Purpose
High content analysis (HCA) has become a leading methodology in phenotypic drug discovery efforts. Typical HCA workflows include imaging cells using an automated microscope and analyzing the data using algorithms designed to quantify one or more specific phenotypes of interest. Due to the richness of high content data, unappreciated phenotypic changes may be discovered in existing image sets using interactive machine-learning based software systems.
Methods
Primary postnatal day four retinal cells from the photoreceptor (PR) labeled QRX-EGFP reporter mice were isolated, seeded, treated with a set of 234 profiled kinase inhibitors and then cultured for one week. The cells were imaged with an Acumen plate-based laser cytometer to determine the number and intensity of GFP-expressing, i.e. PR, cells. Wells with values greater than twice the standard deviation of vehicle-treated wells for either number of objects expressing GFP or mean GFP total object intensities above an average level of 8877 RFU were re-imaged at a higher resolution with an INCell2000 automated microscope The INCell images were analyzed with an open source HCA analysis tool, PhenoRipper (Rajaram et al., 2012) to identify the high GFP-inducing treatments that additionally resulted in the most diverse phenotypes compared to the vehicle control samples.
Results
The pyrimidinopyrimidone kinase inhibitor CHEMBL-1766490, a pan kinase inhibitor whose major known targets are p38α and the Src family member lck, was identified as an inducer of photoreceptor neuritogenesis by PhenoRipper, a cell-independent image analysis tool. This finding was corroborated using an alternate cell-based method of image analysis that measures quantitative differences in the mean neurite length in GFP expressing cells.
Conclusions
Interacting with data using machine learning algorithms may complement traditional HCA approaches by leading to the discovery of small molecule-induced cellular phenotypes in addition to those upon which the investigator is initially focusing.