Deconvolution of subcellular protrusion heterogeneity and the underlying actin regulator dynamics from live cell imaging

Nat Commun. 2018 Apr 27;9(1):1688. doi: 10.1038/s41467-018-04030-0.

Abstract

Cell protrusion is morphodynamically heterogeneous at the subcellular level. However, the mechanism of cell protrusion has been understood based on the ensemble average of actin regulator dynamics. Here, we establish a computational framework called HACKS (deconvolution of heterogeneous activity in coordination of cytoskeleton at the subcellular level) to deconvolve the subcellular heterogeneity of lamellipodial protrusion from live cell imaging. HACKS identifies distinct subcellular protrusion phenotypes based on machine-learning algorithms and reveals their underlying actin regulator dynamics at the leading edge. Using our method, we discover "accelerating protrusion", which is driven by the temporally ordered coordination of Arp2/3 and VASP activities. We validate our finding by pharmacological perturbations and further identify the fine regulation of Arp2/3 and VASP recruitment associated with accelerating protrusion. Our study suggests HACKS can identify specific subcellular protrusion phenotypes susceptible to pharmacological perturbation and reveal how actin regulator dynamics are changed by the perturbation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Actin Cytoskeleton / drug effects
  • Actin Cytoskeleton / physiology
  • Actin-Related Protein 2-3 Complex / antagonists & inhibitors
  • Actin-Related Protein 2-3 Complex / metabolism
  • Actins / metabolism*
  • Animals
  • Cell Adhesion Molecules / metabolism
  • Cell Line
  • Cell Line, Tumor
  • Cell Movement / drug effects
  • Cell Movement / physiology*
  • Cluster Analysis
  • Humans
  • Indoles / pharmacology
  • Intravital Microscopy
  • Machine Learning*
  • Microfilament Proteins / metabolism
  • Models, Biological*
  • Phosphoproteins / metabolism
  • Potoroidae
  • Pseudopodia / physiology*
  • Software

Substances

  • Actin-Related Protein 2-3 Complex
  • Actins
  • CK-0944666
  • Cell Adhesion Molecules
  • Indoles
  • Microfilament Proteins
  • Phosphoproteins
  • vasodilator-stimulated phosphoprotein