Cell Painting

What is cell painting?

Cell painting is a type of phenotypic assay and a powerful application of high-content screening. Cells are "painted" by staining specific cellular compartments with different fluorescent bioprobes simultaneously, followed by imaging and analysis to extract hundreds to thousands of features in order to phenotypically profile the cells and elucidate their behaviour.

Origin of cell painting technique

The first iteration of cell painting, without naming it as such, was published in a 2013 paper by Gustafsdottir and colleagues at the Broad Institute of Harvard and MIT. The assay was then slightly modified into its current configuration by Bray and colleagues, who coined the term "Cell Painting”, in a 2016 publication that describes the process in detail.

The cell painting process

The cell painting process is dependent on the use of known reference compounds to "train" image analysis algorithms to generate multiparametric data that is subsequently filtered using machine learning approaches to reduce the overall complexity of the multidimensional data. The highly-dimensional data is displayed using tools such as PCA (Principal Component Analysis) or t-SNE (t-Distributed Stochastic Neighbor Embedding) that allow for clustering of similar phenotypic profiles that may "suggest" a mechanism or mode of action (MOA) for unknown compounds by comparison with reference compounds of known MOA.

At a high-level, the process of cell painting incorporates high-throughput robotics and automation to seed cells and deliver compounds to microplates, the use of multiple fluorescent bioprobes to stain cell compartments, acquisition of images, image analysis, and machine and deep learning data analysis tools to enrich and summarize findings of complex multidimensional data.

Cell painting for phenotypic drug discovery

With cell painting, computational and cell biology combine to provide a deeper understanding of the impact of genetic or exogenous perturbagens, with the aim of identifying therapeutics, investigating human gene function, or assessing environmental toxicants.

Since the first publications describing the technique, cell painting has been rapidly adopted for phenotypic drug discovery and basic research. Implementing the assay comes with some challenges, ranging from the choice of cell model, appropriate labeling reagents, and optimizing instrumentation for detection, to making sense of the thousands of features that can be generated during data analysis.

References:

1. Gustafsdottir, S.M., et al., Multiplex cytological profiling assay to measure diverse cellular states. PLoS One, 2013. 8(12): p. e80999.
2. Bray, M.A., et al., Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes. Nat Protoc, 2016. 11(9): p. 1757-74.