P-OGC32 Copper-dependent cell death is a cancer specific vulnerability in oesophageal adenocarcinoma and provides the opportunity for future biomarker-stratified clinical trials

Abstract

Abstract Background Oesophageal adenocarcinoma (OAC) is of increasing global concern due to increasing incidence, lack of effective treatments, and poor prognosis. Therapeutic target discovery and clinical trials have been hindered by the heterogeneity of the disease, dominance of large-scale genomic rearrangements, and lack of driver mutations. We have profiled small-molecule compounds using an innovative high content imaging assay in a panel of transformed and non-transformed oesophageal cell lines to identify OAC-specific cytotoxic compounds, new therapeutic targets, potential drug repurposing opportunities, and chemical starting points for the treatment of OAC. Methods We have comprehensively profiled 19,555 small-molecule compounds using an innovative high content assay to quantify 1000’s of subcellular imaging features to capture important phenotypes missed by standard approaches. Prioritised molecules then underwent functional, transcriptomic, and metabolomic characterisation across panels of oesophageal cell lines and patient-derived organoids for the identification of OAC-specific drug mechanisms. Results We identified 72 lead compounds as exhibiting OAC-specific cytotoxicity and characterised three of the most potent and selective compounds in depth, each of different proposed classes and chemical structures. Using several orthogonal methods we uncovered a unified mechanism of action and a targetable vulnerability in OAC involving copper-dependent cell death. Strikingly no phenotypic effects or changes in gene-expression were observed following treatment with these compounds in non-transformed oesophageal cell lines or normal gastric organoids providing support for this mechanism as a cancer-specific phenomenon. Conclusions We have applied high content imaging, transcriptomic and metabolomic analyses to reveal a unique vulnerability in OAC. We have defined a unified mechanism of OAC-specific copper-dependent cell death for the three highly potent compounds. Finally, through the integration of transcriptomic and metabolomics analyses we gained insight into drug sensitivity and provide the basis for a future biomarker-stratified clinical trial of these drugs in OAC.