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A screen for morphological complexity identifies regulators of switch-like transitions between discrete cell shapes

Nature Cell Biology volume 15, pages 860–871 (2013)Cite this article

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Abstract

The way in which cells adopt different morphologies is not fully understood. Cell shape could be a continuous variable or restricted to a set of discrete forms. We developed quantitative methods to describe cell shape and show that Drosophila haemocytes in culture are a heterogeneous mixture of five discrete morphologies. In an RNAi screen of genes affecting the morphological complexity of heterogeneous cell populations, we found that most genes regulate the transition between discrete shapes rather than generating new morphologies. In particular, we identified a subset of genes, including the tumour suppressor PTEN, that decrease the heterogeneity of the population, leading to populations enriched in rounded or elongated forms. We show that these genes have a highly conserved function as regulators of cell shape in both mouse and human metastatic melanoma cells.

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Figure 1: Automated morphological profiling.
Figure 2: N, L, C, T and R cells.
Figure 3: Hierarchical clustering of QMSs. Average linkage clustering of 284 5-feature QMSs comprising L, C, T and R SVM Z-scores as well as PZ scores.
Figure 4: Morphological complexity is a phenotype that can be altered by RNAi.
Figure 5: Kc cells exist as discrete subpopulations.
Figure 6: Melanoma cells make switch-like transitions between discrete morphologies on Col-I.
Figure 7: Loss of PTEN alters the exploration of shape space.
Figure 8: A conserved set of genes promotes rounding in Drosophila, mouse and human cells.

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Acknowledgements

We are indebted to the Drosophila RNAi Screening Center staff at Harvard Medical School for their invaluable assistance. We especially thank I. Flockhart for assistance with data management. We thank J. Wang, X. Zhou and P. Bradley for their initial involvement in this study. We are grateful to N. Dhomen and R. Marais for melanoma cell lines. Work was financially supported in part by NCI grants (Grants R01CA121225 and U54CA149196) to S.T.C.W. and CRUK grants to C.B. (Grant 13478) and C.J.M. (Grant C107/A10433). N.P. is an Investigator of the Howard Hughes Medical Institute. A.S. is a Marie Curie Intra-European Fellow. C.J.M. is a Gibb Life Fellow of CRUK. C.B. is a Research Career Development Fellow of the Wellcome Trust.

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Author notes

  1. Zheng Yin and Amine Sadok: These authors contributed equally to this work

Authors and Affiliations

  1. NCI Center for Modeling Cancer Development, The Methodist Hospital Research Institute, Weill Cornell Medical College, 6670 Bertner Avenue, R6 South, Texas 77030, Houston, USA

    Zheng Yin, Xiaofeng Xia, Fuhai Li & Stephen T. C. Wong

  2. Department of Systems Medicine and Bioengineering, The Methodist Hospital Research Institute, Weill Cornell Medical College, 6670 Bertner Avenue, R6 South, Texas 77030, Houston, USA

    Zheng Yin, Xiaofeng Xia, Fuhai Li & Stephen T. C. Wong

  3. Division of Cancer Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, UK

    Amine Sadok, Heba Sailem, Afshan McCarthy, Mar Arias Garcia, Louise Evans, Alexis R. Barr, Christopher J. Marshall & Chris Bakal

  4. Department of Genetics, Harvard Medical School and Howard Hughes Medical Institute, 77 Avenue Louis Pasteur, Massachusetts 02215, Boston, USA

    Norbert Perrimon

  5. Department of Radiology, The Methodist Hospital, Weill Cornell Medical College, Houston, Texas 77030, USA

    Stephen T. C. Wong

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Contributions

Z.Y. performed the bulk of statistical analysis of RNAi screening data and wrote the Supplementary Note. A.S. designed and performed all RNAi and cell line characterization experiments in mouse and human melanoma cells and contributed to writing of the manuscript. H.S. performed the analysis of live-cell melanoma cell imaging experiments and contributed to visualization of statistical results. A.M. performed all mouse work. X.X. and F.L. performed processing of images generated in Drosophila RNAi screen. M.A.G. and L.E. performed experiments describing penetrance of effects of different dsRNAs. A.R.B. contributed to writing and editing of the manuscript and the Supplementary Note. N.P. participated in the initial design of the study. S.T.C.W. coordinated image processing and statistical analysis. C.J.M. participated in design of melanoma experiments and contributed to writing the manuscript. C.B. participated in the design of experiments and statistical analysis, performed the Drosophila RNAi screen, performed the live-cell imaging assays, coordinated experimental and computational analysis, and wrote the manuscript.

Corresponding authors

Correspondence to Stephen T. C. Wong or Chris Bakal.

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The authors declare no competing financial interests.

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Yin, Z., Sadok, A., Sailem, H. et al. A screen for morphological complexity identifies regulators of switch-like transitions between discrete cell shapes. Nat Cell Biol 15, 860–871 (2013). https://doi.org/10.1038/ncb2764

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