Image based modeling of bleb site selection

Formation and closure of macropinocytic cups in Dictyostelium

Macropinocytosis is a conserved endocytic process by which cells engulf droplets of medium into micron-sized vesicles. We use light-sheet microscopy to define an underlying set of principles by which macropinocytic cups are shaped and closed in Dictyostelium amoebae. Cups form around domains of PIP3 stretching almost to their lip and are supported by a specialized F-actin scaffold from lip to base. They are shaped by a ring of actin polymerization created by recruiting Scar/WAVE and Arp2/3 around PIP3 domains, but how cups evolve over time to close and form a vesicle is unknown. Custom 3D analysis shows that PIP3 domains expand from small origins, capturing new membrane into the cup, and crucially, that cups close when domain expansion stalls. We show that cups can close in two ways: either at the lip, by inwardly directed actin polymerization, or the base, by stretching and delamination of the membrane. This provides the basis for a conceptual mechanism whereby closure is brought about by a combination of stalled cup expansion, continued actin polymerization at the lip, and membrane tension. We test this through the use of a biophysical model, which can recapitulate both forms of cup closure and explain how 3D cup structures evolve over time to mediate engulfment.

Domain Adapted Multitask Learning for Segmenting Amoeboid Cells in Microscopy

The method proposed in this paper is a robust combination of multi-task learning and unsupervised domain adaptation for segmenting amoeboid cells in microscopy. A highlight of this work is the manner in which the model's hyperparameters are estimated. The detriments of ad-hoc parameter estimation are well known, but this issue remains largely unaddressed in the context of CNN-based segmentation. Using a novel min-max formulation of the segmentation cost function our proposed method analytically estimates the model's hyperparameters, while simultaneously learning the CNN weights during training. This end-to-end framework provides a consolidated mechanism to harness the potential of multi-task learning to isolate and segment clustered cells from low contrast brightfield images, and it simultaneously leverages deep domain adaptation to segment fluorescent cells without explicit pixel-level re- annotation of the data. Experimental validations on multi-cellular images strongly suggest the effectiveness of the proposed technique, and our quantitative results show at least 15% and 10% improvement in cell segmentation on brightfield and fluorescence images respectively compared to contemporary supervised segmentation methods.

Blebs—Formation, Regulation, Positioning, and Role in Amoeboid Cell Migration

In the context of development, tissue homeostasis, immune surveillance, and pathological conditions such as cancer metastasis and inflammation, migrating amoeboid cells commonly form protrusions called blebs. For these spherical protrusions to inflate, the force for pushing the membrane forward depends on actomyosin contraction rather than active actin assembly. Accordingly, blebs exhibit distinct dynamics and regulation. In this review, we first examine the mechanisms that control the inflation of blebs and bias their formation in the direction of the cell’s leading edge and present current views concerning the role blebs play in promoting cell locomotion. While certain motile amoeboid cells exclusively form blebs, others form blebs as well as other protrusion types. We describe factors in the environment and cell-intrinsic activities that determine the proportion of the different forms of protrusions cells produce.

A role for myosin II clusters and membrane energy in cortex rupture for Dictyostelium discoideum

Blebs, pressure driven protrusions of the cell membrane, facilitate the movement of eukaryotic cells such as the soil amoeba Dictyostelium discoideum, white blood cells and cancer cells. Blebs initiate when the cell membrane separates from the underlying cortex. A local rupture of the cortex, has been suggested as a mechanism by which blebs are initiated. However, much clarity is still needed about how cells inherently regulate rupture of the cortex in locations where blebs are expected to form. In this work, we examine the role of membrane energy and the motor protein myosin II (myosin) in facilitating the cell driven rupture of the cortex. We perform under-agarose chemotaxis experiments, using Dictyostelium discoideum cells, to visualize the dynamics of myosin and calculate changes in membrane energy in the blebbing region. To facilitate a rapid detection of blebs and analysis of the energy and myosin distribution at the cell front, we introduce an autonomous bleb detection algorithm that takes in discrete cell boundaries and returns the coordinate location of blebs with its shape characteristics. We are able to identify by microscopy naturally occurring gaps in the cortex prior to membrane detachment at sites of bleb nucleation. These gaps form at positions calculated to have high membrane energy, and are associated with areas of myosin enrichment. Myosin is also shown to accumulate in the cortex prior to bleb initiation and just before the complete disassembly of the cortex. Together our findings provide direct spatial and temporal evidence to support cortex rupture as an intrinsic bleb initiation mechanism and suggests that myosin clusters are associated with regions of high membrane energy where its contractile activity leads to a rupture of the cortex at points of maximal energy.

Chemokine-biased robust self-organizing polarization of migrating cells in vivo

Bleb-driven cell migration plays important roles in diverse biological processes. Here, we present the mechanism for polarity establishment and maintenance in blebbing cells in vivo. We show that actin polymerization defines the leading edge, the position where blebs form. We show that the cell front can direct the formation of the rear by facilitating retrograde flow of proteins that limit the generation of blebs at the opposite aspect of the cell. Conversely, localization of bleb-inhibiting proteins at one aspect of the cell results in the establishment of the cell front at the opposite side. These antagonistic interactions result in robust polarity that can be initiated in a random direction, or oriented by a chemokine gradient.

To study the mechanisms controlling front-rear polarity in migrating cells, we used zebrafish primordial germ cells (PGCs) as an in vivo model. We find that polarity of bleb-driven migrating cells can be initiated at the cell front, as manifested by actin accumulation at the future leading edge and myosin-dependent retrograde actin flow toward the other side of the cell. In such cases, the definition of the cell front, from which bleb-inhibiting proteins such as Ezrin are depleted, precedes the establishment of the cell rear, where those proteins accumulate. Conversely, following cell division, the accumulation of Ezrin at the cleavage plane is the first sign for cell polarity and this aspect of the cell becomes the cell back. Together, the antagonistic interactions between the cell front and back lead to a robust polarization of the cell. Furthermore, we show that chemokine signaling can bias the establishment of the front-rear axis of the cell, thereby guiding the migrating cells toward sites of higher levels of the attractant. We compare these results to a theoretical model according to which a critical value of actin treadmilling flow can initiate a positive feedback loop that leads to the generation of the front-rear axis and to stable cell polarization. Together, our in vivo findings and the mathematical model, provide an explanation for the observed nonoriented migration of primordial germ cells in the absence of the guidance cue, as well as for the directed migration toward the region where the gonad develops.

Zebrafish Primordial Germ Cell Migration

Similar to many other organisms, zebrafish primordial germ cells (PGCs) are specified at a location distinct from that of gonadal somatic cells. Guided by chemotactic cues, PGCs migrate through embryonic tissues toward the region where the gonad develops. In this process, PGCs employ a bleb-driven amoeboid migration mode, characterized by low adhesion and high actomyosin contractility, a strategy used by other migrating cells, such as leukocytes and certain types of cancer cells. The mechanisms underlying the motility and the directed migration of PGCs should be robust to ensure arrival at the target, thereby contributing to the fertility of the organism. These features make PGCs an excellent model for studying guided single-cell migration in vivo. In this review, we present recent findings regarding the establishment and maintenance of cell polarity that are essential for motility and discuss the mechanisms by which cell polarization and directed migration are controlled by chemical and physical cues.

Mathematical modelling in cell migration: tackling biochemistry in changing geometries

Directed cell migration poses a rich set of theoretical challenges. Broadly, these are concerned with (1) how cells sense external signal gradients and adapt; (2) how actin polymerisation is localised to drive the leading cell edge and Myosin-II molecular motors retract the cell rear; and (3) how the combined action of cellular forces and cell adhesion results in cell shape changes and net migration. Reaction-diffusion models for biological pattern formation going back to Turing have long been used to explain generic principles of gradient sensing and cell polarisation in simple, static geometries like a circle. In this minireview, we focus on recent research which aims at coupling the biochemistry with cellular mechanics and modelling cell shape changes. In particular, we want to contrast two principal modelling approaches: (1) interface tracking where the cell membrane, interfacing cell interior and exterior, is explicitly represented by a set of moving points in 2D or 3D space and (2) interface capturing. In interface capturing, the membrane is implicitly modelled analogously to a level line in a hilly landscape whose topology changes according to forces acting on the membrane. With the increased availability of high-quality 3D microscopy data of complex cell shapes, such methods will become increasingly important in data-driven, image-based modelling to better understand the mechanochemistry underpinning cell motion.

Actin cytoskeleton in mesenchymal-to-amoeboid transition of cancer cells

During development of metastasis, tumor cells migrate through different tissues and encounter different extracellular matrices. An ability of cells to adapt mechanisms of their migration to these diverse environmental conditions, called migration plasticity, gives tumor cells an advantage over normal cells for long distant dissemination. Different modes of individual cell motility-mesenchymal and amoeboid-are driven by different molecular mechanisms, which largely depend on functions of the actin cytoskeleton that can be modulated in a wide range by cellular signaling mechanisms in response to environmental conditions. Various triggers can switch one motility mode to another, but regulations of these transitions are incompletely understood. However, understanding of the mechanisms driving migration plasticity is instrumental for finding anti-cancer treatment capable to stop cancer metastasis. In this review, we discuss cytoskeletal features, which allow the individually migrating cells to switch between mesenchymal and amoeboid migrating modes, called mesenchymal-to-amoeboid transition (MAT). We briefly describe main characteristics of different cell migration modes, and then discuss the triggering factors that initiate MAT with special attention to cytoskeletal features essential for migration plasticity.

Pressure sensing through Piezo channels controls whether cells migrate with blebs or pseudopods

Cells migrating within the body perform vital functions in development and for defense and repair of tissues. In this dense environment, cells encounter mechanical forces and constraints not experienced when moving under buffer, and, accordingly, many change how they move. We find that gentle squashing, which mimics mechanical resistance, causes cells to move using blebs—a form of projection driven by fluid pressure—rather than pseudopods. This behavior depends on the Piezo stretch-operated ion channel in the cell membrane and calcium fluxes into the cell. Piezo is highly conserved and is required for light touch sensation; this work extends its functions into migrating cells.

Blebs and pseudopods can both power cell migration, with blebs often favored in tissues, where cells encounter increased mechanical resistance. To investigate how migrating cells detect and respond to mechanical forces, we used a “cell squasher” to apply uniaxial pressure to Dictyostelium cells chemotaxing under soft agarose. As little as 100 Pa causes a rapid (<10 s), sustained shift to movement with blebs rather than pseudopods. Cells are flattened under load and lose volume; the actin cytoskeleton is reorganized, with myosin II recruited to the cortex, which may pressurize the cytoplasm for blebbing. The transition to bleb-driven motility requires extracellular calcium and is accompanied by increased cytosolic calcium. It is largely abrogated in cells lacking the Piezo stretch-operated channel; under load, these cells persist in using pseudopods and chemotax poorly. We propose that migrating cells sense pressure through Piezo, which mediates calcium influx, directing movement with blebs instead of pseudopods.

QuimP: analyzing transmembrane signalling in highly deformable cells

Summary

Transmembrane signalling plays important physiological roles, with G protein-coupled cell surface receptors being particularly important therapeutic targets. Fluorescent proteins are widely used to study signalling, but analyses of image time series can be challenging, in particular when cells change shape. QuimP software semi-automatically tracks spatio-temporal patterns of fluorescence at the cell membrane at high spatial resolution. This makes it a unique tool for studying transmembrane signalling, particularly during cell migration in immune or cancer cells for example.

Availability and implementation

QuimP (http://warwick.ac.uk/quimp) is a set of Java plugins for Fiji/ImageJ (http://fiji.sc) installable through the Fiji Updater (http://warwick.ac.uk/quimp/wiki-pages/installation). It is compatible with Mac, Windows and Unix operating systems, requiring version >1.45 of ImageJ and Java 8. QuimP is released as open source (https://github.com/CellDynamics/QuimP) under an academic licence.

Supplementary information

Supplementary data are available at Bioinformatics online.

Advances in geometric techniques for analyzing blebbing in chemotaxing Dictyostelium cells

We present a technical platform that allows us to monitor and measure cortex and membrane dynamics during bleb-based chemotaxis. Using D. discoideum cells expressing LifeAct-GFP and crawling under agarose containing RITC-dextran, we were able to simultaneously visualize the actin cortex and the cell membrane throughout bleb formation. Using these images, we then applied edge detect to generate points on the cell boundary with coordinates in a coordinate plane. Then we fitted these points to a curve with known x and y coordinate functions. The result was to parameterize the cell outline. With the parameterization, we demonstrate how to compute data for geometric features such as cell area, bleb area and edge curvature. This allows us to collect vital data for the analysis of blebbing.

3D mapping of native extracellular matrix reveals cellular responses to the microenvironment

Cells and extracellular matrix (ECM) are mutually interdependent: cells guide self-assembly of ECM precursors, and the resulting ECM architecture supports and instructs cells. Though bidirectional signaling between ECM and cells is fundamental to cell biology, it is challenging to gain high-resolution structural information on cellular responses to the matrix microenvironment. Here we used cryo-scanning transmission electron tomography (CSTET) to reveal the nanometer- to micron-scale organization of major fibroblast ECM components in a native-like context, while simultaneously visualizing internal cell ultrastructure including organelles and cytoskeleton. In addition to extending current models for collagen VI fibril organization, three-dimensional views of thick cell regions and surrounding matrix showed how ECM networks impact the structures and dynamics of intracellular organelles and how cells remodel ECM. Collagen VI and fibronectin were seen to distribute in fundamentally different ways in the cell microenvironment and perform distinct roles in supporting and interacting with cells. This work demonstrates that CSTET provides a new perspective for the study of ECM in cell biology, highlighting labeled extracellular elements against a backdrop of unlabeled but morphologically identifiable cellular features with nanometer resolution detail.

Interaction and fusion dynamics between cellular blebs

Membrane blebbing, as a mechanism for cells to regulate their internal pressure and membrane tension, is believed to play important roles in processes such as cell migration, spreading and apoptosis. However, the fundamental question of how different blebs interact with each other during their life cycles remains largely unclear. Here, we report a combined theoretical and experimental investigation to examine how the growth and retraction of a cellular bleb are influenced by neighboring blebs as well as the fusion dynamics between them. Specifically, a boundary integral model was developed to describe the shape evolution of cell membrane during the blebbing/retracting process. We showed that a drop in the intracellular pressure will be induced by the formation of a bleb whose retraction then restores the pressure level. Consequently, the volume that a second bleb can reach was predicted to heavily depend on its initial weakened size and the time lag with respect to the first bleb, all in quantitative agreement with our experimental observations. In addition, it was found that as the strength of membrane-cortex adhesion increases, the possible coalescence of two neighboring blebs changes from smooth fusion to abrupt coalescence and eventually to no fusion at all. Phase diagrams summarizing the dependence of such transition on key physical factors, such as the intracellular pressure and bleb separation, were also obtained.

The actin cortex at a glance

Precisely controlled cell deformations are key to cell migration, division and tissue morphogenesis, and have been implicated in cell differentiation during development, as well as cancer progression. In animal cells, shape changes are primarily driven by the cellular cortex, a thin actomyosin network that lies directly underneath the plasma membrane. Myosin-generated forces create tension in the cortical network, and gradients in tension lead to cellular deformations. Recent studies have provided important insight into the molecular control of cortical tension by progressively unveiling cortex composition and organization. In this Cell Science at a Glance article and the accompanying poster, we review our current understanding of cortex composition and architecture. We then discuss how the microscopic properties of the cortex control cortical tension. While many open questions remain, it is now clear that cortical tension can be modulated through both cortex composition and organization, providing multiple levels of regulation for this key cellular property during cell and tissue morphogenesis.

Summary: A summary of the composition, architecture, mechanics and function of the cellular actin cortex, which determines the shape of animal cells, and, thus, provides the foundation for cell and tissue morphogenesis.

A combined experimental and theoretical investigation on cellular blebbing

Although accumulating evidence has demonstrated the important role of membrane blebbing in various cellular processes, the fundamental question of how the initiation/evolution of blebs are influenced by physical factors like membrane-cortex interactions and intracellular pressure remains unclear. Here, we report a combined modeling and experimental study to address this outstanding issue. Specifically, boundary integral method was used to track the motion of membrane (in 3D) during blebbing while possible rupture of the bilayer-cortex adhesion has also been taken into account. We showed that, for a given differential pressure across the cell membrane, the size of the weakened cortex must be over a critical value for blebbing to occur and the steady-state volume of a bleb is proportional to its initial growth rate, all in good agreement with recent experiments. The predicted shape evolution of blebs also matches well with our observations. Finally, a blebbing map, summarizing the essential physics involved, was obtained which exhibits three distinct regimes: no bleb formation corresponding to a low intracellular pressure or a small weakened cortex region; bleb formed with a fixed width when the disrupted cortex zone is very large; and a growing bleb resulted from progressive membrane-cortex detachment under intermediate weakened cortex size.