title: Multiscale feature analysis of salivary gland branching morphogenesis.
abstract: Pattern formation in developing tissues involves dynamic spatio-temporal changes in cellular organization and subsequent evolution of functional adult structures. Branching morphogenesis is a developmental mechanism by which patterns are generated in many developing organs, which is controlled by underlying molecular pathways. Understanding the relationship between molecular signaling, cellular behavior and resulting morphological change requires quantification and categorization of the cellular behavior. In this study, tissue-level and cellular changes in developing salivary gland in response to disruption of ROCK-mediated signaling by are modeled by building cell-graphs to compute mathematical features capturing structural properties at multiple scales. These features were used to generate multiscale cell-graph signatures of untreated and ROCK signaling disrupted salivary gland organ explants. From confocal images of mouse submandibular salivary gland organ explants in which epithelial and mesenchymal nuclei were marked, a multiscale feature set capturing global structural properties, local structural properties, spectral, and morphological properties of the tissues was derived. Six feature selection algorithms and multiway modeling of the data was performed to identify distinct subsets of cell graph features that can uniquely classify and differentiate between different cell populations. Multiscale cell-graph analysis was most effective in classification of the tissue state. Cellular and tissue organization, as defined by a multiscale subset of cell-graph features, are both quantitatively distinct in epithelial and mesenchymal cell types both in the presence and absence of ROCK inhibitors. Whereas tensor analysis demonstrate that epithelial tissue was affected the most by inhibition of ROCK signaling, significant multiscale changes in mesenchymal tissue organization were identified with this analysis that were not identified in previous biological studies. We here show how to define and calculate a multiscale feature set as an effective computational approach to identify and quantify changes at multiple biological scales and to distinguish between different states in developing tissues.
authors.affiliation: Rensselaer Polytechnic Institute, Computer Science Department, Troy, New York, United States of America.
authors.forename: Cemal Cagatay
authors.initials: CC
authors.lastname: Bilgin
authors.forename: Shayoni
authors.initials: S
authors.lastname: Ray
authors.forename: Banu
authors.initials: B
authors.lastname: Baydil
authors.forename: William P
authors.initials: WP
authors.lastname: Daley
authors.forename: Melinda
authors.initials: M
authors.lastname: Larsen
authors.forename: Bülent
authors.initials: B
authors.lastname: Yener
mesh_terms: D000818:Animals; D001185:Artificial Intelligence; D002467:Cell Nucleus / Q000187:drug effects / Q000378:metabolism; D003196:Computer Graphics; D004847:Epithelial Cells / Q000166:cytology / Q000187:drug effects / Q000378:metabolism; D008648:Mesoderm / Q000166:cytology / Q000187:drug effects; D051379:Mice; D008954:Models, Biological; D057054:Molecular Imaging; D009024:Morphogenesis / Q000187:drug effects; D047428:Protein Kinase Inhibitors / Q000494:pharmacology; D015203:Reproducibility of Results; D012469:Salivary Glands / Q000166:cytology / Q000254:growth & development* / Q000378:metabolism; D015398:Signal Transduction / Q000187:drug effects; D054460:rho-Associated Kinases / Q000037:antagonists & inhibitors / Q000378:metabolism
chemical_list: D047428:Protein Kinase Inhibitors; D054460:rho-Associated Kinases