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

SUMMARY/ABSTRACT 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 and remaining poorly recapitulated by current in vitro and animal model systems. We have generated 116 patient- and healthy donor-derived organoids (PDOs) spanning normal oesophagogastric tissue, BO and OAC. These PDOs capture population diversity and recapitulate phenotypic, genomic and transcriptomic features of their respective disease stages. We develop a single cell-derived clonal organoid approach and show that this enables us to capture the heterogeneity and isolate high-risk, subclonal populations that are difficult to discern and maintain in bulk PDO cultures. Using this platform, we demonstrate functional importance of this biobank across the pre-malignant to invasive disease spectrum, including a role for BO in shaping fibroblast phenotype within assembloids, and diverse responses of OAC to chemotherapy, radiotherapy and targeted CDK4/6 inhibition. HIGHLIGHTS Patient- and healthy donor-derived organoids (PDOs) provide a functional platform of disease progression and heterogeneity across normal gastric, non-dysplastic and dysplastic Barrett oesophagus (BO) and oesophageal adenocarcinoma (OAC). We provide a quantitative phenotypic and molecular framework to assess the provenance and fidelity of each PDO model given the heterogeneity of this disease. PDOs recapitulate key features of non-dysplastic and dysplastic BO, as well as invasive OAC. Single cell-derived clonal organoids (sc-organoids) isolate and maintain high-risk subclonal populations. OAC PDOs mirror known population level variation in response to systemic anti-cancer therapies. Competing Interest Statement R.C.F. is a co-founder and shareholder in Cyted Health, sits on the advisory board for AstraZeneca and CRUK Functional Genomics Centre, and consults for AstraZeneca and 23andMe. C.M.J. has received consultancy fees from Candesic for work outside the scope of this manuscript. M.dP. received consultancy from Medtronic and Olympus for work outside the scope of this manuscript. SG.J. is currently an employee of MedGenome Labs Private Ltd., Chennai, India. X.L. is currently an employee of AstraZeneca, Cambridge, UK. C.C. is currently affiliated with Wellcome Sanger Institute, Cambridge, UK. T.S.C. is currently affiliated with King's College London, London, UK. Footnotes - New results and figures have been added to the Results section: OAC PDOs reproducibly show variable responses to anti-cancer therapies in keeping with their molecular and phenotypic heterogeneity. - Author list updated. - Declaration of Interest updated.