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Mukashyaka P, Kumar P, Mellert DJ, Nicholas S, Noorbakhsh J, Brugiolo M, Courtois ET, Anczukow O, Liu ET, Chuang JH. High-throughput deconvolution of 3D organoid dynamics at cellular resolution for cancer pharmacology with Cellos. Nat Commun 2023; 14:8406. [PMID: 38114489 PMCID: PMC10730814 DOI: 10.1038/s41467-023-44162-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 12/01/2023] [Indexed: 12/21/2023] Open
Abstract
Three-dimensional (3D) organoid cultures are flexible systems to interrogate cellular growth, morphology, multicellular spatial architecture, and cellular interactions in response to treatment. However, computational methods for analysis of 3D organoids with sufficiently high-throughput and cellular resolution are needed. Here we report Cellos, an accurate, high-throughput pipeline for 3D organoid segmentation using classical algorithms and nuclear segmentation using a trained Stardist-3D convolutional neural network. To evaluate Cellos, we analyze ~100,000 organoids with ~2.35 million cells from multiple treatment experiments. Cellos segments dye-stained or fluorescently-labeled nuclei and accurately distinguishes distinct labeled cell populations within organoids. Cellos can recapitulate traditional luminescence-based drug response of cells with complex drug sensitivities, while also quantifying changes in organoid and nuclear morphologies caused by treatment as well as cell-cell spatial relationships that reflect ecological affinity. Cellos provides powerful tools to perform high-throughput analysis for pharmacological testing and biological investigation of organoids based on 3D imaging.
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Affiliation(s)
- Patience Mukashyaka
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | - Pooja Kumar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - David J Mellert
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Shadae Nicholas
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Javad Noorbakhsh
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Mattia Brugiolo
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Elise T Courtois
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Olga Anczukow
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA
| | - Edison T Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT, USA.
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