bims-rimeca 2021-12-12 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2021–12–12
eight papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics

Methyltransferase-Like 3-Mediated m6A Methylation of Hsa_circ_0058493 Accelerates Hepatocellular Carcinoma Progression by Binding to YTH Domain-Containing Protein 1.
m6A methyltransferase METTL3 promotes oral squamous cell carcinoma progression through enhancement of IGF2BP2-mediated SLC7A11 mRNA stability.
ALKBH5 Is Lowly Expressed in Esophageal Squamous Cell Carcinoma and Inhibits the Malignant Proliferation and Invasion of Tumor Cells.
TTP protects against acute liver failure by regulating CCL2 and CCL5 through m6A RNA methylation.
GR-mediated transcriptional regulation of m6A metabolic genes contributes to diet-induced fatty liver in hens.
M6A methylation-mediated elevation of SM22α inhibits the proliferation and migration of vascular smooth muscle cells and ameliorates intimal hyperplasia in type 2 diabetes mellitus.
Genome-wide map of N6-methyladenosine circular RNAs identified in mice model of severe acute pancreatitis.
The methyltransferase METTL3 negatively regulates nonalcoholic steatohepatitis (NASH) progression.

Front Cell Dev Biol. 2021 ;9 762588

Methyltransferase-Like 3-Mediated m6A Methylation of Hsa_circ_0058493 Accelerates Hepatocellular Carcinoma Progression by Binding to YTH Domain-Containing Protein 1.

Anqi Wu, Yuhao Hu, Yao Xu, Jing Xu, Xinyue Wang, Aiting Cai, Ruoyu Liu, Lin Chen, Feng Wang.

  Circular RNAs (circRNAs) are highly correlated with the progression and prognosis of hepatocellular carcinoma (HCC). In addition, mounting evidence has revealed that N6-methyladenosine (m6A) methylation, a common RNA modification, is involved in the progression of malignancies. In this research, a novel circRNA, hsa_circ_0058493, was proven to be upregulated in HCC, which was correlated with the prognosis of HCC patients. Experimentally, hsa_circ_0058493 knockdown suppressed the growth and metastasis of HCC cells in vivo and in vitro. On the contrary, the overexpression of hsa_circ_0058493 in HCC cells had the opposite effect in vitro. Mechanistic experiments revealed that hsa_circ_0058493 contained m6A methylation sites and that methyltransferase-like 3 (METTL3) mediated the degree of methylation modification of hsa_circ_0058493. Furthermore, YTH domain-containing protein 1 (YTHDC1) could bind to hsa_circ_0058493 and promote its intracellular localization from the nucleus to the cytoplasm. In addition, both si-METTL3 and si-YTHDC1 suppressed HCC cell growth and metastasis, whereas rescue experiments confirmed that overexpression of hsa_circ_0058493 inverted the inhibitory effects of si-METTL3 and si-YTHDC1 on HCC cells. Taken together, this study explored the oncogenic role of m6A-modified hsa_circ_0058493 and found to accelerate HCC progression via the METTL3-hsa_circ_0058493-YTHDC1 axis, indicating a potential therapeutic target for this deadly disease.

Keywords:  HCC; METTL3; N6-methyladenosine; YTHDC1; circular RNA; hsa_circ_0058493

DOI:  https://doi.org/10.3389/fcell.2021.762588
Am J Cancer Res. 2021 ;11(11): 5282-5298

m6A methyltransferase METTL3 promotes oral squamous cell carcinoma progression through enhancement of IGF2BP2-mediated SLC7A11 mRNA stability.

Le Xu, Qingxiang Li, Yifei Wang, Lin Wang, Yuxing Guo, Rong Yang, Na Zhao, Na Ge, Yixiang Wang, Chuanbin Guo.

As the key enzyme of the N6-methyladenosine (m6A) in eukaryotic messenger RNA, METTL3 plays an important role in tumor progression, but the exact mechanism by which METTL3 controls oral squamous cell carcinoma (OSCC) progression remains unclear. In this study, METTL3 expression in OSCC samples was analyzed by qPCR and immunohistochemistry. The effects of METTL3 suppression on OSCC cell lines were measured by CCK-8, Ki67 flow cytometry analysis, invasion transwell and wound healing assays. MeRIP-seq and RNA-seq analyses were performed to explore target gene of METTL3. RIP-qPCR and RNA stability assays were performed to explore the mechanism by which METTL3 regulated the target genes. Triptolide was used to evaluate its specific treatment effects on METTL3 in OSCC cells. BALB/c nude mice were used to establish orthotopic and subcutaneous xenograft models to verify the in vitro results. The results showed that METTL3 was upregulated in OSCC tissues compared with OSCC adjacent normal tissues, and its expression was associated with T stage, lymphatic metastasis and prognosis. METTL3 suppression impaired OSCC cells proliferation, invasion, and migration. MeRIP-seq and RNA-seq analysis identified that SLC7A11 mRNA was the m6A target of METTL3, which was verified by meRIP-qPCR, qPCR and western blot. METTL3 depletion decreased the stability of SLC7A11 mRNA, and IGF2BP2 as m6A reader was involved in this process. Moreover, METTL3 knockdown attenuated the binding between SLC7A11 mRNA and IGF2BP2, finally leading to accelerate SLC7A11 mRNA degradation. Triptolide inhibited METTL3-mediated SLC7A11 expression, thus suppressing malignancy of OSCC cells. In conclusion, the new finding of the manuscript is that METTL3 enhances the mRNA stability of SLC7A11 via m6A-mediated binding of IGF2BP2, which thus promotes OSCC progression, and triptolide inhibits OSCC by suppressing METTL3-SLC7A11 axis. Triptolide has a potential to be as an effective anti-OSCC drug targeted to METTL3.

Keywords: IGF2BP2; METTL3; N6-methyladenosine; Oral squamous cell carcinoma; SLC7A11; Triptolide
Comput Math Methods Med. 2021 ;2021 1001446

ALKBH5 Is Lowly Expressed in Esophageal Squamous Cell Carcinoma and Inhibits the Malignant Proliferation and Invasion of Tumor Cells.

Jinqiu Li, Hongqiang Liu, Shanglin Dong, Yunbo Zhang, Xiao Li, Jing Wang.

Background: Modification of N6-methyladenosine (m6A) and RNA m6A regulatory factors is required in cancer advancement. The contribution of m6A and its alteration in esophageal squamous cell carcinoma (ESCC) is still unclear.
Results: ALKBH5 was lowly expressed in ESCC tissues, which the total m6A level was increased in ESCC tissue than the presentation in normal healthy tissue. The pcDNA3.1-ALKBH5 recombinant plasmid was transfected into KYSE-150 and Eca-109 cells. The overexpression of ALKBH5 is responsible for a significant reduction of the total m6A levels in Eca-109 and KYSE150 cells, inhibiting the proliferation capability, migration, and cell invasion.
Conclusions: ALKBH5 as a demethylase was lowly expressed in cancer progression of ESCC and acts as a crucial component in ESCC progression.

DOI: https://doi.org/10.1155/2021/1001446
JCI Insight. 2021 Dec 08. pii: e149276. [Epub ahead of print]6(23):

TTP protects against acute liver failure by regulating CCL2 and CCL5 through m6A RNA methylation.

Pingping Xiao, Mingxuan Li, Mengsi Zhou, Xuejun Zhao, Cheng Wang, Jinglin Qiu, Qian Fang, Hong Jiang, Huifen Dong, Rui Zhou.

  Tristetraprolin (TTP), an important immunosuppressive protein regulating mRNA decay through recognition of the AU-rich elements (AREs) within the 3'-UTRs of mRNAs, participates in the pathogenesis of liver diseases. However, whether TTP regulates mRNA stability through other mechanisms remains poorly understood. Here, we report that TTP was upregulated in acute liver failure (ALF), resulting in decreased mRNA stabilities of CCL2 and CCL5 through promotion of N6-methyladenosine (m6A) mRNA methylation. Overexpression of TTP could markedly ameliorate hepatic injury in vivo. TTP regulated the mRNA stabilization of CCL2 and CCL5. Interestingly, increased m6A methylation in CCL2 and CCL5 mRNAs promoted TTP-mediated RNA destabilization. Moreover, induction of TTP upregulated expression levels of WT1 associated protein, methyltransferase like 14, and YT521-B homology N6-methyladenosine RNA binding protein 2, which encode enzymes regulating m6A methylation, resulting in a global increase of m6A methylation and amelioration of liver injury due to enhanced degradation of CCL2 and CCL5. These findings suggest a potentially novel mechanism by which TTP modulates mRNA stabilities of CCL2 and CCL5 through m6A RNA methylation, which is involved in the pathogenesis of ALF.

Keywords:  Chemokines; Hepatitis; Hepatology; Inflammation

DOI:  https://doi.org/10.1172/jci.insight.149276
J Anim Sci Biotechnol. 2021 Dec 07. 12(1): 117

GR-mediated transcriptional regulation of m6A metabolic genes contributes to diet-induced fatty liver in hens.

Yue Feng, Yanlin Li, Wenduo Jiang, Yun Hu, Yimin Jia, Ruqian Zhao.

   BACKGROUND: Glucocorticoid receptor (GR) mediated corticosterone-induced fatty liver syndrome (FLS) in the chicken by transactivation of Fat mass and obesity associated gene (FTO), leading to demethylation of N6-methyladenosine (m6A) and post-transcriptional activation of lipogenic genes. Nutrition is considered the main cause of FLS in the modern poultry industry. Therefore, this study was aimed to investigate whether GR and m6A modification are involved in high-energy and low protein (HELP) diet-induced FLS in laying hens, and if true, what specific m6A sites of lipogenic genes are modified and how GR mediates m6A-dependent lipogenic gene activation in HELP diet-induced FLS in the chicken.
RESULTS: Laying hens fed HELP diet exhibit excess (P < 0.05) lipid accumulation and lipogenic genes activation in the liver, which is associated with significantly increased (P < 0.05) GR expression that coincided with global m6A demethylation. Concurrently, the m6A demethylase FTO is upregulated (P < 0.05), whereas the m6A reader YTHDF2 is downregulated (P < 0.05) in the liver of FLS chickens. Further analysis identifies site-specific demethylation (P < 0.05) of m6A in the mRNA of lipogenic genes, including FASN, SREBP1 and SCD. Moreover, GR binding to the promoter of FTO gene is highly enriched (P < 0.05), while GR binding to the promoter of YTHDF2 gene is diminished (P < 0.05).
CONCLUSIONS: These results implicate a possible role of GR-mediated transcriptional regulation of m6A metabolic genes on m6A-depenent post-transcriptional activation of lipogenic genes and shed new light in the molecular mechanism of FLS etiology in the chicken.

Keywords:  Chicken; FTO; Fatty liver syndrome; GR; Lipogenesis; YTHDF2; m6A

DOI:  https://doi.org/10.1186/s40104-021-00642-7
Biol Chem. 2021 Dec 07.

M6A methylation-mediated elevation of SM22α inhibits the proliferation and migration of vascular smooth muscle cells and ameliorates intimal hyperplasia in type 2 diabetes mellitus.

Bao-Fu Zhang, Zi-Heng Wu, Jie Deng, Hao-Jie Jin, Wei-Biao Chen, Sai Zhang, Xiu-Jie Liu, Wan-Tie Wang, Xiang-Tao Zheng.

  Abnormal proliferation of vascular smooth muscle cells (VSMCs) induced by insulin resistance facilitates intimal hyperplasia of type 2 diabetes mellitus (T2DM) and N6-methyladenosine (m6A) methylation modification mediates the VSMC proliferation. This study aimed to reveal the m6A methylation modification regulatory mechanism. In this study, m6A demethylase FTO was elevated in insulin-treated VSMCs and T2DM mice with intimal injury. Functionally, FTO knockdown elevated m6A methylation level and further restrained VSMC proliferation and migration induced by insulin. Mechanistically, FTO knockdown elevated Smooth muscle 22 alpha (SM22α) expression and m6A-binding protein IGF2BP2 enhanced SM22α mRNA stability by recognizing and binding to m6A methylation modified mRNA. In vivo studies confirmed that the elevated m6A modification level of SM22α mRNA mitigated intimal hyperplasia in T2DM mice. Conclusively, m6A methylation-mediated elevation of SM22α restrained VSMC proliferation and migration and ameliorated intimal hyperplasia in T2DM.

Keywords:  N6-methyladenosine (m6A); Type 2 diabetes mellitus (T2DM); intimal hyperplasia; vascular smooth muscle cells (VSMCs)

DOI:  https://doi.org/10.1515/hsz-2021-0296
World J Gastroenterol. 2021 Nov 21. 27(43): 7530-7545

Genome-wide map of N6-methyladenosine circular RNAs identified in mice model of severe acute pancreatitis.

Jun Wu, Xiao-Hui Yuan, Wen Jiang, Yi-Chen Lu, Qi-Lin Huang, Yi Yang, Hua-Ji Qie, Jiang-Tao Liu, Hong-Yu Sun, Li-Jun Tang.

   BACKGROUND: Severe acute pancreatitis (SAP) is a deadly inflammatory disease with complex pathogenesis and lack of effective therapeutic options. N6-methyladenosine (m6A) modification of circRNAs plays important roles in physiological and pathological processes. However, the roles of m6A circRNA in the pathological process of SAP remains unknown.
AIM: To identify transcriptome-wide map of m6A circRNAs and to determine their biological significance and potential mechanisms in SAP.
METHODS: The SAP in C57BL/6 mice was induced using 4% sodium taurocholate salt. The transcriptome-wide map of m6A circRNAs was identified by m6A-modified RNA immunoprecipitation sequencing. The biological significance of circRNAs with differentially expressed m6A peaks was evaluated through gene ontology and Kyoto Encyclopedia of Genes and Genomes analysis. The underlying mechanism of m6A circRNAs in SAP was analyzed by constructing of m6A circRNA-microRNA networks. The expression of demethylases was determined by quantitative polymerase chain reaction and western blot to deduce the possible mechanism of reversible m6A process in SAP.
RESULTS: Fifty-seven circRNAs with differentially expressed m6A peaks were identified by m6A-modified RNA immunoprecipitation sequencing, of which 32 were upregulated and 25 downregulated. Functional analysis of these m6A circRNAs in SAP found some important pathways involved in the pathogenesis of SAP, such as regulation of autophagy and protein digestion. In m6A circRNA-miRNA networks, several important miRNAs participated in the occurrence and progression of SAP were found to bind to these m6A circRNAs, such as miR-24-3p, miR-26a, miR-92b, miR-216b, miR-324-5p and miR-762. Notably, the total m6A level of circRNAs was reduced, while the demethylase alkylation repair homolog 5 was upregulated in SAP.
CONCLUSION: m6A modification of circRNAs may be involved in the pathogenesis of SAP. Our findings may provide novel insights to explore the possible pathogenetic mechanism of SAP and seek new potential therapeutic targets for SAP.

Keywords:  Circular RNAs; Epigenetic analysis; MeRIP-seq; N6-methyladenosine; Severe acute pancreatitis

DOI:  https://doi.org/10.3748/wjg.v27.i43.7530
Nat Commun. 2021 Dec 10. 12(1): 7213

The methyltransferase METTL3 negatively regulates nonalcoholic steatohepatitis (NASH) progression.

Xinzhi Li, Bingchuan Yuan, Min Lu, Yuqin Wang, Na Ding, Chunhong Liu, Ming Gao, Zhicheng Yao, Shiyan Zhang, Yujun Zhao, Liwei Xie, Zheng Chen.

Nonalcoholic steatohepatitis (NASH) is a key step in the progression of nonalcoholic fatty liver (NAFL) to cirrhosis. However, the molecular mechanisms of the NAFL-to-NASH transition are largely unknown. Here, we identify methyltransferase like 3 (METTL3) as a key negative regulator of NASH pathogenesis. Hepatocyte-specific deletion of Mettl3 drives NAFL-to-NASH progression by increasing CD36-mediated hepatic free fatty acid uptake and CCL2-induced inflammation, which is due to increased chromatin accessibility in the promoter region of Cd36 and Ccl2. Antibody blockade of CD36 and CCL2 ameliorates NASH progression in hepatic Mettl3 knockout mice. Hepatic overexpression of Mettl3 protects against NASH progression by inhibiting the expression of CD36 and CCL2. Mechanistically, METTL3 directly binds to the promoters of the Cd36 and Ccl2 genes and recruits HDAC1/2 to induce deacetylation of H3K9 and H3K27 in their promoters, thus suppressing Cd36 and Ccl2 transcription. Furthermore, METTL3 is translocated from the nucleus to the cytosol in NASH, which is associated with CDK9-mediated phosphorylation of METTL3. Our data reveal a mechanism by which METTL3 negatively regulates hepatic Cd36 and Ccl2 gene transcription via a histone modification pathway for protection against NASH progression.

DOI: https://doi.org/10.1038/s41467-021-27539-3