Cell painting transfer increases screening hit rate. (3rd March 2023)

• Record Type: Journal Article
• Authors: Cohen, Ethan; Corbe, Maxime; Franco, Cláudio A.; Vasconcelos, Francisca F.; Perez, Franck; Del Nery, Elaine; Bollot, Guillaume; Genovesio, Auguste
• Is Part Of: Biological imaging. Volume 3(2023)
• Publication Date: 2023-03-03
• Subjects: high content screening -- transfer learning -- cell painting -- drug discovery; Imaging systems in biology -- Periodicals; 570.28
• DOI: 10.1017/S2633903X23000077
• Languages: English
• ISSNs: 2633-903X

Abstract

Abstract: Drug discovery uses high throughput screening to identify compounds that interact with a molecular target or that alter a phenotype favorably. The cautious selection of molecules used for such a screening is instrumental and is tightly related to the hit rate. In this work, we wondered if cell painting, a general-purpose image-based assay, could be used as an efficient proxy for compound selection, thus increasing the success rate of a specific assay. To this end, we considered cell painting images with 30, 000 molecules treatments, and selected compounds that produced a visual effect close to the positive control of an assay, by using the Frechet Inception Distance. We then compared the hit rates of such a preselection with what was actually obtained in real screening campaigns. As a result, cell painting would have permitted a significant increase in the success rate and, even for one of the assays, would have allowed to reach 80% of the hits with 10 times fewer compounds to test. We conclude that images of a cell painting assay can be directly used for compound selection prior to screening, and we provide a simple quantitative approach in order to do so.