bims-rimeca 2020-10-18 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2020–10–18
eleven papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics

HBXIP promotes gastric cancer via METTL3-mediated MYC mRNA m6A modification.
The m6A Methyltransferase METTL3 Is Functionally Implicated in DLBCL Development by Regulating m6A Modification in PEDF.
Connecting METTL3 and intratumoural CD33+ MDSCs in predicting clinical outcome in cervical cancer.
The role of m6A-related genes in the prognosis and immune microenvironment of pancreatic adenocarcinoma.
Advances in the role of m6A RNA modification in cancer metabolic reprogramming.
TRADES: Targeted RNA Demethylation by SunTag System.
The Role of N6-Methyladenosine Methylation in the Progression of Endometrial Cancer.
Magnetic microbeads-based amperometric immunoplatform for the rapid and sensitive detection of N6-methyladenosine to assist in metastatic cancer cells discrimination.
M6A Demethylase FTO Plays a Tumor Suppressor Role in Thyroid Cancer.
Fluorescein-based monitoring of RNA N6-methyladenosine at single-nucleotide resolution.
Distinct 5-methylcytosine profiles of circular RNA in human hepatocellular carcinoma.

Aging (Albany NY). 2020 Oct 13. 12

HBXIP promotes gastric cancer via METTL3-mediated MYC mRNA m6A modification.

Zhi Yang, Xiaodi Jiang, Deming Li, Xiaofeng Jiang.

  Gastric cancer (GC) is one of the most common malignancies worldwide with limited treatment options and distinct geographical distribution even in countries such as China. Genetic alterations during its carcinogenesis need urgent elucidation. In this study, we propose an intriguing hypothesis that the hepatitis B X-interacting protein (HBXIP) may function as an oncogene in GC. We harvested 45 GC tissues and matched the paracancerous tissues. The c-myc proto-oncogene (MYC) N6-methyladenosine (m6A) mRNA methylation was detected by m6A RNA immunoprecipitation and dot-blot assays. Expressions of HBXIP, methyltransferase like 3 (METTL3) and MYC were all determined to be upregulated in both GC tissues and cells. Silencing HBXIP led to a decreased expression of METTL3, which inhibited GC cell proliferation, migration and invasion while promoting their apoptosis. Furthermore, METTL3 enhanced MYC m6A methylation and increased MYC translation, which could potentiate the proliferation, migration and invasion of GC cells. Finally, the HBXIP knockdown impeded the tumorigenicity of GC cells in vivo. Based on the findings of this study, we conclude that HBXIP plays an oncogenic role in GC via METTL3-mediated MYC mRNA m6A modification. The study offers a comprehensive understanding of HBXIP as a potential therapeutic target to limit GC progression.

Keywords:  Hepatitis B X-interacting protein; METTL3; MYC; N6-methyladenosine methylation; gastric cancer

DOI:  https://doi.org/10.18632/aging.103767
Front Genet. 2020 ;11 955

The m6A Methyltransferase METTL3 Is Functionally Implicated in DLBCL Development by Regulating m6A Modification in PEDF.

Yingying Cheng, Yuanyuan Fu, Ying Wang, Jinbi Wang.

  Diffuse large B-cell lymphoma (DLBCL) is the most common subtype of lymphoma, whose treatment still has a major challenge of achieving a satisfactory curative effect. The underlying mechanisms also have not been fully illustrated. N 6-Methyladenosine (m6A) has been identified as the most prevalent internal modification of mRNAs present in eukaryotes, which is involved in the pathogenesis of cancers. It remains unclear how m6A mRNA methylation is functionally linked to the pathogenesis of DLBCL. In this study, we sought to explore the roles of METTL3 on DLBCL development. The results showed that m6A level for RNA methylation and the expression level of METTL3 were upregulated in DLBCL tissues and cell lines. Functionally, downregulated METTL3 expression in DLBCL cells inhibited the cell proliferation ability. Further mechanism analysis indicated that METTL3 knockdown abates the m6A methylation and total mRNA level of pigment epithelium-derived factor (PEDF). However, Wnt/β-catenin signaling was not thus activated. Overexpressed PEDF abrogates the inhibition of cell proliferation in DLBCL cells that is caused by METTL3 silence. In summary, the above-mentioned results demonstrated that the METTL3 promotes DLBCL progression by regulating the m6A level of PEDF.

Keywords:  DLBCL; METTL3; N6-methyladenosine; PEDF; proliferation

DOI:  https://doi.org/10.3389/fgene.2020.00955
J Transl Med. 2020 Oct 15. 18(1): 393

Connecting METTL3 and intratumoural CD33+ MDSCs in predicting clinical outcome in cervical cancer.

Huan-He Ni, Lin Zhang, He Huang, Shu-Qin Dai, Jiang Li.

   BACKGROUND: Methyltransferase-like 3 (METTL3) is a member of the m6A methyltransferase family and acts as an oncogene in cancers. Recent studies suggest that host innate immunity is regulated by the enzymes controlling m6A epitranscriptomic changes. Here, we aim to explore the associations between the levels of METTL3 and CD33+ myeloid-derived suppressor cells (MDSCs) in tumour tissues and the survival of patients with cervical cancer (CC).
METHODS: Specimens of paraffin embedded tumour from 197 CC patients were collected. The expression levels of METTL3 and CD33 were measured by immunohistochemical (IHC) staining. The clinical associations of the IHC variants were analysed by Pearson's or Spearman's chi-square tests. Overall survival (OS) and disease-free survival (DFS) were estimated by the Kaplan-Meier method and log-rank test. Hazard ratios (HRs) and independent significance were obtained via Cox proportional hazards models for multivariate analyses. METTL3 in CD33+ cells or CC-derived cells was knocked down by METTL3-specific siRNA, and MDSC induction in vitro was performed in a co-culture system in the presence of METTL3-siRNA and METTL3-knockdown-CC-derived cells compared with that of the corresponding controls.
RESULTS: We found that tumour tissues displayed increased levels of METTL3 and CD33+ MDSCs compared with tumour-adjacent tissues from the same CC patients. Importantly, METTL3 expression was positively related to the density of CD33+ cells in tumour tissues (P = 0.011). We further found that the direct CD33+CD11b+HLA-DR- MDSC induction and tumour-derived MDSC induction in vitro were decreased in the absence of METTL3. The level of METTL3 in tumour microenvironments was significantly related to advanced tumour stage. The levels of METTL3 and CD33+ MDSCs in tumour tissues were notably associated with reduced DFS or OS. Cox model analysis revealed that the level of METTL3 in tumour cells was an independent factor for patient survival, specifically for DFS (HR = 3.157, P = 0.022) and OS (HR = 3.271, P = 0.012), while the CD33+ MDSC number was an independent predictor for DFS (HR: 3.958, P = 0.031). Interestingly, in patients with advanced-disease stages (II-IV), METTL3 in tumour cells was an independent factor for DFS (HR = 6.725, P = 0.010) and OS (HR = 5.140, P = 0.021), while CD33+ MDSC density was an independent factor for OS (HR = 8.802, P = 0.037).
CONCLUSION: Our findings suggest that CD33+ MDSC expansion is linked to high levels of METTL3 and that METTL3 and CD33+ MDSCs are independent prognostic factors in CC.

Keywords:  CD33; Cervical cancer; METTL3; Prognosis; Tumour microenvironment

DOI:  https://doi.org/10.1186/s12967-020-02553-z
PeerJ. 2020 ;8 e9602

The role of m6A-related genes in the prognosis and immune microenvironment of pancreatic adenocarcinoma.

Rong Tang, Yiyin Zhang, Chen Liang, Jin Xu, Qingcai Meng, Jie Hua, Jiang Liu, Bo Zhang, Xianjun Yu, Si Shi.

   Background: Pancreatic adenocarcinoma (PAAD) is among the most lethal diseases and has a dismal prognosis; however, efficient treatment is currently limited. Several studies have observed epigenetic variation during tumorigenesis, suggesting the potential role of RNA methylation, especially N6-methyladenosine (m6A) modification, as a novel epigenetic modification mediating PAAD prognosis.
Methods: The expression levels of m6A-related genes were downloaded from The Cancer Genome Atlas-Pancreatic Adenocarcinoma (TCGA) and Genotype-Tissue Expression (GTEx) projects, and the findings were validated in four Expression Omnibus (GEO) datasets. A predictive model was constructed using a lasso regression and evaluated by a survival analysis and receiver operating characteristic curve. Consensus clustering identified two distinct subgroups with different immune activity signatures based on the expression pattern of m6A-related genes. The relationship between the mutation state of m6A-related genes and infiltration of immune cells was established and visualized using Tumor Immune Estimation Resource (https://cistrome.shinyapps.io/timer/).
Results: Fourteen of twenty-one m6A-related genes were differentially expressed between PAAD and normal tissues in TCGA-GTEx cohort. Among these genes, HNRNPC, IGF2BP2 and YTHDF1 were further validated in four GEO datasets. Moreover, an m6A-based model exhibited moderate accuracy in predicting overall survival in PAAD samples. Additionally, potential m6A modification targets were screened by selecting genes from a set of 23,391 genes that not only harbored the most m6A-modified sites but also showed a robust correlation with PAAD survival. Moreover, we correlated the expression level of m6A-related genes with the immune microenvironment of pancreatic cancer for the first time. Specifically, both arm-level gain and deletion of ALKBH5 decreased the infiltration of CD8+T cells (P < 0.05 and P < 0.01, respectively).
Conclusion: Collectively, our findings suggest a novel anticancer strategy for restoring balanced RNA methylation in tumor cells and guide clinical physicians in developing a new practical approach for considering the impact of related genes on prognosis.

Keywords:  Gemcitabine resistance; Immunity; Pancreatic adenocarcinoma; Prognosis; RNA methylation; m6A

DOI:  https://doi.org/10.7717/peerj.9602
Cell Biosci. 2020 ;10 117

Advances in the role of m6A RNA modification in cancer metabolic reprogramming.

Xiu Han, Lin Wang, Qingzhen Han.

  N6-methyladenosine (m6A) modification is the most common internal modification of eukaryotic mRNA and is widely involved in many cellular processes, such as RNA transcription, splicing, nuclear transport, degradation, and translation. m6A has been shown to plays important roles in the initiation and progression of various cancers. The altered metabolic programming of cancer cells promotes their cell-autonomous proliferation and survival, leading to an indispensable hallmark of cancers. Accumulating evidence has demonstrated that this epigenetic modification exerts extensive effects on the cancer metabolic network by either directly regulating the expression of metabolic genes or modulating metabolism-associated signaling pathways. In this review, we summarized the regulatory mechanisms and biological functions of m6A and its role in cancer metabolic reprogramming.

Keywords:  Cancer metabolic reprogramming; Detection techniques; Glycolysis; N6-methyladenosine

DOI:  https://doi.org/10.1186/s13578-020-00479-z
Adv Sci (Weinh). 2020 Oct;7(19): 2001402

TRADES: Targeted RNA Demethylation by SunTag System.

Jing Mo, Zonggui Chen, Shanshan Qin, Shu Li, Chuangang Liu, Lu Zhang, Ruoxi Ran, Ying Kong, Fang Wang, Songmei Liu, Yu Zhou, Xiaolian Zhang, Xiaocheng Weng, Xiang Zhou.

  N6-methyladenosine (m6A) is rapidly being studied and uncovered to play a significant role in various biological processes as well as in RNA fate and functions, while the effects of defined m6A sites are rarely characterized for the lack of convenient tools. To provide an applicable method to remove m6A modification at specific loci, an m6A editing system called "targeted RNA demethylation by SunTag system (TRADES)" is engineered. In this system, the targeting element dCas13b is fused to ten copies of GCN4 peptides which can recruit multiple scFv-fusion RNA demethylase to demethylate the target m6A site. Owing to this design, TRADES is more flexible to the indistinct m6A sites for its wide editing window. By site-specific demethylation of messenger RNA (mRNA) SON A2699, the lifetime of SON RNA is successfully prolonged in HeLa cells. Meanwhile, TRADES negligibly influences the lifetime of other non-targeted transcripts. TRADES also can regulate the gene expression of target transcript in an m6A-dependent manner. Moreover, the interference occuring for HBV and HIV replications demonstrates that the TRADES system holds potential in viral life cycle regulation and clinical applications.

Keywords:  N6‐methyladenosine; RNA modification; gene expression; nucleic acids; site‐specific demethylation

DOI:  https://doi.org/10.1002/advs.202001402
Cancer Biother Radiopharm. 2020 Oct 14.

The Role of N6-Methyladenosine Methylation in the Progression of Endometrial Cancer.

Kewei Song, Hongxia Xu, Changhe Wang.

  Purpose: N6-methyladenosine (m6A) methylation was the most abundant internal modification on messenger RNAs in eukaryotes. This study intended to explore the role of m6A methylation in endometrial cancer (EC). Materials and Methods: The m6A-sequencing data "GSE93911" of human EC were downloaded from Gene Expression Omnibus database. Hisat2 software and MACS2 were used to perform the alignment of reads and m6A methylation peak calling, and the peaks were annotated using Chipseeker. Then, differential m6A methylation peaks between normal and tumor samples were analyzed, followed by the functional enrichment analysis of the differentially methylated genes in promoter and 3' untranslated region (UTR) using Clusterprofiler. Based on the 450K methylated chip data, gene expression and clinical data in The Cancer Genome Atlas, the differentially methylated genes were verified, followed by Cox univariate/multivariate regression analysis and survival analysis. Finally, a risk prognosis model was constructed. Results: The m6A peak number was decreased in EC. The distribution of m6A peaks was highly enriched near transcriptional start site, in promoter, UTR, intron and exon, followed by distal intergenic. A total of 581 differentially methylated genes (361 hyper- and 220 hypomethylated genes) were identified in promoter and UTR regions that were enriched in insulin resistance (IR) and extracellular matrix (ECM). A total of 181 genes with significant differential expressions and differential methylation site in EC were selected. Of which, 31 genes were correlated with survival, and an 11-gene risk prognosis model was identified, including GDF7, BNC2, SLC8A1, B4GALNT3, DHCR24, ESRP1, HOXB9, IGSF9, KIAA1324, MSnX1, and PHGDH. Conclusion: The m6A methylation regulated EC progression by targeting the genes related to IR and ECM. A 11-gene risk prognosis model was identified to predict survival of patients with EC.

Keywords:  Msh homeobox 1; N6-methyladenosine methylation; endometrial cancer

DOI:  https://doi.org/10.1089/cbr.2020.3912
Biosens Bioelectron. 2020 Oct 08. pii: S0956-5663(20)30697-7. [Epub ahead of print]171 112708

Magnetic microbeads-based amperometric immunoplatform for the rapid and sensitive detection of N6-methyladenosine to assist in metastatic cancer cells discrimination.

Eloy Povedano, María Gamella, Rebeca M Torrente-Rodríguez, Ana Montero-Calle, María Pedrero, Guillermo Solís-Fernández, Fernando Navarro-Villoslada, Rodrigo Barderas, Susana Campuzano, José M Pingarrón.

  This work describes the preparation of an immunoplatform for the sensitive and selective determination of N6-methyladenosine (m6A). The simple and fast protocol involves for the first time the use of micromagnetic immunoconjugates to establish a direct competitive assay between the m6A target and a biotinylated RNA oligomer bearing a single m6A enzymatically labelled with a commercial conjugate of streptavidin-peroxidase (Strep-HRP) as tracer. The cathodic current change measured in the presence of H2O2/hydroquinone (HQ) at screen-printed carbon electrodes (SPCEs) upon surface capturing the magnetic bioconjugates is inversely proportional to the m6A target concentration. After evaluating the effect of key variables, the analytical characteristics were established for the determination of three different targets: the N6-methyladenosine-5'-triphosphate (m6ATP) ribonucleotide, a short synthetic RNA oligomer bearing a single m6A and the positive control provided in a commercial colorimetric kit for m6A-RNA quantification. The obtained results show that this immunoplatform is competitive with other methods reported to date, achieving an improved sensitivity (limit of detection of 0.9 pM for the short synthetic oligomer) using a much simpler and faster protocol (~1 h) and disposable electrodes for the transduction. Furthermore, the applicability for discriminating the metastatic potential of cancer cells by directly analyzing a small amount of raw total RNA without enriching or fragmenting was also preliminary assessed.

Keywords:  Amperometry; Disposable electrodes; Immunosensor; Magnetic microbeads; Metastatic cancer cells; m6A

DOI:  https://doi.org/10.1016/j.bios.2020.112708
DNA Cell Biol. 2020 Oct 15.

M6A Demethylase FTO Plays a Tumor Suppressor Role in Thyroid Cancer.

Run Tian, Shidong Zhang, Daxin Sun, Chunhua Bei, Di Li, Chuanjun Zheng, Xin Song, Mengshi Chen, Shengkui Tan, Xiaonian Zhu, Huixia Zhang.

  The purpose of this study was to investigate the expression and clinical significance of N6-methyladenosine demethylase FTO in thyroid cancer. Bioinformatic analysis showed that FTO expression was downregulated in thyroid cancer tissues and correlated with lymph node metastasis in thyroid cancer patients. We conducted experimental verification by collecting Asian samples. The results of quantitative reverse transcription-PCR showed that the mRNA expression of FTO in the blood of 30 thyroid cancer patients was lower than that of the control population. At the same time, we found that FTO expression was negative in tissues of 16/56 (28.57%) thyroid cancer cases and 4/40 (10.00%) nontumor thyroid cases through the immunohistochemical method, indicating a lower FTO expression in thyroid cancer tissues than nontumor thyroid tissues (p < 0.05). In addition, the protein expression of FTO was significantly related to the tumor grade and lymph node metastasis in thyroid cancer patients (p < 0.05), but not to other clinicopathological features. Multivariate logistic regression analysis showed that FTO expression was an independent risk factor for tumor grade. Survival analysis showed no significant difference in the disease-free survival time of thyroid cancer patients between high expression and low expression groups of FTO. Furthermore, bioinformatic analysis found that promoter DNA methylation and copy number variation might cause downregulated FTO and then affect TP53 pathways in thyroid cancer. We found that FTO expression was downregulated in thyroid cancer tissues and related to the progression of thyroid cancer, suggesting a tumor suppressor role of FTO in thyroid cancer.

Keywords:  FTO; m6A modification; metastasis; prognosis; thyroid cancer

DOI:  https://doi.org/10.1089/dna.2020.5956
J Mol Cell Biol. 2020 Oct 16. pii: mjaa057. [Epub ahead of print]

Fluorescein-based monitoring of RNA N6-methyladenosine at single-nucleotide resolution.

Xiao-Min Liu, Shen Wang, Xianqing Gan, Shu-Bing Qian, Jun Zhou.

DOI: https://doi.org/10.1093/jmcb/mjaa057
Am J Transl Res. 2020 ;12(9): 5719-5729

Distinct 5-methylcytosine profiles of circular RNA in human hepatocellular carcinoma.

Yuting He, Qiyao Zhang, Qingyuan Zheng, Xiao Yu, Wenzhi Guo.

Recent studies have indicated that several circular RNAs (circRNAs) can affect the occurrence and development of hepatocellular carcinoma (HCC). Post-transcriptional methylation modifications, including 5-methylcytosine (m5C) modification, are closely related to the tumorigenesis of cancers. However, the map of m5C modification of circRNA in HCC remains to be investigated. In this study, we performed MeRIP-seq to identify m5C sites on circRNA of human HCC tissues and paired adjacent non-tumor tissues. Further, we analyzed the relationship between m5C and HCC. Moreover, we performed a bioinformatics analysis to predict the function of specific methylated transcripts. We found that there was a significant difference in m5C between HCC tissues and paired non-tumor tissues, suggesting potential critical roles of m5C of circRNA in HCC development. In addition, the Gene Ontology (GO) analysis results indicated that the unique distribution pattern of circRNA m5C in HCC was associated with specific metabolism-associated pathways. In conclusion, our findings suggest a possible association between HCC and m5C of circRNA. Additionally, our results provide new insights into a novel function of m5C RNA methylation of circRNA in HCC progression.

Keywords: 5-methylcytosine; MeRIP-seq; RNA methylation; circRNA; hepatocellular carcinoma