DNA Methylation-based Molecular Subtype Analysis Of T Cell Acute Lymphoblastic Leukemia

T-cell acute lymphoblastic leukemia is a malignant clonal disease of blood system with high heterogeneity of immunophenotype.Genomic DNA methylation modification is an important epigenetic regulation of T-ALL,which maintains homeostasis in normal and tumor cells.Recent studies have confirmed that DNA methyltransferase DNMT family and demethylase active tet protein family play an important role in the continuous and dynamic regulation of various subtype cell populations and maintaining heterogeneity in the occurrence and development of T-ALL.However,the research on the mechanism of maintaining molecular heterogeneity,cell source and maintaining cell properties of T-ALL cells has not been reported.Therefore,it is of great significance to reclassify and identify T-ALL cells based on DNA methylation and explore the mechanism.The purpose of this study is to reveal the potential regulatory mechanism of DNA methylation in the occurrence,evolution and maintenance of T-ALL cell heterogeneity by using bioinformatics research methods.Firstly,we analyzed the expression profiles of T-ALL and AML,and found that NOTCH2 and CBX2,the fate determinants related to DNA methylation modifying enzymes,may be involved in the occurrence,development and lineage differentiation of T-ALL.The consistent results were verified by the expression of T-ALL cell lines BE13,Jurkat,Molt4 and RPMI-8402.Next,the DNA methylation map of 65 T-ALL patients was used to screen the promoter differentially methylated region with biological significance as the basic condition for cell typing,and eight T-ALL cell subtypes were found by cluster analysis.Next,in order to reveal the ancestors of cells,we use the comparative analysis of cell transcription spectrum in the development stage of T cells.According to the distribution and functional enrichment of CIMP gene group,it is found that cluster 2,4 and 7 subtypes show the characteristics of hematopoietic progenitor cells,and other subtypes may come from other developmental stages of T cells.There are specific upstream gene groups of DMR in cluster 2,4 and 7.In order to determine the genes regulated by DNA methylation modifying enzymes,the correlation between them and DNMT or TET family members was analyzed.It was found that these genes are mainly regulated by DNMT1 and TET3 enzymes in T cell development.Then we analyzed the transcription factor targets of the upstream gene groups of cluster 2 and 7 DMR,constructed PPI network,and predicted and verified the competitive or synergistic relationship between methyltransferase or demethyltransferase and transcription factors.In this study,T-ALL identity was identified by methylation combined with cell-specific transcription spectrum,the potential mechanism of DNA methylation modifying enzymes in the process of identity recognition and fate regulation was clarified,and the epigenetic mechanism of clonal and heterogeneous leukemia was clarified.This study lays a theoretical foundation for the individualized diagnosis and treatment of leukemia.