bims-rimeca 2020-11-01 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2020–11–01
ten papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics

N6-methyladenosine METTL3 promotes cervical cancer tumorigenesis and Warburg effect through YTHDF1/HK2 modification.
YTHDF2 mediates the mRNA degradation of the tumor suppressors to induce AKT phosphorylation in N6-methyladenosine-dependent way in prostate cancer.
FTO demethylates m6A modifications in HOXB13 mRNA and promotes endometrial cancer metastasis by activating the WNT signaling pathway.
Hematopoietic Gene Expression Regulation Through m6A Methylation Predicts Prognosis in Stage III Colorectal Cancer.
To Develop and Validate the Combination of RNA Methylation Regulators for the Prognosis of Patients with Gastric Cancer.
Prognosis Analysis and Validation of m6A Signature and Tumor Immune Microenvironment in Glioma.
Prognostic Value of YTHDF2 in Clear Cell Renal Cell Carcinoma.
YTHDF3 Induces the Translation of m6A-Enriched Gene Transcripts to Promote Breast Cancer Brain Metastasis.
2'-O-Methylation can increase the abundance and lifetime of alternative RNA conformational states.
Site-specific RNA methylation by a methyltransferase ribozyme.

Cell Death Dis. 2020 Oct 24. 11(10): 911

N6-methyladenosine METTL3 promotes cervical cancer tumorigenesis and Warburg effect through YTHDF1/HK2 modification.

Qianqing Wang, Xiangcui Guo, Li Li, Zhihui Gao, Xiaoke Su, Mei Ji, Juan Liu.

N6-methyladenosine (m6A) serves as the most common and conserved internal transcriptional modification. However, the roles of m6A on cervical cancer (CC) tumorigenesis are still unclear. Here, results indicated that METTL3 was significantly upregulated in CC tissue and cells, which was closely correlated with the lymph node metastasis and poor prognosis of CC patients. MeRIP-Seq analysis revealed the m6A profiles in CC cells. Functionally, METTL3 promoted the proliferation and Warburg effect (aerobic glycolysis) of CC cells. Mechanistically, METTL3 targeted the 3'-Untranslated Region (3'-UTR) of hexokinase 2 (HK2) mRNA. Moreover, METTL3 recruited YTHDF1, a m6A reader, to enhance HK2 stability. These findings demonstrated that METTL3 enhanced the HK2 stability through YTHDF1-mediated m6A modification, thereby promoting the Warburg effect of CC, which might promote a novel insight for the CC treatment.

DOI: https://doi.org/10.1038/s41419-020-03071-y
Mol Cancer. 2020 Oct 29. 19(1): 152

YTHDF2 mediates the mRNA degradation of the tumor suppressors to induce AKT phosphorylation in N6-methyladenosine-dependent way in prostate cancer.

Jiangfeng Li, Haiyun Xie, Yufan Ying, Hong Chen, Huaqing Yan, Liujia He, Mingjie Xu, Xin Xu, Zhen Liang, Ben Liu, Xiao Wang, Xiangyi Zheng, Liping Xie.

   BACKGROUND: N6-methyladenosine (m6A) is the most abundant modification in mRNA of humans. Emerging evidence has supported the fact that m6A is comprehensively involved in various diseases especially cancers. As a crucial reader, YTHDF2 usually mediates the degradation of m6A-modified mRNAs in m6A-dependent way. However, the function and mechanisms of m6A especially YTHDF2 in prostate cancer (PCa) still remain elusive.
METHODS: To investigate the functions and mechanisms of YTHDF2 in PCa, in vitro, in vivo biofunctional assays and epigenetics experiments were performed. Endogenous expression silencing of YTHDF2 and METTL3 was established with lentivirus-based shRNA technique. Colony formation, flow cytometry and trans-well assays were performed for cell function identifications. Subcutaneous xenografts and metastatic mice models were combined with in vivo imaging system to investigate the phenotypes when knocking down YTHDF2 and METTL3. m6A RNA immunoprecipitation (MeRIP) sequencing, mRNA sequencing, RIP-RT-qPCR and bioinformatics analysis were mainly used to screen and validate the direct common targets of YTHDF2 and METTL3. In addition, TCGA database was also used to analyze the expression pattern of YTHDF2, METTL3 and the common target LHPP in PCa, and their correlation with clinical prognosis.
RESULTS: The upregulated YTHDF2 and METTL3 in PCa predicted a worse overall survival rate. Knocking down YTHDF2 or METTL3 markedly inhibited the proliferation and migration of PCa in vivo and in vitro. LHPP and NKX3-1 were identified as the direct targets of both YTHDF2 and METTL3. YTHDF2 directly bound to the m6A modification sites of LHPP and NKX3-1 to mediate the mRNA degradation. Knock-down of YTHDF2 or METTL3 significantly induced the expression of LHPP and NKX3-1 at both mRNA and protein level with inhibited phosphorylated AKT. Overexpression of LHPP and NKX3-1 presented the consistent phenotypes and AKT phosphorylation inhibition with knock-down of YTHDF2 or METTL3. Phosphorylated AKT was consequently confirmed as the downstream of METTL3/YTHDF2/LHPP/NKX3-1 to induce tumor proliferation and migration.
CONCLUSION: We propose a novel regulatory mechanism in which YTHDF2 mediates the mRNA degradation of the tumor suppressors LHPP and NKX3-1 in m6A-dependent way to regulate AKT phosphorylation-induced tumor progression in prostate cancer. We hope our findings may provide new concepts of PCa biology.

Keywords:  M6A; Prostate cancer; RNA degradation; RNA methylation; YTHDF2

DOI:  https://doi.org/10.1186/s12943-020-01267-6
RNA Biol. 2020 Oct 25.

FTO demethylates m6A modifications in HOXB13 mRNA and promotes endometrial cancer metastasis by activating the WNT signaling pathway.

Lin Zhang, Yicong Wan, Zihan Zhang, Yi Jiang, Jinghe Lang, Wenjun Cheng, Lan Zhu.

  Although many studies have confirmed the relationship between obesity and endometrial cancer (EC), the molecular mechanism between obesity and EC progression has not been elucidated. Overexpression of fat mass and the obesity associated protein FTO leads to weight gain, although recently it has been discovered that FTO can serve as a demethylase which erases N6-methyladenosine (m6A) modification and regulates the metabolization of mRNAs. In this study, we found high expression of FTO in metastatic EC and that this action promote both metastasis and invasion in vivo and in vitro. Mechanistically, FTO can catalyze demethylation modification in 3'UTR region of HOXB13 mRNA, thereby abolishing m6A modification recognition with the YTHDF2 protein. Decreasing HOXB13 mRNA decay and increasing HOXB13 protein expression was accompanied by WNT signaling pathway activation and the expression of downstream proteins, leading to tumor metastasis and invasion. We also found the WNT signaling pathway inhibitor ICG-001 can block HOXB13 gene-induced tumor metastasis, therefore ICG-001 may be a promising molecular intervention. This study provides insight into the relationship between obesity and the pathogenesis of endometrial cancer while highlighting future areas of research.

Keywords:  Cancer metastasis; Endometrial cancer; FTO; HOXB13; m6A

DOI:  https://doi.org/10.1080/15476286.2020.1841458
Front Oncol. 2020 ;10 572708

Hematopoietic Gene Expression Regulation Through m6A Methylation Predicts Prognosis in Stage III Colorectal Cancer.

Zheng Zhou, Shaobo Mo, Ruiqi Gu, Weixing Dai, Xinhui Zou, Lingyu Han, Long Zhang, Renjie Wang, Guoxiang Cai.

   Background: Methylation of N6 adenosine (m6A) plays important regulatory roles in diverse biological processes. The purpose of this research was to explore the potential mechanism of m6A modification level on the clinical outcome of stage III colorectal cancer (CRC).
Methods: Gene set variation analysis (GSVA) and gene set enrichment analysis (GSEA) were adopted to reveal the signal pathway which was most likely affected by m6A methylation. The linear models for microarray data (LIMMA) method and the least absolute shrink-age and selection operator (LASSO) Cox regression model were used to identify the signature. The signature can sensitively separate the patients into high and low risk indicating the relapse-free survival (RFS) time based on time-dependent receiver operating characteristic (ROC) analysis. Then, the multi-gene signature was validated in GSE14333 and the Cancer Genome Atlas (TCGA) cohort. The number of the samples in GSE14333 and TCGA cohort are 63 and 150. Finally, two nomograms were set up and validated to predict prognosis of patients with stage III CRC.
Results: The hematopoietic cell lineage (HCL) signaling pathway was disclosed through GSEA and GSVA. Seven HCL-related genes were determined in the LASSO model to construct signature, with AUC 0.663, 0.708, and 0.703 at 1-, 3-, and 5-year RFS, respectively. Independent datasets analysis and stratification analysis indicated that the HCL-related signature was reliable in distinguishing high- and low-risk stage III CRC patients. Two nomograms incorporating the signature and pathological N stage were set up, which yielded good discrimination and calibration in the predictions of prognosis for stage III CRC patients.
Conclusions: A novel HCL-related signature was developed as a predictive model for survival rate of stage III CRC patients. Nomograms based on the signature were advantageous to facilitate personalized counseling and treatment in stage III CRC.

Keywords:  colorectal cancer; m6A; prognosis; signature; stage III

DOI:  https://doi.org/10.3389/fonc.2020.572708
Onco Targets Ther. 2020 ;13 10785-10795

To Develop and Validate the Combination of RNA Methylation Regulators for the Prognosis of Patients with Gastric Cancer.

Jun Zhang, Hai-Yan Piao, Yue Wang, Xiang-Yu Meng, Dong Yang, Yan Zhao, Zhi-Chao Zheng.

   Background: Gastric cancer (GC) accounts for high mortality. RNA methylation has recently gained interest as markers in specific tumors. This study aimed to uncover the function of the roles of 25 RNA methylation regulators in GC.
Methods: RNA sequence and clinical data were downloaded from The Cancer Genome Atlas (TCGA) database. "STRING" and R were performed to analyze the correlation among the methylase. COX and LASSO were performed to screen for prognostic associated RNA methylation regulators. A prognostic model was established based on the expression of methylase. RT-PCR and immunohistochemistry detected the expression of methylase in GC cells and tissue. Kaplan-Meier curve and Cox analysis were applied to evaluate the effectiveness of the model.
Results: The prediction model was established based on the expression of m6A RNA methylation regulators FTO (fat mass and obesity-associated) and RBM15 (RNA binding motif protein 15). Based on the model, GC patients were divided into "high risk" and "low risk" groups to compare the differences in survival. The model was re-evaluated with the clinical data of our center.
Conclusion: The two-methylase combination model was an independent prognostic factor of GC.

Keywords:  RNA methylation; gastric cancer; least absolute shrinkage and selection operator; prognosis; survival analysis

DOI:  https://doi.org/10.2147/OTT.S276239
Front Oncol. 2020 ;10 541401

Prognosis Analysis and Validation of m6A Signature and Tumor Immune Microenvironment in Glioma.

Shaojian Lin, Houshi Xu, Anke Zhang, Yunjia Ni, Yuanzhi Xu, Tong Meng, Mingjie Wang, Meiqing Lou.

  Glioma is one of the most typical intracranial tumors, comprising about 80% of all brain malignancies. Several key molecular signatures have emerged as prognostic biomarkers, which indicate room for improvement in the current approach to glioma classification. In order to construct a more veracious prediction model and identify the potential prognosis-biomarker, we explore the differential expressed m6A RNA methylation regulators in 665 gliomas from TCGA-GBM and TCGA-LGG. Consensus clustering was applied to the m6A RNA methylation regulators, and two glioma subgroups were identified with a poorer prognosis and a higher grade of WHO classification in cluster 1. The further chi-squared test indicated that the immune infiltration was significantly enriched in cluster 1, indicating a close relation between m6A regulators and immune infiltration. In order to explore the potential biomarkers, the weighted gene co-expression network analysis (WGCNA), along with Least absolute shrinkage and selection operator (LASSO), between high/low immune infiltration and m6A cluster 1/2 groups were utilized for the hub genes, and four genes (TAGLN2, PDPN, TIMP1, EMP3) were identified as prognostic biomarkers. Besides, a prognostic model was constructed based on the four genes with a good prediction and applicability for the overall survival (OS) of glioma patients (the area under the curve of ROC achieved 0.80 (0.76-0.83) and 0.72 (0.68-0.76) in TCGA and Chinese Glioma Genome Atlas (CGGA), respectively). Moreover, we also found PDPN and TIMP1 were highly expressed in high-grade glioma from The Human Protein Atlas database and both of them were correlated with m6A and immune cell marker in glioma tissue samples. In conclusion, we construct a novel prognostic model which provides new insights into glioma prognosis. The PDPN and TIMP1 may serve as potential biomarkers for prognosis of glioma.

Keywords:  WGCNA; glioma; immune infiltration; m6A; prognostic model

DOI:  https://doi.org/10.3389/fonc.2020.541401
Front Oncol. 2020 ;10 1566

Prognostic Value of YTHDF2 in Clear Cell Renal Cell Carcinoma.

Zhongyi Mu, Dan Dong, Mingli Sun, Liwen Li, Ning Wei, Bin Hu.

  m6A, the main form of mRNA modification, participates in regulating multiple normal and pathological biological events, especially in tumorigenesis. However, there is little known about the association of m6A-related genes with prognosis of clear cell renal cell cancer (ccRCC). Therefore, the prognostic value of m6A-related genes was investigated using Kaplan-Meier curves of overall survival (OS) with the log-rank test and Cox regression analysis. The differential expression of YTHDF2 mRNA in ccRCC and tumor-adjacent normal tissues and associated with clinicopathological characteristics was also analyzed. The alteration of cancer signaling pathways was screened by Gene Set Enrichment Analysis (GSEA). Univariate analysis showed that 15 m6A-related genes (including YTHDF2) were closely related to prognosis. Multivariate analysis further confirmed that YTHDF2 could serve as an independent prognostic factor for the OS of ccRCC patients (P < 0.001). Low-level expression of YTHDF2 had poor prognosis in ccRCC patients with lower tumor-node-metastasis (TNM) stage, age > 61, non-distant metastasis, non-lymph node metastasis, female gender, and higher histological grade (P < 0.05). Moreover, YTHDF2 expression in ccRCC tissues (N = 529) is significantly lower than that of tumor-adjacent normal tissues (N = 72, P = 0.0086). Furthermore, GSEA demonstrated that AKT/mTOR/GSK3 pathway, EIF4 pathway, CHREBP2 pathway, MET pathway, NFAT pathway, FAS pathway, EDG1 pathway, and CTCF pathway are altered in tumors with high YTHDF2 expression. Taken together, our results demonstrated that YTHDF2 (an m6A-related gene) could serve as a potential prognostic biomarker of ccRCC, and targeting epigenetic modification may be a novel therapeutic strategy for the treatment of ccRCC.

Keywords:  The Cancer Genome Atlas; YTHDF2; clear cell renal cell cancer; m6A-related genes; prognosis

DOI:  https://doi.org/10.3389/fonc.2020.01566
Cancer Cell. 2020 Oct 16. pii: S1535-6108(20)30498-0. [Epub ahead of print]

YTHDF3 Induces the Translation of m6A-Enriched Gene Transcripts to Promote Breast Cancer Brain Metastasis.

Guoqiang Chang, Lei Shi, Youqiong Ye, Hailing Shi, Lixian Zeng, Shweta Tiwary, Jason T Huse, Lei Huo, Li Ma, Yongjie Ma, Sicong Zhang, Jianwei Zhu, Victoria Xie, Peng Li, Leng Han, Chuan He, Suyun Huang.

  Brain metastasis is a major cause of cancer mortality, but its molecular mechanisms are severely understudied. In addition, little is known regarding the role of m6A reader YTHDF3 in human diseases. Here, we show that YTHDF3 overexpression clinically correlates with brain metastases in breast cancer patients. YTHDF3 promotes cancer cell interactions with brain endothelial cells and astrocytes, blood-brain barrier extravasation, angiogenesis, and outgrow. Mechanistically, YTHDF3 enhances the translation of m6A-enriched transcripts for ST6GALNAC5, GJA1, and EGFR, all associated with brain metastasis. Furthermore, overexpression of YTHDF3 in brain metastases is attributed to increased gene copy number and the autoregulation of YTHDF3 cap-independent translation by binding to m6A residues within its own 5' UTR. Our work uncovers an essential role of YTHDF3 in controlling the interaction between cancer cells and brain microenvironment, thereby inducing brain metastatic competence.

Keywords:  YTHDF3; brain metastasis; epigenetic regulation; gene amplification; m(6)A RNA methylation

DOI:  https://doi.org/10.1016/j.ccell.2020.10.004
Nucleic Acids Res. 2020 Oct 26. pii: gkaa928. [Epub ahead of print]

2'-O-Methylation can increase the abundance and lifetime of alternative RNA conformational states.

Hala Abou Assi, Atul K Rangadurai, Honglue Shi, Bei Liu, Mary C Clay, Kevin Erharter, Christoph Kreutz, Christopher L Holley, Hashim M Al-Hashimi.

2'-O-Methyl (Nm) is a highly abundant post-transcriptional RNA modification that plays important biological roles through mechanisms that are not entirely understood. There is evidence that Nm can alter the biological activities of RNAs by biasing the ribose sugar pucker equilibrium toward the C3'-endo conformation formed in canonical duplexes. However, little is known about how Nm might more broadly alter the dynamic ensembles of flexible RNAs containing bulges and internal loops. Here, using NMR and the HIV-1 transactivation response (TAR) element as a model system, we show that Nm preferentially stabilizes alternative secondary structures in which the Nm-modified nucleotides are paired, increasing both the abundance and lifetime of low-populated short-lived excited states by up to 10-fold. The extent of stabilization increased with number of Nm modifications and was also dependent on Mg2+. Through phi-value analysis, the Nm modification also provided rare insights into the structure of the transition state for conformational exchange. Our results suggest that Nm could alter the biological activities of Nm-modified RNAs by modulating their secondary structural ensembles as well as establish the utility of Nm as a tool for the discovery and characterization of RNA excited state conformations.

DOI: https://doi.org/10.1093/nar/gkaa928
Nature. 2020 Oct 28.

Site-specific RNA methylation by a methyltransferase ribozyme.

Carolin P M Scheitl, Mohammad Ghaem Maghami, Ann-Kathrin Lenz, Claudia Höbartner.

Nearly all classes of coding and non-coding RNA undergo post-transcriptional modification, including RNA methylation. Methylated nucleotides are among the evolutionarily most-conserved features of transfer (t)RNA and ribosomal (r)RNA1,2. Many contemporary methyltransferases use the universal cofactor S-adenosylmethionine (SAM) as a methyl-group donor. SAM and other nucleotide-derived cofactors are considered to be evolutionary leftovers from an RNA world, in which ribozymes may have catalysed essential metabolic reactions beyond self-replication3. Chemically diverse ribozymes seem to have been lost in nature, but may be reconstructed in the laboratory by in vitro selection. Here we report a methyltransferase ribozyme that catalyses the site-specific installation of 1-methyladenosine in a substrate RNA, using O6-methylguanine as a small-molecule cofactor. The ribozyme shows a broad RNA-sequence scope, as exemplified by site-specific adenosine methylation in various RNAs. This finding provides fundamental insights into the catalytic abilities of RNA, serves a synthetic tool to install 1-methyladenosine in RNA and may pave the way to in vitro evolution of other methyltransferase and demethylase ribozymes.

DOI: https://doi.org/10.1038/s41586-020-2854-z