Traject3d allows label-free identification of distinct co-occurring phenotypes within 3D culture by live imaging

Freckmann, E. C. et al. (2022) Traject3d allows label-free identification of distinct co-occurring phenotypes within 3D culture by live imaging. Nature Communications, 13, 5317. (doi: 10.1038/s41467-022-32958-x) (PMID:36085324) (PMCID:PMC9463449)

[img] Text
279114.pdf - Published Version
Available under License Creative Commons Attribution.



Single cell profiling by genetic, proteomic and imaging methods has expanded the ability to identify programmes regulating distinct cell states. The 3-dimensional (3D) culture of cells or tissue fragments provides a system to study how such states contribute to multicellular morphogenesis. Whether cells plated into 3D cultures give rise to a singular phenotype or whether multiple biologically distinct phenotypes arise in parallel is largely unknown due to a lack of tools to detect such heterogeneity. Here we develop Traject3d (Trajectory identification in 3D), a method for identifying heterogeneous states in 3D culture and how these give rise to distinct phenotypes over time, from label-free multi-day time-lapse imaging. We use this to characterise the temporal landscape of morphological states of cancer cell lines, varying in metastatic potential and drug resistance, and use this information to identify drug combinations that inhibit such heterogeneity. Traject3d is therefore an important companion to other single-cell technologies by facilitating real-time identification via live imaging of how distinct states can lead to alternate phenotypes that occur in parallel in 3D culture.

Item Type:Articles
Additional Information:This work was supported by the following grants; NIH K99CA163535 (D.M.B.), CRUK C596/A19481 (M.Na.), CRUK C7932/A25170 (K.N.), CRUK C596/A17196 and A31287 (E.S., AR.-F., L.M., A.H., M.Ne, D.S.), MR/L017997/1), (M.S), A17196, A25233, A29996 (J.P.M.), A29801 (C.M.), A22904 (H.Y.L.), IAA/CRUK (A26825 and A28223), O.J.S and T.RM.L. E.C.F. was supported by a University of Glasgow Industrial Partnership PhD studentship co-funded by Essen Bioscience, Sartorius Group. We thank M. Henry (University of Iowa) and K. Pienta for providing cell lines (Johns Hopkins Medicine International). We thank R. Carstens for ESRP1/2 shRNA plasmids.
Glasgow Author(s) Enlighten ID:Roman-Fernandez, Dr Alvaro and McGarry, Ms Lynn and Bryant, Dr David and Leung, Professor Hing and Strachan, Mr David and Sandilands, Dr Emma and Neilson, Dr Matthew and Freckmann, Eva and Salji, Mr Mark and Nacke, Marisa and Nikolatou, Konstantina and Miller, Professor Crispin and Morton, Dr Jennifer and Sansom, Professor Owen and Cumming, Erin
Authors: Freckmann, E. C., Sandilands, E., Cumming, E., Neilson, M., Roman-Fernandez, A., Nikolatou, K., Nacke, M., Lannagan, T. R.M., Hedley, A., Strachan, D., Salji, M., Morton, J. P., McGarry, L., Leung, H. Y., Sansom, O. J., Miller, C. J., and Bryant, D. M.
College/School:College of Medical Veterinary and Life Sciences > School of Cancer Sciences
Journal Name:Nature Communications
Publisher:Nature Research
ISSN (Online):2041-1723
Copyright Holders:Copyright © The Author(s) 2022
First Published:First published in Nature Communications 13: 5317
Publisher Policy:Reproduced under a Creative Commons license

University Staff: Request a correction | Enlighten Editors: Update this record

Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
170638Non-Clinical Training Award Cycle 2David BryantCancer Research UK (CRUK)C596/A19481Institute of Cancer Sciences
300448Non-clinical Training Award Cycle 3 2017Owen SansomCancer Research UK (CRUK)C7932/A25170CS - Beatson Institute for Cancer Research
170128Quantitative proteomic analysis of castrate-resistant prostate cancerHing LeungMedical Research Council (MRC)MR/L017997/1Institute of Cancer Sciences
174328Precision-Panc: a dynamic therapeutic development platform for pancreatic cancerOwen SansomCancer Research UK (CRUK)C7932/A25233CS - Beatson Institute for Cancer Research
301989ACRClerate: Colorectal Cancer Stratified Medicine NetworkOwen SansomCancer Research UK (CRUK)C7932/A26825CS - Beatson Institute for Cancer Research