A machine learning approach for generating temporal logic classifications of complex model behaviours

How growth cones detect small concentration differences of guidance cues for correct steering remains a long-standing puzzle. Commissural axons engage planar cell polarity (PCP) signaling components to turn anteriorly in a Wnt gradient after midline crossing. We found here that Frizzled3, a Wnt receptor, undergoes endocytosis via filopodia tips. Wnt5a increases Frizzled3 endocytosis, which correlates with filopodia elongation. We discovered an unexpected antagonism between Dishevelleds, which may function as a signal amplification mechanism in filopodia where PCP signaling is activated: Dishevelled2 blocks Dishevelled1-induced Frizzled3 hyperphosphorylation and membrane accumulation. A key component of apical-basal polarity (A-BP) signaling, aPKC, also inhibits Dishevelled1-induced Frizzled3 hyperphosphorylation. Celsr3, another PCP component, is required in commissural neurons for anterior turning. Frizzled3 hyperphosphorylation is increased in Celsr3 mutant mice, where PCP signaling is impaired, suggesting Frizzled3 hyperphosphorylation does correlate with loss of PCP signaling in vivo. Furthermore, we found that the small GTPase, Arf6, which is required for Frizzled3 endocytosis, is essential for Wnt-promoted outgrowth, highlighting the importance of Frizzled3 recycling in PCP signaling in growth cone guidance. In a Wnt5a gradient, more Frizzled3 endocytosis and activation of atypical protein kinase C was observed on the side of growth cones facing higher Wnt5a concentration, suggesting that spatially controlled Frizzled3 endocytosis is part of the key mechanism for growth cone steering.

During vertebrate gastrulation, convergence and extension (C and E) of the primary anteroposterior (AP) embryonic axis is driven by polarized mediolateral (ML) cell intercalations and is influenced by AP axial patterning. Nodal signaling is essential for patterning of the AP axis while planar cell polarity (PCP) signaling polarizes cells with respect to this axis, but how these two signaling systems interact during C and E is unclear. We find that the neuroectoderm of Nodal-deficient zebrafish gastrulae exhibits reduced C and E cell behaviors, which require Nodal signaling in both cell- and non-autonomous fashions. PCP signaling is partially active in Nodal-deficient embryos and its inhibition exacerbates their C and E defects. Within otherwise naïve zebrafish blastoderm explants, however, Nodal induces C and E in a largely PCP-dependent manner, arguing that Nodal acts both upstream of and in parallel with PCP during gastrulation to regulate embryonic axis extension cooperatively.

During vertebrate gastrulation, convergence and extension (C and E) of the primary anteroposterior (AP) embryonic axis is driven by polarized mediolateral (ML) cell intercalations and is influenced by AP axial patterning. Nodal signaling is essential for patterning of the AP axis while planar cell polarity (PCP) signaling polarizes cells with respect to this axis, but how these two signaling systems interact during C and E is unclear. We find that the neuroectoderm of Nodal-deficient zebrafish gastrulae exhibits reduced C and E cell behaviors, which require Nodal signaling in both cell- and non-autonomous fashions. PCP signaling is partially active in Nodal-deficient embryos and its inhibition exacerbates their C and E defects. Within otherwise naïve zebrafish blastoderm explants, however, Nodal induces C and E in a largely PCP-dependent manner, arguing that Nodal acts both upstream of and in parallel with PCP during gastrulation to regulate embryonic axis extension cooperatively.

The anterior visceral endoderm (AVE), a signalling centre within the simple epithelium of the visceral endoderm (VE), is required for anterior-posterior axis specification in the mouse embryo. AVE cells migrate directionally within the VE, thereby properly positioning the future anterior of the embryo and orientating the primary body axis. AVE cells consistently come to an abrupt stop at the border between the anterior epiblast and extra-embryonic ectoderm, which represents an end-point to their proximal migration. Little is known about the underlying basis for this barrier and how surrounding cells in the VE respond to or influence AVE migration. We use high-resolution 3D reconstructions of protein localisation patterns and time-lapse microscopy to show that AVE cells move by exchanging neighbours within an intact epithelium. Cell movement and mixing is restricted to the VE overlying the epiblast, characterised by the enrichment of Dishevelled-2 (Dvl2) to the lateral plasma membrane, a hallmark of Planar Cell Polarity (PCP) signalling. AVE cells halt upon reaching the adjoining region of VE overlying the extra-embryonic ectoderm, which displays reduced neighbour exchange and in which Dvl2 is excluded specifically from the plasma membrane. Though a single continuous sheet, these two regions of VE show distinct patterns of F-actin localisation, in cortical rings and an apical shroud, respectively. We genetically perturb PCP signalling and show that this disrupts the localisation pattern of Dvl2 and F-actin and the normal migration of AVE cells. In Nodal null embryos, membrane localisation of Dvl2 is reduced, while in mutants for the Nodal inhibitor Lefty1, Dvl2 is ectopically membrane localised, establishing a role for Nodal in modulating PCP signalling. These results show that the limits of AVE migration are determined by regional differences in cell behaviour and protein localisation within an otherwise apparently uniform VE. In addition to coordinating global cell movements across epithelia (such as during convergence extension), PCP signalling in interplay with TGFβ signalling can demarcate regions of differing behaviour within epithelia, thereby modulating the movement of cells within them.

Propulsion of contaminants out of the lungs by coordinated action of motile cilia is essential for airway function. Multiciliated airway epithelial cells undergoing ciliogenesis generate hundreds of basal bodies that traffic to the surface, elongate motile axonemes and align with the tissue axis for coordinated motility. The mechanisms of cilia polarization remain poorly explored. We showed that a conserved set of planar cell polarity (PCP) proteins polarize airway epithelial cilia: PCP proteins localize asymmetrically to the cell cortex, revealing that PCP signaling starts before ciliogenesis; in PCP mutant epithelia, molecular and morphological polarity are disrupted; and PCP mutants display defective airway clearance, highlighting the requirement for ciliary alignment. Studying the cytoskeleton, a target of PCP signaling, we uncovered two temporally-distinct, cell type-specific, planar polarized microtubule (MT) networks. Prior to ciliogenesis, MTs are necessary in all cells for PCP protein asymmetry. Subsequently, after basal bodies dock, MTs are observed to contact the polarized appendages of basal bodies, and PCP-regulated, ciliated cell-specific MTs, stably anchored by their plus ends to the proximal cortex, are required for basal body distribution and alignment. Our evidence suggests that MTs have two separable PCP functions: MTs are first required in every cell for trafficking PCP proteins to the cortex, and later they interact with and directly align cilia. Our studies reveal strong conservation of PCP mechanisms initially described in Drosophila, and cilia alignment by PCP-oriented MTs provides the first mechanistic description of how asymmetric PCP proteins at the cortex orient cilia along the cell surface.

Composition of software artifacts modelled using Colored Petri nets

Planar cell polarity (PCP) describes the orientation of a cell within the plane of an epithelial cell layer. During tissue development, epithelial cells normally align their PCP so that they face in the same direction. This alignment allows cells to move in a common direction, or to generate structures with a common orientation. A classic system for studying the coordination of epithelial PCP is the developing Drosophila wing. The alignment of epithelial PCP during pupal wing development allows the production of an array of cell hairs that point towards the wing tip. Multiple studies have established that the Frizzled (Fz) PCP signaling pathway coordinates wing PCP. Recently, we have found that the same pathway also controls the formation of ridges on the Drosophila wing membrane. However, in contrast to hair polarity, ridge orientation differs between the anterior and posterior wing. How can the Fz PCP pathway generate a different relationship between hair and ridge orientation in different parts of the wing? In this Extra View article, we discuss membrane ridge development drawing upon our recent PLoS Genetics paper and other, published and unpublished, data. We also speculate upon how our findings impact the ongoing debate concerning the interaction of the Fz PCP and Fat/Dachsous pathways in the control of PCP.

Convergent extension movements occur ubiquitously in animal development. This special type of cell movement is controlled by the Wnt/planar cell polarity (PCP) pathway. Here we show that Xenopus paraxial protocadherin (XPAPC) functionally interacts with the Wnt/PCP pathway in the control of convergence and extension (CE) movements in Xenopus laevis. XPAPC functions as a signalling molecule that coordinates cell polarity of the involuting mesoderm in mediolateral orientation and thus selectively promotes convergence in CE movements. XPAPC signals through the small GTPases Rho A and Rac 1 and c-jun N-terminal kinase (JNK). Loss of XPAPC function blocks Rho A-mediated JNK activation. Despite common downstream components, XPAPC and Wnt/PCP signalling are not redundant, and the activity of both, XPAPC and PCP signalling, is required to coordinate CE movements.

In addition to the ubiquitous apical-basal polarity, epithelial cells are often polarized within the plane of the tissue – the phenomenon known as planar cell polarity (PCP). In Drosophila, manifestations of PCP are visible in the eye, wing, and cuticle. Several components of the PCP signaling have been characterized in flies and vertebrates, including the heterotrimeric Go protein. However, Go signaling partners in PCP remain largely unknown. Using a genetic screen we uncover Kermit, previously implicated in G protein and PCP signaling, as a novel binding partner of Go. Through pull-down and genetic interaction studies, we find that Kermit interacts with Go and another PCP component Vang, known to undergo intracellular relocalization during PCP establishment. We further demonstrate that the activity of Kermit in PCP differentially relies on the motor proteins: the microtubule-based dynein and kinesin motors and the actin-based myosin VI. Our results place Kermit as a potential transducer of Go, linking Vang with motor proteins for its delivery to dedicated cellular compartments during PCP establishment.

Blastocyst implantation is a complex process requiring coordination of a dynamic sequence of embryo-uterine interactions. Blood vessels enter the uterus from the mesometrium, demarcating the uterus into mesometrial (M) and antimesometrial (AM) domains. Implantation occurs along the uterine longitudinal axis within specialized implantation chambers (crypts) that originate within the evaginations directed from the primary lumen toward the AM domain. The morphological orientation of crypts in rodent uteri was recognized more than a century ago, but the mechanism remained unknown. Here we provide evidence that planar cell polarity (PCP) signaling orchestrates directed epithelial evaginations to form crypts for implantation in mice. Uterine deletion of Vang-like protein 2, but not Vang-like protein 1, conferred aberrant PCP signaling, misdirected epithelial evaginations, defective crypt formation, and blastocyst attachment, leading to severely compromised pregnancy outcomes. The study reveals a previously unrecognized role for PCP in executing spatial cues for crypt formation and implantation. Because PCP is an evolutionarily conserved phenomenon, our study is likely to inspire implantation studies of this signaling pathway in humans and other species.

In planar cell polarity (PCP) signaling, distinct molecular subcomplexes segregate to opposite sides of each cell, where they interact across intercellular junctions to form asymmetric clusters. Although proximal-distal asymmetry within PCP clusters is the defining feature of PCP signaling, the mechanism by which this asymmetry develops remains unclear. Here, we developed a method to count the number of monomers of core PCP proteins within individual clusters in live animals and used it to infer the underlying molecular dynamics of cluster assembly and polarization. Measurements over time and space in wild type and in strategically chosen mutants demonstrate that cluster assembly is required for polarization, and together with mathematical modeling provide evidence that clusters become increasingly asymmetric and correctly oriented as they increase in size. We propose that cluster assembly dynamics amplify weak and noisy inputs into a robust cellular output, in this case cell and tissue-level polarization.

It was recently suggested that a proximal to distal gradient of the protocadherin Dachsous (Ds) acts as a cue for planar cell polarity (PCP) in the Drosophila wing, orienting cell-cell interactions by inhibiting the activity of the protocadherin Fat (Ft). This Ft-Ds signaling model is based on mutant loss-of-function phenotypes, leaving open the question of whether Ds is instructive or permissive for PCP. We developed tools for misexpressing ds and ft in vitro and in vivo, and have used these to test aspects of the model. First, this model predicts that Ds and Ft can bind. We show that Ft and Ds mediate preferentially heterophilic cell adhesion in vitro, and that each stabilizes the other on the cell surface. Second, the model predicts that artificial gradients of Ds are sufficient to reorient PCP in the wing; our data confirms this prediction. Finally, loss-of-function phenotypes suggest that the gradient of ds expression is necessary for correct PCP throughout the wing. Surprisingly, this is not the case. Uniform levels of ds drive normally oriented PCP and, in all but the most proximal regions of the wing, uniform ds rescues the ds mutant PCP phenotype. Nor are distal PCP defects increased by the loss of spatial information from the distally expressed four-jointed (fj) gene, which encodes putative modulator of Ft-Ds signaling. Thus, while our results support the existence of Ft-Ds binding and show that it is sufficient to alter PCP, ds expression is permissive or redundant with other PCP cues in much of the wing.

Disheveled mediated planar cell polarity signaling is required in the second heart field lineage for outflow tract morphogenesis

Epithelial planar cell polarity (PCP) is evident in the cellular organization of many tissues in vertebrates and invertebrates. In mammals, PCP signalling governs convergent extension during gastrulation and the organization of a wide variety of structures, including the orientation of body hair and sensory hair cells of the inner ear. In Drosophila melanogaster, PCP is manifest in adult tissues, including ommatidial arrangement in the compound eye and hair orientation in wing cells. PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Mutations in PCP-pathway-associated genes cause aberrant orientation of body hair or inner-ear sensory cells in mice, or misorientation of ommatidia and wing hair in D. melanogaster. Here we provide mechanistic insight into Frizzled/Dishevelled signalling regulation. We show that the ankyrin-repeat protein Diego binds directly to Dishevelled and promotes Frizzled signalling. Dishevelled can also be bound by the Frizzled PCP antagonist Prickle. Strikingly, Diego and Prickle compete with one another for Dishevelled binding, thereby modulating Frizzled/Dishevelled activity and ensuring tight control over Frizzled PCP signalling.

Wnt proteins are secreted glycoproteins regulating biological processes in cell migration and tissue patterning during embryogenesis via highly conserved signaling pathways and are often deregulated in tumor progression and metastasis. Dishevelled is a crucial signal transduction protein at the branching point between the distinct pathways, governing the pathways through its different domains. Pukrop et al. have shown that noncanonical Wnt 5a enhances invasiveness of the breast cancer cell line MCF-7. While the canonical Wnt/β-catenin-signaling pathway is a necessary prerequisite it seems that the noncanonical planar cell polarity (PCP) signaling pathway exerts the active part. Building on these results I further investigated the invasiveness of MCF-7 cell clones and compared clones either overexpressing a Dishevelled wild type construct (DVL wt) or a Dishevelled construct with a knockout for the PCP signaling domains PDZ and DEP (DVL Δ PDZ Δ DEP). According to our hypothesis the PCP pathway in DVL Δ PDZ Δ DEP should be blocked thereby resulting in an inhibition of Wnt 5a-enhanced invasiness. Intriguingly both cell clones showed increased invasiveness following Wnt 5a stimulation. Immunofluorescence staining revealed distinct subcellular distribution patterns of the constructs: While the localization of DVL wt was consistent with the homogenous, mainly membrane-bound distribution pattern of endogenous Dishevelled; DVL Δ PDZ Δ DEP accumulated in a peri- and intranuclear fashion. Staining of further constructs with different combinations of domains showed an association of the distribution pattern depending on the presence of the DEP domain. Constructs lacking DEP showed the same para- and intranuclear distribution pattern as seen with DVL Δ PDZ Δ DEP. Hence membrane-binding of DVL Δ PDZ Δ DEP being necessary for Wnt 5a-induced signaling transduction could not take place. Regarding its impaired membrane recruitment it can therefore be concluded that DVL Δ PDZ Δ DEP could not function as a competitive antagonist to endogenous Dishevelled. Further testing showed that Wnt 5a-induced enhanced invasiveness was most likely achieved by endogenous Disheveled still expressed in the clones. This presumption is supported by the fact that the clone containing DVL Δ PDZ Δ DEP had a similarly increased invasiveness in comparison to normal MCF-7. In conclusion the DEP domain of Dishevelled is an essential prerequisite for membrane-binding thus ensuring a Wnt-induced signal transduction.