1
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Fujiwara H. Dynamic duo: Cell-extracellular matrix interactions in hair follicle development and regeneration. Dev Biol 2024; 516:20-34. [PMID: 39059679 DOI: 10.1016/j.ydbio.2024.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 06/20/2024] [Accepted: 07/23/2024] [Indexed: 07/28/2024]
Abstract
Ectodermal organs, such as hair follicles, originate from simple epithelial and mesenchymal sheets through a complex developmental process driven by interactions between these cell types. This process involves dermal condensation, placode formation, bud morphogenesis, and organogenesis, and all of these processes require intricate interactions among various tissues. Recent research has emphasized the crucial role of reciprocal and dynamic interactions between cells and the extracellular matrix (ECM), referred to as the "dynamic duo", in the development of ectodermal organs. These interactions provide spatially and temporally changing biophysical and biochemical cues within tissues. Using the hair follicle as an example, this review highlights two types of cell-ECM adhesion units-focal adhesion-type and hemidesmosome-type adhesion units-that facilitate communication between epithelial and mesenchymal cells. This review further explores how these adhesion units, along with other cell-ECM interactions, evolve during hair follicle development and regeneration, underscoring their importance in guiding both developmental and regenerative processes.
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2
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Almet AA, Tsai YC, Watanabe M, Nie Q. Inferring pattern-driving intercellular flows from single-cell and spatial transcriptomics. Nat Methods 2024; 21:1806-1817. [PMID: 39187683 PMCID: PMC11466815 DOI: 10.1038/s41592-024-02380-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 07/23/2024] [Indexed: 08/28/2024]
Abstract
From single-cell RNA-sequencing (scRNA-seq) and spatial transcriptomics (ST), one can extract high-dimensional gene expression patterns that can be described by intercellular communication networks or decoupled gene modules. These two descriptions of information flow are often assumed to occur independently. However, intercellular communication drives directed flows of information that are mediated by intracellular gene modules, in turn triggering outflows of other signals. Methodologies to describe such intercellular flows are lacking. We present FlowSig, a method that infers communication-driven intercellular flows from scRNA-seq or ST data using graphical causal modeling and conditional independence. We benchmark FlowSig using newly generated experimental cortical organoid data and synthetic data generated from mathematical modeling. We demonstrate FlowSig's utility by applying it to various studies, showing that FlowSig can capture stimulation-induced changes to paracrine signaling in pancreatic islets, demonstrate shifts in intercellular flows due to increasing COVID-19 severity and reconstruct morphogen-driven activator-inhibitor patterns in mouse embryogenesis.
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Affiliation(s)
- Axel A Almet
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
| | - Yuan-Chen Tsai
- Department of Anatomy & Neurobiology, University of California, Irvine, Irvine, CA, USA
- Sue & Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA
- School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Momoko Watanabe
- Department of Anatomy & Neurobiology, University of California, Irvine, Irvine, CA, USA
- Sue & Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA
- School of Medicine, University of California, Irvine, Irvine, CA, USA
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA.
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA.
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA.
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3
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Paul S, Adetunji J, Hong T. Widespread biochemical reaction networks enable Turing patterns without imposed feedback. Nat Commun 2024; 15:8380. [PMID: 39333132 PMCID: PMC11436923 DOI: 10.1038/s41467-024-52591-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 09/11/2024] [Indexed: 09/29/2024] Open
Abstract
Understanding self-organized pattern formation is fundamental to biology. In 1952, Alan Turing proposed a pattern-enabling mechanism in reaction-diffusion systems containing chemical species later conceptualized as activators and inhibitors that are involved in feedback loops. However, identifying pattern-enabling regulatory systems with the concept of feedback loops has been a long-standing challenge. To date, very few pattern-enabling circuits have been discovered experimentally. This is in stark contrast to ubiquitous periodic patterns and symmetry in biology. In this work, we systematically study Turing patterns in 23 elementary biochemical networks without assigning any activator or inhibitor. These mass action models describe post-synthesis interactions applicable to most proteins and RNAs in multicellular organisms. Strikingly, we find ten simple reaction networks capable of generating Turing patterns. While these network models are consistent with Turing's theory mathematically, there is no apparent connection between them and commonly used activator-feedback intuition. Instead, we identify a unifying network motif that enables Turing patterns via regulated degradation pathways with flexible diffusion rate constants of individual molecules. Our work reveals widespread biochemical systems for pattern formation, and it provides an alternative approach to tackle the challenge of identifying pattern-enabling biological systems.
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Affiliation(s)
- Shibashis Paul
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, Knoxville, TN, 37916, USA
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, 75080, USA
| | - Joy Adetunji
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee, Knoxville, Knoxville, TN, 37916, USA
| | - Tian Hong
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, 75080, USA.
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4
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Desmarquet-Trin Dinh C, Manceau M. Structure, function and formation of the amniote skin pattern. Dev Biol 2024; 517:203-216. [PMID: 39326486 DOI: 10.1016/j.ydbio.2024.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 09/10/2024] [Accepted: 09/23/2024] [Indexed: 09/28/2024]
Abstract
From feather and hair dotted arrays to pigmented stripes and spots, the spatial distribution of skin appendages and colouration often forms visible ornaments crucial for fitness in the coat of birds and mammals. These geometrical motifs are extremely diverse in nature. Yet, phenotypic surveys evidenced common themes in variation: the orientation, appendage-specificity or pigmentation of a given region may be conserved across groups or species. Here, we review naturalist observations of natural variation in the anatomy and ecological function of the skin pattern in amniotes. We then describe several decades of genetics, mathematical modelling and experimental embryology work aiming at understanding the molecular and morphogenetic mechanisms responsible for pattern formation. We discuss how these studies provided evidence that the morphological trends and differences representative of the phenotypic landscape of skin patterns in wild amniote species is rooted in the mechanisms controlling the production of distinct compartments in the embryonic skin.
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Affiliation(s)
| | - Marie Manceau
- Centre for Interdisciplinary Research in Biology, Collège de France, Université PSL, CNRS, INSERM, France.
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5
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Lee SH, Platt S, Lim CH, Ito M, Myung P. The development of hair follicles and nail. Dev Biol 2024; 513:3-11. [PMID: 38759942 DOI: 10.1016/j.ydbio.2024.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 05/06/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024]
Abstract
The hair follicle and nail unit develop and regenerate through epithelial-mesenchymal interactions. Here, we review some of the key signals and molecular interactions that regulate mammalian hair follicle and nail formation during embryonic development and how these interactions are reutilized to promote their regeneration during adult homeostasis and in response to skin wounding. Finally, we highlight the role of some of these signals in mediating human hair follicle and nail conditions.
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Affiliation(s)
- Soung-Hoon Lee
- The Ronald O. Perelman Department of Dermatology and Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Sarah Platt
- Department of Dermatology, Yale School of Medicine, New Haven, CT, USA
| | - Chae Ho Lim
- The Ronald O. Perelman Department of Dermatology and Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Mayumi Ito
- The Ronald O. Perelman Department of Dermatology and Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Peggy Myung
- Department of Dermatology, Yale School of Medicine, New Haven, CT, USA; Department of Pathology, Yale School of Medicine, New Haven, CT, USA.
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6
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Drake PM, Franz-Odendaal TA. Hydrocortisone treatment as a tool to study conjunctival placode induction. Dev Dyn 2024. [PMID: 39096180 DOI: 10.1002/dvdy.729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 06/27/2024] [Accepted: 07/10/2024] [Indexed: 08/05/2024] Open
Abstract
BACKGROUND Conjunctival placodes are a series of placodes that develop into the conjunctival (scleral) papillae and ultimately induce a series of scleral ossicles in the eyes of many vertebrates. This study establishes a hydrocortisone injection procedure (incl. dosage) that consistently inhibits all conjunctival papillae in the embryonic chicken eye. The effects of this hydrocortisone treatment on apoptosis, vasculature, and placode-related gene expression were assessed. RESULTS Hydrocortisone treatment does not increase apoptotic cell death or have a major effect on the ciliary artery or vascular plexus in the eye. β-catenin and Eda expression levels were not significantly altered following hydrocortisone treatment, despite the absence of conjunctival papillae. Notably, Fgf20 expression was significantly reduced following hydrocortisone treatment, and the distribution of β-catenin was altered. CONCLUSIONS Our study showed that conjunctival papillae induction begins as early as HH27.5 (E5.5). Hydrocortisone treatment reduces Fgf20 expression independently of β-catenin and Eda and may instead affect other members of the Wnt/β-catenin or Eda/Edar pathways, or it may affect the ability of morphogens to diffuse through the extracellular matrix. This study contributes to a growing profile of gene expression data during placode development and enhances our understanding of how some vertebrate eyes develop these fascinating bones.
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Affiliation(s)
- Paige M Drake
- Department of Medical Neuroscience, Dalhousie University, Halifax, Nova Scotia, Canada
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7
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Mao Y, Wickström SA. Mechanical state transitions in the regulation of tissue form and function. Nat Rev Mol Cell Biol 2024; 25:654-670. [PMID: 38600372 DOI: 10.1038/s41580-024-00719-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2024] [Indexed: 04/12/2024]
Abstract
From embryonic development, postnatal growth and adult homeostasis to reparative and disease states, cells and tissues undergo constant changes in genome activity, cell fate, proliferation, movement, metabolism and growth. Importantly, these biological state transitions are coupled to changes in the mechanical and material properties of cells and tissues, termed mechanical state transitions. These mechanical states share features with physical states of matter, liquids and solids. Tissues can switch between mechanical states by changing behavioural dynamics or connectivity between cells. Conversely, these changes in tissue mechanical properties are known to control cell and tissue function, most importantly the ability of cells to move or tissues to deform. Thus, tissue mechanical state transitions are implicated in transmitting information across biological length and time scales, especially during processes of early development, wound healing and diseases such as cancer. This Review will focus on the biological basis of tissue-scale mechanical state transitions, how they emerge from molecular and cellular interactions, and their roles in organismal development, homeostasis, regeneration and disease.
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Affiliation(s)
- Yanlan Mao
- Laboratory for Molecular Cell Biology, University College London, London, UK.
- Institute for the Physics of Living Systems, University College London, London, UK.
| | - Sara A Wickström
- Department of Cell and Tissue Dynamics, Max Planck Institute for Molecular Biomedicine, Münster, Germany.
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Helsinki Institute of Life Science, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland.
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8
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Matas-Gil A, Endres RG. Unraveling biochemical spatial patterns: Machine learning approaches to the inverse problem of stationary Turing patterns. iScience 2024; 27:109822. [PMID: 38827409 PMCID: PMC11140185 DOI: 10.1016/j.isci.2024.109822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/14/2024] [Accepted: 04/24/2024] [Indexed: 06/04/2024] Open
Abstract
The diffusion-driven Turing instability is a potential mechanism for spatial pattern formation in numerous biological and chemical systems. However, engineering these patterns and demonstrating that they are produced by this mechanism is challenging. To address this, we aim to solve the inverse problem in artificial and experimental Turing patterns. This task is challenging since patterns are often corrupted by noise and slight changes in initial conditions can lead to different patterns. We used both least squares to explore the problem and physics-informed neural networks to build a noise-robust method. We elucidate the functionality of our network in scenarios mimicking biological noise levels and showcase its application using an experimentally obtained chemical pattern. The findings reveal the significant promise of machine learning in steering the creation of synthetic patterns in bioengineering, thereby advancing our grasp of morphological intricacies within biological systems while acknowledging existing limitations.
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Affiliation(s)
- Antonio Matas-Gil
- Department of Life Sciences & Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London SW7 2BU, UK
| | - Robert G. Endres
- Department of Life Sciences & Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London SW7 2BU, UK
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9
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Ramos R, Swedlund B, Ganesan AK, Morsut L, Maini PK, Monuki ES, Lander AD, Chuong CM, Plikus MV. Parsing patterns: Emerging roles of tissue self-organization in health and disease. Cell 2024; 187:3165-3186. [PMID: 38906093 PMCID: PMC11299420 DOI: 10.1016/j.cell.2024.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 02/22/2024] [Accepted: 05/08/2024] [Indexed: 06/23/2024]
Abstract
Patterned morphologies, such as segments, spirals, stripes, and spots, frequently emerge during embryogenesis through self-organized coordination between cells. Yet, complex patterns also emerge in adults, suggesting that the capacity for spontaneous self-organization is a ubiquitous property of biological tissues. We review current knowledge on the principles and mechanisms of self-organized patterning in embryonic tissues and explore how these principles and mechanisms apply to adult tissues that exhibit features of patterning. We discuss how and why spontaneous pattern generation is integral to homeostasis and healing of tissues, illustrating it with examples from regenerative biology. We examine how aberrant self-organization underlies diverse pathological states, including inflammatory skin disorders and tumors. Lastly, we posit that based on such blueprints, targeted engineering of pattern-driving molecular circuits can be leveraged for synthetic biology and the generation of organoids with intricate patterns.
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Affiliation(s)
- Raul Ramos
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
| | - Benjamin Swedlund
- Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Anand K Ganesan
- Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA; Department of Dermatology, University of California, Irvine, Irvine, CA, USA
| | - Leonardo Morsut
- Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Alfred E. Mann Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
| | - Philip K Maini
- Mathematical Institute, University of Oxford, Oxford, UK
| | - Edwin S Monuki
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA; Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, CA, USA
| | - Arthur D Lander
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA.
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Maksim V Plikus
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA; Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, USA.
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10
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Huycke TR, Häkkinen TJ, Miyazaki H, Srivastava V, Barruet E, McGinnis CS, Kalantari A, Cornwall-Scoones J, Vaka D, Zhu Q, Jo H, Oria R, Weaver VM, DeGrado WF, Thomson M, Garikipati K, Boffelli D, Klein OD, Gartner ZJ. Patterning and folding of intestinal villi by active mesenchymal dewetting. Cell 2024; 187:3072-3089.e20. [PMID: 38781967 PMCID: PMC11166531 DOI: 10.1016/j.cell.2024.04.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/30/2023] [Accepted: 04/26/2024] [Indexed: 05/25/2024]
Abstract
Tissue folds are structural motifs critical to organ function. In the intestine, bending of a flat epithelium into a periodic pattern of folds gives rise to villi, finger-like protrusions that enable nutrient absorption. However, the molecular and mechanical processes driving villus morphogenesis remain unclear. Here, we identify an active mechanical mechanism that simultaneously patterns and folds the intestinal epithelium to initiate villus formation. At the cellular level, we find that PDGFRA+ subepithelial mesenchymal cells generate myosin II-dependent forces sufficient to produce patterned curvature in neighboring tissue interfaces. This symmetry-breaking process requires altered cell and extracellular matrix interactions that are enabled by matrix metalloproteinase-mediated tissue fluidization. Computational models, together with in vitro and in vivo experiments, revealed that these cellular features manifest at the tissue level as differences in interfacial tensions that promote mesenchymal aggregation and interface bending through a process analogous to the active dewetting of a thin liquid film.
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Affiliation(s)
- Tyler R Huycke
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA; Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Teemu J Häkkinen
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA; Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Hikaru Miyazaki
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA; Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Vasudha Srivastava
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Emilie Barruet
- Department of Pediatrics, Cedars-Sinai Guerin Children's, Los Angeles, CA, USA
| | - Christopher S McGinnis
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Ali Kalantari
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA; Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Jake Cornwall-Scoones
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Dedeepya Vaka
- Department of Pediatrics, Cedars-Sinai Guerin Children's, Los Angeles, CA, USA
| | - Qin Zhu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Hyunil Jo
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Roger Oria
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Comprehensive Cancer Center, Helen Diller Family Cancer Research Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Therapeutic Sciences, Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Valerie M Weaver
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; Comprehensive Cancer Center, Helen Diller Family Cancer Research Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Therapeutic Sciences, Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Matt Thomson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Krishna Garikipati
- Departments of Mechanical Engineering, and Mathematics, University of Michigan, Ann Arbor, MI, USA
| | - Dario Boffelli
- Department of Pediatrics, Cedars-Sinai Guerin Children's, Los Angeles, CA, USA
| | - Ophir D Klein
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA; Department of Pediatrics, Cedars-Sinai Guerin Children's, Los Angeles, CA, USA.
| | - Zev J Gartner
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
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11
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Takaya K, Sunohara A, Sakai S, Aramaki-Hattori N, Okabe K, Kishi K. Twist2 contributes to skin regeneration and hair follicle formation in mouse fetuses. Sci Rep 2024; 14:10854. [PMID: 38740788 PMCID: PMC11091223 DOI: 10.1038/s41598-024-60684-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 04/26/2024] [Indexed: 05/16/2024] Open
Abstract
Unlike adult mammalian wounds, early embryonic mouse skin wounds completely regenerate and heal without scars. Analysis of the underlying molecular mechanism will provide insights into scarless wound healing. Twist2 is an important regulator of hair follicle formation and biological patterning; however, it is unclear whether it plays a role in skin or skin appendage regeneration. Here, we aimed to elucidate Twist2 expression and its role in fetal wound healing. ICR mouse fetuses were surgically wounded on embryonic day 13 (E13), E15, and E17, and Twist2 expression in tissue samples from these fetuses was evaluated via in situ hybridization, immunohistochemistry, and reverse transcription-quantitative polymerase chain reaction. Twist2 expression was upregulated in the dermis of E13 wound margins but downregulated in E15 and E17 wounds. Twist2 knockdown on E13 left visible marks at the wound site, inhibited regeneration, and resulted in defective follicle formation. Twist2-knockdown dermal fibroblasts lacked the ability to undifferentiate. Furthermore, Twist2 hetero knockout mice (Twist + /-) formed visible scars, even on E13, when all skin structures should regenerate. Thus, Twist2 expression correlated with skin texture formation and hair follicle defects in late mouse embryos. These findings may help develop a therapeutic strategy to reduce scarring and promote hair follicle regeneration.
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Affiliation(s)
- Kento Takaya
- Department of Plastic and Reconstructive Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Ayano Sunohara
- Department of Plastic and Reconstructive Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Shigeki Sakai
- Department of Plastic and Reconstructive Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Noriko Aramaki-Hattori
- Department of Plastic and Reconstructive Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Keisuke Okabe
- Department of Plastic and Reconstructive Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Kazuo Kishi
- Department of Plastic and Reconstructive Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan.
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12
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Tan CT, Lim CY, Lay K. Modelling Human Hair Follicles-Lessons from Animal Models and Beyond. BIOLOGY 2024; 13:312. [PMID: 38785794 PMCID: PMC11117913 DOI: 10.3390/biology13050312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/26/2024] [Accepted: 04/27/2024] [Indexed: 05/25/2024]
Abstract
The hair follicle is a specialized appendage of the skin that is critical for multiple functions, including thermoregulation, immune surveillance, and sebum production. Mammals are born with a fixed number of hair follicles that develop embryonically. Postnatally, these hair follicles undergo regenerative cycles of regression and growth that recapitulate many of the embryonic signaling pathways. Furthermore, hair cycles have a direct impact on skin regeneration in homeostasis, cutaneous wound healing, and disease conditions such as alopecia. Here, we review the current knowledge of hair follicle formation during embryonic development and the post-natal hair cycle, with an emphasis on the molecular signaling pathways underlying these processes. We then discuss efforts to capitalize on the field's understanding of in vivo mechanisms to bioengineer hair follicles or hair-bearing skin in vitro and how such models may be further improved to develop strategies for hair regeneration.
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Affiliation(s)
- Chew Teng Tan
- A*STAR Skin Research Labs (A*SRL), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, Singapore 138648, Singapore
| | - Chin Yan Lim
- A*STAR Skin Research Labs (A*SRL), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, Singapore 138648, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Kenneth Lay
- A*STAR Skin Research Labs (A*SRL), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, #06-06 Immunos, Singapore 138648, Singapore
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13
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Dhouailly D. The avian ectodermal default competence to make feathers. Dev Biol 2024; 508:64-76. [PMID: 38190932 DOI: 10.1016/j.ydbio.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/24/2023] [Accepted: 01/05/2024] [Indexed: 01/10/2024]
Abstract
Feathers originate as protofeathers before birds, in pterosaurs and basal dinosaurs. What characterizes a feather is not only its outgrowth, but its barb cells differentiation and a set of beta-corneous proteins. Reticula appear concomitantly with feathers, as small bumps on plantar skin, made only of keratins. Avian scales, with their own set of beta-corneous proteins, appear more recently than feathers on the shank, and only in some species. In the chick embryo, when feather placodes form, all the non-feather areas of the integument are already specified. Among them, midventral apterium, cornea, reticula, and scale morphogenesis appear to be driven by negative regulatory mechanisms, which modulate the inherited capacity of the avian ectoderm to form feathers. Successive dermal/epidermal interactions, initiated by the Wnt/β-catenin pathway, and involving principally Eda/Edar, BMP, FGF20 and Shh signaling, are responsible for the formation not only of feather, but also of scale placodes and reticula, with notable differences in the level of Shh, and probably FGF20 expressions. This sequence is a dynamic and labile process, the turning point being the FGF20 expression by the placode. This epidermal signal endows its associated dermis with the memory to aggregate and to stimulate the morphogenesis that follows, involving even a re-initiation of the placode.
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Affiliation(s)
- Danielle Dhouailly
- Department of Biology and Chemistry, University Grenoble-Alpes, Institute for Advanced Biosciences, 38700, La Tronche, France.
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14
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Biggs LC, Miroshnikova YA. Nuclear mechanotransduction on skin stem cell fate regulation. Curr Opin Cell Biol 2024; 87:102328. [PMID: 38340567 DOI: 10.1016/j.ceb.2024.102328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 02/12/2024]
Abstract
Mammalian skin is a highly dynamic and regenerative organ that has long been recognized as a mechanically active composite of tissues withstanding daily compressive and tensile forces that arise from body movement. Importantly, cell- and tissue-scale mechanical signals are critical regulators of skin morphogenesis and homeostasis. These signals are sensed at the cellular periphery and transduced by mechanosensitive proteins within the plasma membrane to the cytoskeletal networks, and eventually into the nucleus to regulate chromatin organization and gene expression. The role of each of these nodes in producing a coherent mechanoresponse at both cell- and tissue-scales is emerging. Here we focus on the key cytoplasmic and nuclear mechanosensitive structures that are critical for the mammalian skin development and homeostatic maintenance. We propose that the mechanical state of the skin, in particular of its nuclear compartment, is a critical rheostat that fine-tunes developmental and homeostatic processes essential for the proper function of the organ.
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Affiliation(s)
- Leah C Biggs
- Department of Cell and Tissue Dynamics, Max Planck Institute for Molecular Biomedicine, 48149 Münster, Germany.
| | - Yekaterina A Miroshnikova
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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15
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Sudderick ZR, Glover JD. Periodic pattern formation during embryonic development. Biochem Soc Trans 2024; 52:75-88. [PMID: 38288903 PMCID: PMC10903485 DOI: 10.1042/bst20230197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/21/2023] [Accepted: 01/08/2024] [Indexed: 02/29/2024]
Abstract
During embryonic development many organs and structures require the formation of series of repeating elements known as periodic patterns. Ranging from the digits of the limb to the feathers of the avian skin, the correct formation of these embryonic patterns is essential for the future form and function of these tissues. However, the mechanisms that produce these patterns are not fully understood due to the existence of several modes of pattern generation which often differ between organs and species. Here, we review the current state of the field and provide a perspective on future approaches to studying this fundamental process of embryonic development.
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Affiliation(s)
- Zoe R. Sudderick
- The Roslin Institute & R(D)SVS, University of Edinburgh, Edinburgh, U.K
| | - James D. Glover
- The Roslin Institute & R(D)SVS, University of Edinburgh, Edinburgh, U.K
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16
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Liu Y, Zhang Y, Chang X, Liu X. MDIC3: Matrix decomposition to infer cell-cell communication. PATTERNS (NEW YORK, N.Y.) 2024; 5:100911. [PMID: 38370122 PMCID: PMC10873161 DOI: 10.1016/j.patter.2023.100911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 05/31/2023] [Accepted: 12/08/2023] [Indexed: 02/20/2024]
Abstract
Crosstalk among cells is vital for maintaining the biological function and intactness of systems. Most existing methods for investigating cell-cell communications are based on ligand-receptor (L-R) expression, and they focus on the study between two cells. Thus, the final communication inference results are particularly sensitive to the completeness and accuracy of the prior biological knowledge. Because existing L-R research focuses mainly on humans, most existing methods can only examine cell-cell communication for humans. As far as we know, there is currently no effective method to overcome this species limitation. Here, we propose MDIC3 (matrix decomposition to infer cell-cell communication), an unsupervised tool to investigate cell-cell communication in any species, and the results are not limited by specific L-R pairs or signaling pathways. By comparing it with existing methods for the inference of cell-cell communication, MDIC3 obtained better performance in both humans and mice.
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Affiliation(s)
- Yi Liu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- School of Mathematics and Statistics, Shandong University, Weihai 364209, China
| | - Yuelei Zhang
- School of Mathematics and Statistics, Shandong University, Weihai 364209, China
| | - Xiao Chang
- Institute of Statistics and Applied Mathematics, Anhui University of Finance and Economics, Bengbu 233030, China
| | - Xiaoping Liu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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17
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Villeneuve C, Hashmi A, Ylivinkka I, Lawson-Keister E, Miroshnikova YA, Pérez-González C, Myllymäki SM, Bertillot F, Yadav B, Zhang T, Matic Vignjevic D, Mikkola ML, Manning ML, Wickström SA. Mechanical forces across compartments coordinate cell shape and fate transitions to generate tissue architecture. Nat Cell Biol 2024; 26:207-218. [PMID: 38302719 PMCID: PMC10866703 DOI: 10.1038/s41556-023-01332-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 12/08/2023] [Indexed: 02/03/2024]
Abstract
Morphogenesis and cell state transitions must be coordinated in time and space to produce a functional tissue. An excellent paradigm to understand the coupling of these processes is mammalian hair follicle development, which is initiated by the formation of an epithelial invagination-termed placode-that coincides with the emergence of a designated hair follicle stem cell population. The mechanisms directing the deformation of the epithelium, cell state transitions and physical compartmentalization of the placode are unknown. Here we identify a key role for coordinated mechanical forces stemming from contractile, proliferative and proteolytic activities across the epithelial and mesenchymal compartments in generating the placode structure. A ring of fibroblast cells gradually wraps around the placode cells to generate centripetal contractile forces, which, in collaboration with polarized epithelial myosin activity, promote elongation and local tissue thickening. These mechanical stresses further enhance compartmentalization of Sox9 expression to promote stem cell positioning. Subsequently, proteolytic remodelling locally softens the basement membrane to facilitate a release of pressure on the placode, enabling localized cell divisions, tissue fluidification and epithelial invagination into the underlying mesenchyme. Together, our experiments and modelling identify dynamic cell shape transformations and tissue-scale mechanical cooperation as key factors for orchestrating organ formation.
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Affiliation(s)
- Clémentine Villeneuve
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Cell and Tissue Dynamics, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Ali Hashmi
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Irene Ylivinkka
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | - Yekaterina A Miroshnikova
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Carlos Pérez-González
- Cell Biology and Cancer Unit, Institut Curie, PSL Research University, CNRS, Paris, France
| | - Satu-Marja Myllymäki
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Cell and Tissue Dynamics Research Program, Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Fabien Bertillot
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Cell and Tissue Dynamics, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Bhagwan Yadav
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Tao Zhang
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | | | - Marja L Mikkola
- Cell and Tissue Dynamics Research Program, Institute of Biotechnology, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - M Lisa Manning
- Department of Physics and BioInspired Institute, Syracuse University, Syracuse, NY, USA.
| | - Sara A Wickström
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Department of Cell and Tissue Dynamics, Max Planck Institute for Molecular Biomedicine, Münster, Germany.
- Helsinki Institute of Life Science, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland.
- Wihuri Research Institute, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland.
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18
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Khatif H, Bazzi H. Generation and characterization of a Dkk4-Cre knock-in mouse line. Genesis 2024; 62:e23532. [PMID: 37435631 DOI: 10.1002/dvg.23532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/13/2023]
Abstract
Ectodermal appendages in mammals, such as teeth, mammary glands, sweat glands and hair follicles, are generated during embryogenesis through a series of mesenchymal-epithelial interactions. Canonical Wnt signaling and its inhibitors are implicated in the early steps of ectodermal appendage development and patterning. To study the activation dynamics of the Wnt target and inhibitor Dickkopf4 (Dkk4) in ectodermal appendages, we used CRSIPR/Cas9 to generate a Dkk4-Cre knock-in mouse (Mus musculus) line, where the Cre recombinase cDNA replaces the expression of endogenous Dkk4. Using Cre reporters, the Dkk4-Cre activity was evident at the prospective sites of ectodermal appendages, overlapping with the Dkk4 mRNA expression. Unexpectedly, a predominantly mesenchymal cell population in the embryo posterior also showed Dkk4-Cre activity. Lineage-tracing suggested that these cells are likely derived from a few Dkk4-Cre-expressing cells in the epiblast at early gastrulation. Finally, our analyses of Dkk4-Cre-expressing cells in developing hair follicle epithelial placodes revealed intra- and inter-placodal cellular heterogeneity, supporting emerging data on the positional and transcriptional cellular variability in placodes. Collectively, we propose the new Dkk4-Cre knock-in mouse line as a suitable model to study Wnt and DKK4 inhibitor dynamics in early mouse development and ectodermal appendage morphogenesis.
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Affiliation(s)
- Houda Khatif
- Department of Dermatology and Venereology, University Hospital of Cologne, University of Cologne, Cologne, Germany
- The Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases (CECAD), Medical Faculty, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany
| | - Hisham Bazzi
- Department of Dermatology and Venereology, University Hospital of Cologne, University of Cologne, Cologne, Germany
- The Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases (CECAD), Medical Faculty, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University of Cologne, Cologne, Germany
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19
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Diez A, Krause AL, Maini PK, Gaffney EA, Seirin-Lee S. Turing Pattern Formation in Reaction-Cross-Diffusion Systems with a Bilayer Geometry. Bull Math Biol 2024; 86:13. [PMID: 38170298 PMCID: PMC10764571 DOI: 10.1007/s11538-023-01237-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 11/06/2023] [Indexed: 01/05/2024]
Abstract
Conditions for self-organisation via Turing's mechanism in biological systems represented by reaction-diffusion or reaction-cross-diffusion models have been extensively studied. Nonetheless, the impact of tissue stratification in such systems is under-explored, despite its ubiquity in the context of a thin epithelium overlying connective tissue, for instance the epidermis and underlying dermal mesenchyme of embryonic skin. In particular, each layer can be subject to extensively different biochemical reactions and transport processes, with chemotaxis - a special case of cross-diffusion - often present in the mesenchyme, contrasting the solely molecular transport typically found in the epidermal layer. We study Turing patterning conditions for a class of reaction-cross-diffusion systems in bilayered regions, with a thin upper layer and coupled by a linear transport law. In particular, the role of differential transport through the interface is explored together with the presence of asymmetry between the homogeneous equilibria of the two layers. A linear stability analysis is carried out around a spatially homogeneous equilibrium state in the asymptotic limit of weak and strong coupling strengths, where quantitative approximations of the bifurcation curve can be computed. Our theoretical findings, for an arbitrary number of reacting species, reveal quantitative Turing conditions, highlighting when the coupling mechanism between the layered regions can either trigger patterning or stabilize a spatially homogeneous equilibrium regardless of the independent patterning state of each layer. We support our theoretical results through direct numerical simulations, and provide an open source code to explore such systems further.
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Affiliation(s)
- Antoine Diez
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University Institute for Advanced Study (KUIAS), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Andrew L Krause
- Mathematical Sciences Department, Durham University, Upper Mountjoy Campus, Stockton Rd, Durham, DH1 3LE, UK
| | - Philip K Maini
- Wolfson Centre For Mathematical Biology, Mathematical Institute, Andrew Wiles Building, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, UK
| | - Eamonn A Gaffney
- Wolfson Centre For Mathematical Biology, Mathematical Institute, Andrew Wiles Building, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, UK.
| | - Sungrim Seirin-Lee
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University Institute for Advanced Study (KUIAS), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
- Department of Mathematical Medicine, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
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20
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Fraga Delfino Kunz C, Gerisch A, Glover J, Headon D, Painter KJ, Matthäus F. Novel Aspects in Pattern Formation Arise from Coupling Turing Reaction-Diffusion and Chemotaxis. Bull Math Biol 2023; 86:4. [PMID: 38038776 PMCID: PMC10692013 DOI: 10.1007/s11538-023-01225-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/11/2023] [Indexed: 12/02/2023]
Abstract
Recent experimental studies on primary hair follicle formation and feather bud morphogenesis indicate a coupling between Turing-type diffusion driven instability and chemotactic patterning. Inspired by these findings we develop and analyse a mathematical model that couples chemotaxis to a reaction-diffusion system exhibiting diffusion-driven (Turing) instability. While both systems, reaction-diffusion systems and chemotaxis, can independently generate spatial patterns, we were interested in how the coupling impacts the stability of the system, parameter region for patterning, pattern geometry, as well as the dynamics of pattern formation. We conduct a classical linear stability analysis for different model structures, and confirm our results by numerical analysis of the system. Our results show that the coupling generally increases the robustness of the patterning process by enlarging the pattern region in the parameter space. Concerning time scale and pattern regularity, we find that an increase in the chemosensitivity can speed up the patterning process for parameters inside and outside of the Turing space, but generally reduces spatial regularity of the pattern. Interestingly, our analysis indicates that pattern formation can also occur when neither the Turing nor the chemotaxis system can independently generate pattern. On the other hand, for some parameter settings, the coupling of the two processes can extinguish the pattern formation, rather than reinforce it. These theoretical findings can be used to corroborate the biological findings on morphogenesis and guide future experimental studies. From a mathematical point of view, this work sheds a light on coupling classical pattern formation systems from the parameter space perspective.
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Affiliation(s)
- Camile Fraga Delfino Kunz
- Frankfurt Institute for Advanced Studies and Department of Computer Science and Mathematics, Goethe-University Frankfurt, Ruth-Moufang-Str. 1, 60438, Frankfurt, Germany
| | - Alf Gerisch
- Department of Mathematics, Technical University Darmstadt, Darmstadt, Germany
| | - James Glover
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Denis Headon
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, EH25 9RG, UK
| | - Kevin John Painter
- Dipartimento Interateneo di Scienze, Progetto e Politiche del Territorio (DIST), Politecnico di Torino, Turin, Italy
| | - Franziska Matthäus
- Frankfurt Institute for Advanced Studies and Department of Computer Science and Mathematics, Goethe-University Frankfurt, Ruth-Moufang-Str. 1, 60438, Frankfurt, Germany.
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21
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Mäkelä OJM, Mikkola ML. Mesenchyme governs hair follicle induction. Development 2023; 150:dev202140. [PMID: 37982496 DOI: 10.1242/dev.202140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/23/2023] [Indexed: 11/21/2023]
Abstract
Tissue interactions are essential for guiding organ development and regeneration. Hair follicle formation relies on inductive signalling between two tissues, the embryonic surface epithelium and the adjacent mesenchyme. Although previous research has highlighted the hair-inducing potential of the mesenchymal component of the hair follicle - the dermal papilla and its precursor, the dermal condensate - the source and nature of the primary inductive signal before dermal condensate formation have remained elusive. Here, we performed epithelial-mesenchymal tissue recombination experiments using hair-forming back skin and glabrous plantar skin from mouse embryos to unveil that the back skin mesenchyme is inductive even before dermal condensate formation. Moreover, the naïve, unpatterned mesenchyme was sufficient to trigger hair follicle formation even in the oral epithelium. Building on previous knowledge, we explored the hair-inductive ability of the Wnt agonist R-spondin 1 and a Bmp receptor inhibitor in embryonic skin explants. Although R-spondin 1 instigated precocious placode-specific transcriptional responses, it was insufficient for hair follicle induction, either alone or in combination with Bmp receptor inhibition. Our findings pave the way for identifying the hair follicle-inducing cue.
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Affiliation(s)
- Otto J M Mäkelä
- Cell and Tissue Dynamics Research Program, Institute of Biotechnology, Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, 00014 Helsinki, Finland
| | - Marja L Mikkola
- Cell and Tissue Dynamics Research Program, Institute of Biotechnology, Helsinki Institute of Life Sciences (HiLIFE), University of Helsinki, 00014 Helsinki, Finland
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22
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Li X, Xie R, Luo Y, Shi R, Ling Y, Zhao X, Xu X, Chu W, Wang X. Cooperation of TGF-β and FGF signalling pathways in skin development. Cell Prolif 2023; 56:e13489. [PMID: 37150846 PMCID: PMC10623945 DOI: 10.1111/cpr.13489] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/27/2023] [Accepted: 04/13/2023] [Indexed: 05/09/2023] Open
Abstract
The skin is a multi-layered structure composed of the epidermis, dermis and hypodermis. The epidermis originates entirely from the ectoderm, whereas the dermis originates from various germ layers depending on its anatomical location; thus, there are different developmental patterns of the skin. Although the regulatory mechanisms of epidermal formation are well understood, mechanisms regulating dermis development are not clear owing to the complex origin. It has been shown that several morphogenetic pathways regulate dermis development. Of these, transforming growth factor-β (TGF-β) and fibroblast growth factor (FGF) signalling pathways are the main modulators regulating skin cell induction, fate decision, migration and differentiation. Recently, the successful generation of human skin by modulating TGF-β and FGF signals further demonstrated the irreplaceable roles of these pathways in skin regeneration. This review provides evidence of the role of TGF-β and FGF signalling pathways in the development of different skin layers, especially the disparate dermis of different body regions. This review also provides new perspectives on the distinct developmental patterns of skin and explores new ideas for clinical applications in the future.
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Affiliation(s)
- Xinxin Li
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
| | - Rongfang Xie
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
| | - Yilin Luo
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
| | - Runlu Shi
- Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate SchoolTsinghua UniversityShenzhenChina
| | - Yuanqiang Ling
- Guangzhou Wishing Tree Hair Medical Technology Limited CompanyGuangzhouChina
| | - Xiaojing Zhao
- Guangzhou Wishing Tree Hair Medical Technology Limited CompanyGuangzhouChina
| | - Xuejuan Xu
- Department of EndocrinologyThe First People's Hospital of FoshanFoshanChina
| | - Weiwei Chu
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
| | - Xusheng Wang
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
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23
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Riddell J, Noureen SR, Sedda L, Glover JD, Ho WKW, Bain CA, Berbeglia A, Brown H, Anderson C, Chen Y, Crichton ML, Yates CA, Mort RL, Headon DJ. Rapid mechanosensitive migration and dispersal of newly divided mesenchymal cells aid their recruitment into dermal condensates. PLoS Biol 2023; 21:e3002316. [PMID: 37747910 PMCID: PMC10553821 DOI: 10.1371/journal.pbio.3002316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 10/05/2023] [Accepted: 08/29/2023] [Indexed: 09/27/2023] Open
Abstract
Embryonic mesenchymal cells are dispersed within an extracellular matrix but can coalesce to form condensates with key developmental roles. Cells within condensates undergo fate and morphological changes and induce cell fate changes in nearby epithelia to produce structures including hair follicles, feathers, or intestinal villi. Here, by imaging mouse and chicken embryonic skin, we find that mesenchymal cells undergo much of their dispersal in early interphase, in a stereotyped process of displacement driven by 3 hours of rapid and persistent migration followed by a long period of low motility. The cell division plane and the elevated migration speed and persistence of newly born mesenchymal cells are mechanosensitive, aligning with tissue tension, and are reliant on active WNT secretion. This behaviour disperses mesenchymal cells and allows daughters of recent divisions to travel long distances to enter dermal condensates, demonstrating an unanticipated effect of cell cycle subphase on core mesenchymal behaviour.
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Affiliation(s)
- Jon Riddell
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Shahzeb Raja Noureen
- Department of Mathematical Sciences, University of Bath, Claverton Down, Bath, United Kingdom
| | - Luigi Sedda
- Lancaster Ecology and Epidemiology Group, Lancaster Medical School, Lancaster University, Lancaster, United Kingdom
| | - James D. Glover
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - William K. W. Ho
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Connor A. Bain
- School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, United Kingdom
| | - Arianna Berbeglia
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Helen Brown
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Calum Anderson
- School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, United Kingdom
| | - Yuhang Chen
- School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, United Kingdom
| | - Michael L. Crichton
- School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh, United Kingdom
| | - Christian A. Yates
- Department of Mathematical Sciences, University of Bath, Claverton Down, Bath, United Kingdom
| | - Richard L. Mort
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, United Kingdom
| | - Denis J. Headon
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
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24
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Huycke TR, Miyazaki H, Häkkinen TJ, Srivastava V, Barruet E, McGinnis CS, Kalantari A, Cornwall-Scoones J, Vaka D, Zhu Q, Jo H, DeGrado WF, Thomson M, Garikipati K, Boffelli D, Klein OD, Gartner ZJ. Patterning and folding of intestinal villi by active mesenchymal dewetting. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.25.546328. [PMID: 37425793 PMCID: PMC10326967 DOI: 10.1101/2023.06.25.546328] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Tissue folding generates structural motifs critical to organ function. In the intestine, bending of a flat epithelium into a periodic pattern of folds gives rise to villi, the numerous finger-like protrusions that are essential for nutrient absorption. However, the molecular and mechanical mechanisms driving the initiation and morphogenesis of villi remain a matter of debate. Here, we identify an active mechanical mechanism that simultaneously patterns and folds intestinal villi. We find that PDGFRA+ subepithelial mesenchymal cells generate myosin II-dependent forces sufficient to produce patterned curvature in neighboring tissue interfaces. At the cell-level, this occurs through a process dependent upon matrix metalloproteinase-mediated tissue fluidization and altered cell-ECM adhesion. By combining computational models with in vivo experiments, we reveal these cellular features manifest at the tissue-level as differences in interfacial tensions that promote mesenchymal aggregation and interface bending through a process analogous to the active de-wetting of a thin liquid film.
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Affiliation(s)
- Tyler R. Huycke
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA, USA
- Equal contribution
| | - Hikaru Miyazaki
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA, USA
- Equal contribution
| | - Teemu J. Häkkinen
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA, USA
- Equal contribution
| | - Vasudha Srivastava
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Emilie Barruet
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Christopher S. McGinnis
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Ali Kalantari
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Jake Cornwall-Scoones
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Dedeepya Vaka
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Qin Zhu
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Hyunil Jo
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - William F. DeGrado
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Matt Thomson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Krishna Garikipati
- Departments of Mechanical Engineering, and Mathematics, University of Michigan, Ann Arbor, USA
| | - Dario Boffelli
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Ophir D. Klein
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Zev J. Gartner
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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25
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Dhouailly D. Evo Devo of the Vertebrates Integument. J Dev Biol 2023; 11:25. [PMID: 37367479 DOI: 10.3390/jdb11020025] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/19/2023] [Accepted: 05/21/2023] [Indexed: 06/28/2023] Open
Abstract
All living jawed vertebrates possess teeth or did so ancestrally. Integumental surface also includes the cornea. Conversely, no other anatomical feature differentiates the clades so readily as skin appendages do, multicellular glands in amphibians, hair follicle/gland complexes in mammals, feathers in birds, and the different types of scales. Tooth-like scales are characteristic of chondrichthyans, while mineralized dermal scales are characteristic of bony fishes. Corneous epidermal scales might have appeared twice, in squamates, and on feet in avian lineages, but posteriorly to feathers. In contrast to the other skin appendages, the origin of multicellular glands of amphibians has never been addressed. In the seventies, pioneering dermal-epidermal recombination between chick, mouse and lizard embryos showed that: (1) the clade type of the appendage is determined by the epidermis; (2) their morphogenesis requires two groups of dermal messages, first for primordia formation, second for appendage final architecture; (3) the early messages were conserved during amniotes evolution. Molecular biology studies that have identified the involved pathways, extending those data to teeth and dermal scales, suggest that the different vertebrate skin appendages evolved in parallel from a shared placode/dermal cells unit, present in a common toothed ancestor, c.a. 420 mya.
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Affiliation(s)
- Danielle Dhouailly
- Department of Biology and Chemistry, Institute for Advanced Biosciences, University Grenoble-Alpes, 38700 La Tronche, France
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26
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Zimm R, Berio F, Debiais-Thibaud M, Goudemand N. A shark-inspired general model of tooth morphogenesis unveils developmental asymmetries in phenotype transitions. Proc Natl Acad Sci U S A 2023; 120:e2216959120. [PMID: 37027430 PMCID: PMC10104537 DOI: 10.1073/pnas.2216959120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 02/07/2023] [Indexed: 04/08/2023] Open
Abstract
Developmental complexity stemming from the dynamic interplay between genetic and biomechanic factors canalizes the ways genotypes and phenotypes can change in evolution. As a paradigmatic system, we explore how changes in developmental factors generate typical tooth shape transitions. Since tooth development has mainly been researched in mammals, we contribute to a more general understanding by studying the development of tooth diversity in sharks. To this end, we build a general, but realistic, mathematical model of odontogenesis. We show that it reproduces key shark-specific features of tooth development as well as real tooth shape variation in small-spotted catsharks Scyliorhinus canicula. We validate our model by comparison with experiments in vivo. Strikingly, we observe that developmental transitions between tooth shapes tend to be highly degenerate, even for complex phenotypes. We also discover that the sets of developmental parameters involved in tooth shape transitions tend to depend asymmetrically on the direction of that transition. Together, our findings provide a valuable base for furthering our understanding of how developmental changes can lead to both adaptive phenotypic change and trait convergence in complex, phenotypically highly diverse, structures.
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Affiliation(s)
- Roland Zimm
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, Lyon Cedex07 69364, France
| | - Fidji Berio
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, Lyon Cedex07 69364, France
- Institut des Sciences de l’Evolution de Montpellier, University of Montpellier, CNRS, Institut de la Recherche pour le Développement, Montpellier34095, France
| | - Mélanie Debiais-Thibaud
- Institut des Sciences de l’Evolution de Montpellier, University of Montpellier, CNRS, Institut de la Recherche pour le Développement, Montpellier34095, France
| | - Nicolas Goudemand
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, Lyon Cedex07 69364, France
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27
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Glover JD, Sudderick ZR, Shih BBJ, Batho-Samblas C, Charlton L, Krause AL, Anderson C, Riddell J, Balic A, Li J, Klika V, Woolley TE, Gaffney EA, Corsinotti A, Anderson RA, Johnston LJ, Brown SJ, Wang S, Chen Y, Crichton ML, Headon DJ. The developmental basis of fingerprint pattern formation and variation. Cell 2023; 186:940-956.e20. [PMID: 36764291 DOI: 10.1016/j.cell.2023.01.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 11/04/2022] [Accepted: 01/10/2023] [Indexed: 02/11/2023]
Abstract
Fingerprints are complex and individually unique patterns in the skin. Established prenatally, the molecular and cellular mechanisms that guide fingerprint ridge formation and their intricate arrangements are unknown. Here we show that fingerprint ridges are epithelial structures that undergo a truncated hair follicle developmental program and fail to recruit a mesenchymal condensate. Their spatial pattern is established by a Turing reaction-diffusion system, based on signaling between EDAR, WNT, and antagonistic BMP pathways. These signals resolve epithelial growth into bands of focalized proliferation under a precociously differentiated suprabasal layer. Ridge formation occurs as a set of waves spreading from variable initiation sites defined by the local signaling environments and anatomical intricacies of the digit, with the propagation and meeting of these waves determining the type of pattern that forms. Relying on a dynamic patterning system triggered at spatially distinct sites generates the characteristic types and unending variation of human fingerprint patterns.
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Affiliation(s)
- James D Glover
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Zoe R Sudderick
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Barbara Bo-Ju Shih
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh EH25 9RG, UK
| | | | - Laura Charlton
- Institute of Mechanical, Process and Energy Engineering, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Andrew L Krause
- Department of Mathematical Sciences, Durham University, Durham DH1 3LE, UK
| | - Calum Anderson
- Institute of Mechanical, Process and Energy Engineering, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Jon Riddell
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Adam Balic
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Jinxi Li
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Fudan University, Shanghai 200433, PRC
| | - Václav Klika
- Department of Mathematics, FNSPE, Czech Technical University in Prague, Prague 16000, Czechia
| | | | - Eamonn A Gaffney
- Mathematical Institute, University of Oxford, Oxford OX2 6GG, UK
| | - Andrea Corsinotti
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Richard A Anderson
- MRC Centre for Reproductive Health, Queens Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Luke J Johnston
- Centre for Genomic & Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Sara J Brown
- Centre for Genomic & Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Sijia Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, PRC
| | - Yuhang Chen
- Institute of Mechanical, Process and Energy Engineering, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Michael L Crichton
- Institute of Mechanical, Process and Energy Engineering, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Denis J Headon
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh EH25 9RG, UK.
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28
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Single-cell chromatin landscapes of mouse skin development. Sci Data 2022; 9:741. [PMID: 36460683 PMCID: PMC9718782 DOI: 10.1038/s41597-022-01839-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 11/09/2022] [Indexed: 12/03/2022] Open
Abstract
The coat of mammals is produced by hair follicles, and hair follicle is an important and complex accessory organ of skin. As a complex physiological regulation process, hair follicle morphogenesis is regulated by a series of signal pathway factors, involves the interaction of multiple cell types and begins in the early embryonic stage. However, its transcriptional regulatory mechanism is unclear. We have therefore utilized single-cell ATAC sequencing to obtain the chromatin accessibility landscapes of 6,928, 6,961 and 7,374 high-quality cells from the dorsal skins of E13.5, E16.5 and P0 mice (Mus musculus), respectively. Based on marker gene activity clustering, we defined 6, 8 and 5 distinct cell types in E13.5, E16.5 and P0 stages, respectively. Furtherly, we integrated the fibroblasts and keratinocytes clusters, performed further analysis and re-clustered. The single cell map of the chromatin open area was drawn from each cell type and the mechanism of cell transcription regulation was explored. Collectively, our data provide a reference for deeply exploring the epigenetic regulation mechanism of mouse hair follicles development.
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29
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Myung P, Andl T, Atit R. The origins of skin diversity: lessons from dermal fibroblasts. Development 2022; 149:dev200298. [PMID: 36444877 PMCID: PMC10112899 DOI: 10.1242/dev.200298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Skin is largely composed of an epidermis that overlies a supporting dermis. Recent advancements in our understanding of how diverse groups of dermal fibroblasts regulate epidermal and hair follicle growth and differentiation have been fueled by tools capable of resolving molecular heterogeneity at a single-cell level. Fibroblast heterogeneity can be traced back to their developmental origin before their segregation into spatially distinct fibroblast subtypes. The mechanisms that drive this lineage diversification during development are being unraveled, with studies showing that both large- and small-scale positional signals play important roles during dermal development. Here, we first delineate what is known about the origins of the dermis and the central role of Wnt/β-catenin signaling in its specification across anatomical locations. We then discuss how one of the first morphologically recognizable fibroblast subtypes, the hair follicle dermal condensate lineage, emerges. Leveraging the natural variation of skin and its appendages between species and between different anatomical locations, these collective studies have identified shared and divergent factors that contribute to the extraordinary diversity of skin.
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Affiliation(s)
- Peggy Myung
- Department of Dermatology, Yale University, New Haven, CT 06510, USA
| | - Thomas Andl
- Burnett School of Biomedical Sciences, Orlando, FL 32827, USA
| | - Radhika Atit
- Department of Biology, Department of Genetics and Genome Sciences, Department of Dermatology, Case Western Reserve University, Cleveland, OH 44106, USA
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30
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[Translated article] RF – What Is the Origin of Morphologic Patterning in Dermatology? An Introduction to Reaction–Diffusion Systems (Turing Patterns). ACTAS DERMO-SIFILIOGRAFICAS 2022; 113:T955-T956. [DOI: 10.1016/j.ad.2022.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/05/2021] [Indexed: 11/30/2022] Open
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31
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Macfarlane FR, Lorenzi T, Painter KJ. The Impact of Phenotypic Heterogeneity on Chemotactic Self-Organisation. Bull Math Biol 2022; 84:143. [PMID: 36319913 PMCID: PMC9626439 DOI: 10.1007/s11538-022-01099-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 10/13/2022] [Indexed: 11/05/2022]
Abstract
The capacity to aggregate through chemosensitive movement forms a paradigm of self-organisation, with examples spanning cellular and animal systems. A basic mechanism assumes a phenotypically homogeneous population that secretes its own attractant, with the well known system introduced more than five decades ago by Keller and Segel proving resolutely popular in modelling studies. The typical assumption of population phenotypic homogeneity, however, often lies at odds with the heterogeneity of natural systems, where populations may comprise distinct phenotypes that vary according to their chemotactic ability, attractant secretion, etc. To initiate an understanding into how this diversity can impact on autoaggregation, we propose a simple extension to the classical Keller and Segel model, in which the population is divided into two distinct phenotypes: those performing chemotaxis and those producing attractant. Using a combination of linear stability analysis and numerical simulations, we demonstrate that switching between these phenotypic states alters the capacity of a population to self-aggregate. Further, we show that switching based on the local environment (population density or chemoattractant level) leads to diverse patterning and provides a route through which a population can effectively curb the size and density of an aggregate. We discuss the results in the context of real world examples of chemotactic aggregation, as well as theoretical aspects of the model such as global existence and blow-up of solutions.
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Affiliation(s)
- Fiona R Macfarlane
- School of Mathematics and Statistics, University of St Andrews, St Andrews, Scotland.
| | - Tommaso Lorenzi
- Department of Mathematical Sciences "G. L. Lagrange", Politecnico di Torino, Turin, Italy
| | - Kevin J Painter
- Inter-university Department of Regional and Urban Studies and Planning, Politecnico di Torino, Turin, Italy
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32
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Zimm R, Oberdick D, Gnetneva A, Schneider P, Cebra-Thomas J, Moustakas-Verho JE. Turing's turtles all the way down: A conserved role of EDAR in the carapacial ridge suggests a deep homology of prepatterns across ectodermal appendages. Anat Rec (Hoboken) 2022; 306:1201-1213. [PMID: 36239299 DOI: 10.1002/ar.25096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/26/2022] [Accepted: 10/03/2022] [Indexed: 11/11/2022]
Abstract
The scutes of the turtle shell are epidermal shields that begin their formation during the early stages of shell development. Like other skin appendages, turtle scutes are hypothesized to be patterned by reaction-diffusion systems. We have previously established ex vivo and in silico systems to study these mechanisms experimentally and have further shown that mathematical models can explain the dynamics of the induction of turtle scute primordia and the generation of final scute architecture. Using these foundations, we expand our current knowledge and test the roles of ectodysplasin and activin signaling in the development of turtle scutes. We find that these molecules play important roles in the prepatterning of scute primordia along the carapacial ridge and show that blocking Edar signaling may lead to a complete loss of marginal scute primordia. We show that it is possible to reproduce these observations using simple mathematical modeling, thereby suggesting a stabilizing role for ectodysplasin within the reaction-diffusion mechanisms. Finally, we argue that our findings further entrench turtle scutes within a class of developmental systems composed of hierarchically nested reaction-diffusion mechanisms, which is conserved across ectodermal organs.
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Affiliation(s)
- Roland Zimm
- Institute of Functional Genomics, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Danielle Oberdick
- Department of Biology, Millersville University, Millersville, Pennsylvania, USA
| | - Anna Gnetneva
- Zoological Institute of the Russian Academy of Sciences, Saint Petersburg, Russia
| | - Pascal Schneider
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
| | - Judith Cebra-Thomas
- Department of Biology, Millersville University, Millersville, Pennsylvania, USA
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33
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Liu Z, Liu Z, Mu Q, Zhao M, Cai T, Xie Y, Zhao C, Qin Q, Zhang C, Xu X, Lan M, Zhang Y, Su R, Wang Z, Wang R, Wang Z, Li J, Zhao Y. Identification of key pathways and genes that regulate cashmere development in cashmere goats mediated by exogenous melatonin. Front Vet Sci 2022; 9:993773. [PMID: 36246326 PMCID: PMC9558121 DOI: 10.3389/fvets.2022.993773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
The growth of secondary hair follicles in cashmere goats follows a seasonal cycle. Melatonin can regulate the cycle of cashmere growth. In this study, melatonin was implanted into live cashmere goats. After skin samples were collected, transcriptome sequencing and histological section observation were performed, and weighted gene co-expression network analysis (WGCNA) was used to identify key genes and establish an interaction network. A total of 14 co-expression modules were defined by WGCNA, and combined with previous analysis results, it was found that the blue module was related to the cycle of cashmere growth after melatonin implantation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that the first initiation of exogenous melatonin-mediated cashmere development was related mainly to the signaling pathway regulating stem cell pluripotency and to the Hippo, TGF-beta and MAPK signaling pathways. Via combined differential gene expression analyses, 6 hub genes were identified: PDGFRA, WNT5A, PPP2R1A, BMPR2, BMPR1A, and SMAD1. This study provides a foundation for further research on the mechanism by which melatonin regulates cashmere growth.
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Affiliation(s)
- Zhihong Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Goat Genetics and Breeding Engineering Technology Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhichen Liu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Qing Mu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Meng Zhao
- Inner Mongolia Autonomous Region Agriculture and Animal Husbandry Technology Extension Center, Hohhot, China
| | - Ting Cai
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Yuchun Xie
- Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Cun Zhao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Qing Qin
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Chongyan Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaolong Xu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Mingxi Lan
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhiying Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Ruijun Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhixin Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Jinquan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Goat Genetics and Breeding Engineering Technology Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Yanhong Zhao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Mutton Sheep Genetics and Breeding, Ministry of Agriculture, Hohhot, China
- Goat Genetics and Breeding Engineering Technology Research Center, Inner Mongolia Agricultural University, Hohhot, China
- *Correspondence: Yanhong Zhao
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34
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Jaiswal A, Singh R. Homeostases of epidermis and hair follicle, and development of basal cell carcinoma. Biochim Biophys Acta Rev Cancer 2022; 1877:188795. [PMID: 36089203 DOI: 10.1016/j.bbcan.2022.188795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/10/2022] [Accepted: 09/03/2022] [Indexed: 10/14/2022]
Abstract
Hedgehog signaling (Hh) plays a critical role in embryogenesis. On the other hand, its overactivity may cause basal cell carcinoma (BCC), the most common human cancer. Further, epidermal and hair follicle homeostases may have a key role in the development of BCC. This article describes the importance of different signaling pathways in the different stages of the two processes. The description of the homeostases brought up the importance of the Notch signaling along with the sonic hedgehog (Shh) and the Wnt pathways. Loss of the Notch signaling adversely affects the late stages of hair follicle formation and allows the bulge cells in the hair follicles to take the fate of the keratinocytes in the interfollicular epidermis. Further, the loss of Notch activity upregulates the Shh and Wnt activities, adversely affecting the homeostases. Notably, the Notch signaling is suppressed in BCC, and the peripheral BCC cells, which have low Notch activity, show drug resistance in comparison to the interior suprabasal BCC cells, which have high Notch activity.
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Affiliation(s)
- Alok Jaiswal
- Department of Chemical Engineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Raghvendra Singh
- Department of Chemical Engineering, Indian Institute of Technology Kanpur, Kanpur 208016, India.
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35
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Ornitz DM, Itoh N. New developments in the biology of fibroblast growth factors. WIREs Mech Dis 2022; 14:e1549. [PMID: 35142107 PMCID: PMC10115509 DOI: 10.1002/wsbm.1549] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 01/28/2023]
Abstract
The fibroblast growth factor (FGF) family is composed of 18 secreted signaling proteins consisting of canonical FGFs and endocrine FGFs that activate four receptor tyrosine kinases (FGFRs 1-4) and four intracellular proteins (intracellular FGFs or iFGFs) that primarily function to regulate the activity of voltage-gated sodium channels and other molecules. The canonical FGFs, endocrine FGFs, and iFGFs have been reviewed extensively by us and others. In this review, we briefly summarize past reviews and then focus on new developments in the FGF field since our last review in 2015. Some of the highlights in the past 6 years include the use of optogenetic tools, viral vectors, and inducible transgenes to experimentally modulate FGF signaling, the clinical use of small molecule FGFR inhibitors, an expanded understanding of endocrine FGF signaling, functions for FGF signaling in stem cell pluripotency and differentiation, roles for FGF signaling in tissue homeostasis and regeneration, a continuing elaboration of mechanisms of FGF signaling in development, and an expanding appreciation of roles for FGF signaling in neuropsychiatric diseases. This article is categorized under: Cardiovascular Diseases > Molecular and Cellular Physiology Neurological Diseases > Molecular and Cellular Physiology Congenital Diseases > Stem Cells and Development Cancer > Stem Cells and Development.
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Affiliation(s)
- David M Ornitz
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Nobuyuki Itoh
- Kyoto University Graduate School of Pharmaceutical Sciences, Sakyo, Kyoto, Japan
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36
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FR - ¿Cómo se originan los distintos patrones morfológicos en dermatología? introducción a los sistemas de reacción-difusión (Patrones de Turing). ACTAS DERMO-SIFILIOGRAFICAS 2022; 113:955-956. [DOI: 10.1016/j.ad.2021.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/23/2021] [Accepted: 04/05/2021] [Indexed: 11/23/2022] Open
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37
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Abstract
Embryoids and organoids hold great promise for human biology and medicine. Herein, we discuss conceptual and technological frameworks useful for developing high-fidelity embryoids and organoids that display tissue- and organ-level phenotypes and functions, which are critically needed for decoding developmental programs and improving translational applications. Through dissecting the layers of inputs controlling mammalian embryogenesis, we review recent progress in reconstructing multiscale structural orders in embryoids and organoids. Bioengineering tools useful for multiscale, multimodal structural engineering of tissue- and organ-level cellular organization and microenvironment are also discussed to present integrative, bioengineering-directed approaches to achieve next-generation, high-fidelity embryoids and organoids.
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Affiliation(s)
- Yue Shao
- Institute of Biomechanics and Medical Engineering, Department of Engineering Mechanics, Tsinghua University, Beijing 100084, China; State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China.
| | - Jianping Fu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
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38
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Qu R, Gupta K, Dong D, Jiang Y, Landa B, Saez C, Strickland G, Levinsohn J, Weng PL, Taketo MM, Kluger Y, Myung P. Decomposing a deterministic path to mesenchymal niche formation by two intersecting morphogen gradients. Dev Cell 2022; 57:1053-1067.e5. [PMID: 35421372 PMCID: PMC9050909 DOI: 10.1016/j.devcel.2022.03.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/03/2022] [Accepted: 03/17/2022] [Indexed: 01/09/2023]
Abstract
Organ formation requires integrating signals to coordinate proliferation, specify cell fates, and shape tissue. Tracing these events and signals remains a challenge, as intermediate states across many critical transitions are unresolvable over real time and space. Here, we designed a unique computational approach to decompose a non-linear differentiation process into key components to resolve the signals and cell behaviors that drive a rapid transition, using the hair follicle dermal condensate as a model. Combining scRNA sequencing with genetic perturbation, we reveal that proliferative Dkk1+ progenitors transiently amplify to become quiescent dermal condensate cells by the mere spatiotemporal patterning of Wnt/β-catenin and SHH signaling gradients. Together, they deterministically coordinate a rapid transition from proliferation to quiescence, cell fate specification, and morphogenesis. Moreover, genetically repatterning these gradients reproduces these events autonomously in "slow motion" across more intermediates that resolve the process. This analysis unravels two morphogen gradients that intersect to coordinate events of organogenesis.
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Affiliation(s)
- Rihao Qu
- Computational Biology & Bioinformatics Program, Yale University, New Haven, CT 06520, USA; Department of Pathology, Yale University, New Haven, CT 06520, USA; Department of Immunobiology, Yale University, New Haven, CT 06520, USA
| | - Khusali Gupta
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Danni Dong
- Department of Dermatology, Yale University, New Haven, CT 06520, USA
| | - Yiqun Jiang
- Department of Dermatology, Yale University, New Haven, CT 06520, USA; Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Boris Landa
- Applied Mathematics Program, Yale University, New Haven, CT 06511, USA
| | - Charles Saez
- Department of Dermatology, Yale University, New Haven, CT 06520, USA
| | | | - Jonathan Levinsohn
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Pei-Lun Weng
- Department of Dermatology, Yale University, New Haven, CT 06520, USA
| | - M Mark Taketo
- Colon Cancer Project, Graduate School of Medicine, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yuval Kluger
- Computational Biology & Bioinformatics Program, Yale University, New Haven, CT 06520, USA; Department of Pathology, Yale University, New Haven, CT 06520, USA; Applied Mathematics Program, Yale University, New Haven, CT 06511, USA; Yale Cancer Center, New Haven, CT 06520, USA
| | - Peggy Myung
- Department of Pathology, Yale University, New Haven, CT 06520, USA; Department of Dermatology, Yale University, New Haven, CT 06520, USA; Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA; Yale Cancer Center, New Haven, CT 06520, USA; Yale Stem Cell Center, New Haven, CT 06520, USA.
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39
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Gallagher KD, Mani M, Carthew RW. Emergence of a geometric pattern of cell fates from tissue-scale mechanics in the Drosophila eye. eLife 2022; 11:72806. [PMID: 35037852 PMCID: PMC8863370 DOI: 10.7554/elife.72806] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 01/15/2022] [Indexed: 12/02/2022] Open
Abstract
Pattern formation of biological structures involves the arrangement of different types of cells in an ordered spatial configuration. In this study, we investigate the mechanism of patterning the Drosophila eye epithelium into a precise triangular grid of photoreceptor clusters called ommatidia. Previous studies had led to a long-standing biochemical model whereby a reaction-diffusion process is templated by recently formed ommatidia to propagate a molecular prepattern across the eye. Here, we find that the templating mechanism is instead, mechanochemical in origin; newly born columns of differentiating ommatidia serve as a template to spatially pattern flows that move epithelial cells into position to form each new column of ommatidia. Cell flow is generated by a source and sink, corresponding to narrow zones of cell dilation and contraction respectively, that straddle the growing wavefront of ommatidia. The newly formed lattice grid of ommatidia cells are immobile, deflecting, and focusing the flow of other cells. Thus, the self-organization of a regular pattern of cell fates in an epithelium is mechanically driven.
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Affiliation(s)
- Kevin D Gallagher
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States,NSF Simons Center for Quantitative Biology, Northwestern UniversityEvanstonUnited States
| | - Madhav Mani
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States,NSF Simons Center for Quantitative Biology, Northwestern UniversityEvanstonUnited States,Department of Engineering Sciences and Applied Mathematics, Northwestern UniversityEvanstonUnited States
| | - Richard W Carthew
- Department of Molecular Biosciences, Northwestern UniversityEvanstonUnited States,NSF Simons Center for Quantitative Biology, Northwestern UniversityEvanstonUnited States
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40
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Hadjivasiliou Z, Hunter G. Talking to your neighbors across scales: Long-distance Notch signaling during patterning. Curr Top Dev Biol 2022; 150:299-334. [DOI: 10.1016/bs.ctdb.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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41
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Krause AL, Gaffney EA, Maini PK, Klika V. Modern perspectives on near-equilibrium analysis of Turing systems. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2021; 379:20200268. [PMID: 34743603 PMCID: PMC8580451 DOI: 10.1098/rsta.2020.0268] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/18/2021] [Indexed: 05/02/2023]
Abstract
In the nearly seven decades since the publication of Alan Turing's work on morphogenesis, enormous progress has been made in understanding both the mathematical and biological aspects of his proposed reaction-diffusion theory. Some of these developments were nascent in Turing's paper, and others have been due to new insights from modern mathematical techniques, advances in numerical simulations and extensive biological experiments. Despite such progress, there are still important gaps between theory and experiment, with many examples of biological patterning where the underlying mechanisms are still unclear. Here, we review modern developments in the mathematical theory pioneered by Turing, showing how his approach has been generalized to a range of settings beyond the classical two-species reaction-diffusion framework, including evolving and complex manifolds, systems heterogeneous in space and time, and more general reaction-transport equations. While substantial progress has been made in understanding these more complicated models, there are many remaining challenges that we highlight throughout. We focus on the mathematical theory, and in particular linear stability analysis of 'trivial' base states. We emphasize important open questions in developing this theory further, and discuss obstacles in using these techniques to understand biological reality. This article is part of the theme issue 'Recent progress and open frontiers in Turing's theory of morphogenesis'.
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Affiliation(s)
- Andrew L. Krause
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, UK
- Department of Mathematical Sciences, Durham University, Upper Mountjoy Campus, Stockton Rd, Durham DH1 3LE, UK
| | - Eamonn A. Gaffney
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, UK
| | - Philip K. Maini
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, UK
| | - Václav Klika
- Department of Mathematics, FNSPE, Czech Technical University in Prague, Trojanova, 13, 12000 Praha, Czech Republic
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42
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Painter KJ, Ptashnyk M, Headon DJ. Systems for intricate patterning of the vertebrate anatomy. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2021; 379:20200270. [PMID: 34743605 PMCID: PMC8580425 DOI: 10.1098/rsta.2020.0270] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/11/2021] [Indexed: 05/05/2023]
Abstract
Periodic patterns form intricate arrays in the vertebrate anatomy, notably the hair and feather follicles of the skin, but also internally the villi of the gut and the many branches of the lung, kidney, mammary and salivary glands. These tissues are composite structures, being composed of adjoined epithelium and mesenchyme, and the patterns that arise within them require interaction between these two tissue layers. In embryonic development, cells change both their distribution and state in a periodic manner, defining the size and relative positions of these specialized structures. Their placement is determined by simple spacing mechanisms, with substantial evidence pointing to a variety of local enhancement/lateral inhibition systems underlying the breaking of symmetry. The nature of the cellular processes involved, however, has been less clear. While much attention has focused on intercellular soluble signals, such as protein growth factors, experimental evidence has grown for contributions of cell movement or mechanical forces to symmetry breaking. In the mesenchyme, unlike the epithelium, cells may move freely and can self-organize into aggregates by chemotaxis, or through generation and response to mechanical strain on their surrounding matrix. Different modes of self-organization may coexist, either coordinated into a single system or with hierarchical relationships. Consideration of a broad range of distinct biological processes is required to advance understanding of biological pattern formation. This article is part of the theme issue 'Recent progress and open frontiers in Turing's theory of morphogenesis'.
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Affiliation(s)
- Kevin J. Painter
- Dipartimento Interateneo di Scienze, Progetto e Politiche del Territorio, Politecnico di Torino, Torino, Italy
| | - Mariya Ptashnyk
- School of Mathematical and Computer Sciences and Maxwell Institute, Heriot-Watt University, Edinburgh, UK
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43
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Pereyra M, Drusko A, Krämer F, Strobl F, Stelzer EHK, Matthäus F. QuickPIV: Efficient 3D particle image velocimetry software applied to quantifying cellular migration during embryogenesis. BMC Bioinformatics 2021; 22:579. [PMID: 34863116 PMCID: PMC8642913 DOI: 10.1186/s12859-021-04474-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 10/15/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The technical development of imaging techniques in life sciences has enabled the three-dimensional recording of living samples at increasing temporal resolutions. Dynamic 3D data sets of developing organisms allow for time-resolved quantitative analyses of morphogenetic changes in three dimensions, but require efficient and automatable analysis pipelines to tackle the resulting Terabytes of image data. Particle image velocimetry (PIV) is a robust and segmentation-free technique that is suitable for quantifying collective cellular migration on data sets with different labeling schemes. This paper presents the implementation of an efficient 3D PIV package using the Julia programming language-quickPIV. Our software is focused on optimizing CPU performance and ensuring the robustness of the PIV analyses on biological data. RESULTS QuickPIV is three times faster than the Python implementation hosted in openPIV, both in 2D and 3D. Our software is also faster than the fastest 2D PIV package in openPIV, written in C++. The accuracy evaluation of our software on synthetic data agrees with the expected accuracies described in the literature. Additionally, by applying quickPIV to three data sets of the embryogenesis of Tribolium castaneum, we obtained vector fields that recapitulate the migration movements of gastrulation, both in nuclear and actin-labeled embryos. We show normalized squared error cross-correlation to be especially accurate in detecting translations in non-segmentable biological image data. CONCLUSIONS The presented software addresses the need for a fast and open-source 3D PIV package in biological research. Currently, quickPIV offers efficient 2D and 3D PIV analyses featuring zero-normalized and normalized squared error cross-correlations, sub-pixel/voxel approximation, and multi-pass. Post-processing options include filtering and averaging of the resulting vector fields, extraction of velocity, divergence and collectiveness maps, simulation of pseudo-trajectories, and unit conversion. In addition, our software includes functions to visualize the 3D vector fields in Paraview.
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Affiliation(s)
- Marc Pereyra
- Frankfurt Institute for Advanced Studies (FIAS) and Goethe Universität Frankfurt am Main, Ruth-Moufang-Straße 1, 60438 Frankfurt am Main, Germany
| | - Armin Drusko
- Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany
| | - Franziska Krämer
- Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue Straße 15, 60438 Frankfurt am Main, Germany
| | - Frederic Strobl
- Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue Straße 15, 60438 Frankfurt am Main, Germany
| | - Ernst H. K. Stelzer
- Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue Straße 15, 60438 Frankfurt am Main, Germany
| | - Franziska Matthäus
- Frankfurt Institute for Advanced Studies (FIAS) and Goethe Universität Frankfurt am Main, Ruth-Moufang-Straße 1, 60438 Frankfurt am Main, Germany
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44
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Bedekar P, Timofeyev I, Warmflash A, Perepelitsa M. Reaction-diffusion models for morphological patterning of hESCs. J Math Biol 2021; 83:55. [PMID: 34727234 DOI: 10.1007/s00285-021-01674-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 07/04/2021] [Accepted: 09/08/2021] [Indexed: 10/19/2022]
Abstract
In this paper we consider mathematical modeling of the dynamics of self-organized patterning of spatially confined human embryonic stem cells (hESCs) treated with BMP4 (gastruloids) described in recent experimental works (Warmflash in Nat Methods 11:847-854, 2014; Chhabra in PloS Biol 17: 3000498, 2019). In the first part of the paper we use the activator-inhibitor equations of Gierer and Meinhardt to identify 3 reaction-diffusion regimes for each of the three morphogenic proteins, BMP4, Wnt and Nodal, based on the characteristic features of the dynamic patterning. We identify appropriate boundary conditions which correspond to the experimental setup and perform numerical simulations of the reaction-diffusion (RD) systems, using the finite element approximation, to confirm that the RD systems in these regimes produce realistic dynamics of the protein concentrations. In the second part of the paper we use analytic tools to address the questions of the existence and stability of non-homogeneous steady states for the reaction-diffusion systems of the type considered in the first part of the paper.
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Affiliation(s)
- Prajakta Bedekar
- Department of Mathematics, University of Houston, Houston, TX, United States
| | - Ilya Timofeyev
- Department of Mathematics, University of Houston, Houston, TX, United States
| | - Aryeh Warmflash
- Laboratory of Systems Stem Cell and Developmental Biology, Department of BioSciences, Rice University, Houston, TX, United States
| | - Misha Perepelitsa
- Department of Mathematics, University of Houston, Houston, TX, United States.
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45
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Pas K, Laboy-Segarra S, Lee J. Systems of pattern formation within developmental biology. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 167:18-25. [PMID: 34619250 DOI: 10.1016/j.pbiomolbio.2021.09.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/19/2021] [Accepted: 09/30/2021] [Indexed: 01/10/2023]
Abstract
Applications of mathematical models to developmental biology have provided helpful insight into various subfields, ranging from the patterning of animal skin to the development of complex organ systems. Systems involved in patterning within morphology present a unique path to explain self-organizing systems. Current efforts show that patterning systems, notably Reaction-Diffusion and specific signaling pathways, provide insight for explaining morphology and could provide novel applications revolving around the formation of biological systems. Furthermore, the application of pattern formation provides a new perspective on understanding developmental biology and pathology research to study molecular mechanisms. The current review is to cover and take a more in-depth overlook at current applications of patterning systems while also building on the principles of patterning of future research in predictive medicine.
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Affiliation(s)
- Kristofor Pas
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX, USA
| | | | - Juhyun Lee
- Department of Bioengineering, University of Texas at Arlington, Arlington, TX, USA; Department of Medical Education, TCU and UNTHSC School of Medicine, Fort Worth, TX, 76107, USA.
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46
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Kaelin CB, McGowan KA, Barsh GS. Developmental genetics of color pattern establishment in cats. Nat Commun 2021; 12:5127. [PMID: 34493721 PMCID: PMC8423757 DOI: 10.1038/s41467-021-25348-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 07/22/2021] [Indexed: 11/09/2022] Open
Abstract
Intricate color patterns are a defining aspect of morphological diversity in the Felidae. We applied morphological and single-cell gene expression analysis to fetal skin of domestic cats to identify when, where, and how, during fetal development, felid color patterns are established. Early in development, we identify stripe-like alterations in epidermal thickness preceded by a gene expression pre-pattern. The secreted Wnt inhibitor encoded by Dickkopf 4 plays a central role in this process, and is mutated in cats with the Ticked pattern type. Our results bring molecular understanding to how the leopard got its spots, suggest that similar mechanisms underlie periodic color pattern and periodic hair follicle spacing, and identify targets for diverse pattern variation in other mammals.
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Affiliation(s)
- Christopher B Kaelin
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Kelly A McGowan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
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47
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Abstract
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.
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48
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Krause AL, Klika V, Maini PK, Headon D, Gaffney EA. Isolating Patterns in Open Reaction-Diffusion Systems. Bull Math Biol 2021; 83:82. [PMID: 34089093 PMCID: PMC8178156 DOI: 10.1007/s11538-021-00913-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 05/13/2021] [Indexed: 01/14/2023]
Abstract
Realistic examples of reaction-diffusion phenomena governing spatial and spatiotemporal pattern formation are rarely isolated systems, either chemically or thermodynamically. However, even formulations of 'open' reaction-diffusion systems often neglect the role of domain boundaries. Most idealizations of closed reaction-diffusion systems employ no-flux boundary conditions, and often patterns will form up to, or along, these boundaries. Motivated by boundaries of patterning fields related to the emergence of spatial form in embryonic development, we propose a set of mixed boundary conditions for a two-species reaction-diffusion system which forms inhomogeneous solutions away from the boundary of the domain for a variety of different reaction kinetics, with a prescribed uniform state near the boundary. We show that these boundary conditions can be derived from a larger heterogeneous field, indicating that these conditions can arise naturally if cell signalling or other properties of the medium vary in space. We explain the basic mechanisms behind this pattern localization and demonstrate that it can capture a large range of localized patterning in one, two, and three dimensions and that this framework can be applied to systems involving more than two species. Furthermore, the boundary conditions proposed lead to more symmetrical patterns on the interior of the domain and plausibly capture more realistic boundaries in developmental systems. Finally, we show that these isolated patterns are more robust to fluctuations in initial conditions and that they allow intriguing possibilities of pattern selection via geometry, distinct from known selection mechanisms.
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Affiliation(s)
- Andrew L Krause
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, UK.
| | - Václav Klika
- Department of Mathematics, FNSPE, Czech Technical University in Prague, Trojanova 13, 120 00, Praha, Czech Republic
| | - Philip K Maini
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, UK
| | - Denis Headon
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Eamonn A Gaffney
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, UK
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49
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Jin S, Guerrero-Juarez CF, Zhang L, Chang I, Ramos R, Kuan CH, Myung P, Plikus MV, Nie Q. Inference and analysis of cell-cell communication using CellChat. Nat Commun 2021; 12:1088. [PMID: 33597522 PMCID: PMC7889871 DOI: 10.1038/s41467-021-21246-9] [Citation(s) in RCA: 2614] [Impact Index Per Article: 871.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 01/08/2021] [Indexed: 01/31/2023] Open
Abstract
Understanding global communications among cells requires accurate representation of cell-cell signaling links and effective systems-level analyses of those links. We construct a database of interactions among ligands, receptors and their cofactors that accurately represent known heteromeric molecular complexes. We then develop CellChat, a tool that is able to quantitatively 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. Applying CellChat to mouse and human skin datasets shows its ability to extract complex signaling patterns. 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 cell-cell communication atlases in diverse tissues.
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Affiliation(s)
- Suoqin Jin
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
| | - Christian F Guerrero-Juarez
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA
| | - Lihua Zhang
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
| | - Ivan Chang
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA
- Research Cyberinfrastructure Center, University of California, Irvine, Irvine, CA, USA
| | - Raul Ramos
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA
| | - Chen-Hsiang Kuan
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Division of Plastic Surgery, Department of Surgery, National Taiwan University, Taipei, Taiwan
| | - Peggy Myung
- Department of Dermatology, Yale University, New Haven, CT, USA
- Department of Pathology, Yale University, New Haven, CT, USA
| | - Maksim V Plikus
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA.
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA.
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, USA.
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA.
- NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, USA.
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA.
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50
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Krause AL, Klika V, Halatek J, Grant PK, Woolley TE, Dalchau N, Gaffney EA. Turing Patterning in Stratified Domains. Bull Math Biol 2020; 82:136. [PMID: 33057872 PMCID: PMC7561598 DOI: 10.1007/s11538-020-00809-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/18/2020] [Indexed: 01/06/2023]
Abstract
Reaction-diffusion processes across layered media arise in several scientific domains such as pattern-forming E. coli on agar substrates, epidermal-mesenchymal coupling in development, and symmetry-breaking in cell polarization. We develop a modeling framework for bilayer reaction-diffusion systems and relate it to a range of existing models. We derive conditions for diffusion-driven instability of a spatially homogeneous equilibrium analogous to the classical conditions for a Turing instability in the simplest nontrivial setting where one domain has a standard reaction-diffusion system, and the other permits only diffusion. Due to the transverse coupling between these two regions, standard techniques for computing eigenfunctions of the Laplacian cannot be applied, and so we propose an alternative method to compute the dispersion relation directly. We compare instability conditions with full numerical simulations to demonstrate impacts of the geometry and coupling parameters on patterning, and explore various experimentally relevant asymptotic regimes. In the regime where the first domain is suitably thin, we recover a simple modulation of the standard Turing conditions, and find that often the broad impact of the diffusion-only domain is to reduce the ability of the system to form patterns. We also demonstrate complex impacts of this coupling on pattern formation. For instance, we exhibit non-monotonicity of pattern-forming instabilities with respect to geometric and coupling parameters, and highlight an instability from a nontrivial interaction between kinetics in one domain and diffusion in the other. These results are valuable for informing design choices in applications such as synthetic engineering of Turing patterns, but also for understanding the role of stratified media in modulating pattern-forming processes in developmental biology and beyond.
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Affiliation(s)
- Andrew L Krause
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, UK.
| | - Václav Klika
- Department of Mathematics, FNSPE, Czech Technical University in Prague, Trojanova 13, 120 00, Prague, Czech Republic
| | - Jacob Halatek
- Microsoft Research, 21 Station Rd, Cambridge, CB1 2FB, UK
| | - Paul K Grant
- Microsoft Research, 21 Station Rd, Cambridge, CB1 2FB, UK
| | - Thomas E Woolley
- Cardiff School of Mathematics, Cardiff University, Senghennydd Road, Cardiff, CF24 4AG, UK
| | - Neil Dalchau
- Microsoft Research, 21 Station Rd, Cambridge, CB1 2FB, UK
| | - Eamonn A Gaffney
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG, UK
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