bims-rimeca 2021-01-10 papers

bims-rimeca

Biomed News

on RNA methylation in cancer

Issue of 2021–01–10
twenty papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics

N6-methyladenosine RNA methylation regulators contribute to the progression of prostate cancer.
The N6-methyladenosine modification posttranscriptionally regulates hepatic UGT2B7 expression.
m6A-RNA Demethylase FTO Inhibitors Impair Self-Renewal in Glioblastoma Stem Cells.
The emerging roles of m6A modification in liver carcinogenesis.
METTL3/YTHDF2 m6A axis accelerates colorectal carcinogenesis through epigenetically suppressing YPEL5.
N6-methyladenosine dynamics in neurodevelopment and aging, and its potential role in Alzheimer's disease.
Genetic variants in m6A regulators are associated with gastric cancer risk.
Hepatitis B virus X protein recruits methyltransferases to affect cotranscriptional N6-methyladenosine modification of viral/host RNAs.
Multifaceted regulation of translation by the epitranscriptomic modification N6-methyadenosine.
Detection of locus-specific N6-methyladenosine modification based on Ag+-assisted ligation and supersandwich signal amplification.
Quantitative profiling of N6-methyladenosine at single-base resolution in stem-differentiating xylem of Populus trichocarpa using Nanopore direct RNA sequencing.
METTL3 is required for maintaining β-cell function.
IGF2BP1 overexpression stabilizes PEG10 mRNA in an m6A-dependent manner and promotes endometrial cancer progression.
Gene Alterations of N6-Methyladenosine (m6A) Regulators in Colorectal Cancer: A TCGA Database Study.
Omeprazole improves chemosensitivity of gastric cancer cells by m6A demethylase FTO-mediated activation of mTORC1 and DDIT3 upregulation.
EGFR/SRC/ERK-stabilized YTHDF2 promotes cholesterol dysregulation and invasive growth of glioblastoma.
Expression and prognostic characteristics of m5 C regulators in low-grade glioma.
The RNA methyltransferase NSUN6 suppresses pancreatic cancer development by regulating cell proliferation.
Molecular Characteristics of N1-Methyladenosine Regulators and Their Correlation with Overall Cancer Survival.
METTL14-regulated PI3K/Akt signaling pathway via PTEN affects HDAC5-mediated epithelial-mesenchymal transition of renal tubular cells in diabetic kidney disease.

J Cancer. 2021 ;12(3): 682-692

N6-methyladenosine RNA methylation regulators contribute to the progression of prostate cancer.

Qunying Wu, Xing Xie, Yiming Huang, Shanshan Meng, Youcheng Li, Huifeng Wang, Yanling Hu.

  Prostate cancer (PCa) is one of the most common epithelial malignant tumors and the fifth leading cause of cancer death in men. An increasing number of studies have demonstrated that N6-methyladenosine (m6A) plays a crucial role in tumorigenesis and tumor development. However, little is known about the role and levels of common m6A regulators and m6A levels in PCa. In this study, we analyzed the characteristic expression of m6A regulators in PCa and castration-resistant prostate cancer (CRPC). UALCAN and cBioPortal were used to estimate the clinical value and genetic alterations of m6A regulators, respectively. The correlation between m6A regulators and androgen receptor (AR) was assessed using Gene Expression Profiling Interactive Analysis (GEPIA) by Pearson correlation statistics. Total m6A levels were detected in transgenic adenocarcinoma of the mouse prostate (TRAMP) mice and PCa cell lines. Results showed that the expression of methyltransferase-like 3 (METTL3) and YTH domain family members, namely, YTHDC2, YTHDF1, and YTHDF2 were generally upregulated in PCa, whereas those of fat mass and obesity-associated protein (FTO), AlkB homolog 5 (ALKBH5), and methyltransferase-like 14 (METTL14) were downregulated. The expression of METTL3, METTL14, Wilms' tumor 1-associating protein (WTAP), YTHDC2, YTHDF1, and YTHDF2 were remarkably higher in CRPC with lymph node metastasis than that in CRPC with bone metastasis, whereas ALKBH5, FTO, and YTHDF3 significantly decreased in CRPC with lymph node metastasis tissues. YTHDF1, YTHDF2, and YTHDC2 were positively correlated with the Gleason grades of PCa, and METTL14, FTO, and ALKBH5 were negatively associated with the Gleason classification. M6A regulators were positively correlated with AR. Patients with a genomic alteration of m6A were associated with poor disease-free survival (DFS). The total m6A levels in TRAMP mice increased dramatically compared with those in tumor-free mice, and m6A levels in LNCaP cell lines were higher than DU145 and PC3 cell lines. In summary, METTL3, METTL14, ALKBH5, FTO, YTHDC2, YTHDF1, and YTHDF2 were abnormally expressed in PCa and related to Gleason classification. Changes in m6A levels maybe contributed to the development and progression of PCa.

Keywords:  N6-methyladenosine; androgen receptor; castration-resistant prostate cancer; prostate cancer; tumorigenesis and progression

DOI:  https://doi.org/10.7150/jca.46379
Biochem Pharmacol. 2020 Dec 30. pii: S0006-2952(20)30638-9. [Epub ahead of print] 114402

The N6-methyladenosine modification posttranscriptionally regulates hepatic UGT2B7 expression.

Kyoko Ondo, Motoki Isono, Masataka Nakano, Shiori Hashiba, Tatsuki Fukami, Miki Nakajima.

UDP-glucuronosyltransferases (UGTs) are enzymes catalyzing the glucuronidation of various endogenous and exogenous compounds. In this study, we examined the possibility that N6-methyladenosine (m6A) modification affects hepatic UGT expression. Treatment of HepaRG cells with 3-deazaadenosine, an inhibitor of RNA methylation, significantly increased UGT1A1, UGT1A3, UGT1A4, UGT1A9, UGT2B7, UGT2B10, and UGT2B15 mRNA levels (1.3- to 2.6-fold). Among them, we focused on UGT2B7 because it most highly contributes to glucuronidation of clinically used drugs. Methylated RNA immunoprecipitation assays revealed that UGT2B7 mRNA in HepaRG cells and human livers is subjected to m6A modification mainly at the 5' untranslated region (UTR) and secondarily at the 3'UTR. UGT2B7 mRNA and protein levels in Huh-7 cells were significantly increased by double knockdown of methyltransferase-like 3 (METTL3) and METTL14, whereas those were decreased by knockdown of fat mass and obesity-associated protein (FTO) or alkB homolog 5, RNA demethylase (ALKBH5), suggesting that m6A modification downregulates UGT2B7 expression. By experiments using actinomycin D, an inhibitor of transcription, it was demonstrated that ALKBH5-mediated demethylation would attenuate UGT2B7 mRNA degradation, whereas METTL3/METTL14 or FTO-mediated m6A modification would alter the transactivity of UGT2B7. Luciferase assays revealed that the promoter region at -118 ∼ -106 has a key role in the decrease in transactivity of UGT2B7 by FTO knockdown. We found that hepatocyte nuclear factor 4α (HNF4α) expression was significantly decreased by knockdown of FTO, indicating that this would be the underlying mechanism of the decreased transactivity of UGT2B7 by knockdown of FTO. Interestingly, treatment with entacapone, which is used for the treatment of Parkinson's disease and is an inhibitor of FTO, decreased HNF4α and UGT2B7 expression. In conclusion, this study clarified that RNA methylation posttranscriptionally controls hepatic UGT2B7 expression.

DOI: https://doi.org/10.1016/j.bcp.2020.114402
ACS Chem Biol. 2021 Jan 07.

m6A-RNA Demethylase FTO Inhibitors Impair Self-Renewal in Glioblastoma Stem Cells.

Sarah Huff, Shashi Kant Tiwari, Gwendolyn M Gonzalez, Yinsheng Wang, Tariq M Rana.

N6-methyladenosine (m6A) has emerged as the most abundant mRNA modification that regulates gene expression in many physiological processes. m6A modification in RNA controls cellular proliferation and pluripotency and has been implicated in the progression of multiple disease states, including cancer. RNA m6A methylation is controlled by a multiprotein "writer" complex including the enzymatic factor methyltransferase-like protein 3 (METTL3) that regulates methylation and two "eraser" proteins, RNA demethylase ALKBH5 (ALKBH5) and fat mass- and obesity-associated protein (FTO), that demethylate m6A in transcripts. FTO can also demethylate N6,2'-O-dimethyladenosine (m6Am), which is found adjacent to the m7G cap structure in mRNA. FTO has recently gained interest as a potential cancer target, and small molecule FTO inhibitors such as meclofenamic acid have been shown to prevent tumor progression in both acute myeloid leukemia and glioblastoma in vivo models. However, current FTO inhibitors are unsuitable for clinical applications due to either poor target selectivity or poor pharmacokinetics. In this work, we describe the structure-based design, synthesis, and biochemical evaluation of a new class of FTO inhibitors. Rational design of 20 small molecules with low micromolar IC50's and specificity toward FTO over ALKBH5 identified two competitive inhibitors FTO-02 and FTO-04. Importantly, FTO-04 prevented neurosphere formation in patient-derived glioblastoma stem cells (GSCs) without inhibiting the growth of healthy neural stem cell-derived neurospheres. Finally, FTO-04 increased m6A and m6Am levels in GSCs consistent with FTO inhibition. These results support FTO-04 as a potential new lead for treatment of glioblastoma.

DOI: https://doi.org/10.1021/acschembio.0c00841
Int J Biol Sci. 2021 ;17(1): 271-284

The emerging roles of m6A modification in liver carcinogenesis.

Xue-Yin Pan, Cheng Huang, Jun Li.

  The 'epitranscriptome', a collective term for chemical modifications that influence the structure, metabolism, and functions of RNA, has recently emerged as vitally important for the regulation of gene expression. N6-methyladenosine (m6A), the most prevalent mammalian mRNA internal modification, has been demonstrated to have a pivotal role in almost all vital bioprocesses, such as stem cell self-renewal and differentiation, heat shock or DNA damage response, tissue development, and maternal-to-zygotic transition. Hepatocellular carcinoma (HCC) is prevalent worldwide with high morbidity and mortality because of late diagnosis at an advanced stage and lack of effective treatment strategies. Epigenetic modifications including DNA methylation and histone modification have been demonstrated to be crucial for liver carcinogenesis. However, the role and underlying molecular mechanism of m6A in liver carcinogenesis are mostly unknown. In this review, we summarize recent advances in the m6A region and how these new findings remodel our understanding of m6A regulation of gene expression. We also describe the influence of m6A modification on liver carcinoma and lipid metabolism to instigate further investigations of the role of m6A in liver biological diseases and its potential application in the development of therapeutic strategies.

Keywords:  Epitranscriptome; Hepatocellular Carcinoma (HCC); N6-methyladenosine

DOI:  https://doi.org/10.7150/ijbs.50003
Mol Oncol. 2021 Jan 07.

METTL3/YTHDF2 m6A axis accelerates colorectal carcinogenesis through epigenetically suppressing YPEL5.

Dan Zhou, Weiwei Tang, Yidan Xu, Yajie Xu, Binbin Xu, Shanshan Fu, Yanting Wang, Fangfang Chen, Yongxiong Chen, Yinshu Han, Gueyhorng Wang.

  N6-methyladenosine (m6A) has emerged as the most prevalent posttranscriptional modification on mRNA that contributes prominently to tumorigenesis. However, the specific function of m6A methyltransferase methyltransferase-like 3 (METTL3) in colorectal cancer (CRC) remains elusive. Herein, we explored the biological function of METTL3 in CRC progression. Clinically, METTL3 was frequently upregulated in CRC tissues, cell lines and plasma samples and its high expression predicted poor prognosis of CRC patients. Functionally, knockdown of METTL3 significantly repressed CRC cell proliferation and migration in vitro, while its overexpression accelerated CRC tumor formation and metastasis both in vitro and in vivo. Mechanistically, METTL3 epigenetically repressed YPEL5 in an m6A-YTHDF2 dependent manner by targeting the m6A site in the coding sequence region of the YPEL5 transcript. Moreover, overexpression of YPEL5 significantly reduced CCNB1 and PCNA expression. Collectively, we identified the pivotal role of METTL3-catalysed m6A modification in CRC tumorigenesis, wherein it facilitates CRC tumor growth and metastasis through suppressing YPEL5 expression in an m6A-YTHDF2 dependent manner, suggesting a promising strategy for the diagnosis and therapy of CRC.

Keywords:  Colorectal cancer; Metastasis; Prognostic biomarker; m6A modification

DOI:  https://doi.org/10.1002/1878-0261.12898
Genome Biol. 2021 Jan 05. 22(1): 17

N6-methyladenosine dynamics in neurodevelopment and aging, and its potential role in Alzheimer's disease.

Andrew M Shafik, Feiran Zhang, Zhenxing Guo, Qing Dai, Kinga Pajdzik, Yangping Li, Yunhee Kang, Bing Yao, Hao Wu, Chuan He, Emily G Allen, Ranhui Duan, Peng Jin.

   BACKGROUND: N6-methyladenosine (m6A) modification is known to impact many aspects of RNA metabolism, including mRNA stability and translation, and is highly prevalent in the brain.
RESULTS: We show that m6A modification displays temporal and spatial dynamics during neurodevelopment and aging. Genes that are temporally differentially methylated are more prone to have mRNA expression changes and affect many pathways associated with nervous system development. Furthermore, m6A shows a distinct tissue-specific methylation profile, which is most pronounced in the hypothalamus. Tissue-specific methylation is associated with an increase in mRNA expression and is associated with tissue-specific developmental processes. During the aging process, we observe significantly more m6A sites as age increases, in both mouse and human. We show a high level of overlap between mouse and human; however, humans at both young and old ages consistently show more m6A sites compared to mice. Differential m6A sites are found to be enriched in alternative untranslated regions of genes that affect aging-related pathways. These m6A sites are associated with a strong negative effect on mRNA expression. We also show that many Alzheimer-related transcripts exhibit decreased m6A methylation in a mouse model of Alzheimer's disease, which is correlated with reduced protein levels.
CONCLUSIONS: Our results suggest that m6A exerts a critical function in both early and late brain development in a spatio-temporal fashion. Furthermore, m6A controls protein levels of key genes involved in Alzheimer's disease-associated pathways, suggesting that m6A plays an important role in aging and neurodegenerative disease.

Keywords:  Aging; Alternative 3′UTR; Alzheimer’s; Epitranscriptomics; Neurodevelopment; Regulation of mRNA levels; Regulation of protein levels; m6A

DOI:  https://doi.org/10.1186/s13059-020-02249-z
Arch Toxicol. 2021 Jan 04.

Genetic variants in m6A regulators are associated with gastric cancer risk.

Xiaowei Wang, Dan Guan, Dafei Wang, Hanting Liu, Yanling Wu, Weida Gong, Mulong Du, Haiyan Chu, Jing Qian, Zhengdong Zhang.

  N6-methyladenosine (m6A) modification plays a vital regulatory role in tumorigenesis and development. In this study, we determined that the mRNA expression of IGF2BP1, IGF2BP2 and IGF2BP3, as the m6A modification genes, was significantly increased in gastric cancer (GC) tissues. Using a logistic regression model, we found that novel single-nucleotide polymorphism (SNP) rs9906944 C > T in IGF2BP1 was remarkably associated with a decreased risk of GC in discovery stage (odds ratio (OR) = 0.75, 95% confidence interval (95% CI): 0.60-0.93, P = 8.51 × 10-3). This finding was repeated in an independent Nanjing population (OR = 0.76, 95% CI: 0.59-0.98, P = 3.45 × 10-2). The combined analysis including 2900 GC cases and 3,536 controls confirmed the association between rs9906944 C > T and GC risk (OR = 0.75, 95% CI: 0.64-0.88, P = 5.76 × 10-4). Furthermore, we found that GC patients with higher IGF2BP1 mRNA expression level had prominent poorer overall survival (hazard ratio (HR) = 1.49, 95% CI: 1.16-1.91, logrank P = 1.50 × 10-3). For the first time, our findings suggested the importance of genetic variants in m6A regulators in GC and indicated that IGF2BP1 plays a crucial role in GC. Genetic variants in m6A modification genes may be used for GC risk prediction.

Keywords:  Gastric cancer; IGF2BP1; Molecular epidemiology; N6-methyladenosine; Susceptibility

DOI:  https://doi.org/10.1007/s00204-020-02958-1
Proc Natl Acad Sci U S A. 2021 Jan 19. pii: e2019455118. [Epub ahead of print]118(3):

Hepatitis B virus X protein recruits methyltransferases to affect cotranscriptional N6-methyladenosine modification of viral/host RNAs.

Geon-Woo Kim, Aleem Siddiqui.

  Chronic hepatitis B virus (HBV) infections are one of the leading causes of cirrhosis and hepatocellular carcinoma. N6-methyladenosine (m6A) modification of cellular and viral RNAs is the most prevalent internal modification that occurs cotranscriptionally. Previously, we reported the dual functional role of m6A modification of HBV transcripts in the viral life cycle. Here, we show that viral HBV X (HBx) protein is responsible for the m6A modifications of viral transcripts. HBV genomes defective in HBx failed to induce m6A modifications of HBV RNAs during infection/transfection, while ectopic expression of HBx restores m6A modifications of the viral RNAs but not the mutant HBx carrying the nuclear export signal. Using chromatin immunoprecipitation assays, we provide evidence that HBx and m6A methyltransferase complexes are localized on the HBV minichromosome to achieve cotranscriptional m6A modification of viral RNAs. HBx interacts with METTL3 and 14 to carry out methylation activity and also modestly stimulates their nuclear import. This role of HBx in mediating m6A modification also extends to host phosphatase and tensin homolog (PTEN) mRNA. This study provides insight into how a viral protein recruits RNA methylation machinery to m6A-modify RNAs.

Keywords:  METTL3/14; N6-methyladenosine modification; cotranscriptional modification; hepatitis B virus; hepatitis B virus X protein

DOI:  https://doi.org/10.1073/pnas.2019455118
Crit Rev Biochem Mol Biol. 2021 Jan 08. 1-21

Multifaceted regulation of translation by the epitranscriptomic modification N6-methyadenosine.

Xiao-Min Liu, Jun Zhou.

  Translation occurring on cytoplasmic mRNA is precisely governed at three consecutive stages, including initiation, elongation and termination. A growing body of evidence has revealed that an emerging epitranscriptomic code N6-methyadenosine (m6A), asymmetrically present in a large subset of coding and non-coding transcripts, is crucially required for mediating the translatomic stability. Through recruiting translation machinery proteins, serving as a physical barrier, or directing RNA structural rearrangement and mRNA looping formation, m6A has been decoded to modulate translational dynamics through potentially influencing the progress of different stages, thereby forming an additional layer of complexity to the regulation of translation. In this review, we summarize the current understanding of how m6A guides mRNA translation under normal and stress conditions, highlighting the divergent molecular mechanisms of multifarious regulation of m6A-mediated translation.

Keywords:  N6-methyadenosine; coding region; mRNA looping; translation regulation; untranslated region

DOI:  https://doi.org/10.1080/10409238.2020.1869174
Analyst. 2021 Jan 04.

Detection of locus-specific N6-methyladenosine modification based on Ag+-assisted ligation and supersandwich signal amplification.

Yanxia Wang, Ji Zheng, Chengjie Duan, Jin Jiao, Youjing Gong, Hai Shi, Yang Xiang.

Emerging evidence reveals that the epitranscriptomic mark N6-methyladenosine (m6A) plays vital roles in organisms, including gene regulation and disease progression. However, developing sensitive methods to detect m6A modification, especially the identification of m6A marks at the single-site level, remains a challenge. Therefore, based on target-specific triggered signal amplification, we developed a highly sensitive electrochemical method to detect site-specific m6A modifications in DNA. In this work, the m6A site in DNA can restrict the ligation assisted by Ag+, and this restriction effect can activate the subsequent strand displacement reaction and hybridization chain reaction (HCR), thus achieving signal amplification from the m6A site, and finally realizing high sensitivity analysis of m6A methylation. Benefiting from the high specificity of base pairs and the extremely weak binding affinity between Ag+ and m6A, the proposed method was used for not only detecting the target DNA with a putative m6A site, but also identifying m6A marks at the single-site level in DNA. In addition, this study does not rely on antibodies and radiolabeling, so it has the advantage of cost-effectiveness. Therefore, we believe that the proposed strategy may provide a new perspective for methylation research, which can be used to test more clinical samples in further research.

DOI: https://doi.org/10.1039/d0an02214d
Genome Biol. 2021 Jan 07. 22(1): 22

Quantitative profiling of N6-methyladenosine at single-base resolution in stem-differentiating xylem of Populus trichocarpa using Nanopore direct RNA sequencing.

Yubang Gao, Xuqing Liu, Bizhi Wu, Huihui Wang, Feihu Xi, Markus V Kohnen, Anireddy S N Reddy, Lianfeng Gu.

  There are no comprehensive methods to identify N6-methyladenosine (m6A) at single-base resolution for every single transcript, which is necessary for the estimation of m6A abundance. We develop a new pipeline called Nanom6A for the identification and quantification of m6A modification at single-base resolution using Nanopore direct RNA sequencing based on an XGBoost model. We validate our method using methylated RNA immunoprecipitation sequencing (MeRIP-Seq) and m6A-sensitive RNA-endoribonuclease-facilitated sequencing (m6A-REF-seq), confirming high accuracy. Using this method, we provide a transcriptome-wide quantification of m6A modification in stem-differentiating xylem and reveal that different alternative polyadenylation (APA) usage shows a different ratio of m6A.

Keywords:  Alternative polyadenylation; N 6-Methyladenosine; Nanopore direct RNA sequencing; Populus trichocarpa; Stem-differentiating xylem

DOI:  https://doi.org/10.1186/s13059-020-02241-7
Metabolism. 2021 Jan 05. pii: S0026-0495(21)00002-0. [Epub ahead of print] 154702

METTL3 is required for maintaining β-cell function.

Xinzhi Li, Yuze Jiang, Xu Sun, Yongsen Wu, Zheng Chen.

  N6-methyladenosine (m6A) mRNA methylation has been shown to regulate obesity and type 2 diabetes. However, whether METTL3, the key methyltransferase for m6A mRNA methylation, regulates β-cell failure in diabetes has not been fully explored. Here, we show that METTL3 is downregulated under the inflammatory and oxidative stress conditions, and islet β-cell-specific deletion of Mettl3 induces β-cell failure and hyperglycemia, which is likely due to decreased m6A modification and reduced expression of insulin secretion-related genes. Overall, METTL3 might be a potential drug target for the treatment of β-cell failure in diabetes.

Keywords:  Cell death; Hyperglycemia; Insulin secretion; Islet β cells; METTL3; m(6)A

DOI:  https://doi.org/10.1016/j.metabol.2021.154702
Theranostics. 2021 ;11(3): 1100-1114

IGF2BP1 overexpression stabilizes PEG10 mRNA in an m6A-dependent manner and promotes endometrial cancer progression.

Lin Zhang, Yicong Wan, Zihan Zhang, Yi Jiang, Zhiyue Gu, Xiaoling Ma, Sipei Nie, Jing Yang, Jinghe Lang, Wenjun Cheng, Lan Zhu.

  Rationale: N6-methyladenosine (m6A) mRNA methylation is the most abundant chemical posttranscriptional modification in mRNA and is involved in the regulation of a number of biological processes. Insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) has recently been reported as having the capacity to recognize m6A sites in mRNA and plays a role in regulating mRNA metabolization. However, it is unclear which genes IGF2BP1 targets to identify m6A sites and what are their respective functions in endometrial cancer (EC). Methods: Quantitative PCR, western blot and immunohistochemistry were used to measure IGF2BP1 expression in EC cell lines and tissues. Xenograft experiments were performed to examine the in vivo role of IGF2BP1 in EC cell growth. RNA-binding protein immunoprecipitation sequencing, methylated RNA-binding protein immunoprecipitation sequencing and RNA-sequencing were also conducted to identify potential IGF2BP1 targets involved in EC regulation. Co-immunoprecipitation and mass spectrometry were used to identify IGF2BP1-interacting proteins. Results: IGF2BP1 expression increased in EC, and high expression of this protein correlated with poor prognosis. IGF2BP1 overexpression/knockdown can promote (and inhibit) cell proliferation and regulate the tumor cell cycle and cancer progression, both in vivo and in vitro. Mechanistically, IGF2BP1 can recognize m6A sites in the 3' untranslated region (3'UTR) of Paternally Expressed Gene 10 (PEG10) mRNA and recruits polyadenylate-binding protein 1 (PABPC1) to enhance PEG10 mRNA stability, which consequently promotes PEG10 protein expression. Additionally, it would appear that a large number of PEG10 proteins bind p16 and p18 gene promoter sequences, thereby repressing expression and accelerating the cell cycle. Conclusion: This investigation found that IGF2BP1 has a crucial role in the m6A-dependent regulatory mechanism for endometrial cancer. This study provides new insights into our understanding of disease progression and provides another potential route for understanding biological functions.

Keywords:  IGF2BP1; N6-methyladenosine; PEG10; cell cycle; endometrial cancer

DOI:  https://doi.org/10.7150/thno.49345
Biomed Res Int. 2020 ;2020 8826456

Gene Alterations of N6-Methyladenosine (m6A) Regulators in Colorectal Cancer: A TCGA Database Study.

Qian Zhang, Yuping Cai, Vadim Kurbatov, Sajid A Khan, Lingeng Lu, Yawei Zhang, Caroline H Johnson.

N6-methyladenosine (m6A) plays an important role in many cancers. However, few studies have examined the role of m6A in colorectal CRC. To examine the effect of m6A on CRC, we studied the genome of 591 CRC cases from The Cancer Genome Atlas (TCGA). The relationship between the messenger RNA (mRNA) expression, copy number variation (CNVs), and mutations of m6A "Writers," "Readers," and "Erasers," prognosis, immune cell infiltration, and genetic mutations in CRC cases were analyzed. CNVs and mutations were found in thirteen m6A regulators. As expected, gain and amplification of m6A regulators increased the mRNA expression of these regulators, while deletion led to reduction in the mRNA expression. Moreover, CNVs and mutation of these regulators were significantly associated with APC, TP53, and microsatellite instability (MSI) status (p < 0.001, p < 0.001, and p = 0.029, respectively). CNVs of m6A regulators also correlated with inferred immune cell infiltration in CRC tissues, especially in colon tissues. Additionally, alterations of RBM15, YTHDF2, YTHDC1, YTHDC2, and METTL14 genes were related to the worse overall survival and disease-free survival (DFS) of CRC patients. Specifically, the deletion status of "Writers" was also correlated to the DFS of CRC patients (p = 0.02). Gene set enrichment analysis found that FTO was involved in mRNA 3' end processing, polyubiquitin binding, and RNA polymerase promoter elongation, while YTHDC1 was related to interferon-alpha and gamma response. In conclusion, a novel relationship was identified between CNVs and mutations of m6A regulators with prognosis and inferred immune function of CRC. These findings will improve the understanding of the relationship of m6A in CRC.

DOI: https://doi.org/10.1155/2020/8826456
Biosci Rep. 2021 Jan 04. pii: BSR20200842. [Epub ahead of print]

Omeprazole improves chemosensitivity of gastric cancer cells by m6A demethylase FTO-mediated activation of mTORC1 and DDIT3 upregulation.

Shui Tu Feng, Guo Qin Qiu, Li Hong Yang, Li Hua Feng, Xin Fan, Fang Ren, Kai da Huang, Yi de Chen.

  The curative effect for patients with advanced gastric cancer is still unsatisfactory. Proton pump inhibitors could be a promising treatment strategy which could sensitize gastric cancer cells to antitumor drugs further, however, the underlying molecular mechanism remains to be further elucidated. In this research. it was found that omeprazole pretreatment could enhance the inhibitory effect of 5-Fu, DDP and TAX on gastric cancer cells. Interestingly, omeprazole pretreatment enhanced the total m6A level of cells due to the decreased FTO. TCGA analysis showed that FTO expression is upregulated in GC tissues and is negatively correlated with disease free survival of GC patients. It was also found that FTO inhibition induced by omeprazole enhanced the activation of mTORC1 signal pathway which inhibited the pro-survival autophagy so as to improve the antitumor efficiency of chemotherapeutic drugs on GC cells. Meanwhile, transcript level of DDIT3, which is an apoptosis-related tumor suppressor gene downstream of mTORC1 was regulated by omeprazole induced FTO silence through an m6A-dependent mechanism. This study, for the first time, found that m6A modification and its eraser FTO may play a role in the improvement of chemosensitivity mediated by proton pump inhibitor omeprazole.

Keywords:  DDIT3; FTO; Omeprazole; autophagy; gastric cancer; m6A modification

DOI:  https://doi.org/10.1042/BSR20200842
Nat Commun. 2021 Jan 08. 12(1): 177

EGFR/SRC/ERK-stabilized YTHDF2 promotes cholesterol dysregulation and invasive growth of glioblastoma.

Runping Fang, Xin Chen, Sicong Zhang, Hui Shi, Youqiong Ye, Hailing Shi, Zhongyu Zou, Peng Li, Qing Guo, Li Ma, Chuan He, Suyun Huang.

Glioblastoma (GBM) is the most common type of adult malignant brain tumor, but its molecular mechanisms are not well understood. In addition, the knowledge of the disease-associated expression and function of YTHDF2 remains very limited. Here, we show that YTHDF2 overexpression clinically correlates with poor glioma patient prognosis. EGFR that is constitutively activated in the majority of GBM causes YTHDF2 overexpression through the EGFR/SRC/ERK pathway. EGFR/SRC/ERK signaling phosphorylates YTHDF2 serine39 and threonine381, thereby stabilizes YTHDF2 protein. YTHDF2 is required for GBM cell proliferation, invasion, and tumorigenesis. YTHDF2 facilitates m6A-dependent mRNA decay of LXRA and HIVEP2, which impacts the glioma patient survival. YTHDF2 promotes tumorigenesis of GBM cells, largely through the downregulation of LXRα and HIVEP2. Furthermore, YTHDF2 inhibits LXRα-dependent cholesterol homeostasis in GBM cells. Together, our findings extend the landscape of EGFR downstream circuit, uncover the function of YTHDF2 in GBM tumorigenesis, and highlight an essential role of RNA m6A methylation in cholesterol homeostasis.

DOI: https://doi.org/10.1038/s41467-020-20379-7
J Cell Mol Med. 2021 Jan 05.

Expression and prognostic characteristics of m5 C regulators in low-grade glioma.

Xiaozhi Li, Yutong Meng.

  Glioma is the most common intracranial malignant tumour. A clear diagnosis and molecular targeted therapy are of great significance for improving the survival time and quality of life of patients with low-grade glioma. 5-methylcytosine methylation is one of the ways of RNA modification, but there are limited studies on the role of m5 C methylation of low-grade glioma. Single-nucleotide variant, RNA expression matrix and corresponding clinical data of low-grade glioma came from public database. The single-nucleotide variant and expression of m5 C regulators were estimated. A prognostic model based on m5 C regulators was constructed by Cox regression. Potential functions of these molecules were assessed by gene set enrichment analysis. DNMT3A mutation was the most frequent among the m5 C regulators in low-grade glioma. NSUN3, TET2, TRDMT1, ALYREF, DNMT3B, DNMT1, NOP2 and NSUN2 were up-regulated. One prognostic model was constructed which had a strong predictive power for the overall survival of low-grade glioma. We studied the expression and prognostic characteristics of m5 C regulators in low-grade glioma, supplied biomarkers for the diagnosis and prognosis and provided the foundation for the study of the pathogenesis of low-grade glioma.

Keywords:  RNA methylation; low-grade glioma; m5C; prognosis

DOI:  https://doi.org/10.1111/jcmm.16221
EBioMedicine. 2021 Jan 05. pii: S2352-3964(20)30571-5. [Epub ahead of print]63 103195

The RNA methyltransferase NSUN6 suppresses pancreatic cancer development by regulating cell proliferation.

Ruimeng Yang, Xing Liang, Hui Wang, Miaomiao Guo, Hui Shen, Yongheng Shi, Qiang Liu, Yongwei Sun, Linhua Yang, Ming Zhan.

   BACKGROUND: Pancreatic cancer (PC) is one of the most lethal solid malignancies in the world due to its excessive cell proliferation and aggressive metastatic features. Emerging evidences revealed the importance of posttranscriptional modifications of RNAs in PC progression. However, knowledge about the 5-methylcytosine (m5C) RNA modification in PC is still extremely limited. In this study, we attempted to explore the expression changes and clinical significances of 12 known m5C-related genes among PC patients.
METHODS: A total of 362 normal and 382 tumor specimens from PC patients were examined for candidate m5C-related gene and protein expression by using quantitative PCR (qPCR) and immunohistochemistry (IHC). The proliferation rate of PC cells was detected by MTS assay. Xenograft mouse models were used to assess the role of NSUN6 in PC tumor formation.
FINDINGS: Through analyzing the four Gene Expression Omnibus (GEO) databases, six m5C-related genes shown significant and consistent alterations were selected for further examination in our 3 independent PC cohorts. Finally, we identified the reduction of NSUN6 as a common feature of all PC sample sets examined. NSUN6 expression correlated with clinicopathologic parameters including T stage, and Ki67+ cell rate. Further assessing the transcriptional profiles of 50 PC tissues, we found biological processes associated with cell proliferation like cell cycle and G2M checkpoint were enriched in NSUN6 lower expression group. Helped by in vitro PC cell lines and in vivo xenograft mouse models, we confirmed the role of NSUN6 in regulating cell proliferation and PC tumor growth. Last but also importantly, we also show the good performance of NSUN6 in evaluating tumor recurrence and survival among PC patients.
INTERPRETATION: Our data suggested that NSUN6 is an important factor involved in regulating cell proliferation of PC, and highlights the potential of novel m5C-based clinical modalities as a therapeutic approach in PC patients.
FUNDING: This study was supported by the National Natural Science Foundation of China (Grant Nos. 81803014, 81802424, and 81802911).

Keywords:  5-methylcytosine; Cell proliferation; NSUN6; Pancreatic cancer

DOI:  https://doi.org/10.1016/j.ebiom.2020.103195
DNA Cell Biol. 2021 Jan 08.

Molecular Characteristics of N1-Methyladenosine Regulators and Their Correlation with Overall Cancer Survival.

Juan Li, Chunting Zhang, Xin Yuan, Yuan Cao.

  N1-methyladenosine (m1A) is a prevalent RNA modification widely affecting RNA structural stability, folding, and interactions with proteins. Recently, there have been increasing reports on the roles of m1A regulators in tumors. However, their mechanisms and clinical relevance remain unclear. This study systematically evaluates the epigenetic characteristics and clinical relevance of m1A regulators using bioinformatic methods. Our results show widespread gene expression changes for m1A regulators, which are related to the activation and inhibition of carcinogenic pathways and overall patient survival. Collectively, this investigation provides new insights into assessing tumor prognosis and targeted therapy.

Keywords:  N1-methyladenosine; overall survival; pan-cancer

DOI:  https://doi.org/10.1089/dna.2020.6214
Cell Death Dis. 2021 Jan 04. 12(1): 32

METTL14-regulated PI3K/Akt signaling pathway via PTEN affects HDAC5-mediated epithelial-mesenchymal transition of renal tubular cells in diabetic kidney disease.

Zhaoxia Xu, Keqi Jia, Hui Wang, Feng Gao, Song Zhao, Fan Li, Jun Hao.

Histone deacetylase 5 (HDAC5) belongs to class II HDAC subfamily and is reported to be increased in the kidneys of diabetic patients and animals. However, little is known about its function and the exact mechanism in diabetic kidney disease (DKD). Here, we found that HDAC5 was located in renal glomeruli and tubular cells, and significantly upregulated in diabetic mice and UUO mice, especially in renal tubular cells and interstitium. Knockdown of HDAC5 ameliorated high glucose-induced epithelial-mesenchymal transition (EMT) of HK2 cells, indicated in the increased E-cadherin and decreased α-SMA, via the downregulation of TGF-β1. Furthermore, HDAC5 expression was regulated by PI3K/Akt signaling pathway and inhibition of PI3K/Akt pathway by LY294002 treatment or Akt phosphorylation mutation reduced HDAC5 and TGF-β1 expression in vitro high glucose-cultured HK2 cells. Again, high glucose stimulation downregulated total m6A RNA methylation level of HK2 cells. Then, m6A demethylase inhibitor MA2 treatment decreased Akt phosphorylation, HDAC5, and TGF-β1 expression in high glucose-cultured HK2 cells. In addition, m6A modification-associated methylase METTL3 and METTL14 were decreased by high glucose at the levels of mRNA and protein. METTL14 not METTL3 overexpression led to PI3K/Akt pathway inactivation in high glucose-treated HK2 cells by enhancing PTEN, followed by HDAC5 and TGF-β1 expression downregulation. Finally, in vivo HDACs inhibitor TSA treatment alleviated extracellular matrix accumulation in kidneys of diabetic mice, accompanied with HDAC5, TGF-β1, and α-SMA expression downregulation. These above data suggest that METTL14-regulated PI3K/Akt signaling pathway via PTEN affected HDAC5-mediated EMT of renal tubular cells in diabetic kidney disease.

DOI: https://doi.org/10.1038/s41419-020-03312-0