bims-rimeca 2021-01-17 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2021–01–17
ten papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics

m6A RNA methylation regulators contribute to malignant development and have a clinical prognostic effect on cervical cancer.
RNA m6 A methylation regulates virus-host interaction and EBNA2 expression during Epstein-Barr virus infection.
R-2-hydroxyglutarate attenuates aerobic glycolysis in leukemia by targeting the FTO/m6A/PFKP/LDHB axis.
m6A RNA methylation regulates the fate of endogenous retroviruses.
MYC promotes cancer progression by modulating m6 A modifications to suppress target gene translation.
Decreased expression of METTL14 predicts poor prognosis and construction of a prognostic signature for clear cell renal cell carcinoma.
ALKBH5-mediated m6A demethylation of FOXM1 mRNA promotes progression of uveal melanoma.
HSM6AP: A high-precision predictor for the Homo sapiens N6-methyladenosine (m^6 A) based on multiple weights and feature stitching.
Ythdf is a N6-methyladenosine reader that modulates Fmr1 target mRNA selection and restricts axonal growth in Drosophila.
Metformin exhibits antiproliferation activity in breast cancer via miR-483-3p/METTL3/m6A/p21 pathway.

Am J Transl Res. 2020 ;12(12): 8137-8146

m6A RNA methylation regulators contribute to malignant development and have a clinical prognostic effect on cervical cancer.

Xiaoqing Ma, Yan Li, Ji Wen, Yu Zhao.

N6-methyladenosine (m6A) RNA methylation, which is related to the occurrence and development of cancer, is dynamically modulated by m6A RNA methylation regulators ("writers", "erasers" and "readers"). In this paper, we demonstrated that most of the 13 major m6A RNA methylation regulators were differently expressed in 306 cervical cancer tissues stratified according to different clinicopathological characteristics. We applied consensus clustering technique to analyze m6A RNA methylation regulators and identified two subgroups of cervical cancer, named RM1/2. Compared with the RM1, the RM2 had a poorer prognosis and lower overall survival (OS). This result suggested that m6A RNA methylation regulators were closely related to cervical cancer. Based on this result, we used m6A RNA methylation regulators to derive a risk marker that not only is an independent prognostic marker but also can predict the clinicopathological characteristics of cervical cancer. In conclusion, m6A RNA methylation regulator is a key player in the malignant progression of cervical cancer and has potential role in the stratification of prognosis and the formulation of treatment strategies.

Keywords: RNA methylation; cervical cancer; m6A; prognosis
Immun Inflamm Dis. 2021 Jan 12.

RNA m6 A methylation regulates virus-host interaction and EBNA2 expression during Epstein-Barr virus infection.

Xiang Zheng, Jia Wang, Xiaoyue Zhang, Yuxin Fu, Qiu Peng, Jianhong Lu, Lingyu Wei, Zhengshuo Li, Can Liu, Yangge Wu, Qun Yan, Jian Ma.

   INTRODUCTION: N6 -methyladenosine (m6 A) is the most prevalent modification that occurs in messenger RNA (mRNA), affecting mRNA splicing, translation, and stability. This modification is reversible, and its related biological functions are mediated by "writers," "erasers," and "readers." The field of viral epitranscriptomics and the role of m6 A modification in virus-host interaction have attracted much attention recently. When Epstein-Barr virus (EBV) infects a human B lymphocyte, it goes through three phases: the pre-latent phase, latent phase, and lytic phase. Little is known about the viral and cellular m6 A epitranscriptomes in EBV infection, especially in the pre-latent phase during de novo infection.
METHODS: Methylated RNA immunoprecipitation sequencing (MeRIP-seq) and MeRIP-RT-qPCR were used to determine the m6 A-modified transcripts during de novo EBV infection. RIP assay was used to confirm the binding of EBNA2 and m6 A readers. Quantitative reverse-transcription polymerase chain reaction (RT-qPCR) and Western blot analysis were performed to test the effect of m6 A on the host and viral gene expression.
RESULTS: Here, we provided mechanistic insights by examining the viral and cellular m6 A epitranscriptomes during de novo EBV infection, which is in the pre-latent phase. EBV EBNA2 and BHRF1 were highly m6 A-modified upon EBV infection. Knockdown of METTL3 (a "writer") decreased EBNA2 expression levels. The emergent m6 A modifications induced by EBV infection preferentially distributed in 3' untranslated regions of cellular transcripts, while the lost m6 A modifications induced by EBV infection preferentially distributed in coding sequence regions of mRNAs. EBV infection could influence the host cellular m6 A epitranscriptome.
CONCLUSIONS: These results reveal the critical role of m6 A modification in the process of de novo EBV infection.

Keywords:  BHRF1; EBNA2; Epstein-Barr virus; METTL3; RNA m6A methylation

DOI:  https://doi.org/10.1002/iid3.396
Mol Cell. 2021 Jan 06. pii: S1097-2765(20)30947-3. [Epub ahead of print]

R-2-hydroxyglutarate attenuates aerobic glycolysis in leukemia by targeting the FTO/m6A/PFKP/LDHB axis.

Ying Qing, Lei Dong, Lei Gao, Chenying Li, Yangchan Li, Li Han, Emily Prince, Brandon Tan, Xiaolan Deng, Collin Wetzel, Chao Shen, Min Gao, Zhenhua Chen, Wei Li, Bin Zhang, Daniel Braas, Johanna Ten Hoeve, Gerardo Javier Sanchez, Huiying Chen, Lai N Chan, Chun-Wei Chen, David Ann, Lei Jiang, Markus Müschen, Guido Marcucci, David R Plas, Zejuan Li, Rui Su, Jianjun Chen.

  R-2-hydroxyglutarate (R-2HG), a metabolite produced by mutant isocitrate dehydrogenases (IDHs), was recently reported to exhibit anti-tumor activity. However, its effect on cancer metabolism remains largely elusive. Here we show that R-2HG effectively attenuates aerobic glycolysis, a hallmark of cancer metabolism, in (R-2HG-sensitive) leukemia cells. Mechanistically, R-2HG abrogates fat-mass- and obesity-associated protein (FTO)/N6-methyladenosine (m6A)/YTH N6-methyladenosine RNA binding protein 2 (YTHDF2)-mediated post-transcriptional upregulation of phosphofructokinase platelet (PFKP) and lactate dehydrogenase B (LDHB) (two critical glycolytic genes) expression and thereby suppresses aerobic glycolysis. Knockdown of FTO, PFKP, or LDHB recapitulates R-2HG-induced glycolytic inhibition in (R-2HG-sensitive) leukemia cells, but not in normal CD34+ hematopoietic stem/progenitor cells, and inhibits leukemogenesis in vivo; conversely, their overexpression reverses R-2HG-induced effects. R-2HG also suppresses glycolysis and downregulates FTO/PFKP/LDHB expression in human primary IDH-wild-type acute myeloid leukemia (AML) cells, demonstrating the clinical relevance. Collectively, our study reveals previously unrecognized effects of R-2HG and RNA modification on aerobic glycolysis in leukemia, highlighting the therapeutic potential of targeting cancer epitranscriptomics and metabolism.

Keywords:  FTO; LDHB; N(6)-methyladenosine (m(6)A) modification; PFKP; R-2HG; RNA stability; YTHDF2; cancer metabolism; glycolysis; leukemia

DOI:  https://doi.org/10.1016/j.molcel.2020.12.026
Nature. 2021 Jan 13.

m6A RNA methylation regulates the fate of endogenous retroviruses.

Tomasz Chelmicki, Emeline Roger, Aurélie Teissandier, Mathilde Dura, Lorraine Bonneville, Sofia Rucli, François Dossin, Camille Fouassier, Sonia Lameiras, Deborah Bourc'his.

Endogenous retroviruses (ERVs) are abundant and heterogenous groups of integrated retroviral sequences that affect genome regulation and cell physiology throughout their RNA-centred life cycle1. Failure to repress ERVs is associated with cancer, infertility, senescence and neurodegenerative diseases2,3. Here, using an unbiased genome-scale CRISPR knockout screen in mouse embryonic stem cells, we identify m6A RNA methylation as a way to restrict ERVs. Methylation of ERV mRNAs is catalysed by the complex of methyltransferase-like METTL3-METTL144 proteins, and we found that depletion of METTL3-METTL14, along with their accessory subunits WTAP and ZC3H13, led to increased mRNA abundance of intracisternal A-particles (IAPs) and related ERVK elements specifically, by targeting their 5' untranslated region. Using controlled auxin-dependent degradation of the METTL3-METTL14 enzymatic complex, we showed that IAP mRNA and protein abundance is dynamically and inversely correlated with m6A catalysis. By monitoring chromatin states and mRNA stability upon METTL3-METTL14 double depletion, we found that m6A methylation mainly acts by reducing the half-life of IAP mRNA, and this occurs by the recruitment of the YTHDF family of m6A reader proteins5. Together, our results indicate that RNA methylation provides a protective effect in maintaining cellular integrity by clearing reactive ERV-derived RNA species, which may be especially important when transcriptional silencing is less stringent.

DOI: https://doi.org/10.1038/s41586-020-03135-1
EMBO Rep. 2021 Jan 11. e51519

MYC promotes cancer progression by modulating m6 A modifications to suppress target gene translation.

Gongwei Wu, Caixia Suo, Ying Yang, Shengqi Shen, Linchong Sun, Shi-Ting Li, Yingli Zhou, Dongdong Yang, Yan Wang, Yongping Cai, Nana Wang, Huafeng Zhang, Yun-Gui Yang, Jie Cao, Ping Gao.

  The MYC oncoprotein activates and represses gene expression in a transcription-dependent or transcription-independent manner. Modification of mRNA emerges as a key gene expression regulatory nexus. We sought to determine whether MYC alters mRNA modifications and report here that MYC promotes cancer progression by down-regulating N6-methyladenosine (m6 A) preferentially in transcripts of a subset of MYC-repressed genes (MRGs). We find that MYC activates the expression of ALKBH5 and reduces m6 A levels in the mRNA of the selected MRGs SPI1 and PHF12. We also show that MYC-regulated m6 A controls the translation of MRG mRNA via the specific m6 A reader YTHDF3. Finally, we find that inhibition of ALKBH5, or overexpression of SPI1 or PHF12, effectively suppresses the growth of MYC-deregulated B-cell lymphomas, both in vitro and in vivo. Our findings uncover a novel mechanism by which MYC suppresses gene expression by altering m6 A modifications in selected MRG transcripts promotes cancer progression.

Keywords:  ALKBH5; MYC; MYC-repressed genes; m6A; oncogenesis

DOI:  https://doi.org/10.15252/embr.202051519
Cancer Cell Int. 2021 Jan 11. 21(1): 46

Decreased expression of METTL14 predicts poor prognosis and construction of a prognostic signature for clear cell renal cell carcinoma.

Yi Wang, Rong Cong, Shouyong Liu, Bingye Zhu, Xing Wang, Qianwei Xing.

   BACKGROUND: METTL14, as one of N6-methyladenosine (m6A) related genes, has been found to be associated with promoting tumorigenesis in different types of cancers. This study was aimed to investigate the prognostic value of METTL14 in clear cell renal cell carcinoma (ccRCC).
METHODS: We collected ccRCC patients' clinicopathological parameters information and 13 m6A related genes expression from The Cancer Genome Atlas (TCGA) database. Univariate and multivariate Cox regression analyses were conducted to investigate whether METTL14 could serve as an independent factor correlated with overall survival (OS). Gene Set Enrichment Analysis (GSEA) was carried out to identify METTL14-related signaling pathways. Moreover, a risk score (RS) was calculated to predict the prognosis of ccRCC. Quantitative real-time PCR (qRT-PCR) was also utilized to verify the expression of METTL14 in clinical specimens.
RESULTS: Differently expressed m6A related genes were identified between ccRCC tissues and normal tissues. Therein, METTL14 was lowly expressed in ccRCC tissues and verified by qRT-PCR (all p < 0.01). Survival analysis indicated that high expression of METTL14 was associated with better OS (p = 1e-05). GSEA results revealed that high METTL14 expression was enriched in ERBB pathway, MAPK pathway, mTOR pathway, TGF-β pathway and Wnt pathway. Moreover, METTL14 was proved to be an independent prognostic factor by means of univariate and multivariate Cox regression analyses. Nomogram integrating both the METTL14 expression and clinicopathologic variables was also established to provide clinicians with a quantitative approach for predicting survival probabilities of ccRCC. Furthermore, a METTL14-based riskscore (RS) was developed with significant OS (p = 6.661e-16) and increased AUC of 0.856. Besides, significant correlated genes with METTL14 were also provided.
CONCLUSIONS: Our results indicated that METTL14 could serve as a favorable prognostic factor for ccRCC. Moreover, this study also provided a prognostic signature to predict prognosis of ccRCC and identified METTL14-related signaling pathways.

Keywords:  Clear cell renal cell carcinoma; METTL14; N6-Methyladenosine; Overall survival; Risk score

DOI:  https://doi.org/10.1186/s12935-020-01738-2
Aging (Albany NY). 2021 Jan 10. 12

ALKBH5-mediated m6A demethylation of FOXM1 mRNA promotes progression of uveal melanoma.

Lili Hao, Jiayang Yin, Hong Yang, Chaoxuan Li, Linxin Zhu, Lian Liu, Jingxiang Zhong.

  In this study, we found that ALKBH5, a key component of the N6-methyladenosine (m6A) methyltransferase complex, was significantly elevated in uveal melanoma (UM) cell lines and that ALKBH5 downregulation inhibited tumor growth in vivo. High ALKBH5 expression predicted worse outcome in patients with UM. EP300-induced H3K27 acetylation activation increased ALKBH5 expression. Downregulation of ALKBH5 inhibited UM cell proliferation, migration, and invasion and increased apoptosis in vitro. Besides, ALKBH5 may promote UM metastasis by inducing epithelial-to-mesenchymal transition (EMT) via demethylation of FOXM1 mRNA, which increases its expression and stability. In sum, our study indicates that AKLBH5-induced m6A demethylation of FOXM1 mRNA promotes UM progression. Therefore, AKLBH5 is a potential prognostic biomarker and therapeutic target in UM.

Keywords:  ALKBH5; FOXM1; m6A demethylation; uveal melanoma

DOI:  https://doi.org/10.18632/aging.202371
RNA Biol. 2021 Jan 14.

HSM6AP: A high-precision predictor for the Homo sapiens N6-methyladenosine (m^6 A) based on multiple weights and feature stitching.

Jing Li, Shida He, Fei Guo, Quan Zou.

  Motivation: Recent studies have shown that RNA methylation modification can affect RNA transcription, metabolism, splicing and stability. In addition, RNA methylation modification has been associated with cancer, obesity and other diseases. Based on information about human genome and machine learning, this paper discusses the effect of the fusion sequence and gene level feature extraction on the accuracy of methylation site recognition. The significant limitation of existing computing tools was exposed by discovered of new features. (1) Most prediction models are based solely on sequence features and use SVM or random forest as classification methods. (2) Limited by the number of samples, the model may not achieve good performance. In order to establish a better prediction model for methylation sites, we must set specific weighting strategies for training samples and find more powerful and informative feature matrices to establish a comprehensive model. Results: In this paper, we present HSM6AP, a high-precision predictor for the Homo sapiens N6-methyladenosine ( m6A ) based on multiple weights and feature stitching. Compared with existing methods, HSM6AP samples were creatively weighted during training, and a wide range of features were explored. Max-Relevance-Max-Distance (MRMD) is employed for feature selection, and the feature matrix is generated by fusing a single feature. The extreme gradient boosting (XGBOOST), an integrated machine learning algorithm based on decision tree, is used for model training and improves model performance through parameter adjustment. Two rigorous independent datasets demonstrated the superiority of HSM6AP in identifying methylation sites. HSM6AP is an advanced predictor that can be directly employed by users (especially non-professional users) to predict methylation sites. Users can access our related tools and datasets at the following website: http://lab.malab.cn/~lijing/HSM6AP.html The codes of our tool can be publicly accessible at https://github.com/lijingtju/HSm6AP.git.

Keywords:  XGBoost; feature stitching; gene-derived features; methylation site; sequence derived feature

DOI:  https://doi.org/10.1080/15476286.2021.1875180
EMBO J. 2021 Jan 11. e104975

Ythdf is a N6-methyladenosine reader that modulates Fmr1 target mRNA selection and restricts axonal growth in Drosophila.

Lina Worpenberg, Chiara Paolantoni, Sara Longhi, Miriam M Mulorz, Tina Lence, Hans-Hermann Wessels, Erik Dassi, Giuseppe Aiello, F X Reymond Sutandy, Marion Scheibe, Raghu R Edupuganti, Anke Busch, Martin M Möckel, Michiel Vermeulen, Falk Butter, Julian König, Michela Notarangelo, Uwe Ohler, Christoph Dieterich, Alessandro Quattrone, Alessia Soldano, Jean-Yves Roignant.

  N6-methyladenosine (m6 A) regulates a variety of physiological processes through modulation of RNA metabolism. This modification is particularly enriched in the nervous system of several species, and its dysregulation has been associated with neurodevelopmental defects and neural dysfunctions. In Drosophila, loss of m6 A alters fly behavior, albeit the underlying molecular mechanism and the role of m6 A during nervous system development have remained elusive. Here we find that impairment of the m6 A pathway leads to axonal overgrowth and misguidance at larval neuromuscular junctions as well as in the adult mushroom bodies. We identify Ythdf as the main m6 A reader in the nervous system, being required to limit axonal growth. Mechanistically, we show that the m6 A reader Ythdf directly interacts with Fmr1, the fly homolog of Fragile X mental retardation RNA binding protein (FMRP), to inhibit the translation of key transcripts involved in axonal growth regulation. Altogether, this study demonstrates that the m6 A pathway controls development of the nervous system and modulates Fmr1 target transcript selection.

Keywords:  Fmr1; RNA modification; Ythdf; m6A; nervous system

DOI:  https://doi.org/10.15252/embj.2020104975
Oncogenesis. 2021 Jan 05. 10(1): 7

Metformin exhibits antiproliferation activity in breast cancer via miR-483-3p/METTL3/m6A/p21 pathway.

Lin Cheng, Xu Zhang, Yu-Zhou Huang, Yu-Lan Zhu, Ling-Yun Xu, Zhi Li, Xin-Yuan Dai, Liang Shi, Xu-Jie Zhou, Ji-Fu Wei, Qiang Ding.

Evidence suggests that metformin might be a potential candidate for breast cancer treatment. Yet, its relevant molecular mechanisms remain to be fully investigated. We found that metformin could suppress the N6-methyladenosine (m6A) level in breast cancer cells significantly. The latter has an essential role in breast cancer progression and is newly considered as a therapeutic target. In this study, we measured the m6A level by m6A colorimetric analysis and dot blot assay. We then performed qRT-PCR, western blot, MeRIP, dual-luciferase reporter assay, and others to explore the m6A-dependent pathway associated with metformin. In vivo effect of metformin was investigated using a mouse tumorigenicity model. In addition, breast cancer and normal tissues were used to determine the role of METTL3 in breast cancer. Metformin could reduce the m6A level via decreasing METTL3 expression mediated by miR-483-3p in breast cancer. METTL3 is known to be able to promote breast cancer cell proliferation by regulating the p21 expression by an m6A-dependent manner. Metformin can take p21 as the main target to inhibit such effect. To specify, this study exhibited that metformin can inhibit breast cancer cell proliferation through the pathway miR-483-3p/METTL3/m6A/p21. Our findings suggest that METTL3 may be considered as a potential therapeutic target of metformin for breast cancer.

DOI: https://doi.org/10.1038/s41389-020-00290-y