m6A "reader" protein YTHDF1 in breast cancer from TCGA databases, which was further validated in a cohort of clinical specimens. Furthermore, functional experiments such as the CCK-8 assay, EdU assay, wound healing assay, transwell invasion assay and cell cycle assay were used to determine the biological role of YTHDF1 in breast cancer. RIP, m6A-IP, and CLIP assays were used to find the target of YTHDF1 and further verification by RT-qPCR, western blot, polysome profiling assay. The protein-protein interaction between YTHDF1 and FOXM1 was detected via co-immunoprecipitation.
RESULTS: Our study showed that YTHDF1 was overexpressed in breast cancer cells and clinical tissues specimens. At the same time, the high expression level of YTHDF1 was positively correlated with tumor size, lymph node invasion, and distant metastasis in breast cancer patients. YTHDF1 depletion repressed the proliferation, invasion and epithelial-mesenchymal transformation (EMT) and induced G0/G1 phase cell cycle arrest of breast cancer cells in vitro and in vivo. We also demonstrated that FOXM1 is a target of YTHDF1. Through recognizing and binding to the m6A-modified mRNA of FOXM1, YTHDF1 accelerated the translation process of FOXM1 and promoted breast cancer metastasis. Whereas overexpression of FOXM1 in breast cancer cells partially counteracted the tumor suppressed effects caused by YTHDF1 silence, which further verified the regulatory relationship between YTHDF1 and FOXM1.
CONCLUSION: Our study reveals a novel YTHDF1/FOXM1 regulatory pathway that contributes to metastasis and progression of breast cancer, suggesting that YTHDF1 might be applied as a potential biomarker and therapeutic target. That also advances our understanding of the tumorigenesis for breast cancer from m6A epigenetic regulation.

Keywords:  Breast cancer; EMT; FOXM1; YTHDF1; m6A

DOI:  https://doi.org/10.1186/s13578-022-00759-w
Front Mol Biosci. 2022 ;9 807418

Classification of Hepatocellular Carcinoma Based on N6-Methylandenosine-Related lncRNAs Profiling.

Lu Yin, Liuzhi Zhou, Shiqi Gao, Yina Feng, Hanzhang Zhu, Jingjing Xiang, Rujun Xu.

  HCC is one of the most common types of malignancies worldwide and the fourth-leading cause of cancer deaths. Thus, there is an urgent need to search for novel targeted therapies in HCC. 186 m6a-related lncRNAs were screened for subsequent analysis. Two distinct m6A modification clusters were identified to be associated with the overall prognosis in TCGA-LIHC based on the m6A-related lncRNAs profiling, followed by univariate Cox regression analysis. In addition, four m6A-related lncRNAs prognostic signatures were developed and validated that could predict the OS of HCC patients, followed by univariate Cox regression, LASSO regression, and multivariate Cox regression analysis. Moreover, four m6A-related lncRNAs were identified to be related to HCC prognosis. ESTIMATE was used to evaluate the stromal score, immune score, ESTIMATE score, and tumor purity of each HCC sample. ssGSEA was performed to identify the enrichment levels of 29 immune signatures in each sample. Finally, quantitative real-time polymerase chain reaction shown that KDM4A-AS1, BACE1-AS, and NRAV expressions were upregulated in HCC patients. We proved that our m6A-related lncRNAs signature had powerful and robust ability for predicting OS of different HCC subgroups.

Keywords:  biomarkers; classification; hepatocellular carcinoma; m6A-related lncRNA; machine learning; prognosis; tumor microenvironment

DOI:  https://doi.org/10.3389/fmolb.2022.807418
Discov Med. 2021 May-Jun;31(164):31(164): 111-120

Gene Signatures and Prognostic Value of m6A RNA Methylation Regulators in Uterine Corpus Endometrial Carcinoma.

Yuanling Feng, Chunfang Yao, Jiayu Shen, Jianwei Zhou.

BACKGROUND: Uterine corpus endometrial carcinoma (UCEC) is the second most common malignancy of female reproductive system. Though most UCEC are diagnosed at an early age, the mortality has increased. It is important to develop new targets for prognosis evaluation and treatment.METHODS: Expression profiles of 19 m6A regulators and UCEC samples' epidemiologic information were obtained from GTEx and TCGA datasets. Nonnegative matrix factorization (NMF) was used to cluster UCEC samples into three groups and overall survival (OS) was compared among them. Multivariate cox proportional hazard model was used to select targets for the construction of m6A-related prognosis prediction signature. A nomogram consisting of m6A-related signature, stage, and histology was provided for clinical application.
RESULTS: Eighteen m6A regulators were found to be differentially expressed between normal sample and UCEC samples. There was a significant difference in the OS probability among three clusters with different expression levels of m6A. VIRMA, YTHDF3, and IGF2BP1 were picked as UCEC prognosis prediction signatures and the prognostic value was confirmed. Risk score estimated by this signature was demonstrated to be the independent prognostic factor for UCEC.
CONCLUSION: Aberrant expression of m6A RNA methylation regulators was significantly associated with the development and prognosis of UCEC. A three-gene signature consisting of VIRMA, YTHDF3, and IGF2BP1 may effectively predict the prognosis of UCEC patients.
Oncogene. 2022 Feb 26.

N7-methylguanosine tRNA modification promotes tumorigenesis and chemoresistance through WNT/β-catenin pathway in nasopharyngeal carcinoma.

Binbin Chen, Wei Jiang, Ying Huang, Jian Zhang, Peng Yu, Lirong Wu, Hao Peng.

Treatment selections are very limited for patients with advanced nasopharyngeal carcinoma (NPC) experiencing disease progression. Uncovering mechanisms underlying NPC progression is crucial for the development of novel treatments. Here we show that N7-methylguanosine (m7G) tRNA modification enzyme METTL1 and its partner WDR4 are significantly elevated in NPC and are associated with poor prognosis. Loss-of-function and gain-of-function assays demonstrated that METTL1/WDR4 promotes NPC growth and metastasis in vitro and in vivo. Mechanistically, ARNT was identified as an upstream transcription factor regulating METTL1 expression in NPC. METTL1 depletion resulted in decreased m7G tRNA modification and expression, which led to impaired codon recognition during mRNA translation, therefore reducing the translation efficiencies of mRNAs with higher m7G codons. METTL1 upregulated the WNT/β-catenin signaling pathway and promoted NPC cell epithelial-mesenchymal transition (EMT) and chemoresistance to cisplatin and docetaxel in vitro and in vivo. Overexpression of WNT3A bypassed the requirement of METTL1 for EMT and chemoresistance. This work uncovers novel insights into tRNA modification-mediated mRNA translation regulation and highlights the critical function of tRNA modification in cancer progression.

DOI: https://doi.org/10.1038/s41388-022-02250-9
J Exp Clin Cancer Res. 2022 Feb 19. 41(1): 69

A reciprocal feedback between N6-methyladenosine reader YTHDF3 and lncRNA DICER1-AS1 promotes glycolysis of pancreatic cancer through inhibiting maturation of miR-5586-5p.

Yuhang Hu, Jiang Tang, Fengyu Xu, Jinhuang Chen, Zhu Zeng, Shengbo Han, Fan Wang, Decai Wang, Mengqi Huang, Yong Zhao, Yan Huang, Wenfeng Zhuo, Gang Zhao.

  BACKGROUND: Glycolysis is a pivotal process in metabolic reprogramming of tumorigenesis. Previous research has indicated that lncRNAs might play crucial roles in glycolysis of various tumors. However, the function of lncRNAs in glycolysis of pancreatic cancer has not been fully elucidated.METHODS: Bio-information analyses were applied to reveal the potential glycolysis-associated lncRNA. RT-PCR and fluorescence in situ hybridization (FISH) assays were applied to detect the expression of antisense RNA1 of DICER1 (DICER1-AS1) in pancreatic cancer tissues and cell lines. Gain- and loss-of-function experiments were performed to evaluate the roles of DICER1-AS1 in glycolysis and tumorigenesis of PC. Mechanistic experiments including luciferase reporter assay, RNA immunoprecipitation (RIP), and chromatin immunoprecipitation (ChIP) were employed to uncover the downstream targets and regulatory mechanism of DICER1-AS1 in glycolysis of PC.
RESULTS: Bio-information analysis indicated that DICER1-AS1 was downregulated in PC and negatively correlated with glycolytic genes expression. Meanwhile, overexpression of DICER1-AS1 inhibited glycolysis, proliferation, and metastasis of PC cells both in vitro and in vivo. Mechanistically, DICER1-AS1 promoted transcription of its sense gene DICER1 by recruiting transcriptional factor YY1 to the DICER1 promoter. Meanwhile, DICER1 promoted maturation of miR-5586-5p which consequently inhibited glycolytic gene expression including LDHA, HK2, PGK1, and SLC2A1. Notably, enhanced interaction between N6-methyladenosine (m6A) reader YTHDF3 and DICER1-AS1 led to degradation of DICER1-AS1 in response to glucose depletion. Moreover, our data revealed that YTHDF3 was a critical target for miR-5586-5p, by which forming a negative feedback with DICER1-AS1 to regulate glycolysis of PC.
CONCLUSION: Our results implicate a negative feedback of m6A reader YTHDF3 and glycolytic lncRNA DICER1-AS1 is involved in glycolysis and tumorigenesis of PC.

Keywords:  DICER1; DICER1-AS1; Glycolysis; LncRNA; Pancreatic cancer; YTHDF3; m6A; miR-5586-5p

DOI:  https://doi.org/10.1186/s13046-022-02285-6
J Bone Oncol. 2022 Apr;33 100412

MiR-451a promotes cell growth, migration and EMT in osteosarcoma by regulating YTHDC1-mediated m6A methylation to activate the AKT/mTOR signaling pathway.

Dong Cao, Shanshan Ge, Mengchun Li.

  Background: Osteosarcoma is the most prevalent primary malignant bone tumor containing mesenchymal cells with poor prognosis. Being a hot spot of anti-tumor therapy researches, AKT/mammalian target of rapamycin (mTOR) signaling pathway could affect various cellular processes including transcription, protein synthesis, apoptosis, autophagy and growth.Materials and methods: The levels of RNA and protein were detected by quantitative real-time polymerase chain reaction (q-PCR) and western blot analyses respectively. Functional assays were carried out to analyze the malignant phenotypes of osteosarcoma cells. RNA-binding protein immunoprecipitation (RIP), Co-immunoprecipitation (Co-IP), RNA pulldown, luciferase reporter and in vitro kinase assays were conducted to uncover the specific mechanism of microRNA-451a (miR-451a) in osteosarcoma cells.
Results: Functionally, miR-451a represses the malignant progression of osteosarcoma. Mechanically, miR-451a could curb the AKT/mTOR pathway via 3-phosphoinositide dependent protein kinase 1 (PDPK1)-mediated phosphorylation modification. After the certification that YTH domain containing 1 (YTHDC1) regulates the m6A phosphorylation modification of PDPK1 mRNA, we further proved that miR-451a-mediated YTHDC1 stabilizes PDPK1 mRNA via m6A-dependent regulation.
Conclusion: This study demonstrated that miR-451a regulates YTHDC1-mediated m6A methylation to activate the AKT/mTOR pathway, stimulating the malignancy of osteosarcoma.

Keywords:  AKT/mTOR signaling pathway; ANOVA, Analysis of variance; Cdna, Complementary DNA; GEO, Gene Expression Omnibus; Osteosarcoma; PDPK1, 3-phosphoinositide dependent protein kinase 1; RIP, Co-IP, Co-immunoprecipitation; SD, Standard deviation; YTHDC1, YTH domain containing 1; m6A methylation; mTOR, Mammalian target of rapamycin; miR-451a; miR-451a, MicroRNA-451a; q-PCR, Quantitative real-time polymerase chain reaction

DOI:  https://doi.org/10.1016/j.jbo.2022.100412
J Immunol Res. 2022 ;2022 1433323

29 m6A-RNA Methylation (Epitranscriptomic) Regulators Are Regulated in 41 Diseases including Atherosclerosis and Tumors Potentially via ROS Regulation - 102 Transcriptomic Dataset Analyses.

Ming Liu, Keman Xu, Fatma Saaoud, Ying Shao, Ruijing Zhang, Yifan Lu, Yu Sun, Charles Drummer, Li Li, Sheng Wu, Satya P Kunapuli, Gerard J Criner, Jianxin Sun, Huimin Shan, Xiaohua Jiang, Hong Wang, Xiaofeng Yang.

We performed a database mining on 102 transcriptomic datasets for the expressions of 29 m6A-RNA methylation (epitranscriptomic) regulators (m6A-RMRs) in 41 diseases and cancers and made significant findings: (1) a few m6A-RMRs were upregulated; and most m6A-RMRs were downregulated in sepsis, acute respiratory distress syndrome, shock, and trauma; (2) half of 29 m6A-RMRs were downregulated in atherosclerosis; (3) inflammatory bowel disease and rheumatoid arthritis modulated m6A-RMRs more than lupus and psoriasis; (4) some organ failures shared eight upregulated m6A-RMRs; end-stage renal failure (ESRF) downregulated 85% of m6A-RMRs; (5) Middle-East respiratory syndrome coronavirus infections modulated m6A-RMRs the most among viral infections; (6) proinflammatory oxPAPC modulated m6A-RMRs more than DAMP stimulation including LPS and oxLDL; (7) upregulated m6A-RMRs were more than downregulated m6A-RMRs in cancer types; five types of cancers upregulated ≥10 m6A-RMRs; (8) proinflammatory M1 macrophages upregulated seven m6A-RMRs; (9) 86% of m6A-RMRs were differentially expressed in the six clusters of CD4+Foxp3+ immunosuppressive Treg, and 8 out of 12 Treg signatures regulated m6A-RMRs; (10) immune checkpoint receptors TIM3, TIGIT, PD-L2, and CTLA4 modulated m6A-RMRs, and inhibition of CD40 upregulated m6A-RMRs; (11) cytokines and interferons modulated m6A-RMRs; (12) NF-κB and JAK/STAT pathways upregulated more than downregulated m6A-RMRs whereas TP53, PTEN, and APC did the opposite; (13) methionine-homocysteine-methyl cycle enzyme Mthfd1 downregulated more than upregulated m6A-RMRs; (14) m6A writer RBM15 and one m6A eraser FTO, H3K4 methyltransferase MLL1, and DNA methyltransferase, DNMT1, regulated m6A-RMRs; and (15) 40 out of 165 ROS regulators were modulated by m6A eraser FTO and two m6A writers METTL3 and WTAP. Our findings shed new light on the functions of upregulated m6A-RMRs in 41 diseases and cancers, nine cellular and molecular mechanisms, novel therapeutic targets for inflammatory disorders, metabolic cardiovascular diseases, autoimmune diseases, organ failures, and cancers.

DOI: https://doi.org/10.1155/2022/1433323
Front Oncol. 2022 ;12 763341

YTHDF2 Inhibits the Migration and Invasion of Lung Adenocarcinoma by Negatively Regulating the FAM83D-TGFβ1-SMAD2/3 Pathway.

Teng Zhao, Mingchao Wang, Xin Zhao, Shuang Weng, Kun Qian, Kejian Shi, Yanfei Gu, Wantao Ying, Xiaohong Qian, Yi Zhang.

  Objective: YTH domain family 2 (YTHDF2) is an important N6-methyladenosine (m6A) reader, but its role in lung adenocarcinoma remains elusive. This study assessed its function in lung adenocarcinoma.Methods: YTHDF2 expression in lung adenocarcinoma was explored using public databases, such as The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumour Analysis Consortium (CPTAC). The effect of YTHDF2 on a lung adenocarcinoma cell line was explored by performing cytological and molecular experiments. Molecules downstream of YTHDF2 were identified using proteomics, and the related pathways were verified through cytological and molecular biology experiments.
Results: YTHDF2 expression was upregulated in lung adenocarcinoma, and patients with high YTHDF2 expression experienced prolonged overall survival. In two lung cancer cell lines, YTHDF2 knockdown inhibited proliferation but promoted migration, invasion, and the epithelial-mesenchymal transition. The proteomic analysis identified 142 molecules downstream of YTHDF2, and 11 were closely related to survival. Further experiments revealed that YTHDF2 inhibited expression of the family with sequence similarity 83D (FAM83D)-TGFβ1-SMAD2/3 pathway components. This study is the first to show that YTHDF2 regulated the downstream TGFβ1-SMAD2/3 pathway through FAM83D in lung adenocarcinoma.
Conclusion: YTHDF2 inhibits the migration and invasion of lung adenocarcinoma cells by regulating the FAM83D-TGFβ1-pSMAD2/3 pathway, which may play an important role in lung cancer metastasis.

Keywords:  FAM83D; N6-methyladenosine; NSCLC; TGFβ1; YTHDF2

DOI:  https://doi.org/10.3389/fonc.2022.763341
J Clin Lab Anal. 2022 Feb 25. e24303

Role of m5 C RNA methylation regulators in colorectal cancer prognosis and immune microenvironment.

Xiaojie Fang, Chenyun Miao, Tianni Zeng, Weijian Chu, Yi Zheng, Xi Sun, Xin Yin, Yanyan Li.

  BACKGROUND: RNA modification has become one of the hot topics of research as it can be used for tumor prognosis. However, its role in various biological processes is still poorly understood. The aim of this study was to investigate the role of m5 C and m1 A regulators on colorectal cancer prognosis using bioinformatics tools. The association between these regulators and differences in patient survival as well as the clinicopathological characteristics and tumor immune microenvironment in colorectal cancer tissues were assessed.METHODS: We selected publicly available colorectal cancer data sets from The Cancer Genome Atlas and used the "limma" package in R to identify differentially expressed genes. The least absolute shrinkage and selection operator regression model was used to calculate the prognostic risk, and a risk prediction model was constructed, to help assess the prognostic values of the differentially expressed genes. Finally, using TISCH and TIMER, we assessed the extent of cellular infiltration in colorectal cancer.
RESULTS: We explored NSUN6 and DNMT3A expression using UALCAN and HPA and found that their expression is significantly increased in colorectal cancer tissues and correlated with sex and TP53 mutation status. Moreover, we found NSUN6 and DNMT3A were related to the infiltration of six major immune cells, with DNMT3A being closely related to dendritic cells, CD4+ T cells, and B cells, whereas NSUN6 to B cells and CD8+ T cells.
CONCLUSION: Our findings suggest that m5 C regulators can predict the clinical prognostic risk and regulate the tumor immune microenvironment in colorectal cancer.

Keywords:  5-methylcytosine; RNA methylation; colorectal cancer; prognostic model; tumor immune microenvironment

DOI:  https://doi.org/10.1002/jcla.24303
ACS Chem Biol. 2022 Feb 25.

Chemical Method to Sequence 5-Formylcytosine on RNA.

Ang Li, Xuemeng Sun, A Emilia Arguello, Ralph E Kleiner.

Epitranscriptomic RNA modifications can regulate biological processes, but there remains a major gap in our ability to identify and measure individual modifications at nucleotide resolution. Here we present Mal-Seq, a chemical method for sequencing 5-formylcytosine (f5C) modifications on RNA based on the selective and efficient malononitrile-mediated labeling of f5C residues to generate adducts that are read as C-to-T mutations upon reverse transcription and polymerase chain reaction amplification. We apply Mal-Seq to characterize the prevalence of f5C at the wobble position of mt-tRNA(Met) in different organisms and tissue types and find that high-level f5C modification is present in mammals but lacking in lower eukaryotes. Our work sheds light on mitochondrial tRNA modifications throughout eukaryotic evolution and provides a general platform for characterizing the f5C epitranscriptome.

DOI: https://doi.org/10.1021/acschembio.1c00707
BMC Res Notes. 2022 Feb 23. 15(1): 81

5-Methylcytosine profiles in mouse transcriptomes suggest the randomness of m5C formation catalyzed by RNA methyltransferase.

Junfeng Liu.

  OBJECTIVE: 5-Methylcytosine (m5C) is a type of chemical modification on the nucleotides and is widespread in both DNA and RNA. Although the DNA m5C has been extensively studied over the past years, the distribution and biological function of RNA m5C still remain to be elucidated. Here, I explored the profiles of RNA m5C in four mouse tissues by applying a RNA cytosine methylation data analysis tool to public mouse RNA m5C data.RESULTS: I found that the methylation rates of cytosine were the same with the averages of methylation level at single-nucleotide level. Furthermore, I gave a mathematical formula to describe the observed relationship and analyzed it deeply. The sufficient necessary condition for the given formula suggests that the methylation levels at most m5C sites are the same in four mouse tissues. Therefore, I proposed a hypothesis that the m5C formation catalyzed by RNA methyltransferase is random and with the same probability at most m5C sites, which is the methylation rate of cytosine. My hypothesis can be used to explain the observed profiles of RNA m5C in four mouse tissues and will be benefit to future studies of the distribution and biological function of RNA m5C in mammals.

Keywords:  Methylation level; Methylation rate; RNA 5-methylcytosine

DOI:  https://doi.org/10.1186/s13104-022-05968-7
Proc Natl Acad Sci U S A. 2022 Mar 01. pii: e2110713119. [Epub ahead of print]119(9):

5-methylcytosine modification by Plasmodium NSUN2 stabilizes mRNA and mediates the development of gametocytes.

Meng Liu, Gangqiang Guo, Pengge Qian, Jianbing Mu, Binbin Lu, Xiaoqin He, Yanting Fan, Xiaomin Shang, Guang Yang, Shijun Shen, Wenju Liu, Liping Wang, Liang Gu, Quankai Mu, Xinyu Yu, Yuemeng Zhao, Richard Culleton, Jun Cao, Lubin Jiang, Thomas E Wellems, Jing Yuan, Cizhong Jiang, Qingfeng Zhang.

  5-methylcytosine (m5C) is an important epitranscriptomic modification involved in messenger RNA (mRNA) stability and translation efficiency in various biological processes. However, it remains unclear if m5C modification contributes to the dynamic regulation of the transcriptome during the developmental cycles of Plasmodium parasites. Here, we characterize the landscape of m5C mRNA modifications at single nucleotide resolution in the asexual replication stages and gametocyte sexual stages of rodent (Plasmodium yoelii) and human (Plasmodium falciparum) malaria parasites. While different representations of m5C-modified mRNAs are associated with the different stages, the abundance of the m5C marker is strikingly enhanced in the transcriptomes of gametocytes. Our results show that m5C modifications confer stability to the Plasmodium transcripts and that a Plasmodium ortholog of NSUN2 is a major mRNA m5C methyltransferase in malaria parasites. Upon knockout of P. yoelii nsun2 (pynsun2), marked reductions of m5C modification were observed in a panel of gametocytogenesis-associated transcripts. These reductions correlated with impaired gametocyte production in the knockout rodent malaria parasites. Restoration of the nsun2 gene in the knockout parasites rescued the gametocyte production phenotype as well as m5C modification of the gametocytogenesis-associated transcripts. Together with the mRNA m5C profiles for two species of Plasmodium, our findings demonstrate a major role for NSUN2-mediated m5C modifications in mRNA transcript stability and sexual differentiation in malaria parasites.

Keywords:  RNA bisulfite sequencing; RNA methyltransferase; epitranscriptomic modifications; gametocytogenesis; gene knockout

DOI:  https://doi.org/10.1073/pnas.2110713119
Gene. 2022 Feb 16. pii: S0378-1119(22)00136-6. [Epub ahead of print] 146317

EZH2 suppresses insulinoma development by epigenetically reducing KIF4A expression via H3K27me3 modification.

Suzhen Zhang, Jun Liu, Feng Li, Mudan Yang, Junping Wang.

  Kinesin family member 4A (KIF4A), located in the human chromosome band Xq13.1, is aberrantly overexpressed in various cancers. Our study intended to assess the expression of KIF4A in insulinoma and to gain new insights into the molecular mechanisms of this rare disease. First, KIF4A was significantly recruited in pancreatic endocrine cells relative to other cell types. A significant correlation existed between the overexpression of KIF4A and the poor survival of pancreatic adenocarcinoma patients. As revealed by CCK-8, TUNEL assay, flow cytometry, wound healing, Matrigel-transwell, senescence-associated β-galactosidase staining, ELISA, and subcutaneous tumor formation analysis in nude mice, knocking down KIF4A significantly inhibited the growth and metastasis of insulinoma cells in vivo and in vitro. Mechanistically, we observed that KIF4A promoter sequences had reduced H3K27me3 modifications, and decline in enhancer of zeste homolog-2 (EZH2) expression promoted KIF4A expression by reducing the modification, thus leading to insulinoma. Moreover, EZH2 knockdown-induced insulinoma cell proliferation was dependent on KIF4A overexpression since KIF4A knockdown eradicated shEZH2-induced proliferation of insulinoma cells. In summary, KIF4A was identified as a possible therapeutic target for insulinoma.

Keywords:  EZH2; Epigenetics; H3K27me3; Insulinoma; KIF4A

DOI:  https://doi.org/10.1016/j.gene.2022.146317