Identification and verification of m7G-Related genes as biomarkers for prognosis of sarcoma

Background: Increasing evidence indicates a crucial role for N7-methylguanosine (m7G) methylation modification in human disease development, particularly cancer, and aberrant m7G levels are closely associated with tumorigenesis and progression via regulation of the expression of multiple oncogenes and tumor suppressor genes. However, the role of m7G in sarcomas (SARC) has not been adequately evaluated. Materials and methods: Transcriptome and clinical data were gathered from the TCGA database for this study. Normal and SARC groups were compared for the expression of m7G-related genes (m7GRGs). The expression of m7GRGs was verified using real-time quantitative PCR (RT-qPCR) in SARC cell lines. Then, differentially expressed genes (DEGs) were identified between high and low m7GRGs expression groups in SARC samples, and GO enrichment and KEGG pathways were evaluated. Next, prognostic values of m7GRGs were evaluated by Cox regression analysis. Subsequently, a prognostic model was constructed using m7GRGs with good prognostic values by Lasso regression analysis. Besides, the relationships between prognostic m7GRGs and immune infiltration, clinical features, cuproptosis-related genes, and antitumor drugs were investigated in patients with SARC. Finally, a ceRNA regulatory network based on m7GRGs was constructed. Results: The expression of ten m7GRGs was higher in the SARC group than in the control group. DEGs across groups with high and low m7GRGs expression were enriched for adhesion sites and cGMP-PKG. Besides, we constructed a prognostic model that consists of EIF4A1, EIF4G3, NCBP1, and WDR4 m7GRGs for predicting the survival likelihood of sarcoma patients. And the elevated expression of these four prognostic m7GRGs was substantially associated with poor prognosis and elevated expression in SARC cell lines. Moreover, we discovered that these four m7GRGs expressions were negatively correlated with CD4+ T cell levels, dendritic cell level and tumor purity, and positively correlated with tumor mutational burden, microsatellite instability, drug sensitivity and cuproptosis-related genes in patients with sarcomas. Then, a triple regulatory network of mRNA, miRNA, and lncRNA was established. Conclusion: The current study identified EIF4A1, EIF4G3, NCBP1, and WDR4 as prognostic genes for SARC that are associated with m7G.These findings extend our knowledge of m7G methylation in SARC and may guide the development of innovative treatment options.

[1]  Na Li,et al.  Ovarian cancer subtypes based on the regulatory genes of RNA modifications: Novel prediction model of prognosis , 2022, Frontiers in Endocrinology.

[2]  E. Fernández-Salas,et al.  AB801 is a potent and selective AXL inhibitor that demonstrates significant anti-tumor activity in combination with standard of care therapeutics , 2022, European Journal of Cancer.

[3]  Wen Fu,et al.  Cuproptosis scoring system to predict the clinical outcome and immune response in bladder cancer , 2022, Frontiers in Immunology.

[4]  Z. Shao,et al.  Single-cell transcriptomics reveals the regulative roles of cancer associated fibroblasts in tumor immune microenvironment of recurrent osteosarcoma , 2022, Theranostics.

[5]  Zhen Zhang,et al.  Cuproptosis-Related Risk Score Predicts Prognosis and Characterizes the Tumor Microenvironment in Hepatocellular Carcinoma , 2022, Frontiers in Immunology.

[6]  Hong Wang,et al.  A Newly Established Cuproptosis-Associated Long Non-Coding RNA Signature for Predicting Prognosis and Indicating Immune Microenvironment Features in Soft Tissue Sarcoma , 2022, Journal of oncology.

[7]  Xianwei Zhang,et al.  A novel Cuproptosis-related LncRNA signature to predict prognosis in hepatocellular carcinoma , 2022, Scientific Reports.

[8]  Min Fu,et al.  Circular RNA EIF4G3 suppresses gastric cancer progression through inhibition of β-catenin by promoting δ-catenin ubiquitin degradation and upregulating SIK1 , 2022, Molecular cancer.

[9]  Xuqing Zhang,et al.  N7-Methylguanosine Regulatory Genes Profoundly Affect the Prognosis, Progression, and Antitumor Immune Response of Hepatocellular Carcinoma , 2022, Frontiers in Surgery.

[10]  Shuibin Lin,et al.  Eliminating METTL1‐mediated accumulation of PMN‐MDSCs prevents hepatocellular carcinoma recurrence after radiofrequency ablation , 2022, Hepatology.

[11]  Xin-yu Li,et al.  m7G Methylation-Related Genes as Biomarkers for Predicting Overall Survival Outcomes for Hepatocellular Carcinoma , 2022, Frontiers in Bioengineering and Biotechnology.

[12]  Lingmin Xie,et al.  A Novel Cuproptosis-Related Prognostic Gene Signature and Validation of Differential Expression in Clear Cell Renal Cell Carcinoma , 2022, Genes.

[13]  T. Golub,et al.  Copper induces cell death by targeting lipoylated TCA cycle proteins , 2022, Science.

[14]  Leo D. Wang,et al.  Clipper: p-value-free FDR control on high-throughput data from two conditions , 2021, Genome Biology.

[15]  Zheng Chen,et al.  MicroRNA-let-7 Targets HMGA2 to Regulate the Proliferation, Migration, and Invasion of Colon Cancer Cell HCT116 , 2021, Evidence-Based Complementary and Alternative Medicine.

[16]  Shuibin Lin,et al.  METTL1/WDR4 mediated m7G tRNA modifications and m7G codon usage promote mRNA translation and lung cancer progression. , 2021, Molecular therapy : the journal of the American Society of Gene Therapy.

[17]  Shiwen Xu,et al.  Aberrant expression of WDR4 affects the clinical significance of cancer immunity in pan-cancer , 2021, Aging.

[18]  Xianping Lu,et al.  Chidamide and Radiotherapy Synergistically Induce Cell Apoptosis and Suppress Tumor Growth and Cancer Stemness by Regulating the MiR-375-EIF4G3 Axis in Lung Squamous Cell Carcinomas , 2021, Journal of oncology.

[19]  Diane Lefaudeux,et al.  Identifying the combinatorial control of signal-dependent transcription factors , 2021, PLoS Comput. Biol..

[20]  Junjie Bao,et al.  Glycogen synthase kinase 3β promotes osteosarcoma invasion and migration via regulating PTEN and phosphorylation of focal adhesion kinase , 2021, Bioscience reports.

[21]  F. Verrecchia,et al.  ICG-001, an Inhibitor of the β-Catenin and cAMP Response Element-Binding Protein Dependent Gene Transcription, Decreases Proliferation but Enhances Migration of Osteosarcoma Cells , 2021, Pharmaceuticals.

[22]  Wei Zhang,et al.  Roles of RNA Methylation on Tumor Immunity and Clinical Implications , 2021, Frontiers in Immunology.

[23]  Xidi Wang,et al.  Oncogenic lncRNA ZNF561-AS1 is essential for colorectal cancer proliferation and survival through regulation of miR-26a-3p/miR-128-5p-SRSF6 axis , 2021, Journal of experimental & clinical cancer research : CR.

[24]  T. Ozaki,et al.  Immunotherapy for sarcomas. , 2021, Japanese journal of clinical oncology.

[25]  G. Brandi,et al.  PD-L1, TMB, MSI, and Other Predictors of Response to Immune Checkpoint Inhibitors in Biliary Tract Cancer , 2021, Cancers.

[26]  T. Nielsen,et al.  Sarcomas: Immune biomarker expression and checkpoint inhibitor trials. , 2020, Cancer treatment reviews.

[27]  Zhongyue Huang,et al.  LINC00511 Promotes Osteosarcoma Tumorigenesis and Invasiveness through the miR-185-3p/E2F1 Axis , 2020, BioMed research international.

[28]  Fan Zhang,et al.  TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment , 2020, bioRxiv.

[29]  Teresa Colombo,et al.  A Census and Categorization Method of Epitranscriptomic Marks , 2020, International journal of molecular sciences.

[30]  J. Xia,et al.  miRNet 2.0: network-based visual analytics for miRNA functional analysis and systems biology , 2020, Nucleic Acids Res..

[31]  Xiaole Shirley Liu,et al.  TIMER2.0 for analysis of tumor-infiltrating immune cells , 2020, Nucleic Acids Res..

[32]  Yabing Chen,et al.  m6A mRNA methylation regulates testosterone synthesis through modulating autophagy in Leydig cells , 2020, Autophagy.

[33]  F. Huang,et al.  WD40 protein Wuho controls germline homeostasis via TRIM-NHL tumor suppressor Mei-p26 in Drosophila , 2020, Development.

[34]  Chenghao Zhang,et al.  The prognostic value of long noncoding RNA SNHG16 on clinical outcomes in human cancers: a systematic review and meta-analysis , 2019, Cancer Cell International.

[35]  Q. Ding,et al.  METTL3-mediated m6A modification of HDGF mRNA promotes gastric cancer progression and has prognostic significance , 2019, Gut.

[36]  Yu-Sheng Chen,et al.  Dynamic methylome of internal mRNA N7-methylguanosine and its regulatory role in translation , 2019, Cell Research.

[37]  Yulong Tan,et al.  NCBP1 promotes the development of lung adenocarcinoma through up‐regulation of CUL4B , 2019, Journal of cellular and molecular medicine.

[38]  Lauren L. Ritterhouse,et al.  Tumor mutational burden , 2019, Cancer cytopathology.

[39]  Edward M Kennedy,et al.  Epitranscriptomic Addition of m5C to HIV-1 Transcripts Regulates Viral Gene Expression. , 2019, Cell host & microbe.

[40]  N. Sonenberg,et al.  The Organizing Principles of Eukaryotic Ribosome Recruitment. , 2019, Annual review of biochemistry.

[41]  Wenling Zhang,et al.  Circ-EIF4G3 promotes the development of gastric cancer by sponging miR-335. , 2019, Pathology, research and practice.

[42]  Andrew J. Bannister,et al.  METTL1 Promotes let-7 MicroRNA Processing via m7G Methylation , 2019, Molecular cell.

[43]  A. Naghavi,et al.  Sarcoma as a Model for Adolescent and Young Adult Care. , 2019, Journal of oncology practice.

[44]  Damian Szklarczyk,et al.  STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets , 2018, Nucleic Acids Res..

[45]  X. Liu,et al.  Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response , 2018, Nature Medicine.

[46]  Victor S Lelyveld,et al.  Mettl1/Wdr4-Mediated m7G tRNA Methylome Is Required for Normal mRNA Translation and Embryonic Stem Cell Self-Renewal and Differentiation. , 2018, Molecular cell.

[47]  J. Marquardt,et al.  Immunotherapy of Hepatocellular Carcinoma , 2018, Oncology Research and Treatment.

[48]  Harrison Pielke-Lombardo,et al.  GSEA-InContext: identifying novel and common patterns in expression experiments , 2018, bioRxiv.

[49]  Janusz M. Bujnicki,et al.  MODOMICS: a database of RNA modification pathways. 2017 update , 2017, Nucleic Acids Res..

[50]  Jun S. Liu,et al.  TIMER: A Web Server for Comprehensive Analysis of Tumor-Infiltrating Immune Cells. , 2017, Cancer research.

[51]  S. Liang,et al.  Ubiquitination of tumor suppressor PML regulates prometastatic and immunosuppressive tumor microenvironment , 2017, The Journal of clinical investigation.

[52]  M. Xie,et al.  Icarisid II inhibits the proliferation of human osteosarcoma cells by inducing apoptosis and cell cycle arrest , 2017, Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine.

[53]  Chuan He,et al.  m6A Demethylase ALKBH5 Maintains Tumorigenicity of Glioblastoma Stem-like Cells by Sustaining FOXM1 Expression and Cell Proliferation Program. , 2017, Cancer cell.

[54]  G. Fornaciari.  Histology of ancient soft tissue tumors: A review. , 2017, International journal of paleopathology.

[55]  Yang Shi,et al.  m6A RNA methylation regulates the UV-induced DNA damage response , 2016, Nature.

[56]  Wade Wang,et al.  Structurally Programmed Assembly of Translation Initiation Nanoplex for Superior mRNA Delivery. , 2017, ACS nano.

[57]  Jie Jin,et al.  FTO Plays an Oncogenic Role in Acute Myeloid Leukemia as a N6-Methyladenosine RNA Demethylase. , 2017, Cancer cell.

[58]  K. Entian,et al.  Tuning the ribosome: The influence of rRNA modification on eukaryotic ribosome biogenesis and function , 2016, RNA biology.

[59]  G. B. Robb,et al.  mRNA capping: biological functions and applications , 2016, Nucleic acids research.

[60]  Samir Adhikari,et al.  Nuclear m(6)A Reader YTHDC1 Regulates mRNA Splicing. , 2016, Molecular cell.

[61]  James R. Eshleman,et al.  Microsatellite Instability as a Biomarker for PD-1 Blockade , 2016, Clinical Cancer Research.

[62]  Olivier Elemento,et al.  5′ UTR m6A Promotes Cap-Independent Translation , 2015, Cell.

[63]  J. Alexander,et al.  Targeted Chemotherapy in Bone and Soft-Tissue Sarcoma. , 2015, The Orthopedic clinics of North America.

[64]  Marco Y. Hein,et al.  mRNA export through an additional cap-binding complex consisting of NCBP1 and NCBP3 , 2015, Nature Communications.

[65]  Chuan He,et al.  N 6 -methyladenosine Modulates Messenger RNA Translation Efficiency , 2015, Cell.

[66]  S. Donaldson,et al.  Recent advances in understanding and managing rhabdomyosarcoma , 2015, F1000prime reports.

[67]  K. Tomczak,et al.  The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge , 2015, Contemporary oncology.

[68]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[69]  E Provenzano,et al.  The malignant phenotype in breast cancer is driven by eIF4A1-mediated changes in the translational landscape , 2015, Cell Death and Disease.

[70]  E. Phizicky,et al.  Two-subunit enzymes involved in eukaryotic post-transcriptional tRNA modification , 2014, RNA biology.

[71]  Chuan He,et al.  FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis , 2014, Cell Research.

[72]  C. Antonescu,et al.  Lessons Learned From the Study of 10,000 Patients With Soft Tissue Sarcoma , 2014, Annals of surgery.

[73]  G. Ke,et al.  Decreased Expression of EIF4A1 After Preoperative Brachytherapy Predicts Better Tumor-Specific Survival in Cervical Cancer , 2014, International Journal of Gynecologic Cancer.

[74]  Hui Zhou,et al.  starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data , 2013, Nucleic Acids Res..

[75]  Zhike Lu,et al.  m6A-dependent regulation of messenger RNA stability , 2013, Nature.

[76]  Dong Chen,et al.  Potential biomarkers for paclitaxel sensitivity in hypopharynx cancer cell. , 2013, International journal of clinical and experimental pathology.

[77]  E. Puré,et al.  Hypoxia-dependent modification of collagen networks promotes sarcoma metastasis. , 2013, Cancer discovery.

[78]  Benjamin E. Gross,et al.  Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal , 2013, Science Signaling.

[79]  Justin Guinney,et al.  GSVA: gene set variation analysis for microarray and RNA-Seq data , 2013, BMC Bioinformatics.

[80]  Isidore Rigoutsos,et al.  Interactive exploration of RNA22 microRNA target predictions , 2012, Bioinform..

[81]  Sridhar Ramaswamy,et al.  Genomics of Drug Sensitivity in Cancer (GDSC): a resource for therapeutic biomarker discovery in cancer cells , 2012, Nucleic Acids Res..

[82]  Guangchuang Yu,et al.  clusterProfiler: an R package for comparing biological themes among gene clusters. , 2012, Omics : a journal of integrative biology.

[83]  Douglas Hanahan,et al.  Accessories to the Crime: Functions of Cells Recruited to the Tumor Microenvironment Prospects and Obstacles for Therapeutic Targeting of Function-enabling Stromal Cell Types , 2022 .

[84]  P. Pandolfi,et al.  A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language? , 2011, Cell.

[85]  Gary D. Bader,et al.  The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function , 2010, Nucleic Acids Res..

[86]  Matthew D. Wilkerson,et al.  ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking , 2010, Bioinform..

[87]  A. Fusco,et al.  Inorganic phosphate inhibits growth of human osteosarcoma U2OS cells via adenylate cyclase/cAMP pathway , 2006, Journal of cellular biochemistry.

[88]  P. Shannon,et al.  Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks , 2003 .

[89]  J. Clardy,et al.  Structural basis of m7GpppG binding to the nuclear cap-binding protein complex , 2002, Nature Structural Biology.

[90]  E. Phizicky,et al.  Two proteins that form a complex are required for 7-methylguanosine modification of yeast tRNA. , 2002, RNA.

[91]  S Minoshima,et al.  Isolation and characterization of a human chromosome 21q22.3 gene (WDR4) and its mouse homologue that code for a WD-repeat protein. , 2000, Genomics.

[92]  Joe D. Lewis,et al.  A cap-binding protein complex mediating U snRNA export , 1995, Nature.

[93]  Joe D. Lewis,et al.  A nuclear cap binding protein complex involved in pre-mRNA splicing , 1994, Cell.

[94]  Markus List,et al.  Immunedeconv: An R Package for Unified Access to Computational Methods for Estimating Immune Cell Fractions from Bulk RNA-Sequencing Data. , 2020, Methods in molecular biology.

[95]  K. Kalia,et al.  Tumor Microenvironment Targeted Nanotherapeutics for Cancer Therapy and Diagnosis: A review. , 2019, Acta biomaterialia.

[96]  A. Jemal,et al.  Cancer statistics, 2019 , 2019, CA: a cancer journal for clinicians.

[97]  W. Neaves.  Leydig cells. , 1975, Contraception.