An Integrative Network Modeling Approach to T CD4 Cell Activation

David Martínez-Méndez; Carlos Villarreal; Luis Mendoza; Leonor Huerta

doi:10.3389/fphys.2020.00380

An Integrative Network Modeling Approach to T CD4 Cell Activation

Front Physiol. 2020 Apr 23:11:380. doi: 10.3389/fphys.2020.00380. eCollection 2020.

Authors

David Martínez-Méndez¹, Carlos Villarreal^{2

3}, Luis Mendoza^{1

3}, Leonor Huerta¹

Affiliations

¹ Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico.
² Instituto de Física, Universidad Nacional Autónoma de México, Mexico City, Mexico.
³ Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico.

Abstract

The adaptive immune response is initiated by the interaction of the T cell antigen receptor/CD3 complex (TCR) with a cognate peptide bound to a MHC molecule. This interaction, along with the activity of co-stimulatory molecules and cytokines in the microenvironment, enables cells to proliferate and produce soluble factors that stimulate other branches of the immune response for inactivation of infectious agents. The intracellular activation signals are reinforced, amplified and diversified by a complex network of biochemical interactions, and includes the activity of molecules that modulate the activation process and stimulate the metabolic changes necessary for fulfilling the cell energy demands. We present an approach to the analysis of the main early signaling events of T cell activation by proposing a concise 46-node hybrid Boolean model of the main steps of TCR and CD28 downstream signaling, encompassing the activity of the anergy factor Ndrg1, modulation of activation by CTLA-4, and the activity of the nutrient sensor AMPK as intrinsic players of the activation process. The model generates stable states that reflect the overcoming of activation signals and induction of anergy by the expression of Ndrg1 in the absence of co-stimulation. The model also includes the induction of CTLA-4 upon activation and its competition with CD28 for binding to the co-stimulatory CD80/86 molecules, leading to stable states that reflect the activation arrest. Furthermore, the model integrates the activity of AMPK to the general pathways driving differentiation to functional cell subsets (Th1, Th2, Th17, and Treg). Thus, the network topology incorporates basic mechanism associated to activation, regulation and induction of effector cell phenotypes. The model puts forth a conceptual framework for the integration of functionally relevant processes in the analysis of the T CD4 cell function.

Keywords: AMPK; Boolean model; CD28; CTLA-4; NDRG1; T CD4 cells; TCR; complex network.