bims-rimeca Biomed News
on RNA methylation in cancer
Issue of 2022‒11‒20
fifty-one papers selected by
Sk Ramiz Islam
Saha Institute of Nuclear Physics
  1. Methyltransferase-like 3 promotes cervical cancer metastasis by enhancing cathepsin L mRNA stability in an m6A-dependent manner.
  2. Analysis of m6A Methylation Patterns and Tumor Microenvironment in Endometrial Cancer.
  3. The roles of RNA N6-methyladenosine in esophageal cancer.
  4. N6-methyladenosine modification governs liver glycogenesis by stabilizing the glycogen synthase 2 mRNA.
  5. Fat mass and obesity-associated protein alleviates Aβ1-40 induced retinal pigment epithelial cells degeneration via PKA/CREB signaling pathway.
  6. The RNA demethylase ALKBH5 promotes the progression and angiogenesis of lung cancer by regulating the stability of the LncRNA PVT1.
  7. Potential impact of WTAP and YTHDF2 on tumor immunity in lung adenocarcinoma.
  8. Construction and validation of a m6A RNA methylation and ferroptosis-related prognostic model for pancreatic cancer by integrated bioinformatics analysis.
  9. Interactive regulation of DNA demethylase gene TET1 and m6A methyltransferase gene METTL3 in myoblast differentiation.
  10. Identification of a five m6A-relevant mRNAs signature and risk score for the prognostication of gastric cancer.
  11. Roles of N6-methyladenosine (m6A) modifications in gynecologic cancers: mechanisms and therapeutic targeting.
  12. METTL14 upregulates TCF1 through m6A mRNA methylation to stimulate osteogenic activity in osteoporosis.
  13. Promotive role of USP29-mediated deubiquitination in malignant proliferation of colorectal cancer cells via the KIAA1429/SOX8 axis.
  14. RNA m5C regulator-mediated modification patterns and the cross-talk between tumor microenvironment infiltration in gastric cancer.
  15. WFDC21P promotes triple-negative breast cancer proliferation and migration through WFDC21P/miR-628/SMAD3 axis.
  16. Early recruitment of PARP-dependent m8A RNA methylation at DNA lesions is subsequently accompanied by active DNA demethylation.
  17. Mettl3-mediated m6A modification of Fgf16 restricts cardiomyocyte proliferation during heart regeneration.
  18. METTL3/m6A/IFIT2 regulates proliferation, invasion and immunity in esophageal squamous cell carcinoma.
  19. m6A modification of circSPECC1 suppresses RPE oxidative damage and maintains retinal homeostasis.
  20. METTL3 boosts glycolysis and cardiac fibroblast proliferation by increasing AR methylation.
  21. m7G regulator-mediated methylation modification patterns define immune cell infiltration and patient survival.
  22. Methyltransferase like 3-mediated N6-methylatidin methylation inhibits vascular smooth muscle cells phenotype switching via promoting phosphatidylinositol 3-kinase mRNA decay.
  23. Bio-Orthogonal Chemistry Conjugation Strategy Facilitates Investigation of N-methyladenosine and Thiouridine Guide RNA Modifications on CRISPR Activity.
  24. Roles of m6A modification in oral cancer (Review).
  25. METTL1 drives tumor progression of bladder cancer via degrading ATF3 mRNA in an m7G-modified miR-760-dependent manner.
  26. N6-methyladenosine-mediated SH3BP5-AS1 upregulation promotes GEM chemoresistance in pancreatic cancer by activating the Wnt signaling pathway.
  27. Detecting RNA modification using direct RNA sequencing: A systematic review.
  28. N6-Methyladenosine modification (m6A) of circRNA-ZNF638 contributes the induced activation of SHF stem cells through miR-361-5p/Wnt5a axis in cashmere goats.
  29. HNRNPA2B1-mediated m6A modification of TLR4 mRNA promotes progression of multiple myeloma.
  30. The biological function of m6A methyltransferase KIAA1429 and its role in human disease.
  31. METTL3-mediated m6A modification stabilizes TERRA and maintains telomere stability.
  32. N6-methyladenosine-modified circular RNA QSOX1 promotes colorectal cancer resistance to anti-CTLA-4 therapy through induction of intratumoral regulatory T cells.
  33. Fusobacterium nucleatum stimulates cell proliferation and promotes PD-L1 expression via IFIT1-related signal in colorectal cancer.
  34. Epitranscriptomic Turbo for Autophagy Boost: m6A reader YTHDF3.
  35. Effect of the m6ARNA gene on the prognosis of thyroid cancer, immune infiltration, and promising immunotherapy.
  36. Identification of the cuproptosis-related molecular subtypes and an immunotherapy prognostic model in hepatocellular carcinoma.
  37. Infection phase-dependent dynamics of the viral and host N6-methyladenosine epitranscriptome in the lifecycle of an oncogenic virus in vivo.
  38. CDH13 is a prognostic biomarker and a potential therapeutic target for patients with clear cell renal cell carcinoma.
  39. Oxidative stress-related patterns determination for establishment of prognostic models, and characteristics of tumor microenvironment infiltration.
  40. The epitranscriptome: RNA modifications in vascular remodelling.
  41. O-GlcNAcylation Coordinates Glutaminolysis by Regulating the Stability and Membrane Trafficking of ASCT2 in Hepatic Stellate Cells.
  42. m7G-quant-seq: Quantitative Detection of RNA Internal N7-Methylguanosine.
  43. LncRNA Airn alleviates diabetic cardiac fibrosis by inhibiting activation of cardiac fibroblasts via a m6A-IMP2-p53 axis.
  44. CX3CL1 promotes cell sensitivity to ferroptosis and is associated with the tumor microenvironment in clear cell renal cell carcinoma.
  45. Molecular subtypes identified by pyroptosis-related genes are associated with tumor microenvironment cell infiltration in colon cancer.
  46. Regulation, genomics, and clinical characteristics of cuproptosis regulators in pan-cancer.
  47. CPSF1 positively regulates NSDHL by alternative polyadenylation and promotes gastric cancer progression.
  48. PRMT6 functionally associates with PRMT5 to promote colorectal cancer progression through epigenetically repressing the expression of CDKN2B and CCNG1.
  49. Lung adenocarcinoma relapse with emerging EGFR mutation following complete response of small cell lung cancer warrants routine re-biopsy: A case report.
  50. Effects of RNA Modification "Writers" of GALNT2 on the Tumor Microenvironment in Cervical Squamous Cell Carcinoma.
  51. RNA 5-Methylcytosine Modification Regulates Vegetative Development Associated with H3K27 Trimethylation in Arabidopsis.
  1. Cancer Sci. 2022 Nov 16.
    Methyltransferase-like 3 promotes cervical cancer metastasis by enhancing cathepsin L mRNA stability in an m6A-dependent manner.
    Pingping Liu, Mingxiu Ju, Xiaojing Zheng, Yinan Jiang, Xingjuan Yu, Baoyue Pan, Rongzhen Luo, Weihua Jia, Min Zheng.
      N6-methyladenosine (m6A) is a highly abundant RNA modification in eukaryotic cells. Methyltransferase-like 3 (METTL3), a major protein in the m6A methyltransferase complex, plays important roles in many malignancies, but its role in cervical cancer metastasis remains uncertain. Here, we found that METTL3 was significantly upregulated in cervical cancer tissue, and its upregulation was associated with a poor prognosis in cervical cancer patients. METTL3 knockdown significantly reduced cervical cancer cell migration and invasion. Conversely, METTL3 overexpression markedly promoted cervical cancer cell metastasis in vitro and in vivo. Furthermore, METTL3 mediated the m6A modification of cathepsin L (CTSL) mRNA at the 5'-untranslated region, and the m6A reader protein insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) bound to the m6A sites and enhanced CTSL mRNA stability. Our results indicated that METTL3 enhanced CTSL mRNA stability via an m6A-IGF2BP2-dependent mechanism, thereby promoting cervical cancer cell metastasis. These findings provide insights into a novel m6A modification pattern involved in cervical cancer development.
    Keywords:  CTSL; METTL3; cervical cancer; m6A; metastasis
    DOI:  https://doi.org/10.1111/cas.15658
  2. Gene. 2022 Nov 14. pii: S0378-1119(22)00872-1. [Epub ahead of print] 147052
    Analysis of m6A Methylation Patterns and Tumor Microenvironment in Endometrial Cancer.
    Junfeng Chen, Xiaomei Luo, Guocheng Wang, Jing Zhang, Yongli Zhang.
      BACKGROUND: The N6-methyladenosine (m6A) modification is the most common epigenetic modification in eukaryotic mRNA. In recent years, lots of studies have shown that the tumor microenvironment (TME) plays a critical role in tumor growth and development. However, there are few studies on the interaction between m6A methylation and the TME in uterine corpus endometrial carcinoma (UCEC).METHODS: Three distinct m6A modification patterns were based on 21 m6A regulators of UCEC patients and tumor-free individuals. We investigated the relationship between m6A modification patterns and associated features of the TME. Differentially expressed genes were selected and the m6A score was established to evaluate the prognosis and immunotherapeutic efficacy of UCEC patients.
    RESULTS: We identified three different m6A modification patterns. The TME infiltrating characteristics were highly consistent with tumors with three distinct immune phenotypes. Besides, our analysis showed that the m6A score was shown to be useful in predicting clinical outcomes. Patients with the low m6A score seemed to have a better prognosis, a stronger immunotherapeutic response, and a higher tumor mutation burden.
    CONCLUSION: Our study explored the influence of m6A modification and TME on the prognosis of cancer patients, which will contribute to the discovery of immunotherapy strategies to improve their prognosis.
    Keywords:  Endometrial cancer; Immunotherapy; RNA methylation; Tumor microenvironment; m(6)A
    DOI:  https://doi.org/10.1016/j.gene.2022.147052
  3. Heliyon. 2022 Nov;8(11): e11430
    The roles of RNA N6-methyladenosine in esophageal cancer.
    Chuan Teng, Fanhua Kong, Jinggang Mo, Weidong Lin, Chong Jin, Kunpeng Wang, Ying Wang.
      Esophageal cancer is a malignant tumour with a high degree of malignancy and high mortality. Its pathogenesis and treatment strategy remain unclear. N6-methyladenosine (m6A) is important for various biological functions in RNA modification and is currently being investigated extensively. It plays an essential role in RNA modification. m6A modification is a dynamic process that reversibly regulates the target RNA through its regulatory factors and plays an important role in several diseases, especially cancer. However, the role of m6A in esophageal cancer remains elusive. RNA modification and splicing are regulated by RNA methylation regulators called 'writers' (methyltransferases), 'erasers' (demethylases) and 'readers' (modified RNA-binding proteins). These regulatory factors recognise and bind to RNA methylation sites, regulate biological functions such as RNA splicing and translation and influence the occurrence, development, invasion and metastasis of tumours. Considering the importance of m6A modification, we reviewed the regulatory mechanisms, biological functions and therapeutic prospects of m6A RNA methylation regulators in esophageal cancer.
    Keywords:  Epigenetics; Esophageal cancer; Immunotherapy; N6-methyladenosine; RNA methylation; m6A
    DOI:  https://doi.org/10.1016/j.heliyon.2022.e11430
  4. Nat Commun. 2022 Nov 17. 13(1): 7038
    N6-methyladenosine modification governs liver glycogenesis by stabilizing the glycogen synthase 2 mRNA.
    Xiang Zhang, Huilong Yin, Xiaofang Zhang, Xunliang Jiang, Yongkang Liu, Haolin Zhang, Yingran Peng, Da Li, Yanping Yu, Jinbao Zhang, Shuli Cheng, Angang Yang, Rui Zhang.
      Hepatic glycogen is the main source of blood glucose and controls the intervals between meals in mammals. Hepatic glycogen storage in mammalian pups is insufficient compared to their adult counterparts; however, the detailed molecular mechanism is poorly understood. Here, we show that, similar to glycogen storage pattern, N6-methyladenosine (m6A) modification in mRNAs gradually increases during the growth of mice in liver. Strikingly, in the hepatocyte-specific Mettl3 knockout mice, loss of m6A modification disrupts liver glycogen storage. On the mechanism, mRNA of Gys2, the liver-specific glycogen synthase, is a substrate of METTL3 and plays a critical role in m6A-mediated glycogenesis. Furthermore, IGF2BP2, a "reader" protein of m6A, stabilizes the mRNA of Gys2. More importantly, reconstitution of GYS2 almost rescues liver glycogenesis in Mettl3-cKO mice. Collectively, a METTL3-IGF2BP2-GYS2 axis, in which METTL3 and IGF2BP2 regulate glycogenesis as "writer" and "reader" proteins respectively, is essential on maintenance of liver glycogenesis in mammals.
    DOI:  https://doi.org/10.1038/s41467-022-34808-2
  5. Cell Biol Int. 2022 Nov 15.
    Fat mass and obesity-associated protein alleviates Aβ1-40 induced retinal pigment epithelial cells degeneration via PKA/CREB signaling pathway.
    Yifan Hu, Jieqiong Chen, Yuwei Wang, Junran Sun, Peirong Huang, Jingyang Feng, Te Liu, Xiaodong Sun.
      Amyloid-β (Aβ) is thought to be a critical pathologic factor of retinal pigment epithelium (RPE) degeneration in age-related macular degeneration (AMD). Aβ induces inflammatory responses in RPE cells and recent studies demonstrate the N6-methyladenosine (m6A) regulatory role in RPE cell inflammation. m6A is a reversible epigenetic posttranslational modification, but its relationship with Aβ-induced RPE degeneration is yet to be thoroughly investigated. The present study explored the role and mechanism of m6A in Aβ-induced RPE degeneration model. This model was induced via intravitreally injecting oligomeric Aβ and the morphology of its retina was analyzed. One of m6A demethylases, the fat mass and obesity-associated (FTO) gene expression, was assessed. An m6A-messenger RNA (mRNA) epitranscriptomic microarray was employed for further bioinformatic analyses. It was confirmed that Aβ induced FTO upregulation within the RPE. Hypopigmentation alterations and structural disorganization were observed in Aβ-treated eyes, and inhibition of FTO exacerbated retinal degeneration and RPE impairment. Moreover, the m6A-mRNA epitranscriptomic microarray suggested that protein kinase A (PKA) was a target of FTO, and the PKA/cyclic AMP-responsive element binding (CREB) signaling pathway was involved in Aβ-induced RPE degeneration. m6A-RNA binding protein immunoprecipitation confirmed that FTO demethylated PKA within the RPE cells of Aβ-treated eyes. Altered expression of PKA and its downstream targets (CREB and brain-derived neurotrophic factor) was confirmed by quantitative reverse-transcription polymerase chain reaction and Western blot analyses. Hence, this study's findings shed light on FTO-mediated m6A modification in Aβ-induced RPE degeneration and indicate potential therapeutic targets for AMD.
    Keywords:  N6-methyladenosine; age-related macular degeneration; amyloid-β; fat mass and obesity-associated protein; m6A-mRNA epi-transcriptomic microarray; retinal pigment epithelium
    DOI:  https://doi.org/10.1002/cbin.11959
  6. Cancer Cell Int. 2022 Nov 15. 22(1): 353
    The RNA demethylase ALKBH5 promotes the progression and angiogenesis of lung cancer by regulating the stability of the LncRNA PVT1.
    Wenyi Shen, Juan Pu, Zhi Zuo, Shanye Gu, Jing Sun, Bing Tan, Lili Wang, Jianmeng Cheng, Yangsong Zuo.
      BACKGROUND: N6-methyladenosine (m6A) is the most common posttranscriptional modification of RNA and plays critical roles in human cancer progression. However, the biological function of m6A methylation requires further studied in cancer, especially in tumor angiogenesis.METHODS: A public database was used to analyze the expression and overall survival of ALKBH5 and PVT1 in lung cancer patients. CCK-8 and colony formation assays were performed to detect cell proliferation, a transwell assay was used to assess cell migration, and a tube formation assay was performed to assess angiogenic potential in vitro. A zebrafish lung cancer xenograft model was used to verify the function of ALKBH5 and PVT1 in vivo. Western blot assays were used to measure the relative protein expression in lung cancer cells. SRAMP predictor analysis and RNA stability experiments were used to examine the potential m6A modification.
    RESULTS: Bioinformatics analysis showed that the expression levels of m6A-related genes were changed significantly in lung cancer tissues compared with normal lung tissues. We then identified that ALKBH5 was upregulated in lung cancer tissues and associated with poor prognosis of lung cancer patients by analyzing a public database. Knockdown of ALKBH5 inhibited the proliferation and migration of cultured lung cancer cell lines. Zebrafish lung cancer xenografts showed that ALKBH5 silencing also suppressed the growth and metastasis of lung cancer cells. Moreover, knockdown of ALKBH5 inhibited the angiogenesis of lung cancer in vitro and in vivo. Mechanistic studies showed that knockdown of ALKBH5 decreased the expression and stability of PVT1 in lung cancer cells. We next observed that PVT1 promoted the progression of lung cancer cells in vitro and in vivo and regulated the expression of VEGFA and angiogenesis in lung cancer. Finally, rescue experiments revealed that ALKBH5 regulated the proliferation, migration and angiogenesis of lung cancer cells, partially through PVT1.
    CONCLUSION: Our results demonstrate that ALKBH5 promotes the progression and angiogenesis of lung cancer by regulating the expression and stability of PVT1, which provides a potential prognostic and therapeutic target for lung cancer patients.
    Keywords:  ALKBH5; Angiogenesis; Lung cancer; PVT1; RNA stability
    DOI:  https://doi.org/10.1186/s12935-022-02770-0
  7. Medicine (Baltimore). 2022 Nov 11. 101(45): e31195
    Potential impact of WTAP and YTHDF2 on tumor immunity in lung adenocarcinoma.
    Xinyu Zhang, Xinsheng Cai.
      WTAP and N6-methyladenosine (m6A) reader proteins (YTHDF2) are N6-methyladenosine (m6A) methyltransferase and m6A reading proteins, respectively. In recent years, the tumor immune environment has received more and more attention in the progress and treatment of cancer. The aim of this study was to investigate the relationship between N6-methyladenosine (m6A) methyltransferase (WTAP)/YTHDF2 and the immunological characteristics of lung adenocarcinoma (LUAD). Based on the expression of WTAP and YTHDF2 in the cancer genome atlas (TCGA) and gene expression omnibus (GEO) database, LUAD patients were divided into 2 clusters by coherently clustering method, and performed gene set enrichment analysis (GSEA) to identify the functional differences. Immunoinvasion analysis was performed using ESTIMATE, CIBERSORT, and single-sample GSEA (ssGSEA), and expression of immune checkpoint inhibitors (ICIs) targets was assessed, while tumor mutation burden (TMB) was calculated in tumor samples. Weighted gene co-expression network analysis (WGCNA) was used to identify the genes related to both WTAP/YTHDF2 expression and immunity. The immunological characteristics between the 2 clusters were externally verified based on GSE39582. The expression of WTAP was higher in cluster 1 and YTHDF2 was lower, but it was opposite in cluster 2. Cluster 1 had stronger immune infiltration, more ICIs target expression, more TMB. In addition, WGCNA identified 22 genes associated with WTAP/YTHDF2 expression and immune score, including TIM3 (HAVCR2) and CD86. WTAP and YTHDF2 influence immune contexture and may be novel prognostic and druggable targets associated with the immune system of LUAD.
    DOI:  https://doi.org/10.1097/MD.0000000000031195
  8. J Gastrointest Oncol. 2022 Oct;13(5): 2553-2564
    Construction and validation of a m6A RNA methylation and ferroptosis-related prognostic model for pancreatic cancer by integrated bioinformatics analysis.
    Tong Wu, Tian-Yang Qian, Ren-Jie Lin, Dan-Dan Jin, Xue-Bin Xu, Meng-Xiang Huang, Jie Ji, Feng Jiang, Ling-Ling Pan, Lan Luo, Yi-Fei Ji, Qiao-Lan Chen, Ming-Bing Xiao.
      Background: Both N6-methyladenosine (m6A) ribonucleic acid (RNA) methylation and ferroptosis regulators are demonstrated to have significant effects on the malignant clinicopathological characteristics of pancreatic adenocarcinoma (PAAD) patients. However, the currently available clinical indexes are not sufficient to predict precise prognostic outcomes pf PAAD patients accurately. This study aims to examine the clinicopathologic features of m6A RNA methylation and ferroptosis regulators in predicting the outcomes of different types of cancer.Methods: As the foundation for this research, the differentially expressed genes (DEGs) between PAAD tissues and adjacent normal tissues were first identified. Next, dimensional reduction analysis (DCA) based on m6A RNA methylation regulators and ferroptosis regulators were performed and DEGs between good/poor prognosis PAAD patient clusters were identified. DEGs were then screened by Cox analysis, and finally a risk signature was established by least absolute shrinkage and selection operator (LASSO) analyses. The prediction model based on risk score was further evaluated by a validation set from Gene Expression Omnibus (GEO) database.
    Results: In total, 4 m6A RNA methylation regulator genes and 29 ferroptosis regulator genes were found to have close causal relationships with the prognosis of PAAD, and a risk score with 3 m6A methylation regulators (i.e., IGF2BP2, IGF2BP3, and METTL16) and 4 ferroptosis regulators (i.e., ENPP2, ATP6V1G2, ITGB4, and PROM2) was constructed and showed to be highly involved in PAAD progression and could serve as effective markers for prognosis with AUC value equaled 0.753 in training set and 0.803 in validation set.
    Conclusions: The combined prediction model, composed of seven regulators of m6A methylation and ferroptosis, in this study more effectively reflects the progression and prognosis of PAAD than previous single genome or epigenetic analysis. Our study provides a broader perspective for the subsequent establishment of prognostic models and the patients may benefit from more precision management.
    Keywords:  Pancreatic cancer; The Cancer Genome Atlas (TCGA); ferroptosis; m6A RNA methylation; prognostic model
    DOI:  https://doi.org/10.21037/jgo-22-941
  9. Int J Biol Macromol. 2022 Nov 11. pii: S0141-8130(22)02639-3. [Epub ahead of print]
    Interactive regulation of DNA demethylase gene TET1 and m6A methyltransferase gene METTL3 in myoblast differentiation.
    Xinran Yang, Chugang Mei, Sayed Haidar Abbas Raza, Xinhao Ma, Jianfang Wang, Jiawei Du, Linsen Zan.
      DNA methylation (5mC) and mRNA N6-methyladenosine (m6A) play an essential role in gene transcriptional regulation. DNA methylation has been well established to be involved in skeletal muscle development. Interacting regulatory mechanisms between DNA methylation and mRNA m6A modification have been identified in a variety of biological processes. However, the effect of m6A on skeletal muscle differentiation and the underlying mechanisms are still unclear. It is also unknown whether there is an interaction between DNA methylation and mRNA m6A modification in skeletal myogenesis. In the present study, we used m6A-IP-qPCR, LC-MS/MS and dot blot assays to determine that the DNA demethylase gene, TET1, exhibited increased m6A levels and decreased mRNA expression during bovine skeletal myoblast differentiation. Dual-luciferase reporter assays and RIP experiments demonstrated that METTL3 suppressed TET1 expression by regulating TET1 mRNA stability in a m6A-YTHDF2-dependent manner. Furthermore, TET1 mediated DNA demethylation of itself, MYOD1 and MYOG, thereby stimulating their expression to promote myogenic differentiation. Ectopic expression of TET1 rescued the effect of METTL3 knockdown on reduced myotubes. In contrast, TET1 knockdown impaired the myogenic differentiation promoted by METTL3 overexpression. Moreover, ChIP experiments found that TET1 could bind and demethylate METTL3 DNA, which enhanced METTL3 expression. In addition, TET1 knockdown decreased m6A levels. ChIP assays also showed that TET1 knockdown contributed to the binding of H3K4me3 and H3K27me3 to METTL3 DNA. Our results revealed a negative feedback regulatory loop between TET1 and METTL3 in myoblast differentiation, which unveiled the interplay among DNA methylation, RNA methylation and histone methylation in skeletal myogenesis.
    Keywords:  DNA methylation; Histone methylation; METTL3; Myoblast differentiation; TET1; mRNA m(6)A methylation
    DOI:  https://doi.org/10.1016/j.ijbiomac.2022.11.081
  10. J Gastrointest Oncol. 2022 Oct;13(5): 2234-2248
    Identification of a five m6A-relevant mRNAs signature and risk score for the prognostication of gastric cancer.
    Lei Yin, Shichun Feng, Yongqiang Sun, Yasu Jiang, Chong Tang, Dongwei Sun.
      Background: N6-methyladenosine (m6A) is the most abundant form of methylation modification in eukaryotic cell messenger RNA (mRNA). However, the role of m6A in gastric cancer (GC), which is one of the most common gastrointestinal malignancies, is unclear. In this study, m6A-relevant mRNA signatures and risk scores were determined to predict the prognosis of GC.Methods: The expression profiles and clinical information of 367 patients were downloaded from The Cancer Genome Atlas (TCGA). Cluster analysis and univariate Cox analysis were performed to identify the regulatory factors of RNA methylation associated with GC prognosis. A co-expression network was constructed using the WGCNA package in R. The correlations between module eigengenes and clinical traits were then calculated to identify the relevant modules. We used univariate Cox analysis to screen for genes that are significantly associated with prognosis in the module. We identified hub genes by least absolute shrinkage and selection operator (LASSO) and multivariate analysis and developed a Cox prognostic model. Finally, the hub gene expression values weighted by the coefficients from the LASSO regression were applied to generate a risk score for each patient, and receiver operating characteristic (ROC) and Kaplan-Meier curves were used to assess the prognostic capacity of the risk scores. The asporin (ASPN) gene in GC cell lines was verified via quantitative polymerase chain reaction (qPCR) and Western blot. Moreover, 5-ethynyl-2'-deoxyuridine (EdU) and transwell assays were applied to evaluate the effects of the proliferation, migration, and invasion abilities in GC cells after ASPN knockdown. Western blot verified the effects of ASPN on the phosphoinositide 3-kinase (PI3K)/serine/threonine kinase (AKT)/mechanistic target of rapamycin kinase (mTOR) pathway and epithelial-mesenchymal transition (EMT) pathway-related gene expression.
    Results: Our results indicated that AARD, ASPN, SLAMF9, MIR3117 and DUSP1 were hub genes affecting the prognosis of GC patients. Besides, we found that ASPN expression was upregulated in GC cells. The knockdown of ASPN expression suppressed GC cell proliferation, migration, and invasion by deactivating the PI3K/AKT/mTOR and EMT pathways, respectively.
    Conclusions: Our findings indicated that ASPN participates in the biological process of GC as an oncogene and may be a promising biomarker in GC.
    Keywords:  Gastric cancer (GC); N6-methyladenosine (m6A); asporin (ASPN)
    DOI:  https://doi.org/10.21037/jgo-22-962
  11. Exp Hematol Oncol. 2022 Nov 12. 11(1): 98
    Roles of N6-methyladenosine (m6A) modifications in gynecologic cancers: mechanisms and therapeutic targeting.
    Jiahua Chen, Bao Guo, Xiaojing Liu, Jing Zhang, Junhui Zhang, Yuan Fang, Suding Zhu, Bing Wei, Yunxia Cao, Lei Zhan.
      Uterine and ovarian cancers are the most common gynecologic cancers. N6-methyladenosine (m6A), an important internal RNA modification in higher eukaryotes, has recently become a hot topic in epigenetic studies. Numerous studies have revealed that the m6A-related regulatory factors regulate the occurrence and metastasis of tumors and drug resistance through various mechanisms. The m6A-related regulatory factors can also be used as therapeutic targets and biomarkers for the early diagnosis of cancers, including gynecologic cancers. This review discusses the role of m6A in gynecologic cancers and summarizes the recent advancements in m6A modification in gynecologic cancers to improve the understanding of the occurrence, diagnosis, treatment, and prognosis of gynecologic cancers.
    Keywords:  Gynecologic cancer; N6-methyladenosine; Prognosis; Treatment; Tumor microenvironment
    DOI:  https://doi.org/10.1186/s40164-022-00357-z
  12. Hum Cell. 2022 Nov 19.
    METTL14 upregulates TCF1 through m6A mRNA methylation to stimulate osteogenic activity in osteoporosis.
    Xuepeng Wang, Chunchun Zou, Maoqiang Li, Changju Hou, Wu Jiang, Zhenyu Bian, Liulong Zhu.
      Alteration of N6-methyladenosine (m6A) is closely linked to spanning biological processes including osteoporosis (OP) development. This research focuses on the function of methyltransferase like 14 (METTL14) in bone turnover and its interaction with T cell factor 1 (TCF1). A mouse model of OP was established by ovariectomy (OVX). The bone mass parameters were evaluated by micro-CT analysis. Mouse MC3T3-E1 cells and mouse bone marrow macrophages (BMMs) were induced for osteogenic or osteoclastic differentiation, respectively, for in vitro experiments. The osteogenesis or osteoclasis activity was analyzed by measuring the biomarkers such as OPG, ALP, NFATC1, CTSK, RANKL, and TRAP. RT-qPCR and IHC assays identified reduced METTL14 expression in bone tissues of osteoporotic patients and ovariectomized mice. Artificial METTL14 overexpression increased bone mass of mice and promoted osteogenesis whereas suppressed osteoclasis both in vivo and in vitro. METTL14 promoted TCF1 expression through m6A mRNA methylation, and TCF1 increased the osteogenic activity by elevating the protein level of RUNX2, a key molecule linked to bone formation. In rescue experiments, TCF1 restored the RUNX2 level and osteogenic activity of cells suppressed by METTL14 silencing. In summary, this research demonstrates that METTL14 plays a protective role against OP by promoting the TCF1/RUNX2 axis.
    Keywords:  METTL14; Osteogenic differentiation; Osteoporosis; RUNX2; TCF1; m6A RNA methylation
    DOI:  https://doi.org/10.1007/s13577-022-00825-y
  13. Bosn J Basic Med Sci. 2022 Nov 10.
    Promotive role of USP29-mediated deubiquitination in malignant proliferation of colorectal cancer cells via the KIAA1429/SOX8 axis.
    Juncai Li, Jianguo Yang, Zhenzhou Chen, Li Liu, Hao Wang, Qican Deng, Yajun Chen, Yong Que, Zhongxue Fu.
      Colorectal cancer (CRC) is regarded as one of the most prevalent neoplasms worldwide, and ubiquitination and N6-methyladenosine (m6A) modification regulate the outgrowth of multiple cancers. This study attempted to explore the effect of ubiquitin-specific peptidases 29 (USP29) on the malignant proliferation of CRC cells via stabilizing Vir-like m6A methyltransferase associated (VIRMA/KIAA1429). First, upregulations of USP29, KIAA1429, and SRY-box transcription factor 8 (SOX8) were found in CRC tissues and cells through real-time quantitative polymerase chain reaction and Western blotting. After transfection of si-USP29, the proliferation of CRC cells was evaluated by the cell counting kit-8, colony formation and 5-ethynyl-2'-deoxyuridine assays, and we observed that depletion of USP29 inhibited the proliferation of CRC cells. Co-immunoprecipitation confirmed the binding of USP29 to KIAA1429. Mechanically, USP29 mediated deubiquitination to stabilize the protein levels of KIAA1429, and KIAA1429 promoted the stability of SOX8 mRNA through m6A modification. Moreover, overexpression of KIAA1429 or SOX8 reversed the inhibitory effects of USP29 depletion on CRC cell proliferation. Finally, the xenograft tumor model revealed the promotive role of USP29 in the proliferation of CRC cells in vivo. Altogether, USP29 facilitates the malignant proliferation of CRC cells via upregulating the KIAA1429/SOX8 axis.
    DOI:  https://doi.org/10.17305/bjbms.2022.7930
  14. Front Immunol. 2022 ;13 905057
    RNA m5C regulator-mediated modification patterns and the cross-talk between tumor microenvironment infiltration in gastric cancer.
    Qiang Zhang, Xiangfei Sun, Jianyi Sun, Jiangshen Lu, Xiaodong Gao, Kuntang Shen, Xinyu Qin.
      The effect of immunotherapy strategy has been affirmed in the treatment of various tumors. Nevertheless, the latent role of RNA 5-methylcytosine (m5C) modification in gastric cancer (GC) tumor microenvironment (TME) cell infiltration is still unclear. We systematically explore the m5C modification patterns of 2,122 GC patients from GEO and TCGA databases by 16 m5C regulators and related these patterns to TME characteristics. LASSO Cox regression was employed to construct the m5Cscore based on the expression of regulators and DEGs, which was used to evaluate the prognosis. All the GC patients were divided into three m5C modification clusters with distinct gene expression characteristics and TME patterns. GSVA, ssGSEA, and TME cell infiltration analysis showed that m5C clusters A, B, and C were classified as immune-desert, immune-inflamed, and immune-excluded phenotype, respectively. The m5Cscore system based on the expression of eight genes could effectively predict the prognosis of individual GC patients, with AUC 0.766. Patients with a lower m5Cscore were characterized by the activation of immunity and experienced significantly longer PFS and OS. Our study demonstrated the non-negligible role of m5C modification in the development of TME complexity and inhomogeneity. Assessing the m5C modification pattern for individual GC patients will help recognize the infiltration characterization and guide more effective immunotherapy treatment.
    Keywords:  5-methylcytosine (m5C); RNA methylation modification; immune; m5Cscore; prognosis; tumor microenvironment
    DOI:  https://doi.org/10.3389/fimmu.2022.905057
  15. Front Oncol. 2022 ;12 1032850
    WFDC21P promotes triple-negative breast cancer proliferation and migration through WFDC21P/miR-628/SMAD3 axis.
    Yu-Bo Wei, Dong-Min Liang, Mei-Ling Zhang, You-Jie Li, Hong-Fang Sun, Qin Wang, Yan Liang, Yan-Mei Li, Ran-Ran Wang, Zhen-Lin Yang, Pingyu Wang, Shu-Yang Xie.
      Long non-coding RNAs (lncRNAs) modulate cell proliferation, cycle, and apoptosis. However, the role of lncRNA-WFDC21P in the tumorigenesis of triple-negative breast cancer (TNBC) remains unclear. Results of this study demonstrated that WFDC21P levels significantly increased in TNBC, which was associated with the poor survival of patients. WFDC21P overexpression significantly promoted TNBC cell proliferation and metastasis. WFDC21P interacted with miR-628-5p, which further suppressed cell proliferation and metastasis by negatively regulating Smad3-related gene expression. Recovery of miR-628-5p weakened the roles of WFDC21P in promoting the growth and metastasis of TNBC cells. Moreover,N6-methyladenosine (m6A) modification upregulated WFDC21P expression in the TNBC cells. WFDC21P and its m6A levels were increased after methyltransferase like 3 (METTL3) overexpression but reduced after METTL3 silencing. The proliferation and metastasis of TNBC cells were promoted by METTL3 overexpression but suppressed by METTL3 silencing. This study demonstrated the vital roles of WFDC21P and its m6A in regulating the proliferation and metastasis of TNBC cells via the WFDC21P/miR-628/SMAD3 axis.
    Keywords:  N6-methyladenosine; WFDC21P; epigenetics; microRNA; triple-negative breast cancer
    DOI:  https://doi.org/10.3389/fonc.2022.1032850
  16. RNA Biol. 2022 Jan;19(1): 1153-1171
    Early recruitment of PARP-dependent m8A RNA methylation at DNA lesions is subsequently accompanied by active DNA demethylation.
    Soňa Legartová, Alena Svobodová Kovaříková, Jana Běhalová Suchánková, Hana Polášek-Sedláčková, Eva Bártová.
      RNA methylation, especially 6-methyladenosine (m6A)-modified RNAs, plays a specific role in DNA damage response (DDR). Here, we also observe that RNA modified at 8-methyladenosine (m8A) is recruited to UVA-damaged chromatin immediately after microirradiation. Interestingly, the level of m8A RNA at genomic lesions was reduced after inhibition of histone deacetylases and DNA methyltransferases. It appears in later phases of DNA damage response, accompanied by active DNA demethylation. Also, PARP inhibitor (PARPi), Olaparib, prevented adenosine methylation at microirradiated chromatin. PARPi abrogated not only m6A and m8A RNA positivity at genomic lesions, but also XRCC1, the factor of base excision repair (BER), did not recognize lesions in DNA. To this effect, Olaparib enhanced the genome-wide level of γH2AX. This histone modification interacted with m8A RNAs to a similar extent as m8A RNAs with DNA. Pronounced interaction properties we did not observe for m6A RNAs and DNA; however, m6A RNA interacted with XRCC1 with the highest efficiency, especially in microirradiated cells. Together, we show that the recruitment of m6A RNA and m8A RNA to DNA lesions is PARP dependent. We suggest that modified RNAs likely play a role in the BER mechanism accompanied by active DNA demethylation. In this process, γH2AX stabilizes m6A/m8A-positive RNA-DNA hybrid loops via its interaction with m8A RNAs. R-loops could represent basic three-stranded structures recognized by PARP-dependent non-canonical m6A/m8A-mediated DNA repair pathway.
    Keywords:  DNA demethylation; DNA repair; RNA methylation; base excision repair; epigenetics
    DOI:  https://doi.org/10.1080/15476286.2022.2139109
  17. Elife. 2022 Nov 18. pii: e77014. [Epub ahead of print]11
    Mettl3-mediated m6A modification of Fgf16 restricts cardiomyocyte proliferation during heart regeneration.
    Fu-Qing Jiang, Kun Liu, Jia-Xuan Chen, Yan Cao, Wu-Yun Chen, Wan-Ling Zhao, Guo-Hua Song, Chi-Qian Liang, Yi-Min Zhou, Huan-Lei Huang, Rui-Jin Huang, Hui Zhao, Kyu-Sang Park, Zhenyu Ju, Dongqing Cai, Xu-Feng Qi.
      Cardiovascular disease is the leading cause of death worldwide due to the inability of adult heart to regenerate after injury. N6-methyladenosine (m6A) methylation catalyzed by the enzyme methyltransferase-like 3 (Mettl3) plays an important role in various physiological and pathological bioprocesses. However, the role of m6A in heart regeneration remains largely unclear. To study m6A function in heart regeneration, we modulated Mettl3 expression in vitro and in vivo. Knockdown of Mettl3 significantly increased the proliferation of cardiomyocytes and accelerated heart regeneration following heart injury in neonatal and adult mice. However, Mettl3 overexpression decreased cardiomyocyte proliferation and suppressed heart regeneration in postnatal mice. Conjoint analysis of methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA-seq identified Fgf16 as a downstream target of Mettl3-mediated m6A modification during postnatal heart regeneration. RIP-qPCR and luciferase reporter assays revealed that Mettl3 negatively regulates Fgf16 mRNA expression in an m6A-Ythdf2-dependent manner. The silencing of Fgf16 suppressed the proliferation of cardiomyocytes. However, the overexpression of ΔFgf16, in which the m6A consensus sequence was mutated, significantly increased cardiomyocyte proliferation and accelerated heart regeneration in postnatal mice compared with wild-type Fgf16. Our data demonstrate that Mettl3 post-transcriptionally reduces Fgf16 mRNA levels through an m6A-Ythdf2-dependen pathway, thereby controlling cardiomyocyte proliferation and heart regeneration.
    Keywords:  Mettl3; cell biology; heart; m6A; mouse; regeneration; regenerative medicine; stem cells
    DOI:  https://doi.org/10.7554/eLife.77014
  18. Front Pharmacol. 2022 ;13 1002565
    METTL3/m6A/IFIT2 regulates proliferation, invasion and immunity in esophageal squamous cell carcinoma.
    Fangfang Ge, Zhenyu Li, Jiaru Hu, Youguang Pu, Fangfang Zhao, Lingsuo Kong.
      Epigenetic regulation plays a critical role in the development, progression, and treatment of tumors. The most common chemical modification of mRNA, called m6A, is essential for controlling mRNA stability, splicing, and translation. Methyltransferase-like 3 (METTL3) is an important m6A methyltransferase. The mechanism of action of METTL3 in esophageal squamous cell carcinoma (ESCC) remains unclear. In this investigation, we sought to clarify the function and clinical importance of METTL3 in ESCC and investigate its underlying mechanisms. We discovered that METTL3 has a significant proliferative effect in ESCC cells by using lentiviral construction of stable cell lines overexpressing METTL3 (METTL3-OE) and knocking down METTL3 (sh-METTL3). To create a xenograft tumor model, we inoculated KYSE510 cells subcutaneously into BALB/c nude mice and discovered that sh-METTL3 inhibited the tumorigenicity of esophageal cancer KYSE510 cells in the nude mouse tumor model. MeRIP-seq and RNA-seq analysis revealed IFIT2 to be a METTL3 target gene. The findings revealed that METTL3 regulates IFIT2 and thus influences malignant biological behaviors such as proliferation, migration, and invasion of ESCC, as well as the immune microenvironment of tumors.
    Keywords:  IFIT2; METTL3; N6-methyladenosine modification; immune infiltration; squamous cell carcinoma
    DOI:  https://doi.org/10.3389/fphar.2022.1002565
  19. Cell Rep. 2022 Nov 15. pii: S2211-1247(22)01545-5. [Epub ahead of print]41(7): 111671
    m6A modification of circSPECC1 suppresses RPE oxidative damage and maintains retinal homeostasis.
    Xue Chen, Ying Wang, Jia-Nan Wang, Qiu-Chen Cao, Ru-Xu Sun, Hong-Jing Zhu, Ye-Ran Zhang, Jiang-Dong Ji, Qing-Huai Liu.
      Age-related macular degeneration (AMD) is a leading cause of irreversible vision loss in the elderly population with unclear pathogenic mechanism. Herein, we detect downregulated circSPECC1 expression in retinal pigment epithelium (RPE) of AMD patients. In RPE cells, circSPECC1 insufficiency leads to oxidative stress-induced ferroptosis, depolarization, and irregular lipid metabolism. Consistently, in mice, circSPECC1 deficiency induces visual impairments and RPE anomalies and interrupts retinal homeostasis. Mechanically, nuclear export of circSPECC1 transcript depends on its N6-methyladenosine (m6A) level with YTHDC1 as the reader. CircSPECC1 directly sponges miR-145-5p to block its interaction with CDKN1A. Overexpressing miR-145-5p aggravates RPE dysfunctions, mimicking circSPECC1 silencing effects. Retinal phenotypes induced by circSPECC1 insufficiency are alleviated by miR-145-5p inhibition and are aggravated by miR-145-5p overexpression. Collectively, circSPECC1, mediated by m6A modification and sponging miR-145-5p, resists oxidative stress injuries and maintains lipid metabolism in RPE. Pharmacological supplementation of circSPECC1 is a promising therapeutic option for atrophic retinopathies like AMD.
    Keywords:  CP: Neuroscience; age-related macular degeneration; circular RNA; m(6)A; oxidative stress; retinal pigment epithelium
    DOI:  https://doi.org/10.1016/j.celrep.2022.111671
  20. Int J Biol Macromol. 2022 Nov 09. pii: S0141-8130(22)02600-9. [Epub ahead of print]
    METTL3 boosts glycolysis and cardiac fibroblast proliferation by increasing AR methylation.
    Yang Zhou, Kai Song, Bin Tu, He Sun, Ji-Fei Ding, Yong Luo, Ji-Ming Sha, Rui Li, Ye Zhang, Jian-Yuan Zhao, Hui Tao.
      Dysregulated glycolysis has been noted in several pathological processes characterized by supporting cell proliferation. Nonetheless, the role of glycolysis reprogramming is not well appreciated in cardiac fibrosis which is accompanied by increased fibroblasts proliferation. In this study, we investigated the cause and consequence of glycolysis reprogramming in cardiac fibrosis, using clinical samples, animal models, and cultured cells. Herein, we report that methyltransferase-like 3 (METTL3) facilitates glycolysis and cardiac fibroblasts proliferation, leading to cardiac fibrosis. The augmentation of glycolysis, an essential event during cardiac fibroblasts proliferation, is dependent on an increased expression of METTL3. A knockdown of METTL3 suppressed glycolysis, and inhibited cardiac fibroblast proliferation and cardiac fibrosis. Mechanistically, METTL3 epigenetically repressed androgen receptor (AR) expression in an m6A-YTHDF2- dependent manner, by targeting the specific AR m6A site. AR could interact with the glycolysis marker HIF-1α, and down-regulation of AR activates HIF-1α signaling, resulting in enhanced glycolysis and cardiac fibroblast proliferation. In contrast, the overexpression of AR significantly reduced the HIF-1α axis, decreased expression of glycolytic enzymes HK3, inhibited glycolysis, and repressed cardiac fibroblasts proliferation. Notably, increased METTL3 and YTHDF2 levels, decreased AR expression, increased HIF-1α and Postn expression and augmented glycolysis, and increased cardiac fibrosis were detected in human atrial fibrillation heart tissues. Our results found a novel mechanism by which METTL3-catalyzed m6A modification in cardiac fibrosis, wherein it facilitated glycolysis and cardiac fibroblasts proliferation by increasing AR methylation in an m6A-YTHDF2- dependent manner and provided new insights strategies to intervene cardiac fibrosis.
    Keywords:  Androgen receptor; Cardiac fibroblasts; Cardiac fibrosis; Extracellular matrix; METTL3; Proliferation
    DOI:  https://doi.org/10.1016/j.ijbiomac.2022.11.042
  21. Front Immunol. 2022 ;13 1022720
    m7G regulator-mediated methylation modification patterns define immune cell infiltration and patient survival.
    Lu Wang, Xing Hu, Xiaoni Liu, Yingmei Feng, Yuan Zhang, Jing Han, Xuqing Liu, Fankun Meng.
      Numerous studies have demonstrated the important roles of epigenetic modifications in tumorigenesis, progression and prognosis. However, in hepatocellular carcinoma, the potential link between N7-methylguanosine (m7G) modification and molecular heterogeneity and tumor microenvironment (TME) remains unclear.Method: We performed a comprehensive evaluation of m7G modification patterns in 816 hepatocellular carcinoma samples based on 24 m7G regulatory factors, identified different m7G modification patterns, and made a systematic correlation of these modification patterns with the infiltration characteristics of immunocytes. Then, we built and validated a scoring tool called m7G score.
    Results: In this study, we revealed the presence of three distinct m7G modification patterns in liver cancer, with remarkable differences in the immunocyte infiltration characteristics of these three subtypes. The m7G scoring system of this study could assess m7G modification patterns in individual hepatocellular carcinoma patients, could predict TME infiltration characteristics, genetic variants and patient prognosis. We also found that the m7G scoring system may be useful in guiding patients' clinical use of medications.
    Conclusions: This study revealed that m7G methylation modifications exerted a significant role in formation of TME in hepatocellular carcinoma. Assessing the m7G modification patterns of single patients would help enhance our perception of TME infiltration characteristics and give significant insights into immunotherapy efficacy.
    Keywords:  drug response; hepatocellular carcinoma; immunotherapy; m7G modification; prognosis; tumor microenvironment
    DOI:  https://doi.org/10.3389/fimmu.2022.1022720
  22. Front Cardiovasc Med. 2022 ;9 913039
    Methyltransferase like 3-mediated N6-methylatidin methylation inhibits vascular smooth muscle cells phenotype switching via promoting phosphatidylinositol 3-kinase mRNA decay.
    Yongchao Zhao, Aichao Xia, Chaofu Li, Xianping Long, Zhixun Bai, Zhimei Qiu, Weidong Xiong, Ning Gu, Youcheng Shen, Ranzun Zhao, Bei Shi.
      N6-methylatidine (m6A) is involved in post-transcriptional metabolism and a variety of pathological processes. However, little is known about the role of m6A in vascular proliferative diseases, particularly in vascular smooth muscle cells (VSMCs) phenotype switching-induced neointimal hyperplasia. In the current study, we discovered that methyltransferase like 3 (METTL3) is a critical candidate for catalyzing a global increase in m6A in response to carotid artery injury and various VSMCs phenotype switching. The inhibited neointimal hyperplasia was obtained after in vivo gene transfer to knock-down Mettl3. In vitro overexpression of Mettl3 resulted in increased VSMC proliferation, migration, and reduced contractile gene expression with a global elevation of m6A modification. In contrast, Mettl3 knockdown reversed this facilitated phenotypic switch in VSMCs, as demonstrated by downregulated m6A, decreased proliferation, migration, and increased expression of contractile genes. Mechanistically, Mettl3 knock-down was found to promote higher phosphatidylinositol 3-kinase (Pi3k) mRNA decay thus inactivating the PI3K/AKT signal to inhibit VSMCs phenotype switching. Overall, our findings highlight the importance of METTL3-mediated m6A in VSMCs phenotype switching and offer a novel perspective on targeting METTL3 as a therapeutic option for VSMCs phenotype switching modulated pathogenesis, including atherosclerosis and restenosis.
    Keywords:  N6-methyladenosine; VSMCs phenotype switching; mRNA decay; methyltransferase like 3; neointimal hyperplasia
    DOI:  https://doi.org/10.3389/fcvm.2022.913039
  23. CRISPR J. 2022 Nov 15.
    Bio-Orthogonal Chemistry Conjugation Strategy Facilitates Investigation of N-methyladenosine and Thiouridine Guide RNA Modifications on CRISPR Activity.
    Alyssa Hoy, Ya Ying Zheng, Jia Sheng, Maksim Royzen.
      The CRISPR-Cas9 system is an important genome editing tool that holds enormous potential toward the treatment of human genetic diseases. Clinical success of CRISPR technology is dependent on the incorporation of modifications into the single-guide RNA (sgRNA). However, chemical synthesis of modified sgRNAs, which are over 100 nucleotides in length, is difficult and low-yielding. We developed a conjugation strategy that utilized bio-orthogonal chemistry to efficiently assemble functional sgRNAs containing nucleobase modifications. The described approach entails the chemical synthesis of two shorter RNA oligonucleotides: a 31-mer containing tetrazine (Tz) group and a 70-mer modified with a trans-cyclooctene (TCO) moiety. The two oligonucleotides were conjugated to form functional sgRNAs. The two-component conjugation methodology was utilized to synthesize a library of sgRNAs containing nucleobase modifications such as N1-methyladenosine (m1A), N6-methyladenosine (m6A), 2-thiouridine (s2U), and 4-thiouridine (s4U). The impact of these RNA modifications on overall CRISPR activity were investigated in vitro and in Cas9-expressing HEK293T cells.
    DOI:  https://doi.org/10.1089/crispr.2022.0065
  24. Int J Oncol. 2023 Jan;pii: 5. [Epub ahead of print]62(1):
    Roles of m6A modification in oral cancer (Review).
    Huimin Liu, Yinyu Wang, Tianyi Xue, Zhijing Yang, Shaoning Kan, Ming Hao, Yang Gao, Dongxu Wang, Weiwei Liu.
      Oral cancer is one of the highly malignant tumors with poor prognosis. The pathogenic mechanisms of oral cancer have remained to be fully elucidated and this brings significant challenges to the treatment. RNA modification is a common intracellular chemical modification that has been related to various pathological processes, such as blood diseases, immune system diseases and cancer. As the most common and abundant RNA modification in eukaryotic mRNA, N6‑methyladenosine (m6A) modification has a crucial role in several cancers, including oral cancer. m6A modification directly affects gene expression levels and regulates various physiological and pathological processes. It has been demonstrated that m6A modification may affect the proliferation, migration and invasion of oral cancer cells by regulating the level of m6A modification. In the present review, the effects of m6A modification on the proliferation and death of oral cancer cells, as well as the occurrence and development of oral cancer, were analyzed in order to provide a new target for treatment. Furthermore, the roles of m6A modification in chemotherapy resistance and potential immunotherapy were analyzed and new treatment ideas were provided.
    Keywords:  RNA modified; m6A autophagy; metastasis; oral cancer; proliferation
    DOI:  https://doi.org/10.3892/ijo.2022.5453
  25. Cell Death Discov. 2022 Nov 17. 8(1): 458
    METTL1 drives tumor progression of bladder cancer via degrading ATF3 mRNA in an m7G-modified miR-760-dependent manner.
    Haiyun Xie, Mingchao Wang, Haifeng Yu, Huan Wang, Lifeng Ding, Ruyue Wang, Wenqin Luo, Zeyi Lu, Qiming Zheng, Liangliang Ren, Zhenwei Zhou, Wenjing Su, Liqun Xia, Gonghui Li.
      7-methylguanosine (m7G) modification is recently found to conservatively exist in RNA internal position besides mRNA caps and mediates the various RNA metabolisms. As the core confirmed transmethylase of m7G modification, METTL1 has been reported in certain human cancers. However, the role of internal m7G at miRNAs and its core writer METTL1 in bladder cancer (BCa) remains to be elucidated. Here, we demonstrated that METTL1 was indispensable for BCa proliferation and metastasis in vitro and in vivo. By combining miRNA sequencing, m7G methylated RNA immunoprecipitation (MeRIP) and RIP, we identified METTL1 promoted the processing of miR-760 in an m7G-dependent manner. Transcription sequencing suggested that METTL1 indirectly degrades tumor suppressor ATF3 mRNA mediated by miR-760. Together, we concluded a regulatory axis composed of METTL1/m7G/miR-760/ATF3 in regulating BCa progression and provided potential therapeutic targets for BCa.
    DOI:  https://doi.org/10.1038/s41420-022-01236-6
  26. Biol Direct. 2022 Nov 17. 17(1): 33
    N6-methyladenosine-mediated SH3BP5-AS1 upregulation promotes GEM chemoresistance in pancreatic cancer by activating the Wnt signaling pathway.
    Chengjie Lin, Yan Wang, Yihong Dong, Shihui Lai, Liang Wang, Shangeng Weng, Xiang Zhang.
      BACKGROUND: Pancreatic cancer (PC) is highly malignant. Chemotherapy is the main treatment strategy, especially for patients with advanced PC. However, chemoresistance has always been a frequently encountered bottleneck. Hence, there is an urgent need to enhance the sensitivity of PC to gemcitabine (GEM).RESULTS: We demonstrated that SH3BP5-AS1 was significantly upregulated in GEM-resistant PC and predicted a poorer prognosis. SH3BP5-AS1 stability was regulated by ALKBH5/IGF2BP1-mediated m6A modification. Loss of SH3BP5-AS1 reduced PC cell migration and invasion and enhanced the sensitivity of PC to GEM, as confirmed by gain- and loss-of-function assays in vitro and in vivo. Bioinformatics analysis revealed that SH3BP5-AS1 acted as a ceRNA against miR-139-5p and directly targeted CTBP1, affecting the biological behavior of PC cells. The mechanistic studies revealed that the upregulation of SH3BP5-AS1 increased CTBP1 expression by directly activating the Wnt signaling pathway, promoting GEM resistance.
    CONCLUSIONS: This study revealed that SH3BP5-AS1 activated Wnt signaling pathway by sponging miR-139-5p, upregulating CTBP1 expression, and contributing to the sensitivity of PC cells to GEM. SH3BP5-AS1 might be a potential target for PC therapy.
    Keywords:  Chemoresistance; N6-methyladenosine; Pancreatic cancer; SH3BP5-AS1; Wnt signaling pathway
    DOI:  https://doi.org/10.1186/s13062-022-00347-5
  27. Comput Struct Biotechnol J. 2022 ;20 5740-5749
    Detecting RNA modification using direct RNA sequencing: A systematic review.
    Xichen Zhao, Yuxin Zhang, Daiyun Hang, Jia Meng, Zhen Wei.
      Post-transcriptional RNA modifications are involved in a range of important cellular processes, including the regulation of gene expression and fine-tuning of the functions of RNA molecules. To decipher the context-specific functions of these post-transcriptional modifications, it is crucial to accurately determine their transcriptomic locations and modification levels under a given cellular condition. With the newly emerged sequencing technology, especially nanopore direct RNA sequencing, different RNA modifications can be detected simultaneously with a single molecular level resolution. Here we provide a systematic review of 15 published RNA modification prediction tools based on direct RNA sequencing data, including their computational models, input-output formats, supported modification types, and reported performances. Finally, we also discussed the potential challenges and future improvements of nanopore sequencing-based methods for RNA modification detection.
    DOI:  https://doi.org/10.1016/j.csbj.2022.10.023
  28. Anim Biosci. 2022 Nov 14.
    N6-Methyladenosine modification (m6A) of circRNA-ZNF638 contributes the induced activation of SHF stem cells through miR-361-5p/Wnt5a axis in cashmere goats.
    Ronghuan Yin, Ronglan Yin, Man Bai, Yixing Fan, Zeying Wang, Yubo Zhu, Qi Zhang, Taiyu Hui, Jincheng Shen, Siyu Feng, Wenlin Bai.
      Objective: The objective of this study was to investigate the effects of N6-Methyladenosine modification-circRNA-zinc finger protein 638 (m6A-circRNA-ZNF638) on the induced activation of secondary hair follicle (SHF) stem cells with its potential mechanisms in cashmere goats.Methods: The m6A modification of ZNF638 was analyzed using Methylation Immunoprecipitation (Me-RIP) with real-time quantitative PCR (RT-qPCR) technique in SHF stem cells. The effects of circRNA-ZNF638 on the induced activation of SHF stem cells in m6A dependence were evaluated through the overexpression of circRNA-ZNF638/its m6A-deficient mutants in circRNA-ZNF638 knockdown SHF stem cells. The competitive binding of miR-361-5p to circRNA-ZNF638/Wnt5a 3'- untranslated region (3'-UTR) was analyzed through Dual-luciferase reporter assay.
    Results: The m6A-circRNA-ZNF638 had significantly higher transcription at anagen SHF bulge of cashmere goats compared with that at telogen, as well as it positively regulated the induced activation of SHF-stem cells in cashmere goats. Mechanismly, m6A-circRNA-ZNF638 sponged miR-361-5p to heighten the transcriptional expression of Wnt5a gene in SHF-stem cells. We further demonstrated that the internal m6A modification within circRNA-ZNF638 is required for mediating the miR-361-5p/Wnt5a pathway to regulate the induced activation of SHF stem cells through an introducing of m6A-deficient mutant of circRNA-ZNF638.
    Conclusion: The circRNA-ZNF638 contributes the proper induced activation of SHF-stem cells in cashmere goats in m6A-dependent manner through miR-361-5p/Wnt5a axis.
    Keywords:  Cashmere Goats; CircRNA-ZNF638; MiR-361-5p; N6-Methyladenosine; SHF Stem Cells; Wnt5a
    DOI:  https://doi.org/10.5713/ab.22.0211
  29. J Transl Med. 2022 Nov 18. 20(1): 537
    HNRNPA2B1-mediated m6A modification of TLR4 mRNA promotes progression of multiple myeloma.
    Lina Quan, Chuiming Jia, Yiwei Guo, Yao Chen, Xinya Wang, Qiuting Xu, Yu Zhang.
      BACKGROUND: Multiple myeloma (MM) is a malignancy of plasma cells that remains incurable. Toll-like receptor 4 (TLR4) acts as a stress-responsive signal, protecting mitochondria during proteasome inhibitor (PI) exposure, maintaining mitochondrial metabolism and increasing drug resistance in MM. However, the mechanism of TLR4 regulation remains elusive.AIMS: The purpose of this study was to investigate the methylation pattern of multiple myeloma and its effect on the expression of HNRNPA2B1 and downstream targets.
    METHODS: The methylation level in MM and normal bone marrow specimens was detected using a colorimetric assay. HNRNPA2B1 gene knockdown was achieved in RPMI 8226 MM cells via adenovirus transfection. CCK8 and flow cytometric assays were used to detect proliferation and apoptosis, respectively. Transcriptome sequencing and m6A methylation MeRIP sequencing were applied, and differentially expressed genes (DEGs) were detected. Three independent NCBI GEO datasets were applied to examine the effects of HNRNPA2B1 and TLR4 expression on MM patient survival.
    RESULTS: HNRNPA2B1 promoted MM progression. Clinical data from database revealed that HNRNPA2B1 was adverse prognostic factor for survival among MM patients. Furthermore, transcriptome sequencing and methylation sequencing showed that HNRNPA2B1 recognized and was enriched at the m6A sites of TLR4 and TLR4 was down-regulated of both the m6A level and transcription level in HNRNPA2B1-knockdown MM cells. Moreover, TLR4 was an adverse survival prognostic factor based on database analysis.
    CONCLUSION: Overall, our study implies that the RNA-binding protein HNRNPA2B1 increases cell proliferation and deregulates cell apoptosis in MM through TLR4 signaling. Our study suggests HNRNPA2B1 as a potential therapeutic target for MM.
    Keywords:  HNRNPA2B1; Multiple myeloma; N6-methyladenosine methylation; TLR4
    DOI:  https://doi.org/10.1186/s12967-022-03750-8
  30. PeerJ. 2022 ;10 e14334
    The biological function of m6A methyltransferase KIAA1429 and its role in human disease.
    Xiaoyu Zhang, Meng Jiao Li, Lei Xia, Hairong Zhang.
      KIAA1429 is a major m6A methyltransferase, which plays important biological and pharmacological roles in both human cancer or non-cancer diseases. KIAA1429 produce a tumorigenic role in various cancers through regulating DAPK3, ID2, GATA3, SMC1A, CDK1, SIRT1 and other targets, promoting cell proliferation, migration, invasion, metastasis and tumor growth . At the same time, KIAA1429 is also effective in non-tumor diseases, such as reproductive system and cardiovascular system diseases. The potential regulatory mechanism of KIAA1429 dependent on m6A modification is related to mRNA, lncRNA, circRNA and miRNAs. In this review, we summarized the current evidence on KIAA1429 in various human cancers or non-cancer diseases and its potential as a prognostic target.
    Keywords:   Cancer; Mechanism; RNA methyltransferase; Therapeutic target; m6A modification; KIAA1429
    DOI:  https://doi.org/10.7717/peerj.14334
  31. Nucleic Acids Res. 2022 Nov 18. pii: gkac1027. [Epub ahead of print]
    METTL3-mediated m6A modification stabilizes TERRA and maintains telomere stability.
    Liping Chen, Canfeng Zhang, Wenbin Ma, Junjiu Huang, Yong Zhao, Haiying Liu.
      Telomeric repeat-containing RNA (TERRA) is a type of long non-coding RNA transcribed from telomeres, and it forms R-loops by invasion into telomeric DNA. Since either an excessive or inadequate number of R-loops leads to telomere instability, the TERRA levels need to be delicately modulated. In this study, we found that m6A modification presents on the subtelomeric regions of TERRA and stabilizes it, and the loss of METTL3 impacts telomere stability. Mechanically, the m6A modification on TERRA is catalyzed by METTL3, recognized and stabilized by the m6A reader YTHDC1. Knockdown of either METTL3 or YTHDC1 enhances TERRA degradation. The m6A-modified TERRA forms R-loops and promotes homologous recombination which is essential for the alternative lengthening of telomeres (ALT) pathway in cancer cells. METTL3 depletion leads to R-loop reduction, telomere shortening and instability. Altogether, these findings reveal that METTL3 protects telomeres by catalyzing m6A modification on TERRA, indicating that inhibition or deletion of METTL3 is potentially a new avenue for ALT cancer therapy.
    DOI:  https://doi.org/10.1093/nar/gkac1027
  32. Drug Resist Updat. 2022 Oct 21. pii: S1368-7646(22)00085-1. [Epub ahead of print]65 100886
    N6-methyladenosine-modified circular RNA QSOX1 promotes colorectal cancer resistance to anti-CTLA-4 therapy through induction of intratumoral regulatory T cells.
    Zhihua Liu, Nanxin Zheng, Juan Li, Chao Li, Dan Zheng, Xue Jiang, Xiaoying Ge, Min Liu, Lianjie Liu, Zhen Song, Leilei Bao, Yangyang Zhan, Xianhua Gao.
      BACKGROUND: Colorectal cancer (CRC) is the 3rd most common cancer worldwide. CircRNAs are promising novel biomarkers for CRC. T regulatory (Treg) cells express the immune checkpoint receptor of cytotoxic T-lymphocyte-associated antigen-4 (CTLA-4) and promote tumor immunological tolerance. We therefore investigate the biological functions and mechanisms of circQSOX1 in CRC tumorigenesis; involvement of circQSOX1 in promoting Treg cell-mediated CRC immune escape in anti-CTLA-4 therapy.METHODS: Bioinformatics analyses were performed for circQSOX1expressions, specific binding sites, and N6-methyladenosine (m6A) motifs of circQSOX1, thatwere further validated with a series of experiments. Functions of circQSOX1 in promoting CRC development, Treg cells-based immune escape, and anti-CTLA-4 therapy response were investigated both in vitro and in vivo.
    RESULTS: High circQSOX1 expression was associated with carcinogenesis and poor clinical outcome of CRC patients. METTL3-mediated RNA m6A modification on circQSOX1 could be read by IGF2BP2 in CRC cells. CircQSOX1 promoted CRC development by regulating miR-326/miR-330-5p/PGAM1 axis. CircQSOX1 regulated glycolysis and promoted immune escape of CRC cells, and inhibits anti-CTLA-4 therapy response in CRC patients.
    CONCLUSION: m6A-modified circQSOX1 facilitated CRC tumorigenesis by sponging miR-326 and miR-330-5p to promotes PGAM1 expression, which further promoted CRC immune escape by activating glycolysis and inactivating the anti-CTLA-4 therapy response of CRC. Combined treatment with sh-circQSOX1 and anti-CTLA-4 could be a strategy to overcome Treg cell-mediated CRC immune therapy resistance.
    Keywords:  Anti-CTLA-4 therapy; CircQSOX1; Colorectal cancer; MiR-326; MiR-330–5p; PGAM1
    DOI:  https://doi.org/10.1016/j.drup.2022.100886
  33. Neoplasia. 2022 Nov 10. pii: S1476-5586(22)00076-8. [Epub ahead of print]35 100850
    Fusobacterium nucleatum stimulates cell proliferation and promotes PD-L1 expression via IFIT1-related signal in colorectal cancer.
    Yaqi Gao, Tianhui Zou, Pingping Xu, Yingchao Wang, Yi Jiang, Ying-Xuan Chen, Haoyan Chen, Jie Hong, Jing-Yuan Fang.
      Fusobacterium nucleatum (F. nucleatum) is enriched in colorectal cancer (CRC) tissues and a high amount of F. nucleatum was associated with an immunosuppressive tumor environment. PD-L1 is an important immune checkpoint expressed on tumor cells and promotes tumor immune escape. Whether PD-L1 is regulated by F. nucleatum is still unclear. We demonstrated that F. nucleatum promoted CRC progression and upregulated PD-L1 protein expression in CRC cell lines. Combined m6A-seq and RNA-seq identified m6A-modified IFIT1 mediating F. nucleatum induced PD-L1 upregulation. IFIT1 mRNA was modified with m6A modifications in 3'UTR and the m6A levels were altered by F. nucleatum treatment. Our results also indicated that IFIT1 served as a potential oncogene in CRC and regulated PD-L1 protein levels through altering PD-L1 ubiquitination. Clinical CRC data confirmed the correlation among F. nucleatum abundance, IFIT1 and PD-L1 expressions. Our work highlighted the function of F. nucleatum in stimulating PD-L1 expression through m6A-modified IFIT1 and provided new aspects for understanding F. nucleatum mediated immune escape.
    Keywords:  Colorectal cancer; F. nucleatum; IFIT1; PD-L1; m(6)A
    DOI:  https://doi.org/10.1016/j.neo.2022.100850
  34. Autophagy. 2022 Nov 14.
    Epitranscriptomic Turbo for Autophagy Boost: m6A reader YTHDF3.
    WeiChao Hao, MeiJuan Dian, JiaHong Wang, Yan Sun, Dong Xiao.
      Mcroautophagy/autophagy plays an important role in maintaining homeostasis during nutrient starvation. However, whether epitranscriptomic events are involved in this process remains unclear. Our recent findings suggest that m6A reader YTHDF3 has an essential role in autophagy induction. Elevated m6A modifications installed by METTL3 enable YTHDF3 to promote autophagosome formation and lysosomal function upon nutrient deficiency. This is due to YTHDF3 binding to the m6A modifications at the coding DNA sequence (CDS) and 3' untranslated region (UTR) around the stop codon of Foxo3 mRNA, recruiting EIF3A and EIF4B to facilitate FOXO3 translation, thus boosting autophagy. In this punctum, we discuss our finding for how YTHDF3 responds to nutrient starvation to promote autophagy flux, providing insights into RNA post-transcriptional modifications linking nutrient cues to autophagic upcycling.
    Keywords:  FOXO3; METTL3; YTHDF3; autophagy; epitranscriptomics; m6A; nutrient starvation
    DOI:  https://doi.org/10.1080/15548627.2022.2146890
  35. Front Immunol. 2022 ;13 995645
    Effect of the m6ARNA gene on the prognosis of thyroid cancer, immune infiltration, and promising immunotherapy.
    Minqi Xia, Shuo Wang, Yingchun Ye, Yi Tu, Tiantian Huang, Ling Gao.
      Background: Accumulating evidence suggests that N6-methyladenosine (m6A) RNA methylation plays an important role in tumor proliferation and growth. However, its effect on the clinical prognosis, immune infiltration, and immunotherapy response of thyroid cancer patients has not been investigated in detail.Methods: Clinical data and RNA expression profiles of thyroid cancer were extracted from the Cancer Genome Atlas-thyroid carcinoma (TCGA-THCA) and preprocessed for consensus clustering. The risk model was constructed based on differentially expressed genes (DEGs) using Least Absolute Shrinkage and Selection Operator (LASSO) and Cox regression analyses. The associations between risk score and clinical traits, immune infiltration, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Set Enrichment Analysis (GSEA), immune infiltration, and immunotherapy were assessed. Immunohistochemistry was used to substantiate the clinical traits of our samples.
    Results: Gene expression analysis showed that 17 genes, except YHTDF2, had significant differences (vs healthy control, P<0.001). Consensus clustering yielded 2 clusters according to their clinical features and estimated a poorer prognosis for Cluster 1 (P=0.03). The heatmap between the 2 clusters showed differences in T (P<0.01), N (P<0.001) and stage (P<0.01). Based on univariate Cox and LASSO regression, a risk model consisting of three high-risk genes (KIAA1429, RBM15, FTO) was established, and the expression difference between normal and tumor tissues of three genes was confirmed by immunohistochemical results of our clinical tissues. KEGG and GSEA analyses showed that the risk DEGs were related mainly to proteolysis, immune response, and cancer pathways. The levels of immune infiltration in the high- and low-risk groups were different mainly in iDCs (P<0.05), NK cells (P<0.05), and type-INF-II (P<0.001). Immunotherapy analysis yielded 30 drugs associated with the expression of each gene and 20 drugs associated with the risk score.
    Conclusions: Our risk model can act as an independent marker for thyroid cancer and provides promising immunotherapy targets for its treatment.
    Keywords:  immune infiltration; immunotherapy; m6A; prognosis; risk model; thyroid cancer
    DOI:  https://doi.org/10.3389/fimmu.2022.995645
  36. BMC Bioinformatics. 2022 Nov 16. 23(1): 485
    Identification of the cuproptosis-related molecular subtypes and an immunotherapy prognostic model in hepatocellular carcinoma.
    Li Zhang, Jingwei Xu, Xiufeng Chu, Hongqiao Zhang, Xueyuan Yao, Jian Zhang, Yanwei Guo.
      BACKGROUND: Cuproptosis, a newly discovered mode of cell death, has been less studied in hepatocellular carcinoma (HCC). Exploring the molecular characteristics of different subtypes of HCC based on cuproptosis-related genes (CRGs) is meaningful to HCC. In addition, immunotherapy plays a pivotal role in treating HCC. Exploring the sensitivity of immunotherapy and building predictive models are critical for HCC.METHODS: The 357 HCC samples from the TCGA database were classified into three subtypes, Cluster 1, Cluster 2, and Cluster 3, based on the expression levels of ten CRGs genes using consensus clustering. Six machine learning algorithms were used to build models that identified the three subtypes. The molecular features of the three subtypes were analyzed and compared from some perspectives. Moreover, based on the differentially expressed genes (DEGs) between Cluster 1 and Cluster 3, a prognostic scoring model was constructed using LASSO regression and Cox regression, and the scoring model was used to predict the efficacy of immunotherapy in the IMvigor210 cohort.
    RESULTS: Cluster 3 had the worst overall survival compared to Cluster 1 and Cluster 2 (P = 0.0048). The AUC of the Catboost model used to identify Cluster 3 was 0.959. Cluster 3 was significantly different from the other two subtypes in gene mutation, tumor mutation burden, tumor microenvironment, the expression of immune checkpoint inhibitor genes and N6-methyladenosine regulatory genes, and the sensitivity to sorafenib. We believe Cluster 3 is more sensitive to immunotherapy from the above analysis results. Therefore, based on the DEGs between Cluster 1 and Cluster 3, we obtained a 7-gene scoring prognostic model, which achieved meaningful results in predicting immunotherapy efficacy in the IMvigor210 cohort (P = 0.013).
    CONCLUSIONS: Our study provides new ideas for molecular characterization and immunotherapy of HCC from machine learning and bioinformatics. Moreover, we successfully constructed a prognostic model of immunotherapy.
    Keywords:  Bioinformatics; Cuproptosis; Hepatocellular carcinoma (HCC); Machine learning; Prognostic model; Subtype
    DOI:  https://doi.org/10.1186/s12859-022-04997-0
  37. J Med Virol. 2022 Nov 18.
    Infection phase-dependent dynamics of the viral and host N6-methyladenosine epitranscriptome in the lifecycle of an oncogenic virus in vivo.
    Guoqing Zhuang, Xuyang Zhao, Jiaxin Jin, Xiaojing Zhu, Rui Wang, Yunyun Zhai, Wenlong Lu, Yifei Liao, Man Teng, Yongxiu Yao, Venugopal Nair, Wen Yao, Aijun Sun, Jun Luo, Gaiping Zhang.
      Dynamic alteration of the epitranscriptome exerts regulatory effects on the lifecycle of oncogenic viruses in vitro. However, little is known about these effects in vivo because of the general lack of suitable animal infection models of these viruses. Using a model of rapid-onset Marek's disease lymphoma in chickens, we investigated changes in viral and host mRNA N6-methyladenosine (m6 A) modification during Marek's disease virus (MDV) infection in vivo. We found that the expression of major epitranscriptomic proteins varies among viral infection phases, reprogramming both the viral and the host epitranscriptomes. Specifically, the METTL3/14 complex was suppressed during the lytic and reactivation phases of the MDV lifecycle, whereas its expression was increased during the latent phase and in MDV-induced tumors. METTL3/14 overexpression inhibits, whereas METTL3/14 knockdown enhances, MDV gene expression and replication. These findings reveal the dynamic features of the mRNA m6 A modification program during viral replication in vivo, especially in relation to key pathways involved in tumorigenesis. This article is protected by copyright. All rights reserved.
    Keywords:  N6-methyladenosine (m6A); epitranscriptome; oncogenic viruses; tumorigenesis
    DOI:  https://doi.org/10.1002/jmv.28324
  38. Am J Cancer Res. 2022 ;12(10): 4520-4544
    CDH13 is a prognostic biomarker and a potential therapeutic target for patients with clear cell renal cell carcinoma.
    Yuan Shao, Wenxia Li, Lin Zhang, Bo Xue, Yongquan Chen, Zikuan Zhang, Dongwen Wang, Bo Wu.
      CDH13 is an atypical member of the cadherin family and is closely related to the clinicopathological factors and prognosis of many types of cancer. However, the role of CDH13 in clear cell renal cell carcinoma (ccRCC) remains unknown. Therefore, we comprehensively analyzed the expression level, diagnostic efficacy, clinical significance, prognostic value, immune infiltration, methylation status, genetic alteration, and biological functions of CDH13 in ccRCC patients. The results showed that CDH13 was significantly upregulated in ccRCC and strongly correlated with better survival, lower cancer stages, and lower tumor grades of ccRCC patients. Additionally, the immune infiltration analysis indicated that CDH13 might play a crucial role in regulating the tumor microenvironment of ccRCC. The results of methylation analysis showed that the epigenetic status of CDH13 was altered, and the prognosis of ccRCC patients was related not only to DNA methylation but also to m6A modification of CDH13. Finally, the results based on clinical samples further elucidated the expression pattern of CDH13 in ccRCC. In conclusion, CDH13 might be a novel prognostic biomarker and therapeutic target for patients with ccRCC. And our study provides new insights into the potential molecular changes and strategies for the treatment of ccRCC.
    Keywords:  CDH13; T-cadherin; biomarker; ccRCC; methylation; prognosis; tumor microenvironment
  39. Front Surg. 2022 ;9 1013794
    Oxidative stress-related patterns determination for establishment of prognostic models, and characteristics of tumor microenvironment infiltration.
    Zihao Bai, Yihua Bai, Changzhong Fang, Wenliang Chen.
      Oxidative stress-mediated excessive accumulation of ROS in the body destroys cell homeostasis and participates in various diseases. However, the relationship between oxidative stress-related genes (ORGs) and tumor microenvironment (TME) in gastric cancer remains poorly understood. For improving the treatment strategy of GC, it is necessary to explore the relationship among them. We describe the changes of ORGs in 732 gastric cancer samples from two data sets. The two different molecular subtypes revealed that the changes of ORGs were associated with clinical features, prognosis, and TME. Subsequently, the OE_score was related to RFS, as confirmed by the correlation between OE_score and TME, TMB, MSI, immunotherapy, stem cell analysis, chemotherapeutic drugs, etc. OE_score can be used as an independent predictive marker for the treatment and prognosis of gastric cancer. Further, a Norman diagram was established to improve clinical practicability. Our research showed a potential role of ORGs in clinical features, prognosis, and tumor microenvironment of gastric cancer. Our research findings broaden the understanding of gastric cancer ORGs as a potential target for individualized treatment of gastric cancer and a new direction to evaluate the prognosis.
    Keywords:  gastric cancer; microsatellite instability; oxidative stress; prognosis; tumor microenvironment
    DOI:  https://doi.org/10.3389/fsurg.2022.1013794
  40. Atherosclerosis. 2022 Nov 09. pii: S0021-9150(22)01500-3. [Epub ahead of print]
    The epitranscriptome: RNA modifications in vascular remodelling.
    A Yaël Nossent.
      RNA transcripts are not finished products. Like proteins undergo posttranslational modifications, RNAs undergo posttranscriptional modifications. Some of these modifications affect processing, stability or turnover of RNAs, others can 'edit' nucleotides, change the RNA's function and rewrite the genetic code. The body of RNA modifications is collectively called the 'epitranscriptome'. The epitranscriptome is dynamically regulated. This is the most clear for N6-methyladenosine (m6A), where both m6A-'writers' and -'erasers' have been identified and are also already being employed in studies on the effects of broad-scale m6A modifications on human disease, including cardiovascular disease. Even though not all modifications are readily reversible like m6A, most, if not all, other modifications are actively regulated in response to stressors, such as ischemia, starvation, or incubation with for example cytokines or oxidized LDL, all important factors in vascular remodelling and cardiovascular disease. Epitranscriptome research in human disease in general and in cardiovascular research is still in its infancy and methods to reliably detect and/or manipulate most RNA modifications are still lacking. Nonetheless, the number of studies on RNA modification and on writer-, eraser-, and reader-protein in various forms of vascular remodelling has increased dramatically over the last three years. This review aimed to discuss the available literature on the most common RNA modifications in different forms of vascular remodelling. Both adaptive vascular remodelling, including postischemic angiogenesis, as well as maladaptive remodelling, like atherosclerosis and aneurysm formation, and their direct consequences, such as myocardial infarction, acute stroke, peripheral artery disease and abdominal aorta aneurysm, have been discussed.
    Keywords:  2'Oribose methylation; A-to-I editing; Angiogenesis; Atherosclerosis; Epitranscriptome; RNA modifications; Vascular remodelling; m1A; m5C; m6A; m7G
    DOI:  https://doi.org/10.1016/j.atherosclerosis.2022.11.004
  41. J Clin Transl Hepatol. 2022 Dec 28. 10(6): 1107-1116
    O-GlcNAcylation Coordinates Glutaminolysis by Regulating the Stability and Membrane Trafficking of ASCT2 in Hepatic Stellate Cells.
    Feixia Wang, Li Chen, Biyun Zhang, Zhanghao Li, Min Shen, Li Tang, Zili Zhang, Jiangjuan Shao, Feng Zhang, Shizhong Zheng, Shanzhong Tan.
      Background and Aims: Recognition of excessive activation of hepatic stellate cells (HSCs) in liver fibrosis prompted us to investigate the regulatory mechanisms of HSCs. We aimed to examine the role of O-GlcNAcylation modification of alanine, serine, cysteine transporter 2 (ASCT2) in HSCs and liver fibrosis.Methods: The expression of O-GlcNAcylation modification in fibrotic mice livers and activated HSCs was analyzed by western blotting. Immunoprecipitation was used to assess the interaction of ASCT2 and O-GlcNAc transferase (OGT). In addition, ASCT2 protein stability was assayed after cycloheximide (CHX) treatment. The O-GlcNAcylation site of ASCT2 was predicted and mutated by site-directed mutagenesis. Real-time PCR, immunofluorescence, kit determinations and Seahorse assays were used to clarify the effect of ASCT2 O-GlcNAcylation on HSC glutaminolysis and HSC activation. Western blotting, immunochemistry, and immunohistofluorescence were used to analyze the effect of ASCT2 O-GlcNAcylation in vivo.
    Results: We observed significantly increased O-GlcNAcylation modification of ASCT2. ASCT2 was found to interact with OGT to regulate ASCT2 stability. We predicted and confirmed that O-GlcNAcylation of ASCT2 at Thr122 site resulted in HSCs activation. We found Thr122 O-GlcNAcylation of ASCT2 mediated membrane trafficking of glutamine transport and attenuated HSC glutaminolysis. Finally, we validated the expression and function of ASCT2 O-GlcNAcylation after injection of AAV8-ASCT2 shRNA in CCl4-induced liver fibrosis mice in vivo.
    Conclusions: Thr122 O-GlcNAcylation regulation of ASCT2 resulted in stability and membrane trafficking-mediated glutaminolysis in HSCs and liver fibrosis. Further studies are required to assess its role as a putative therapeutic target.
    Keywords:  ASCT2; Liver fibrosis; O-GlcNacylation; Stability; Trafficking
    DOI:  https://doi.org/10.14218/JCTH.2021.00413
  42. ACS Chem Biol. 2022 Nov 18.
    m7G-quant-seq: Quantitative Detection of RNA Internal N7-Methylguanosine.
    Li-Sheng Zhang, Cheng-Wei Ju, Chang Liu, Jiangbo Wei, Qing Dai, Li Chen, Chang Ye, Chuan He.
      Methods for the precise detection and quantification of RNA modifications are critical to uncover functional roles of diverse RNA modifications. The internal m7G modification in mammalian cytoplasmic tRNAs is known to affect tRNA function and impact embryonic stem cell self-renewal, tumorigenesis, cancer progression, and other cellular processes. Here, we introduce m7G-quant-seq, a quantitative method that accurately detects internal m7G sites in human cytoplasmic tRNAs at single-base resolution. The efficient chemical reduction and mild depurination can almost completely convert internal m7G sites into RNA abasic sites (AP sites). We demonstrate that RNA abasic sites induce a mixed variation pattern during reverse transcription, including G → A or C or T mutations as well as deletions. We calculated the total variation ratio to quantify the m7G modification fraction at each methylated site. The calibration curves of all relevant motif contexts allow us to more quantitatively determine the m7G methylation level. We detected internal m7G sites in 22 human cytoplasmic tRNAs from HeLa and HEK293T cells and successfully estimated the corresponding m7G methylation stoichiometry. m7G-quant-seq could be applied to monitor the tRNA m7G methylation level change in diverse biological processes.
    DOI:  https://doi.org/10.1021/acschembio.2c00792
  43. Biol Direct. 2022 Nov 16. 17(1): 32
    LncRNA Airn alleviates diabetic cardiac fibrosis by inhibiting activation of cardiac fibroblasts via a m6A-IMP2-p53 axis.
    Tingwei Peng, Mingchuan Liu, Lang Hu, Dong Guo, Di Wang, Bingchao Qi, Gaotong Ren, Chenchen Hu, Feng Zhang, Hyung J Chun, Liqiang Song, Jianqiang Hu, Yan Li.
      BACKGROUND: Cardiac fibrosis is a leading cause of cardiac dysfunction in patients with diabetes. However, the underlying mechanisms of cardiac fibrosis remain unclear. This study aimed to investigate the role of the long non-coding RNA (LncRNA) Airn in the pathogenesis of cardiac fibrosis in diabetic cardiomyopathy (DCM) and its underlying mechanism.METHODS: Diabetes mellitus (DM) was induced in mice by streptozotocin injection. An intramyocardial adeno-associated virus (AAV) was used to manipulate Airn expression. The functional significance and underlying mechanisms in DCM fibrosis were investigated both in vitro and in vivo.
    RESULTS: Diabetic hearts showed a significant impairment in cardiac function, accompanied by obviously increased cardiac fibrosis. Interestingly, lncRNA Airn expression was significantly decreased in both diabetic hearts and high glucose (HG)-treated cardiac fibroblasts (CFs). AAV-mediated Airn reconstitution prevented cardiac fibrosis and the development of DCM, while Airn knockdown induced cardiac fibrosis phenotyping DCM. As in vitro, Airn reversed HG-induced fibroblast-myofibroblast transition, aberrant CFs proliferation and section of collagen I. In contrast, Airn knockdown mimicked a HG-induced CFs phenotype. Mechanistically, we identified that Airn exerts anti-fibrotic effects by directly binding to insulin-like growth factor 2 mRNA-binding protein 2 (IMP2) and further prevents its ubiquitination-dependent degradation. Moreover, we revealed that Airn/IMP2 protected p53 mRNA from degradation in m6A manner, leading to CF cell cycle arrest and reduced cardiac fibrosis. As a result, ablation of p53 blunted the inhibitory effects of Airn on fibroblast activation and cardiac fibrosis.
    CONCLUSIONS: Our study demonstrated for the first time that Airn prevented the development of cardiac fibrosis in diabetic heart via IMP2-p53 axis in an m6A dependent manner. LncRNA Airn could be a promising therapeutic target for cardiac fibrosis in DCM.
    Keywords:  Diabetic cardiomyopathy; Fibroblast proliferation; Fibrosis; LncRNA-Airn; P53; m6A modification
    DOI:  https://doi.org/10.1186/s13062-022-00346-6
  44. BMC Cancer. 2022 Nov 17. 22(1): 1184
    CX3CL1 promotes cell sensitivity to ferroptosis and is associated with the tumor microenvironment in clear cell renal cell carcinoma.
    Qiming Gong, Zhiting Guo, Wenjuan Sun, Xiuri Du, Yan Jiang, Fahui Liu.
      BACKGROUND: An increasing number of studies have demonstrated that CX3CL1 is involved in the development of tumors and may thus be considered a new potential therapeutic target for them. However, the function of CX3CL1 in clear cell renal cell carcinoma (ccRCC) remains poorly defined.METHODS: The pan-cancer expression pattern and prognostic value of CX3CL1 were evaluated in this study. Moreover, the relationship of CX3CL1 expression with the tumor microenvironment, especially the tumor immune microenvironment, was analyzed. Our analyses employed public repository data. Additionally, we generated stable CX3CL1-overexpressing 786-O cells to determine the role of CX3CL1 in vitro via cell viability and transwell assays. A xenograft tumor model was used to determine the role of CX3CL1 in vivo. The association between CX3CL1 and ferroptosis sensitivity of tumor cells was assessed using Ferrostatin-1.
    RESULTS: Our findings indicated the involvement of CX3CL1 in the occurrence and development of ccRCC by acting as a tumor suppressor. We also found that ccRCC patients with high CX3CL1 expression showed better clinical outcomes than those with low CX3CL1 expression. The findings of our epigenetic study suggested that the expression of CX3CL1 in ccRCC is correlated with its DNA methylation level. Furthermore, the CX3CL1 expression level was closely related to the infiltration level of CD8+ T cells into the tumor microenvironment (TME). CX3CL1 showed different predictive values in different immunotherapy cohorts. Finally, CX3CL1 overexpression inhibited tumor cell proliferation and metastasis and promoted tumor ferroptosis sensitivity in ccRCC.
    CONCLUSIONS: This study revealed the role of CX3CL1 as a tumor suppressor in ccRCC. Our findings indicated that CX3CL1 plays a crucial role in regulating the ccRCC TME and is a potential predictor of immunotherapy outcomes in ccRCC. We also found that CX3CL1 can promote ferroptosis sensitivity in ccRCC cells.
    Keywords:  CX3CL1; Clear cell renal cell carcinoma; Ferroptosis; Immunotherapy; Tumor microenvironment
    DOI:  https://doi.org/10.1186/s12885-022-10302-2
  45. Aging (Albany NY). 2022 Nov 16. 14
    Molecular subtypes identified by pyroptosis-related genes are associated with tumor microenvironment cell infiltration in colon cancer.
    Yiting Ling, Yinda Wang, Chenxi Cao, Lianzhong Feng, Binzhong Zhang, Senjuan Li.
      The important role of pyroptosis in tumor progression has been well characterized in recent years. However, little is known about the impact of tumor pyroptosis characteristics on patient prognosis and tumor microenvironment (TME) as well as efficacy of immunotherapy. In this study, we successfully classified colon cancer samples into three pyroptosis characterizations with different prognosis and TME cell infiltration patterns based on the expression of pyroptosis-related genes. Cluster 2, with the characterizations of immunosuppression, was classified as immune-desert cell infiltration patterns. Cluster 3, with the patterns of immune-inflamed cell infiltration, had the feature of an activated innate and adaptive immunity and significant prolonged survival. The activation of stromal pathways including EMT, angiogenesis and TGF-β in cluster 1 may mediate the impaired immune penetration of this cluster, which was classified as immune-excluded cell infiltration patterns. Our results demonstrated the PyroSig signature was a robust and independent biomarker for predicting patient prognosis. Patients with low PyroSig signature was confirmed to be correlated with treatment advantages and significant prolonged survival in two anti-checkpoint immunotherapy cohorts. This study identified three pyroptosis-related subtypes with distinct molecular features, clinical and microenvironment cell infiltration patterns in colon cancer, which could promote individualized immunotherapy for colon cancer.
    Keywords:  immune response; immunotherapy; prognosis; pyroptosis; tumor microenvironment
    DOI:  https://doi.org/10.18632/aging.204379
  46. Front Oncol. 2022 ;12 934076
    Regulation, genomics, and clinical characteristics of cuproptosis regulators in pan-cancer.
    Cankun Zhou, Chaomei Li, Yuhua Zheng, Xiaobin Huang.
      Background: Cuproptosis, a copper-dependent controlled cell death, is a novel form of cell death that differs from known cell death mechanisms; however, its overall regulation in cancer remains elusive.Methods: Multiple open-source bioinformatic platforms were used to comprehensively elucidate the expression levels, prognostic efficiency, potential biological functions, genomic and epigenetic characteristics, immune microenvironment, and drug sensitivity of cuproptosis regulators (ATP7A, ATP7B, DLAT, DLD, FDX1, GLS, LIAS, LIPT1, MTF1, NLRP3, PDHA1, PDHB, and SLC31A1) in pan-cancer.
    Results: Cuproptosis-related genes (CRGs) were upregulated in most cancers tested. In KIRC, KIRP, LGG, MESO, and PCPG, most highly expressed CRGs predicted a better prognosis but poorer prognosis in patients with ACC, LIHC, and UCEC. Pathway analysis confirmed that cuproptosis regulators were associated with the metabolism-related pathways. The expression of MTF1, NLRP3, and SLC31A1 was positively related with ImmuneScore, StromalScore, and ESTIMATEScore in almost all types of tumor, whereas ATP7B, DLAT, DLD, LIAS, PDHA1, and PDHB were significantly negatively correlated with the scores. In addition, CRGs were significantly correlated with RNA stemness score, DNA stemness score, microsatellite instability, and tumor mutational burden. The expression of ATP7A, ATP7B, LIAS, and DLAT was significantly positively correlated with the drug sensitivity of Docetaxel. ATP7A, LIAS, and FDX1 were significantly negatively correlated with the drug sensitivity of UNC0638, XMD13-2, YM201636, and KIN001-260.
    Conclusions: The altered genomic and clinical characteristics of cuproptosis regulators were comprehensively elucidated, providing a preliminary basis for understanding the functions of cuproptosis in pan-cancer.
    Keywords:  cuproptosis; genomics; immune; pan-cancer; tumor microenvironment
    DOI:  https://doi.org/10.3389/fonc.2022.934076
  47. Am J Cancer Res. 2022 ;12(10): 4566-4583
    CPSF1 positively regulates NSDHL by alternative polyadenylation and promotes gastric cancer progression.
    Weibiao Kang, Yang Yang, Changyu Chen, Changjun Yu.
      Gastric cancer (GC) is a common malignancies with unfavourable prognosis. As one of the most common RNA modifications in nature, alternative polyadenylation (APA) plays a critical role in the progression of carcinomas. CPSF1 is a critical APA-related factor and is involved in many cancers. Nevertheless, the roles and underlying mechanisms of CPSF1 remain unclear in GC. In this work, we identified that CPSF1 is significantly upregulated in GC and that high CPSF1 expression indicates an unfavourable prognosis in GC patients. Moreover, CPSF1 expression levels were closely associated with tumour size, TNM stage and lymph node metastasis. CPSF1 depletion dramatically weakened GC cell proliferation and metastasis. We then performed RNA sequencing and found numerous downstream genes involved the regulation of CPSF1 with remarkable changes in 3'UTR length, among which NSDHL was positively regulated by CPSF1 and promoted GC progression. In addition, rescue assays demonstrated that NSDHL mediated the carcinogenic effect of CPSF1, and this process potentially involved APA. Therefore, this study showed that CPSF1 promotes GC progression, at least in part, by enhancing NSDHL and offered new insights into therapeutic targets for GC.
    Keywords:  APA; CPSF1; NSDHL; gastric cancer; progression
  48. Exp Cell Res. 2022 Nov 15. pii: S0014-4827(22)00406-2. [Epub ahead of print] 113413
    PRMT6 functionally associates with PRMT5 to promote colorectal cancer progression through epigenetically repressing the expression of CDKN2B and CCNG1.
    Yuzhong Chen, Wanqing Liang, Jun Du, Jiachi Ma, Rongrui Liang, Min Tao.
      BACKGROUND: Protein arginine methyltransferase 6 (PRMT6) is a type I arginine methyltransferase that asymmetrically dimethylates histone H3 arginine 2 (H3R2me2a). However, the biological roles and underlying molecular mechanisms of PRMT6 in colorectal cancer (CRC) remain unclear.METHODS: PRMT6 expression in CRC tissue was examined using immunohistochemistry. The effect of PRMT6 on CRC cells was investigated in vitro and in vivo. Mass spectrometry, co-immunoprecipitation and GST pulldown assays were performed to identify interaction partners of PRMT6. RNA-seq, chromatin immunoprecipitation, Western blot and qRT-PCR assays were used to investigate the mechanism of PRMT6 in gene regulation.
    RESULTS: PRMT6 is significantly upregulated in CRC tissues and facilitates cell proliferation of CRC cells in vitro and in vivo. Through RNA-seq analysis, CDKN2B (p15INK4b) and CCNG1 were identified as new transcriptional targets of PRMT6. PRMT6-dependent H3R2me2a mark was predominantly deposited at the promoters of CDKN2B and CCNG1 in CRC cells. Furthermore, PRMT5 was firstly characterized as an interaction partner of PRMT6. Notably, H3R2me2a coincides with PRMT5-mediated H4R3me2s and H3R8me2s marks at the promoters of CDKN2B and CCNG1 genes, thus leading to transcriptional repression of these genes.
    CONCLUSIONS: PRMT6 functionally associates with PRMT5 to promote CRC progression through epigenetically repressing the expression of CDKN2B and CCNG1. These insights raise the possibility that combinational intervention of PRMT6 and PRMT5 may be a promising strategy for CRC therapy.
    Keywords:  CCNG1; CDKN2B; PRMT5; PRMT6; Proliferation
    DOI:  https://doi.org/10.1016/j.yexcr.2022.113413
  49. Front Oncol. 2022 ;12 1024655
    Lung adenocarcinoma relapse with emerging EGFR mutation following complete response of small cell lung cancer warrants routine re-biopsy: A case report.
    Minna Zhang, Yi Tang, Junlei Wang, Qian Liu, Bing Xia.
      Transformation of small cell lung cancer (SCLC) to lung adenocarcinoma (LUAD) is rarely reported. Here, we report a case initially presented with SCLC and was diagnosed as LUAD when the lesion relapsed at the same site. A 56-year-old patient with SCLC who received etoposide and cisplatin chemotherapy combined with radiotherapy achieved a complete radiological response. After 28 months of stable disease, a computed tomography scan revealed a new lesion at the same site as the primary tumor. Pathological examination suggested a LUAD with an emerging EGFR exon 19 deletion. The patient was then treated with icotinib and achieved a near-complete radiological response. Nineteen months later, the patient developed resistance caused by EGFR T790M mutation and received treatment with osimertinib. At the last follow-up in January 2022, the patient was symptom-free. This case warrants re-biopsy and genetic testing as a routine operation when SCLC relapses at the same site as the primary tumor for an extended period, and prospective investigation is required.
    Keywords:  EGFR; histological transformation; lung adenocarcinoma; non-small cell lung cancer; small cell lung cancer
    DOI:  https://doi.org/10.3389/fonc.2022.1024655
  50. J Environ Pathol Toxicol Oncol. 2022 ;41(4): 25-38
    Effects of RNA Modification "Writers" of GALNT2 on the Tumor Microenvironment in Cervical Squamous Cell Carcinoma.
    Shizhang Wang, Lin Chen.
      Cervical squamous cell carcinoma (CESC) is one of the most common causes of cancer-related deaths in women. RNA modification "writers" modulate and alter RNA molecular activity and have been implicated in the origin and development of cancer. We explored the effects of RNA modification writers on the tumor microenvironment in CESC and their prognostic value. RNA modification writers were altered at the genetic and transcriptional levels in CESC sample data downloaded from The Cancer Genome Atlas and Gene Expression Omnibus databases. A principal component analysis (PCA) score model was established based on the genes screened by Cox regression analysis and random forest dimensionality reduction. A survival analysis of CESC patients revealed significant differences between patients with high and low scores. The gene set variation analysis method was used for a functional enrichment analysis. The relative abundance of immune cells in CESCs was quantified using the CIBERSORT algorithm. There were significant differences in multiple signaling pathways and immune cells between the patients with high and low scores. Based on Genomics of Drug Sensitivity in Cancer data, we analyzed the genetic mutations in CESCs and predicted the therapeutic effects of multiple anticancer drugs. Patients with high scores showed significant resistance. Finally, the N-acetylgalactosaminyltransferase 2 (GALNT2) was highly expressed in CESCs and was associated with multiple immune cells and the formation of the extracellular matrix. PCA score based on RNA modification writers is closely associated with immune infiltration in the tumor microenvironment and could be used as a reference for prognosis and medication in CESC patients.
    DOI:  https://doi.org/10.1615/JEnvironPatholToxicolOncol.2022042887
  51. Adv Sci (Weinh). 2022 Nov 16. e2204885
    RNA 5-Methylcytosine Modification Regulates Vegetative Development Associated with H3K27 Trimethylation in Arabidopsis.
    Daolei Zhang, Weijun Guo, Ting Wang, Yifan Wang, Liang Le, Fan Xu, Yue Wu, Hada Wuriyanghan, Zinmay Renee Sung, Li Pu.
      Methylating RNA post-transcriptionally is emerging as a significant mechanism of gene regulation in eukaryotes. The crosstalk between RNA methylation and histone modification is critical for chromatin state and gene expression in mammals. However, it is not well understood mechanistically in plants. Here, the authors report a genome-wide correlation between RNA 5-cytosine methylation (m5 C) and histone 3 lysine27 trimethylation (H3K27me3) in Arabidopsis. The plant-specific Polycomb group (PcG) protein EMBRYONIC FLOWER1 (EMF1) plays dual roles as activators or repressors. Transcriptome-wide RNA m5 C profiling revealed that m5 C peaks are mostly enriched in chromatin regions that lacked H3K27me3 in both wild type and emf1 mutants. EMF1 repressed the expression of m5 C methyltransferase tRNA specific methyltransferase 4B (TRM4B) through H3K4me3, independent of PcG-mediated H3K27me3 mechanism. The 5-Cytosine methylation on targets is increased in emf1 mutants, thereby decreased the mRNA transcripts of photosynthesis and chloroplast genes. In addition, impairing EMF1 activity reduced H3K27me3 levels of PcG targets, such as starch genes, which are de-repressed in emf1 mutants. Both EMF1-mediated promotion and repression of gene activities via m5 C and H3K27me3 are required for normal vegetative growth. Collectively, t study reveals a previously undescribed epigenetic mechanism of RNA m5 C modifications and histone modifications to regulate gene expression in eukaryotes.
    Keywords:  Arabidopsis; EMBRYONIC FLOWER1; RNA 5-cytosine methylation; histone 3 lysine27 trimethylation; vegetative growth
    DOI:  https://doi.org/10.1002/advs.202204885
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