bims-rimeca 2020-11-22 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2020–11–22
seven papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics

RNA m6A methyltransferase METTL3 facilitates colorectal cancer by activating m6A-GLUT1-mTORC1 axis and is a therapeutic target.
YTHDF1-enhanced iron metabolism depends on TFRC m6A methylation.
Stabilization of ERK-Phosphorylated METTL3 by USP5 Increases m6A Methylation.
m6A methyltransferase Wilms' tumor 1-associated protein facilitates cell proliferation and cisplatin resistance in NK/T cell lymphoma by regulating dual-specificity phosphatases 6 expression via m6A RNA methylation.
m6A RNA Methylation Regulators Participate in the Malignant Progression and Have Clinical Prognostic Value in Lung Adenocarcinoma.
N6-methyladenosine methyltransferase plays a role in hypoxic preconditioning partially through the interaction with lncRNA H19.
[Research Advances of m⁶A RNA Methylation in Non-small Cell Lung Cancer].

Gastroenterology. 2020 Nov 17. pii: S0016-5085(20)35402-0. [Epub ahead of print]

RNA m6A methyltransferase METTL3 facilitates colorectal cancer by activating m6A-GLUT1-mTORC1 axis and is a therapeutic target.

Huarong Chen, Shanshan Gao, Weixin Liu, Chi-Chun Wong, Jianfeng Wu, Jingtong Wu, Dabin Liu, Hongyan Gou, Wei Kang, Jianning Zhai, Chuangen Li, Hao Su, Shiyan Wang, Fraser Soares, Jiahuai Han, Housheng Hansen He, Jun Yu.

   BACKGROUND & AIMS: RNA N6-methyladenosine (m6A) modification has recently emerged as a new regulatory mechanism in cancer progression. We aimed to explore the role of m6A regulatory enzyme METTL3 in colorectal cancer (CRC) pathogenesis and its potential as a therapeutic target.
METHODS: The expression and clinical implication of METTL3 were investigated in multiple human CRC cohorts. The underlying mechanisms of METTL3 in CRC were investigated by integrative m6A-sequencing, RNA-sequencing and ribosome profiling analyses. The efficacy of targeting METTL3 in CRC treatment was elucidated in CRC cell lines, patient-derived CRC organoids and Mettl3 knockout mouse models.
RESULTS: Using targeted CRISPR/Cas9 dropout screening, we identified METTL3 as the top essential m6A regulatory enzyme in CRC. METTL3 was overexpressed in 62.2% (79/127) and 88.0% (44/50) of primary CRC from two independent cohorts. High METTL3 expression predicted poor survival in CRC patients (n=374, P < .01). Functionally, silencing METTL3 suppressed tumorigenesis in CRC cells, human-derived primary CRC organoids and Mettl3 knockout mouse models. We discovered the novel functional m6A methyltransferase domain of METTL3 in CRC cells by domain-focused CRISPR screen and mutagenesis assays. Mechanistically, METTL3 directly induced m6A-GLUT1-mTORC1 axis as identified by integrated m6A-sequencing, RNA-sequencing, Ribosome-sequencing and functional validation. METTL3 induced GLUT1 translation in m6A-dependent manner, which subsequently promoted glucose uptake and lactate production, leading to the activation of mTORC1 signaling and CRC development. Furthermore, inhibition of mTORC1 potentiated the anticancer effect of METTL3 silencing in CRC patient-derived organoids and METTL3 transgenic mouse models.
CONCLUSIONS: METTL3 promotes CRC by activating m6A-GLUT1-mTORC1 axis. METTL3 is a promising therapeutic target for the treatment of CRC.

Keywords:  Colorectal cancer; N(6)-Methyladenosine; glucose metabolism; mTORC1

DOI:  https://doi.org/10.1053/j.gastro.2020.11.013
Theranostics. 2020 ;10(26): 12072-12089

YTHDF1-enhanced iron metabolism depends on TFRC m6A methylation.

Jing Ye, Zhanggui Wang, Xiaozhen Chen, Xiaohua Jiang, Zhihuai Dong, Sunhong Hu, Wenya Li, Yuehui Liu, Bing Liao, Weidong Han, Jiaying Shen, Mang Xiao.

  Background: Among head and neck squamous cell carcinomas (HNSCCs), hypopharyngeal squamous cell carcinoma (HPSCC) has the worst prognosis. Iron metabolism, which plays a crucial role in tumor progression, is mainly regulated by alterations to genes and post-transcriptional processes. The recent discovery of the N6-methyladenosine (m6A) modification has expanded the realm of previously undiscovered post-transcriptional gene regulation mechanisms in eukaryotes. Many studies have demonstrated that m6A methylation represents a distinct layer of epigenetic deregulation in carcinogenesis and tumor proliferation. However, the status of m6A modification and iron metabolism in HPSCC remains unknown. Methods: Bioinformatics analysis, sample analysis, and transcriptome sequencing were performed to evaluate the correlation between m6A modification and iron metabolism. Iron metabolic and cell biological analyses were conducted to evaluate the effect of the m6A reader YTHDF1 on HPSCC proliferation and iron metabolism. Transcriptome-wide m6A-seq and RIP-seq data were mapped to explore the molecular mechanism of YTHDF1 function in HPSCC. Results: YTHDF1 was found to be closely associated with ferritin levels and intratumoral iron concentrations in HPSCC patients at Sir Run Run Shaw Hospital. YTHDF1 induced-HPSCC tumorigenesis depends on iron metabolism in vivo in vitro. Mechanistically, YTHDF1 methyltransferase domain interacts with the 3'UTR and 5'UTR of TRFC mRNA, then further positively regulates translation of m6A-modified TFRC mRNA. Gain-of-function and loss-of-function analyses validated the finding showing that TFRC is a crucial target gene for YTHDF1-mediated increases in iron metabolism. Conclusion: YTHDF1 enhanced TFRC expression in HPSCC through an m6A-dependent mechanism. From a therapeutic perspective, targeting YTHDF1 and TFRC-mediated iron metabolism may be a promising strategy for HPSCC.

Keywords:  Hypopharyngeal squamous cell carcinoma; Iron metabolism; N6-methyladenosine (m6A) modification; TFRC; YTHDF1

DOI:  https://doi.org/10.7150/thno.51231
Mol Cell. 2020 Nov 19. pii: S1097-2765(20)30733-4. [Epub ahead of print]80(4): 633-647.e7

Stabilization of ERK-Phosphorylated METTL3 by USP5 Increases m6A Methylation.

Hui-Lung Sun, Allen C Zhu, Yawei Gao, Hideki Terajima, Qili Fei, Shun Liu, Linda Zhang, Zijie Zhang, Bryan T Harada, Yu-Ying He, Marc B Bissonnette, Mien-Chie Hung, Chuan He.

  N6-methyladenosine (m6A) is the most abundant mRNA modification and is installed by the METTL3-METTL14-WTAP methyltransferase complex. Although the importance of m6A methylation in mRNA metabolism has been well documented recently, regulation of the m6A machinery remains obscure. Through a genome-wide CRISPR screen, we identify the ERK pathway and USP5 as positive regulators of the m6A deposition. We find that ERK phosphorylates METTL3 at S43/S50/S525 and WTAP at S306/S341, followed by deubiquitination by USP5, resulting in stabilization of the m6A methyltransferase complex. Lack of METTL3/WTAP phosphorylation reduces decay of m6A-labeled pluripotent factor transcripts and traps mouse embryonic stem cells in the pluripotent state. The same phosphorylation can also be found in ERK-activated human cancer cells and contribute to tumorigenesis. Our study reveals an unrecognized function of ERK in regulating m6A methylation.

Keywords:  ERK; METTL3 phosphorylation; USP5; m(6)A methylation; stem cell differentiation

DOI:  https://doi.org/10.1016/j.molcel.2020.10.026
IUBMB Life. 2020 Nov 17.

m6A methyltransferase Wilms' tumor 1-associated protein facilitates cell proliferation and cisplatin resistance in NK/T cell lymphoma by regulating dual-specificity phosphatases 6 expression via m6A RNA methylation.

HongYan Ma, LiYun Shen, Hua Yang, HongTao Gong, XingJun Du, JunBo Li.

  Nasal-type natural killer/T-cell lymphoma (NKTCL) is an aggressive malignancy with poor survival outcomes that is relatively resistant to chemotherapy. N6-Methyladenosine (m6A) modification, the most prevalent modification of eukaryotic messenger RNA, is involved in the progression of various tumors. However, it is unclear whether it has a physiological role in NKTCL development. To address this question, we probed its function and molecular mechanisms in NKTCL. Initially, we demonstrated that Wilms' tumor 1-associated protein (WTAP), a major RNA N6-adenosine methyltransferase, was obviously upregulated in human NKTCL cell lines (YTS and SNK-6 cells), compared with normal NK cells. Functionally, depletion of WTAP noticeably repressed proliferation and facilitated apoptosis in YTS and SNK-6 cells. Moreover, intervention of WTAP evidently prohibited NKTCL cell chemotherapy resistance to cisplatin, as reflected by a lower inhibition of cell viability and decreased expression of drug resistance-associated protein expression MRP-1 and P-gp in YTS and SNK-6 cells. With regard to the mechanism, we revealed that WTAP enhanced dual-specificity phosphatases 6 (DUSP6) expression by increasing m6A levels of DUSP6 mRNA transcript, leading to oncogenic functions in NKTCL. Interestingly, WTAP contributed to the progression and chemotherapy sensitivity of NKTCL by stabilizing DUSP6 mRNA in an m6A-dependent manner. Taken together, these findings uncovered a critical function for WTAP-guided m6A methylation and identified DUSP6 as an important target of m6A modification in the regulation of chemotherapy resistance in NKTCL oncogenesis. This study highlights WTAP as a potential therapeutic target of NKTCL treatment.

Keywords:  DUSP6; N6-Methyladenosine; NK/T cell lymphoma; WTAP; cisplatin resistance

DOI:  https://doi.org/10.1002/iub.2410
Front Genet. 2020 ;11 994

m6A RNA Methylation Regulators Participate in the Malignant Progression and Have Clinical Prognostic Value in Lung Adenocarcinoma.

Fangwei Li, Hong Wang, Huirong Huang, Li Zhang, Dan Wang, Yixin Wan.

  Abnormal methylation of N6 adenosine (m6A) in RNA plays a crucial role in the pathogenesis of many types of tumors. However, little is known about m6A RNA methylation in lung adenocarcinoma. This study aimed to identify the value of m6A RNA methylation regulators in the malignant progression and clinical prognosis of lung adenocarcinoma. The RNA-seq transcriptome data and corresponding clinical information of lung adenocarcinoma were downloaded from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) database. Then the identification of differentially expressed m6A RNA methylation regulators between cancer samples and normal control samples, different subgroups by consensus expression of these regulators and the prognostic signature were achieved using R software with multiple corresponding packages. The results showed that the expression levels of HNRNPC, YTHDF1, KIAA1429, RBM15, YTHDF2, and METTL3 in cancer group were significantly up-regulated (P < 0.05), while expression levels of FTO, ZC3H13, METTL14, YTHDC1 and WTAP in cancer group were significantly down-regulated (P < 0.05) compared with control group. Two subgroups identified by consensus expression of these regulators were closely related to the clinicopathological features, clinical outcomes and malignancy of lung adenocarcinoma. In addition, a 3-gene risk signature including KIAA1429, RBM15, and HNRNPC was constructed and the lung adenocarcinoma patients in TCGA database were divided into high-risk group and low-risk group based on the median risk score. In conclusion, the prognostic signature-based risk score calculated according to the expression levels of KIAA1429, RBM15, and HNRNPC, was not only strongly associated with clinical outcomes and clinicopathological features, but also an independent prognostic factor in lung adenocarcinoma.

Keywords:  demethylation; lung adenocarcinoma; m6A; methylation; prognostic signature

DOI:  https://doi.org/10.3389/fgene.2020.00994
Acta Biochim Biophys Sin (Shanghai). 2020 Nov 17. pii: gmaa130. [Epub ahead of print]

N6-methyladenosine methyltransferase plays a role in hypoxic preconditioning partially through the interaction with lncRNA H19.

Yamin Su, Rongfeng Xu, Rui Zhang, Yangyang Qu, Wenjie Zuo, Zhenjun Ji, Haihua Geng, Min Pan, Genshan Ma.

  N6-methyladenosine (m6A), a methylation in the N6 position of adenosine especially in the mRNA, exerts diverse physiological and pathological functions. However, the precise role of m6A methylation in hypoxic preconditioning (HPC) is still unknown. Here, we observed that HPC treatment protected H9c2 cells against H2O2-induced injury, upregulated the m6A level in the total RNA and the expression of methyltransferase like 3 (METTL3), methyltransferase like 14 (METTL14), and long noncoding RNA (lncRNA) H19. Either knockdown of METTL3 or METTL14 notably reversed the HPC-induced enhancement of cell viability, anti-apoptosis ability, and H19 expression. Methylated RNA immunoprecipitation (IP) indicated that knockdown of METTL3 or METTL14 decreased m6A level in the lncRNA H19. Gain-of-function assay demonstrated that H19 overexpression could partially rescue the decreased protection mediated by METTL3 or METTL14 knockdown in HPC-treated H9c2 cells. RNA binding protein immunoprecipitation (RIP) assay showed that METTL3 and METTL14 could directly bind with H19. Our study identified a novel pattern of posttranscriptional regulation in HPC treatment. Since METTL3, METTL14, and lncRNA H19 were involved in HPC protection, they could be considered as potential biomarkers and therapeutic targets in HPC-derived cardiac rehabilitation and therapeutic approaches.

Keywords:  N6-methyladenosine; hypoxic preconditioning; lncRNA H19; methyltransferase like 14; methyltransferase like 3

DOI:  https://doi.org/10.1093/abbs/gmaa130
Zhongguo Fei Ai Za Zhi. 2020 Nov 20. 23(11): 961-969

[Research Advances of m⁶A RNA Methylation in Non-small Cell Lung Cancer].

Hongli Pan, Xuebing Li, Chen Chen, Yaguang Fan, Qinghua Zhou.

  N6-methyladenosine is one of the most prevalent mRNA modification in eukaryotes. The regulation of this pervasive mark is a dynamic and reversible process. m⁶A RNA methylation is catalyzed by m⁶A writers, removed by m⁶A erasers and recognized by m⁶A readers, thereby regulating multiple RNA processes including alternative splicing, nuclear export, degradation and translation. Accumulated evidence suggests that m⁶A modification plays a crucial role in the pathogenic mechanism and malignant progression in non-small cell lung cancer (NSCLC), including cell survival, proliferation, migration, invasion, tumor metastasis and drug resistance. Moreover, the expression of m⁶A and its related proteins are dysregulated in clinical samples and circulating tumor cells (CTCs) of lung cancer patients, indicating that m⁶A modification may serve as a novel potential biomarker for the diagnosis and prognosis of lung cancer. In this review, by summarizing a great number of recent reports related to m⁶A's function and its modulators, we aim to provide a new insight on the early diagnosis and drug development in NSCLC therapy. .

Keywords:  Epigenetic modification; Lung neoplasms; N6-methyladenosine; RNA methylation

DOI:  https://doi.org/10.3779/j.issn.1009-3419.2020.102.35