Integration of Multi-omics Data Revealed the Orphan CpG Islands and Enhancer-dominated Cis-regulatory Network in Glioma

Abstract

Background: The complex transcriptional regulatory network leads to the poor prognosis of glioma. The role of orphan CpG islands (oCGIs) in the transcriptional regulatory network has been overlooked. Establishing a sophisticated transcriptional regulatory system is paramount.Methods: We constructed different cis-regulatory models through mutual information and Bayesian networks. We utilized eleven machine learning algorithms to develop classifiers that could effectively integrate multi-omics datasets. we utilized single-cell multi-omics data construct a higher-resolution cis-regulatory network. To investigate the binding interaction between oCGIs and transcription factors, we utilized chromatin immunoprecipitation assay and qRT-PCR. Furthermore, we assessed the proliferative status of various glioma subtypes using the MTT assay and immunohistochemistry.Results: The cis-regulatory network dominated by oCGIs and enhancers was significantly active in the glioma subtypes, mainly characterized by glioblastoma (Cluster 2). Direct regulation of target genes by oCGIs or enhancers is of great importance in the cis-regulatory network. Furthermore, based on single-cell multi-omics data, we found that the highly activated cis-regulatory network in Cluster 2 sustains the high proliferative potential of glioma cells. The upregulation of oCGIs and enhancers related genes in Cluster 2 results in glioma patients exhibiting resistance to radiotherapy and chemotherapy. These findings were further validated through glioma cell line related experiments.Conclusion: Our study systematically elucidated the cis-regulatory role of oCGIs for the first time. The comprehensive characterization of the multi-omics features of the oCGIs- and enhancers-dominated cis-regulatory network offers a novel insight into the pathogenesis of glioma and provides new strategies to treat this challenging disease.