Summary
A bioRxiv preprint reports that Cell Painting PLUS uses additional organelle-resolved imaging to improve morphological profiling of compounds. In tests of 284 compounds in U2OS cells, it performed better than conventional Cell Painting for identifying compounds that interfere with lysosome function.
Researchers report that Cell Painting PLUS (CPP), an expanded cell-imaging assay, improved the profiling of compounds that interfere with lysosome function compared with conventional Cell Painting. The study, posted as a bioRxiv preprint, tested an annotated library of 284 compounds in U2OS cells and compared predictions based on the two assays.
Cell Painting profiles the visible changes compounds cause in cells, providing a way to compare their effects across multiple cellular features. The researchers say conventional Cell Painting is useful for high-throughput profiling, but its limited number of imaging channels restricts how specifically it can distinguish changes in different cell structures.
A more detailed view of cell structures
CPP expands the imaging readouts to produce spatially resolved images of mitochondria, lysosomes, actin, Golgi, RNA, DNA and the endoplasmic reticulum. These additional views can help distinguish compounds that produce similar overall changes in a cell but affect different structures or processes.
The team assessed mechanism-of-action (MoA) prediction using Pearson correlation and morphological-profile analyses. MoA describes the biological process or target through which a compound has an effect. In this approach, a compound’s cellular profile is compared with profiles associated with compounds whose actions are already annotated. It is a way to guide predictions from cell responses, rather than a direct measurement of a compound binding to a particular target.
What the comparison found
With three reference compounds per MoA, both CPP and conventional Cell Painting predicted DNA replication antagonists and histamine inhibitors with high sensitivity, according to the authors. CPP performed better for compounds that interfere with lysosome function. The authors also report that its additional organelle channels helped reveal subtle off-target effects that the original assay missed.
The findings suggest that adding more cell-structure-specific imaging can improve the distinctions made by morphological profiling, particularly for some compound effects. The authors present CPP as a high-content platform that could complement target-based approaches, which examine particular molecular targets or pathways.
The evidence comes from cell-based experiments in U2OS cells, and the report is a preprint. How well the profiling results generalise to other cell types or biological settings is not described in the abstract.