Probing the rules of cell coordination in live tissues by interpretable machine learning based on graph neural networks.

Robustness in developing and homeostatic tissues is supported by various types of spatiotemporal cell-to-cell interactions. Although live imaging and cell tracking are powerful in providing direct evidence of cell coordination rules, extracting and comparing these rules across many tissues with potentially different length and timescales of coordination requires a versatile framework of analysis. Here we demonstrate that graph neural network (GNN) models are suited for this purpose, by showing how they can be applied to predict cell fate in tissues and utilized to infer the cell interactions governing the multicellular dynamics. Analyzing the live mammalian epidermis data, where spatiotemporal graphs constructed from cell tracks and cell contacts are given as inputs, GNN discovers distinct neighbor cell fate coordination rules that depend on the region of the body. This approach demonstrates how the GNN framework is powerful in inferring general cell interaction rules from live data without prior knowledge of the signaling involved.

Non-monotonic fluidization generated by fluctuating edge tensions in confluent tissues.

In development and homeostasis, multi-cellular systems exhibit spatial and temporal heterogeneity in their biochemical and mechanical properties. Nevertheless, it remains unclear how spatiotemporally heterogeneous forces affect the dynamical and mechanical properties of confluent tissue. To address this question, we study the dynamical behavior of the two-dimensional cellular vertex model for epithelial monolayers in the presence of fluctuating cell-cell interfacial tensions, which is a biologically relevant source of mechanical spatiotemporal heterogeneity. In particular, we investigate the effects of the amplitude and persistence time of fluctuating tension on the tissue dynamics. We unexpectedly find that the long-time diffusion constant describing cell rearrangements depends non-monotonically on the persistence time, while it increases monotonically as the amplitude increases. Our analysis indicates that at low and intermediate persistence times tension fluctuations drive motion of vertices and promote cell rearrangements, while at the highest persistence times the tension in the network evolves so slowly that rearrangements become rare.

Tracheal motile cilia in mice require CAMSAP3 for the formation of central microtubule pair and coordinated beating.

Motile cilia of multiciliated epithelial cells undergo synchronized beating to produce fluid flow along the luminal surface of various organs. Each motile cilium consists of an axoneme and a basal body (BB), which are linked by a "transition zone" (TZ). The axoneme exhibits a characteristic 9+2 microtubule arrangement important for ciliary motion, but how this microtubule system is generated is not yet fully understood. Here we show that calmodulin-regulated spectrin-associated protein 3 (CAMSAP3), a protein that can stabilize the minus-end of a microtubule, concentrates at multiple sites of the cilium-BB complex, including the upper region of the TZ or the axonemal basal plate (BP) where the central pair of microtubules (CP) initiates. CAMSAP3 dysfunction resulted in loss of the CP and partial distortion of the BP, as well as the failure of multicilia to undergo synchronized beating. These findings suggest that CAMSAP3 plays pivotal roles in the formation or stabilization of the CP by localizing at the basal region of the axoneme and thereby supports the coordinated motion of multicilia in airway epithelial cells.

Tracing the origin of hair follicle stem cells.

Tissue stem cells are generated from a population of embryonic progenitors through organ-specific morphogenetic events1,2. Although tissue stem cells are central to organ homeostasis and regeneration, it remains unclear how they are induced during development, mainly because of the lack of markers that exclusively label prospective stem cells. Here we combine marker-independent long-term 3D live imaging and single-cell transcriptomics to capture a dynamic lineage progression and transcriptome changes in the entire epithelium of the mouse hair follicle as it develops. We found that the precursors of different epithelial lineages were aligned in a 2D concentric manner in the basal layer of the hair placode. Each concentric ring acquired unique transcriptomes and extended to form longitudinally aligned, 3D cylindrical compartments. Prospective bulge stem cells were derived from the peripheral ring of the placode basal layer, but not from suprabasal cells (as was previously suggested3). The fate of placode cells is determined by the cell position, rather than by the orientation of cell division. We also identified 13 gene clusters: the ensemble expression dynamics of these clusters drew the entire transcriptional landscape of epithelial lineage diversification, consistent with cell lineage data. Combining these findings with previous work on the development of appendages in insects4,5, we describe the 'telescope model', a generalized model for the development of ectodermal organs in which 2D concentric zones in the placode telescope out to form 3D longitudinally aligned cylindrical compartments.

Cell cycle-dependent active stress drives epithelia remodeling.

Epithelia have distinct cellular architectures which are established in development, reestablished after wounding, and maintained during tissue homeostasis despite cell turnover and mechanical perturbations. In turn, cell shape also controls tissue function as a regulator of cell differentiation, proliferation, and motility. Here, we investigate cell shape changes in a model epithelial monolayer. After the onset of confluence, cells continue to proliferate and change shape over time, eventually leading to a final architecture characterized by arrested motion and more regular cell shapes. Such monolayer remodeling is robust, with qualitatively similar evolution in cell shape and dynamics observed across disparate perturbations. Here, we quantify differences in monolayer remodeling guided by the active vertex model to identify underlying order parameters controlling epithelial architecture. When monolayers are formed atop an extracellular matrix with varied stiffness, we find the cell density at which motion arrests varies significantly, but the cell shape remains constant, consistent with the onset of tissue rigidity. In contrast, pharmacological perturbations can significantly alter the cell shape at which tissue dynamics are arrested, consistent with varied amounts of active stress within the tissue. Across all experimental conditions, the final cell shape is well correlated to the cell proliferation rate, and cell cycle inhibition immediately arrests cell motility. Finally, we demonstrate cell cycle variation in junctional tension as a source of active stress within the monolayer. Thus, the architecture and mechanics of epithelial tissue can arise from an interplay between cell mechanics and stresses arising from cell cycle dynamics.

Adherens junction regulates cryptic lamellipodia formation for epithelial cell migration.

Collective migration of epithelial cells plays crucial roles in various biological processes such as cancer invasion. In migrating epithelial sheets, leader cells form lamellipodia to advance, and follower cells also form similar motile apparatus at cell-cell boundaries, which are called cryptic lamellipodia (c-lamellipodia). Using adenocarcinoma-derived epithelial cells, we investigated how c-lamellipodia form and found that they sporadically grew from around E-cadherin-based adherens junctions (AJs). WAVE and Arp2/3 complexes were localized along the AJs, and silencing them not only interfered with c-lamellipodia formation but also prevented follower cells from trailing the leaders. Disruption of AJs by removing αE-catenin resulted in uncontrolled c-lamellipodia growth, and this was brought about by myosin II activation and the resultant contraction of AJ-associated actomyosin cables. Additional observations indicated that c-lamellipodia tended to grow at mechanically weak sites of the junction. We conclude that AJs not only tie cells together but also support c-lamellipodia formation by recruiting actin regulators, enabling epithelial cells to undergo ordered collective migration.

Reorientation behavior in the helical motility of light-responsive spiral droplets.

The physico-chemical processes supporting life's purposeful movement remain essentially unknown. Self-propelling chiral droplets offer a minimalistic model of swimming cells and, in surfactant-rich water, droplets of chiral nematic liquid crystals follow the threads of a screw. We demonstrate that the geometry of their trajectory is determined by both the number of turns in, and the handedness of, their spiral organization. Using molecular motors as photo-invertible chiral dopants allows converting between right-handed and left-handed trajectories dynamically, and droplets subjected to such an inversion reorient in a direction that is also encoded by the number of spiral turns. This motile behavior stems from dynamic transmission of chirality, from the artificial molecular motors to the liquid crystal in confinement and eventually to the helical trajectory, in analogy with the chirality-operated motion and reorientation of swimming cells and unicellular organisms.

Hydrodynamic rotlet dipole driven by spinning chiral liquid crystal droplets.

Chirality is an essential evolutionary-conserved physical aspect of swimming microorganisms. However, the role of chirality on the hydrodynamics of such microswimmers is still being elucidated. Hydrodynamic theories have so far predicted that, under a torque-free condition satisfied in the system of microswimmers, a rotlet dipole generating a twisting flow is the leading-order singularity of the chiral flow field. Nevertheless, such a chiral flow field has never been experimentally detected. Here we explore a hydrodynamic field generated in a system of a chiral microswimmer, where a droplet of a cholesteric liquid crystal (CLC) exhibits helical and spinning motions in surfactant solutions due to a chiral nonequilibrium cross coupling between the rotation and the Marangoni flow. Combining measurement of the flow field around the spinning CLC droplets and a computational flow modeling, we revealed that the CLC droplets generate a flow field of a rotlet dipole. Remarkably, we found that the chiral component of the flow field decays with distance r as r^{-3}, which is consistent with the theoretical prediction for the flow field produced by a point singularity of a rotlet dipole. Our findings will promote the understanding of roles of chirality on the hydrodynamics in active matter as well as liquid crystals.

Theoretical model of chirality-induced helical self-propulsion.

We recently reported the experimental realization of a chiral artificial microswimmer exhibiting helical self-propulsion [T. Yamamoto and M. Sano, Soft Matter 13, 3328 (2017)1744-683X10.1039/C7SM00337D]. In the experiment, cholesteric liquid crystal (CLC) droplets dispersed in surfactant solutions swam spontaneously, driven by the Marangoni flow, in helical paths whose handedness is determined by the chirality of the component molecules of CLC. To study the mechanism of the emergence of the helical self-propelled motion, we propose a phenomenological model of the self-propelled helical motion of the CLC droplets. Our model is constructed by symmetry argument in chiral systems, and it describes the dynamics of CLC droplets with coupled time-evolution equations in terms of a velocity, an angular velocity, and a tensor variable representing the symmetry of the helical director field of the droplet. We found that helical motions as well as other chiral motions appear in our model. By investigating bifurcation behaviors between each chiral motion, we found that the chiral coupling terms between the velocity and the angular velocity, the structural anisotropy of the CLC droplet, and the nonlinearity of model equations play a crucial role in the emergence of the helical motion of the CLC droplet.

Chirality-induced helical self-propulsion of cholesteric liquid crystal droplets.

We report the first experimental realization of a chiral artificial microswimmer exhibiting helical motion without any external fields. We discovered that a cholesteric liquid crystal (CLC) droplet with a helical director field swims in a helical path driven by the Marangoni flow in an aqueous surfactant solution. We also showed that the handedness of the helical path is reversed when that of the CLC droplet is reversed by replacing the chiral dopant with the enantiomer. In contrast, nematic liquid crystal (NLC) droplets exhibited ballistic motions. These results suggest that the helical motion of the CLC droplets is driven by chiral couplings between the Marangoni flow and rotational motion via the helical director field of CLC droplets.

Identification and characterization of an increased glycoprotein in aging: age-associated translocation of cathepsin D.

We found that 14 N-glycosylated proteins were accumulated in the rat cerebral cortex cytosolic fraction in the aging process by a comparative study with two-dimensional gel electrophoresis and concanavalin A staining. All proteins had high mannose and/or hybrid-type N-glycans, as indicated by the fact that they were sensitive to endoglycosidase H digestion. Three of these cytosolic glycoproteins were identified as cathepsin D, a lysosomal protease, by tryptic digestion and nano liquid chromatography electrospray ionization quadrupole time of flight mass spectrometry. The increase of cytosolic cathepsin D during aging was not due to lysosomal membrane disruption, as shown by the fact that the activities of beta-hexosaminidase and beta-glucuronidase, other lysosomal enzymes, did not increase in the cytosolic fraction. Although the total amount of cathepsin D increased during aging, the amount of cathepsin D in the microsomal fraction did not change, indicating a selective increase of cytosolic cathepsin D. This phenomenon was also observed in the hippocampus, cerebellum, kidney, liver, and spleen. Based on these results, we propose that cytosolic cathepsin D is a new biomarker of aging.