Regulatory chromatin rewiring promotes metabolic switching during adaptation to oncogenic receptor tyrosine kinase inhibition

Abstract

Oesophageal adenocarcinoma (OAC) patients show poor survival rates and there are few targeted molecular therapies available. However, components of the receptor tyrosine kinase (RTK) driven pathways are commonly mutated in OAC, typified by high frequency amplifications of the RTK ERBB2. ERBB2 can be therapeutically targeted, but this has limited clinical benefit due to the acquisition of drug resistance. Here we examined how OAC cells adapt to ERBB2 inhibition as they transition to a drug resistant state. ERBB2 inhibition triggers widespread remodelling of the accessible chromatin landscape and the underlying gene regulatory networks. The transcriptional regulators HNF4A and PPARGC1A play a key role in this network rewiring. Initially, inhibition of cell cycle associated gene expression programmes is observed, with compensatory increases in the programmes driving changes in metabolic activity. Both PPARGC1A and HNF4A are required for the acquisition of resistance to ERBB2 inhibition and PPARGC1A is instrumental in promoting a switch to dependency on oxidative phosphorylation. Our work therefore reveals the molecular pathways that support the acquisition of a resistant state and points to potential new therapeutic strategies to combat cellular adaptation and ensuing drug resistance.

Oncogenic ERRB2 signals through the AP-1 transcription factor to control mesenchymal-like properties of oesophageal adenocarcinoma

“…pINDUCER20-GFP-AFOS (ADS5006) (17) was packaged into lentivirus and OE19, KYAE1 and ESO26 cells were then transduced with lentivirus as described previously (9). Polyclonal cells were selected for 2 weeks using 250 g/mL G418 (ThermoFisher Scientific, 10131027).…”

“…RT-qPCR was performed as described previously (9). Primers used are listed in Supplementary Table S6.…”

“…Western blots were performed as described previously (9). Antibodies used: anti-GFP (Santa Cruz, sc-8334, 1:2,000), anti-ERK (Cell Signaling Technologies, 4695S, 1:1,000).…”

“…dnFOS was induced in OE19-dnFOS (28) and KYAE1-dnFOS cells for 48 hours before RNA was isolated and sequenced and analysed as described previously (9). Differentially expressed genes were determined using DESeq2 (29).…”

“…To bridge this knowledge gap, we recently studied the effects of pharmacological ERBB2 inhibition on the gene regulatory pathways operational in OAC cells as they transition to a drug resistant state (9). In that study we focussed on the programmes that become newly operational following ERBB2 inhibition, and demonstrated a role for the transcription factor HNF4A and also the transcriptional co-activator PPARGC1A in rewiring the metabolic pathways to allow cells to survive and subsequently acquire a resistant state.…”