bims-rimeca Biomed News
on RNA methylation in cancer
Issue of 2021‒07‒04
seventeen papers selected by
Sk Ramiz Islam
Saha Institute of Nuclear Physics

  1. Biomolecules. 2021 Jun 18. pii: 908. [Epub ahead of print]11(6):
      RNA methylation at the nitrogen sixth of adenosine (m6A, N6-methyladenosine) is the most abundant RNA modification which plays a crucial role in all RNA metabolic aspects. Recently, m6A modification has been assigned to mediate the biological processes of cancer cells, but their significance in HNSCC development is still poorly described. Thus, the main aim of this study was to globally quantify m6A modification by the mass spectrometry approach and determine the mRNA expression level of selected m6A RNA methyltransferase (METTL3), demethylase (FTO), and m6A readers (YTHDF2, YTHDC2) in 45 HNSCC patients and 4 cell lines (FaDu, Detroit 562, A-253 and SCC-15) using qPCR. In the results, we have not observed differences in the global amount of m6A modification and the mRNA level of the selected genes between the cancerous and paired-matched histopathologically unchanged tissues from 45 HNSCC patients. However, we have found a positive correlation between selected RNA methylation machinery genes expression and m6A abundance on total RNA and characterized the transcript level of those genes in the HNSCC cell lines. Moreover, the lack of global m6A differences between cancerous and histopathologically unchanged tissues suggests that m6A alterations in specific RNA sites may specifically influence HNSCC tumorigenesis.
    Keywords:  RNA methylation; head and neck squamous cell carcinoma; m6A RNA modification
  2. Bioengineered. 2021 Dec;12(1): 3159-3176
      N6-methyladenosine (m6A) RNA methylation regulators play a regulatory role in tumor pathogenesis and development. However, the role of m6A regulator genes in ovarian cancer (OC) has not been fully elucidated. This study aims to investigate the mRNA expressions, clinicopathological features, and prognostic values of m6A regulators in OC. Here, we demonstrate that the 17 m6A RNA methylation regulators are differentially expressed in ovarian cancer and normal tissues. By using consensus clustering, all ovarian cancer patients can be divided into two subgroups (cluster 1 and 2) based on the expression of 17 m6A RNA methylation regulators. Using Gene Set Enrichment Analysis, we identified that cluster 1 was most connected to oxidative phosphorylation pathways. Regression models identified that prognosis is associated with HNRNPA2B1, KIAA1429, and WTAP. qRT-PCR result show that the expression trends of HNRNPA2B1 and KIAA1429 are consistent with the predicted results. Multivariate Cox regression analysis results show that the risk score was an independent predictive factor in OV. The overall survival of high-risk patients was significantly shorter than that of low-risk patients. ROC curve analysis showed that the prognostic signature precisely predicted the 5-year survival of OV patients. A nomogram was developed to predict each patient's survival probability and well calibrated and showed a satisfactory discrimination. Dendritic fraction, macrophage fraction, and neutrophil fraction showed higher fraction in high-risk patients. In conclusion, m6A RNA methylation regulators are vital participants in ovarian cancer pathology, and three-gene mRNA levels are valuable factors for prognosis predictions.
    Keywords:  Ovarian cancer; immune cells infiltration; m6A; prognosis; tcga
  3. Biomed Res Int. 2021 ;2021 9959212
      Increasing evidences have revealed that N6-methyladenosine (m6A) RNA methylation regulators participate in the tumorigenesis and development of multiple tumors. So far, there has been little comprehension about the effects of m6A RNA methylation regulators on lower-grade gliomas (LGG). Here, we systematically investigated the expression profiles and prognostic significance of 36 m6A RNA methylation regulators in LGG patients from the TCGA and CGGA databases. Most of the m6A RNA methylation regulators are differentially expressed in LGG tissues as compared with normal brain tissues and glioblastoma (GBM) tissues. The consensus clustering for these m6A RNA methylation regulators identified three clusters. Patients in cluster 3 exhibited worse prognosis. In addition, we constructed an m6A-related prognostic signature, which exhibited excellent performance in prognostic stratification of LGG patients according to the results of the Kaplan-Meier curves, ROC curves, and univariate and multivariate Cox regression analyses. In addition, a significant correlation was observed between the m6A-related prognostic signature and the immune landscape of the LGG microenvironment. The high-risk group exhibited higher immune scores, stromal scores, and ESTIMATE scores but lower tumor purity and lower abundance of activated NK cells. Moreover, the expression level of immune checkpoints was positively correlated with the risk score. To conclude, the current research systematically demonstrated the prognostic roles of m6A RNA methylation regulators in LGG.
  4. Front Genet. 2021 ;12 656114
      Background: N6-methyladenosine (m6A) RNA modification is vital for cancers because methylation can alter gene expression and even affect some functional modification. Our study aimed to analyze m6A RNA methylation regulators and m6A-related genes to understand the prognosis of early lung adenocarcinoma.Methods: The relevant datasets were utilized to analyze 21 m6A RNA methylation regulators and 5,486 m6A-related genes in m6Avar. Univariate Cox regression analysis, random survival forest analysis, Kaplan-Meier analysis, Chi-square analysis, and multivariate cox analysis were carried out on the datasets, and a risk prognostic model based on three feature genes was constructed.
    Results: Respectively, we treated GSE31210 (n = 226) as the training set, GSE50081 (n = 128) and TCGA data (n = 400) as the test set. By performing univariable cox regression analysis and random survival forest algorithm in the training group, 218 genes were significant and three prognosis-related genes (ZCRB1, ADH1C, and YTHDC2) were screened out, which could divide LUAD patients into low and high-risk group (P < 0.0001). The predictive efficacy of the model was confirmed in the test group GSE50081 (P = 0.0018) and the TCGA datasets (P = 0.014). Multivariable cox manifested that the three-gene signature was an independent risk factor in LUAD. Furthermore, genes in the signature were also externally validated using the online database. Moreover, YTHDC2 was the important gene in the risk score model and played a vital role in readers of m6A methylation.
    Conclusion: The findings of this study suggested that associated with m6A RNA methylation regulators and m6A-related genes, the three-gene signature was a reliable prognostic indicator for LUAD patients, indicating a clinical application prospect to serve as a potential therapeutic target.
    Keywords:  RNA methylation regulators; lung adenocarcinoma; m6A; m6A-related genes; prognostic signature
  5. Viruses. 2021 Jun 01. pii: 1049. [Epub ahead of print]13(6):
      There are over 100 different chemical RNA modifications, collectively known as the epitranscriptome. N6-methyladenosine (m6A) is the most commonly found internal RNA modification in cellular mRNAs where it plays important roles in the regulation of the mRNA structure, stability, translation and nuclear export. This modification is also found in viral RNA genomes and in viral mRNAs derived from both RNA and DNA viruses. A growing body of evidence indicates that m6A modifications play important roles in regulating viral replication by interacting with the cellular m6A machinery. In this review, we will exhaustively detail the current knowledge on m6A modification, with an emphasis on its function in virus biology.
    Keywords:  RNA modification; epitranscriptomics; m6A; viral infection
  6. Genes (Basel). 2021 Jun 30. pii: 1019. [Epub ahead of print]12(7):
      Dynamic modifications on RNA, frequently termed both, "RNA epigenetics" and "epitranscriptomics", offer one of the most exciting emerging areas of gene regulation and biomedicine. Similar to chromatin-based epigenetic mechanisms, writers, readers, and erasers regulate both the presence and interpretation of these modifications, thereby adding further nuance to the control of gene expression. In particular, the most abundant modification on mRNAs, N6-methyladenosine (m6A), catalyzed by methyltransferase-like 3 (METTL3) has been shown to play a critical role in self-renewing somatic epithelia, fine-tuning the balance between development, differentiation, and cancer, particularly in the case of squamous cell carcinomas (SCCs), which in aggregate, outnumber all other human cancers. Along with the development of targeted inhibitors of epitranscriptomic modulators (e.g., METTL3) now entering clinical trials, the field holds significant promise for treating these abundant cancers. Here, we present the most current summary of this work, while also highlighting the therapeutic potential of these discoveries.
    Keywords:  METTL3; RNA; cancer; development; differentiation; epigenetics; epithelial; epitranscriptomics; m6A
  7. Life (Basel). 2021 Jun 26. pii: 619. [Epub ahead of print]11(7):
      N6-methyladenosine (m6A) RNA modification is the most abundant modification method in mRNA, and it plays an important role in the occurrence and development of many cancers. This paper mainly discusses the role of m6A RNA methylation regulators in lung adenocarcinoma (LUAD) to identify novel prognostic biomarkers. The gene expression data of 19 m6A methylation regulators in LUAD patients and its relevant clinical parameters were extracted from The Cancer Genome Atlas (TCGA) database. We selected three significantly differentially expressed m6A regulators in LUAD to construct the risk signature, and evaluated its prognostic prediction efficiency using the receiver operating characteristic (ROC) curve. Kaplan-Meier survival analysis and Cox regression analysis were used to identify the independent prognostic significance of the risk signature. The ROC curve indicated that the area under the curve (AUC) was 0.659, which means that the risk signature had a good prediction efficiency. The results of the Kaplan-Meier survival analysis and Cox regression analysis showed that the risk score can be used as an independent prognostic factor for LUAD. In addition, we explored the differential signaling pathways and cellular processes related to m6A methylation regulators in LUAD.
    Keywords:  lung adenocarcinoma; m6A methylation; prognostic signature; survival analysis
  8. J Cell Mol Med. 2021 Jun 27.
      This research systematically profiled the global N6-methyladenosine modification pattern of circular RNAs (circRNAs) in glioblastoma (GBM). Based on RNA methylation sequencing (MeRIP sequencing or N6-methyladenosine sequencing) and RNA sequencing, we described the N6-methyladenosine modification status and gene expression of circRNAs in GBM and normal brain tissues. N6-methyladenosine-related circRNAs were immunoprecipitated and validated by real-time quantitative PCR. Bioinformatics analysis and related screening were carried out. Compared with those of the NC group, the circRNAs from GBM exhibited 1370 new N6-methyladenosine peaks and 1322 missing N6-methyladenosine peaks. Among the loci associated with altered N6-methyladenosine peaks, 1298 were up-regulated and 1905 were down-regulated. The N6-methyladenosine level tended to be positively correlated with circRNA expression. Bioinformatics analysis was used to predict the biological function of N6-methyladenosine-modified circRNAs and the corresponding signalling pathways. In addition, through PCR validation combined with clinical data mining, we identified five molecules of interest (BUB1, C1S, DTHD1, F13A1 and NDC80) that could be initial candidates for further study of the function and mechanism of N6-methyladenosine-mediated GBM development. In conclusion, our findings demonstrated the N6-methyladenosine modification pattern of circRNAs in human GBM, revealing the possible roles of N6-methyladenosine-mediated novel noncoding RNAs in the origin and progression of GBM.
    Keywords:  CircRNA; GBM; N6-methyladenosine modification; decoration pattern; glioblastoma; ncRNA; noncoding RNA
  9. Nucleic Acids Res. 2021 Jun 28. pii: gkab517. [Epub ahead of print]
      N6-methyladenosine (m6A) is a common modification on endogenous RNA transcripts in mammalian cells. Technologies to precisely modify the RNA m6A levels at specific transcriptomic loci empower interrogation of biological functions of epitranscriptomic modifications. Here, we developed a bidirectional dCasRx epitranscriptome editing platform composed of a nuclear-localized dCasRx conjugated with either a methyltransferase, METTL3, or a demethylase, ALKBH5, to manipulate methylation events at targeted m6A sites. Leveraging this platform, we specifically and efficiently edited m6A modifications at targeted sites, reflected in gene expression and cell proliferation. We employed the dCasRx epitranscriptomic editor system to elucidate the molecular function of m6A-binding proteins YTHDF paralogs (YTHDF1, YTHDF2 and YTHDF3), revealing that YTHDFs promote m6A-mediated mRNA degradation. Collectively, our dCasRx epitranscriptome perturbation platform permits site-specific m6A editing for delineating of functional roles of individual m6A modifications in the mammalian epitranscriptome.
  10. Front Mol Biosci. 2021 ;8 675683
      N6-methyladenosine (m6A) RNA modification is the most common internal mRNA modification in mammals and has been reported to play a key role in gene expression regulation. In this study, we detected a high level of m6A methylation of the PLOD2 3'-untranslated regions (3'UTR) in renal cell carcinoma (RCC). Furthermore, we found that the high expression level of PLOD2 was a prognostic indicator for patients with RCC. A dm6ACRISPR demethylation system was performed to accurately and specifically demethylate 3'UTR of PLOD2 and caused an inactivation of PLOD2 expression. Furthermore, we also performed many in vitro experiments to confirm that PLOD2 exerted tumor promoter effects by promoting tumor proliferation and migration. In conclusion, PLOD2 mRNA demethylated by dCas13b-ALKBH5 might provide a new light on the treatment for RCC.
    Keywords:  (N6-methyladenosine); CRISPR; PLOD2; dCas13b; renal cell cancer
  11. RNA. 2021 Jun 29. pii: rna.078777.121. [Epub ahead of print]
      Polyadenylated nuclear (PAN) RNA is a long non-coding transcript involved in Kaposi's sarcoma-associated herpesvirus (KSHV) lytic reactivation and regulation of cellular and viral gene expression. We have previously shown that PAN RNA has a dynamic secondary structure and protein binding profile that can be influenced by the epitranscriptomic modifications. N6-methyladenosine (m6A) is one of the most abundant chemical signatures found in viral RNA genomes and virus-encoded RNAs. Here, we combined an antibody-independent next-generation mapping with direct RNA sequencing to address the epitranscriptomic status of PAN RNA in KSHV infected cells. We showed that PAN m6A status is dynamic, reaching the highest number of modifications at the late lytic stages of KSHV infection. Using a newly developed method, termed Selenium-modified deoxythymidine triphosphate (SedTTP)- Reverse Transcription (RT) and Ligation Assisted PCR analysis of m6A (SLAP), we gained insight into the fraction of modification at identified sites. By applying comprehensive proteomic approaches, we identified writers and erasers that regulate the m6A status of PAN, and readers that can convey PAN m6A phenotypic effects. We verified the temporal and spatial subcellular availability of the methylome components for PAN modification by performing confocal microscopy analysis. Additionally, the RNA biochemical probing (SHAPE-MaP) outlined local and global structural alterations invoked by m6A in the context of full-length PAN RNA. This work represents the first comprehensive overview of the dynamic interplay that takes place between the cellular epitranscriptomic machinery and a specific viral RNA in the context of KSHV infected cells.
    Keywords:  N6-methyladenosine; SHAPE-MaP; lncRNA; methylome; polyadenylated nuclear RNA
  12. Front Cell Dev Biol. 2021 ;9 672248
      Background: The purpose of this study was to determine the association between m6A-modified lncRNAs, immune infiltration, and PD-L1 expression in patients with primary head and neck squamous cell carcinoma (HNSCC) and the prognostic value of m6A RNA methylation-related lncRNAs in HNSCC. Methods: We downloaded the RNA-seq transcriptome data and the clinical information for HNSCC from the TCGA databases and used consensus clustering analysis to divide the samples into two groups. To identify a risk signature, least absolute shrinkage and selection operator (LASSO) analyses were conducted. the association between m6A-modified lncRNAs, immune infiltration, and PD-L1 expression were detected by using the R packages. What is more, we used cBioPortal tools to identify genomic alterations and PD-L1 mutations and Gene set enrichment analysis (GSEA) was utilized to predict downstream access of two clusters. Results: Notably, lncRNAs play significant roles in tumorigenesis and development. In total, we identified two subtypes of HNSCC according to consensus clustering of the m6A RNA methylation-related lncRNAs, and the T, grade and age were proven to be related to the subtypes. The Cox regression and LASSO analyses identified a risk signature including GRHL3-AS1, AL121845.4, AC116914.2, AL513190.1. The prognostic value of the risk signature was then proven. The selected gene PD-L1 mutations and the immune infiltration in both groups were further explored. Conclusion: Collectively, our study elucidated the important role of m6A RNA methylation- related lncRNAs in tumor microenvironment of HNSCC. The proposed m6A RNA methylation- related lncRNAs might serve as crucial mediators of tumor microenvironment of HNSCC, representing promising therapeutic targets in improving immunotherapeutic efficacy.
    Keywords:  HNSCC; PD-L1; biomarker; lncRNA; m6A regulators; survival analysis; tumor microenvironment
  13. Front Oncol. 2021 ;11 657466
      RNA methylation is a novel epigenetic modification that can be used to evaluate tumor prognosis. However, the underlying mechanisms are unclear. This study aimed to investigate the genetic characteristics of 5-methylcytosine (m5C) and N1-methyladenosine (m1A) regulators in lung squamous cell carcinoma (LUSC) and the prognostic value and immune-related effects of m5C regulators. To this end, we selected the public LUSC dataset from the Cancer Genome Atlas and Gene Expression Omnibus. The least absolute shrinkage and selection operator regression model was used to identify prognostic risk signatures. We used the UALCAN and Human Protein Atlas databases to study the expression of target gene mRNA/protein expression. Furthermore, the Tumor Immune Single Cell Hub and the Tumor Immune Estimation Resource were used to evaluate the degree of immune cell infiltration. Most of the m5C and m1A regulators showed significantly different expression between LUSC and normal samples. The m5C regulators were associated with poor prognosis. In addition, a prognostic risk signature was developed based on two m5C regulators, NOP2/Sun RNA methyltransferase 3 (NSUN3), and NOP2/Sun RNA methyltransferase 4 (NSUN4). Compared with normal lung tissues, the expression of NSUN3 and NSUN4 in the LUSC TCGA dataset was increased, which was related to clinicopathological characteristics and survival. NSUN3 and NSUN4 were related to the infiltration of six major immune cells; especially NSUN3, which was closely related to CD8+ T cells, while NSUN4 was closely related to neutrophils. Our findings suggest that m5C regulators can predict the clinical prognosis risk and regulate the tumor immune microenvironment in LUSC.
    Keywords:  5-methylcytosine; RNA methylation; lung squamous cell carcinoma; prognosis; tumor; tumor immune microenvironment
  14. FEBS Open Bio. 2021 Jun 29.
      Lung adenocarcinoma (LUAD) accounts for almost 40% of lung cancers, leading to significant associated morbidity and mortality rates. However, the mechanism of LUAD tumorigenesis remains far from clear. Here, we scanned downregulated genes involved in LUAD sourced from Cancer Genome Atlas and Gene Expression Omnibus data and focused on G protein-coupled receptor 133 (GPR133). We offer compelling evidence that GPR133 was expressed at low levels in the setting of LUAD and higher expression was positively related with a better prognosis among LUAD patients. Functionally, GPR133 inhibited cell proliferation and tumor growth in vitro and in vivo. Regarding the mechanism, flow cytometry assays and western blot assays showed that GPR133 enhanced p21 and decreased cyclin B1 expression, thus triggered LUAD cells at G2/M-phase arrest. Consistent with this, we evaluated the expression levels of cell-cycle biomarkers and found that Bioinformatics analysis combined with N6 -methyladenosine (m6 A; methylation at the N6 position in adenosine) RNA immunoprecipitation-qPCR (MeRIP-qPCR) assay indicated that GPR133 expression was downregulated by this modification. Moreover, we observed that methyltransferase-like 3 was impaired in LUAD and that it is able to significantly increase levels of GPR133 by enhancing its RNA stability. In conclusion, we found that GPR133 expression was downregulated in LUAD via m6 A modification. Increasing GPR133 levels could suppress LUAD cell proliferation and tumor growth.
    Keywords:  G protein-coupled receptor 133; cell cycle; lung adenocarcinoma; proliferation
  15. Apoptosis. 2021 Jul 01.
      As a nucleic acid demethylase, Fat and obesity associated gene (FTO) plays a vital role in modulating adipose metabolism. However, it is still unknown how FTO affects apoptosis in adipocytes. In this study, we found that overexpression of FTO inhibited the expression of pro-apoptosis factors Caspase-3, Caspase-9 and Bax and mitochondrial unfolded protein response (UPRmt) markers HSP60 and ClpP in vivo and in vitro. Particularly, overexpression of FTO inhibited mitochondria-dependent apoptosis in adipocytes. Further studies revealed that FTO suppressed UPRmt by reducing HSP60 mRNA N6-methyladenosine (m6A) modification. Moreover, FTO inhibited the activation of Caspase-3 via JAK2/STAT3 signaling pathway in adipocytes. Further experiments showed that pro-apoptosis gene Bax was upregulated by UPRmt-activated PKR/eIF2α/ATF5 axis in adipocytes. In summary, this study confirms that FTO reduces adipocytes apoptosis by activiting JAK2/STAT3 signaling pathway and inhibiting UPRmt, revealing a novel mechanism of FTO on adipocytes apoptosis, which provides some new potential therapy for treating obesity and related metabolic syndromes.
    Keywords:  Adipocytes; Apoptosis; FTO; UPRmt; m6A
  16. Front Oncol. 2021 ;11 697949
      Background: LncRNA dysregulation and the tumor microenvironment (TME) have been shown to play a vital role in the progression and prognosis of colon cancer (CC). We aim to reveal the potential molecular mechanism from the perspective of lncRNA in the TME and provide the candidate biomarkers for CC prognosis.Methods: ESTIMATE analysis was used to divide the CC patients into high and low immune or stromal score groups. The expression array of lncRNA was re-annotated by Seqmap. Microenvironment-associated lncRNAs were filtered through differential analysis. The m6A-associated lncRNAs were screened by Pearson correlation analysis. Lasso Cox regression analyses were performed to construct the m6A- and tumor microenvironment-related lncRNA prognostic model (m6A-TME-LM). Survival analysis was used to assess the prognostic efficacy of candidate lncRNAs. Enrichment analyses annotated the candidate genes' functions.
    Results: We obtained 25 common differentially expressed lncRNAs (DELs) associated with immune microenvironment and m6A-related genes for subsequent lasso analysis. Four out of these DELs were selected for the m6A-TME-LM. All the four lncRNAs were related to overall survival, and a test set testified the result. Further stratification analysis of the m6A-TME-LM retained its ability to predict OS for male and chemotherapy adjuvant patients and performed an excellent prognostic efficacy in the TNM stage III and IV subgroups. Network analysis also found the four lncRNAs mediated co-expression network was associated with tumor development.
    Conclusion: We constructed the m6A-TME-LM, which could provide a better prognostic prediction of CC.
    Keywords:  N6-methylandenosine (m6A); colon cancer; lncRNA - long noncoding RNA; prognostic biomarker; tumor microenvironment
  17. Biol Res. 2021 Jun 29. 54(1): 18
      BACKGROUND: Ovarian cancer is one of the most common malignancies often resulting in a poor prognosis. 5-methylcytosine (m5C) is a common epigenetic modification with roles in eukaryotes. However, the expression and function of m5C regulatory factors in ovarian cancer remained unclear.RESULTS: Two molecular subtypes with different prognostic and clinicopathological features were identified based on m5C regulatory factors. Meanwhile, functional annotation showed that in the two subtypes, 452 differentially expressed genes were significantly related to the malignant progression of ovarian cancer. Subsequently, four m5C genes were screened to construct a risk marker predictive of overall survival and indicative of clinicopathological features of ovarian cancer, also the robustness of the risk marker was verified in external dataset and internal validation set. multifactorial cox regression analysis and nomogram demonstrated that risk score was an independent prognostic factor for ovarian cancer prognosis.
    CONCLUSION: In conclusion, our results revealed that m5C-related genes play a critical role in tumor progression in ovarian cancer. Further detection of m5C methylation could provide a novel targeted therapy for treating ovarian cancer.
    Keywords:  5-methylcytosine; Molecular subtypes; Ovarian cancer; Risk score