Stress-shape misalignment in confluent cell layers.

In tissue formation and repair, the epithelium undergoes complex patterns of motion driven by the active forces produced by each cell. Although the principles governing how the forces evolve in time are not yet clear, it is often assumed that the contractile stresses within the cell layer align with the axis defined by the body of each cell. Here, we simultaneously measured the orientations of the cell shape and the cell-generated contractile stresses, observing correlated, dynamic domains in which the stresses were systematically misaligned with the cell body. We developed a continuum model that decouples the orientations of contractile stress and cell body. The model recovered the spatial and temporal dynamics of the regions of misalignment in the experiments. These findings reveal that the cell controls its contractile forces independently from its shape, suggesting that the physical rules relating cell forces and cell shape are more flexible than previously thought.

Active nematics with deformable particles.

The hydrodynamic theory of active nematics has been often used to describe the spatio-temporal dynamics of cell flows and motile topological defects within soft confluent tissues. Those theories, however, often rely on the assumption that tissues consist of cells with a fixed, anisotropic shape and do not resolve dynamical cell shape changes due to flow gradients. In this paper we extend the continuum theory of active nematics to include cell shape deformability. We find that circular cells in tissues must generate sufficient active stress to overcome an elastic barrier to deforming their shape in order to drive tissue-scale flows. Above this threshold the systems enter a dynamical steady-state with regions of elongated cells and strong flows coexisting with quiescent regions of isotropic cells.

Activity-driven tissue alignment in proliferating spheroids.

We extend the continuum theory of active nematic fluids to study cell flows and tissue dynamics inside multicellular spheroids, spherical, self-assembled aggregates of cells that are widely used as model systems to study tumour dynamics. Cells near the surface of spheroids have better access to nutrients and therefore proliferate more rapidly than those in the resource-depleted core. Using both analytical arguments and three-dimensional simulations, we find that the proliferation gradients result in flows and in gradients of activity both of which can align the orientation axis of cells inside the aggregates. Depending on environmental conditions and the intrinsic tissue properties, we identify three distinct alignment regimes: spheroids in which all the cells align either radially or tangentially to the surface throughout the aggregate and spheroids with angular cell orientation close to the surface and radial alignment in the core. The continuum description of tissue dynamics inside spheroids not only allows us to infer dynamic cell parameters from experimentally measured cell alignment profiles, but more generally motivates novel mechanisms for controlling the alignment of cells within aggregates which has been shown to influence the mechanical properties and invasive capabilities of tumors.

Activity gradients in two- and three-dimensional active nematics.

We numerically investigate how spatial variations of extensile or contractile active stress affect bulk active nematic systems in two and three dimensions. In the absence of defects, activity gradients drive flows which re-orient the nematic director field and thus act as an effective anchoring force. At high activity, defects are created and the system transitions into active turbulence, a chaotic flow state characterized by strong vorticity. We find that in two-dimensional (2D) systems active torques robustly align +1/2 defects parallel to activity gradients, with defect heads pointing towards contractile regions. In three-dimensional (3D) active nematics disclination lines preferentially lie in the plane perpendicular to activity gradients due to active torques acting on line segments. The average orientation of the defect structures in the plane perpendicular to the line tangent depends on the defect type, where wedge-like +1/2 defects align parallel to activity gradients, while twist defects are aligned anti-parallel. Understanding the response of active nematic fluids to activity gradients is an important step towards applying physical theories to biology, where spatial variations of active stress impact morphogenetic processes in developing embryos and affect flows and deformations in growing cell aggregates, such as tumours.

Coupled differentiation and division of embryonic stem cells inferred from clonal snapshots.

The deluge of single-cell data obtained by sequencing, imaging and epigenetic markers has led to an increasingly detailed description of cell state. However, it remains challenging to identify how cells transition between different states, in part because data are typically limited to snapshots in time. A prerequisite for inferring cell state transitions from such snapshots is to distinguish whether transitions are coupled to cell divisions. To address this, we present two minimal branching process models of cell division and differentiation in a well-mixed population. These models describe dynamics where differentiation and division are coupled or uncoupled. For each model, we derive analytic expressions for each subpopulation's mean and variance and for the likelihood, allowing exact Bayesian parameter inference and model selection in the idealised case of fully observed trajectories of differentiation and division events. In the case of snapshots, we present a sample path algorithm and use this to predict optimal temporal spacing of measurements for experimental design. We then apply this methodology to an in vitro dataset assaying the clonal growth of epiblast stem cells in culture conditions promoting self-renewal or differentiation. Here, the larger number of cell states necessitates approximate Bayesian computation. For both culture conditions, our inference supports the model where cell state transitions are coupled to division. For culture conditions promoting differentiation, our analysis indicates a possible shift in dynamics, with these processes becoming more coupled over time.