bims-rimeca Biomed News
on RNA methylation in cancer
Issue of 2023‒04‒16
forty papers selected by
Sk Ramiz Islam
Saha Institute of Nuclear Physics
  1. m6A regulator-mediated RNA methylation modification patterns are involved in the regulation of the immune microenvironment in ischaemic cardiomyopathy.
  2. N6-methyladenosine regulator-mediated methylation modification patterns and immune infiltration characterization in Polycystic Ovary Syndrome (PCOS).
  3. METTL3 enhances dentinogenesis differentiation of dental pulp stem cells via increasing GDF6 and STC1 mRNA stability.
  4. Functions of N6-methyladenosine in cancer metabolism: from mechanism to targeted therapy.
  5. Integrated analysis of transcriptome-wide m6A methylation in a Cd-induced kidney injury rat model.
  6. The emerging importance role of m6A modification in liver disease.
  7. LncRNA DGUOK-AS1 facilitates non-small cell lung cancer growth and metastasis through increasing TRPM7 stability via m6A modification.
  8. Cancer-associated fibroblasts promote migration and invasion of non-small cell lung cancer cells via METTL3-mediated RAC3 m6A modification.
  9. IGF2BP3 Regulates TMA7-mediated Autophagy and Cisplatin Resistance in Laryngeal Cancer via m6A RNA Methylation.
  10. M6A-modified circRBM33 promotes prostate cancer progression via PDHA1-mediated mitochondrial respiration regulation and presents a potential target for ARSI therapy.
  11. N6-methyladenosine-methylomic landscape of lung tissues of mice with chronic obstructive pulmonary disease.
  12. YBX2 modulates mRNA stability via interaction with YTHDF2 in endometrial cancer cells.
  13. Depletion of the m6A demethylases FTO and ALKBH5 impairs growth and metastatic capacity through EMT phenotype change in clear cell renal cell carcinoma.
  14. Targeted Demethylation of the TGFβ1 mRNA Promotes Myoblast Proliferation via Activating the SMAD2 Signaling Pathway.
  15. RNA methylation-related genes of m6A, m5C, and m1A predict prognosis and immunotherapy response in cervical cancer.
  16. Donor graft METTL3 gene transfer ameliorates rat liver transplantation ischemia-reperfusion injury by enhancing HO-1 expression in an m6A-dependent manner.
  17. Cobalt induces neurodegeneration through FTO-triggered autophagy impairment by targeting TSC1 in an m6A-YTHDF2-dependent manner.
  18. RUNX1-IT1 favors breast cancer carcinogenesis through regulation of IGF2BP1/GPX4 axis.
  19. METTL14 is a chromatin regulator independent of its RNA N6-methyladenosine methyltransferase activity.
  20. The m6A methylation landscape, molecular characterization and clinical relevance in prostate adenocarcinoma.
  21. DARS2 is a prognostic biomarker and correlated with immune infiltrates and cuproptosis in lung adenocarcinoma.
  22. Biological function analysis of ARHGAP39 as an independent prognostic biomarker in hepatocellular carcinoma.
  23. 5-methyladenosine regulators play a crucial role in development of chronic hypersensitivity pneumonitis and idiopathic pulmonary fibrosis.
  24. FTO promotes cervical cancer cell proliferation, colony formation, migration and invasion via the regulation of the BMP4/Hippo/YAP1/TAZ pathway.
  25. Evaluation of epitranscriptome-wide N6-methyladenosine differential analysis methods.
  26. NR3C1/Glucocorticoid receptor activation promotes pancreatic β-cell autophagy overload in response to glucolipotoxicity.
  27. N6-methyladenosine RNA methylation modulates liquid‒liquid phase separation in plants.
  28. Analysis of the prognostic significance and potential mechanisms of lncRNAs related to m6A methylation in laryngeal cancer.
  29. IGF2BP2 promotes lncRNA DANCR stability mediated glycolysis and affects the progression of FLT3-ITD + acute myeloid leukemia.
  30. Chemical Space Virtual Screening against Hard-to-Drug RNA Methyltransferases DNMT2 and NSUN6.
  31. Long noncoding RNA DIAPH2-AS1 promotes neural invasion of gastric cancer via stabilizing NSUN2 to enhance the m5C modification of NTN1.
  32. Prognostic Value and Genome Signature of m6A/m5C Regulated Genes in Early-Stage Lung Adenocarcinoma.
  33. Ubiquitin-proteasome system-mediated ubiquitination modification patterns and characterization of tumor microenvironment infiltration, stemness and cellular senescence in low-grade glioma.
  34. Sestrin2-mediated disassembly of stress granules dampens aerobic glycolysis to overcome glucose starvation.
  35. Fatty Acid Excess Dysregulates CARF to Initiate the Development of Hepatic Steatosis.
  36. An in vivo CRISPR screen identifies that SNRPC promotes triple-negative breast cancer progression.
  37. TJP1 promotes vascular mimicry in bladder cancer by facilitating VEGFA expression and transcriptional activity through TWIST1.
  38. The kinesin light chain-2, a target of mRNA stabilizing protein HuR, inhibits p53 protein phosphorylation to promote radioresistance in NSCLC.
  39. Accumulation of m 6 A exhibits stronger correlation with MAPT than β-amyloid pathology in an APP NL-G-F /MAPT P301S mouse model of Alzheimer's disease.
  40. Downregulation of KIAA1199 alleviated the activation, proliferation, and migration of hepatic stellate cells by the inhibition of epithelial-mesenchymal transition.
  1. Sci Rep. 2023 Apr 11. 13(1): 5904
    m6A regulator-mediated RNA methylation modification patterns are involved in the regulation of the immune microenvironment in ischaemic cardiomyopathy.
    Peng-Fei Zheng, Xiu-Qin Hong, Zheng-Yu Liu, Zhao-Fen Zheng, Peng Liu, Lu-Zhu Chen.
      The role of RNA N6-methyladenosine (m6A) modification in the regulation of the immune microenvironment in ischaemic cardiomyopathy (ICM) remains largely unclear. This study first identified differential m6A regulators between ICM and healthy samples, and then systematically evaluated the effects of m6A modification on the characteristics of the immune microenvironment in ICM, including the infiltration of immune cells, the human leukocyte antigen (HLA) gene, and HALLMARKS pathways. A total of seven key m6A regulators, including WTAP, ZCH3H13, YTHDC1, FMR1, FTO, RBM15 and YTHDF3, were identified using a random forest classifier. A diagnostic nomogram based on these seven key m6A regulators could effectively distinguish patients with ICM from healthy subjects. We further identified two distinct m6A modification patterns (m6A cluster-A and m6A cluster-B) that are mediated by these seven regulators. Meanwhile, we also noted that one m6A regulator, WTAP, was gradually upregulated, while the others were gradually downregulated in the m6A cluster-A vs. m6A cluster-B vs. healthy subjects. In addition, we observed that the degree of infiltration of the activated dendritic cells, macrophages, natural killer (NK) T cells, and type-17 T helper (Th17) cells gradually increased in m6A cluster-A vs. m6A cluster-B vs. healthy subjects. Furthermore, m6A regulators, including FTO, YTHDC1, YTHDF3, FMR1, ZC3H13, and RBM15 were significantly negatively correlated with the above-mentioned immune cells. Additionally, several differential HLA genes and HALLMARKS signalling pathways between the m6A cluster-A and m6A cluster-B groups were also identified. These results suggest that m6A modification plays a key role in the complexity and diversity of the immune microenvironment in ICM, and seven key m6A regulators, including WTAP, ZCH3H13, YTHDC1, FMR1, FTO, RBM15, and YTHDF3, may be novel biomarkers for the accurate diagnosis of ICM. Immunotyping of patients with ICM will help to develop immunotherapy strategies with a higher level of accuracy for patients with a significant immune response.
    DOI:  https://doi.org/10.1038/s41598-023-32919-4
  2. J Ovarian Res. 2023 Apr 12. 16(1): 73
    N6-methyladenosine regulator-mediated methylation modification patterns and immune infiltration characterization in Polycystic Ovary Syndrome (PCOS).
    Sihan Zhou, Rui Hua, Song Quan.
      BACKGROUND: Polycystic ovary syndrome (PCOS) is a multisystem-related disease whose pathophysiology is still unclear. Several regulators of N6-methyladenosine (m6A) modification were confirmed to play a regulatory role in PCOS. Nonetheless, the roles of m6A regulators in PCOS are not fully demonstrated.MATERIALS AND METHODS: Four mRNA expression profiling microarrays were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed m6A regulators between PCOS and normal patients were identified by R software. A random forest modal and nomogram were developed to assess the relationship between m6A regulators and the occurrence risk of PCOS. A consensus clustering method was utilized to distinctly divide PCOS patients into two m6A subtypes (m6A cluster A/B). The patterns of differential expression and immune infiltration were explored between the two m6A clusters.
    RESULTS: In this study, 22 significant m6A regulators were identified between healthy controls and PCOS patients. The random forest model determined three optimal m6A regulators which are related to the occurrence risk of PCOS, including YTHDF1, RBM15 and METTL14. A nomogram was established based on these genes, and its predictive reliability was validated by decision curve analysis. The consensus clustering algorithm distinctly divided PCOS cases into two m6A subtypes. The ssGSEA algorithm found that the immune infiltration was markedly enriched in m6A cluster B than in cluster A. The m6A-pattern related differentially expressed genes (DEGs) of the two m6A subtypes were demonstrated by differential expression analysis. We found that they were enriched in immune-related genes and various infection pathways. Based on the m6A-pattern related DEGs, the PCOS patients were classified into two m6A-pattern related genomic subtypes (gene clusters A and B).
    CONCLUSIONS: The present study provided evidence concerning the different modification patterns of m6A regulators in PCOS compared with normal patients. This study will help clarify the overall impact of m6A modification patterns and related immune infiltration on PCOS.
    Keywords:  Bioinformatics analysis; M6A regulators; N6-methyladenosine; Polycystic ovary syndrome
    DOI:  https://doi.org/10.1186/s13048-023-01147-9
  3. BMC Oral Health. 2023 04 11. 23(1): 209
    METTL3 enhances dentinogenesis differentiation of dental pulp stem cells via increasing GDF6 and STC1 mRNA stability.
    Yue Pan, Ying Liu, Dixin Cui, Sihan Yu, Yachuan Zhou, Xin Zhou, Wei Du, Liwei Zheng, Mian Wan.
      BACKGROUND: The dentinogenesis differentiation of dental pulp stem cells (DPSCs) is controlled by the spatio-temporal expression of differentiation related genes. RNA N6-methyladenosine (m6A) methylation, one of the most abundant internal epigenetic modification in mRNA, influences various events in RNA processing, stem cell pluripotency and differentiation. Methyltransferase like 3 (METTL3), one of the essential regulators, involves in the process of dentin formation and root development, while mechanism of METTL3-mediated RNA m6A methylation in DPSC dentinogenesis differentiation is still unclear.METHODS: Immunofluorescence staining and MeRIP-seq were performed to establish m6A modification profile in dentinogenesis differentiation. Lentivirus were used to knockdown or overexpression of METTL3. The dentinogenesis differentiation was analyzed by alkaline phosphatase, alizarin red staining and real time RT-PCR. RNA stability assay was determined by actinomycin D. A direct pulp capping model was established with rat molars to reveal the role of METTL3 in tertiary dentin formation.
    RESULTS: Dynamic characteristics of RNA m6A methylation in dentinogenesis differentiation were demonstrated by MeRIP-seq. Methyltransferases (METTL3 and METTL14) and demethylases (FTO and ALKBH5) were gradually up-regulated during dentinogenesis process. Methyltransferase METTL3 was selected for further study. Knockdown of METTL3 impaired the DPSCs dentinogenesis differentiation, and overexpression of METTL3 promoted the differentiation. METTL3-mediated m6A regulated the mRNA stabiliy of GDF6 and STC1. Furthermore, overexpression of METTL3 promoted tertiary dentin formation in direct pulp capping model.
    CONCLUSION: The modification of m6A showed dynamic characteristics during DPSCs dentinogenesis differentiation. METTL3-mediated m6A regulated in dentinogenesis differentiation through affecting the mRNA stability of GDF6 and STC1. METTL3 overexpression promoted tertiary dentin formation in vitro, suggesting its promising application in vital pulp therapy (VPT).
    Keywords:  Dentinogenesis; Epigenesis; METTL3; Mesenchymal stem cells; RNA stability
    DOI:  https://doi.org/10.1186/s12903-023-02836-z
  4. Biomark Res. 2023 Apr 13. 11(1): 40
    Functions of N6-methyladenosine in cancer metabolism: from mechanism to targeted therapy.
    Jiayi He, Furong Liu, Zhanguo Zhang.
      N6-methyladenosine (m6A) is the most abundant modification of eukaryotic mRNA and is involved in almost every stage of RNA metabolism. The m6A modification on RNA has been demonstrated to be a regulator of the occurrence and development of a substantial number of diseases, especially cancers. Increasing evidence has shown that metabolic reprogramming is a hallmark of cancer and is crucial for maintaining the homeostasis of malignant tumors. Cancer cells rely on altered metabolic pathways to support their growth, proliferation, invasion and metastasis in an extreme microenvironment. m6A regulates metabolic pathways mainly by either directly acting on metabolic enzymes and transporters or indirectly influencing metabolism-related molecules. This review discusses the functions of the m6A modification on RNAs, its role in cancer cell metabolic pathways, the possible underlying mechanisms of its effects and the implication of this modification in cancer therapy.
    Keywords:  Cancer; Metabolic reprogramming; N6-methyladenosine
    DOI:  https://doi.org/10.1186/s40364-023-00483-8
  5. Ecotoxicol Environ Saf. 2023 Apr 11. pii: S0147-6513(23)00407-4. [Epub ahead of print]256 114903
    Integrated analysis of transcriptome-wide m6A methylation in a Cd-induced kidney injury rat model.
    Shuangjing Li, Han Zhou, Yufen Liang, Qian Yang, Jiachen Zhang, Weitong Shen, Lijian Lei.
      BACKGROUND: Accumulating evidence has demonstrated that N6-methyladenosine (m6A) plays important roles in a variety of diseases. However, the specific functions of m6A in CdCl2-induced kidney injury remain unclear.OBJECTIVE: Here, we investigate a transcriptome-wide map of m6A modifications and explore the effects of m6A on Cd-induced kidney injury.
    MATERIALS AND METHODS: The rat kidney injury model was constructed by subcutaneous injection of CdCl2 (0.5, 1.0, and 2.0 mg/kg). The m6A levels were measured by colorimetry. The level of expression of m6A-related enzymes were detected by reverse transcription quantitative real-time PCR analysis. Transcriptome-wide m6A methylome in CdCl2 (2.0 mg/kg) and the control group were profiled by methylated RNA immunoprecipitation sequencing (MeRIP-seq). Subsequently, the sequencing data were analyzed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG), while gene set enrichment analysis (GSEA) confirmed the functional enrichment pathways of sequencing genes. In addition, a protein-protein interaction (PPI) network was applied to select hub genes.
    RESULTS: The levels of m6A and m6A regulators (METTL3, METTL14, WTAP, YTHDF2) were significantly increased in CdCl2 groups. We identified a total of 2615 differentially expressed m6A peaks, 868 differentially expressed genes and 200 genes with significant changes in both m6A modification and gene expression levels. GO, KEGG, and GSEA analyses indicated that these genes were mainly enriched in inflammation and metabolism-related pathways such as in IL-17 signaling and fatty acid metabolism. According the result of the conjoint analysis, we identified the top ten hub genes (Fos, Hsp90aa1, Gata3, Fcer1g, Cftr, Cspg4, Atf3, Cdkn1a, Ptgs2, and Npy) which may be regulated by m6A and involve in CdCl2-induced kidney damage.
    CONCLUSION: This study established a m6A transcriptional map in a CdCl2-induced kidney injury model and suggested that m6A may affect CdCl2 induced kidney injury via regulated the inflammation and metabolism related gene.
    Keywords:  CdCl(2)-induced kidney injury; M(6)A methylation; MeRIP-seq; PPI network; RNA-seq
    DOI:  https://doi.org/10.1016/j.ecoenv.2023.114903
  6. Biomed Pharmacother. 2023 Apr 08. pii: S0753-3322(23)00457-2. [Epub ahead of print]162 114669
    The emerging importance role of m6A modification in liver disease.
    Sheng Wang, Songsen Gao, Wufei Ye, Yueran Li, Jiajie Luan, Xiongwen Lv.
      N6-methyladenosine (m6A) modification, as one of the most common types of inner RNA modification in eukaryotes, plays a multifunctional role in normal and abnormal biological processes. This type of modification is modulated by m6A writer, eraser and reader, which in turn impact various processes of RNA metabolism, such as RNA processing, translation, nuclear export, localization and decay. The current academic view holds that m6A modification exerts a crucial role in the post-transcriptional modulation of gene expression, and is involved in multiple cellular functions, developmental and disease processes. However, the potential molecular mechanism and specific role of m6A modification in the development of liver disease have not been fully elucidated. In our review, we summarized the latest research progress on m6A modification in liver disease, and explored how these novel findings reshape our knowledge of m6A modulation of RNA metabolism. In addition, we also illustrated the effect of m6A on liver development and regeneration to prompt further exploration of the mechanism and role of m6A modification in liver physiology and pathology, providing new insights and references for the search of potential therapeutic targets for liver disease.
    Keywords:  HCC; Liver disease; METTL3; m6A modification
    DOI:  https://doi.org/10.1016/j.biopha.2023.114669
  7. Transl Oncol. 2023 Apr 08. pii: S1936-5233(23)00047-5. [Epub ahead of print]32 101661
    LncRNA DGUOK-AS1 facilitates non-small cell lung cancer growth and metastasis through increasing TRPM7 stability via m6A modification.
    Yimin Feng, Fengjuan Wu, Yuanning Wu, Zihan Guo, Xiang Ji.
      BACKGROUND: N6-methyladenosine (m6A) modification plays key roles in tumor progression. LncRNA deoxyguanosine kinase antisense RNA 1 (DGUOK-AS1) has been reported as a promoter in tumors, but its role and mechanism in non-small cell lung cancer (NSCLC) development remain uncertain.METHODS: Cell proliferation, migration, invasion and angiogenesis were investigated via CCK-8, colony formation, transwell, and tube formation assays, respectively. The location of DGUOK-AS1 was detected via FISH assay. The interaction relationship among DGUOK-AS1, IGF2BP2 and TRPM7 was confirmed by RIP and MeRIP assays. The effects of DGUOK-AS1 on NSCLC growth and metastasis in vivo were investigated using xenograft and pulmonary metastatic models.
    RESULTS: DGUOK-AS1 was upregulated in NSCLC. DGUOK-AS1 silencing inhibited NSCLC cell proliferation, migration, invasion and angiogenesis. DGUOK-AS1 was mostly expressed in cytoplasm, and positively regulated IGF2BP2. METTL3/IGF2BP2 axis could increase TRPM7 mRNA stability in m6A-dependent manner. TRPM7 overexpression reversed the inhibitive function of DGUOK-AS1 silencing on NSCLC development. DGUOK-AS1 knockdown suppressed NSCLC cell growth and metastasis in nude mice.
    CONCLUSION: DGUOK-AS1 silencing restrains NSCLC cell growth and metastasis through decreasing TRPM7 stability via regulation of the METTL3/IGF2BP2-mediated m6A modification.
    Keywords:  DGUOK-AS1; Growth; Metastasis; NSCLC; m6A modification
    DOI:  https://doi.org/10.1016/j.tranon.2023.101661
  8. Int J Biol Sci. 2023 ;19(5): 1616-1632
    Cancer-associated fibroblasts promote migration and invasion of non-small cell lung cancer cells via METTL3-mediated RAC3 m6A modification.
    Mengmeng Chen, Qicheng Zhang, Sijia Zheng, Xueru Guo, Limin Cao, Yinghui Ren, Yongmei Qian, Min Wang, Xiang Wu, Ke Xu.
      Cancer progression depends on the communication between tumor cells and tumor microenvironment. Cancer-associated fibroblasts (CAFs) are a major component of stromal cells. CAFs promote cancer metastasis; however, it has not been evaluated whether N6-methyladenosine (m6A) modification is responsible for CAFs' role in metastasis. In the present study, we found that CAFs promoted migration and invasion of non-small cell lung cancer (NSCLC) cells by elevating m6A modification in NSCLC cells. Methyltransferase-like 3 (METTL3) in NSCLC cells mediated CAFs' effect on m6A modification, and was regulated by CAFs-secreted vascular endothelial growth factor A (VEGFA). METTL3 knockdown in NSCLC cells dramatically inhibited cell migration and invasion, and suppressed tumor growth in vivo. Database analysis revealed that METTL3 was associated with poor prognosis of lung cancer. The mechanism study showed that METTL3 increased m6A level of RAC3 mRNA, resulting in increased stability and translation of RAC3 mRNA. RAC3 was responsible for the CAFs' promoting effect on cell migration via the AKT/NF-κB pathway. This study established a CAF-METTL3-RAC3 m6A modification-dependent regulation system in NSCLC metastasis, suggesting potential candidates for metastasis treatment.
    Keywords:  Cancer-associated fibroblasts; Lung cancer; METTL3; Metastasis; RAC3; m6A
    DOI:  https://doi.org/10.7150/ijbs.79467
  9. Int J Biol Sci. 2023 ;19(5): 1382-1400
    IGF2BP3 Regulates TMA7-mediated Autophagy and Cisplatin Resistance in Laryngeal Cancer via m6A RNA Methylation.
    Like Yang, Bingrui Yan, Lingmei Qu, Jingyuan Ren, Qiuying Li, Jingting Wang, Xuan Kan, Ming Liu, Yakun Wang, Yanan Sun, Chao Wang, Peng Wang.
      Translation machinery associated 7 homolog (TMA7) is closely related to proliferation-related diseases. However, the function and regulatory mechanism of TMA7 in laryngeal squamous cell carcinoma (LSCC) remain unclear. The present study aimed to investigate the effect of TMA7 on the occurrence and development of LSCC and to study the mechanism of TMA7. TMA7 is upregulated in LSCC tissues and associated with poor prognosis. After TMA7 downregulation, the autophagy level was increased, and the proliferation, migration, and invasion of LSCC cells were inhibited. The m6A methylated reader IGF2BP3 enhanced the stability of TMA7 and reduced the level of autophagy. TMA7 interacted directly with UBA2. Furthermore, the activation of the IGF2BP3-regulated TMA7-UBA2-PI3K pathway is the primary mechanism by which TMA7 inhibits autophagy and promotes the progression of LSCC. The current study revealed that IGF2BP3-mediated TMA7 m6A modification promotes LSCC progression and cisplatin-resistance through UBA2-PI3K pathway, providing new insights into the autophagy-related mechanism, potential biomarkers, and therapeutic targets for LSCC.
    Keywords:  LSCC; TMA7; UBA2; autophagy.; cisplatin resistance; m6A RNA modification
    DOI:  https://doi.org/10.7150/ijbs.80921
  10. Int J Biol Sci. 2023 ;19(5): 1543-1563
    M6A-modified circRBM33 promotes prostate cancer progression via PDHA1-mediated mitochondrial respiration regulation and presents a potential target for ARSI therapy.
    Chuanfan Zhong, Zining Long, Taowei Yang, Shuo Wang, Weibo Zhong, Feng Hu, Jeremy Yuen-Chun Teoh, Jianming Lu, Xiangming Mao.
      N6-Methyladenosine (m6A) is the most prevalent RNA modification in various types of RNA, including circular RNAs (circRNAs). Mounting evidence has shown that circRNAs may play critical roles in diverse malignancies. However, the biological relevance of m6A modification of circRNAs in prostate cancer (PCa) remains unclear and needs to be elucidated. Our data showed that circRBM33 was m6A-modified and was more highly expressed in PCa cells than in normal cells/tissues. The in vitro and in vivo experiments showed that downregulation/upregulation of circRBM33 inhibited/promoted tumour growth and invasion, respectively. Decreasing m6A levels rescued the tumour-promoting effect of circRBM33. Additionally, once modified by m6A, circRBM33 interacts with FMR1 by forming a binary complex that sustains the mRNA stability of PDHA1, a downstream target gene. Suppressed/overexpressed circRBM33 lowered/enhanced the ATP production, the acetyl-CoA levels and the NADH/NAD+ ratio. Moreover, depletion of circRBM33 significantly increased the response sensitivity to androgen receptor signalling inhibitor (ARSI) therapy, including enzalutamide and darolutamide, in prostate tumours. Our study suggested that the m6A-mediated circRBM33-FMR1 complex can activate mitochondrial metabolism by stabilizing PDHA1 mRNA, which promotes PCa progression, and can attenuate circRBM33 increased ARSI effectiveness in PCa treatment. This newly discovered circRNA may serve as a potential therapeutic target for PCa.
    Keywords:  ARSI therapy; N6-methyladenosine; Prostate cancer; circRBM33; mitochondrial respiration
    DOI:  https://doi.org/10.7150/ijbs.77133
  11. Front Immunol. 2023 ;14 1137195
    N6-methyladenosine-methylomic landscape of lung tissues of mice with chronic obstructive pulmonary disease.
    Tingting Hu, Lijuan Xu, Min Jiang, Fengbo Zhang, Qifeng Li, Zhiwei Li, Chao Wu, Jianbing Ding, Fengsen Li, Jing Wang.
      Chronic obstructive pulmonary disease (COPD), a common respiratory disease, can be divided into stable phase and acute exacerbation phase (AECOPD) and is characterized by inflammation and hyper-immunity. Methylation of N6-methyladenosine (m6A) is an epigenetic modification that regulates the expression and functions of genes by influencing post-transcriptional RNA modifications. Its influence on the immune regulation mechanism has attracted great attention. Herein, we present the m6Amethylomic landscape and observe how the methylation of m6A participates in the pathological process of COPD. The m6A modification of 430 genes increased and that of 3995 genes decreased in the lung tissues of mice with stable COPD. The lung tissues of mice with AECOPD exhibited 740 genes with hypermethylated m6A peak and 1373 genes with low m6A peak. These differentially methylated genes participated in signaling pathways related to immune functions. To further clarify the expression levels of differentially methylated genes, RNA immunoprecipitation sequencing (MeRIP-seq) and RNA-sequencing data were jointly analyzed. In the stable COPD group, 119 hypermethylated mRNAs (82 upregulated and 37 downregulated mRNAs) and 867 hypomethylated mRNAs (419 upregulated and 448 downregulated mRNAs) were differentially expressed. In the AECOPD group, 87 hypermethylated mRNAs (71 upregulated and 16 downregulated mRNAs) and 358 hypomethylated mRNAs (115 upregulated and 243 downregulated mRNAs) showed differential expression. Many mRNAs were related to immune function and inflammation. Together, this study provides important evidence on the role of RNA methylation of m6A in COPD.
    Keywords:  COPD; MeRIP-seq; N6-methyladenosine; lung tissue; m6A; mouse
    DOI:  https://doi.org/10.3389/fimmu.2023.1137195
  12. Exp Cell Res. 2023 Apr 06. pii: S0014-4827(23)00133-7. [Epub ahead of print]427(1): 113586
    YBX2 modulates mRNA stability via interaction with YTHDF2 in endometrial cancer cells.
    Ying Cai, Na Li, Huaibiao Li.
      RNA-binding proteins (RBPs) fine-tune gene expression by modulating RNA stability, translation, and degradation. RBPs are involved in the development of endometrial cancer. In particular, Y-box-binding protein 2 (YBX2), a germ cell-specific member of the YBX family, has been reported to maintain cancer stem cell-like phenotypes in endometrial cancer. However, the mechanism by which YBX2 modulates mRNA stability in endometrial cancer cells remains unknown. In this study, we examined the effects of the ectopic expression of YBX2 in endometrial adenocarcinoma-derived Ishikawa cells. We found that elevated levels of YBX2 delayed cell proliferation, without increasing cell apoptosis. Transcriptomic analysis revealed disturbances in gene expression caused by YBX2. Interestingly, heat shock protein family A (Hsp70) member 6 (HSPA6) levels were downregulated due to the reduced mRNA stability after YBX2 binding. YBX2 facilitated the formation of relatively stable cytoplasmic granules in tumor cells via its mRNA binding domain. Moreover, N6-methyladenosine (m6A) reader proteins are recruited by YBX2 granules via the cold-shock domain. Notably, knockdown of YTH N6-methyladenosine RNA-binding protein F2 (YTHDF2), an m6A reader, ameliorated the reduction in HSPA6 mRNA levels induced by YBX2, indicating the synergistic effects of YBX2 and YTHDF2 on mRNA stability. Therefore, YBX2 regulates RNA stability by interacting with the m6A reader proteins.
    Keywords:  HSPA6; RNA stability; RNA-binding protein; YBX2; YTHDF2
    DOI:  https://doi.org/10.1016/j.yexcr.2023.113586
  13. Am J Transl Res. 2023 ;15(3): 1744-1755
    Depletion of the m6A demethylases FTO and ALKBH5 impairs growth and metastatic capacity through EMT phenotype change in clear cell renal cell carcinoma.
    Wei Hu, Niklas Klümper, Doris Schmidt, Manuel Ritter, Jörg Ellinger, Stefan Hauser.
      BACKGROUND: N6-methyladenosine (m6A) is one of the most common RNA modifications in eukaryotes and has effects on RNA structure and stability. Recent studies have shown that m6A methylation is involved in human carcinogenesis. In the present study, we investigated the effects of m6A demethylases FTO and ALKBH5 on renal cell carcinoma (RCC) cell lines.METHODS: The epithelial-mesenchymal in vitro knockdowns of FTO and ALKBH5 induced by antisense oligonucleotides (LNA-GapmeR system) were established in RCC cell lines. Their effects on migration and proliferation were investigated subsequently. The influence of FTO and ALKBH5 knockdown on key epithelial-mesenchymal transition (EMT) genes was analyzed.
    RESULTS: Inactivation of FTO and ALKBH5 resulted in decreased proliferation and motility in all cell lines examined (ACHN, Caki-1, 769-P). Vimentin (VIM) was downregulated after the knockdown of FTO and ALKBH5, indicating an EMT switch.
    CONCLUSIONS: Knockdown of the m6A erasers FTO and ALKBH5 inhibits the malignant potential in the cell cultures studied by means of an EMT switch.
    Keywords:  ALKBH5; FTO; clear cell renal cell carcinoma (ccRCC); epithelial-mesenchymal transition (EMT); m6A-erasers
  14. Cells. 2023 Mar 24. pii: 1005. [Epub ahead of print]12(7):
    Targeted Demethylation of the TGFβ1 mRNA Promotes Myoblast Proliferation via Activating the SMAD2 Signaling Pathway.
    Kaiping Deng, Zhipeng Liu, Xiaodan Li, Zhen Zhang, Yixuan Fan, Qunhao Huang, Yanli Zhang, Feng Wang.
      Recent evidence suggested that N6-methyladenosine (m6A) methylation can determine m6A-modified mRNA fate and play an important role in skeletal muscle development. It was well known that transforming growth factor beta 1 (TGFβ1) is involved in a variety of cellular processes, such as proliferation, differentiation, and apoptosis. However, little is known about the m6A-mediated TGFβ1 regulation in myogenesis. Here, we observed an increase in endogenous TGFβ1 expression and activity during myotube differentiation. However, the knockdown of TGFβ1 inhibits the proliferation and induces cell apoptosis of myoblast. Moreover, we found that m6A in 5'-untranslated regions (5'UTR) of TGFβ1 promote its decay and inhibit its expression, leading to the blockage of the TGFβ1/SMAD2 signaling pathway. Furthermore, the targeted specific demethylation of TGFβ1 m6A using dCas13b-FTO significantly increased the TGFβ1-mediated activity of the SMAD2 signaling pathway, promoting myoblast proliferation. These findings suggest that TGFβ1 is an essential regulator of myoblast growth that is negatively regulated by m6A. Overall, these results highlight the critical role of m6A-mediated post-transcriptional regulation in myogenesis.
    Keywords:  TGFβ1; cell proliferation; dCas13b; m6A; myoblast
    DOI:  https://doi.org/10.3390/cells12071005
  15. Ann Med. 2023 Dec;55(1): 2190618
    RNA methylation-related genes of m6A, m5C, and m1A predict prognosis and immunotherapy response in cervical cancer.
    Yan Wang, Yiwen Mao, Caizhi Wang, Xuefeng Jiang, Qionglan Tang, Lingling Wang, Jialei Zhu, Mengqiu Zhao.
      PURPOSE: To investigate the prognostic value of N6-methyladenosine (m6A)-, 5-methylcytosine (m5C)-, and N1-methyladenosine (m1A)-related genes in cervical cancer (CESC) and predicting immunotherapy response.METHODS: We downloaded cervical cancer mRNA expression profiles, clinical data, and m6A, m5C, m1A-related genes from public databases, and subjected them to serial bioinformatics analysis and clinical sample validation.
    RESULTS: Differential analysis revealed 106 methylation-related differential genes (MEDs), including 44 differentially downregulated and 62 upregulated genes. We then obtained methylation models containing 10 genes by univariate and multifactorial COX analysis. High risk genes with HR > 1 include IQGAP3, PTBP1, STAC3, CUX1, SLC2A1, and CA2, and low risk genes with HR < 1 include IGBP1, DUOX1, CHAF1A, and STAC3. We verified the accuracy of the model from inside TCGA and outside GSE39001 (AUC = 0.729). K-M analysis showed shorter survival times in the High-risk group, and Immunocytic infiltration analysis showed model genes closely associated with six immune cells. The high-risk group may benefit more effectively from immunosuppressive therapy, especially anti-CTLA-4 therapy (p < .05). We also screened nine drugs for potential treatment and verified the expression of three key genes SLC2A1, CUX1, and CA2 using immunohistochemistry and RT-qPCR experiments with clinical samples.
    CONCLUSION: We identified a prognostic model using m6A/m5C/m1A-related genes in cervical cancer, which can predict survival time and correlate with immune cell infiltration. Additionally, anti-CTLA-4 may be used as an immunotherapeutic agent for cervical cancer.KEY MESSAGESCervical cancer still has a high mortality rate, we aim to establish a strong prognostic index and new treatment goals for improving patient survival.The role of three types of RNA methylation modifications, m6A, m5C, and m1A, in cervical cancer, remains unknown. Therefore, it is essential to explore the potential molecular mechanisms of m6A, m5C, and m1A methylation regulation in cervical cancer.We also screened nine drugs for potential treatment and anti-CTLA-4 may be used as an immunotherapeutic agent for cervical cancer. We verified the expression of three key genes SLC2A1, CUX1, and CA2.
    Keywords:  Cervical cancer; immune infiltration; immunosuppressive therapy; m1A; m5C; m6A; potential drug therapy
    DOI:  https://doi.org/10.1080/07853890.2023.2190618
  16. Clin Immunol. 2023 Apr 06. pii: S1521-6616(23)00104-3. [Epub ahead of print] 109325
    Donor graft METTL3 gene transfer ameliorates rat liver transplantation ischemia-reperfusion injury by enhancing HO-1 expression in an m6A-dependent manner.
    Song Xiang, Yihua Wang, Dengliang Lei, Yunhai Luo, Dadi Peng, Kezhen Zong, Yanyao Liu, Zuotian Huang, Shaojiang Mo, Xingyu Pu, Jinli Zheng, Zhongjun Wu.
      Ischemia-reperfusion injury (IRI) is one of the most common complications in liver transplantation. METTL3 regulates inflammation and various cellular stress responses via modulating RNA m6A modification level. Here, the study aimed to investigate the role and mechanism of METTL3 in IRI after rat orthotopic liver transplantation. Firstly, m6A dot blot assay showed that total RNA m6A modification level in grafts was down-regulated, which echoed with the downregulation of METTL3. Furthermore, METTL3 pretreatment in donor significantly reduced liver grafts necrosis formation, apoptosis, improved liver function and depressed the proinflammatory cytokine/chemokine expression. Mechanistically, western blot and immunohistochemical showed that METTL3 inhibited apoptosis via upregulating HO-1. Moreover, MeRIP-qPCR assay revealed that METTL3 promoted HO-1 expression in an m6A-dependent manner. Additionally, METTL3 alleviated primary hepatocytes apoptosis by upregulating HO-1 under hypoxia/reoxygenation condition. Taken together, these results demonstrated that METTL3 exerted a cytoprotective role against IRI via inducing HO-1 in an m6A-dependent manner.
    Keywords:  HO-1; Ischemia-reperfusion injury; Liver transplantation; METTL3; N(6)-methyladenosine
    DOI:  https://doi.org/10.1016/j.clim.2023.109325
  17. J Hazard Mater. 2023 Apr 06. pii: S0304-3894(23)00637-4. [Epub ahead of print]453 131354
    Cobalt induces neurodegeneration through FTO-triggered autophagy impairment by targeting TSC1 in an m6A-YTHDF2-dependent manner.
    Jianping Tang, Fuli Zheng, Xu Liu, Yanjun Li, Zhenkun Guo, Xinpei Lin, Jinfu Zhou, Yu Zhang, Guangxia Yu, Hong Hu, Wenya Shao, Siying Wu, Huangyuan Li.
      Cobalt is the most widely used heavy metal pollutant in medicine and industry. Excessive cobalt exposure can adversely affect human health. Neurodegenerative symptoms have been observed in cobalt-exposed populations; however, the underlying mechanisms remain largely unknown. In this study, we demonstrate that the N6-methyladenosine (m6A) demethylase fat mass and obesity-associated gene (FTO) mediates cobalt-induced neurodegeneration by impairing autophagic flux. Cobalt-induced neurodegeneration was exacerbated through FTO genetic knockdown or repression of demethylase activity, but was alleviated by FTO overexpression. Mechanistically, we showed that FTO regulates TSC1/2-mTOR signaling pathway by targeting TSC1 mRNA stability in an m6A-YTHDF2 manner, which resulted in autophagosome accumulation. Furthermore, FTO decreases lysosome-associated membrane protein-2 (LAMP2) to inhibit the integration of autophagosomes and lysosomes, leading to autophagic flux damage. In vivo experiments further identified that central nervous system (CNS)-Fto-specific knockout resulted in serious neurobehavioral and pathological damage as well as TSC1-related autophagy impairment in cobalt-exposed mice. Interestingly, FTO-regulated autophagy impairment has been confirmed in patients with hip replacement. Collectively, our results provide novel insights into m6A-modulated autophagy through FTO-YTHDF2 targeted TSC1 mRNA stability, revealing cobalt is a novel epigenetic hazard that induces neurodegeneration. These findings suggest the potential therapeutic targets for hip replacement in patients with neurodegenerative damage.
    Keywords:  Autophagic flux; Cobalt chloride; Epigenetic hazard; MRNA stability; Neurodegenerative damage
    DOI:  https://doi.org/10.1016/j.jhazmat.2023.131354
  18. Discov Oncol. 2023 Apr 10. 14(1): 42
    RUNX1-IT1 favors breast cancer carcinogenesis through regulation of IGF2BP1/GPX4 axis.
    Shengting Wang, Yufang Wang, Qian Li, Kaixuan Zeng, Xiaoming Li, Xinghua Feng.
      Breast cancer is the most common malignancy among women and the leading cause of cancer deaths, with complicated pathogenesis that is largely unknown. In this study, we identified a novel long non-coding RNA (lncRNA) as a critical driver of breast cancer tumorigenesis. RUNX1 intronic transcript 1 (RUNX1-IT1) was notably overexpressed in human breast cancer tissues, and knockdown of RUNX1-IT1 inhibited breast cancer cell viability and invasion, as well as tumor growth in orthotopic transplantation model. Further, RUNX1-IT1 repressed ferroptosis, a novel iron-dependent form of regulated cell death, via increasing glutathione peroxidase 4 (GPX4) expression. Specifically, RUNX1-IT1 directly bound to N6-methyladenosine m6A reader IGF2BP1 and promoted the formation of (insulin like growth factor 2 mRNA binding protein 1) IGF2BP1 liquid-liquid phase separation (LLPS) biomolecular condensates, resulting in more IGF2BP1 occupation on GPX4 mRNA, increasing GPX4 mRNA stability. Moreover, high RUNX1-IT1 was linked to poor prognosis, and a strong positive correlation between RUNX1-IT1 and GPX4 was observed in clinical breast cancer tissues. Taken together, our data reveal that RUNX1-IT1 promotes breast cancer carcinogenesis through blocking ferroptosis via elevating GPX4, targeting of the previously unappreciated regulatory axis of RUNX1-IT1/IGF2BP1/GPX4 may be a promising treatment for patient with breast cancer.
    Keywords:  Breast cancer; Ferroptosis; Long non-coding RNA; m6A reader; mRNA stability
    DOI:  https://doi.org/10.1007/s12672-023-00652-z
  19. Protein Cell. 2023 Feb 23. pii: pwad009. [Epub ahead of print]
    METTL14 is a chromatin regulator independent of its RNA N6-methyladenosine methyltransferase activity.
    Xiaoyang Dou, Lulu Huang, Yu Xiao, Chang Liu, Yini Li, Xinning Zhang, Lishan Yu, Ran Zhao, Lei Yang, Chuan Chen, Xianbin Yu, Boyang Gao, Meijie Qi, Yawei Gao, Bin Shen, Shuying Sun, Chuan He, Jun Liu.
      METTL3 and METTL14 are two components that form the core heterodimer of the main RNA m6A methyltransferase complex (MTC) that installs m6A. Surprisingly, depletion of METTL3 or METTL14 displayed distinct effects on stemness maintenance of mouse embryonic stem cell (mESC). While comparable global hypo-methylation in RNA m6A was observed in Mettl3 or Mettl14 knockout mESCs, respectively. Mettl14 knockout led to a globally decreased nascent RNA synthesis, whereas Mettl3 depletion resulted in transcription upregulation, suggesting that METTL14 might possess an m6A-independent role in gene regulation. We found that METTL14 colocalizes with the repressive H3K27me3 modification. Mechanistically, METTL14, but not METTL3, binds H3K27me3 and recruits KDM6B to induce H3K27me3 demethylation independent of METTL3. Depletion of METTL14 thus led to a global increase in H3K27me3 level along with a global gene suppression. The effects of METTL14 on regulation of H3K27me3 is essential for the transition from self-renewal to differentiation of mESCs. This work reveals a regulatory mechanism on heterochromatin by METTL14 in a manner distinct from METTL3 and independently of m6A, and critically impacts transcriptional regulation, stemness maintenance, and differentiation of mESCs.
    Keywords:  H3K27me3; METTL14; chromatin; m6A-independent; mESC differentiation
    DOI:  https://doi.org/10.1093/procel/pwad009
  20. Front Immunol. 2023 ;14 1086907
    The m6A methylation landscape, molecular characterization and clinical relevance in prostate adenocarcinoma.
    Chao Li, Dongyi Peng, Yu Gan, Lei Zhou, Weibin Hou, Bingzhi Wang, Peng Yuan, Wei Xiong, Long Wang.
      Background: Despite the recent progress of therapeutic strategies in treating prostate cancer (PCa), the majority of patients still eventually relapse, experiencing dismal outcomes. Therefore, it is of utmost importance to identify novel viable targets to increase the effectiveness of treatment. The present study aimed to investigate the potential relationship between N6-methyladenosine (m6A) RNA modification and PCa development and determine its clinical relevance.Methods: Through systematic analysis of the TCGA database and other datasets, we analyzed the gene expression correlation and mutation profiles of m6A-related genes between PCa and normal tissues. Patient samples were divided into high- and low-risk groups based on the results of Least Absolute Shrinkage and Selection Operator (LASSO) Cox analysis. Subsequently, differences in biological processes and genomic characteristics of the two risk groups were determined, followed by functional enrichment analysis and gene set enrichment (GSEA) analysis. Next, we constructed the protein-protein interaction (PPI) network of differentially expressed genes between patients in high- and low-risk groups, along with the mRNA-miRNA-lncRNA network. The correlation analysis of tumor-infiltrating immune cells was further conducted to reveal the differences in immune characteristics between the two groups.
    Results: A variety of m6A-related genes were identified to be differentially expressed in PCa tissues as compared with normal tissues. In addition, the PPI network contained 278 interaction relationships and 34 m6A-related genes, and the mRNA-miRNA-lncRNA network contained 17 relationships, including 91 miRNAs. Finally, the immune characteristics analysis showed that compared with the low-risk group, the levels of M1 and M2 macrophages in the high-risk group significantly increased, while the levels of mast cells resting and T cells CD4 memory resting significantly decreased.
    Conclusions: This study provides novel findings that can further the understanding of the role of m6A methylation during the progression of PCa, which may facilitate the invention of targeted therapeutic drugs.
    Keywords:  RNA N6-methyladenosine; immune infiltration; molecular characterization; prognosis; prostate adenocarcinoma
    DOI:  https://doi.org/10.3389/fimmu.2023.1086907
  21. Am J Cancer Res. 2023 ;13(3): 818-834
    DARS2 is a prognostic biomarker and correlated with immune infiltrates and cuproptosis in lung adenocarcinoma.
    Xu-Sheng Liu, Jing Zeng, Yao-Hua Zhang, Yu Zhang, Yan Gao, Chao Liu, Zhi-Jun Pei.
      Overexpression of DARS2 may enhance the progression of hepatocellular carcinoma (HCC). However, there are few extensive reports on DARS2 function in lung adenocarcinoma (LUAD). The differential expression of DARS2 was detected by genomics and in vitro experiments, and the effect of DARS2 expression on LUAD cell activity was analyzed. Functional enrichment analysis was performed to explore possible signal pathways involved in the biological functions of DARS2 and its co-expressed genes. Utilizing TIMER and GEPIA datasets, the association between DARS2 expression and immunological infiltrating cells was analyzed. At the same time, the association between DARS2 expression pattern and LUAD m6A modification and cuproptosis was examined utilizing TCGA and GEO datasets. The level of DARS2 in LUAD increased, and inhibition of DARS2 expression could significantly inhibit the proliferation of LUAD cells. ROC curves showed that DARS2 overexpression could accurately diagnose LUAD and lead to a significant decline in the survival rates of OS, DSS, and PFI in LUAD. Enrichment analysis showed that DARS2 and its co-expressed genes were closely associated with chromosome segregation and the cell cycle. TIMER and GEPIA database analysis demonstrated that the DARS2 expression pattern was adversely correlated with the infiltration of B cells and Tfh cells. TCGA and GEO dataset examination revealed that DARS2 expression was significantly linked to four m6A-related genes and one cuproptosis-related gene. DARS2 expression is increased in LUAD patients and is closely associated with LUAD immune cell infiltration, modification of m6A, and cuproptosis. DARS2 is a potential reliable prognostic biomarker of LUAD.
    Keywords:  DARS2; cuproptosis; immune infiltration; lung adenocarcinoma; m6A modification
  22. Aging (Albany NY). 2023 Apr 05. 15
    Biological function analysis of ARHGAP39 as an independent prognostic biomarker in hepatocellular carcinoma.
    Yongqi Ding, Yiyang Gong, Hong Zeng, Xuanrui Zhou, Zichuan Yu, Jingying Pan, Minqin Zhou, Shiwen Liu, Wei Lai.
      Hepatocellular carcinoma (HCC) is the most common subtype of liver cancer, with a high morbidity and low survival rate. Rho GTPase activating protein 39 (ARHGAP39) is a crucial activating protein of Rho GTPases, a novel target in cancer therapy, and it was identified as a hub gene for gastric cancer. However, the expression and role of ARHGAP39 in hepatocellular carcinoma remain unclear. Accordingly, the cancer genome atlas (TCGA) data were used to analyze the expression and clinical value of ARHGAP39 in hepatocellular carcinoma. Further, the LinkedOmics tool suggested functional enrichment pathways for ARHGAP39. To investigate in depth the possible role of ARHGAP39 on immune infiltration, we analyzed the relationship between ARHGAP39 and chemokines in HCCLM3 cells. Finally, the GSCA website was used to explore drug resistance in patients with high ARHGAP39 expression. Studies have shown that ARHGAP39 is highly expressed in hepatocellular carcinoma and relevant to clinicopathological features. In addition, the overexpression of ARHGAP39 leads to a poor prognosis. Besides, co-expressed genes and enrichment analysis showed a correlation with the cell cycle. Notably, ARHGAP39 may worsen the survival of hepatocellular carcinoma patients by increasing the level of immune infiltration through chemokines. Moreover, N6-methyladenosine (m6A) modification-related factors and drug sensitivity were also found to be associated with ARHGAP39. In brief, ARHGAP39 is a promising prognostic factor for hepatocellular carcinoma patients that is closely related to cell cycle, immune infiltration, m6A modification, and drug resistance.
    Keywords:  ARHGAP39; biomarker; hepatocellular carcinoma; immune infiltration; prognosis
    DOI:  https://doi.org/10.18632/aging.204635
  23. Sci Rep. 2023 Apr 12. 13(1): 5941
    5-methyladenosine regulators play a crucial role in development of chronic hypersensitivity pneumonitis and idiopathic pulmonary fibrosis.
    Yiyi Zhou, Zhenli Hu, Qinying Sun, Yuchao Dong.
      5-methyladenosine (m5C) modification regulates gene expression and biological functions in oncologic areas. However, the effect of m5C modification in chronic hypersensitivity pneumonitis (CHP) and idiopathic pulmonary fibrosis (IPF) remains unknown. Expression data for 12 significant m5C regulators were obtained from the interstitial lung disease dataset. Five candidate m5C regulators, namely tet methylcytosine dioxygenase 2, NOP2/Sun RNA methyltransferase 5, Y-box binding protein 1, tRNA aspartic acid methyltransferase 1, and NOP2/Sun RNA methyltransferase 3 were screened using random forest and nomogram models to predict risks of pulmonary fibrosis. Next, we applied the consensus clustering method to stratify the samples with different m5C patterns into two groups (cluster A and B). Finally, we calculated immune cell infiltration scores via single-sample gene set enrichment analysis, then compared immune cell infiltration, related functions as well as the expression of programmed cell death 1 (PD-1, PDCD1) and programmed death protein ligand-1 (PD-L1, CD274) between the two clusters. Principal component analysis of m5C-related scores across the 288 samples revealed that cluster A had higher immune-related expression than B. Notably, T helper cell (Th) 2 type cytokines and Th1 signatures were more abundant in clusters A and B, respectively. Our results suggest that m5C is associated with and plays a crucial role in development of pulmonary fibrosis. These m5C patterns could be potential biomarkers for identification of CHP and IPF, and guide future development of immunotherapy or other new drugs strategies for pulmonary fibrosis.
    DOI:  https://doi.org/10.1038/s41598-023-32452-4
  24. Exp Cell Res. 2023 Apr 06. pii: S0014-4827(23)00132-5. [Epub ahead of print]427(1): 113585
    FTO promotes cervical cancer cell proliferation, colony formation, migration and invasion via the regulation of the BMP4/Hippo/YAP1/TAZ pathway.
    Jinyuan Huang, Jing Yang, Yudi Zhang, Dan Lu, Yinmei Dai.
      Cervical cancer is the fourth most common malignancy tumor worldwide with high incidence and mortality. Accumulating evidence indicated that through an m6A-dependent or m6A-independent mechanism, fat mass and obesity associated gene (FTO) exhibits the tumor-promoting and suppressive roles of FTO involved in various cancers, including cervical cancer. This study aims to verify the biological function and potential mechanisms of FTO in cervical cancer cell proliferation, colony formation, migration, and invasion in vitro as well as tumor growth in vivo. Herein, we confirmed that knockdown of FTO inhibits cell proliferation, colony formation, migration, and invasion of cervical cancer cells in vitro via cell counting kit-8 (CCK8) assay, colony formation assay, and transwell migration and invasion assay. The demethylase activity of FTO is required for cell proliferation, colony formation, migration, and invasion of cervical cancer cells in vitro. RNA sequencing, online database analysis, and western blotting revealed that FTO regulated the BMP4/Hippo/YAP1/TAZ pathway. In addition, FTO upregulates the expression of BMP4 in an m6A-dependent manner and binds to the N-terminal of BMP4 to form a dimer at the C-terminal in cervical cancer cells through protein-protein interaction. We further discovered that BMP4 treatment promoted cell proliferation, colony formation, migration, and invasion of cervical cancer cells, and rescue experiments validated that BMP4 treatment reversed the inhibition of FTO knockdown on the Hippo/YAP1/TAZ pathway and the progression of cervical cancer cells in vitro. Notably, the knockdown of FTO significantly suppressed xenograft tumor growth and the protein level of BMP4 in vivo. Collectively, our results demonstrate that the FTO promotes cervical cancer progression in vitro and in vivo via the regulation of the BMP4/Hippo/YAP1/TAZ pathway, suggesting that FTO acts as an oncogenic molecule and the FTO/BMP4 Hippo/YAP1/TAZ axis may serve as valuable targets for cervical cancer treatment.
    Keywords:  BMP4; Cervical cancer; FTO; Hippo/YAP1/TAZ pathway; m6A-dependent manner
    DOI:  https://doi.org/10.1016/j.yexcr.2023.113585
  25. Brief Bioinform. 2023 Apr 10. pii: bbad139. [Epub ahead of print]
    Evaluation of epitranscriptome-wide N6-methyladenosine differential analysis methods.
    Daoyu Duan, Wen Tang, Runshu Wang, Zhenxing Guo, Hao Feng.
      RNA methylation has emerged recently as an active research domain to study post-transcriptional alteration in gene expression regulation. Various types of RNA methylation, including N6-methyladenosine (m6A), are involved in human disease development. As a newly developed sequencing biotechnology to quantify the m6A level on a transcriptome-wide scale, MeRIP-seq expands RNA epigenetics study in both basic and clinical applications, with an upward trend. One of the fundamental questions in RNA methylation data analysis is to identify the Differentially Methylated Regions (DMRs), by contrasting cases and controls. Multiple statistical approaches have been recently developed for DMR detection, but there is a lack of a comprehensive evaluation for these analytical methods. Here, we thoroughly assess all eight existing methods for DMR calling, using both synthetic and real data. Our simulation adopts a Gamma-Poisson model and logit linear framework, and accommodates various sample sizes and DMR proportions for benchmarking. For all methods, low sensitivities are observed among regions with low input levels, but they can be drastically boosted by an increase in sample size. TRESS and exomePeak2 perform the best using metrics of detection precision, FDR, type I error control and runtime, though hampered by low sensitivity. DRME and exomePeak obtain high sensitivities, at the expense of inflated FDR and type I error. Analyses on three real datasets suggest differential preference on identified DMR length and uniquely discovered regions, between these methods.
    Keywords:  Differentially Methylated Regions; Epigenomics; MeRIP-seq; N6-methyladenosine; RNA Methylation
    DOI:  https://doi.org/10.1093/bib/bbad139
  26. Autophagy. 2023 Apr 11.
    NR3C1/Glucocorticoid receptor activation promotes pancreatic β-cell autophagy overload in response to glucolipotoxicity.
    Tijun Wu, Yixue Shao, Xirui Li, Tao Wu, Ling Yu, Jin Liang, Yaru Zhang, Jiahui Wang, Tong Sun, Yunxia Zhu, Xiaoai Chang, Shusen Wang, Fang Chen, Xiao Han.
      Diabetes is a complex and heterogeneous disorder characterized by chronic hyperglycemia. Its core cause is progressively impaired insulin secretion by pancreatic β-cell failures, usually upon a background of pre-existing insulin resistance. Recent studies demonstrate that macroautophagy/autophagy is essential to maintain architecture and function of β-cells, whereas excessive autophagy is also involved in β-cell dysfunction and death. It has been poorly understood whether autophagy plays a protective or harmful role in β-cells, while we report here that it is dependent on NR3C1/glucocorticoid receptor activation. We proved that deleterious hyperactive autophagy happened only upon NR3C1 activation in β-cells under glucolipotoxic conditions, which eventually promoted diabetes. The transcriptome and the N6-methyladenosine (m6A) methylome revealed that NR3C1-enhancement upregulated the RNA demethylase FTO (fat mass and obesity associated) protein in β-cells, which caused diminished m6A modifications on mRNAs of four core Atg (autophagy related) genes (Atg12, Atg5, Atg16l2, Atg9a) and, hence, hyperactive autophagy and defective insulin output; by contrast, FTO inhibition, achieved by the specific FTO inhibitor Dac51, prevented NR3C1-instigated excessive autophagy activation. Importantly, Dac51 effectively alleviated impaired insulin secretion and glucose intolerance in hyperglycemic β-cell specific NR3C1 overexpression mice. Our results determine that the NR3C1-FTO-m6A modifications-Atg genes axis acts as a key mediator of balanced autophagic flux in pancreatic β-cells, which offers a novel therapeutic target for the treatment of diabetes.
    Keywords:  Autophagy; FTO; NR3C1; diabetes; m6A; pancreatic β-cell
    DOI:  https://doi.org/10.1080/15548627.2023.2200625
  27. Plant Cell. 2023 Apr 10. pii: koad103. [Epub ahead of print]
    N6-methyladenosine RNA methylation modulates liquid‒liquid phase separation in plants.
    Hunseung Kang, Tao Xu.
      Membraneless biomolecular condensates form distinct subcellular compartments that enable a cell to orchestrate numerous biochemical reactions in a spatiotemporal-specific and dynamic manner. Liquid‒liquid phase separation (LLPS) facilitates the formation of membraneless biomolecular condensates, which are crucial for many cellular processes in plants, including embryogenesis, the floral transition, photosynthesis, pathogen defense, and stress responses. The main component required for LLPS is a protein harboring key characteristic features, such as intrinsically disordered regions, low-complexity sequence domains, and prion-like domains. RNA is an additional component involved in LLPS. Increasing evidence indicates that modifications in proteins and RNAs play pivotal roles in LLPS. In particular, recent studies have indicated that N6-methyladenosine (m6A) modification of messenger RNA is crucial for LLPS in plants and animals. In this review, we provide an overview of recent developments in the role of mRNA methylation in LLPS in plant cells. Moreover, we highlight the major challenges in understanding the pivotal roles of RNA modifications and elucidating how m6A marks are interpreted by RNA-binding proteins crucial for LLPS.
    DOI:  https://doi.org/10.1093/plcell/koad103
  28. Biotechnol Genet Eng Rev. 2023 Apr 13. 1-26
    Analysis of the prognostic significance and potential mechanisms of lncRNAs related to m6A methylation in laryngeal cancer.
    Jingtu Cen, Lihua Wang, Haopeng Zhang, Yu Guo.
      Objective to investigate the prognostic significance and potential mechanism analysis of m6A methylation-associated lncRNAs in laryngeal cancer. Methods based on the expression of m6A-associated lncRNAs, the samples were divided into two clusters and least absolute value and selection operator (LASSO) regression analysis was performed to build and validate prognostic models. In addition, the relationships between risk scores, clusters, arginine synthase (SMS), tumor microenvironment, clinicopathological features, immune infiltration, immune checkpoints, and tumor mutation burden were analyzed. Finally, the relationship between SMS and m6A-associated IncRNAs was analyzed and SMS-associated pathways were enriched by gene set enrichment analysis (GSEA). Results a total of 95 lncRNAs were associated with the expression of 22 m6A methylation regulators in laryngeal cancer, 14 of which were prognostic lncRNAs. These lncRNAs were divided into two clusters and evaluated. Clinicopathological features did not show significant differences. However, the two clusters differed significantly in terms of naive B cells, memory B cells, naive CD4 T cells, T helper cells and immune score. lASSO regression analysis showed that risk score was a significant predictor of progression-free survival. Conclusion low expression of m6A-related lncRNAs involved in laryngeal cancer development in laryngeal cancer tissues can be used as an indicator to diagnose patients with laryngeal cancer, reduce patient prognosis, be an independent risk factor affecting patient prognosis and be able to assess patient prognosis.
    Keywords:  Prognostic biomarker; SMS; laryngeal cancer; lncRNAs; m6a
    DOI:  https://doi.org/10.1080/02648725.2023.2198630
  29. Apoptosis. 2023 Apr 15.
    IGF2BP2 promotes lncRNA DANCR stability mediated glycolysis and affects the progression of FLT3-ITD + acute myeloid leukemia.
    Shenghao Wu, Changwei Chi, Shanshan Weng, Wenjin Zhou, Zhen Liu.
      Internal tandem duplication (ITD) is the most common type of FLT3 mutation (FLT3-ITD), accounting for about 25% of AML patients. The expression of DANCR in FLT3-ITD AML had not been paid attention to, and whether its regulatory relationship with IGF2BP2 can affect the progression of FLT3-ITD AML was unclear. Our study sought to verify the biological role of IGF2BP2 as an m6A reading protein in FLT3-ITD AML. To further explore the role and mechanism of DANCR in AML, and provide a basis for the screening of biomarkers and the development of targeted drugs. The results show that IGF2BP2 was upregulated in FLT3-ITD+ AML patients and cells. Si-IGF2BP2 could inhibit the proliferation, glycolytic and promote the apoptosis in MV4-11 cells. IGF2BP2 could promote the DANCR RNA stability. This discovery will provide new horizons for early screening and targeted therapy of FLT3-ITD+ AML.
    Keywords:  Acute myeloid leukemia (AML); FLT3-ITD; Glycolysis; IGF2BP2; N6-methyladenosine
    DOI:  https://doi.org/10.1007/s10495-023-01846-0
  30. Int J Mol Sci. 2023 Mar 24. pii: 6109. [Epub ahead of print]24(7):
    Chemical Space Virtual Screening against Hard-to-Drug RNA Methyltransferases DNMT2 and NSUN6.
    Robert A Zimmermann, Tim R Fischer, Marvin Schwickert, Zarina Nidoieva, Tanja Schirmeister, Christian Kersten.
      Targeting RNA methyltransferases with small molecules as inhibitors or tool compounds is an emerging field of interest in epitranscriptomics and medicinal chemistry. For two challenging RNA methyltransferases that introduce the 5-methylcytosine (m5C) modification in different tRNAs, namely DNMT2 and NSUN6, an ultra-large commercially available chemical space was virtually screened by physicochemical property filtering, molecular docking, and clustering to identify new ligands for those enzymes. Novel chemotypes binding to DNMT2 and NSUN6 with affinities down to KD,app = 37 µM and KD,app = 12 µM, respectively, were identified using a microscale thermophoresis (MST) binding assay. These compounds represent the first molecules with a distinct structure from the cofactor SAM and have the potential to be developed into activity-based probes for these enzymes. Additionally, the challenges and strategies of chemical space docking screens with special emphasis on library focusing and diversification are discussed.
    Keywords:  DNMT2; NSUN6; RNA methyltransferases; chemical spaces; molecular docking; ultra-large molecular libraries; virtual screening
    DOI:  https://doi.org/10.3390/ijms24076109
  31. Cell Death Dis. 2023 04 10. 14(4): 260
    Long noncoding RNA DIAPH2-AS1 promotes neural invasion of gastric cancer via stabilizing NSUN2 to enhance the m5C modification of NTN1.
    Ying Li, Yiwen Xia, Tianlu Jiang, Zetian Chen, Yikai Shen, Jie Lin, Li Xie, Chao Gu, Jialun Lv, Chen Lu, Diancai Zhang, Hao Xu, Li Yang, Zekuan Xu, Linjun Wang.
      Neural invasion (NI) is a vital pathological characteristic of gastric cancer (GC), which correlates with tumor recurrence and a worse prognosis. Long noncoding RNAs (lncRNAs) play critical roles in various biological processes. However, the involvement of lncRNAs in NI of GC (GC-NI) remains unclear. DIAPH2-AS1 was upregulated in NI-positive GC tissues, which was confirmed by qRT-PCR. The higher expression of DIAPH2-AS1 predicted NI and worse survival for GC patients. Both in vitro and in vivo experiments, including wound-healing assay, Transwell assay, DRG-GC cells co-culture model, the mouse sciatic nerve model, and the lung metastasis model, indicated that DIAPH2-AS1 promoted the migration, invasion, and NI potential of GC cells. Mechanistically, pulldown assay and RNA immunoprecipitation assay revealed that DIAPH2-AS1 interacted with NSUN2. Subsequent experiments indicated that DIAPH2-AS1 stabilized NSUN2 from ubiquitin-proteasomal degradation via masking the K577 and K579 of NSUN2. The protection of DIAPH2-AS1 on NSUN2 improved the stability of NTN1 mRNA via m5C modification, which finally induced GC-NI. Our work uncovered DIAPH2-AS1 as a novel oncogenic lncRNA in GC-NI and validated the DIAPH2-AS1-NSUN2-NTN1 axis as a potential therapeutic target for NI-positive GC.
    DOI:  https://doi.org/10.1038/s41419-023-05781-5
  32. Int J Mol Sci. 2023 Mar 30. pii: 6520. [Epub ahead of print]24(7):
    Prognostic Value and Genome Signature of m6A/m5C Regulated Genes in Early-Stage Lung Adenocarcinoma.
    Long Tian, Yan Wang, Jie Tian, Wenpeng Song, Lu Li, Guowei Che.
      RNA modifications implicate pathological and prognosis significance in cancer development and progression, of which, m6A and m5C are representative regulators. These RNA modifications could produce effects on the function of other RNA by regulating gene expression. Thus, in this study, we aimed to explore the correlation between m6A/m5C regulators and early-stage lung adenocarcinoma (LUAD). Only the early-stage LUAD samples were included in this investigation, and the RNA-seq dataset of The Cancer Genome Atlas (TCGA) cohort was utilized to evaluate the expression of 37 m6A/m5C regulated genes. Based on the expression level of these 37 genes, early-stage LUAD patients were divided into 2 clusters, which were performed by consensus clustering, and the m6A/m5C subtypes had significantly different prognostic outcomes (p < 0.001). Cluster1, which has a better prognosis, was characterized by the C3 (inflammatory) immune subtype, low immune infiltration, chemokine expression, major histocompatibility complex (MHC) expression, and immune checkpoint molecule expression. Furthermore, compared with cluster1, cluster2 showed a T cell exhaustion state, characterized by a high expression of immune checkpoint genes, and immune cells, such as T cells, CD8+ T cells, cytotoxic lymphocytes, NK cells, and so on. In addition, patients in cluster2 were with high tumor mutational burden (TMB) and numerous significant mutated oncogene and tumor suppressor genes, such as WNT10B, ERBB4, SMARCA4, TP53, and CDKN2A (p < 0.001). A total of 19 genes were mostly related to the prognosis of LUAD and were upregulated in cluster2 (p < 0.05), showing a positive correlation with the mRNA expression of 37 m6A/m5C regulated genes. The predictive risk model was constructed using Cox and LASSO (least absolute shrinkage and selection operator) regression analysis. Finally, a seven-gene m6A/m5C risk model, comprising of METTL3, NPLOC4, RBM15, YTHDF1, IGF2BP1, NSUN3, and NSUN7, was constructed to stratify the prognosis of early-stage LUAD (p = 0.0049, AUC = 0.791). The high-risk score was associated with a poorer prognosis. This model was also validated using two additional GEO datasets: GSE72094 (p = 0.011, AUC = 0.736) and GSE50081 (p = 0.012, AUC = 0.628). In summary, it was established that the m6A/m5C-regulated genes performed a crosstalk function in the mRNA expression of early-stage LUAD. By interacting with other mRNA genes, m6A/m5C modification disturbs DNA replication and the tumor immune microenvironment (TIME). The seven-gene risk model may be a critical tool for the prognostic assessment of early-stage LUAD.
    Keywords:  early-stage LUAD; genome feature; m5C; m6A; prognosis
    DOI:  https://doi.org/10.3390/ijms24076520
  33. Aging (Albany NY). 2023 Apr 11. 15
    Ubiquitin-proteasome system-mediated ubiquitination modification patterns and characterization of tumor microenvironment infiltration, stemness and cellular senescence in low-grade glioma.
    Jun Gu, Lijun Pang, Donghua Yan, Chunming Wang, Yuekun Song, Zhengshuai Jin, Zhenwei Xu, Yuanqing Mao, Shengzhe Liu, Sheng Chen.
      The Ubiquitin-proteasome system (UPS) performs a crucial role in immune activation and tumorigenesis. Nevertheless, the comprehensive role of the ubiquitin-proteasome system in the low-grade glioma (LGG) tumor microenvironment (TME) remains unknown. Ubiquitination modification patterns in LGG patients and corresponding characteristics of tumor immune traits, CSC stemness, and cellular senescence were evaluated via a comprehensive analysis of 20 ubiquitination modification regulators. For quantification of the ubiquitination modification status of individual patients, the UM-score was constructed and associated with TME characteristics, clinical features, cancer stem cell stemness, cellular senescence, prognosis, and immunotherapy efficacy. We identified that alterations in multiple ubiquitination regulators are linked to patient survival and the shaping of the tumor microenvironment. We found two different styles of ubiquitination modification in patients with low-grade glioma (immune-inflamed differentiation and immune-exclude dedifferentiation), characterized by high and low UM-score, and the two regulatory patterns of ubiquitination modification on immunity, stemness feature, and cellular senescence. We demonstrate that the UM-score could forecast the subtype of LGG, the immunologic infiltration traits, the biological process, the stemness feature, and the cellular senescence trait. Notably, the UM-score was related to immunotherapeutic efficacy, implying that modifying ubiquitination modification patterns by targeting ubiquitination modification regulators or ubiquitination modification pattern signature genes to reverse unfavorable TME properties will provide new insights into cancer immunotherapy. This research indicated that the ubiquitin-proteasome system is crucial in the formation of TME complexity and multiformity. The UM-score can determine ubiquitination modification status in individual patients, bringing about more personalized and effective immunotherapeutic tactics.
    Keywords:  cancer stem cell; cellular senescence; low-grade glioma; tumor microenvironment; ubiquitination modification
    DOI:  https://doi.org/10.18632/aging.204650
  34. Cell Death Discov. 2023 Apr 14. 9(1): 127
    Sestrin2-mediated disassembly of stress granules dampens aerobic glycolysis to overcome glucose starvation.
    Mingyue Li, Rick Francis Thorne, Ruijie Wang, Leixi Cao, Fangyuan Cheng, Xuedan Sun, Mian Wu, Jianli Ma, Lianxin Liu.
      Sestrins are a small gene family of pleiotropic factors whose actions promote cell adaptation to a range of stress conditions. In this report we disclose the selective role of Sestrin2 (SESN2) in dampening aerobic glycolysis to adapt to limiting glucose conditions. Removal of glucose from hepatocellular carcinoma (HCC) cells inhibits glycolysis associated with the downregulation of the rate-limiting glycolytic enzyme hexokinase 2 (HK2). Moreover, the accompanying upregulation of SESN2 through an NRF2/ATF4-dependent mechanism plays a direct role in HK2 regulation by destabilizing HK2 mRNA. We show SESN2 competes with insulin like growth factor 2 mRNA binding protein 3 (IGF2BP3) for binding with the 3'-UTR region of HK2 mRNA. Interactions between IGF2BP3 and HK2 mRNA result in their coalescence into stress granules via liquid-liquid phase separation (LLPS), a process which serves to stabilize HK2 mRNA. Conversely, the enhanced expression and cytoplasmic localization of SESN2 under glucose deprivation conditions favors the downregulation of HK2 levels via decreases in the half-life of HK2 mRNA. The resulting dampening of glucose uptake and glycolytic flux inhibits cell proliferation and protect cells from glucose starvation-induced apoptotic cell death. Collectively, our findings reveal an intrinsic survival mechanism allowing cancer cells to overcome chronic glucose shortages, also providing new mechanistic insights into SESN2 as an RNA-binding protein with a role in reprogramming of cancer cell metabolism.
    DOI:  https://doi.org/10.1038/s41420-023-01411-3
  35. Cells. 2023 Apr 01. pii: 1069. [Epub ahead of print]12(7):
    Fatty Acid Excess Dysregulates CARF to Initiate the Development of Hepatic Steatosis.
    Kamrul M Hasan, Meher Parveen, Alondra Pena, Francisco Bautista, Juan Carlos Rivera, Roxana Ramirez Huerta, Erica Martinez, Jorge Espinoza-Derout, Amiya P Sinha-Hikim, Theodore C Friedman.
      CARF (CDKN2AIP) regulates cellular fate in response to various stresses. However, its role in metabolic stress is unknown. We found that fatty livers from mice exhibit low CARF expression. Similarly, overloaded palmitate inhibited CARF expression in HepG2 cells, suggesting that excess fat-induced stress downregulates hepatic CARF. In agreement with this, silencing and overexpressing CARF resulted in higher and lower fat accumulation in HepG2 cells, respectively. Furthermore, CARF overexpression lowered the ectopic palmitate accumulation in HepG2 cells. We were interested in understanding the role of hepatic CARF and underlying mechanisms in the development of NAFLD. Mechanistically, transcriptome analysis revealed that endoplasmic reticulum (ER) stress and oxidative stress pathway genes significantly altered in the absence of CARF. IRE1α, GRP78, and CHOP, markers of ER stress, were increased, and the treatment with TUDCA, an ER stress inhibitor, attenuated fat accumulation in CARF-deficient cells. Moreover, silencing CARF caused a reduction of GPX3 and TRXND3, leading to oxidative stress and apoptotic cell death. Intriguingly, CARF overexpression in HFD-fed mice significantly decreased hepatic steatosis. Furthermore, overexpression of CARF ameliorated the aberrant ER function and oxidative stress caused by fat accumulation. Our results further demonstrated that overexpression of CARF alleviates HFD-induced insulin resistance assessed with ITT and GTT assay. Altogether, we conclude that excess fat-induced reduction of CARF dysregulates ER functions and lipid metabolism leading to hepatic steatosis.
    Keywords:  CARF (CDKN2AIP); ER-stress; NAFLD; hepatic steatosis; lipo-toxicity; metabolic stress; oxidative stress
    DOI:  https://doi.org/10.3390/cells12071069
  36. Cancer Res. 2023 Apr 14. pii: CAN-22-0536. [Epub ahead of print]
    An in vivo CRISPR screen identifies that SNRPC promotes triple-negative breast cancer progression.
    Xun-Xi Lu, Wen-Xiao Yang, Yu-Chen Pei, Hong Luo, Xiaoguang Li, Yun-Jin Wang, Guo-Liang Zhang, Hong Ling, Zhiming Shao, Xin Hu.
      Dysregulation of RNA-binding proteins (RBPs) is one of the characteristics of cancer. Investigating the biological functions and molecular mechanisms of abnormal RBPs can help uncover new cancer biomarkers and treatment strategies. To identify oncogenic RBPs in triple-negative breast cancer (TNBC), we employed an in vivo CRISPR screen and a TNBC progression model, which revealed small nuclear ribonucleoprotein polypeptide C (SNRPC), a subunit of the U1 small nuclear ribonucleoprotein particle (U1 snRNP), as a key modulator of TNBC progression. SNRPC was frequently upregulated, which corresponded to poor prognosis in TNBC patients. SNRPC ablation significantly impaired the proliferation, migration and invasion of TNBC cells in vitro and in vivo. In addition, SNRPC was essential for the stability of U1 snRNP and contributed to the RNA Pol II-controlled transcriptional program. Knockdown of SNRPC decreased RNA Pol II enrichment on a subset of oncogenes (TNFAIP2, E2F2 and CDK4) and reduced their expression levels. Furthermore, SNRPC deletion was confirmed to inhibit TNBC progression partially through regulation of the TNFAIP2-Rac1-β-catenin signaling pathway. Taken together, this data suggests that SNRPC plays an oncogenic role in TNBC, is a marker of poor prognosis, and may be a valuable therapeutic target for patients with intractable TNBC.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-22-0536
  37. Transl Oncol. 2023 Apr 07. pii: S1936-5233(23)00052-9. [Epub ahead of print]32 101666
    TJP1 promotes vascular mimicry in bladder cancer by facilitating VEGFA expression and transcriptional activity through TWIST1.
    Zhao-Xia Dong, Sze-Hoi Chan, Shu-Na Chen, Miao Li, Xing-Ding Zhang, Xue-Qi Liu.
      Tight junction protein 1 (TJP1) is a recently identified prominent regulator of bladder cancer (BLCA) angiogenesis and tumorigenesis. Vascular mimicry (VM) is a newly described tumor feature and is correlated with an increased risk of tumor metastasis. However, the relationship between TJP1 expression and VM in bladder cancer remains elusive. In the present study, we report a novel function for TJP1 in accommodating VM to promote tumor progression. We found that the elevated TJP1 expression was positively related to VM in patients and xenograft tumor models in bladder cancer. Enforced expression of TJP1 increased VM of BLCA cells in vitro and in vivo by elevating Vascular endothelial growth factor A (VEGFA) levels. Furthermore, VM induced by TJP1 overexpression was significantly blocked by the VEGFA and VEGFR inhibitors (Bevacizumab and Sunitinib). Mechanistically, TJP1 promoted VEGFA transcriptional and protein level in a TWIST1-dependent manner. Taken together, our study reveals that TJP1-regulated VEGFA overexpression may indicate a potential therapeutic target for clinical intervention in the early tumor neovascularization of bladder cancer.
    Keywords:  Bladder cancer; TJP1; VEGFA; Vascular mimicry
    DOI:  https://doi.org/10.1016/j.tranon.2023.101666
  38. Thorac Cancer. 2023 Apr 13.
    The kinesin light chain-2, a target of mRNA stabilizing protein HuR, inhibits p53 protein phosphorylation to promote radioresistance in NSCLC.
    Simiao Qiao, Yuhang Jiang, Na Li, Xiaoxia Zhu.
      BACKGROUND: Radioresistance hinders radiotherapy for the treatment of lung cancer. Kinesin light chain-2 (KLC2) has been found to be upregulated in lung cancer and also to be associated with poor prognosis. This study aimed to investigate the effect of KLC2 on radiosensitivity in lung cancer.METHODS: The radioresistant role of KLC2 was determined by colony formation, neutral comet assay, and γH2AX immunofluorescent staining assay. We further verified the function of KLC2 in a xenograft tumor model. The downstream of KLC2 was identified through gene set enrichment analysis and validated by western blot. Finally, we analyzed clinical data from the TCGA database to reveal the upstream transcription factor of KLC2, which was validated by RNA binding protein immunoprecipitation assay.
    RESULTS: Here, we found that downregulation of KLC2 could significantly reduce colony formation, increase γH2AX level, and double-stranded DNA breaks in vitro. Meanwhile, overexpressed KLC2 significantly increased the proportion of the S phase in lung cancer cells. KLC2 knockdown could activate P53 pathway, and ultimately promoting radiosensitivity. The mRNA of KLC2 was observed to bind with Hu-antigen R (HuR). The mRNA and protein expression of KLC2 in lung cancer cells was significantly reduced when combined with siRNA-HuR. Interestingly, KLC2 overexpression significantly increased the expression of HuR in lung cancer cells.
    CONCLUSION: Taken together, these results indicated that HuR-KLC2 forms a positive feedback loop, which decreases the phosphorylation of p53 and thereby weaken the radiosensitivity of lung cancer cells. Our findings highlight the potential prognosis and therapeutic target value of KLC2 in lung cancer patients treated with radiotherapy.
    Keywords:  HuR; NSCLC; kinesin light chain-2; p53; radioresistance
    DOI:  https://doi.org/10.1111/1759-7714.14886
  39. bioRxiv. 2023 Mar 28. pii: 2023.03.28.534515. [Epub ahead of print]
    Accumulation of m 6 A exhibits stronger correlation with MAPT than β-amyloid pathology in an APP NL-G-F /MAPT P301S mouse model of Alzheimer's disease.
    Lulu Jiang, Rebecca Roberts, Melissa Wong, Lushuang Zhang, Chelsea Joy Webber, Alper Kilci, Matthew Jenkins, Guangxin Sun, Sherif Rashad, Jingjing Sun, Peter C Dedon, Sarah Anne Daley, Weiming Xia, Alejandro Rondón Ortiz, Luke Dorrian, Takashi Saito, Takaomi C Saido, Benjamin Wolozin.
      The study for the pathophysiology study of Alzheimer's disease (AD) has been hampered by lack animal models that recapitulate the major AD pathologies, including extracellular β-amyloid (Aβ) deposition, intracellular aggregation of microtubule associated protein tau (MAPT), inflammation and neurodegeneration. We now report on a double transgenic APP NL-G-F MAPT P301S mouse that at 6 months of age exhibits robust Aβ plaque accumulation, intense MAPT pathology, strong inflammation and extensive neurodegeneration. The presence of Aβ pathology potentiated the other major pathologies, including MAPT pathology, inflammation and neurodegeneration. However, MAPT pathology neither changed levels of amyloid precursor protein nor potentiated Aβ accumulation. The APP NL-G-F /MAPT P301S mouse model also showed strong accumulation of N 6 -methyladenosine (m 6 A), which was recently shown to be elevated in the AD brain. M6A primarily accumulated in neuronal soma, but also co-localized with a subset of astrocytes and microglia. The accumulation of m6A corresponded with increases in METTL3 and decreases in ALKBH5, which are enzymes that add or remove m 6 A from mRNA, respectively. Thus, the APP NL- G-F /MAPT P301S mouse recapitulates many features of AD pathology beginning at 6 months of aging.
    DOI:  https://doi.org/10.1101/2023.03.28.534515
  40. Open Med (Wars). 2023 ;18(1): 20230689
    Downregulation of KIAA1199 alleviated the activation, proliferation, and migration of hepatic stellate cells by the inhibition of epithelial-mesenchymal transition.
    Jingmei Liu, Suhong Xia, Ping Han, Mingyu Zhang, Jingwen Wu, Jiazhi Liao.
      KIAA1199, a major glycosaminoglycan component of the extracellular matrix, was reported to induce a fibrosis-like process. However, the relationship between KIAA1199 and liver fibrosis remains unclear. The liver fibrosis mouse model was established with carbon tetrachloride (CCl4). Here, we found that KIAA1199 was upregulated in CCl4-induced liver fibrosis. The expression of KIAA1199 was also increased in TGF-β-stimulated LX-2 cells. To clarify the impact of KIAA1199 in hepatic stellate cells (HSCs), we downregulated the expression of KIAA1199 in LX-2 cells by RNA interference. Cell proliferation, apoptosis, and migration were determined by CCK-8, flow cytometry, and transwell assay. We found that KIAA1199 knockdown reduced the expression of fibrosis markers α-SMA and COL1A1. Depletion of KIAA1199 inhibited cell proliferation by downregulating cyclin B1 and cyclin D1 and promoted cell apoptosis by upregulating Bax and downregulating Bcl-2. Moreover, KIAA1199 knockdown decreased matrix metalloproteinase-2 (MMP-2) and MMP-9 expression to inhibit the migration ability of LX-2 cells. Silencing KIAA1199 also suppressed the epithelial-mesenchymal transition phenomenon. Collectively, our study revealed that KIAA1199 knockdown alleviated the activation, proliferation, and migration of HSCs, while promoting apoptosis of HSCs, which suggests that KIAA1199 may be a potential regulator of liver fibrosis.
    Keywords:  KIAA1199; hepatic stellate cells; liver fibrosis
    DOI:  https://doi.org/10.1515/med-2023-0689
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