Intron 1–Mediated Regulation of <i>EGFR</i> Expression in EGFR-Dependent Malignancies Is Mediated by AP-1 and BET Proteins

Abstract

The epidermal growth factor receptor (EGFR) is overexpressed in numerous solid tumors and is the subject of extensive therapeutic efforts. Much of the research on EGFR is focused on protein dynamics and downstream signaling; however, few studies have explored its transcriptional regulation. Here, we identified two enhancers (CE1 and CE2) present within the first intron of the <i>EGFR</i> gene in models of glioblastoma (GBM) and head and neck squamous cell carcinoma (HNSCC). CE1 and CE2 contain open chromatin and H3K27Ac histone marks, enhance transcription in reporter assays, and interact with the <i>EGFR</i> promoter. Enhancer genetic deletion by CRISPR/Cas9 significantly reduces <i>EGFR</i> transcript levels, with double deletion exercising an additive effect. Targeted repression of CE1 and CE2 by dCas9-KRAB demonstrates repression of transcription similar to that of genomic deletion. We identify AP-1 transcription factor family members in concert with BET bromodomain proteins as modulators of CE1 and CE2 activity in HNSCC and GBM through <i>de novo</i> motif identification and validate their presence. Genetic inhibition of AP-1 or pharmacologic disruption of BET/AP-1 binding results in downregulated EGFR protein and transcript levels, confirming a role for these factors in CE1 and CE2. Our results identify and characterize these novel enhancers, shedding light on the role that epigenetic mechanisms play in regulating <i>EGFR</i> transcription in EGFR-dependent cancers. IMPLICATIONS: We identify critical constituent enhancers present in the first intron of the <i>EGFR</i> gene, and provide a rationale for therapeutic targeting of <i>EGFR</i> intron 1 enhancers through perturbation of AP-1 and BET in EGFR-positive malignancies.