DNA Methylation Analysis Identifies Immune-related LncRNAs In Pan-central Nervous System Tumor

Objective:DNA methylation(DNA Methylation)is a common and important epigenetic modification.Studies have shown that DNA methylation plays an important role in tissue development and various complex diseases(such as cancer,cardiovascular disease,etc.).Long non-coding RNA(lncRNA)is one of the key regulators of gene expression.The expression of lncRNA changes in various diseases and plays an important role in immune regulation.Numerous studies have shown that the dysregulation of lncRNA expression is tightly regulated by DNA methylation.Central nervous system(CNS)tumors are one of the most common tumor types in children.However,there is still a lack of knowledge about the epigenetic regulation of immunerelated lncRNAs in different types of pediatric CNS tumors.Methods:The DNA methylation profiles of 2,257 pediatric CNS tumor samples covering 61 WHO-defined CNS tumor types were first collected from the Gene Expression Omnibus(GEO)database and the Array Express database,and the DNA methylation profiles were collected from the Gene Expression Omnibus(GEO)database and Array Express database.The profiles were combined with lncRNA annotation to identify lncRNAs that were epigenetically regulated.Next,paediatric CNS tumors were reclassified into different molecular clusters based on methylation signatures,and the effectiveness of the new classification was assessed using a likelihood ratio model.For CNS clusters based on methylation signatures,immune cell infiltration in patients with each cluster was calculated and compared using MethyCIBERSORT.In addition,differences in immune regulation between clusters were further investigated by collecting multiple immune signatures through the literature.In order to systematically determine the functional pathways regulated by DNA methylation,quantitative differentially methylated regions(QDMRs)were determined based on the quantitative method QDMR software,and then the functional enrichment analysis of differentially methylated genes was performed using the metascape online tool to identify each Cluster-related molecular functional pathways.To further evaluate the correlation between IncRNA methylation and immune cell infiltration in each cluster by calculating the Spearman correlation coefficient(SCC)between lncRNA methylation levels and the proportion of immune cells,by investigating their association with immune cells The correlation of cell infiltration and potential regulatory target genes further identified immune-related IncRNAs.The number of IncRNAs associated with immune cell infiltration was analyzed,and the correlation between different immune cells and IncRNA methylation between clusters was further analyzed.1,811 protein-coding genes involved in 17 immune-related pathways were obtained.Next,the closest homeopathically regulated protein-coding genes were identified for each immune cell infiltration-related IncRNA based on genomic location.If the nearest protein-coding gene is annotated in an immune-related pathway,this IncRNA is considered to be involved in the regulation of immune-related pathways.The differentially methylated IncRNAs in each cluster were then identified based on the "one vs.rest" approach.Finally,through literature mining,lncRNAs that can serve as potential biomarkers in pediatric CNS tumors were identified.Results:The epigenetic regulation of IncRNAs in 61 CNS tumors was finally determined,and IncRNAs were divided into three methylation patterns of hyper,inter,and hypo according to the methylation level of children’s tumors.The properties of IncRNAs with different methylation types are different.The hypo-type IncRNAs have higher GC content,exon number,CpG number and conservation score,while the hypertype IncRNAs show the opposite pattern.Next,we revealed the ubiquitous IncRNA methylation heterogeneity in pediatric pan-CNS tumors,reclassified CNS tumors into 14 different molecular clusters based on the pattern of IncRNA methylation,and the intraclass samples had High Pearson correlation.In addition,it was found that after adding methylation signature-based cluster classification,the likelihood ratio model also showed higher significance,indicating that methylation signature-based cancer cluster classification could better reflect the clinical differences of patients.Further,through the computational results of MethyCIBERSORT,the immune microenvironment of patients with tumor molecular clusters was studied,and it was found that each tumor cluster had a different degree of immune cell infiltration,among which endothelial cells and fibroblasts accounted for a large proportion.Among the clusters,there are significant differences in immune signature scores.In particular,patients in the C5 cluster have generally higher levels of immune signature methylation,and Treg immune cells account for the largest proportion,indicating that regulatory T cells may hinder CNS nerve damage.or recovery from psychological stress.In addition,these clusters are also involved in functional pathways such as neurodevelopment and immune regulation.Then,through a comprehensive analysis of the proportion of lncRNA methylation and immune cell infiltration,it was found that lncRNA methylation was significantly associated with immune cell infiltration in different tumor clusters,and 32 lncRNAs and 10 types of immune cell infiltration were identified.degree is significantly correlated.The number of lncRNAs associated with immune infiltration was significantly different between molecular clusters,and there were differences in the types of immune cells involved.LncRNAs with methylation perturbations may play important roles in tumors by regulating genes in immunerelated pathways.Finally,16 candidate immune-related lncRNAs in CNS tumors were identified as potential biomarkers for subsequent functional verification.Conclusion:This study systematically analyzed the lncRNA regulatory map under epigenetic regulation in pediatric pan-central nervous system tumors,and revealed the important role of lncRNA in immune regulation.The results of the study found that lncRNA methylation profiles can reveal tumor molecular clusters with different methylation patterns,and tumor patients with different clusters have significantly different immune microenvironment differences.By analyzing the correlation between IncRNA methylation levels and the tumor immune microenvironment,potential immune-related IncRNA molecular markers in pediatric tumors were identified,providing an important resource for promoting the development of new immunotherapy targets and therapeutic strategies in CNS tumors.New insights.