Co-activation of super-enhancer-driven CCAT1 by TP63 and SOX2 promotes squamous cancer progression

Yuan Jiang,Li Chen,Moli Huang ,Jianwen Deng ,Lian‐Di Liao ,Maya Jeitany,Chunquan Li ,Li‐Yan Xu ,Benjamin P Berman,Jin-Fen Xiao,Jia‐Jie Hao ,Anand Mayakonda,Deepika Kanojia,Qiao-Yang Sun,Jian‐Jun Xie ,En‐Min Li ,Liang Xu,Yan‐Yi Jiang ,Ming-Rong Wang,De‐Chen Lin ,Masaharu Hazawa,Ling-Wen Ding,Xingang Bi ,Harmik J Soukiasian,H Phillip Koeffler

doi:10.1038/s41467-018-06081-9

Abstract

Squamous cell carcinomas (SCCs) are aggressive malignancies. Previous report demonstrated that master transcription factors (TFs) TP63 and SOX2 exhibited overlapping genomic occupancy in SCCs. However, functional consequence of their frequent co-localization at super-enhancers remains incompletely understood. Here, epigenomic profilings of different types of SCCs reveal that TP63 and SOX2 cooperatively and lineage-specifically regulate long non-coding RNA (lncRNA) CCAT1 expression, through activation of its super-enhancers and promoter. Silencing of CCAT1 substantially reduces cellular growth both in vitro and in vivo, phenotyping the effect of inhibiting either TP63 or SOX2. ChIRP analysis shows that CCAT1 forms a complex with TP63 and SOX2, which regulates EGFR expression by binding to the super-enhancers of EGFR, thereby activating both MEK/ERK1/2 and PI3K/AKT signaling pathways. These results together identify a SCC-specific DNA/RNA/protein complex which activates TP63/SOX2-CCAT1-EGFR cascade and promotes SCC tumorigenesis, advancing our understanding of transcription dysregulation in cancer biology mediated by master TFs and super-enhancers.

Highlights

Squamous cell carcinomas (SCCs) are aggressive malignancies
To explore whether and how super-enhancers are regulated by SCC master transcription factors (TFs) (TP63 and SOX2), we first performed chromatin immunoprecipitation sequencing (ChIP-seq) with antibodies against H3K27 acetylation (H3K27ac), TP63, and SOX2
Given our earlier findings that TP63- and SOX2-occupied regions were strongly enriched for H3K27ac modification, we primarily focused on genes that were downregulated following the silencing of these two TFs

Summary

Introduction

Squamous cell carcinomas (SCCs) are aggressive malignancies. Previous report demonstrated that master transcription factors (TFs) TP63 and SOX2 exhibited overlapping genomic occupancy in SCCs. Epigenomic profilings of different types of SCCs reveal that TP63 and SOX2 cooperatively and lineagespecifically regulate long non-coding RNA (lncRNA) CCAT1 expression, through activation of its super-enhancers and promoter. ChIRP analysis shows that CCAT1 forms a complex with TP63 and SOX2, which regulates EGFR expression by binding to the super-enhancers of EGFR, thereby activating both MEK/ERK1/2 and PI3K/AKT signaling pathways These results together identify a SCC-specific DNA/ RNA/protein complex which activates TP63/SOX2-CCAT1-EGFR cascade and promotes SCC tumorigenesis, advancing our understanding of transcription dysregulation in cancer biology mediated by master TFs and super-enhancers. The most notable SCC-specific genomic lesions target several transcription factors (TFs) with prominent functions in both healthy and neoplastic squamous cells, including SOX2, TP63, ZNF750, and NOTCH family genes. Further mechanistic exploration demonstrates a complex interplay between CCAT1, TP63, and SOX2 in the transcriptional activation of EGFR, resulting in the hyper-activation of EGFR downstream pathways in SCC cells

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Results

Conclusion