bims-rimeca 2021-03-14 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2021–03–14
twenty papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics

Development and Validation of an m6A RNA Methylation Regulators-Based Signature for Predicting the Prognosis of Adrenocortical Carcinoma.
Chromatin and transcriptional regulation by reversible RNA methylation.
YTH Domain Proteins: A Family of m6A Readers in Cancer Progression.
Mapping messenger RNA methylations at single base resolution.
N6-methyladenosine modification of HIV-1 RNA suppresses type-I interferon induction in differentiated monocytic cells and primary macrophages.
RNA m6A reader IMP2/IGF2BP2 promotes pancreatic β-cell proliferation and insulin secretion by enhancing PDX1 expression.
Mettl14-mediated m6A modification modulates neuron apoptosis during the repair of spinal cord injury by regulating the transformation from pri-mir-375 to miR-375.
N6-methyladenosine RNA modification suppresses antiviral innate sensing pathways via reshaping double-stranded RNA.
Deficiency of Mettl3 in Bladder Cancer Stem Cells Inhibits Bladder Cancer Progression and Angiogenesis.
MiR-4729 regulates TIE1 mRNA m6A modification and angiogenesis in hemorrhoids by targeting METTL14.
Succinylation Regulators Promote Clear Cell Renal Cell Carcinoma by Immune Regulation and RNA N6-Methyladenosine Methylation.
METTL3-mediated m6A mRNA modification of FBXW7 suppresses lung adenocarcinoma.
N6-methyladenosine reader YTHDC2 and eraser FTO may determine hepatocellular carcinoma prognoses after transarterial chemoembolization.
A Ten-N6-Methyladenosine (m6A)-Modified Gene Signature Based on a Risk Score System Predicts Patient Prognosis in Rectum Adenocarcinoma.
RNA modifications as a common denominator between tRNA and mRNA.
m6A-Mediated Upregulation of LINC00857 Promotes Pancreatic Cancer Tumorigenesis by Regulating the miR-150-5p/E2F3 Axis.
Downregulation of lncRNA ZNF582-AS1 due to DNA hypermethylation promotes clear cell renal cell carcinoma growth and metastasis by regulating the N(6)-methyladenosine modification of MT-RNR1.
N-methyladenosine reader YTHDF2-mediated long noncoding RNA FENDRR degradation promotes cell proliferation in endometrioid endometrial carcinoma.
Analysis and Validation of circRNA-miRNA Network in Regulating m6A RNA Methylation Modulators Reveals CircMAP2K4/miR-139-5p/YTHDF1 Axis Involving the Proliferation of Hepatocellular Carcinoma.
Regulation of translation by methylation multiplicity of 18S rRNA.

Front Endocrinol (Lausanne). 2021 ;12 568397

Development and Validation of an m6A RNA Methylation Regulators-Based Signature for Predicting the Prognosis of Adrenocortical Carcinoma.

Chengquan Shen, Jing Liu, Xiaokun Yang, Wei Jiao, Yonghua Wang.

   Background: Adrenocortical carcinoma (ACC) is an aggressive and rare neoplasm that originates from the cortex of the adrenal gland. N6-methyladenosine (m6A) RNA methylation, the most common form of mRNA modification, has been reported to be correlated with the occurrence and development of the malignant tumor. This study aims to identify the significance of m6A RNA methylation regulators in ACC and construct a m6A based signature to predict the prognosis of ACC patients.
Materials and methods: RNA-seq data from The Cancer Genome Atlas (TCGA) database was used to identify the expression level of m6A RNA methylation regulators in ACC. An m6A based signature was further constructed and its prognostic and predictive values were assessed by survival analysis and nomogram.
Results: 11 m6A RNA regulators were differentially expressed in ACC and three m6A RNA regulators were finally selected in a signature to predict the prognosis of ACC patients. Survival analysis indicated that high risk scores were closely related to poor survival outcomes in ACC patients. Univariate and multivariate Cox regression analyses demonstrated that the m6A based signature was an independent prognostic factor for ACC patients. A nomogram with clinical factors and the m6A based signature was also constructed to superiorly predict the prognosis of ACC patients. The expression levels of m6A RNA methylation regulators, which were contained in the signature, were also verified in human ACC tissues and normal tissues by using vitro experiments.
Conclusion: We identified and validated an m6A based signature, which can be used as an independent prognostic factor in evaluating the prognosis of ACC patients. Further clinical trials and experimental explorations are needed to confirm our observations and mechanisms underlying prognostic values of these m6A RNA methylation regulators in ACC.

Keywords:  The Cancer Genome Atlas; adrenocortical carcinoma; m6A RNA methylation regulators; prognosis; signature

DOI:  https://doi.org/10.3389/fendo.2021.568397
Curr Opin Cell Biol. 2021 Mar 08. pii: S0955-0674(20)30155-1. [Epub ahead of print]70 109-115

Chromatin and transcriptional regulation by reversible RNA methylation.

Jiangbo Wei, Chuan He.

  Dynamic RNA modifications have been a burgeoning area in the last decade since the concept of 'RNA epigenetics' was proposed [1]. N6-methyladenosine (m6A) is the most abundant mRNA modification in eukaryotic cells. It can be installed by 'writers', removed by 'erasers,' recognized by 'readers,' and dynamically regulate the fate of methylated RNA. Until recently, the roles of reversible RNA methylation in chromatin and transcriptional regulation were not adequately studied. We discuss the new discoveries and insights into the chromatin and transcriptional regulation by m6A through two pathways: 1) effects of m6A on mRNAs encoding histone modifiers and transcriptional factors; 2) m6A regulation of chromatin-associated regulatory RNAs. Additionally, we provide an outlook on how the transcriptional regulation by RNA m6A could add an additional critical layer to transcriptional regulation.

Keywords:  Transcriptional regulation; carRNAs; m(6)A

DOI:  https://doi.org/10.1016/j.ceb.2020.11.005
Front Oncol. 2021 ;11 629560

YTH Domain Proteins: A Family of m6A Readers in Cancer Progression.

Yirong Xu, Wei Zhang, Feng Shen, Xi Yang, Huilan Liu, Shengbin Dai, Xinchen Sun, Junxing Huang, Qing Guo.

  N6-methyladenosine (m6A) is the most abundant internal modification in eukaryotic messenger RNAs (mRNAs). m6A RNA methylation is involved in all stages of RNA life cycle, from RNA processing, nuclear output, translation regulation to RNA degradation, indicating that m6A has various functions affecting RNA metabolism positively or negatively. Reading proteins are vital in regulating the translation and stability of m6A mRNAs positively or negatively. Recent studies have enhanced the understanding of the molecular mechanism of the YT521-B homology (YTH) domain family and the modification of m6A. This study aimed to review the specific mechanisms, functions, and interactions of the YTH domain protein family. It also discussed future research directions, thus providing new ideas for the clinical diagnosis and targeted therapy of cancer.

Keywords:  YTH domain; YTHDC1-2; YTHDF1-3; cancer; m6A modification

DOI:  https://doi.org/10.3389/fonc.2021.629560
Curr Opin Chem Biol. 2021 Mar 05. pii: S1367-5931(21)00011-9. [Epub ahead of print]63 28-37

Mapping messenger RNA methylations at single base resolution.

Jie Cao, Xiao Shu, Xin-Hua Feng, Jianzhao Liu.

  The messenger RNA (mRNA) methylations in mammalian cells have been found to contain N6-methyladenosine (m6A), N6-2'-O-dimethyladenosine (m6Am), 7-methylguanosine (m7G), 1-methyladenosine (m1A), 5-methylcytosine (m5C), and 2'-O-methylation (2'-OMe). Their regulatory functions in control of mRNA fate and gene expression are being increasingly uncovered. To unambiguously understand the critical roles of mRNA methylations in physiological and pathological processes, mapping these methylations at single base resolution is highly required. Here, we will review the progresses made in methylation sequencing methodologies developed mainly in recent two years, with an emphasis on chemical labeling-assisted single base resolution methods, and discuss the problems and prospects as well.

Keywords:  Chemical labeling methods; Single base resolution; m(6)A; m(7)G; mRNA methylation

DOI:  https://doi.org/10.1016/j.cbpa.2021.02.001
PLoS Pathog. 2021 Mar 10. 17(3): e1009421

N6-methyladenosine modification of HIV-1 RNA suppresses type-I interferon induction in differentiated monocytic cells and primary macrophages.

Shuliang Chen, Sameer Kumar, Constanza E Espada, Nagaraja Tirumuru, Michael P Cahill, Lulu Hu, Chuan He, Li Wu.

N6-methyladenosine (m6A) is a prevalent RNA modification that plays a key role in regulating eukaryotic cellular mRNA functions. RNA m6A modification is regulated by two groups of cellular proteins, writers and erasers that add or remove m6A, respectively. HIV-1 RNA contains m6A modifications that modulate viral infection and gene expression in CD4+ T cells. However, it remains unclear whether m6A modifications of HIV-1 RNA modulate innate immune responses in myeloid cells that are important for antiviral immunity. Here we show that m6A modification of HIV-1 RNA suppresses the expression of antiviral cytokine type-I interferon (IFN-I) in differentiated human monocytic cells and primary monocyte-derived macrophages. Transfection of differentiated monocytic U937 cells with HIV-1 RNA fragments containing a single m6A-modification significantly reduced IFN-I mRNA expression relative to their unmodified RNA counterparts. We generated HIV-1 with altered m6A levels of RNA by manipulating the expression of the m6A erasers (FTO and ALKBH5) or pharmacological inhibition of m6A addition in virus-producing cells, or by treating HIV-1 RNA with recombinant FTO in vitro. HIV-1 RNA transfection or viral infection of differentiated U937 cells and primary macrophages demonstrated that HIV-1 RNA with decreased m6A levels enhanced IFN-I expression, whereas HIV-1 RNA with increased m6A modifications had opposite effects. Our mechanistic studies indicated that m6A of HIV-1 RNA escaped retinoic acid-induced gene I (RIG-I)-mediated RNA sensing and activation of the transcription factors IRF3 and IRF7 that drive IFN-I gene expression. Together, these findings suggest that m6A modifications of HIV-1 RNA evade innate immune sensing in myeloid cells.

DOI: https://doi.org/10.1371/journal.ppat.1009421
Mol Metab. 2021 Mar 08. pii: S2212-8778(21)00049-1. [Epub ahead of print] 101209

RNA m6A reader IMP2/IGF2BP2 promotes pancreatic β-cell proliferation and insulin secretion by enhancing PDX1 expression.

Laura Regué, Liping Zhao, Fei Ji, Hua Wang, Joe Avruch, Ning Dai.

  Type 2 diabetes (T2D) is a common metabolic disease. Variants in IMP2 (IGF2BP2) associated with increased risk of T2D impair insulin secretion. However, the underlying mechanism is not known. IMP2 is an RNA binding protein that preferentially recognize N6-methyladenosine (m6A) modified mRNAs. Here we report that the deletion of IMP2 in pancreatic β-cells leads to reduced compensatory β-cell proliferation and function in mice. Mechanically, IMP2 directly binds to Pdx1 mRNA and stimulates its translation in a m6A dependent manner. In addition, IMP2 also orchestrates IGF2-AKT-GSK3-PDX1 signaling to promotes insulin secretion. In human EndoC-βH1 cells, the expression of IMP2 is capable to enhance cell proliferation, PDX1 expression, IGF2 signaling as well as insulin secretion. Our work therefore reveals IMP2 as a critical regulator of β-cell function and highlights the importance of posttranscriptional gene expression in T2D pathology.

Keywords:  IMP2/IGF2BP2; T2D; insulin secretion; m6A; post-transcriptional gene expression regulation

DOI:  https://doi.org/10.1016/j.molmet.2021.101209
Cell Biosci. 2021 Mar 11. 11(1): 52

Mettl14-mediated m6A modification modulates neuron apoptosis during the repair of spinal cord injury by regulating the transformation from pri-mir-375 to miR-375.

Haoyu Wang, Jing Yuan, Xiaoqian Dang, Zhibin Shi, Wenrui Ban, Dong Ma.

   BACKGROUND: Spinal cord injury (SCI) is a disabling disorder, resulting in neurological impairments. This study investigated the mechanism of methyltransferase-like 14 (Mettl14) on apoptosis of spinal cord neurons during SCI repair by mediating pri-microRNA (miR) dependent N6-methyladenosine (m6A) methylation.
METHODS: The m6A content in total RNA and Mettl14 levels in spinal cord tissues of SCI rats were detected. Mettl14 expression was intervened in SCI rats to examine motor function, neuron apoptosis, and recovery of neurites. The cell model of SCI was established and intervened with Mettl14. miR-375, related to SCI and positively related to Mettl14, was screened out. The expression of miR-375 and pri-miR-375 after Mettl14 intervention was detected. The expression of pri-miR-375 combined with DiGeorge critical region 8 (DGCR8) and that modified by m6A was detected. Furthermore, the possible downstream gene and pathway of miR-375 were analysed. SCI cell model with Mettl14 intervention was combined with Ras-related dexamethasone-induced 1 (RASD1)/miR-375 intervention to observe the apoptosis.
RESULTS: Mettl14 level and m6A content in spinal cord tissue were significantly increased. After Mettl14 knockdown, the injured motor function was restored and neuron apoptosis was reduced. In vitro, Mettl14 silencing reduced the apoptosis of SCI cells; miR-375 was reduced and pri-miR-375 was increased; miR-375 targeted RASD1. Silencing Mettl14 inactivated the mTOR pathway. The apoptosis in cells treated with silencing Mettl14 + RASD1/miR-375 was inhibited.
CONCLUSIONS: Mettl14-mediated m6A modification inhibited RASD1 and induced the apoptosis of spinal cord neurons in SCI by promoting the transformation of pri-miR-375 to mature miR-375.

Keywords:  Mettl14; Pri‐mir‐375; RASD1; Spinal cord injury; m6A modification; miR-375

DOI:  https://doi.org/10.1186/s13578-020-00526-9
Nat Commun. 2021 03 11. 12(1): 1582

N6-methyladenosine RNA modification suppresses antiviral innate sensing pathways via reshaping double-stranded RNA.

Weinan Qiu, Qingyang Zhang, Rui Zhang, Yangxu Lu, Xin Wang, Huabin Tian, Ying Yang, Zijuan Gu, Yanan Gao, Xin Yang, Guanshen Cui, Baofa Sun, Yanan Peng, Hongyu Deng, Hua Peng, Angang Yang, Yun-Gui Yang, Pengyuan Yang.

Double-stranded RNA (dsRNA) is a virus-encoded signature capable of triggering intracellular Rig-like receptors (RLR) to activate antiviral signaling, but whether intercellular dsRNA structural reshaping mediated by the N6-methyladenosine (m6A) modification modulates this process remains largely unknown. Here, we show that, in response to infection by the RNA virus Vesicular Stomatitis Virus (VSV), the m6A methyltransferase METTL3 translocates into the cytoplasm to increase m6A modification on virus-derived transcripts and decrease viral dsRNA formation, thereby reducing virus-sensing efficacy by RLRs such as RIG-I and MDA5 and dampening antiviral immune signaling. Meanwhile, the genetic ablation of METTL3 in monocyte or hepatocyte causes enhanced type I IFN expression and accelerates VSV clearance. Our findings thus implicate METTL3-mediated m6A RNA modification on viral RNAs as a negative regulator for innate sensing pathways of dsRNA, and also hint METTL3 as a potential therapeutic target for the modulation of anti-viral immunity.

DOI: https://doi.org/10.1038/s41467-021-21904-y
Front Cell Dev Biol. 2021 ;9 627706

Deficiency of Mettl3 in Bladder Cancer Stem Cells Inhibits Bladder Cancer Progression and Angiogenesis.

Ganping Wang, Yarong Dai, Kang Li, Maosheng Cheng, Gan Xiong, Xiaochen Wang, Shuang Chen, Zhi Chen, Jianwen Chen, Xiuyun Xu, Rong-Song Ling, Liang Peng, Demeng Chen.

  RNA N6-methyladenosine is a key step of posttranscriptional modulation that is involved in governing gene expression. The m6A modification catalyzed by Mettl3 has been widely recognized as a critical epigenetic regulation process for tumorigenic properties in various cancer cell lines, including bladder cancer. However, the in vivo function of Mettl3 in bladder cancer remains largely unknown. In our study, we found that ablation of Mettl3 in bladder urothelial attenuates the oncogenesis and tumor angiogenesis of bladder cancer using transgenic mouse model. In addition, conditional knockout of Mettl3 in K14+ bladder cancer stem cell population leads to inhibition of bladder cancer progression. Coupled with the global transcriptome sequencing and methylated RNA immunoprecipitation sequencing results, we showed that deletion of Mettl3 leads to the suppression of tyrosine kinase endothelial (TEK) and vascular endothelial growth factor A (VEGF-A) through reduced abundance of m6A peaks on a specific region. In addition, the depletion of Mettl3 results in the decrease in both messenger RNA (mRNA) and protein levels of TEK and VEGF-A in vitro. Taken together, Mettl3-mediated m6A modification is required for the activation of TEK-VEGF-A-mediated tumor progression and angiogenesis. Our findings may provide theoretical basis for bladder cancer treatment targeting Mettl3.

Keywords:  Mettl3; angiogenesis; bladder cancer; cancer stem cell; m6A

DOI:  https://doi.org/10.3389/fcell.2021.627706
Ann Transl Med. 2021 Feb;9(3): 232

MiR-4729 regulates TIE1 mRNA m6A modification and angiogenesis in hemorrhoids by targeting METTL14.

Te Liu, Haikun Zhou, Hong Lu, Chunsheng Luo, Qingming Wang, Yunhua Peng, Wei Yang, Yaojie Xin.

   Background: Hemorrhoids are a frequently-occurring disease of the anorectal system that is often accompanied by vascular hyperplasia and edema. A METTL14-mediated RNA N-6 methyladenosine (m6A) modification can improve mRNA stability and increase its transcriptional and translational activities, closely related to the occurrence of many diseases.
Methods: Western blot, qPCR, and immunofluorescence staining were used to detect the levels of gene and protein expression. Haematoxylin and eosin staining was used for histopathological examination. RNA immunoprecipitation-PCR and RNA dot blotting were used to detect mRNA m6A modification.
Results: Obvious signs of angiogenesis (CD31+/vWF+) were identified in the hemorrhoids. High levels of METTL14 expression on vascular endothelial cells (CD31+) suggested that angiogenesis was accompanied by differential modification of m6A RNA. It was subsequently found that the level of miR-4729 expression was significantly decreased in hemorrhoid tissues. The luciferase reporter enzyme assay results suggested that miR-4729 silenced its expression by targeting the 3'UTR of METTL14 mRNA. MiR-4729 overexpression in human umbilical vein endothelial cells (HUVECs) inhibited the proliferation and migration of HUVECs in vitro and vascular structure formation in the outer matrix. MiR-4729 overexpression significantly inhibited endogenous METTL14 expression in HUVECs and reduced the entire m6A RNA modification, especially the level of m6A methylation at the specific site of the 3' UTR of TIE1 mRNA. Moreover, miR-4729 overexpression significantly inhibited the molecular loop of the TIE1/VEGFA signaling pathway in HUVECs.
Conclusions: Our findings confirmed that the down-regulation of miR-4729 in hemorrhoid vascular endothelial cells was one of the main reasons for vascular proliferation. The overexpression of miR-4729 in vascular endothelial cells decreased the global mRNA methylation and TIE1 mRNA 3'UTR-specific site methylation by silencing METTL14 expression, reducing TIE1 mRNA stability, down-regulating the TIE1/VEGFA signal molecular loop expression, and weakening angiogenesis ability.

Keywords:  Hemorrhoids; METTL14; TIE1; microRNA; vascular hyperplasia

DOI:  https://doi.org/10.21037/atm-20-3399
Front Cell Dev Biol. 2021 ;9 622198

Succinylation Regulators Promote Clear Cell Renal Cell Carcinoma by Immune Regulation and RNA N6-Methyladenosine Methylation.

Wenqing Lu, Xiaofang Che, Xiujuan Qu, Chunlei Zheng, Xianghong Yang, Bowen Bao, Zhi Li, Duo Wang, Yue Jin, Yizhe Wang, Jiawen Xiao, Jianfei Qi, Yunpeng Liu.

  Succinylation is a newly discovered and multienzyme-regulated post-translational modification (PTM) that is associated with the initiation and progression of cancer. Currently, no systematic analyses on the role of succinylation regulators in tumors have been reported. In this study, we performed a comprehensive pan-cancer analysis on four well-known succinylation regulators (CPT1A, KAT2A, SIRT5, and SIRT7). We found that these regulators played specific and critical roles in the prognosis of clear cell renal cell carcinoma (ccRCC). We constructed a risk score (RS) based on two independent prognostic prediction factors, CPT1A and KAT2A, and subsequently developed a nomogram model containing the RS, which showed good accuracy in the prediction of overall survival (OS) in ccRCC patients. Furthermore, we used the similar expression pattern of four succinylation regulators according to consensus clustering analysis to divide the patients into three clusters that exhibited prominently different OS as well as clinicopathological characteristics. Differently expressed genes (DEGs) and pathway enrichment analyses of three clusters indicated that succinylation regulators might promote malignant progression of ccRCC by regulating the infiltration of immune cells and RNA N6-methyladenosine (m6A) methylation. Importantly, our data suggest that CPT1A and SIRT5 might up-regulate and down-regulate the expression of LRPPRC and EIF3B, respectively. Our study systematically analyzed the prognostic predictive values of four succinylation regulators and revealed their potential mechanisms in ccRCC aggressiveness. These data provide new insight into the understanding of succinylation modification and present clinical evidence for its role in ccRCC treatments.

Keywords:  RNA N6-methyladenosine methylation; clear cell renal cell carcinoma; immune; prognosis; succinylation regulators

DOI:  https://doi.org/10.3389/fcell.2021.622198
J Exp Clin Cancer Res. 2021 Mar 06. 40(1): 90

METTL3-mediated m6A mRNA modification of FBXW7 suppresses lung adenocarcinoma.

Yingtong Wu, Ning Chang, Yong Zhang, Xinxin Zhang, Leidi Xu, Yinggang Che, Tianyun Qiao, Bin Wu, Ying Zhou, Jun Jiang, Jie Xiong, Jian Zhang, Jian Zhang.

   BACKGROUND: FBXW7 m6A modification plays an important role in lung adenocarcinoma (LUAD) progression; however, the underlying mechanisms remain unclear.
METHODS: The correlation between FBXW7 and various genes related to m6A modification was analyzed using The Cancer Genome Atlas database. The regulatory effects of METTL3 on FBXW7 mRNA m6A modification were examined in a cell model, and the underlying mechanism was determined by methylated RNA immunoprecipitation, RNA immunoprecipitation, luciferase reporter, and mutagenesis assays. In vitro experiments were performed to further explore the biological effects of METTL3-mediated FBXW7 m6A modification on LUAD development.
RESULTS: Decreased FBXW7 expression was accompanied by downregulated METTL3 expression in human LUAD tissues and was associated with a worse prognosis for LUAD in The Cancer Genome Atlas database. m6A was highly enriched in METTL3-mediated FBXW7 transcripts, and increased m6A modification in the coding sequence region increased its translation. Functionally, METTL3 overexpression or knockdown affected the apoptosis and proliferation phenotype of LUAD cells by regulating FBXW7 m6A modification and expression. Furthermore, FBXW7 overexpression in METTL3-depleted cells partially restored LUAD cell suppression in vitro and in vivo.
CONCLUSIONS: Our findings reveal that METTL3 positively regulates FBXW7 expression and confirm the tumor-suppressive role of m6A-modified FBXW7, thus providing insight into its epigenetic regulatory mechanisms in LUAD initiation and development.

Keywords:  Epigenetic modification; FBXW7; Lung adenocarcinoma; METTL3; m6A

DOI:  https://doi.org/10.1186/s13046-021-01880-3
Arch Toxicol. 2021 Mar 13.

N6-methyladenosine reader YTHDC2 and eraser FTO may determine hepatocellular carcinoma prognoses after transarterial chemoembolization.

Jiandong Liu, Dongyang Wang, Jianyuan Zhou, Leirong Wang, Nasha Zhang, Liqing Zhou, Jiajia Zeng, Jibing Liu, Ming Yang.

  Transarterial chemoembolization (TACE) has significantly improved overall survival (OS) of unresectable hepatocellular carcinoma (HCC) patients. Unfortunately, a portion of patients show no therapeutic responses to TACE. N6-methyladenosine (m6A) as well as its epigenetic writers, erasers, and readers play a crucial role in HCC development. However, it is still largely unclear how functional small nucleotide polymorphisms (SNPs) in m6A-regulating genes contribute to prognosis of TACE-treated HCC patients. In this study, potential functional SNPs were systematically evaluated to identify their roles in the prognosis of HCC patients after TACE in a Chinese Han population. Employing multiple databases, we successfully annotated 55 candidate SNPs. After genotyping these SNPs in our TACE cohort, we identified three genetic variants in YTHDC2 (rs6594732, rs10071816, and rs2303718) and one SNP in FTO (rs7202116) having statistically significant associations with the OS of HCC patients treated with TACE. For example, multivariate Cox proportional hazards model indicated that the rs7202116 GG genotype carriers had markedly shorter OS and an 87% increased death risk compared with the AA carriers after TACE therapy (P = 0.002). When investigating functional relevance of these SNPs, we observed an allelic regulation of rs7202116 on FTO expression in HCC tissue samples, with higher tumor suppressor FTO expression among the A allele carriers. Our findings reported the first evidence supporting the prognostic value of m6A reader YTHDC2 and m6A eraser FTO SNPs in TACE-treated HCC patients. Importantly, our data implicated that m6A-regulating genes may be targets to improve therapeutic strategy for unresectable HCC patients.

Keywords:  FTO; Hepatocellular carcinoma; TACE; YTHDC2; m6A

DOI:  https://doi.org/10.1007/s00204-021-03021-3
Front Oncol. 2020 ;10 567931

A Ten-N6-Methyladenosine (m6A)-Modified Gene Signature Based on a Risk Score System Predicts Patient Prognosis in Rectum Adenocarcinoma.

Wei Huang, Gen Li, Zihang Wang, Lin Zhou, Xin Yin, Tianshu Yang, Pei Wang, Xu Teng, Yajuan Feng, Hefen Yu.

   Objectives: The study aims to analyze the expression of N6-methyladenosine (m6A)-modified genes in rectum adenocarcinoma (READ) and identify reliable prognostic biomarkers to predict the prognosis of READ.
Materials and Methods: RNA sequence data of READ and corresponding clinical survival data were obtained from The Cancer Genome Atlas (TCGA) database. N6-methyladenosine (m6A)-modified genes in READ were downloaded from the "m6Avar" database. Differentially expressed m6A-modified genes in READ stratified by different clinicopathological characteristics were identified using the "limma" package in R. Protein-protein interaction (PPI) network and co-expression analysis of differentially expressed genes (DEGs) were performed using "STRING" and Cytoscape, respectively. Principal component analysis (PCA) was done using R. In addition, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were used to functionally annotate the differentially expressed genes in different subgroups. Univariate Cox regression analyses were conducted to identify the powerful independent prognostic factors in READ associated with overall survival (OS). A robust likelihood-based survival model was built using the "rbsurv" package to screen for survival-associated signature genes. The Support Vector Machine (SVM) was used to predict the prognosis of READ through the risk score of survival-associated signature genes. Correlation analysis were carried out using GraphPad prism 8.
Results: We screened 974 differentially expressed m6A-modified genes among four types of READ samples. Two READ subgroups (group 1 and group 2) were identified by K means clustering according to the expression of DEGs. The two subgroups were significantly different in overall survival and pathological stages. Next, 118 differentially expressed genes between the two subgroups were screened and the expression of 112 genes was found to be related to the prognosis of READ. Next, a panel of 10 survival-associated signature genes including adamtsl1, csmd2, fam13c, fam184a, klhl4, olfml2b, pdzd4, sec14l5, setbp1, tmem132b was constructed. The signature performed very well for prognosis prediction, time-dependent receiver-operating characteristic (ROC) analysis displaying an area under the curve (AUC) of 0.863, 0.8721, and 0.8752 for 3-year survival rate, prognostic status, and pathological stage prediction, respectively. Correlation analysis showed that the expression levels of the 10 m6A-modified genes were positively correlated with that of m6A demethylase FTO and ALKBH5.
Conclusion: This study identified potential m6A-modified genes that may be involved in the pathophysiology of READ and constructed a novel gene expression panel for READ risk stratification and prognosis prediction.

Keywords:  READ; gene signature; m6A; prognostic prediction; risk score

DOI:  https://doi.org/10.3389/fonc.2020.567931
Curr Genet. 2021 Mar 08.

RNA modifications as a common denominator between tRNA and mRNA.

Ofri Levi, Yoav S Arava.

  Recent studies underscore RNA modifications as a novel mechanism to coordinate expression and function of different genes. While modifications on the sugar or base moieties of tRNA are well known, their roles in mRNA regulation are only starting to emerge. Interestingly, some modifications are present in both tRNA and mRNA, and here we discuss the functional significance of these common features. We describe key modifications that are present in both RNA types, elaborate on proteins that interact with them, and indicate recent works that identify roles in communicating tRNA processes and mRNA regulation. We propose that as tools are developed, the shortlist of features that are common between types of RNA will greatly expand and proteins that interact with them will be identified. In conclusion, the presence of the same modification in both RNA types provides an intersect between tRNA processes and mRNA regulation and implies a novel mechanism for connecting diverse cellular processes.

Keywords:  Inosine; Pseudouridine; RNA binding proteins; RNA modifications; Translation; m5C; m6A; mRNA; tRNA

DOI:  https://doi.org/10.1007/s00294-021-01168-1
Front Oncol. 2021 ;11 629947

m6A-Mediated Upregulation of LINC00857 Promotes Pancreatic Cancer Tumorigenesis by Regulating the miR-150-5p/E2F3 Axis.

Xiangrui Meng, Yanyao Deng, Shuhan He, Li Niu, Hongwei Zhu.

  The mortality and morbidity rates of pancreatic cancer (PC) have been increasing over the past two decades. Recent evidence indicates that long non-coding RNAs (lncRNAs) are usually dysregulated in the tumorigenesis and progression of PC. In the present study, we showed that the expression of LINC00857 was upregulated in PC and associated with poor prognosis based on the Gene Expression Profiling Interactive Analysis (GEPIA) database and validated in our PC tissues and cell lines. N6-Methyladenosine (m6A) was highly enriched within LINC00857 and enhanced its RNA stability. Knockdown of LINC00857 remarkably inhibited the proliferation and promoted the apoptosis of PC cells. Then, by using bioinformation analysis and verified experiments, we identified that LINC00857 functioned as a competing endogenous RNA (ceRNA) for sponging miR-150-5p, leading to the upregulation of its target E2F3 in PC cells. Taken above, our study revealed a potential ceRNA regulatory pathway in which LINC00857 modulates E2F3 expression by binding to miR-150-5p, ultimately promoting tumorigenesis in PC. LINC00857/miR-150-5p/E2F3 regulatory axis may be taken as an alternative therapeutic target for treating PC.

Keywords:  E2F3; LINC00857; M6A; MiR-150-5p; pancreatic cancer

DOI:  https://doi.org/10.3389/fonc.2021.629947
J Exp Clin Cancer Res. 2021 Mar 10. 40(1): 92

Downregulation of lncRNA ZNF582-AS1 due to DNA hypermethylation promotes clear cell renal cell carcinoma growth and metastasis by regulating the N(6)-methyladenosine modification of MT-RNR1.

Wuping Yang, Kenan Zhang, Lei Li, Yawei Xu, Kaifang Ma, Haibiao Xie, Jingcheng Zhou, Lin Cai, Yanqing Gong, Kan Gong.

   BACKGROUND: Emerging evidence confirms that lncRNAs (long non-coding RNAs) are potential biomarkers that play vital roles in tumors. ZNF582-AS1 is a novel lncRNA that serves as a potential prognostic marker of cancers. However, the specific clinical significance and molecular mechanism of ZNF582-AS1 in ccRCC (clear cell renal cell carcinoma) are unclear.
METHODS: Expression level and clinical significance of ZNF582-AS1 were determined by TCGA-KIRC data and qRT-PCR results of 62 ccRCCs. DNA methylation status of ZNF582-AS1 promoter was examined by MSP, MassARRAY methylation and demethylation analysis. Gain-of-function experiments were conducted to investigate the biological roles of ZNF582-AS1 in the phenotype of ccRCC. The subcellular localization of ZNF582-AS1 was detected by RNA FISH. iTRAQ, RNA pull-down and RIP-qRT-PCR were used to identify the downstream targets of ZNF582-AS1. rRNA MeRIP-seq and MeRIP-qRT-PCR were utilized to examine the N(6)-methyladenosine modification status. Western blot and immunohistochemistry assays were used to determine the protein expression level.
RESULTS: ZNF582-AS1 was downregulated in ccRCC, and decreased ZNF582-AS1 expression was significantly correlated with advanced tumor stage, higher pathological stage, distant metastasis and poor prognosis. Decreased ZNF582-AS1 expression was caused by DNA methylation at the CpG islands within its promoter. ZNF582-AS1 overexpression inhibited cell proliferative, migratory and invasive ability, and increased cell apoptotic rate in vitro and in vivo. Mechanistically, we found that ZNF582-AS1 overexpression suppressed the N(6)-methyladenosine modification of MT-RNR1 by reducing rRNA adenine N(6)-methyltransferase A8K0B9 protein level, resulting in the decrease of MT-RNR1 expression, followed by the inhibition of MT-CO2 protein expression. Furthermore, MT-RNR1 overexpression reversed the decreased MT-CO2 expression and phenotype inhibition of ccRCC induced by increased ZNF582-AS1 expression.
CONCLUSIONS: This study demonstrates for the first time that ZNF582-AS1 functions as a tumor suppressor gene in ccRCC and ZNF582-AS1 may serve as a potential biomarker and therapeutic target of ccRCC.

Keywords:  DNA methylation; MT-RNR1; N(6)-methyladenosine modification; ZNF582-AS1; ccRCC

DOI:  https://doi.org/10.1186/s13046-021-01889-8
Lab Invest. 2021 Mar 10.

N-methyladenosine reader YTHDF2-mediated long noncoding RNA FENDRR degradation promotes cell proliferation in endometrioid endometrial carcinoma.

Jie Shen, Xiao-Ping Feng, Ru-Bing Hu, Hao Wang, Yan-Li Wang, Jian-Hua Qian, Yun-Xiao Zhou.

Dysregulation of long noncoding RNA (LncRNA) FENDDR has been shown to be closely related to the progression of several cancers. However, its role and upstream regulatory mechanism in endometrioid endometrial carcinoma (EEC) remains unclear. This study was conducted using the cancerous tissues of EEC patients (n = 60), EEC cell lines, and a xenograft mouse model. The expression level of LncRNA FENDRR was decreased and the N-methyladenosine (m6A) methylation levels of LncRNA FENDRR was elevated in cancerous tissues of EEC patients. In vitro experiments demonstrated that YTH domain-containing 2 (YTHDF2), an m6A reader, recognized the abundance of m6A-modified LncRNA FENDRR in EEC cells and promoted its degradation. LncRNA FENDRR overexpression suppressed cell proliferation and facilitated cell apoptosis in the EEC cell line HEC-1B by reducing the protein level of SRY-related HMG box transcription factor 4 (SOX4). Interference of LncRNA FENDRR reversed the inhibitory effect of sh-YTHDF2 on cell proliferation and the promoting effect of sh-YTHDF2 on cell apoptosis in HEC-1B cells by silencing FENDRR. Finally, in vivo experiments confirmed that overexpression of LncRNA FENDRR retarded the growth of EEC cells. In conclusion, YTHDF2-mediated LncRNA FENDRR degradation promotes cell proliferation by elevating SOX4 expression in EEC.

DOI: https://doi.org/10.1038/s41374-021-00543-3
Front Oncol. 2021 ;11 560506

Analysis and Validation of circRNA-miRNA Network in Regulating m6A RNA Methylation Modulators Reveals CircMAP2K4/miR-139-5p/YTHDF1 Axis Involving the Proliferation of Hepatocellular Carcinoma.

Fanwu Chi, Yong Cao, Yuhan Chen.

  The m6A RNA methylation modulators play a crucial role in regulating hepatocellular carcinoma (HCC) progression. The circular RNA (circRNA) regulatory network in regulating m6A RNA methylation modulators in HCC remains largely unknown. In this study, 5 prognostic m6A RNA methylation modulators in HCC were identified from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) projects. The differentially expressed microRNAs (DEmiRNAs) and circRNAs (DEcircRNAs) between paired tumor and normal tissues were screened out from TCGA and or Gene Expression Omnibus (GEO) database to construct the circRNA-miRNA- m6A RNA methylation modulator regulatory network, which included three m6A RNA methylation modulators (HNRNPC, YTHDF1, and YTHDF2), 11 DEmiRNAs, and eight DEcircRNAs. Among the network, hsa-miR-139-5p expression was negatively correlated with YTHDF1. Hsa-miR-139-5p low or YTHDF1 high expression was correlated with high pathological grade, advanced stage and poor survival of HCC. Additionally, cell cycle, base excision repair, and homologous recombination were enriched in YTHDF1 high expression group by GSEA. A hub circRNA regulatory network was constructed based on hsa-miR-139-5p/YTHDF1 axis. Furthermore, hsa_circ_0007456(circMAP2K4) was validated to promote HCC cell proliferation by binding with hsa-miR-139-5p to promote YTHDF1 expression. Taken together, we identified certain circRNA regulatory network related to m6A RNA methylation modulators and provided clues for mechanism study and therapeutic targets for HCC.

Keywords:  circular RNA; hepatocellular carcinoma; m6A RNA methylation modulator; microRNA; regulatory network

DOI:  https://doi.org/10.3389/fonc.2021.560506
Cell Rep. 2021 Mar 09. pii: S2211-1247(21)00139-X. [Epub ahead of print]34(10): 108825

Regulation of translation by methylation multiplicity of 18S rRNA.

Kuanqing Liu, Daniel A Santos, Jeffrey A Hussmann, Yun Wang, Benjamin M Sutter, Jonathan S Weissman, Benjamin P Tu.

N6-methyladenosine (m6A) is a conserved ribonucleoside modification that regulates many facets of RNA metabolism. Using quantitative mass spectrometry, we find that the universally conserved tandem adenosines at the 3' end of 18S rRNA, thought to be constitutively di-methylated (m62A), are also mono-methylated (m6A). Although present at substoichiometric amounts, m6A at these positions increases significantly in response to sulfur starvation in yeast cells and mammalian cell lines. Combining yeast genetics and ribosome profiling, we provide evidence to suggest that m6A-bearing ribosomes carry out translation distinctly from m62A-bearing ribosomes, featuring a striking specificity for sulfur metabolism genes. Our work thus reveals methylation multiplicity as a mechanism to regulate translation.

DOI: https://doi.org/10.1016/j.celrep.2021.108825