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Seal S, Trapotsi MA, Spjuth O, Singh S, Carreras-Puigvert J, Greene N, Bender A, Carpenter AE. A Decade in a Systematic Review: The Evolution and Impact of Cell Painting. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.04.592531. [PMID: 38766203 PMCID: PMC11100607 DOI: 10.1101/2024.05.04.592531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
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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Affiliation(s)
- Srijit Seal
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, United Kingdom
| | - Maria-Anna Trapotsi
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0AA, United Kingdom
| | - Ola Spjuth
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Box 591, SE-75124, Uppsala, Sweden
| | - Shantanu Singh
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0AA, United Kingdom
| | - Jordi Carreras-Puigvert
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Box 591, SE-75124, Uppsala, Sweden
| | - Nigel Greene
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, MA 02451, USA
| | - Andreas Bender
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, United Kingdom
| | - Anne E. Carpenter
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States
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Seal S, Trapotsi MA, Spjuth O, Singh S, Carreras-Puigvert J, Greene N, Bender A, Carpenter AE. A Decade in a Systematic Review: The Evolution and Impact of Cell Painting. ARXIV 2024:arXiv:2405.02767v1. [PMID: 38745696 PMCID: PMC11092692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
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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Affiliation(s)
- Srijit Seal
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, United Kingdom
| | - Maria-Anna Trapotsi
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0AA, United Kingdom
| | - Ola Spjuth
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Box 591, SE-75124, Uppsala, Sweden
| | - Shantanu Singh
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge, CB2 0AA, United Kingdom
| | - Jordi Carreras-Puigvert
- Department of Pharmaceutical Biosciences and Science for Life Laboratory, Uppsala University, Box 591, SE-75124, Uppsala, Sweden
| | - Nigel Greene
- Imaging and Data Analytics, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, MA 02451, USA
| | - Andreas Bender
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, United Kingdom
| | - Anne E. Carpenter
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States
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Stossi F, Singh PK, Marini M, Safari K, Szafran AT, Tostado AR, Candler CD, Mancini MG, Mosa EA, Bolt MJ, Labate D, Mancini MA. SPACe (Swift Phenotypic Analysis of Cells): an open-source, single cell analysis of Cell Painting data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.586132. [PMID: 38585902 PMCID: PMC10996526 DOI: 10.1101/2024.03.21.586132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Phenotypic profiling by high throughput microscopy has become one of the leading tools for screening large sets of perturbations in cellular models. Of the numerous methods used over the years, the flexible and economical Cell Painting (CP) assay has been central in the field, allowing for large screening campaigns leading to a vast number of data-rich images. Currently, to analyze data of this scale, available open-source software ( i.e. , CellProfiler) requires computational resources that are not available to most laboratories worldwide. In addition, the image-embedded cell-to-cell variation of responses within a population, while collected and analyzed, is usually averaged and unused. Here we introduce SPACe ( S wift P henotypic A nalysis of Ce lls), an open source, Python-based platform for the analysis of single cell image-based morphological profiles produced by CP experiments. SPACe can process a typical dataset approximately ten times faster than CellProfiler on common desktop computers without loss in mechanism of action (MOA) recognition accuracy. It also computes directional distribution-based distances (Earth Mover's Distance - EMD) of morphological features for quality control and hit calling. We highlight several advantages of SPACe analysis on CP assays, including reproducibility across multiple biological replicates, easy applicability to multiple (∼20) cell lines, sensitivity to variable cell-to-cell responses, and biological interpretability to explain image-based features. We ultimately illustrate the advantages of SPACe in a screening campaign of cell metabolism small molecule inhibitors which we performed in seven cell lines to highlight the importance of testing perturbations across models.
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Weisbart E, Kumar A, Arevalo J, Carpenter AE, Cimini BA, Singh S. Cell Painting Gallery: an open resource for image-based profiling. ARXIV 2024:arXiv:2402.02203v1. [PMID: 38351939 PMCID: PMC10862924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Affiliation(s)
- Erin Weisbart
- Broad Institute of MIT and Harvard, Cambridge MA, USA; Department: Imaging Platform
| | - Ankur Kumar
- Broad Institute of MIT and Harvard, Cambridge MA, USA; Department: Imaging Platform
| | - John Arevalo
- Broad Institute of MIT and Harvard, Cambridge MA, USA; Department: Imaging Platform
| | - Anne E. Carpenter
- Broad Institute of MIT and Harvard, Cambridge MA, USA; Department: Imaging Platform
| | - Beth A. Cimini
- Broad Institute of MIT and Harvard, Cambridge MA, USA; Department: Imaging Platform
| | - Shantanu Singh
- Broad Institute of MIT and Harvard, Cambridge MA, USA; Department: Imaging Platform
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Dumbell R, Cox RD. The genetics of adipose tissue metabolism. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231478. [PMID: 38328570 PMCID: PMC10846938 DOI: 10.1098/rsos.231478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/15/2024] [Indexed: 02/09/2024]
Affiliation(s)
- Rebecca Dumbell
- Dept of Biosciences, School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Roger D. Cox
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus Oxfordshire, Harwell OX11 0RD, UK
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