Robust Classification of Small-Molecule Mechanism of Action Using a Minimalist High-Content Microscopy Screen and Multidimensional Phenotypic Trajectory Analysis

PloS One
Nathaniel R TwarogAnang A Shelat

Abstract

Phenotypic screening through high-content automated microscopy is a powerful tool for evaluating the mechanism of action of candidate therapeutics. Despite more than a decade of development, however, high content assays have yielded mixed results, identifying robust phenotypes in only a small subset of compound classes. This has led to a combinatorial explosion of assay techniques, analyzing cellular phenotypes across dozens of assays with hundreds of measurements. Here, using a minimalist three-stain assay and only 23 basic cellular measurements, we developed an analytical approach that leverages informative dimensions extracted by linear discriminant analysis to evaluate similarity between the phenotypic trajectories of different compounds in response to a range of doses. This method enabled us to visualize biologically-interpretable phenotypic tracks populated by compounds of similar mechanism of action, cluster compounds according to phenotypic similarity, and classify novel compounds by comparing them to phenotypically active exemplars. Hierarchical clustering applied to 154 compounds from over a dozen different mechanistic classes demonstrated tight agreement with published compound mechanism classification. Using 11 phen...Continue Reading

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Citations

Nov 24, 2017·International Journal of Molecular Sciences·Kenji Tanabe
Mar 20, 2021·Cell Chemical Biology·Slava ZieglerHerbert Waldmann
Jun 12, 2019·ACS Chemical Biology·William J GodinezBrian Y Feng

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Methods Mentioned

BETA
light scattering
PCA
Example

Software Mentioned

GE InCell Analyzer Workstation

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