ERBB2 signalling and tumour resistance through chromatin landscape rewiring in oesophageal adenocarcinoma

Abstract

Oesophageal adenocarcinoma (OAC) has poor patient survival rates, a rising incidence rate and limited treatment options. These problems are compounded by a limited understanding of the molecular causes of OAC. The receptor tyrosine kinase ERBB2 (HER2) is amplified in approximately 25% of OAC cases and ERBB2-postive OAC tumours are treated using the ERBB2-specific inhibitor trastuzumab. However, therapy resistance poses a major challenge. We aimed to investigate both the function of ERBB2 in OAC, and how resistance to ERBB2 inhibitors arises in OAC. ERBB2 regulates cellular signalling pathways such as the MAPK/ERK and PI3K/AKT signalling pathways, which ultimately regulate gene expression. We show that ERBB2 regulates and drives the cell cycle in OAC cells. We have identified an ERBB2-AP-1 signalling/gene-regulatory axis that is activated in OAC and our analysis predicts that AP-1 regulates processes associated with metastasis in OAC cells. To study how resistance to ERBB2 inhibitors arises in ERBB2 positive OAC we used the EGFR/ERBB2 inhibitor lapatinib. In ERBB2 positive OAC cells lapatinib inhibits ERBB2 signalling, induces apoptosis and inhibits cell proliferation. However, after 5 weeks lapatinib treatment, surviving cells develop resistance and are able to re-commence proliferation, despite ERBB2 remaining inhibited. To attempt to understand the molecular basis of resistance, we investigated changes to the regulatory chromatin landscape and transcriptome in cells treated with lapatinib for 1, 7 and 35 days. Following ERBB2 inhibition in OAC cells, there is widespread remodelling of the accessible chromatin landscape and transcriptome. Gene regulatory changes indicate that OAC cells respond to ERBB2 inhibition by rewiring their metabolism. Two distinct gene regulatory networks are associated with resistance, one driven by the transcription factor HNF4A, and another driven by the transcriptional co-activator PPARGC1A. Loss of either HNF4A or PPARGC1A impairs the emergence of resistance. Whilst PPARGC1A has been shown to co-activate HNF4A in other cell types, in OAC cells PPARGC1A and HNF4A bind to distinct genomic loci, suggesting that they are functioning in two distinct biological pathways. Analysis of transcription factor motifs enriched at PPARGC1A binding sites suggests that PPARGC1A binds to its established partner transcription factor NRF1 in OAC cells. PPARGC1A activity is enhanced by ERBB2 inhibition and PPARGC1A regulates mitochondrial respiration, which OAC cells have increased dependency upon after ERBB2 inhibition. Co-treatment of ERBB2 positive OAC cells lines with lapatinib and the mutant IDH2 inhibitor enasidenib impairs the emergence of resistance illustrating that strategies targeting either PPARGC1A, HNF4A, or the processes regulated by these two transcription regulatory proteins could overcome resistance to ERBB2 inhibitors in OAC.

Date of Award	4 Jun 2021
Original language	English
Awarding Institution	The University of Manchester
Supervisor	Andrew Sharrocks (Supervisor) & Chiara Francavilla (Supervisor)