bims-rimeca Biomed News
on RNA methylation in cancer
Issue of 2022–07–24
eleven papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics
  1. PLAA suppresses ovarian cancer metastasis via METTL3-mediated m6A modification of TRPC3 mRNA.
  2. The N6-methyladenosine writer WTAP contributes to the induction of immune tolerance post kidney transplantation by targeting regulatory T cells.
  3. RNA m1A methylation regulates glycolysis of cancer cells through modulating ATP5D.
  4. Mutual regulation between N6-methyladenosine (m6A) modification and circular RNAs in cancer: impacts on therapeutic resistance.
  5. Alternative splicing of METTL3 explains apparently METTL3-independent m6A modifications in mRNA.
  6. N6-methyladenosine modification-mediated mRNA metabolism is essential for human pancreatic lineage specification and islet organogenesis.
  7. Extracellular vesicles derived from human umbilical cord mesenchymal stem cells alleviate osteoarthritis of the knee in mice model by interacting with METTL3 to reduce m6A of NLRP3 in macrophage.
  8. Reactivity-dependent profiling of RNA 5-methylcytidine dioxygenases.
  9. Effects of the m6Am methyltransferase PCIF1 on cell proliferation and survival in gliomas.
  10. CFDP1 promotes hepatocellular carcinoma progression through activating NEDD4/PTEN/PI3K/AKT signaling pathway.
  11. Transcriptome Profiling of N7-Methylguanosine Modification of Messenger RNA in Drug-Resistant Acute Myeloid Leukemia.
  1. Oncogene. 2022 Jul 22.
    PLAA suppresses ovarian cancer metastasis via METTL3-mediated m6A modification of TRPC3 mRNA.
    Zhangjin Shen, Lingkai Gu, Yuwan Liu, Lingfang Wang, Jiawei Zhu, Sangsang Tang, Xinyi Wei, Jiaying Wang, Songfa Zhang, Xinyu Wang, Xiaodong Cheng, Xing Xie, Weiguo Lu.
      Wide metastasis contributes to a high death rate in ovarian cancer, and understanding of the molecular mechanism helps to find effective targets for metastatic ovarian cancer therapy. It has been found that phospholipase A2-activating protein (PLAA) is inactivated in some cancers, but its role in cancer metastasis remains unknown. Here, we found that PLAA was significantly downregulated in ovarian cancer highly metastatic cell lines and patients, and the low expression of PLAA was associated with poorer prognosis and high-risk clinicopathological features of patients. PLAA inhibited the migration and invasion of ovarian cancer cells and metastasis of transplanted tumor in the orthotopic xenograft mouse model. Meanwhile, PLAA inhibited metastasis of ovarian cancer by inhibiting transient receptor potential channel canonical 3 (TRPC3)-mediated the intracellular Ca2+ level. Mechanistically, PLAA inhibited methyltransferase-like 3 (METTL3) expression through the ubiquitin-mediated degradation, and METTL3 stabilized TRPC3 mRNA expression via N6-methyladenosine (m6A) modification. Our study verified the function and mechanism of the PLAA-METTL3-TRPC3 axis involved in ovarian cancer metastasis, with a view to providing a potential therapeutic approach for ovarian cancer.
    DOI:  https://doi.org/10.1038/s41388-022-02411-w
  2. Lab Invest. 2022 Jul 21.
    The N6-methyladenosine writer WTAP contributes to the induction of immune tolerance post kidney transplantation by targeting regulatory T cells.
    Zhigang Wang, Yuanbo Qi, Yonghua Feng, Hongen Xu, Junxiang Wang, Luyu Zhang, Jie Zhang, Xinyue Hou, Guiwen Feng, Wenjun Shang.
      N6-methyladenosine (m6A) modification is involved in diverse immunoregulation, while the relationship between m6A modification and immune tolerance post kidney transplantation remains unclear. Expression of Wilms tumor 1-associating protein (WTAP), an m6A writer, was firstly detected in tolerant kidney transplant recipients (TOL). Then the role of WTAP on regulatory T (Treg) cell differentiation and function in CD4+ T cells from kidney transplant recipients with immune rejection (IR) was investigated. The potential target of WTAP and effect of WTAP on immune tolerance in vivo were subsequently verified. WTAP was upregulated in CD4+ T cells of TOL and positively correlated with Treg cell proportion. In vitro, WTAP overexpression promoted Treg cell differentiation and enhanced Treg cell-mediated suppression toward naïve T cells. Forkhead box other 1 (Foxo1) was identified as a target of WTAP. WTAP enhanced m6A modification of Foxo1 mRNA in coding sequence (CDS) region, leading to up-regulation of Foxo1. Overexpression of m6A demethylase removed the effect of WTAP overexpression, while Foxo1 overexpression reversed these effects. WTAP overexpression alleviated allograft rejection in model mice, as evidenced by reduced inflammatory response and increased Treg population. Our study suggests that WTAP plays a positive role in induction of immune tolerance post kidney transplant by promoting Treg cell differentiation and function.
    DOI:  https://doi.org/10.1038/s41374-022-00811-w
  3. Proc Natl Acad Sci U S A. 2022 Jul 12. 119(28): e2119038119
    RNA m1A methylation regulates glycolysis of cancer cells through modulating ATP5D.
    Yingmin Wu, Zhuojia Chen, Guoyou Xie, Haisheng Zhang, Zhaotong Wang, Jiawang Zhou, Feng Chen, Jiexin Li, Likun Chen, Hongxin Niu, Hongsheng Wang.
      Studies on biological functions of RNA modifications such as N6-methyladenosine (m6A) in mRNA have sprung up in recent years, while the roles of N1-methyladenosine (m1A) in cancer progression remain largely unknown. We find m1A demethylase ALKBH3 can regulate the glycolysis of cancer cells via a demethylation activity dependent manner. Specifically, sequencing and functional studies confirm that ATP5D, one of the most important subunit of adenosine 5'-triphosphate synthase, is involved in m1A demethylase ALKBH3-regulated glycolysis of cancer cells. The m1A modified A71 at the exon 1 of ATP5D negatively regulates its translation elongation via increasing the binding with YTHDF1/eRF1 complex, which facilitates the release of message RNA (mRNA) from ribosome complex. m1A also regulates mRNA stability of E2F1, which directly binds with ATP5D promoter to initiate its transcription. Targeted specific demethylation of ATP5D m1A by dm1ACRISPR system can significantly increase the expression of ATP5D and glycolysis of cancer cells. In vivo data confirm the roles of m1A/ATP5D in tumor growth and cancer progression. Our study reveals a crosstalk of mRNA m1A modification and cell metabolism, which expands the understanding of such interplays that are essential for cancer therapeutic application.
    Keywords:  ATP5D; cancer cell; m1A; metabolism
    DOI:  https://doi.org/10.1073/pnas.2119038119
  4. Mol Cancer. 2022 07 18. 21(1): 148
    Mutual regulation between N6-methyladenosine (m6A) modification and circular RNAs in cancer: impacts on therapeutic resistance.
    Hong Lin, Yuxi Wang, Pinghan Wang, Fangyi Long, Ting Wang.
      The resistance of tumor cells to therapy severely impairs the efficacy of treatment, leading to recurrence and metastasis of various cancers. Clarifying the underlying mechanisms of therapeutic resistance may provide new strategies for overcoming cancer resistance. N6-methyladenosine (m6A) is the most prevalent RNA modification in eukaryotes, and is involved in the regulation of RNA splicing, translation, transport, degradation, stability and processing, thus affecting several physiological processes and cancer progression. As a novel type of multifunctional non-coding RNAs (ncRNAs), circular RNAs (circRNAs) have been demonstrated to play vital roles in anticancer therapy. Currently, accumulating studies have revealed the mutual regulation of m6A modification and circRNAs, and their interaction can further influence the sensitivity of cancer treatment. In this review, we mainly summarized the recent advances of m6A modification and circRNAs in the modulation of cancer therapeutic resistance, as well as their interplay and potential mechanisms, providing promising insights and future directions in reversal of therapeutic resistance in cancer.
    Keywords:  Cancer; Circular RNA; Interplay; N6-methyladenosine; Therapeutic resistance
    DOI:  https://doi.org/10.1186/s12943-022-01620-x
  5. PLoS Biol. 2022 Jul;20(7): e3001683
    Alternative splicing of METTL3 explains apparently METTL3-independent m6A modifications in mRNA.
    Hui Xian Poh, Aashiq H Mirza, Brian F Pickering, Samie R Jaffrey.
      N6-methyladenosine (m6A) is a highly prevalent mRNA modification that promotes degradation of transcripts encoding proteins that have roles in cell development, differentiation, and other pathways. METTL3 is the major methyltransferase that catalyzes the formation of m6A in mRNA. As 30% to 80% of m6A can remain in mRNA after METTL3 depletion by CRISPR/Cas9-based methods, other enzymes are thought to catalyze a sizable fraction of m6A. Here, we reexamined the source of m6A in the mRNA transcriptome. We characterized mouse embryonic stem cell lines that continue to have m6A in their mRNA after Mettl3 knockout. We show that these cells express alternatively spliced Mettl3 transcript isoforms that bypass the CRISPR/Cas9 mutations and produce functionally active methyltransferases. We similarly show that other reported METTL3 knockout cell lines express altered METTL3 proteins. We find that gene dependency datasets show that most cell lines fail to proliferate after METTL3 deletion, suggesting that reported METTL3 knockout cell lines express altered METTL3 proteins rather than have full knockout. Finally, we reassessed METTL3's role in synthesizing m6A using an exon 4 deletion of Mettl3 and found that METTL3 is responsible for >95% of m6A in mRNA. Overall, these studies suggest that METTL3 is responsible for the vast majority of m6A in the transcriptome, and that remaining m6A in putative METTL3 knockout cell lines is due to the expression of altered but functional METTL3 isoforms.
    DOI:  https://doi.org/10.1371/journal.pbio.3001683
  6. Nat Commun. 2022 Jul 18. 13(1): 4148
    N6-methyladenosine modification-mediated mRNA metabolism is essential for human pancreatic lineage specification and islet organogenesis.
    Xiaojie Ma, Jie Cao, Ziyu Zhou, Yunkun Lu, Qin Li, Yan Jin, Guo Chen, Weiyun Wang, Wenyan Ge, Xi Chen, Zhensheng Hu, Xiao Shu, Qian Deng, Jiaqi Pu, Chengzhen Liang, Junfen Fu, Jianzhao Liu, Saiyong Zhu.
      Pancreatic differentiation from human pluripotent stem cells (hPSCs) provides promising avenues for investigating development and treating diseases. N6-methyladenosine (m6A) is the most prevalent internal messenger RNA (mRNA) modification and plays pivotal roles in regulation of mRNA metabolism, while its functions remain elusive. Here, we profile the dynamic landscapes of m6A transcriptome-wide during pancreatic differentiation. Next, we generate knockout hPSC lines of the major m6A demethylase ALKBH5, and find that ALKBH5 plays significant regulatory roles in pancreatic organogenesis. Mechanistic studies reveal that ALKBH5 deficiency reduces the mRNA stability of key pancreatic transcription factors in an m6A and YTHDF2-dependent manner. We further identify that ALKBH5 cofactor α-ketoglutarate can be applied to enhance differentiation. Collectively, our findings identify ALKBH5 as an essential regulator of pancreatic differentiation and highlight that m6A modification-mediated mRNA metabolism presents an important layer of regulation during cell-fate specification and holds great potentials for translational applications.
    DOI:  https://doi.org/10.1038/s41467-022-31698-2
  7. Stem Cell Res Ther. 2022 Jul 16. 13(1): 322
    Extracellular vesicles derived from human umbilical cord mesenchymal stem cells alleviate osteoarthritis of the knee in mice model by interacting with METTL3 to reduce m6A of NLRP3 in macrophage.
    Hao Zhou, Xun Shen, Chen Yan, Wu Xiong, Zemeng Ma, Zhenggang Tan, Jinwen Wang, Yao Li, Jiuxiang Liu, Ao Duan, Feng Liu.
       BACKGROUND: Osteoarthritis (OA) is a prevalent degenerative joint disease that not only significantly impairs the quality of life of middle-aged and elderly individuals but also imposes a significant financial burden on patients and society. Due to their significant biological properties, extracellular vesicles (EVs) have steadily received great attention in OA treatment. This study aimed to investigate the influence of EVs on chondrocyte proliferation, migration, and apoptosis and their protective efficacy against OA in mice.
    METHODS: The protective impact of EVs derived from human umbilical cord mesenchymal stem cells (hucMSCs-EVs) on OA in mice was investigated by establishing a mouse OA model by surgically destabilizing the medial meniscus (DMM). Human chondrocytes were isolated from the cartilage of patients undergoing total knee arthroplasty (TKA) and cultured with THP-1 cells to mimic the in vivo inflammatory environment. Levels of inflammatory factors were then determined in different groups, and the impacts of EVs on chondrocyte proliferation, migration, apoptosis, and cartilage extracellular matrix (ECM) metabolism were explored. N6-methyladenosine (m6A) level of mRNA and methyltransferase-like 3 (METTL3) protein expression in the cells was also measured in addition to microRNA analysis to elucidate the molecular mechanism of exosomal therapy.
    RESULTS: The results indicated that hucMSCs-EVs slowed OA progression, decreased osteophyte production, increased COL2A1 and Aggrecan expression, and inhibited ADAMTS5 and MMP13 overexpression in the knee joint of mice via decreasing pro-inflammatory factor secretion. The in vitro cell line analysis revealed that EVs enhanced chondrocyte proliferation and migration while inhibiting apoptosis. METTL3 is responsible for these protective effects. Further investigations revealed that EVs decreased the m6A level of NLRP3 mRNA following miR-1208 targeted binding to METTL3, resulting in decreased inflammatory factor release and preventing OA progression.
    CONCLUSION: This study concluded that hucMSCs-EVs inhibited the secretion of pro-inflammatory factors and the degradation of cartilage ECM after lowering the m6A level of NLRP3 mRNA with miR-1208 targeting combined with METTL3, thereby alleviating OA progression in mice and providing a novel therapy for clinical OA treatment.
    Keywords:  Extracellular vesicles (EVs); Human umbilical cord mesenchymal stem cells; METTL3; NLRP3; Osteoarthritis; m6A; miR-1208
    DOI:  https://doi.org/10.1186/s13287-022-03005-9
  8. Nat Commun. 2022 Jul 19. 13(1): 4176
    Reactivity-dependent profiling of RNA 5-methylcytidine dioxygenases.
    A Emilia Arguello, Ang Li, Xuemeng Sun, Tanner W Eggert, Elisabeth Mairhofer, Ralph E Kleiner.
      Epitranscriptomic RNA modifications can regulate fundamental biological processes, but we lack approaches to map modification sites and probe writer enzymes. Here we present a chemoproteomic strategy to characterize RNA 5-methylcytidine (m5C) dioxygenase enzymes in their native context based upon metabolic labeling and activity-based crosslinking with 5-ethynylcytidine (5-EC). We profile m5C dioxygenases in human cells including ALKBH1 and TET2 and show that ALKBH1 is the major hm5C- and f5C-forming enzyme in RNA. Further, we map ALKBH1 modification sites transcriptome-wide using 5-EC-iCLIP and ARP-based sequencing to identify ALKBH1-dependent m5C oxidation in a variety of tRNAs and mRNAs and analyze ALKBH1 substrate specificity in vitro. We also apply targeted pyridine borane-mediated sequencing to measure f5C sites on select tRNA. Finally, we show that f5C at the wobble position of tRNA-Leu-CAA plays a role in decoding Leu codons under stress. Our work provides powerful chemical approaches for studying RNA m5C dioxygenases and mapping oxidative m5C modifications and reveals the existence of novel epitranscriptomic pathways for regulating RNA function.
    DOI:  https://doi.org/10.1038/s41467-022-31876-2
  9. Biochim Biophys Acta Mol Basis Dis. 2022 Jul 19. pii: S0925-4439(22)00169-7. [Epub ahead of print] 166498
    Effects of the m6Am methyltransferase PCIF1 on cell proliferation and survival in gliomas.
    Shangfeng Gao, Junbo Zhou, Zhiyuan Hu, Shicheng Zhang, Yue Wu, Preethi Priyanka Musunuru, Tong Zhang, Liquan Yang, Xiang Luo, Jin Bai, Qingming Meng, Rutong Yu.
       BACKGROUND: Previous studies have suggested an important role for N6-methyladenosine (m6A) modification in the proliferation of glioma cells. N6, 2'-O-dimethyladenosine (m6Am) is another methylated form affecting the fate and function of most RNA. PCIF1 has recently been identified as the sole m6Am methyltransferase in mammalian mRNA. However, it remains unknown about the role of PCIF1 in the growth and survival of glioma cells.
    METHODS: We constructed glioma cell lines that stably downregulated/upregulated PCIF1, established intracranial xenograft models using these cell lines, and employed the following methods for investigations: CCK-8, EdU, colony formation, flow cytometry, qRT-PCR, Western blot, and immunohistochemistry.
    FINDINGS: Downregulating PCIF1 promoted glioma cell proliferation, while overexpressing PCIF1 showed the opposite effects. Overexpression of PCIF1 blocked cell cycle progression and induced apoptosis in glioma cells, which was further confirmed by alterations in the expression of cell checkpoint proteins and apoptotic markers. Interestingly, disruption of PCIF1 methyltransferase activity slightly reversed the effect of PCIF1 overexpression on cell proliferation, but had no significant reversal effects on cell cycle progression or apoptosis. Knockdown of PCIF1 promoted the growth of gliomas, while overexpressing PCIF1 inhibited tumor growth and prolonged the survival time of tumor-bearing mice. In addition, the mRNA and protein levels of PCIF1 were gradually decreased with the increase of WHO grade in glioma tissues, but there was no significant correlation with patient survival.
    INTERPRETATION: These results indicated that PCIF1 played a suppressing role in glioma growth and survival, which may not entirely depend on its methyltransferase activity.
    Keywords:  Apoptosis; Glioblastoma; Methyltransferase; PCIF1; Proliferation
    DOI:  https://doi.org/10.1016/j.bbadis.2022.166498
  10. Cancer Med. 2022 Jul 21.
    CFDP1 promotes hepatocellular carcinoma progression through activating NEDD4/PTEN/PI3K/AKT signaling pathway.
    Yan Zhou, Jiannan Qiu, Siyuan Liu, Peng Wang, Ding Ma, Guang Zhang, Yin Cao, Lili Hu, Zhongxia Wang, Junhua Wu, Chunping Jiang.
       BACKGROUND AND AIMS: It is being increasingly reported that the Cranio Facial Development Protein 1 (CFDP1) plays a significant role in the onset and progression of tumors. Nonetheless, the underlying mechanisms associated with CFDP1 that contribute to hepatocellular carcinoma (HCC) and the specific biological role of CFDP1 remain vague.
    METHODS: The Gene Expression Omnibus (GEO) database was analyzed to obtain the gene expression profiles as well as the matching clinical data of HCC patients. The gene co-expression network was developed by means of weighted gene co-expression network analysis (WGCNA) to screen for possible biomarkers that could be used for the purpose of predicting prognosis. The Cancer Genome Atlas (TCGA) and Gene Expression Profile Interaction Analysis (GEPIA) databases were used to assess the relationship between survival and expression. In addition, we identified the underlying mechanism associated with CFDP1 by analyzing the KEGG pathway database, applying the GSEA and GeneCards analysis method. We performed a sequence of experiments (in vivo and in vitro) for the purpose of investigating the specific function of CFDP1 in liver cancer.
    RESULTS: The obtained results revealed high expression of CFDP1 in HCC tissues and cell lines. A positive correlation between the overexpression of CFDP1 and the adverse clinicopathological features was observed. Moreover, we observed that the low recurrence-free survival and overall survival were associated with CFDP1 overexpression. In addition, GeneCards and GSEA analysis showed that CFDP1 may interact with NEDD4 and participate in PTEN regulation. Meanwhile, CFDP1 can promote the malignant development of liver cancer in vivo and in vitro. The western blotting technique was also employed so as to examine the samples, and the findings demonstrated that CFDP1 enhanced the malignancy of HCC via the NEDD4-mediated PTEN/PI3K/AKT pathway.
    CONCLUSION: We highlighted that CFDP1 played an oncogenic role in HCC and was identified as a possible clinical prognostic factor and a potential novel therapeutic target for HCC.
    Keywords:  CFDP1; NEDD4; PI3K/AKT signaling pathway; hepatocellular carcinoma
    DOI:  https://doi.org/10.1002/cam4.4919
  11. Front Oncol. 2022 ;12 926296
    Transcriptome Profiling of N7-Methylguanosine Modification of Messenger RNA in Drug-Resistant Acute Myeloid Leukemia.
    Bing Zhang, Dong Li, Ran Wang.
      Acute myeloid leukemia (AML) is an aggressive hematological tumor caused by the malignant transformation of myeloid progenitor cells. Although intensive chemotherapy leads to an initial therapeutic response, relapse due to drug resistance remains a significant challenge. In recent years, accumulating evidence has suggested that post-transcriptional methylation modifications are strongly associated with tumorigenesis. However, the mRNA profile of m7G modification in AML and its role in drug-resistant AML are unknown. In this study, we used MeRIP-seq technology to establish the first transcriptome-wide m7G methylome profile for AML and drug-resistant AML cells, and differences in m7G between the two groups were analyzed. In addition, bioinformatics analysis was conducted to explore the function of m7G-specific methylated transcripts. We found significant differences in m7G mRNA modification between AML and drug-resistant AML cells. Furthermore, bioinformatics analysis revealed that differential m7G-modified mRNAs were associated with a wide range of cellular functions. Importantly, down-methylated m7G modification was significantly enriched in ABC transporter-related mRNAs, which are widely recognized to play a key role in multidrug resistance. Our results provide new insights into a novel function of m7G methylation in drug resistance progression of AML.
    Keywords:  N7-methylguanosine(m7G); acute myeloid leukemia (AML); bioinformatics analysis; drug-resistant; messenger RNA (mRNA)
    DOI:  https://doi.org/10.3389/fonc.2022.926296
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