Multiplex Cytological Profiling Assay to Measure Diverse Cellular States

Gústafsdóttir, Sigrún M.; Ljosa, Vebjorn; Sokolnicki, Katherine L; Wilson, Joshua; Walpita, Deepika; Kemp, Melissa M.; Seiler, Kathleen Petri; Carrel, Hyman A.; Golub, Todd R.; Schreiber, Stuart L.; Clemons, Paul A.; Carpenter, Anne E.; Shamji, Alykhan F.

doi:10.1371/journal.pone.0080999

Cited by 249 publications

(338 citation statements)

References 22 publications

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“…Hierarchical clustering of well-annotated BIO compounds based on their MC profiles grouped compounds with similar biological effects together (SI Appendix, Fig. S1), confirming results from earlier studies (19,24).…”

Section: Compound Sets With Diverse Cell Morphology Profiles Have DIVsupporting

confidence: 82%

“…The DOS set was selected without taking any bioactivity data into account. Changes in cell morphology were measured after 48 h of treatment, using a multiplexed-cytological (MC) "cell-painting" assay (19). Cells were stained with six different fluorescent markers to distinguish cellular compartments and organelles.…”

Section: Resultsmentioning

confidence: 99%

“…Cells were stained with six different fluorescent markers to distinguish cellular compartments and organelles. Automated microscopy and image analysis led to profiles of 812 morphology features (19).…”

Section: Resultsmentioning

confidence: 99%

“…To avoid the impracticalities of conducting numerous independent assays on a novel set of small molecules, we chose two recently developed profiling technologies where up to 1,000 measurements can be made from a single well. The methods capture cell morphology (19) and gene expression (20) to characterize complex cell states. Unbiased profiling has been shown to capture the mechanistic details of a wide range of bioactivities (4,5,21) and we hypothesized it would assist in defining the composition of performance-diverse small-molecule libraries for cell-based screening.…”

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confidence: 99%

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Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling

Wawer¹,

Li²,

Gústafsdóttir³

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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195

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High-throughput screening has become a mainstay of small-molecule probe and early drug discovery. The question of how to build and evolve efficient screening collections systematically for cellbased and biochemical screening is still unresolved. It is often assumed that chemical structure diversity leads to diverse biological performance of a library. Here, we confirm earlier results showing that this inference is not always valid and suggest instead using biological measurement diversity derived from multiplexed profiling in the construction of libraries with diverse assay performance patterns for cell-based screens. Rather than using results from tens or hundreds of completed assays, which is resource intensive and not easily extensible, we use high-dimensional image-based cell morphology and gene expression profiles. We piloted this approach using over 30,000 compounds. We show that small-molecule profiling can be used to select compound sets with high rates of activity and diverse biological performance.chemical diversity | biological performance diversity | biological activity | chemical similarity P rofiling small molecules based on multiple biological activity measurements can illuminate mechanisms of action by comparing profiles with compounds whose mechanisms of action are known (1-5). Here, we describe a previously unidentified use of small-molecule profiling-enabling the creation of activityenriched and performance-diverse compound libraries for smallmolecule probe and drug discovery.Biochemical and cell-based high-throughput screening (HTS) is routinely used to discover novel bioactive molecules through unbiased testing of up to several million compounds per screen (6). However, despite ongoing advances in throughput, compound libraries will always represent only a small fraction of all relevant compounds theoretically accessible through chemical synthesis (a concept often referred to as "chemical space") (7). Library composition therefore presents a strong source of bias and potential limitation for any screening endeavor.There is little dissent about the notion that a good screening collection should yield many high-quality hits for a wide range of biological targets or phenotypes. In other words, it should be enriched for bioactive compounds and have high biological performance diversity. A high percentage of compounds lacking any activity will contribute to high cost and low performance of a high-throughput screen. A practical example is a compound collection containing a high percentage of compounds that fail to penetrate cell membranes-such a library will be unlikely to perform effectively in a cell-based HTS exploring an intracellular process. Similarly, a screening collection of compounds with highly redundant biological activities will be less efficient than an equally sized library with diverse performance (Fig. 1). A systematic path to reach these goals, however, remains elusive. One common practice is analyzing structural features of compounds to maximize chemical structural diversity. Ho...

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Section: Compound Sets With Diverse Cell Morphology Profiles Have DIVsupporting

confidence: 82%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

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Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling

Wawer¹,

Li²,

Gústafsdóttir³

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

195

177

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show abstract

“…For example, gene-expression analysis, as exemplified by a yeast compendia [16] and connectivity map profiling, [17] enables a comparison of unknown compounds with a bioactive set for similarity searching. Cell painting [18] also takes a similarity approach, instead using cell morphology for compound comparison. More sophisticated computational analyses have evolved to take an assayagnostic approach to inference generation.…”

Section: Phenotypic Discoveries In Drug Developmentmentioning

confidence: 99%

The resurgence of phenotypic screening in drug discovery and development

Wagner

2015

Expert Opinion on Drug Discovery

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Vacuolin‐1 inhibits autophagy by impairing lysosomal maturation via PIKfyve inhibition

et al. 2016

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Lysosomal protein degradation via autophagy strictly regulates cellular protein homoeostasis. Herein we performed high-content screening to identify compounds that inhibit autophagy pathways. We obtained 11 hit compounds and performed cluster analysis using cellular morphological information. Vacuolin-1, which induces the formation of giant vacuoles and is a target unknown compound, clustered with the known PIKfyve inhibitor YM201636. We further confirmed that vacuolin-1 is a potent PIKfyve inhibitor, and we finally concluded that PIKfyve inhibitors are novel chemical tools for regulating autophagy.

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Multiplex Cytological Profiling Assay to Measure Diverse Cellular States

Cited by 249 publications

References 22 publications

Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling

Toward performance-diverse small-molecule libraries for cell-based phenotypic screening using multiplexed high-dimensional profiling

The resurgence of phenotypic screening in drug discovery and development

Vacuolin‐1 inhibits autophagy by impairing lysosomal maturation via PIKfyve inhibition

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