Selection of Optimal Cell Lines for High-Content Phenotypic Screening

Heinrich, Louise; Kumbier, Karl; Li, Li; Altschuler, Steven J.; Wu, Lani F.

doi:10.1021/acschembio.2c00878

Cited by 8 publications

(6 citation statements)

References 27 publications

(49 reference statements)

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“…13B ). We next tested compounds ( 1 - 3 ) against a panel of nine diverse cancer cell lines (Supplementary Table 5 ) using cell painting 40 and high-content imaging to maximize the detection of activity and infer mechanism of action 41 . Phenotypic profiles generated using a customized image analysis pipeline provided in-depth quantification of cell morphology and biomarker staining in comparison with 28 reference compounds across six diverse drug categories with distinguishable phenotypes 42 (Supplementary Fig.…”

Section: Resultsmentioning

confidence: 99%

Small molecule in situ resin capture provides a compound first approach to natural product discovery

Bogdanov,

Salib,

Chase

et al. 2024

Nat Commun

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Culture-based microbial natural product discovery strategies fail to realize the extraordinary biosynthetic potential detected across earth’s microbiomes. Here we introduce Small Molecule In situ Resin Capture (SMIRC), a culture-independent method to obtain natural products directly from the environments in which they are produced. We use SMIRC to capture numerous compounds including two new carbon skeletons that were characterized using NMR and contain structural features that are, to the best of our knowledge, unprecedented among natural products. Applications across diverse marine habitats reveal biome-specific metabolomic signatures and levels of chemical diversity in concordance with sequence-based predictions. Expanded deployments, in situ cultivation, and metagenomics facilitate compound discovery, enhance yields, and link compounds to candidate producing organisms, although microbial community complexity creates challenges for the later. This compound-first approach to natural product discovery provides access to poorly explored chemical space and has implications for drug discovery and the detection of chemically mediated biotic interactions.

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Section: Resultsmentioning

confidence: 99%

Small molecule in situ resin capture provides a compound first approach to natural product discovery

Bogdanov,

Salib,

Chase

et al. 2024

Nat Commun

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“…12). Furthermore, we found that the real-time capability allowed removal of wells with outlier characteristics before compound treatment, ensuring a reliable and repeatable starting phenotypic state 35 . Such pre-drug assessment is not possible with end-point assays, including high-content imaging which requires cell fixing.…”

Section: Discussionmentioning

confidence: 97%

“…A549 has been shown to be an effective cell model for high-content phenotypic screening 35 . In our work, the A549 clustering analysis revealed interesting insights about MOA of various compounds and their effects on live-cell function.…”

Section: Mechanism Of Action (Moa) Identification Using High-dimensio...mentioning

confidence: 99%

A semiconductor 96-microplate platform for electrical-imaging based high-throughput phenotypic screening

Chitale,

Wu,

Mukherjee

et al. 2023

Preprint

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Recent advancements in high-throughput screening have focused on using multi-parametric readouts to characterize drug compound effects. While high-content imaging is commonly used, it only captures endpoint images of fixed cells. Here, we report a semiconductor 96-microplate platform which performs real-time, label-free impedance imaging of live-cells. An array of 64x64=4,096 electrodes/well provides spatial resolution of 25 micrometres and enables multi-frequency, field-based measurements to capture >20 morphological and functional parameters. This represents a major advancement over current electronic microplates which use 2 electrodes/well for single parameter measurement. Unique characteristics including tissue barrier, cell-surface attachment, transepithelial water transport, cell size and motility are captured every 5-15 min during the experiment time-course. Eleven cell types ranging from primary epithelial to suspension are functionally characterized and proof-of-concept screens using 341 FDA approved compounds highlight the ability to perform mechanism of action (MOA) profiling. Compounds increasing tissue barrier with a previously unreported MOA were identified, an illustrative example of phenotypic discovery in the context of gut barrier diseases. The combination of MOA profiling and direct translatability of functional phenotypes promises to unlock new avenues in phenotypic high-throughput screening.

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“…21,22 In a recent study, the selection of optimal cell lines for high content screening was investigated because different cell lines can result in different sensitivities to detect different MoAs. 23 In total 3,214 small molecule annotated (i.e. containing information about their putative target and MoA) compounds (including FDA approved drugs) were profiled with Cell Painting on six different cell lines.…”

Section: Discussionmentioning

confidence: 99%

A Decade in a Systematic Review: The Evolution and Impact of Cell Painting

Seal,

Trapotsi,

Spjuth

et al. 2024

Preprint

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High-content image-based assays have fueled significant discoveries in the life sciences in the past decade (2013-2023), including novel insights into disease etiology, mechanism of action, new therapeutics, and toxicology predictions. Here, we systematically review the substantial methodological advancements and applications of Cell Painting. Advancements include improvements in the Cell Painting protocol, assay adaptations for different types of perturbations and applications, and improved methodologies for feature extraction, quality control, and batch effect correction. Moreover, machine learning methods recently surpassed classical approaches in their ability to extract biologically useful information from Cell Painting images. Cell Painting data have been used alone or in combination with other - omics data to decipher the mechanism of action of a compound, its toxicity profile, and many other biological effects. Overall, key methodological advances have expanded Cell Painting’s ability to capture cellular responses to various perturbations. Future advances will likely lie in advancing computational and experimental techniques, developing new publicly available datasets, and integrating them with other high-content data types.

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Selection of Optimal Cell Lines for High-Content Phenotypic Screening

Cited by 8 publications

References 27 publications

Small molecule in situ resin capture provides a compound first approach to natural product discovery

Small molecule in situ resin capture provides a compound first approach to natural product discovery

A semiconductor 96-microplate platform for electrical-imaging based high-throughput phenotypic screening

A Decade in a Systematic Review: The Evolution and Impact of Cell Painting

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