bims-rimeca Biomed News
on RNA methylation in cancer
Issue of 2021–05–30
seven papers selected by
Sk Ramiz Islam, Saha Institute of Nuclear Physics
  1. Post-translational modification of RNA m6A demethylase ALKBH5 regulates ROS-induced DNA damage response.
  2. The Role of RNA Methyltransferase METTL3 in Hepatocellular Carcinoma: Results and Perspectives.
  3. Could partial nonstarch polysaccharides ameliorate cancer by altering m6A RNA methylation in hosts through intestinal microbiota?
  4. Identification of m6A methyltransferase-related lncRNA signature for predicting immunotherapy and prognosis in patients with hepatocellular carcinoma.
  5. Quantitative Proteomic Analysis Revealed Broad Roles of N6-Methyladenosine in Heat Shock Response.
  6. Loss of m6A demethylase ALKBH5 promotes post-ischemic angiogenesis via post-transcriptional stabilization of WNT5A.
  7. ALKBH5-modified HMGB1-STING Activation Contributes to Radiation Induced Liver Disease Via Innate Immune Response.
  1. Nucleic Acids Res. 2021 May 28. pii: gkab415. [Epub ahead of print]
    Post-translational modification of RNA m6A demethylase ALKBH5 regulates ROS-induced DNA damage response.
    Fang Yu, Jiangbo Wei, Xiaolong Cui, Chunjie Yu, Wei Ni, Jörg Bungert, Lizi Wu, Chuan He, Zhijian Qian.
      Faithful genome integrity maintenance plays an essential role in cell survival. Here, we identify the RNA demethylase ALKBH5 as a key regulator that protects cells from DNA damage and apoptosis during reactive oxygen species (ROS)-induced stress. We find that ROS significantly induces global mRNA N6-methyladenosine (m6A) levels by modulating ALKBH5 post-translational modifications (PTMs), leading to the rapid and efficient induction of thousands of genes involved in a variety of biological processes including DNA damage repair. Mechanistically, ROS promotes ALKBH5 SUMOylation through activating ERK/JNK signaling, leading to inhibition of ALKBH5 m6A demethylase activity by blocking substrate accessibility. Moreover, ERK/JNK/ALKBH5-PTMs/m6A axis is activated by ROS in hematopoietic stem/progenitor cells (HSPCs) in vivo in mice, suggesting a physiological role of this molecular pathway in the maintenance of genome stability in HSPCs. Together, our study uncovers a molecular mechanism involving ALKBH5 PTMs and increased mRNA m6A levels that protect genomic integrity of cells in response to ROS.
    DOI:  https://doi.org/10.1093/nar/gkab415
  2. Front Cell Dev Biol. 2021 ;9 674919
    The Role of RNA Methyltransferase METTL3 in Hepatocellular Carcinoma: Results and Perspectives.
    Fan Pan, Xin-Rong Lin, Li-Ping Hao, Xiao-Yuan Chu, Hai-Jun Wan, Rui Wang.
      Hepatocellular carcinoma (HCC) is the 6th most prevalent cancer and the 4th leading cause of cancer-related death worldwide. Mechanisms explaining the carcinogenesis of HCC are not clear yet. In recent years, rapid development of N6-methyladenosine (m6A) modification provides a fresh approach to disclosing this mystery. As the most prevalent mRNA modification in eukaryotes, m6A modification is capable to post-transcriptionally affect RNA splicing, stability, and translation, thus participating in a variety of biological and pathological processes including cell proliferation, apoptosis, tumor invasion and metastasis. METTL3 has been recognized as a pivotal methyltransferase and essential to the performance of m6A modification. METTL3 can regulate RNA expression in a m6A-dependent manner and contribute to the carcinogenesis, tumor progression, and drug resistance of HCC. In the present review, we are going to make a clear summary of the known roles of METTL3 in HCC, and explicitly narrate the potential mechanisms for these roles.
    Keywords:  Hepatocellular carcinoma; METTL3; RNA modification; drug-resistance; m6A
    DOI:  https://doi.org/10.3389/fcell.2021.674919
  3. Crit Rev Food Sci Nutr. 2021 May 26. 1-16
    Could partial nonstarch polysaccharides ameliorate cancer by altering m6A RNA methylation in hosts through intestinal microbiota?
    Jianming Luo, Juntong Yu, Xichun Peng.
      There is a growing scientific view that the improvement of cancer by nonstarch polysaccharides (NSPs) is mediated by intestinal microbiota. Intestinal bacteria affect the supply of methyl donor substances and influence N6-methyladenosine (m6A) RNA methylation. As one of the epigenetic/epitranscriptomic modifications, m6A RNA methylation is closely related to the initiation and progression of cancers. This review summarizes the cancer-improving effects of NSPs through modulation of intestinal microbiota. It also summarizes the relationship between intestinal bacteria and the supply of methyl donor substances. Moreover, it also provides a summary of the effects of m6A RNA methylation on various types of cancer. The proposed mechanism is that, dietary consumed NSPs are utilized by specific intestinal bacteria and further reshape the microbial structure. Methyl donor substances will be directly or indirectly generated by the reshaped-microbiota, and affect the m6A RNA methylation of cancer-related and pro-carcinogenic inflammatory cytokine genes. Therefore, NSPs may change the m6A RNA methylation by affecting the methyl donor supply produced by intestinal microbiota and ameliorate cancer. This review discussed the possibility of cancer improvement of bioactive NSPs achieved by impacting RNA methylation via the intestinal microbiota, and it will offer new insights for the application of NSPs toward specific cancer prevention.
    Keywords:  Cancer; intestinal microbiota; m6A RNA methylation; methyl donor; nonstarch polysaccharides
    DOI:  https://doi.org/10.1080/10408398.2021.1927975
  4. Biosci Rep. 2021 May 24. pii: BSR20210760. [Epub ahead of print]
    Identification of m6A methyltransferase-related lncRNA signature for predicting immunotherapy and prognosis in patients with hepatocellular carcinoma.
    Lili Li, Rongrong Xie, Guangrong Lu.
      N6-methyladenosine (m6A) methyltransferase has been shown to be an oncogene in a variety of cancers. Nevertheless, the relationship between the long non-coding RNAs (lncRNAs) and hepatocellular carcinoma (HCC) remains elusive. We integrated the gene expression data of 371 HCC and 50 normal tissues from The Cancer Genome Atlas (TCGA) database. Differentially expressed protein-coding genes (DE-PCGs)/lncRNAs (DE-lncRs) analysis and univariate regression & Kaplan-Meier (K-M) analysis were performed to identify m6A methyltransferase‑related lncRNAs. Three prognostic lncRNAs were selected by univariate and LASSO Cox regression analyses to construct the m6A methyltransferase-related lncRNA signature. Multivariate Cox regression analyses illustrated that this signature was an independent prognostic factor for overall survival (OS) prediction. The Gene Set Enrichment Analysis (GSEA) suggested that the m6A methyltransferase-related lncRNAs were involved in the immune-related biological processes and pathways. Besides, we discovered that the lncRNAs signature was correlated with the tumor microenvironment (TME) and the expression of critical immune checkpoints. Tumor Immune Dysfunction and Exclusion (TIDE) analysis revealed that the lncRNAs could predict the clinical response to immunotherapy. Our study had originated a prognostic signature for HCC based on the potential prognostic m6A methyltransferase-related lncRNAs. This study had deepened the understanding of the TME status of HCC patients and laid a theoretical foundation for the choice of immunotherapy.
    Keywords:  Hepatocellular carcinoma; Immune cells infiltration; Immune checkpoint; LncRNAs; N6-methyladenosine
    DOI:  https://doi.org/10.1042/BSR20210760
  5. J Proteome Res. 2021 May 27.
    Quantitative Proteomic Analysis Revealed Broad Roles of N6-Methyladenosine in Heat Shock Response.
    Weili Miao, Yen-Yu Yang, Yinsheng Wang.
      As optimum temperature is essential for all living organisms, heat shock represents a challenging problem for their survival. Therefore, cellular response to heat shock is among the most extensively investigated stress response pathways; however, how the human proteome responds to heat shock has not been comprehensively investigated. In this study, we employed stable isotope labeling by amino acids in cell culture (SILAC), together with liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis, to fulfill an in-depth analysis of the alterations in the human proteome in M14 human melanoma cells in response to heat shock stress. We found that, after heat shock, 284 and 278 out of the 4319 quantified proteins were with substantially diminished and elevated expressions, respectively. We also examined the alterations in human kinome after heat shock by using our recently developed targeted proteomic method relying on parallel-reaction monitoring. Our results showed that the expression levels of 11 and 22 kinase proteins were increased and decreased, respectively, by at least 1.5-fold upon heat shock. By interrogating publicly available RNA-seq and m6A sequencing data, we observed that the elevated expression of more than 30 proteins, including CHEK1 and CCND3 kinases, could occur via an m6A-mediated mechanism. Furthermore, our results from single-base elongation and ligation-based quantitative polymerase chain reaction (qPCR) amplification (SELECT) and luciferase reporter assays revealed that heat shock gave rise to elevated m6A levels at A280 and A286 sites in the 5'-untranslated region of HSPH1 mRNA, thereby leading to increased translation of HSPH1 protein. Together, our discovery and targeted proteomic methods revealed the reprogramming of human proteome and kinome upon heat shock stress and provided insights into cellular responses toward heat shock stress.
    Keywords:  N6-methyladenosine; epitranscriptomics; heat shock; heat shock proteins; kinase; kinome; parallel-reaction monitoring; quantitative proteomics
    DOI:  https://doi.org/10.1021/acs.jproteome.1c00191
  6. Clin Transl Med. 2021 May;11(5): e402
    Loss of m6A demethylase ALKBH5 promotes post-ischemic angiogenesis via post-transcriptional stabilization of WNT5A.
    Yongchao Zhao, Jingjing Hu, Xiaolei Sun, Kun Yang, Lebing Yang, Lingqiu Kong, Beijian Zhang, Fuhai Li, Chaofu Li, Bei Shi, Kai Hu, Aijun Sun, Junbo Ge.
       BACKGROUND: Post-ischemic angiogenesis is critical for blood flow recovery and ischemic tissue repair. N6-methyladenosine (m6A) plays essential roles in numerous biological processes. However, the impact and connected mechanism of m6A on post-ischemic angiogenesis are not fully understood.
    METHODS: AlkB homolog 5 (ALKBH5) was screened out among several methyltransferases and demethylases involved in dynamic m6A regulation. Cardiac microvascular endothelial cells (CMECs) angiogenesis and WNT family member 5A (WNT5A) stability were analyzed upon ALKBH5 overexpression with adenovirus or knockdown with small interfering RNAs in vitro. The blood flow recovery, capillary, and small artery densities were evaluated in adeno-associated virus (AAV)-ALKBH5 overexpression or ALKBH5 knockout (KO) mice in a hind-limb ischemia model. The same experiments were conducted to explore the translational value of transient silencing of ALKBH5 with adenovirus.
    RESULTS: ALKBH5 was significantly upregulated in hypoxic CMECs and led to a global decrease of m6A level. ALKBH5 overexpression further reduced m6A level in normoxic and hypoxic CMECs, impaired proliferation, migration, and tube formation only in hypoxic CMECs. Conversely, ALKBH5 knockdown preserved m6A levels and promoted angiogenic phenotypes in hypoxic but not in normoxic CMECs. Mechanistically, ALKBH5 regulated WNT5A expression through post-transcriptional mRNA modulation in an m6A-dependent manner, which decreased its stability and subsequently impeded angiogenesis in hypoxic CMECs. Furthermore, ALKBH5 overexpression hindered blood flow recovery and reduced CD31 and alpha-smooth muscle actin expression in hind-limb ischemia mice. As expected, ALKBH5-KO mice exhibited improved blood flow recovery, increased capillary, and small artery densities after hind-limb ischemia, and similar beneficial effects were observed in mice with transient adenoviral ALKBH5 gene silencing.
    CONCLUSION: We demonstrate that ALKBH5 is a negative regulator of post-ischemic angiogenesis via post-transcriptional modulation and destabilization of WNT5A mRNA in an m6A-dependent manner. Targeting ALKBH5 may be a potential therapeutic option for ischemic diseases, including peripheral artery disease.
    Keywords:  AlkB homolog 5; N6-methyladenosine; peripheral arterial disease; post-ischemic angiogenesis
    DOI:  https://doi.org/10.1002/ctm2.402
  7. Int J Radiat Oncol Biol Phys. 2021 May 24. pii: S0360-3016(21)00657-X. [Epub ahead of print]
    ALKBH5-modified HMGB1-STING Activation Contributes to Radiation Induced Liver Disease Via Innate Immune Response.
    Genwen Chen, Qianqian Zhao, Baoying Yuan, Biao Wang, Yang Zhang, Zongjuan Li, Shisuo Du, Zhaochong Zeng.
       PURPOSE: Radiation therapy (RT), vital for treatment of primary liver cancer, comes with unavoidable liver injury, which limits its implementation. N6-methyladenosine (m6A) methylation is involved in many molecular functions. However, its role in radiation-induced liver diseases (RILD) remains unknown. Here, we intend to investigate the role of m6A methylation in RILD.
    METHODS AND MATERIALS: Methylated RNA-immunoprecipitation sequencing (MeRIP-seq) and RNA transcriptome sequencing (RNA-seq) were used to reveal the methylation pattern of human hepatic stellate cells (HSCs) exposed to irradiation. C3H/HeN mice and STING-deficient mice underwent X-ray irradiation of 24 Gy in three fractions. The m6A methylation of HMGB1 transcript was validated using MeRIP, RIP, luciferase assays and mRNA decay assay.
    RESULTS: Human HSCs showed significant differences in methylation patterns after 8 Gy of X-ray irradiation. Irradiation recruited AlkB Homolog 5 (ALKBH5) to demethylate m6A residues in the 3' untranslated region (UTR) of High-Mobility Group Box 1 (HMGB1), which resulted in activation of STING-IRF3 signaling. Changes in transcription of the 3'UTR of HMGB1 occurred after knockdown of ALKBH5, which were eliminated after m6A residue mutation. Strikingly, ALKBH5 deficiency or HMGB1 silencing both attenuated type I interferon production and decreased hepatocyte apoptosis. In vivo depletion of ALKBH5 abolished upregulation of HMGB1-mediated STING signaling and decreased liver inflammation, which was consistent with STING-/- mice treated with irradiation. Notably, YTHDF2, a m6A reader protein, directly bound to HMGB1 m6A-modified sites and promoted its degradation.
    CONCLUSIONS: ALKBH5-dependent HMGB1 expression mediates STING-IRF3 innate immune response in RILD.
    Keywords:  ALKBH5; STING signaling; innate immune response; irradiation; m6A methylation
    DOI:  https://doi.org/10.1016/j.ijrobp.2021.05.115
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