Polyclonal and clonal organoid models of Barrett oesophagus and oesophageal adenocarcinoma reveal heterogeneity in progression and therapy response

Oesophageal adenocarcinoma (OAC) is a major cause of morbidity and mortality. OAC and its precursor, Barrett oesophagus (BO), are defined by substantial early heterogeneity, complicating prevention and treatment of OAC. This diversity is poorly recapitulated by current in vitro and animal model systems. We have generated 91 patient- and healthy donor- derived organoids (PDOs) spanning normal oesophagogastric tissue (n=29), BO (n=13), dysplasia (n=8) and OAC (n=41). These PDOs capture population heterogeneity and recapitulate phenotypic, genomic and transcriptomic features of their respective disease stages. We develop a single cell-derived clonal organoid (sc-organoid) approach, with which we isolate 28 additional organoid lines representing subclonal populations that are difficult to discern and maintain in bulk PDO cultures, and which may represent clones at high risk of progression. Using this platform, we demonstrate functional utility across the pre-malignant to invasive disease spectrum, including recapitulation of step-wise disease progression, subclonal phylogenetic structure, and diverse responses of OAC to systemic anti-cancer therapies and radiotherapy.