Advertisement

Rho GTPases pp 47-56 | Cite as

EdgeProps: A Computational Platform for Correlative Analysis of Cell Dynamics and Near-Edge Protein Activity

  • Anastasia Zhurikhina
  • Timothy Qi
  • Klaus M. Hahn
  • Timothy C. Elston
  • Denis TsygankovEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1821)

Abstract

Developing molecular tools to visualize and control Rho GTPase signaling in living cells has been instrumental in elucidating the mechanisms of cytoskeletal reorganization and causal relationships between activation events in cell function. An indispensable part of such studies is the quantitative characterization of the spatiotemporal GTPase activity. Here we present a computational pipeline, EdgeProps, designed for comparative/correlative analysis of cell dynamics (edge velocity) and near-edge protein activity (intensity of a fluorescent signal). The tool offers a user-friendly interface with three functional modules for processing, visualization, and statistical characterization of single-cell imaging data.

Key words

GTPase activity Image analysis Morphodynamics Protrusive activity Correlation 

Notes

Acknowledgments

This work was supported by US Army Research Office (ARO) Grant W911NF-17-1-0395 to DT and US Army Research Office (ARO) Grant W911NF-15-1-0631 to TE and KH.

References

  1. 1.
    Machacek M, Hodgson L, Welch C, Elliott H, Pertz O, Nalbant P, Abell A, Johnson GL, Hahn KM, Danuser G (2009) Coordination of Rho GTPase activities during cell protrusion. Nature 461:99–103CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Carlson HJ, Campbell RE (2009) Genetically encoded FRET-based biosensors for multiparameter fluorescence imaging. Curr Opin Biotechnol 20:19–27CrossRefPubMedGoogle Scholar
  3. 3.
    Hochreiter B, Garcia AP, Schmid JA (2015) Fluorescent proteins as genetically encoded FRET biosensors in life sciences. Sensors 15:26281–26314CrossRefPubMedGoogle Scholar
  4. 4.
    Karginov AV, Tsygankov D, Berginski M, Chu PH, Trudeau ED, Yi JJ, Gomez S, Elston TC, Hahn KM (2014) Dissecting motility signaling through activation of specific Src-effector complexes. Nat Chem Biol 10:286–290CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Chu PH, Tsygankov D, Berginski ME, Dagliyan O, Gomez SM, Elston TC, Karginov AV, Hahn KM (2014) Engineered kinase activation reveals unique morphodynamic phenotypes and associated trafficking for Src family isoforms. Proc Natl Acad Sci U S A 111:12420–12425CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Etienne-Manneville S, Hall A (2002) Rho GTPases in cell biology. Nature 420:629–635CrossRefPubMedGoogle Scholar
  7. 7.
    Hodge RG, Ridley AJ (2016) Regulating Rho GTPases and their regulators. Nat Rev Mol Cell Biol 17:496–510CrossRefGoogle Scholar
  8. 8.
    Wennerberg K, Der CJ (2004) Rho-family GTPases: it’s not only Rac and Rho (and I like it). J Cell Sci 117:1301–1312CrossRefPubMedGoogle Scholar
  9. 9.
    Tsygankov D, Bilancia CG, Vitriol EA, Hahn KM, Peifer M, Elston TC (2014) CellGeo: a computational platform for the analysis of shape changes in cells with complex geometries. J Cell Biol 204:443–460CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    MacNevin CJ, Toutchkine A, Marston DJ, Hsu CW, Tsygankov D, Li L, Liu B, Qi T, Nguyen DV, Hahn KM (2016) Ratiometric imaging using a single dye enables simultaneous visualization of Rac1 and Cdc42 activation. J Am Chem Soc 138:2571–2575CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Prewitt JMS, Mendelsohn ML (1966) The analysis of cell images. Ann N Y Acad Sci 128:1035–1053CrossRefPubMedGoogle Scholar
  12. 12.
    Otsu N (1979) A threshold selection method from gray-level histograms. IEEE Transact Syst Man Cyb 9:62–66CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Anastasia Zhurikhina
    • 1
  • Timothy Qi
    • 2
  • Klaus M. Hahn
    • 2
    • 3
  • Timothy C. Elston
    • 2
  • Denis Tsygankov
    • 1
    Email author
  1. 1.Wallace H. Coulter Department of Biomedical EngineeringGeorgia Institute of Technology and Emory University School of MedicineAtlantaUSA
  2. 2.Department of PharmacologyThe University of North Carolina at Chapel HillChapel HillUSA
  3. 3.Lineberger Comprehensive Cancer CenterUniversity of North Carolina School of MedicineChapel HillUSA

Personalised recommendations