The PECAn image and statistical analysis pipeline identifies Minute cell competition genes and features.

Autor: Baumgartner ME; School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, BS8 1TD, UK. michael.baumgartner@pennmedicine.upenn.edu.; Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA. michael.baumgartner@pennmedicine.upenn.edu., Langton PF; School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, BS8 1TD, UK., Logeay R; School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, BS8 1TD, UK., Mastrogiannopoulos A; School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, BS8 1TD, UK., Nilsson-Takeuchi A; School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, BS8 1TD, UK.; Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK., Kucinski I; The Wellcome Trust/Cancer Research UK Gurdon Institute and Zoology Department, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.; Wellcome & MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge, UK., Lavalou J; School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, BS8 1TD, UK., Piddini E; School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, BS8 1TD, UK. eugenia.piddini@bristol.ac.uk.
Jazyk: angličtina
Zdroj: Nature communications [Nat Commun] 2023 May 10; Vol. 14 (1), pp. 2686. Date of Electronic Publication: 2023 May 10.
DOI: 10.1038/s41467-023-38287-x
Abstrakt: Investigating organ biology often requires methodologies to induce genetically distinct clones within a living tissue. However, the 3D nature of clones makes sample image analysis challenging and slow, limiting the amount of information that can be extracted manually. Here we develop PECAn, a pipeline for image processing and statistical data analysis of complex multi-genotype 3D images. PECAn includes data handling, machine-learning-enabled segmentation, multivariant statistical analysis, and graph generation. This enables researchers to perform rigorous analyses rapidly and at scale, without requiring programming skills. We demonstrate the power of this pipeline by applying it to the study of Minute cell competition. We find an unappreciated sexual dimorphism in Minute cell growth in competing wing discs and identify, by statistical regression analysis, tissue parameters that model and correlate with competitive death. Furthermore, using PECAn, we identify several genes with a role in cell competition by conducting an RNAi-based screen.
(© 2023. The Author(s).)
Databáze: MEDLINE
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