An analysis toolbox to explore mesenchymal migration heterogeneity reveals adaptive switching between distinct modes

Mesenchymal (lamellipodial) migration is heterogeneous, although whether this reflects progressive variability or discrete, 'switchable' migration modalities, remains unclear. We present an analytical toolbox, based on quantitative single-cell imaging data, to interrogate this heterogeneity. Integrating supervised behavioral classification with multivariate analyses of cell motion, membrane dynamics, cell-matrix adhesion status and F-actin organization, this toolbox here enables the detection and characterization of two quantitatively distinct mesenchymal migration modes, termed 'Continuous' and 'Discontinuous'. Quantitative mode comparisons reveal differences in cell motion, spatiotemporal coordination of membrane protrusion/retraction, and how cells within each mode reorganize with changed cell speed. These modes thus represent distinctive migratory strategies. Additional analyses illuminate the macromolecular- and cellular-scale effects of molecular targeting (fibronectin, talin, ROCK), including 'adaptive switching' between Continuous (favored at high adhesion/full contraction) and Discontinuous (low adhesion/inhibited contraction) modes. Overall, this analytical toolbox now facilitates the exploration of both spontaneous and adaptive heterogeneity in mesenchymal migration.

Download Full-text

Changes in E-cadherin rigidity sensing regulate cell adhesion

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1618676114 ◽

2017 ◽

Vol 114 (29) ◽

pp. E5835-E5844 ◽

Cited By ~ 34

Author(s):

Caitlin Collins ◽

Aleksandra K. Denisin ◽

Beth L. Pruitt ◽

W. James Nelson

Keyword(s):

Cell Adhesion ◽

Signaling Molecules ◽

Membrane Dynamics ◽

Cell Contact ◽

Adhesion Assay ◽

Cell Periphery ◽

Actin Organization ◽

Rigidity Sensing ◽

E Cadherin ◽

Cell Cell

Mechanical cues are sensed and transduced by cell adhesion complexes to regulate diverse cell behaviors. Extracellular matrix (ECM) rigidity sensing by integrin adhesions has been well studied, but rigidity sensing by cadherins during cell adhesion is largely unexplored. Using mechanically tunable polyacrylamide (PA) gels functionalized with the extracellular domain of E-cadherin (Ecad-Fc), we showed that E-cadherin–dependent epithelial cell adhesion was sensitive to changes in PA gel elastic modulus that produced striking differences in cell morphology, actin organization, and membrane dynamics. Traction force microscopy (TFM) revealed that cells produced the greatest tractions at the cell periphery, where distinct types of actin-based membrane protrusions formed. Cells responded to substrate rigidity by reorganizing the distribution and size of high-traction-stress regions at the cell periphery. Differences in adhesion and protrusion dynamics were mediated by balancing the activities of specific signaling molecules. Cell adhesion to a 30-kPa Ecad-Fc PA gel required Cdc42- and formin-dependent filopodia formation, whereas adhesion to a 60-kPa Ecad-Fc PA gel induced Arp2/3-dependent lamellipodial protrusions. A quantitative 3D cell–cell adhesion assay and live cell imaging of cell–cell contact formation revealed that inhibition of Cdc42, formin, and Arp2/3 activities blocked the initiation, but not the maintenance of established cell–cell adhesions. These results indicate that the same signaling molecules activated by E-cadherin rigidity sensing on PA gels contribute to actin organization and membrane dynamics during cell–cell adhesion. We hypothesize that a transition in the stiffness of E-cadherin homotypic interactions regulates actin and membrane dynamics during initial stages of cell–cell adhesion.

Download Full-text

Modelling collective cell motion: are on- and off-lattice models equivalent?

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2019.0378 ◽

2020 ◽

Vol 375 (1807) ◽

pp. 20190378 ◽

Cited By ~ 2

Author(s):

Josué Manik Nava-Sedeño ◽

Anja Voß-Böhme ◽

Haralampos Hatzikirou ◽

Andreas Deutsch ◽

Fernando Peruani

Keyword(s):

Wound Repair ◽

Collective Motion ◽

Scale Effects ◽

Lattice Models ◽

Population Level ◽

Collective Migration ◽

Fruiting Body Formation ◽

Bacterial Patterns ◽

Dynamical Description ◽

Cell Motion

Biological processes, such as embryonic development, wound repair and cancer invasion, or bacterial swarming and fruiting body formation, involve collective motion of cells as a coordinated group. Collective cell motion of eukaryotic cells often includes interactions that result in polar alignment of cell velocities, while bacterial patterns typically show features of apolar velocity alignment. For analysing the population-scale effects of these different alignment mechanisms, various on- and off-lattice agent-based models have been introduced. However, discriminating model-specific artefacts from general features of collective cell motion is challenging. In this work, we focus on equivalence criteria at the population level to compare on- and off-lattice models. In particular, we define prototypic off- and on-lattice models of polar and apolar alignment, and show how to obtain an on-lattice from an off-lattice model of velocity alignment. By characterizing the behaviour and dynamical description of collective migration models at the macroscopic level, we suggest the type of phase transitions and possible patterns in the approximative macroscopic partial differential equation descriptions as informative equivalence criteria between on- and off-lattice models. This article is part of the theme issue ‘Multi-scale analysis and modelling of collective migration in biological systems’.

Download Full-text

The Pleckstrin Homology Domain Proteins Slm1 and Slm2 Are Required for Actin Cytoskeleton Organization in Yeast and Bind Phosphatidylinositol-4,5-Bisphosphate and TORC2

Molecular Biology of the Cell ◽

10.1091/mbc.e04-07-0564 ◽

2005 ◽

Vol 16 (4) ◽

pp. 1883-1900 ◽

Cited By ~ 92

Author(s):

Maria Fadri ◽

Alexes Daquinag ◽

Shimei Wang ◽

Tao Xue ◽

Jeannette Kunz

Keyword(s):

Cell Growth ◽

Actin Cytoskeleton ◽

Membrane Dynamics ◽

Effector Proteins ◽

Pleckstrin Homology Domain ◽

Ph Domain ◽

Pleckstrin Homology ◽

Yeast Saccharomyces Cerevisiae ◽

Actin Organization ◽

Cytoskeleton Organization

Phosphatidylinositol-4,5-bisphosphate [PtdIns(4,5)P2] is a key second messenger that regulates actin and membrane dynamics, as well as other cellular processes. Many of the effects of PtdIns(4,5)P2are mediated by binding to effector proteins that contain a pleckstrin homology (PH) domain. Here, we identify two novel effectors of PtdIns(4,5)P2in the budding yeast Saccharomyces cerevisiae: the PH domain containing protein Slm1 and its homolog Slm2. Slm1 and Slm2 serve redundant roles essential for cell growth and actin cytoskeleton polarization. Slm1 and Slm2 bind PtdIns(4,5)P2through their PH domains. In addition, Slm1 and Slm2 physically interact with Avo2 and Bit61, two components of the TORC2 signaling complex, which mediates Tor2 signaling to the actin cytoskeleton. Together, these interactions coordinately regulate Slm1 targeting to the plasma membrane. Our results thus identify two novel effectors of PtdIns(4,5)P2regulating cell growth and actin organization and suggest that Slm1 and Slm2 integrate inputs from the PtdIns(4,5)P2and TORC2 to modulate polarized actin assembly and growth.

Download Full-text

Computational Methods for Single-Cell Imaging and Omics Data Integration

Frontiers in Molecular Biosciences ◽

10.3389/fmolb.2021.768106 ◽

2022 ◽

Vol 8 ◽

Author(s):

Ebony Rose Watson ◽

Atefeh Taherian Fard ◽

Jessica Cara Mar

Keyword(s):

Single Cell ◽

Biomedical Research ◽

Cell Imaging ◽

New Technologies ◽

Single Cells ◽

Tissue Level ◽

Machine Learning Algorithms ◽

Multidimensional Data ◽

Imaging Data ◽

Single Cell Imaging

Integrating single cell omics and single cell imaging allows for a more effective characterisation of the underlying mechanisms that drive a phenotype at the tissue level, creating a comprehensive profile at the cellular level. Although the use of imaging data is well established in biomedical research, its primary application has been to observe phenotypes at the tissue or organ level, often using medical imaging techniques such as MRI, CT, and PET. These imaging technologies complement omics-based data in biomedical research because they are helpful for identifying associations between genotype and phenotype, along with functional changes occurring at the tissue level. Single cell imaging can act as an intermediary between these levels. Meanwhile new technologies continue to arrive that can be used to interrogate the genome of single cells and its related omics datasets. As these two areas, single cell imaging and single cell omics, each advance independently with the development of novel techniques, the opportunity to integrate these data types becomes more and more attractive. This review outlines some of the technologies and methods currently available for generating, processing, and analysing single-cell omics- and imaging data, and how they could be integrated to further our understanding of complex biological phenomena like ageing. We include an emphasis on machine learning algorithms because of their ability to identify complex patterns in large multidimensional data.

Download Full-text

Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane

The Journal of Cell Biology ◽

10.1083/jcb.200404119 ◽

2004 ◽

Vol 167 (6) ◽

pp. 1099-1112 ◽

Cited By ~ 114

Author(s):

Marcello Marelli ◽

Jennifer J. Smith ◽

Sunhee Jung ◽

Eugene Yi ◽

Alexey I. Nesvizhskii ◽

...

Keyword(s):

Mass Spectrometry ◽

Large Scale ◽

Secretory Pathway ◽

Subcellular Fractionation ◽

Membrane Dynamics ◽

Small Gtpase ◽

Quantitative Mass Spectrometry ◽

Actin Organization ◽

Associated Proteins ◽

Peroxisome Membrane

We have combined classical subcellular fractionation with large-scale quantitative mass spectrometry to identify proteins that enrich specifically with peroxisomes of Saccharomyces cerevisiae. In two complementary experiments, isotope-coded affinity tags and tandem mass spectrometry were used to quantify the relative enrichment of proteins during the purification of peroxisomes. Mathematical modeling of the data from 306 quantified proteins led to a prioritized list of 70 candidates whose enrichment scores indicated a high likelihood of them being peroxisomal. Among these proteins, eight novel peroxisome-associated proteins were identified. The top novel peroxisomal candidate was the small GTPase Rho1p. Although Rho1p has been shown to be tethered to membranes of the secretory pathway, we show that it is specifically recruited to peroxisomes upon their induction in a process dependent on its interaction with the peroxisome membrane protein Pex25p. Rho1p regulates the assembly state of actin on the peroxisome membrane, thereby controlling peroxisome membrane dynamics and biogenesis.

Download Full-text

A stochastic transcriptional switch model for single cell imaging data

Biostatistics ◽

10.1093/biostatistics/kxv010 ◽

2015 ◽

Vol 16 (4) ◽

pp. 655-669 ◽

Cited By ~ 23

Author(s):

Kirsty L. Hey ◽

Hiroshi Momiji ◽

Karen Featherstone ◽

Julian R.E. Davis ◽

Michael R.H. White ◽

...

Keyword(s):

Single Cell ◽

Cell Imaging ◽

Imaging Data ◽

Single Cell Imaging ◽

Transcriptional Switch

Download Full-text

Review of PIP2 in Cellular Signaling, Functions and Diseases

International Journal of Molecular Sciences ◽

10.3390/ijms21218342 ◽

2020 ◽

Vol 21 (21) ◽

pp. 8342

Author(s):

Kalpana Mandal

Keyword(s):

Molecular Mechanisms ◽

Membrane Dynamics ◽

Actin Dynamics ◽

Cellular Functions ◽

Phosphatidylinositol Bisphosphate ◽

Cell Matrix ◽

Intracellular Proteins ◽

Specific Proteins ◽

Cellular Compartments ◽

Cell Matrix Adhesion

Phosphoinositides play a crucial role in regulating many cellular functions, such as actin dynamics, signaling, intracellular trafficking, membrane dynamics, and cell–matrix adhesion. Central to this process is phosphatidylinositol bisphosphate (PIP2). The levels of PIP2 in the membrane are rapidly altered by the activity of phosphoinositide-directed kinases and phosphatases, and it binds to dozens of different intracellular proteins. Despite the vast literature dedicated to understanding the regulation of PIP2 in cells over past 30 years, much remains to be learned about its cellular functions. In this review, we focus on past and recent exciting results on different molecular mechanisms that regulate cellular functions by binding of specific proteins to PIP2 or by stabilizing phosphoinositide pools in different cellular compartments. Moreover, this review summarizes recent findings that implicate dysregulation of PIP2 in many diseases

Download Full-text