1. ΔNp63α is a super enhancer-enriched master factor controlling the basal-to-luminal differentiation transcriptional program and gene regulatory networks in nasopharyngeal carcinoma.
- Author
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Cai J, Chen S, Yi M, Tan Y, Peng Q, Ban Y, Yang J, Li X, Zeng Z, Xiong W, McCarthy JB, Li G, Li X, and Xiang B
- Subjects
- Animals, Apoptosis, Biomarkers, Tumor genetics, Biomarkers, Tumor metabolism, Carcinoma, Basal Cell genetics, Carcinoma, Basal Cell metabolism, Cell Proliferation, Enhancer Elements, Genetic, Epigenesis, Genetic, Female, Gene Expression Profiling, Humans, Male, Mice, Mice, Inbred BALB C, Mice, Nude, Middle Aged, Nasopharyngeal Carcinoma genetics, Nasopharyngeal Carcinoma metabolism, Nasopharyngeal Neoplasms genetics, Nasopharyngeal Neoplasms metabolism, Prognosis, Transcription Factors genetics, Tumor Cells, Cultured, Tumor Suppressor Proteins genetics, Xenograft Model Antitumor Assays, Carcinoma, Basal Cell pathology, Cell Differentiation, Gene Expression Regulation, Neoplastic, Gene Regulatory Networks, Nasopharyngeal Carcinoma pathology, Nasopharyngeal Neoplasms pathology, Transcription Factors metabolism, Tumor Suppressor Proteins metabolism
- Abstract
Nasopharyngeal carcinoma (NPC) originates via malignant transformation of the pseudostratified nasopharyngeal epithelium, composed of basal and luminal cells. Super enhancers (SEs) are large clusters of cis-elements involved in the regulation of gene expression through epigenetic regulatory mechanisms. In this study, we demonstrated that basal cell-specific proteins are highly expressed, whereas luminal cell proteins are downregulated in NPC, implying a perturbation of basal-to-luminal differentiation during NPC development. We characterized NPC cell models according to different molecular signatures associated with their differentiation status and found that distinct SE landscapes are tightly associated with basal or luminal-like molecular signatures in NPC cells. Furthermore, the transcription of ΔNP63α, a prominent isoform of TP63, was found to be driven by SEs in NPC cells. Data from chromatin immunoprecipitation (ChIP)-sequencing showed that ΔNP63α largely occupied regions of SEs associated with basal cell-specific genes. Silencing of ΔNP63α led to a loss of H3K27ac occupancy at basal-type SEs and triggered a basal-to-luminal gene expression signature switch, suggesting that ΔNP63α is a master factor contributing to the perturbation of luminal differentiation. Integrative transcriptomics analysis also revealed that ΔNP63α acts as a core factor involved in the dysregulation of gene expression in NPC. Furthermore, ΔNP63α enhanced EGF-stimulated NF-κB activation in NPC cells by activating SE-mediated EGFR transcription. Finally, depletion of ΔNP63α in NPC cells induced robust growth inhibition of NPC cells in vitro and in vivo. Our data revealed that ΔNP63α-dependent SE reprogramming contributes to the blockade of luminal differentiation and uncontrolled proliferation in NPC., (© The Author(s) 2019. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)
- Published
- 2020
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