Institute for Regeneration and Repair

Drug repurposing for oesophageal cancer

Using imaging microscopy and phenotypic screening to identify drug repurposing and potential new drug discovery

Oesophageal Cancer is the seventh most common cancer type and sixth most common cause of cancer mortality worldwide. This is a complex heterogeneous disease characterized by large scale genomic rearrangements and no common oncogenic drivers, confounding modern target-based drug discovery strategies. As a consequence prognosis is poor and 5-year survival rates are < 20%, global incidence has been increasing steadily over several decades, thus oesophageal cancer represents a major global health problem.

Using automated high content imaging microscopy we conducted a high throughput screen of 20,000 small molecule compounds across six human oesophageal cancer cell lines representing the broad genetic heterogeneity of disease and two non-transformed tissue matched control cell lines. Using a “Cell Painting” assay and bespoke image analysis algorithm we extracted 720 features per cell in every image to obtain a multiparametric phenotypic fingerprint for every cell following compound treatment. Phenotypic fingerprints were interrogated by multivariate statistics and machine learning models to classify cell phenotype and drug mechanism-of-action. This high content screening data set is comprised of 3.9million images (30Tb data). This single phenotypic screen identified several drug repurposing opportunities, potential new therapeutic targets and 4 attractive chemical starting points for novel drug discovery programs targeting oesophageal cancer.


  1. Hughes RE, Elliott RJR, Li X, Munro AF, Makda A, Carter RN, Morton NM, Fujihara K, Clemons NJ, Fitzgerald R, O'Neill JR, Hupp T, Carragher NO. Multiparametric High-Content Cell Painting Identifies Copper Ionophores as Selective Modulators of Esophageal Cancer Phenotypes. ACS Chem Biol. 2022 Jul 15;17(7):1876-1889. doi: 10.1021/acschembio.2c00301.
  2. Hughes RE, Elliott RJR, Munro AF, Makda A, O'Neill JR, Hupp T, Carragher NO. High-Content Phenotypic Profiling in Esophageal Adenocarcinoma Identifies Selectively Active Pharmacological Classes of Drugs for Repurposing and Chemical Starting Points for Novel Drug Discovery. SLAS Discov. 2020 Aug;25(7):770-782. doi: 10.1177/2472555220917115.
  3. Hughes RE, Elliott RJR, Dawson JC, Carragher NO. High-content phenotypic and pathway profiling to advance drug discovery in diseases of unmet need. Cell Chem Biol. 2021 Mar 18;28(3):338-355. doi: 10.1016/j.chembiol.2021.02.015.