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Plikus, M. V.

Publications and source records attributed to Plikus, M. V..

9 recordsLinked to original sources

Study of Principles Governing Epithelial Cell Clustering and Collective Motion In Vitro

In epithelial wounds, physically enlarged cells emerge along injury edges where they interact with regular-size cells during collective migration to repair tissue continuity. Although such large cells are often interpreted as migration leaders, recent observations suggest that regular-size cells can reciprocally influence them and that mixed-size cell clusters engage in distinct rotational motion before merging into confluent sheets. How cell size, polarity and adhesive coupling jointly control distinct collective migration modes remains unclear. Because many features of collective epithelial migration, including large and regular-size cell phenotypes, are conserved between in vivo and in vitro systems, here we developed a multi-scale computational model of interacting epithelial cells in two-dimensional culture with dynamic cell-substrate adhesion, cell-cell interactions, protrusion-based polarity, and contact-induced myosin redistribution as polarity regulator. We also explicitly modeled two functionally distinct cell states, featuring regular and large sizes respectively. Simulations showed that symmetric and asymmetric myosin redistribution at cell-cell junctions can produce stable cell contacts and persistent rotational motions by cell doublets. Intriguingly, in mixed-size cell clusters, straight translation can arise both from leader-like large cell and regular-size cell-mediated motion, whereas rotation emerges when large-cell-generated torque overcomes translation while cell-cell adhesion is maintained. Thus, collective migration mode depends on the balance among myosin-driven torque, regular-size cell-mediated translation, substrate coupling, and cell-cell adhesion. These modeling results suggest that collective epithelial migration can emerge in vitro from reciprocal biomechanical interactions between distinct cell states, rather than from leader-like cell behavior alone, and that such interactions can produce a predator-prey-like pursuit-escape mode of collective migration. Our model also provides a framework for investigating the biochemical and biomechanical regulation of collective cellular migration. It can be readily extended from in vitro to in vivo context and can incorporate the effects of substrate topology and soluble signaling factor-driven chemotaxis. Author summaryWhen epithelial cells repair a wound, they move as coordinated groups rather than as isolated individuals. Cells of different sizes may contribute in distinct but connected ways. We developed a computational model to examine how a large cell and neighboring regular-size cells move together. In the model, cells attach to the underlying surface and one another, form protrusions that set their direction, and redistribute the force-generating protein myosin after contact. We found that group motion depends on a balance among surface attachment, cell-cell adhesion, movement of regular-size cells toward the large cell, and myosin-driven turning of the large cell. Depending on this balance, a mixed-size cluster can travel along a nearly straight path or rotate persistently, exhibiting pursuit-and-escape-like interactions between the large cell and surrounding regular-size cells. Rotation occurs when the large cells turning effect outweighs the translational motion driven by regular-size cells, while cell-cell adhesion keeps the cluster together. Our results show that collective migration can emerge from reciprocal mechanical interactions between cells in different states, not only from a "leader" cell acting alone. The model also provides experimentally testable predictions for how cell size, adhesion, and internal myosin distribution shape cell cluster movement.

cell biology↗

A scRNA-seq atlas of chronic inflammatory skin diseases

Inflammatory skin diseases (ISDs) affect up to 25% of the global population. Yet, large-scale comparative single-cell RNA-sequencing (scRNA-seq) analyses between ISDs are still missing. Here, we integrated scRNA-seq datasets spanning 27 skin diseases from 50 studies, comprising over 2 million cells from 441 samples. Using the healthy skin cell atlas as reference, we could build a robust ISD atlas that enabled us to differentiate universal inflammatory signatures and disease-specific ones. This highlighted, for example, a shared gene program between keratinocytes in atopic dermatitis and parapsoriasis, not present in cutaneous T-cell lymphoma, confirms the plasticity of Th17 cells throughout ISDs, defines specific macrophage signatures in acne, and reveals a yet undescribed role of mural cells in ISDs. This demonstrates the power of the ISD atlas as a resource to resolve disease-specific immune mechanisms. The complete atlas is available through an interactive online portal at https://isd-atlas.derma.meduniwien.ac.at.

immunology↗

CellChat for systematic analysis of cell-cell communication from single-cell and spatially resolved transcriptomics

Recent advances in single-cell sequencing technologies offer an opportunity to explore cell-cell communication in tissues systematically and with reduced bias. A key challenge is the integration between known molecular interactions and measurements into a framework to identify and analyze complex cell-cell communication networks. Previously, we developed a computational tool, named CellChat that infers and analyzes cell-cell communication networks from single-cell RNA-sequencing (scRNA-seq) data within an easily interpretable framework. CellChat quantifies the signaling communication probability between two cell groups using a simplified mass action-based model, which incorporates the core interaction between ligands and receptors with multi-subunit structure along with modulation by cofactors. CellChat v2 is an updated version that includes direct incorporation of spatial locations of cells, if available, to infer spatially proximal cell-cell communication, additional comparison functionalities, expanded database of ligand-receptor pairs along with rich annotations, and an Interactive CellChat Explorer. Here we provide a step-by-step protocol for using CellChat v2 that can be used for both scRNA-seq and spatially resolved transcriptomic data, including inference and analysis of cell-cell communication from one dataset and identification of altered signaling across different datasets. The key steps of applying CellChat v2 to spatially resolved transcriptomics are described in detail. The R implementation of CellChat v2 toolkit and tutorials with the graphic outputs are available at https://github.com/jinworks/CellChat. This protocol typically takes around 20 minutes, and no specialized prior bioinformatics training is required to complete the task.

bioinformatics↗

Convergent deployment of ancestral programs during the evolution of mammalian flight membranes

Lateral flight membranes, or patagia, have evolved repeatedly in diverse mammalian lineages. While little is known about patagium development, its recurrent evolution may suggest a shared molecular basis. By combining transcriptomics, developmental experiments, and mouse transgenics, we demonstrate that lateral WNT5A expression in the marsupial sugar glider (Petaurus breviceps) promotes the differentiation of its patagium primordium. We further show that this function of WNT5A reprises ancestral roles in skin morphogenesis predating mammalian flight and has been convergently employed during patagium evolution in eutherian bats. Moreover, we find that many genes involved in limb development have been re-deployed during patagium outgrowth in both the sugar glider and bat. Taken together, our findings reveal that deeply conserved molecular toolkits underpin the evolutionary transition to flight in mammals.

developmental biology↗

Genomic and anatomical comparisons of skin support independent adaptation to life in water by cetaceans and hippos

The macroevolutionary transition from terra firma to obligatory inhabitance of the marine hydrosphere has occurred twice in the history of Mammalia: Cetacea and Sirenia. In the case of Cetacea (whales, dolphins, porpoises), molecular phylogenies provide unambiguous evidence that fully aquatic cetaceans and semiaquatic hippopotamids (hippos) are each others closest living relatives. Ancestral reconstructions further suggest that some adaptations to the aquatic realm evolved in the common ancestor of Cetancodonta (Cetacea+Hippopotamidae). An alternative hypothesis is that these adaptations evolved independently in cetaceans and hippos. Here, we focus on the integumentary system and evaluate these hypotheses by integrating new histological data for cetaceans and hippos, the first genome-scale data for pygmy hippopotamus, and comprehensive genomic screens and molecular evolutionary analyses for protein-coding genes that have been inactivated in hippos and cetaceans. We identified ten skin-related genes that are inactivated in both cetaceans and hippos, including genes that are related to sebaceous glands, hair follicles, and epidermal differentiation. However, none of these genes exhibit inactivating mutations that are shared by cetaceans and hippos. Mean dates for the inactivation of skin genes in these two clades serve as proxies for phenotypic changes and suggest that hair reduction/loss, the loss of sebaceous glands, and changes to the keratinization program occurred ~16 million years earlier in cetaceans (~46.5 Ma) than in hippos (~30.5 Ma). These results, together with histological differences in the integument and prior analyses of oxygen isotopes from stem hippopotamids ("anthracotheres"), support the hypothesis that aquatic adaptations evolved independently in hippos and cetaceans.

evolutionary biology↗

Inference and analysis of cell-cell communication using CellChat

Understanding global communications among cells requires accurate representation of cell-cell signaling links and effective systems-level analyses of those links. We constructed a database of interactions among ligands, receptors and their cofactors that accurately represents known heteromeric molecular complexes. Based on mass action models, we then developed CellChat, a tool that is able to quantitively infer and analyze intercellular communication networks from single-cell RNA-sequencing (scRNA-seq) data. CellChat predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Through manifold learning and quantitative contrasts, CellChat classifies signaling pathways and delineates conserved and context-specific pathways across different datasets. Applications of CellChat to several mouse skin scRNA-seq datasets for embryonic development and adult wound healing shows its ability to extract complex signaling patterns, both previously known as well as novel. Our versatile and easy-to-use toolkit CellChat and a web-based Explorer (http://www.cellchat.org/) will help discover novel intercellular communications and build a cell-cell communication atlas in diverse tissues.

bioinformatics↗

Activating an adaptive immune response from a hydrogel scaffold imparts regenerative wound healing.

Biomaterial scaffolds represent a promising approach for material-based tissue regeneration. We previously developed microporous annealed particle (MAP) hydrogels - a flowable, microparticle-based hydrogel in which neighboring hydrogel particles are linked in situ to form a porous scaffold that accelerates wound healing. To promote more extensive tissue ingrowth before scaffold degradation, we aimed to slow scaffold degradation by switching the chirality of the crosslinking peptides from L-peptides to D-peptides. Unexpectedly, despite showing the predicted slower enzymatic degradation in vitro, D-peptide crosslinked MAP hydrogel (D-MAP) hastened material degradation in vivo and imparted significant tissue regeneration to healed cutaneous wounds, including increased tensile strength and hair neogenesis. By themselves, D-chiral peptides were poor activators of macrophage innate immune signaling in vivo, but MAP particles elicit IL-33 type 2 myeloid cell recruitment which is amplified in vivo in the presence of D-peptides. Remarkably, D-MAP elicited significant antigen-specific immunity against the D-chiral peptides, and an intact adaptive immune system was required for the hydrogel-induced skin regeneration. These findings demonstrate that the generation of an adaptive immune response from a biomaterial is sufficient to induce cutaneous regenerative healing despite faster scaffold degradation.

bioengineering↗

Rapidly cycling stem cells regenerate the intestine independent of Lgr5high cells

The +4 cells in intestinal crypts are DNA damage-resistant and contribute to regeneration. However, their exact identity and the mechanism underlying +4 cell-mediated regeneration remain unclear. Using lineage tracing, we show that cells marked by an Msi1 reporter (Msi1+) are enriched at the +4 position in intestinal crypts and exhibit DNA damage resistance. Single-cell RNA sequencing reveals that the Msi1+ cells are heterogeneous with the majority being intestinal stem cells (ISCs). The DNA damage-resistant subpopulation of Msi1+ cells is characterized by low-to-negative Lgr5 expression and is more rapidly cycling than Lgr5high radio-sensitive crypt base columnar stem cells (CBCs); they enable fast repopulation of the intestinal epithelium independent of CBCs that are largely depleted after irradiation. Furthermore, relative to CBCs, Msi1+ cells preferentially produce Paneth cells during homeostasis and upon radiation repair. Together, we demonstrate that the DNA damage-resistant Msi1+ cells are rapidly cycling ISCs that maintain and regenerate the intestinal epithelium.

cell biology↗

Stromal ISLR promotes intestinal regeneration and cancer by suppressing epithelial Hippo signaling

The YAP signaling activation in epithelial cells is essential for intestinal regeneration and tumorigenesis. However, the molecular mechanism linking stromal signals to YAP-mediated intestinal regeneration and tumorigenesis is poorly defined. Here we report a stroma-epithelia YAP signaling axis essential for stromal cells to modulate epithelial cell growth during intestinal regeneration and tumorigenesis. Specifically, upon inflammation and in cancer, an oncogenic transcription factor ETS1 in stromal cells induces expression of a secreted protein ISLR that can directly binds to a transmembrane protocadherin FAT1 on the surface of epithelial cells. This binding suppressed the Hippo signaling by disrupting MST1-FAT1 association, resulting in YAP signaling activation. Deletion of Islr in stromal cells in mice markedly impaired intestinal regeneration, and suppressed tumorigenesis in the colon. Moreover, the expression of stromal cell-specific ISLR and ETS1 significantly increased in inflamed mucosa of human IBD patients and in human colorectal adenocarcinoma, accounting for the epithelial YAP hyperactivation. Collectively, our findings uncovered a molecular mechanism governing signals for communication between stroma and epithelium during tissue regeneration and tumorigenesis.

cancer biology↗