Integration of transcriptional and epigenetic regulation of TFEB reveals dual functional roles in Pan-cancer [ChIP-seq]

Transcription factor EB (TFEB) mainly regulates the autophagy-lysosomal pathway, associated with many diseases, including cancer. However, the role of TFEB in pan-cancer has not been investigated systematically. In this study, we comprehensively analyzed TFEB targets under three stresses in Hela cells by cross-validation of RNA-seq and ChIP-seq. 1,712 novel TFEB targets have not been reported in the Gene Set Enrichment Analysis and ChIP Enrichment Analysis databases. We further investigated their distributions and roles among the pan-cancer co-expression networks across 32 cancers constructed by multiscale embedded gene co-expression network analysis (MEGENA) based on the Cancer Genome Atlas (TCGA) cohort. Specifically, TFEB might serve as a hidden player with multifaceted functions in regulating pan-cancer risk factors, e.g., CXCL2, PKMYT1, and BUB1, associated with cell cycle and immunosuppression. TFEB might also regulate protective factors, e.g., CD79A, related to immune promotion in the tumour microenvironment. We further developed a Shiny app website to present the comprehensive regulatory targets of TFEB under various stimuli, intending to support further research on TFEB functions. Summarily, we provided references for the TFEB downstream targets responding to three stresses and the dual roles of TFEB and its targets in pan-cancer, which are promising anticancer targets that warrant further exploration. Chromatin immunoprecipitation sequencing of one input sample and two replicates of Hela cells expressing 3×Flag-TFEB without treatment or with treatment of CCCP, sucrose and Torin1. To investigate regulatory targets of TFEB under three different stresses , we did ChIP-seq for Hela cells expressing 3×Flag-TFEB without treatment or with treatment of CCCP, sucrose and Torin1. Each group has three replicates. We then performed TFEB binding site profiling analysis using ChIP-seq data from the four groups, i.e., Ctrl, CCCP-stimuli, Sucrose-stimuli, and Torin-1 stimuli. By comparing the differential binding sites of TFEB between three stimuli groups and the Ctrl group, we identified the potential TFEB regulatory target genes.