bims-rimeca Biomed News
on RNA methylation in cancer
Issue of 2022‒10‒23
forty-four papers selected by
Sk Ramiz Islam
Saha Institute of Nuclear Physics
  1. FTO-mediated autophagy promotes progression of clear cell renal cell carcinoma via regulating SIK2 mRNA stability.
  2. METTL14 promotes migration and invasion of choroidal melanoma by targeting RUNX2 mRNA via m6A modification.
  3. N6-methyladenosine of Socs1 modulates macrophage inflammatory response in different stiffness environments.
  4. N6-methyladenosine modification in trophoblasts promotes circSETD2 expression, inhibits miR-181a-5p, and elevates MCL1 transcription to reduce apoptosis of trophoblasts.
  5. mRNAs encoding neurodevelopmental regulators have equal N6-methyladenosine stoichiometry in Drosophila neuroblasts and neurons.
  6. RNA m6A reader IGF2BP3 promotes metastasis of triple-negative breast cancer via SLIT2 repression.
  7. RNA m6 A methylation in cancer.
  8. Comprehensive analysis of N6-methyladenosine-related lncRNAs reveals distinct hepatocellular carcinoma subtypes with immunotherapeutic implications.
  9. Biological functions of RNA modification patterns that define tumor microenvironment and survival outcomes in testicular germ cell tumors.
  10. RNA-m6A modification of HDGF mediated by Mettl3 aggravates the progression of atherosclerosis by regulating macrophages polarization via energy metabolism reprogramming.
  11. LDHA is a prognostic biomarker on the immune response in pancreatic adenocarcinoma and associated with m6A modification.
  12. Emerging role of mRNA methylation in regulating the hallmarks of cancer.
  13. Biological roles of adenine methylation in RNA.
  14. Silencing of YTHDF1 Attenuates Cerebral Stroke by Inducing PTEN Degradation and Activating the PTEN/AKT/mTOR Pathway.
  15. Gene signature of m6A RNA regulators in diagnosis, prognosis, treatment, and immune microenvironment for cervical cancer.
  16. m6A-binding protein IGF2BP1 promotes the malignant phenotypes of lung adenocarcinoma.
  17. The m6A-methylated mRNA pattern and the activation of the Wnt signaling pathway under the hyper-m6A-modifying condition in the keloid.
  18. METTL3-mediated N6-methyladenosine modification and HDAC5/YY1 promote IFFO1 downregulation in tumor development and chemo-resistance.
  19. LCAT1 is an oncogenic LncRNA by stabilizing the IGF2BP2-CDC6 axis.
  20. Identification of miR-30c-5p as a tumor suppressor by targeting the m6 A reader HNRNPA2B1 in ovarian cancer.
  21. Transcriptome-wide m6A methylome analysis uncovered the changes of m6A modification in oral pre-malignant cells compared with normal oral epithelial cells.
  22. METTL3 modulates chromatin and transcription dynamics during cell fate transition.
  23. Relationship between M6A methylation regulator and prognosis in patients with hepatocellular carcinoma after transcatheter arterial chemoembolization.
  24. Integrative analysis of m3C associated genes reveals METTL2A as a potential oncogene in breast Cancer.
  25. Identification and verification of IGFBP3 and YTHDC1 as biomarkers associated with immune infiltration and mitophagy in hypertrophic cardiomyopathy.
  26. Crosstalk among N6-methyladenosine modification and RNAs in central nervous system injuries.
  27. Comprehensive analysis of m7G modification patterns based on potential m7G regulators and tumor microenvironment infiltration characterization in lung adenocarcinoma.
  28. An Analysis of BMP1 Associated with m6A Modification and Immune Infiltration in Pancancer.
  29. The emerging importance of METTL5-mediated ribosomal RNA methylation.
  30. Endothelial CYP2J2 overexpression restores the BRB via METTL3-mediated ANXA1 upregulation.
  31. Cancer-Associated Fibroblasts Hinder Lung Squamous Cell Carcinoma Oxidative Stress-Induced Apoptosis via METTL3 Mediated m6A Methylation of COL10A1.
  32. Identification of N6-methylandenosine related lncRNA signatures for predicting the prognosis and therapy response in colorectal cancer patients.
  33. Expression pattern and clinical value of Key RNA methylation modification regulators in ischemic stroke.
  34. METTL3 mediates chemoresistance by enhancing AML homing and engraftment via ITGA4.
  35. Study on the prognosis, immune and drug resistance of m6A-related genes in lung cancer.
  36. PCBP2 Reduced Oxidative Stress-Induced Apoptosis in Glioma through cGAS/STING Pathway by METTL3-Mediated m6A Modification.
  37. Quantitative and single nucleotide RNA m6 A detection technology boosts clinical research based on tissue and cell free RNA modification.
  38. Mammalian N1-adenosine PARylation is a reversible DNA modification.
  39. Detection technologies for RNA modifications.
  40. Identification of a novel m5C/m6A-related gene signature for predicting prognosis and immunotherapy efficacy in lung adenocarcinoma.
  41. The 5-Hydroxymethylcytosine Landscape of Prostate Cancer.
  42. SP1-induced lncRNA MCF2L-AS1 promotes cisplatin resistance in ovarian cancer by regulating IGF2BP1/IGF2/MEK/ERK axis.
  43. Photo-Facilitated Detection and Sequencing of 5-Formylcytidine RNA.
  44. YTHDC2 Promotes Malignant Phenotypes of Breast Cancer Cells.
  1. Int J Biol Sci. 2022 ;18(15): 5943-5962
    FTO-mediated autophagy promotes progression of clear cell renal cell carcinoma via regulating SIK2 mRNA stability.
    Yawei Xu, Jingcheng Zhou, Lei Li, Wuping Yang, Zedan Zhang, Kenan Zhang, Kaifang Ma, Haibiao Xie, Zheng Zhang, Lin Cai, Yanqing Gong, Kan Gong.
      The progression of clear cell renal cell carcinoma (ccRCC) remains a major challenge in clinical practice, and elucidation of the molecular drivers of malignancy progression is critical for the development of effective therapeutic targets. Recent studies have demonstrated that N6-methyladenosine (m6A) is the most abundant modification of eukaryotic mRNA and plays a key role in tumorigenesis and progression. However, the biological roles and underlying mechanisms of m6A-mediated autophagy in cancers especially in ccRCC remain poorly elucidated. m6A dot blot assay, m6A RNA methylation assay kit and immunofluorescence analysis were used to profile m6A levels in tissue samples and their correlation with autophagic flux. Expression patterns and clinical significance of fat mass and obesity-associated protein (FTO) were determined through bioinformatics analysis, real-time PCR, western blotting, immunohistochemistry. RNA-seq, MeRIP-seq, MeRIP-qRT-PCR, RIP-qRT-PCR, transmission electron microscopy, immunofluorescence analysis and luciferase reporter assay were used to investigate the underlying mechanism of the FTO-autophagy axis. The role of FTO and autophagy in ccRCC progression was evaluated both in vitro and in vivo. Here we found that m6A modification was suppressed and closely related to autophagic flux in ccRCC. Elevated FTO was inhibited by rapamycin, whereas silencing FTO enhanced autophagic flux and impaired ccRCC growth and metastasis. SIK2 was identified as a functional target of m6A-mediated autophagy, thereby prompting FTO to play a conserved and important role in inhibiting autophagy and promoting tumorigenesis through an m6A-IGF2BP2 dependent mechanism. Moreover, the small molecule inhibitor FB23-2 targeting FTO inhibited tumor growth and prolonged survival in the patient-derived xenograft (PDX) model mice, suggesting that FTO is a potential effective therapeutic target for ccRCC. Our findings uncovered the crucial role of FTO/autophagy/SIK2 axis in modulating the progression of ccRCC, suggesting that FTO may serve as a valuable prognostic biomarker and promising therapeutic target in ccRCC.
    Keywords:  FTO; SIK2; autophagy; ccRCC
    DOI:  https://doi.org/10.7150/ijbs.77774
  2. J Cell Mol Med. 2022 Oct 20.
    METTL14 promotes migration and invasion of choroidal melanoma by targeting RUNX2 mRNA via m6A modification.
    Xi Zhang, Xiaonan Zhang, Tengyue Liu, Zhe Zhang, Chiyuan Piao, Hong Ning.
      The modification of N6-methyladenosine is involved in the progression of various cancers. This study aimed to clarify its regulatory mechanism in the pathogenesis of choroidal melanoma. Expression of methyltransferase-like 14 in choroidal melanoma or normal choroidal tissues was determined by Western blot and immunohistochemistry. The impacts of methyltransferase-like 14 on invasion and migration of choroidal melanoma cells were determined using functional and animal experiments. The interaction between methyltransferase-like 14 and its downstream target was identified by methylated RNA immunoprecipitation and a dual-luciferase reporter assay. Additionally, Wnt/β-catenin signalling pathway was evaluated by Western blot. Methyltransferase-like 14 was upregulated in choroidal melanoma compared to the normal choroidal tissues. Overexpression or knockdown of methyltransferase-like 14 enhanced or inhibited the invasion and migration of choroidal melanoma cells, respectively, both in vivo and in vitro. Methyltransferase-like 14 directly targeted downstream runt-related transcription factor 2 mRNA, depending on N6-methyladenosine. Additionally, the Wnt/β-catenin signalling pathway was activated by methyltransferase-like 14 in choroidal melanoma cells. Our study identified a novel RNA regulatory mechanism in which runt-related transcription factor 2 was upregulated by enhanced expression of methyltransferase-like 14 via N6-methyladenosine modification, thus facilitating migration and invasion of choroidal melanoma cells.
    Keywords:  N6-methyladenosine; Wnt/β-catenin signalling; choroidal melanoma; methyltransferase-like 14; runt-related transcription factor 2
    DOI:  https://doi.org/10.1111/jcmm.17577
  3. Int J Biol Sci. 2022 ;18(15): 5753-5769
    N6-methyladenosine of Socs1 modulates macrophage inflammatory response in different stiffness environments.
    Zhekai Hu, Yuqing Li, Weihao Yuan, Lijian Jin, Wai Keung Leung, Chengfei Zhang, Yanqi Yang.
      Macrophages exhibit diverse functions within various tissues during the inflammatory response, and the physical properties of tissues also modulate the characteristics of macrophages. However, the underlying N6-methyladenosine (m6A)-associated molecular mechanisms remain unclear. Accordingly, we examined the potential role of m6A in macrophage activation and stiffness sensing. Intriguingly, we found that the macrophage inflammatory response and global levels of m6A were stiffness-dependent and that this was due to mechanically loosening the chromatin and epigenetic modification (H3K36me2 and HDAC3). In addition, we targeted suppressor of cytokine signalling 1 (Socs1) m6A methylation in a stiffness-dependent manner by screening the sequencing data and found that a higher stiffness hydrogel activated Jak-STAT and NFκB signalling and suppressed Fto gene expression. Next, by using the CRISPR/Cas9 system to knockout the FTO gene in macrophages, we demonstrated that FTO affects the stiffness-controlled macrophage inflammatory response by sustaining the negative feedback generated by SOCS1. Finally, we determined that the m6A reader YTHDF1 binds Socs1 mRNA and thereby maintains expression of SOCS1. Our results suggest that the FTO/Socs1/YTHDF1 regulatory axis is vital to the stiffness-controlled macrophage inflammatory response and that the deletion of FTO affects the negative feedback control exerted by SOCS1. Our findings increase understanding of the regulatory mechanisms involved in macrophage activation and the control of inflammation.
    Keywords:  FTO; Hydrogel stiffness; SOCS1; inflammatory response; m6A
    DOI:  https://doi.org/10.7150/ijbs.74196
  4. Environ Toxicol. 2022 Oct 19.
    N6-methyladenosine modification in trophoblasts promotes circSETD2 expression, inhibits miR-181a-5p, and elevates MCL1 transcription to reduce apoptosis of trophoblasts.
    Yajun Xia, Dan Wang, Hongbo Guan, Ying Wang, Guiyu Song.
      Preeclampsia (PE) is an obstetric disorder. N6-methyladenosine (m6A) modification is related to PE trophoblast biological behaviors. This study explored the mechanism of m6A-modified circSETD2 in trophoblast biological behaviors. Chorionic trophoblast apoptosis and circSETD2 expression in PE rat models were detected. HTR8/SVneo cells were induced by CoCl2 to establish PE trophoblast models. circSETD2 was silenced or overexpressed to evaluate its effect on cell proliferation, invasion, and apoptosis. m6A level of circSETD2 in trophoblasts was changed by pcDNA3.1-METTL3 and pcDNA3.1-FTO. The targeting relations among miR-181a-5p, circSETD2, and MCL1 were verified by dual-luciferase assay. miR-181a-5p and MCL1 expressions were interfered with to confirm the effect of m6A-modified circSETD2. m6A methylation level was changed in PE rats for in vivo validation. PE rats showed diminished circSETD2 expression and increased apoptosis index. circSETD2 overexpression promoted trophoblast proliferation and invasion, and reduced apoptosis. METTL3 overexpression increased total m6A, circSETD2 m6A, and circSETD2 levels. m6A modification mediated circSETD2 upregulation. circSETD2 was a sponge of miR-181a-5p to elevate MCL1 transcription. miR-181a-5p overexpression or MCL1 silencing annulled the role of m6A-modified circSETD2. circSETD2 inhibition negated suppression of METTL3 overexpression on chorionic trophoblast apoptosis in vivo. Collectively, m6A modification of circSETD2 suppressed miR-181a-5p and increased MCL1 transcription, thus regulating trophoblasts.
    Keywords:  MCL1; apoptosis; circSETD2; m6A modification; miR-181a-5p; preeclampsia; proliferation; trophoblast
    DOI:  https://doi.org/10.1002/tox.23683
  5. Neural Dev. 2022 Oct 15. 17(1): 9
    mRNAs encoding neurodevelopmental regulators have equal N6-methyladenosine stoichiometry in Drosophila neuroblasts and neurons.
    Josephine D Sami, Robert C Spitale, Michael D Cleary.
      N6-methyladenosine (m6A) is the most prevalent internal mRNA modification in metazoans and is particularly abundant in the central nervous system. The extent to which m6A is dynamically regulated and whether m6A contributes to cell type-specific mRNA metabolism in the nervous system, however, is largely unknown. To address these knowledge gaps, we mapped m6A and measured mRNA decay in neural progenitors (neuroblasts) and neurons of the Drosophila melanogaster larval brain. We identified 867 m6A targets; 233 of these are novel and preferentially encode regulators of neuroblast proliferation, cell fate-specification and synaptogenesis. Comparison of the neuroblast and neuron m6A transcriptomes revealed that m6A stoichiometry is largely uniform; we did not find evidence of neuroblast-specific or neuron-specific m6A modification. While m6A stoichiometry is constant, m6A targets are significantly less stable in neuroblasts than in neurons, potentially due to m6A-independent stabilization in neurons. We used in vivo quantitative imaging of m6A target proteins in Mettl3 methyltransferase null brains and Ythdf m6A reader overexpressing brains to assay metabolic effects of m6A. Target protein levels decreased in Mettl3 null brains and increased in Ythdf overexpressing brains, supporting a previously proposed model in which m6A enhances translation of target mRNAs. We conclude that m6A does not directly regulate mRNA stability during Drosophila neurogenesis but is rather deposited on neurodevelopmental transcripts that have intrinsic low stability in order to augment protein output.
    DOI:  https://doi.org/10.1186/s13064-022-00166-4
  6. FASEB J. 2022 Nov;36(11): e22618
    RNA m6A reader IGF2BP3 promotes metastasis of triple-negative breast cancer via SLIT2 repression.
    Tongtong Jiang, Xinyi He, Zhining Zhao, Xiao Zhang, Ting Wang, Lintao Jia.
      Triple-negative breast cancer (TNBC) is a group of fatal malignancies characterized by high metastatic capacity, the underlying mechanisms of which remain largely elusive. We have found here that insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3) is highly expressed in TNBC and correlates clinically with distant metastasis-free survival of TNBC patients. IGF2BP3 promotes the migration and invasion capabilities of TNBC cells dependent upon cellular RNA N6-methyladenosine (m6A) modification. Mechanistically, IGF2BP3 binds to and destabilizes m6A-methylated mRNA of the extracellular matrix glycoprotein, SLIT2, impairs its downstream signaling via the cognate receptor ROBO1, and consequently triggers the activation of canonical PI3K/AKT and MEK/ERK pathways. The IGF2BP3/SLIT2 axis is critically involved in the regulation of TNBC metastasis in vivo. These findings shed light into the regulatory network of distant metastasis of breast cancer and provide rationale for targeting the m6A machinery in the treatment of TNBC.
    Keywords:  IGF2BP; N6-methyladenosine (m6A); RNA modification; SLIT2; breast cancer; metastasis
    DOI:  https://doi.org/10.1096/fj.202200751RR
  7. Mol Oncol. 2022 Oct 19.
    RNA m6 A methylation in cancer.
    Zhaotong Wang, Jiawang Zhou, Haisheng Zhang, Lichen Ge, Jiexin Li, Hongsheng Wang.
      N6 -methyladenosine (m6 A) is one of the most abundant internal modifications in eukaryotic messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs). It is a reversible and dynamic RNA modification that has been observed in both internal coding segments and untranslated regions. Studies indicate that m6 A modifications play important roles in translation, RNA splicing, export, degradation, and ncRNA processing control. In this review, we focus on the profiles and biological functions of RNA m6 A methylation on both mRNAs and ncRNAs. The dynamic modification of m6 A and its potential roles in cancer development are discussed. Moreover, we discuss the possibility of m6 A modifications serving as potential biomarkers for cancer diagnosis and targets for therapy.
    Keywords:  cancers; m6A; m6A modulators; mRNA; ncRNA; therapy
    DOI:  https://doi.org/10.1002/1878-0261.13326
  8. Am J Transl Res. 2022 ;14(9): 6504-6520
    Comprehensive analysis of N6-methyladenosine-related lncRNAs reveals distinct hepatocellular carcinoma subtypes with immunotherapeutic implications.
    Xiaodong Xie, Hongyin Liang, Qing Ruan, Xiao Ma, Chuan Xie, Zhulin Luo, Lijun Tang, Long Cheng, Tao Wang.
      Accumulating studies have demonstrated critical roles of N6-methyladenosine (m6A) modification and long noncoding RNAs (lncRNAs) in the biological processes leading to occurrence, development and chemoresistance of cancers. However, the specific identities and functional roles of lncRNAs associated with m6A modification in hepatocellular carcinoma (HCC) remain elusive. In this study, eighty-two prognostic m6A-related lncRNAs (m6A-LncRNAs) were identified in HCC datasets. Patients with HCC were classified into three subtypes (C1, C2 and C3) based on the expression of the m6A-LncRNAs. The three subtypes showed significant differences in clinical features, immune and stromal infiltration signatures, and immunotherapy sensitivity. Subclass C1 was notable for high immune and stromal cell infiltration and active immune responses, low serum α-fetoprotein (AFP) levels and high sensitivity to immune checkpoint inhibitors (ICIs). Subclass C2 showed high metabolic activities and absence of immune infiltration with favorable prognosis. Subclass C3 was associated with an exhausted immune environment, high serum AFP and poor prognosis. Notably, subclass C3 displayed high expression of immune checkpoints but failed to respond to ICIs. Finally, 12 m6A-LncRNA signatures were identified for HCC classification and validated in an external dataset. This integrated analysis indicated that the interactions between m6A methylation and lncRNAs are involved in immune and stromal cell infiltration in HCC, and may provide novel insights into precision diagnostics as well as therapeutics for HCC patients.
    Keywords:  M6A; hepatocellular carcinoma; immune microenvironment
  9. Am J Transl Res. 2022 ;14(9): 6484-6503
    Biological functions of RNA modification patterns that define tumor microenvironment and survival outcomes in testicular germ cell tumors.
    Weijun Tang, Jinke Qian, Shilei Qian.
      BACKGROUND: Accumulating evidence has indicated that aberrant RNA modifications are associated with malignant progression and the immune microenvironment in various tumors. However, the function of RNA modification regulators in testicular germ cell tumors (TGCTs) remains to be discovered. This study aimed to investigate the biological functions of RNA modification regulators in testicular germ cell tumors and identify their potential clinical predictive value.METHODS: Expression level of 75 RNA modification regulators was acquired to generate differential expression patterns. RNA modification regulatory genes were applied to construct a progression-free survival (PFS) risk model. Meanwhile, three RNA modification clusters were identified using consensus clustering. Subsequently, the infiltration characteristics of cells in the microenvironment as well as the antitumor drug candidates have been further analyzed. Finally, to further validate our results, we examined the expression and biological behavior of seven selected RNA modification regulators both in TGCT cell lines and clinical tissues.
    RESULTS: We collected the differentially expressed regulators of RNA modification. RNA modification risk signature was developed to stratify the prognosis of TGCT patients. Furthermore, we found significant differences in immune microenvironment between subgroups. Ultimately, seven selected RNA modification regulators were further verified.
    CONCLUSIONS: We generated and validated a risk signature related to RNA modification which could accurately predict the relapse risk in TGCT patients. This risk signature was correlated with immune cells infiltration among tumor microenvironments. Furthermore, we screened antitumor drug candidates and evaluated the sensitivity and efficacy of class chemotherapeutic drugs, which could provide reference for clinical drug use.
    Keywords:  RNA modification risk signature; anti-cancer drugs; bioinformation analysis; immune microenvironment; testicular germ cell tumor
  10. Biochem Biophys Res Commun. 2022 Oct 10. pii: S0006-291X(22)01425-5. [Epub ahead of print]635 120-127
    RNA-m6A modification of HDGF mediated by Mettl3 aggravates the progression of atherosclerosis by regulating macrophages polarization via energy metabolism reprogramming.
    Longbin Zheng, Xiang Chen, Quanwen Yin, Jiaming Gu, Jiajing Chen, Minghong Chen, Yunjia Zhang, Mengdie Dong, Hong Jiang, Ning Yin, Hongshan Chen, Xuesong Li.
      Macrophage polarization plays a crucial role in atherosclerosis (AS), which is closely associated with energy metabolism. However, the underlying mechanism remains elusive. Hepatoma-derived growth factor (HDGF) has been reported to promote tumor metastasis via energy metabolism reprogramming. In this study, we aimed to investigate the role and underlying mechanism of HDGF in regulating macrophage polarization and AS. Our results suggested the elevated expression of HDGF in aortas from atherosclerotic patients and ApoeKO mice, as well as M1 macrophages. The specific deficiency of HDGF in macrophages resulted in a significant reduction of plaque area, inflammation and M1 macrophages content in ApoeKO mouse model of AS. Consistent with the in vivo data, the specific deficiency of HDGF attenuated the inflammation, glycolysis, and lipids accumulation in M1 macrophages, and rescued the mitochondrial dysfunction. Mechanistically, HDGF plays a crucial role in atherogenesis by regulating the M1 macrophages polarization through energy metabolism reprogramming. The expression level of methyltransferase Mettl3 elevated significantly in M1 macrophages, which contributed to enhancing mRNA stability and protein expression of HDGF via N6-methyladenosine (m6A) RNA methylation. Taken together, our study revealed a novel mechanism underlying the macrophage polarization, which may be a potential therapy for AS.
    Keywords:  Atherosclerosis; HDGF; Inflammation; Macrophage polarization; m6A
    DOI:  https://doi.org/10.1016/j.bbrc.2022.10.032
  11. J Cancer Res Clin Oncol. 2022 Oct 21.
    LDHA is a prognostic biomarker on the immune response in pancreatic adenocarcinoma and associated with m6A modification.
    Zhen Tan, Jiang Liu, Jin Xu, Bo Zhang, Xianjun Yu, Wei Wang, Chen Liang.
      PURPOSE: N6-methyladenosine (m6A) is tightly associated with the progression of pancreatic ductal adenocarcinoma (PDAC). Another prominent feature of PDAC is metabolic reprogramming, which provides sufficient nutrients to support rapid cell growth via the tumor microenvironment. However, the underlying influences of m6A-associated metabolic genes on the PDAC microenvironment remain poorly understood. Therefore, we sought to construct a survival prediction model using m6A-related genes to clarify the molecular characteristics of PDAC.METHODS: In the present study, m6A-related metabolic genes were obtained from The Cancer Genome Atlas (TCGA) pancreatic adenocarcinoma dataset and subjected to coexpression analysis. Consensus clustering recognized two distinct subgroups with different immune cell infiltration patterns according to the expression of m6A-associated metabolic genes. Multivariate Cox regression analyses and least absolute shrinkage and selection operator (LASSO) analysis were adopted to create an m6A-related metabolism model. A nomogram including clinical features and the risk score based on the expression of m6A-related metabolism regulators was constructed.
    RESULTS: A four-gene signature comprising ATP8B2, GMPS, LDHA and SDR39U1 was built to predict the overall survival (OS) of PDAC patients. This signature also robustly predicted survival in two independent validation cohorts from the International Cancer Genome Consortium (ICGC) and ArrayExpress (E-MTAB-6134). The four-gene signature divided patients into high- and low-risk groups with distinct OS values as verified by the log-rank test. Among the four genes, LDHA was upregulated in both PDAC tissues and cell lines.
    CONCLUSIONS: Collectively, we analyzed the immune microenvironment, predicted drug sensitivity and assessed the implications of the mutation landscape based on the crosstalk between m6A regulators and metabolic rewiring, and we also constructed a novel signature based on m6A-associated metabolic genes to predict PDAC prognosis.
    Keywords:  Immune microenvironment; M6A; Metabolic reprogramming; Molecular oncology; Pancreatic cancer
    DOI:  https://doi.org/10.1007/s00432-022-04400-8
  12. Biochimie. 2022 Oct 13. pii: S0300-9084(22)00269-3. [Epub ahead of print]
    Emerging role of mRNA methylation in regulating the hallmarks of cancer.
    Gargi Sarraf, Ravindresh Chhabra.
      The dynamic chemical modifications of DNA, RNA, and proteins can transform normal cells into malignant ones. While the DNA and protein modifications in cancer have been described extensively in the literature, there are fewer reports about the role of RNA modifications in cancer. There are over 100 forms of RNA modifications and one of these, mRNA methylation, plays a critical role in the malignant properties of the cells. mRNA methylation is a reversible modification responsible for regulating protein expression at the post-transcriptional level. Despite being discovered in the 1970s, a complete understanding of the different proteins involved and the mechanism behind mRNA methylation remains largely unknown. However, these mRNA methylations have been shown to foster cancer hallmarks via specific cellular targets inside the cell. In this review, we provide a brief overview of mRNA methylation and its emerging role in regulating the various hallmarks of cancer.
    Keywords:  Epitranscriptomics; Methyltransferases; YTHDC; m5C; m6A
    DOI:  https://doi.org/10.1016/j.biochi.2022.10.005
  13. Nat Rev Genet. 2022 Oct 19.
    Biological roles of adenine methylation in RNA.
    Konstantinos Boulias, Eric Lieberman Greer.
      N6-Methyladenosine (m6A) is one of the most abundant modifications of the epitranscriptome and is found in cellular RNAs across all kingdoms of life. Advances in detection and mapping methods have improved our understanding of the effects of m6A on mRNA fate and ribosomal RNA function, and have uncovered novel functional roles in virtually every species of RNA. In this Review, we explore the latest studies revealing roles for m6A-modified RNAs in chromatin architecture, transcriptional regulation and genome stability. We also summarize m6A functions in biological processes such as stem-cell renewal and differentiation, brain function, immunity and cancer progression.
    DOI:  https://doi.org/10.1038/s41576-022-00534-0
  14. Mol Biotechnol. 2022 Oct 19.
    Silencing of YTHDF1 Attenuates Cerebral Stroke by Inducing PTEN Degradation and Activating the PTEN/AKT/mTOR Pathway.
    Xiaohong Li, Peng An, Fang Han, Meihong Yu, Zhenfei Yu, Ying Li.
      N6-methyladenosine (m6A) methylation regulates pathological processes of cerebral stroke, which can lead to disability and death. Herein, we explored the role of a m6A "reader" YTHDF1 in stroke. MCAO (middle cerebral artery occlusion) rat model and hypoxia/reoxygenation (H/R)-induced neurocytes cell model were established. TTC staining assay assessed the infarction area and TUNEL assay analyzed apoptosis. Neurological score was analyzed to evaluate the brain function. Cell counting kit-8, LDH release, and flow cytometry assessed cellular proliferation, cell death, and cell apoptosis in vitro. The expression of YTHDF1, PTEN, and the factors in the PI3K/AKT/mTOR pathway was measured using western blot. The interaction between YTHDF1 and PTEN was confirmed luciferase assay and RNA immunoprecipitation assay. The results indicated that YTHDF1 was upregulated in the brain tissues of MCAO mice and H/R-treated cells. Knockdown of YTHDF1 inhibited the infarct area, neuron damage, and apoptosis. Additionally, YTHDF1 depletion promoted viability and inhibited apoptosis of H/R-treated cells. Moreover, YTHDF1 inactivated the PI3K/AKT/mTOR pathway. Mechanistically, YTHDF1 binds to PTEN to increase PTEN mRNA stability. Overexpressing PTEN rescued the effects of YTHDF1 depletion on cell viability and apoptosis. In conclusion, silencing of YTHDF1 decelerated the progression of cerebral stroke through promoting PTEN degradation and activating the PTEN/AKT/mTOR pathway, suggesting that YTHDF1 has the potential to be a therapeutic target for stroke.
    Keywords:  Ischemia–reperfusion injury; M6A methylation; PTEN/AKT/mTOR pathway; Stroke; YTHDF1
    DOI:  https://doi.org/10.1007/s12033-022-00575-0
  15. Sci Rep. 2022 Oct 21. 12(1): 17667
    Gene signature of m6A RNA regulators in diagnosis, prognosis, treatment, and immune microenvironment for cervical cancer.
    Shizhi Wang, Bo Ding, Shiyuan Wang, Wenjing Yan, Qianqian Xia, Dan Meng, Shuqian Xie, Siyuan Shen, Bingjia Yu, Haohan Liu, Jing Hu, Xing Zhang.
      Continuing studies imply that m6A RNA modification is involved in the development of cervical cancer (CC), but lack strong support on recurrence and diagnosis prediction. In this research, a comprehensive analysis of 33 m6A regulators was performed to fulfill them. Here, we performed diagnostic and prognosis models and identified key regulators, respectively. Then the CC patients were separated into two clusters in accordance with 33 regulators, and participants in the cluster 1 had a worse prognosis. Subsequently, the m6AScore was calculated to quantify the m6A modification pattern based on regulators and we found that patients in cluster 1 had higher m6AScore. Afterwards, immune microenvironment, cell infiltration, escape analyses and tumor burden mutation analyses were executed, and results showed that m6AScore was correlated with them, but to a limited extent. Interestingly, HLAs and immune checkpoint expression, and immunophenoscore in patients with high-m6AScores were significantly lower than those in the low-m6AScore group. These suggested the m6AScores might be used to predict the feasibility of immunotherapy in patients. Results provided a distinctive perspective on m6A modification and theoretical basis for CC diagnosis, prognosis, clinical treatment strategies, and potential mechanism exploration.
    DOI:  https://doi.org/10.1038/s41598-022-22211-2
  16. Front Oncol. 2022 ;12 989817
    m6A-binding protein IGF2BP1 promotes the malignant phenotypes of lung adenocarcinoma.
    Hansheng Wu, Haijie Xu, Shujie Huang, Yong Tang, Jiming Tang, Haiyu Zhou, Liang Xie, Guibin Qiao.
      Background: Lung adenocarcinoma (LUAD), the most common type of lung cancer, poses a significant threat to the life of patients. N6-methyladenosine modification is the most abundant epigenetic modification and may play an important role in the lung carcinogenesis. IGF2BP1 is a newly discovered m6A-binding protein, but little is known about its role in LUAD.Methods: Data from TCGA, GEO, Kaplan-Meier Plotter, and GEPIA databases were systematically analyzed to access the expression and prognostic value of IGF2BP1 on LUAD. Real-time polymerase chain reaction, Western blot, and immunohistochemistry were performed to detect the mRNA and protein level of IGF2BP1 in LUAD tissues and para-carcinoma tissues. Functional cell experiments, including Cell Counting Kit-8 assay, Transwell invasion assay, wound healing assay, Annexin V-FITC/PI double-staining assay, and TUNEL assay, were used to investigate the functions of IGF2BP1 on LUAD cell proliferation, invasion, migration, and apoptosis, respectively. The top 50 genes that were positively or negatively related to the expression of IGF2BP1 were identified, and pathway enrichment analysis was performed. m6A modification sites within IGF2BP1-related genes were predicted by SRAMP.
    Result: 16 m6A regulators were significantly differentially expressed in LUAD tissues. IGF2BP1 was upregulated in LUAD tissues compared with para-carcinoma tissues. High expression of IGF2PB1 was significantly associated with higher clinical stages and poor prognosis of LUAD patients. Furthermore, our functional experiments indicated that IGF2BP1 facilitated cell proliferation, invasion, and migration and suppressed apoptosis in LUAD. Functional enrichment analysis of IGF2BP1-related genes indicated enrichment in several pathways related to oncogenesis. Additionally, m6A modification sites were detected within IGF2BP1-related genes.
    Conclusions: Our findings demonstrate that IGF2BP1 plays a contributory role in the development and progression of LUAD. IGF2BP1 has the potential to become a prognostic predictor and therapeutic target for LUAD.
    Keywords:  IGF2BP1; N6-methyladenosine; bioinformatic; lung adenocarcinoma; prognosis
    DOI:  https://doi.org/10.3389/fonc.2022.989817
  17. Front Cell Dev Biol. 2022 ;10 947337
    The m6A-methylated mRNA pattern and the activation of the Wnt signaling pathway under the hyper-m6A-modifying condition in the keloid.
    Can-Xiang Lin, Zhi-Jing Chen, Qi-Lin Peng, Ke-Rong Xiang, Du-Qing Xiao, Ruo-Xi Chen, Taixing Cui, Yue-Sheng Huang, Hong-Wei Liu.
      Purpose: The present study was carried out to investigate the global m6A-modified RNA pattern and possible mechanisms underlying the pathogenesis of keloid. Method: In total, 14 normal skin and 14 keloid tissue samples were first collected on clinics. Then, three samples from each group were randomly selected to be verified with the Western blotting to determine the level of methyltransferase and demethylase. The total RNA of all samples in each group was isolated and subjected to the analysis of MeRIP sequencing and RNA sequencing. Using software of MeTDiff and htseq-count, the m6A peaks and differentially expressed genes (DEGs) were determined within the fold change >2 and p-value < 0.05. The top 10 pathways of m6A-modified genes in each group and the differentially expressed genes were enriched by the Kyoto Encyclopedia of Genes and Genomes signaling pathways. Finally, the closely associated pathway was determined using the Western blotting and immunofluorescence staining. Results: There was a higher protein level of WTAP and Mettl3 in the keloid than in the normal tissue. In the keloid samples, 21,020 unique m6A peaks with 6,573 unique m6A-associated genetic transcripts appeared. In the normal tissue, 4,028 unique m6A peaks with 779 m6A-associated modified genes appeared. In the RNA sequencing, there were 847 genes significantly changed between these groups, transcriptionally. The genes with m6A-methylated modification and the upregulated differentially expressed genes between two tissues were both mainly related to the Wnt signaling pathway. Moreover, the hyper-m6A-modified Wnt/β-catenin pathway in keloid was verified with Western blotting. From the immunofluorescence staining results, we found that the accumulated fibroblasts were under a hyper-m6A condition in the keloid, and the Wnt/β-Catenin signaling pathway was mainly activated in the fibroblasts. Conclusion: The fibroblasts in the keloid were under a cellular hyper-m6A-methylated condition, and the hyper-m6A-modified highly expressed Wnt/β-catenin pathway in the dermal fibroblasts might promote the pathogenesis of keloid.
    Keywords:  RNA sequencing; fibroblasts; keloid; m6A modification; the Wnt signaling pathway
    DOI:  https://doi.org/10.3389/fcell.2022.947337
  18. Cancer Lett. 2022 Oct 15. pii: S0304-3835(22)00458-X. [Epub ahead of print] 215971
    METTL3-mediated N6-methyladenosine modification and HDAC5/YY1 promote IFFO1 downregulation in tumor development and chemo-resistance.
    Ye Zhang, Jian-Ge Qiu, Xiao-Yu Jia, Yu Ke, Ming-Kun Zhang, David Stieg, Wen-Jing Liu, Ling-Zhi Liu, Lin Wang, Bing-Hua Jiang.
      Ovarian cancer (OC) is a malignant tumor that seriously threatens women's health. Due to the difficulty of early diagnosis, most patients exhibit advanced disease or peritoneal metastasis at diagnosis. We discovered that IFFO1 is a novel tumor suppressor, but its role in tumorigenesis, development and chemoresistance is unknown. In this study, IFFO1 levels were downregulated across cancers, leading to the acceleration of tumor development, metastasis and/or cisplatin resistance. Overexpression of IFFO1 inhibited the translocation of β-catenin to the nucleus and decreased tumor metastasis and cisplatin resistance. Furthermore, we demonstrated that IFFO1 was regulated at both the transcriptional and posttranscriptional levels. At the transcriptional level, the recruitment of HDAC5 inhibited IFFO1 expression, which is mediated by the transcription factor YY1, and the METTL3/YTHDF2 axis regulated the mRNA stability of IFFO1 in an m6A-dependent manner. Mice injected with IFFO1-overexpressing cells had lower ascites volumes and tumor weights throughout the peritoneal cavity than those injected with parental cells expressing the vector control. In conclusion, we demonstrated that IFFO1 is a novel tumor suppressor that inhibits tumor metastasis and reverses drug resistance in ovarian cancer. IFFO1 was downregulated at both the transcriptional level and posttranscriptional level by histone deacetylase and RNA methylation, respectively, and the IFFO1 signaling pathway was identified as a potential therapeutic target for cancer.
    Keywords:  Chemoresistance; HDAC5; IFFO1; METTL3; Tumor metastasis
    DOI:  https://doi.org/10.1016/j.canlet.2022.215971
  19. Cell Death Dis. 2022 Oct 18. 13(10): 877
    LCAT1 is an oncogenic LncRNA by stabilizing the IGF2BP2-CDC6 axis.
    Juze Yang, Xinyi Qian, Qiongzi Qiu, Lingling Xu, Meidie Pan, Jia Li, Jiayi Ren, Bingjian Lu, Ting Qiu, Enguo Chen, Kejing Ying, Honghe Zhang, Yan Lu, Pengyuan Liu.
      Long non-coding RNAs (lncRNAs) is known to play vital roles in modulating tumorigenesis. We previously reported that LCAT1, a novel lncRNA, promotes the growth and metastasis of lung cancer cells both in vitro and in vivo. However, the underlying mechanism(s) of LCAT1 as an oncogenic regulator remains elusive. Here, we showed that LCAT1 physically interacts with and stabilizes IGF2BP2, an m6A reader protein, by preventing its degradation via autolysosomes. IGF2BP2 is overexpressed in lung cancer tissues, which is associated with poor survival of non-small cell lung cancer patients, suggesting its oncogenic role. Biologically, IGF2BP2 depletion inhibits growth and survival as well as the migration of lung cancer cells. Mechanistically, the LCAT1/IGF2BP2 complex increased the levels of CDC6, a key cell cycle regulator, by stabilizing its mRNA in an m6A-dependent manner. Like IGF2BP2, CDC6 is also overexpressed in lung cancer tissues with poor patient survival, and CDC6 knockdown has oncogenic inhibitory activity. Taken together, the LCAT1-IGF2BP2-CDC6 axis appears to play a vital role in promoting the growth and migration of lung cancer cells, and is a potential therapeutic target for lung cancer. Importantly, our finding also highlights a previously unknown critical role of LCAT1 in m6A-dependent gene regulation by preventing autolytic degradation of IGF2BP2.
    DOI:  https://doi.org/10.1038/s41419-022-05316-4
  20. Cancer Med. 2022 Oct 18.
    Identification of miR-30c-5p as a tumor suppressor by targeting the m6 A reader HNRNPA2B1 in ovarian cancer.
    Qiulei Wu, Guoqing Li, Lanqing Gong, Jing Cai, Le Chen, Xiaohan Xu, Xiaoli Liu, Jing Zhao, Ya Zeng, Rui Gao, Lili Yu, Zehua Wang.
      BACKGROUND: microRNAs (miRNAs) and N6-methyladenosine (m6 A) play important roles in ovarian cancer (OvCa). However, the mechanisms by which miRNAs regulate m6 A in OvCa have not been elucidated so far.METHODS: To screen m6 A-related miRNAs, Pearson's correlation analysis of miRNAs and m6 A regulators was implemented using The Cancer Genome Atlas database (TCGA). To determine the level of m6 A, RNA m6 A quantitative assays were used. Then, colony formation assays, EdU assays, wound healing assays, and Transwell assays were performed. The dual-luciferase reporter assay was used to confirm the miRNA target genes. Protein-protein interaction (PPI) analysis of the target genes was performed, and hub genes were discovered using the cytoHubba/Cytoscape software. The underlying molecular mechanisms were explored by bioinformatics and RNA stability assays.
    RESULTS: A total of 126 miRNAs were identified as m6 A-related miRNAs by Pearson's correlation analysis. Among them, the high level of miR-30c-5p was associated with good prognosis in OvCa patients. In vitro, the miR-30c-5p agomir lowered the m6 A level and inhibited OvCa cell proliferation, migration, and invasion. The hub target genes of miR-30c-5p were identified as (i) XPO1, (ii) AGO1, (iii) HNRNPA2B1, of which m6 A reader HNRNPA2B1 was highly expressed in OvCa tissues and related with poor prognosis. In vitro, knockdown of HNRNPA2B1 significantly reduced m6 A level and hampered the proliferation and migration of OvCa cells. The inhibition of m6 A reader HNRNPA2B1 attenuated the suppression of proliferation and migration and the low m6 A level induced by the miR-30c-5p downregulation. Mechanistically, m6 A reader HNRNPA2B1 might regulate CDK19 mRNA stability to alter m6 A level.
    CONCLUSIONS: miR-30c-5p inhibits OvCa progression and reduces the m6 A level by inhibiting m6 A reader HNRNPA2B1, thus providing new insights into the m6 A regulatory mechanism in OvCa.
    Keywords:  Biological function; HNRNPA2B1; m6A level; miR-30c-5p; ovarian cancer
    DOI:  https://doi.org/10.1002/cam4.5246
  21. Front Oncol. 2022 ;12 939449
    Transcriptome-wide m6A methylome analysis uncovered the changes of m6A modification in oral pre-malignant cells compared with normal oral epithelial cells.
    Xun Chen, Liutao Chen, Yuquan Tang, Yi He, Kuangwu Pan, Linyu Yuan, Weihong Xie, Shangwu Chen, Wei Zhao, Dongsheng Yu.
      As the most common post-transcriptional RNA modification, m6A methylation extensively regulates the structure and function of RNA. The dynamic and reversible modification of m6A is coordinated by m6A writers and erasers. m6A reader proteins recognize m6A modification on RNA, mediating different downstream biological functions. mRNA m6A modification and its corresponding regulators play an important role in cancers, but its characteristics in the precancerous stage are still unclear. In this study, we used oral precancerous DOK cells as a model to explore the characteristics of transcriptome-wide m6A modification and major m6A regulator expression in the precancerous stage compared with normal oral epithelial cell HOEC and oral cancer cell SCC-9 through MeRIP-seq and RT-PCR. Compared with HOEC cells, we found 1180 hyper-methylated and 1606 hypo-methylated m6A peaks and 354 differentially expressed mRNAs with differential m6A peaks in DOK cells. Although the change of m6A modification in DOK cells was less than that in SCC-9 cells, mRNAs with differential m6A in both cell lines were enriched into many identical GO terms and KEGG pathways. Among the 20 known m6A regulatory genes, FTO, ALKBH5, METTL3 and VIRMA were upregulated or downregulated in DOK cells, and the expression levels of 10 genes such as METTL14/16, FTO and IGF2BP2/3 were significantly changed in SCC-9 cells. Our data suggest that precancerous cells showed, to some extent, changes of m6A modification. Identifying some key m6A targets and corresponding regulators in precancerous stage may provide potential intervention targets for the prevention of cancer development through epigenetic modification in the future.
    Keywords:  MeRIP sequencing; dysplastic oral keratinocyte (DOK); human oral epithelial cell (HOEC); m6A modification; m6A regulatory genes; oral squamous cell carcinoma cell; precancerous cells
    DOI:  https://doi.org/10.3389/fonc.2022.939449
  22. Cell Mol Life Sci. 2022 Oct 20. 79(11): 559
    METTL3 modulates chromatin and transcription dynamics during cell fate transition.
    Xiao-Min Liu, Yuanhui Mao, Shen Wang, Jun Zhou, Shu-Bing Qian.
      Transcriptional programming plays a key role in determining the cell state. Timely reconfiguration of chromatin structure and attenuation of pluripotent genes are required for efficient embryonic stem cell (ESC) differentiation. Here, we identify METTL3, a core N6-methyladenosine (m6A) catalyzing enzyme, as a crucial modulator of dynamic transcription and chromatin accessibility upon ESC-derived cardiac differentiation. Genome-wide analysis of chromatin-associated RNAs revealed that depletion of METTL3 failed to dramatically attenuate the transcription of pluripotent genes, as well as activate nascent cardiomyocyte-specific transcripts upon differentiation. Consistently, ATAC-seq analysis showed that loss of METTL3 markedly attenuated the dynamic alteration of chromatin accessibility at both promoters and gene bodies, resulting in reduced sensitivity of ESC chromatin structure to cardiac differentiation signal. Furthermore, we found that METTL3 negatively regulated the histone modifications H3K4me3 and H3K36me3, which are involved in METTL3-modulated dynamic chromatin architecture during cell state transition. Unexpectedly, using chromatin-associated m6A sequencing, we found that nuclear m6A underwent a dramatic increase upon differentiation, which correlates with the decrease of chromatin accessibility. Collectively, our findings reveal that METTL3 and nuclear m6A epitranscriptome couple with chromatin state to ensure transcriptional regulation of cell fate transition.
    Keywords:  Cell differentiation; Chromatin accessibility; METTL3; Transcription
    DOI:  https://doi.org/10.1007/s00018-022-04590-x
  23. Heliyon. 2022 Oct;8(10): e10931
    Relationship between M6A methylation regulator and prognosis in patients with hepatocellular carcinoma after transcatheter arterial chemoembolization.
    Deliang Huang, Dejing Huang.
      Background: Patients with mid-stage HCC (hepatocellular carcinoma) may benefit from transcatheter arterial chemoembolization (TACE). However, patient efficacy varies widely, and the detailed assessment index is unknown. The most general methylation alteration in mRNA (Messenger RNA), N6-methyladenosine (m6A), is controlled by the m6A regulator, which is associated with the emergence of tumors. To include the molecular causes of cancer, competition with ceRNA (endogenous RNA) networks is crucial. However, the exact processes they contribute to TACE HCC remain uncertain. The purpose of this study was tantamount to investigating the possible function of ceRNA networks and m6A regulators in patients with TACE HCC.Methods: Genes Associated with m6A were discovered using the TACE GEO (Gene Expression Omnibus) dataset. An additional estimate of M6A-associated DEGs (differentially expressed genes) was used to create a predictive response model, which is required. LncRNA-miRNA and miRNA-mRNA interactions were then predicted, the regulatory ceRNA network was set up using Cytoscape software, and target genes were identified using GEPIA online analysis. The connection between immunological checkpoints, immune cell marker genes, and target genes for immune cells was also examined.
    Results: The detection of 4 m6A-associated DEGs, the development and evaluation of 2 Machine learning models, and the development of risk models that accurately predicted the response rate of specific patients. Additionally, we obtained two miRNAs (micro RNAs)and six lncRNAs (Long non-coding RNAs), forming an 8-pair ceRNA network, and the target gene LRPPRC deletion of one copy number and gene expression was highly correlated with the amount of Tregs immune cells. LRPPRC was related positively with NRP1, IRF5, and ITGAM and negatively with CCR7 and CD8B among immune cell marker genes. We also discovered that LRPPRC correlates positively with immune checkpoint CD274 cells.
    Conclusion: The response of HCC patients to TACE therapy may be predicted using a model based on four gene expression data. We also developed a ceRNA network for TACE HCC related to m6A, which offered suggestions for more research into its molecular processes and possible prognostic indicators.
    Keywords:  HCC; TACE; ceRNA network; m6A
    DOI:  https://doi.org/10.1016/j.heliyon.2022.e10931
  24. J Transl Med. 2022 Oct 20. 20(1): 476
    Integrative analysis of m3C associated genes reveals METTL2A as a potential oncogene in breast Cancer.
    Shuai Wang, Huiting Li, Jiheng Liu, Qianqian Zhang, Wei Xu, Juanjuan Xiang, Li Fang, Ping Xu, Zheng Li.
      RNA methylation modifications, especially m6A mRNA modification, are known to be extensively involved in tumor development. However, the relationship between N3-methylcytidine (m3C) related genes and tumorigenesis has rarely been studied. In this research, we found that m3C-related genes were expressed at different levels and affected patients' prognosis across multiple cancer types from The Cancer Genome Atlas and multi-omics levels. Importantly, methyltransferase-like proteins 2A (METTL2A) had a high amplification frequency (~ 7%) in patients with breast invasive carcinoma (BRCA), and its overexpression was an independent predictor of poor overall survival. Enrichment analysis of associated genes revealed that METTL2A may activate DNA synthesis and cell proliferation pathways in BRCA cells. Through drug sensitivity analysis, Trifluridine, PD407824, and Taselisib were shown to be effective drugs for METTL2A-positive BRCA patients. Overall, our research conducts a holistic view of the expression level and prognostic signature of m3C-related genes with multiple malignancies. Importantly, METTL2A has been intensely explored as a potential oncogene in BRCA, to aid the development of potential drug agents for precision therapy in breast cancer patients.
    Keywords:  Breast cancer; METTL2A; METTL2B; METTL6; METTL8; N3-methylcytidine
    DOI:  https://doi.org/10.1186/s12967-022-03683-2
  25. Front Genet. 2022 ;13 986995
    Identification and verification of IGFBP3 and YTHDC1 as biomarkers associated with immune infiltration and mitophagy in hypertrophic cardiomyopathy.
    Yao Li, Wei Zhang, Yan Dai, Keping Chen.
      Background: Hypertrophic cardiomyopathy (HCM) is the main cause of sudden cardiac death among young adults, yet its pathogenesis remains vague. N6-methyladenosine (m6A) methylation modification was involved in various cardiovascular diseases such as coronary heart disease and heart failure, although its influence on HCM remains unclear. This study aimed to explore the potential role of m6A in the diagnosis and pathogenesis of HCM. Methods: GSE36961 including 106 HCM and 39 controls was used in the study. The HCM-related m6A regulators were selected using support vector machine recursive feature elimination and random forest algorithm. A significant gene signature was then established using least absolute shrinkage and selection operator and then verified by GSE130036. Subgroup classification of HCM was performed based on the expression of m6A biomarkers. Gene set variation analysis was employed to explore the functional difference between distinct subgroups. Weighted gene co-expression network analysis was used to determine the m6A-related hub module. Single-sample gene set enrichment analysis was conducted to assess the immune and mitophagy features between subgroups. Besides, transfection of recombinant plasmids with targeted genes into H9c2 cells was performed to further verify the function of the significant biomarkers. Results: Significant difference existed in m6A landscape between HCM and control patients, among which IGFBP3 and YTHDC1 were identified as the independent biomarkers of HCM. Highly infiltrated immune cells (MDSC, macrophages, etc.), more enriched immune-related pathways (TNFα signaling via NFκB and IL6-JAK-STAT3 signaling) and cardiac remodeling-associated pathways (epithelial mesenchymal transition, angiogenesis, etc.) were identified in the subgroup with higher IGFBP3. Consistently, overexpression of IGFBP3 in H9c2 cells led to upregulation of extracellular-matrix-related genes (COL1A2, COL3A1 and MMP9) and inflammation-related genes (TNFα and IL6). Besides, higher YTHDC1 expression seemed to be consistent with less-activated mitophagy (PINK1-PRKN mediated mitophagy) and energy metabolism. Further experiments demonstrated that overexpression of YTHDC1 resulted in up-regulation of PINK and PRKN in cardiomyocytes, which are essential genes mediating mitophagy. Conclusion: Two m6A readers (IGFBP3 and YTHDC1) well distinguished HCM and may facilitate clinical diagnosis. IGFBP3 may play a role in the immune-microenvironments and remodeling of cardiac tissues, while YTHDC1 may influence mitophagy and energy metabolism in HCM.
    Keywords:  N6-methyladenosine methylation modification; energy metabolism; hypertrophic cardiomyopathy; immune infiltration; mitophagy
    DOI:  https://doi.org/10.3389/fgene.2022.986995
  26. Front Cell Neurosci. 2022 ;16 1013450
    Crosstalk among N6-methyladenosine modification and RNAs in central nervous system injuries.
    Mi Tian, Lei Mao, Li Zhang.
      Central nervous system (CNS) injuries, including traumatic brain injury (TBI), intracerebral hemorrhage (ICH) and ischemic stroke, are the most common cause of death and disability around the world. As the most common modification on ribonucleic acids (RNAs), N6-methyladenosine (m6A) modification has recently attracted great attentions due to its functions in determining the fate of RNAs through changes in splicing, translation, degradation and stability. A large number of studies have suggested that m6A modification played an important role in brain development and involved in many neurological disorders, particularly in CNS injuries. It has been proposed that m6A modification could improve neurological impairment, inhibit apoptosis, suppress inflammation, reduce pyroptosis and attenuate ferroptosis in CNS injuries via different molecules including phosphatase and tensin homolog (PTEN), NLR family pyrin domain containing 3 (NLRP3), B-cell lymphoma 2 (Bcl-2), glutathione peroxidase 4 (GPX4), and long non-coding RNA (lncRNA). Therefore, m6A modification showed great promise as potential targets in CNS injuries. In this article, we present a review highlighting the role of m6A modification in CNS injuries. Hence, on the basis of these properties and effects, m6A modification may be developed as therapeutic agents for CNS injury patients.
    Keywords:  apoptosis; central nervous system injuries; downstream molecules; inflammation; m6A modification; neurological impairment
    DOI:  https://doi.org/10.3389/fncel.2022.1013450
  27. Front Genet. 2022 ;13 996950
    Comprehensive analysis of m7G modification patterns based on potential m7G regulators and tumor microenvironment infiltration characterization in lung adenocarcinoma.
    Shouzheng Ma, Jun Zhu, Mengmeng Wang, Jianfei Zhu, Wenchen Wang, Yanlu Xiong, Runmin Jiang, Lei Liu, Tao Jiang.
      Background: The non-negligible role of epigenetic modifications in cancer development and tumor microenvironment (TME) has been demonstrated in recent studies. Nonetheless, the potential regulatory role of N7-methylguanosine (m7G) modification in shaping and impacting the TME remains unclear. Methods: A comprehensive analysis was performed to explore the m7G modification patterns based on 24 potential m7G regulators in 817 lung adenocarcinoma (LUAD) patients, and the TME landscape in distinct m7G modification patterns were evaluated. The m7G score was established based on principal component analysis (PCA) to quantify m7G modification patterns and evaluate the TME cell infiltrating characteristics of individual tumors. Further, correlation analyses of m7Gscore with response to chemotherapy and immunotherapy were performed. Results: We identified three distinct m7G modification patterns with the biological pathway enrichment and TME cell infiltrating characteristics corresponded to immune-desert, immune-inflamed and immune-excluded phenotype, respectively. We further demonstrated the m7Gscore could predict the TME infiltrating characteristics, tumor mutation burden (TMB), response to immunotherapy and chemotherapy, as well as prognosis of individual tumors. High m7Gscore was associated with increased component of immune cell infiltration, low TMB and survival advantage, while low m7Gscore was linked to decreased immune cell infiltration and increased TMB. Additionally, patients with lower m7Gscore demonstrated significant therapeutic advantages. Conclusion: This study demonstrated the regulatory mechanisms of m7G modification on TME formation and regulation of lung adenocarcinoma. Identification of individual tumor m7G modification patterns will contribute to the understanding of TME characterization and guiding more effective immunotherapy strategies.
    Keywords:  N7-methylguanosine (m7G); immunotherapy; lung adenocarcinoma; mutation burden; tumor microenvironment
    DOI:  https://doi.org/10.3389/fgene.2022.996950
  28. Dis Markers. 2022 ;2022 7899961
    An Analysis of BMP1 Associated with m6A Modification and Immune Infiltration in Pancancer.
    Yiyi Zhou, Shuangshuang Xu, Qinying Sun, Yuchao Dong.
      Background: This research explores the underlying link between diagnosis and therapy between bone morphogenetic protein 1 (BMP1) and various cancers.Methods: Three immunotherapeutic cohorts, by the composition of IMvigor210, GSE35640, and GSE78220 were obtained from previously published articles and the Gene Expression Omnibus database. The different expressions of BMP1 in various clinical parameters were conducted, and prognostic analysis was executed utilizing Cox proportional hazard regression and Gene Expression Profiling Interactive Analysis. Moreover, the correlation between BMP1 and tumor microenvironment was analyzed using ESTIMATE and CIBERSORT algorithms. Tumor mutational burden and microsatellite instability were also included. The correlation between m6A modification and the gene expression level was analyzed using Tumor IMmune Estimation Resource, the University of Alabama at Birmingham Cancer data analysis portal. Gene Set Cancer Analysis analyzed the correlation of BMP1 expression level with copy number variations and methylation. Furthermore, the correlation between BMP1 and therapeutic response after antineoplastic drug use was illustrated for further discussion.
    Results: BMP1 expression had significant differences in 14 cancers. It presented an intimate relationship with immune-relevant biomarkers. A variation analysis indicated that BMP1 had a significant association with immunotherapeutic response. The expression level of BMP1 was closely associated with insulin-like growth factor binding protein 3, an m6A modification relative gene. Except for a few cancer types, methylation negatively correlated with BMP1, and copy number variations positively correlated with BMP1. Notably, low BMP1 expression was connected with immunotherapeutic response in the cohorts, and its expression was related to increased sectional sensitivity of drugs.
    Conclusion: BMP1 may serve as a potential biomarker for prognostic prediction and immunologic infiltration in diversified cancers, providing a new thought approach for oncotherapy.
    DOI:  https://doi.org/10.1155/2022/7899961
  29. Exp Mol Med. 2022 Oct 21.
    The emerging importance of METTL5-mediated ribosomal RNA methylation.
    Elena M Turkalj, Caroline Vissers.
      The study of the epitranscriptome has thus far focused largely on mRNA methylation. Recent human genetics studies suggest that methylation of ribosomal RNA also contributes to brain development and cognition. In particular, the m6A modification at the A-1832 position of the 18S rRNA is installed by METTL5. Mutations or deletions of Mettl5 in humans and mice, respectively, cause abnormal translation and gene expression that in turn mediates stem cell behaviors such as differentiation. In this review, we provide an overview of the current knowledge of the methyltransferase METTL5, as well as the molecular biology surrounding m6A on rRNA and how it regulates cell behavior.
    DOI:  https://doi.org/10.1038/s12276-022-00869-y
  30. FASEB J. 2022 Nov;36(11): e22619
    Endothelial CYP2J2 overexpression restores the BRB via METTL3-mediated ANXA1 upregulation.
    Bowen Zhao, Jingqiu Huang, Xiaotong Lou, Ke Yao, Meng Ye, Qianxue Mou, Zheng Wen, Qiming Duan, Hong Zhang, Yin Zhao.
      Blood-retinal barrier (BRB) breakdown is responsible for multiple ocular diseases, such as diabetic retinopathy, age-related macular degeneration, and retinal vascular occlusive diseases. Increased vascular permeability contributes to vasogenic edema and tissue damage, with consequent adverse effects on vision. Herein, we found that endothelial CYP2J2 overexpression maintained BRB integrity after ischemia-reperfusion injury and consequently protected against retinal ganglion cell loss. Oxidative stress repressed endothelial ANXA1 expression in vivo and in vitro. CYP2J2 upregulated methyltransferase-like 3 (METTL3) expression and hence promoted ANXA1 translation via ANXA1 m6 A modification in endothelium under oxidative stress. CYP2J2 maintained the distribution of endothelial tight junctions and adherens junctions in an ANXA1-dependent manner. Endothelial ANXA1 plays an indispensable role in vascular homeostasis and stabilization during development. Endothelial ANXA1 deletion disrupted retinal vascular perfusion as well as BRB integrity. CYP2J2 metabolites restored BRB integrity in the presence of ANXA1. Our findings identified the CYP2J2-METTL3-ANXA1 pathway as a potential therapeutic target for relieving BRB impairments.
    Keywords:  ANXA1; BRB; CYP2J2; endothelial junctions; vascular development; vascular integrity
    DOI:  https://doi.org/10.1096/fj.202201061RR
  31. Oxid Med Cell Longev. 2022 ;2022 4320809
    Cancer-Associated Fibroblasts Hinder Lung Squamous Cell Carcinoma Oxidative Stress-Induced Apoptosis via METTL3 Mediated m6A Methylation of COL10A1.
    Yuchan Li, Xiaoxue Li, Muwen Deng, Changda Ye, Yuanhong Peng, Yan Lu.
      Background: Cancer-associated fibroblasts (CAFs) within the tumor microenvironment are key players in tumorigenesis and tumor development. Nevertheless, the regulatory mechanisms of CAFs on lung squamous cell carcinoma- (LUSC-) associated remain poorly elucidated.Methods: The microarray dataset GSE22874, containing 30 specimens of primary culture of normal fibroblasts (NFs) and 8 specimens of cancer-associated fibroblasts (CAFs) samples derived from LUSC, was retrieved from the Gene Expression Omnibus (GEO) database and then calculated by using the R language (limma package) to identify differentially expressed genes (DEGs). CAF-conditioned medium (CAF-CM) was collected and used to culture LUSC cells, followed by assessment of cell proliferation, apoptosis, and oxidative stress levels by using CCK-8, annexin V-FITC/PI double staining and ELISA assays. Subsequently, COL10A1 was knocked down in CAFs to assess the role of COL10A1 in CAF regulation of LUSC behavior. Bioinformatics online analysis and MeRIP were applied to predict and test the m6A modification of COL10A1 mRNA and the regulatory relationship with METTL3. Rescue experiments were next performed to explore the effects of METTL3 and COL10A1 in CAFs on LUSC cell proliferation, apoptosis, and oxidative stress. LUSC tumor cells with or without (COL10A1-silenced) CAFs were subcutaneously inoculated in nude mice to evaluate the effect of COL10A1 in CAFs on LUSC tumor growth.
    Results: Elevated expression of COL10A1 was found in LUSC-derived CAFs by GSE22874 dataset analysis. We discovered that COL10A1 and METTL3 was expressed in both LUSC cells and matched CAFs, while COL10A1 expression was prominently higher in CAFs than in LUSC cells. CAF-CM memorably encouraged LUSC cell proliferation and suppressed apoptosis-induced oxidative stress, which was reversed by interfering with COL10A1 expression in CAFs, suggesting that COL10A1 might be secreted by CAFs into the culture medium to exert its effects inside LUSC cells. Global m6A modification was decreased in METTL3 knocked down CAFs. M6A modification, expression levels, and stability of COL10A1 mRNA were impaired upon METTL3 knockdown in CAFs. Overexpression of COL10A1 in CAFs partially reversed the effect of METTL3 knockdown on the malignant behavior of LUSC cells. In vivo studies confirmed that CAFs accelerated LUSC tumor growth, and this effect was counteracted by COL10A1 silencing.
    Conclusions: COL10A1 secreted by CAFs could facilitate LUSC cell proliferation and repress apoptosis-induced oxidative stress, and the mechanism was due to elevated expression mediated by METTL3 promoting its mRNA m6A modification, thereby accelerating tumor growth.
    DOI:  https://doi.org/10.1155/2022/4320809
  32. Front Genet. 2022 ;13 947747
    Identification of N6-methylandenosine related lncRNA signatures for predicting the prognosis and therapy response in colorectal cancer patients.
    Zhiyong Li, Yang Liu, Huijie Yi, Ting Cai, Yunwei Wei.
      Despite recent advances in surgical and multimodal therapies, the overall survival (OS) of advanced colorectal cancer (CRC) patients remains low. Thus, discerning sensitive prognostic biomarkers to give the optimistic treatment for CRC patients is extremely critical. N6-methyladenosine (m6A) and long noncoding RNAs (lncRNAs) play an important role in CRC progression. Nonetheless, few studies have focused on the impact of m6A-related lncRNAs on the prognosis, tumor microenvironment (TME) and treatment of CRC. In this study, 1707 m6A-related lncRNAs were identified through Pearson correlation analysis and Weighted co-expression network analysis (WGCNA) using The Cancer Genome Atlas (TCGA) cohort. Then, 28 m6A-related prognostic lncRNAs were screened by univariate Cox regression analysis, followed by identifying two clusters by consensus clustering analysis. A prognostic model consisted of 8 lncRNA signatures was constructed by the least absolute shrinkage and selection operator (LASSO). Kaplan-Meier curve analysis and a nomogram were performed to investigate the prognostic ability of this model. The risk score of prognostic model act as an independent risk factor for OS rate. Functional enrichment analysis indicated that lncRNA signatures related tumor immunity. The low-risk group characterized by increased microsatellite instability-high (MSI-H), mutation burden, and immunity activation, indicated favorable odds of OS. Moreover, the lncRNA signatures were significantly associated with the cancer stem cell (CSC) index and drug sensitivity. In addition, 3 common immune genes shared by the lncRNA signatures were screened out. We found that these immune genes were widely distributed in 2 cell types of TME. Finally, a ceRNA network was constructed to identify ZEB1-AS1 regulatory axis in CRC. We found that ZEB1-AS1 was significantly overexpressed in tumor tissues, and was related to the metastasis of EMT and the chemoresistance of 5-Fu in CRC. Therefore, our study demonstrated the important role of m6A-related lncRNAs in TME remodeling. Moreover, these results illustrated the levels of ZEB1-AS1 might be valuable for predicting the progression and prognosis of CRC, and further provided a new target for the diagnosis and treatment of CRC patients.
    Keywords:  5-fluorouracil8; N6-methylandenosine2; colorectal cancer1; genetic alteration5; immune cell infiltration6; long non-coding RNA3; prognostic4; single-cell sequencing7
    DOI:  https://doi.org/10.3389/fgene.2022.947747
  33. Front Genet. 2022 ;13 1009145
    Expression pattern and clinical value of Key RNA methylation modification regulators in ischemic stroke.
    Xinyue Zhang, Yuanlin Wang, Beibei Dong, Yi Jiang, Dan Liu, Keliang Xie, Yonghao Yu.
      Ischemic stroke (IS) is one of the major causes of death and disability worldwide, and effective diagnosis and treatment methods are lacking. RNA methylation, a common epigenetic modification, plays an important role in disease progression. However, little is known about the role of RNA methylation modification in the regulation of IS. The aim of this study was to investigate RNA methylation modification patterns and immune infiltration characteristics in IS through bioinformatics analysis. We downloaded gene expression profiles of control and IS model rat brain tissues from the Gene Expression Omnibus database. IS profiles were divided into two subtypes based on RNA methylation regulators, and functional enrichment analyses were conducted to determine the differentially expressed genes (DEGs) between the subtypes. Weighted gene co-expression network analysis was used to explore co-expression modules and genes based on DEGs. The IS clinical diagnosis model was successfully constructed and four IS characteristic genes (GFAP, GPNMB, FKBP9, and CHMP5) were identified, which were significantly upregulated in IS samples. Characteristic genes were verified by receiver operating characteristic curve and real-time quantitative PCR analyses. The correlation between characteristic genes and infiltrating immune cells was determined by correlation analysis. Furthermore, GPNMB was screened using the protein-protein interaction network, and its regulatory network and the potential therapeutic drug chloroquine were predicted. Our finding describes the expression pattern and clinical value of key RNA methylation modification regulators in IS and novel diagnostic and therapeutic targets of IS from a new perspective.
    Keywords:  RNA methylation modification; characteristic gene; epigenetics; immune infiltration; ischemic stroke
    DOI:  https://doi.org/10.3389/fgene.2022.1009145
  34. Leukemia. 2022 Oct 20.
    METTL3 mediates chemoresistance by enhancing AML homing and engraftment via ITGA4.
    Mingying Li, Jingjing Ye, Yuan Xia, Meng Li, Guosheng Li, Xiang Hu, Xiuhua Su, Dongmei Wang, Xin Zhao, Fei Lu, Jingxin Li, Daoxin Ma, Tao Sun, Chunyan Ji.
      Chemoresistant leukemia relapse is one of the most common causes of death for acute myeloid leukemia (AML) patients and the homing/engraftment in bone marrow (BM) are crucial steps for AML cells to acquire chemoresistance by interacting with stromal cell components. No crosstalk between m6A modification and homing/engraftment has been reported. Here, we performed comprehensive high-throughput analyses, including RNA sequencing of CR (complete remission) and relapsed AML patients, and reverse-phase protein arrays of chemoresistant cells to identify METTL3 as a key player regulating AML chemoresistance. Then, METTL3-mediated m6A modification was proved to induce the chemoresistance in vitro and in vivo. Furthermore, AML homing/engraftment was discovered being enhanced by upregulated-METTL3 in chemoresistant cells. And the homing/engraftment and drug-resistance associated phenotypes of chemoresistant cells could be reversed by a METTL3 inhibitor. Mechanistically, METTL3 extended the half-life of ITGA4 mRNA by m6A methylation, and then, increased expression of ITGA4 protein to enhance homing/engraftment of AML cells. The results provide insights into the function of m6A modification on the interaction between AML cells and BM niches and clarify the relationship between METTL3 and AML homing/engraftment, suggesting a therapeutic strategy for the treatment of refractory/relapsed AML with METTL3 inhibitors.
    DOI:  https://doi.org/10.1038/s41375-022-01696-w
  35. BMC Bioinformatics. 2022 Oct 19. 23(1): 437
    Study on the prognosis, immune and drug resistance of m6A-related genes in lung cancer.
    Yang Yang, Zhouyao Qian, Mingyang Feng, Weiting Liao, Qiuji Wu, Feng Wen, Qiu Li.
      BACKGROUND: Few studies have demonstrated that the relationship between m6A-related genes and the prognosis, tumor microenvironment and drug resistance of LC.METHODS: The main results were analyzed with bioinformatics methods.
    RESULTS: Hence, we found 10 m6A-related genes expressed less in tumor samples in comparison with normal ones. Using consensus clustering, all LC patients were grouped into 2 subgroups according to the overall expression of 10 differential expressed m6A-related genes. In two clusters, the OS and immune characteristics were different. We analyzed the predictive potential of 10 m6A-related genes in the prognosis of LC, and obtained a risk prognosis model on the strength of ZC3H13, CBLL1, ELAVL1 and YTHDF1 as the hub candidate genes through LASSO cox. The expression of 4 hub m6A-related genes was validated by IHC in the HPA database. The infiltration level of dendritic cell, CD4+ T cell and neutrophil that were affected by CNV level of m6A-related genes in LUAD and LUSC patients. Moreover, based on GSCALite database, we found that LUSC patients with hypermethylation tended to have a better overall survival. In terms of drug sensitivity, etoposide correlated negatively with ELAVL1, HNRNPC, RBM15B, YTHDF2 and CBLL1. ZC3H13 had positively association with afatinib, while HNRNPC was positively associated with dasatinib, erlotinib, lapatinib and TGX221. Crizotinib had a negative correlation with ELAVL1, CBLL1, HNRNPC and RBM15B.
    CONCLUSION: In conclusion, m6A-related genes are important participants in LC and the expression levels of ZC3H13, CBLL1, ELAVL1 and YTHDF1 are significant for prediction and treatment of LC. Researches of drug resistance based on m6A-related genes need to pay more attention for producing new therapeutic strategies of LC and CBLL1 may contribute to target treatment for further research.
    Keywords:  Drug resistance; Genes; Immune; Lung cancer; Prognosis; m6A
    DOI:  https://doi.org/10.1186/s12859-022-04984-5
  36. Oxid Med Cell Longev. 2022 ;2022 9049571
    PCBP2 Reduced Oxidative Stress-Induced Apoptosis in Glioma through cGAS/STING Pathway by METTL3-Mediated m6A Modification.
    Xiang Chen, Mingchuan Yu, Wei Xu, Peng Kun, Wenbing Wan, Xiao Yuhong, Jing Ye, Yu Liu, Jun Luo.
      Purpose: The most prevalent primary malignant tumor of CNS is glioma, which has a dismal prognosis. The theory of oxidative stress is one of the important theories in the study of its occurrence and development mechanism. In this study, the impacts of PCBP2 on glioma sufferers and the possible mechanisms were examined.Methods: Patients with glioma were obtained from May 2017 to July 2018. Quantitative PCR, microarray analysis, western blot analysis, and immunofluorescence were used in this experiment.
    Results: PCBP2 mRNA expression level and protein expression in patients with glioma were upregulated compared with paracancerous tissue. OS and DFS of PCBP2 low expression in patients with glioma were higher than those of PCBP2 high expression. PCBP2 promoted the progression and metastasis of glioma. PCBP2 reduced oxidative stress-induced apoptosis of glioma. PCBP2 suppressed the cGAS/STING pathway of glioma. PCBP2 protein interlinked with cGAS and cGAS was one target for PCBP2. METTL3-mediated m6A modification increases PCBP2 stability.
    Conclusion: Along the cGAS-STING signal pathway, PCBP2 decreased the apoptosis that oxidative stress-induced glioma caused, which might be a potential target to suppress oxidative stress-induced apoptosis of glioma.
    DOI:  https://doi.org/10.1155/2022/9049571
  37. Clin Transl Med. 2022 Oct;12(10): e1082
    Quantitative and single nucleotide RNA m6 A detection technology boosts clinical research based on tissue and cell free RNA modification.
    Lulu Hu.
      
    Keywords:  RNA m6A; quantitative; sequencing technology; single nucleotide
    DOI:  https://doi.org/10.1002/ctm2.1082
  38. Nat Commun. 2022 Oct 17. 13(1): 6138
    Mammalian N1-adenosine PARylation is a reversible DNA modification.
    Michael U Musheev, Lars Schomacher, Amitava Basu, Dandan Han, Laura Krebs, Carola Scholz, Christof Niehrs.
      Poly-ADP-ribosylation (PARylation) is regarded as a protein-specific modification. However, some PARPs were recently shown to modify DNA termini in vitro. Here, we use ultrasensitive mass spectrometry (LC-MS/MS), anti-PAR antibodies, and anti-PAR reagents to show that mammalian DNA is physiologically PARylated and to different levels in primary tissues. Inhibition of PAR glycohydrolase (PARG) increases DNA PARylation, supporting that the modification is reversible. DNA PARylation requires PARP1 and in vitro PARP1 PARylates single-stranded DNA, while PARG reverts the modification. DNA PARylation occurs at the N1-position of adenosine residues to form N1-Poly(ADP-ribosyl)-deoxyadenosine. Through partial hydrolysis of mammalian gDNA we identify PAR-DNA via the diagnostic deamination product N1-ribosyl-deoxyinosine to occur in vivo. The discovery of N1-adenosine PARylation as a DNA modification establishes the conceptual and methodological framework to elucidate its biological relevance and extends the role of PARP enzymes.
    DOI:  https://doi.org/10.1038/s41467-022-33731-w
  39. Exp Mol Med. 2022 Oct 21.
    Detection technologies for RNA modifications.
    Yan Zhang, Liang Lu, Xiaoyu Li.
      To date, more than 170 chemical modifications have been characterized in RNA, providing a new layer of gene expression regulation termed the 'epitranscriptome'. RNA modification detection methods and tools advance the functional studies of the epitranscriptome. According to the detection throughput and principles, existing RNA modification detection technologies can be categorized into four classes, including quantification methods, locus-specific detection methods, next-generation sequencing-based detection technologies and nanopore direct RNA sequencing-based technologies. In this review, we summarize the current knowledge about these RNA modification detection technologies and discuss the challenges for the existing detection tools, providing information for a comprehensive understanding of the epitranscriptome.
    DOI:  https://doi.org/10.1038/s12276-022-00821-0
  40. Front Genet. 2022 ;13 990623
    Identification of a novel m5C/m6A-related gene signature for predicting prognosis and immunotherapy efficacy in lung adenocarcinoma.
    Yiming Ma, Jun Yang, Tiantai Ji, Fengyun Wen.
      Lung adenocarcinoma (LUAD) is the most prevalent subtype of non-small cell lung cancer (NSCLC) and is associated with high mortality rates. However, effective methods to guide clinical therapeutic strategies for LUAD are still lacking. The goals of this study were to analyze the relationship between an m5C/m6A-related signature and LUAD and construct a novel model for evaluating prognosis and predicting drug resistance and immunotherapy efficacy. We obtained data from LUAD patients from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets. Based on the differentially expressed m5C/m6A-related genes, we identified distinct m5C/m6A-related modification subtypes in LUAD by unsupervised clustering and compared the differences in functions and pathways between different clusters. In addition, a risk model was constructed using multivariate Cox regression analysis based on prognostic m5C/m6A-related genes to predict prognosis and immunotherapy response. We showed the landscape of 36 m5C/m6A regulators in TCGA-LUAD samples and identified 29 differentially expressed m5C/m6A regulators between the normal and LUAD groups. Two m5C/m6A-related subtypes were identified in 29 genes. Compared to cluster 2, cluster 1 had lower m5C/m6A regulator expression, higher OS (overall survival), higher immune activity, and an abundance of infiltrating immune cells. Four m5C/m6A-related gene signatures consisting of HNRNPA2B1, IGF2BP2, NSUN4, and ALYREF were used to construct a prognostic risk model, and the high-risk group had a worse prognosis, higher immune checkpoint expression, and tumor mutational burden (TMB). In patients treated with immunotherapy, samples with high-risk scores had higher expression of immune checkpoint genes and better immunotherapeutic efficacy than those with low-risk scores. We concluded that the m5C/m6A regulator-related risk model could serve as an effective prognostic biomarker and predict the therapeutic sensitivity of chemotherapy and immunotherapy.
    Keywords:  LUAD; RNA methylation; drug sensitivity; immunotherapy; prognosis
    DOI:  https://doi.org/10.3389/fgene.2022.990623
  41. Cancer Res. 2022 Oct 17. OF1-OF15
    The 5-Hydroxymethylcytosine Landscape of Prostate Cancer.
    Martin Sjöström, Shuang G Zhao, Samuel Levy, Meng Zhang, Yuhong Ning, Raunak Shrestha, Arian Lundberg, Cameron Herberts, Adam Foye, Rahul Aggarwal, Junjie T Hua, Haolong Li, Anna Bergamaschi, Corinne Maurice-Dror, Ashutosh Maheshwari, Sujun Chen, Sarah W S Ng, Wenbin Ye, Jessica Petricca, Michael Fraser, Lisa Chesner, Marc D Perry, Thaidy Moreno-Rodriguez, William S Chen, Joshi J Alumkal, Jonathan Chou, Alicia K Morgans, Tomasz M Beer, George V Thomas, Martin Gleave, Paul Lloyd, Tierney Phillips, Erin McCarthy, Michael C Haffner, Amina Zoubeidi, Matti Annala, Robert E Reiter, Matthew B Rettig, Owen N Witte, Lawrence Fong, Rohit Bose, Franklin W Huang, Jianhua Luo, Anders Bjartell, Joshua M Lang, Nupam P Mahajan, Primo N Lara, Christopher P Evans, Phuoc T Tran, Edwin M Posadas, Chuan He, Xiao-Long Cui, Jiaoti Huang, Wilbert Zwart, Luke A Gilbert, Christopher A Maher, Paul C Boutros, Kim N Chi, Alan Ashworth, Eric J Small, Housheng H He, Alexander W Wyatt, David A Quigley, Felix Y Feng.
      Analysis of DNA methylation is a valuable tool to understand disease progression and is increasingly being used to create diagnostic and prognostic clinical biomarkers. While conversion of cytosine to 5-methylcytosine (5mC) commonly results in transcriptional repression, further conversion to 5-hydroxymethylcytosine (5hmC) is associated with transcriptional activation. Here we perform the first study integrating whole-genome 5hmC with DNA, 5mC, and transcriptome sequencing in clinical samples of benign, localized, and advanced prostate cancer. 5hmC is shown to mark activation of cancer drivers and downstream targets. Furthermore, 5hmC sequencing revealed profoundly altered cell states throughout the disease course, characterized by increased proliferation, oncogenic signaling, dedifferentiation, and lineage plasticity to neuroendocrine and gastrointestinal lineages. Finally, 5hmC sequencing of cell-free DNA from patients with metastatic disease proved useful as a prognostic biomarker able to identify an aggressive subtype of prostate cancer using the genes TOP2A and EZH2, previously only detectable by transcriptomic analysis of solid tumor biopsies. Overall, these findings reveal that 5hmC marks epigenomic activation in prostate cancer and identify hallmarks of prostate cancer progression with potential as biomarkers of aggressive disease.SIGNIFICANCE: In prostate cancer, 5-hydroxymethylcytosine delineates oncogene activation and stage-specific cell states and can be analyzed in liquid biopsies to detect cancer phenotypes. See related article by Wu and Attard, p. 3880.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-22-1123
  42. J Gynecol Oncol. 2022 Aug 23.
    SP1-induced lncRNA MCF2L-AS1 promotes cisplatin resistance in ovarian cancer by regulating IGF2BP1/IGF2/MEK/ERK axis.
    Yan Zhu, Lijuan Yang, Jianqing Wang, Yan Li, Youguo Chen.
      OBJECTIVE: Cisplatin resistance is a huge problem encountered in ovarian cancer treatment. Our study probed the roles and the underlying mechanisms of lncRNA MCF2L-AS1 in ovarian cancer cisplatin-resistance.METHODS: SKOV3 and IGROV-1 cells were subjected to gradually increasing concentrations of cisplatin to construct ovarian cancer cisplatin-resistance cells. Cell proliferation was evaluated by cell counting kit-8 and colony formation assays. Cell apoptosis was assessed using Annexin V and PI staining. The relationships between SP1, MCF2L-AS1 and insulin-like growth factor-2 mRNA binding protein 1 (IGF2BP1) were verified by RNA pull-down, RIP, ChIP and dual-luciferase reporter gene assay, respectively. Tumor xenograft experiment was employed to evaluate the effects of MCF2L-AS1 silencing on ovarian cancer cisplatin-resistance in vivo. TUNEL staining and immunohistochemistry were performed in tumor tissue.
    RESULTS: MCF2L-AS1 and IGF2BP1 were upregulated in cisplatin-resistant cells. MCF2L-AS1 silencing suppressed cell proliferation of cisplatin-resistant cells, while promoted the apoptosis, suggesting that MCF2L-AS1 knockdown suppressed ovarian cancer cells cisplatin-resistance. Meanwhile, MCF2L-AS1 silencing enhanced cisplatin sensitivity in ovarian cancer parental cells and IGF2BP1 overexpression impaired cisplatin sensitivity of parental cells. MCF2L-AS1 activated IGF2/MEK/ERK pathway through interacting with IGF2BP1. Transcription factor SP1 activated MCF2L-AS1 expression. MCF2L-AS1 knockdown inhibited ovarian cancer cisplatin-resistance in vivo.
    CONCLUSION: SP1-induced MCF2L-AS1 promoted ovarian cancer cisplatin-resistance through activation of IGF2/MEK/ERK pathway via interacting with IGF2BP1.
    Keywords:  Cisplatin; IGF2/MEK/ERK Signaling Pathway; IGF2BP1; LncRNA MCF2L-AS1; Ovarian Cancer; SP1
    DOI:  https://doi.org/10.3802/jgo.2022.33.e75
  43. Angew Chem Int Ed Engl. 2022 Oct 17.
    Photo-Facilitated Detection and Sequencing of 5-Formylcytidine RNA.
    Xiao-Yang Jin, Zu-Rui Huang, Li-Jun Xie, Li Liu, Da-Li Han, Liang Cheng.
      5-Formylcytidine f5C is one of the epigenetic nucleotides in tRNA. Despite the evident importance of f5C in gene expression regulation, little is known about its exact amount and position. To capture this information, we developed a modification-specific functionalization with a semi-stabilized ylide. The chemical labelling exhibited a high selectivity towards f5C and allowed distinction from similar 5-formyluridine. We realized a detection strategy based on the fluorescence signal of the cyclization product 4,5-pyridin-2-amine-cytidine paC, which exhibited a high quantum yield. The results clearly identified f5C with a limit of detectionat 0.58 nM. This method altered the hydrogen bonding activities of f5C and modulated of its reverse transcription signature in sequencing profile. We showed that f5C can be detected from tRNA segments with a single-base resolution. Taken together, this approach represents a sensitive, antibody-free and applicable detection and sequencing to f5C RNA.
    Keywords:  5-formylcytidine; Chemical labelling; Photochemical cyclization; RNA modification; sequencing
    DOI:  https://doi.org/10.1002/anie.202210652
  44. J Oncol. 2022 ;2022 9188920
    YTHDC2 Promotes Malignant Phenotypes of Breast Cancer Cells.
    Atsushi Tanabe, Takatoshi Nakayama, Jo Kashiyanagi, Hitoshi Yamaga, Yoshihiko Hirohashi, Toshihiko Torigoe, Fukino Satomi, Hiroaki Shima, Hideki Maeda, Goro Kutomi, Ichiro Takemasa, Hiroeki Sahara.
      YTH domain-containing 2 (YTHDC2) is known to be an important regulator for RNA metabolism. Here, we show that YTHDC2 is essential for breast cancer tumorigenesis and metastasis. We examined YTHDC2 expression levels by immunohistochemistry in human breast tumor tissues from 99 patients and found a significantly positive correlation between the YTHDC2 expression level and the tumor stage. We established YTHDC2-knocked-down cell lines using four breast cancer cell lines with different subtypes. Knockdown of YTHDC2 attenuated the sphere-forming and the metastatic ability of breast cancer cells. Although stemness and EMT markers, such as SOX2, c-MYC, and NANOG, were downregulated in several YTHDC2-knocked-down breast cancer cells, a common target gene of YTHDC2 in breast cancer cells was not identified. These findings suggest that while YTHDC2 is involved in malignant progression of breast cancers, the mechanism by which YTHDC2 regulates those phenotypes is different between subtypes of breast cancers.
    DOI:  https://doi.org/10.1155/2022/9188920
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