Grantee: University of Arizona, Tucson, AZ, USA
Researcher: Pierre A. Deymier, Ph.D.
Grant Title: Theoretical and experimental investigations of architecture-dependent signaling in multicellular networks
https://doi.org/10.37717/220020222
Program Area: Studying Complex Systems
Grant Type: Research Award
Amount: $437,060
Year Awarded: 2010
Duration: 3 years
Multi-level organization and dynamics is a hallmark feature of most biological systems. This is particularly true in cellular tissues in which single cells are organized into multi-cellular tissues which are further assembled into complex organs. Central to the proper behavior in these biological systems is a cross-level interdependence. To date, limited studies of signaling in multicellular networks have demonstrated that the architecture of multi-cellular systems can have a significant impact on the behavior of individual cells as well as their emerging collective behavior. From, emerging properties and functions of multicellular structures to health and structural reorganization of tissues, architecture-dependent signals serve as pathways to transmit information that encodes the cues and regulates the working of the constitutive elements (e.g. cells, groups of cells).
Over the past decade, questions concerning the interactions between cells and their environment/architecture have received increasing attention from tumorigenesis, to tissue engineering to angiogenesis. For instance, there is strong evidence that the branching architecture of the mammary gland and associated cellular signaling are major regulators of epithelial cell function [1,2] or disregulation [3]. The disfunction of interactions between the genome, metabolism, and tissue can impact the probability of cancer [4,5] and a normal organ architecture can suppress tumor formation and prevent malignant phenotypes even in grossly abnormal cells [6]. Tissue engineering in its attempt to construct functional tissues faces the challenge of arranging cells (e.g. scaffolding via decellularization of allograph tissue) in a three-dimensional configuration with an architecture analogous to the native tissue, that supports molecular signals with the spatial and temporal characteristics that can sustain appropriate development and function [7-9]. Also, downstream and upstream signal conduction between endothelial cells along the walls of vessels is playing an important role in circulatory function of formed vasculatures, vascular network remodeling, vasculogenesis and neovascularisation [10].
A particularly relevant aspect is the emerging behavior of a multicellular architecture in which celllevel functions, such as intracellular pathways, integrate with multicellular architectures through cellto- cell interactions. Central to this problem is that cellular networks inherently combine dynamical and structural complexity. Early progress on modeling coupled dynamical systems was limited to spaceindependent coupling or regular network topologies. Further progress to circumvent the difficulty associated with the combined complexity of the dynamics and of the architecture was achieved by taking a complementary approach where the dynamics of the network nodes is set aside and the emphasis is placed on the complexity of the network architecture [11]. These models have had great impact on network science and relevance across numerous disciplines ranging from physical sciences, to social sciences to computer science and life sciences.
Yet despite the tremendous progresses in network science, there is a risk in explaining the biology of multicellular architecture from a purely network point of view without considering the complexity of the intracellular pathways occurring at the network nodes. Specifically, we are still lacking a fundamental framework for understanding the integration of lower-order activity (e.g. cell signaling) with higher-order, multicellular architecture to produce a multilevel description of biological organization and function in tissues. Furthermore, most experiments describe the impact of one level on another and not the key aspects of the important regulatory loops, central dynamical features. Moreover, in studies where some insight into the role a single molecule might play across multiple orders or levels (e.g. knockout mouse studies), there remains a paucity of conceptual models that fully integrate the highly dynamic and complex nature of many-ordered biological systems.
From a theoretical perspective, Othmer and Scriven [12] developed, following Turing's pioneering mathematical treatise of morphogenesis [13], an analysis technique in which the information about the underlying network topology, through a connectivity matrix, is decoupled from that of the intracellular reaction pathway mechanism, thus enabling progress in multicellular network research that includes complexity at both low and high levels. In a series of studies [14,15], our research led us to use the Green's function-based Interface Response Theory (IRT) [16], a method originally developed for tackling composite media in condensed matter physics, to augment Scriven-Othmer's method to solve coupled dynamical networks with nontrivial connectivity matrices and therefore integrate natural biological organization from the cellular level to complex network architectures. We used this approach to calculate analytically the spectrum of propagating compositional waves in models of multicellular architectures and to study putative signal conduction dynamics across networks of endothelial cells. Compositional waves originating from simulated intracellular Ca2+ and inositol triphosphate (IP3) negative feedback loops in endothelial cells were shown to be shaped by the connection topologies of networks. Considering models of networks constituted of a main chain of endothelial cells and multiple side chains in ordered, defected, or disordered topologies; we showed that transmission spectra of compositional waves encode architectural information separately in terms of spatial arrangement and branch length via scattering and resonant filtering, respectively.
This discovery has striking implications on the role of calcium signaling on cross-level interdependence in multicellular architectures in terms of signal generation and decoding. For example, the generation of architecture-dependent signaling necessitates cellular control over calcium and IP3 self-regulation as well as control over oscillation frequency via calcium regulation of IP3 concentration. On the other hand, decoding of structural information by individual cells would also need cellular control on frequency dependent intracellular pathways such as frequency-dependent protein phosphorylation by a Ca2+ -calmodulin activated kinase which was shown to be ubiquitous in wide variety of cell types [17]. Therefore, it seems more likely that our calcium-based frequencyencoded wave-like signaling is operative in a range of multicellular architectures and tissues. For instance in the transformation of preformed vasculatures, vessel branching would tend to reinforce cellular response by positional order potentially leading to additional regularity in the architecture. As the spatial extent of the architecture is strongly influenced by the reaction for key cellular compounds, the same mechanisms could be applied in many biological structures such as various organs, muscles, connective tissues or the nervous system.
These implications highlight the need for careful research on the effects of long-range conductive signals emerging from cross-level interactions that may play a role in the function and development of multicellular architectures. They also highlight the growing need for the combined development of theoretical and experimental research approaches that can describe the dynamical response at the cellular level of complex multicellular structures. The problem of extracting dynamical data on calcium-based signaling in natural biological tissues is a difficult one due to the uncontrollable nature of the architecture, due to the presence of extracellular matrix and to its variable cellular composition. Without a means for testing the predictions of theoretical models in the form of controlled experiments there is little hope to make significant progress in shedding light on the cross-level interactions leading to architecture-dependent signaling. Decoupled experiment and theoretical research have little chance of establish a clear picture of this emerging paradigm.
This proposal focuses on the development of a new approach with complementary integration of theoretical and experimental methods for studying the cross-level interactions in multicellular architectures and their effect on collective dynamic behavior. The intent is to produce calcium-based cross-level protocols that exist in biological systems, describe new types of higher-order behaviors arising from lower-order phenomena, and make predictions concerning the mechanisms underlying the dynamics of multi-order biological systems. The theoretical approach to be used focuses on the exploration of the linear and non-linear behavior of calcium-based signaling in model networks of endothelial cells through Green's function IRT methodologies. This research will also pioneer the use of microengineered geometrically-constrained networks of endothelial cells to serve as platforms to arbitrate the theoretical predictions in terms of the effect of network topology on the spatiotemporal characteristics of emerging calcium signals. Geometrically unconstrained networks patterned by a direct-write tissue printing tool will be used to interrogate single cell response as well as the response of entire networks (such as remodeling) to structure-dependent signals. This joint approach will profoundly impact the field of cross-level interdependence in multicellular networks as there have not been previously methods for correlating reliably and systematically theoretical predictions with experimental observations in homologous model networks.
The proposed research focuses on the study of prototypical networks of nearly one-dimensional chains of endothelial cells. The success of this joint experimental and theoretical work will lead to unambiguous understanding of cross-level signaling that could not be studied in less controllable tissues. The proposed methods will allow us to identify the effects of structural features on the dynamics of the cellular networks and separate spectral characteristics of the complex behavior of the dynamical networks resulting from organizational (scattering) and structural (resonances) processes.
Our goal is to develop a new model-based theoretical and experimental framework to shed light on the poorly understood phenomenon of cross-level interactions in complex and dynamic multicellular structures. While there is considerable amount of knowledge on the behavior of individual cells, there is only a beginning of recognition that the unit of function in higher organisms is not the individual cell, but the tissue itself. Indeed, tissue architecture and/or microenvironment influence lower-order biology at the intracellular level and vice versa. The proposed research leverages progresses in modeling of the dynamics of complex network system, progresses in microengineering of multicellular structures and tissue engineering to develop the necessary approaches to understanding multicellular architecture and the procedures that govern the transmission of information between its cellular constitutive elements.
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