A Minimal Regulatory Network of Extrinsic and Intrinsic Factors Recovers Observed Patterns of CD4+ T Cell Differentiation and Plasticity

PLoS Comput Biol. 2015 Jun 19;11(6):e1004324. doi: 10.1371/journal.pcbi.1004324. eCollection 2015 Jun.

Abstract

CD4+ T cells orchestrate the adaptive immune response in vertebrates. While both experimental and modeling work has been conducted to understand the molecular genetic mechanisms involved in CD4+ T cell responses and fate attainment, the dynamic role of intrinsic (produced by CD4+ T lymphocytes) versus extrinsic (produced by other cells) components remains unclear, and the mechanistic and dynamic understanding of the plastic responses of these cells remains incomplete. In this work, we studied a regulatory network for the core transcription factors involved in CD4+ T cell-fate attainment. We first show that this core is not sufficient to recover common CD4+ T phenotypes. We thus postulate a minimal Boolean regulatory network model derived from a larger and more comprehensive network that is based on experimental data. The minimal network integrates transcriptional regulation, signaling pathways and the micro-environment. This network model recovers reported configurations of most of the characterized cell types (Th0, Th1, Th2, Th17, Tfh, Th9, iTreg, and Foxp3-independent T regulatory cells). This transcriptional-signaling regulatory network is robust and recovers mutant configurations that have been reported experimentally. Additionally, this model recovers many of the plasticity patterns documented for different T CD4+ cell types, as summarized in a cell-fate map. We tested the effects of various micro-environments and transient perturbations on such transitions among CD4+ T cell types. Interestingly, most cell-fate transitions were induced by transient activations, with the opposite behavior associated with transient inhibitions. Finally, we used a novel methodology was used to establish that T-bet, TGF-β and suppressors of cytokine signaling proteins are keys to recovering observed CD4+ T cell plastic responses. In conclusion, the observed CD4+ T cell-types and transition patterns emerge from the feedback between the intrinsic or intracellular regulatory core and the micro-environment. We discuss the broader use of this approach for other plastic systems and possible therapeutic interventions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • CD4-Positive T-Lymphocytes / immunology*
  • Cell Differentiation / immunology*
  • Cell Plasticity / immunology*
  • Cellular Microenvironment
  • Computational Biology
  • Cytokines / metabolism
  • Models, Immunological*
  • Signal Transduction / immunology*

Substances

  • Cytokines

Grants and funding

This work was supported by grants from: Consejo Nacional de Ciencia y Tecnología México (www.conacyt.mx): 180380 to CV and ERAB, and 180098 to (ERAB). Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica Universidad Nacional Autónoma de México (dgapa.unam.mx/html/papiit/papit.html): IN203113; IN204011; IN226510-3 and IN203814 to ERAB. Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica Universidad Nacional Autónoma de México (dgapa.unam.mx/html/papiit/papit.html): IN200514 to LM. MEMS acknowledges support from the graduate program “Doctorado en Ciencias Biomédicas, de la Universidad Nacional Autónoma de México”. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.