Abstract
The CD4+ T cell lineages Th1, Th2, Th17, and Treg, are mammalian cell types that differentiate from the common precursor naive CD4+ T cell. While there is a wealth of experimental data regarding the molecular and cellular signals involved in the differentiation of CD4+ T cells in vitro, there is still no consensus regarding the structure of the network of interactions at the molecular and cellular levels controlling this differentiation process. In this work, a virtual culture of cells is constructed by interconnecting several instances of an updated version of the regulatory network controlling the differentiation process of CD4+ T cells in mice. The virtual culture is a multi-compartment model with an instance of a regulatory network inside each compartment, thus simulating a simplified version of a cell culture in a well-stirred reactor. The virtual culture is able to describe the stable molecular expression patterns described for fully differentiated CD4+ T cells in mice, as well as the differentiation process from a precursor to a given effector cell in response to specific molecular stimuli.
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Acosta-Rodriguez, E. V., Rivino, L., Geginat, J., Jarrossay, D., Gattorno, M., Lanzavecchia, A., Sallusto, F., & Napolitani, G. (2007). Surface phenotype and antigenic specificity of human interleukin 17-producing T helper memory cells. Nat. Immunol., 8, 639–646.
Akdis, C. A. (2008). New insights into mechanisms of immunoregulation in 2007. J. Allergy Clin. Immunol., 122, 700–709.
Albert, R., & Wang, R. S. (2009). Discrete dynamic modeling of cellular signaling networks. Methods Enzymol., 467, 281–306.
Bettelli, E., Carrier, Y., Gao, W., Korn, T., Strom, T. B., Oukka, M., Weiner, H. L., & Kuchroo, V. K. (2006). Reciprocal developmental pathways for the generation of pathogenic effector Th17 and regulatory T cells. Nature, 441, 235–238.
Bornholdt, S. (2008). Boolean network models of cellular regulation: prospects and limitations. J. R. Soc. Interface, 5, S85–S94.
Busse, D., de la Rosa, M., Hobiger, K., Thurley, K., Flossdorf, M., Scheffold, A., & Höfer, T. (2010). Competing feedback loops shape IL-2 signaling between helper and regulatory T lymphocytes in cellular microenvironments. Proc. Natl. Acad. Sci. USA, 107, 3058–3063.
Chang, J. T., Segal, B. M., Nakanishi, K., Okamura, H., & Shevach, E. M. (2000). The costimulatory effect of IL-18 on the induction of antigenspecific IFN-gamma production by resting T cells is IL-12 dependent and is mediated by up-regulation of the IL-12 receptor beta2 subunit. Eur. J. Immunol., 30, 1113–1119.
Chen, X. P., Losman, J. A., & Rothman, P. (2000). SOCS proteins, regulators of intracellular signaling. Immunity, 13, 287–290.
Chen, W., Jin, W., Hardegen, N., Lei, K., Li, L., Marinos, N., McGrady, G., & Wahl, S. M. (2003). Conversion of peripheral CD4+CD25− naive T cells to CD4+CD25+ regulatory T cells by TGF-β induction of transcription factor Foxp3. J. Exp. Med., 198, 1875–1886.
De Jong, H. (2002). Modeling and simulation of genetic regulatory systems: a literature review. J. Comput. Biol., 9, 67–103.
Di Cara, A., Garg, A., De Micheli, G., Xenarios, I., & Mendoza, L. (2007). Dynamic simulation of regulatory networks using SQUAD. BMC Bioinform., 8, 462.
Diehl, S., Anguita, J., Hoffmeyer, A., Zapton, T., Ihle, J. N., Fikrig, E., & Rincón, M. (2000). Inhibition of Th1 differentiation by IL-6 is mediated by SOCS1. Immunity, 13, 805–815.
Elser, B., Lohoff, M., Kock, S., Giaisi, M., Kirchhoff, S., Krammer, P. H., & Li-Weber, M. (2002). IFN-γ represses IL-4 expression via IRF-1 and IRF-2. Immunity, 17, 703–712.
Fantini, M. C., Becker, C., Monteleone, G., Pallone, F., Galle, P. R., & Neurath, M. F. (2004). Cutting edge: TGF-β induces a regulatory phenotype in CD4+CD25− T cells through Foxp3 induction and down-regulation of Smad7. J. Immunol., 172, 5149–5153.
Folcik, V. A., An, G. C., & Orosz, C. G. (2007). The Basic Immune Simulator: an agent-based model to study the interactions between innate and adaptive immunity. Theor. Biol. Med. Model., 4, 39.
Gavin, M. A., Rasmussen, J. P., Fontenot, J. D., Vasta, V., Manganiello, V. C., Beavo, J. A., & Rudensky, A. Y. (2007). Foxp3-dependent programme of regulatory T-cell differentiation. Nature, 445, 771–775.
Geard, N., & Willadsen, K. (2009). Dynamical approaches to modeling developmental gene regulatory networks. Birth Defects Res. C, Embryo Today, 87, 131–142.
Goodbourn, S., Didcock, L., & Randal, R. E. (2000). Interferons: cell signalling, immune modulation, antiviral responses and virus countermeasures. J. Gen. Virol., 81, 2341–2364.
Hamalainen, H., Zhou, H., Chou, W., Hashizume, H., Heller, R., & Lahesmaa, R. (2001). Distinct gene expression profiles of human type 1 and type 2 T helper cells. Genome Biol., 2, RESEARCH0022.
Heinrich, P. C., Behrmann, I., Müller-Newen, G., Schaper, F., & Graeve, L. (1998). Interleukin-6-type cytokine signalling through the gp130/Jak/STAT pathway. Biochem. J., 334, 297–314.
Hosken, N. A., Shibuya, K., Heath, A. W., Murphy, K. M., & O’Garra, A. (1995). The effect of antigen dose on CD4+ T helper cell phenotype development in a T cell receptor-alpha betatransgenic model. J. Exp. Med., 182, 1579–1584.
Huang, S. (2009). Reprogramming cell fates: reconciling rarity with robustness. BioEssays, 31, 546–560.
Huang, Y., & Wange, R. L. (2004). T cell receptor signaling: beyond complex complexes. J. Biol. Chem., 279, 28827–28830.
Ivanov, I. I., McKenzie, B. S., Zhou, L., Tadokoro, C. E., Lepelley, A., Lafaille, J. J., Cua, D. J., & Littman, D. R. (2006). The orphan nuclear receptor RORγt directs the differentiation program of proinflammatory IL−17+ T helper cells. Cell, 126, 1121–1133.
Kanakaraj, P., Ngo, K., Wu, Y., Angulo, A., Ghazal, P., Harris, C. A., Siekierka, J. J., Peterson, P. A., & Fung-Leung, W. P. (1999). Defective interleukin (IL)-18-mediated natural killer and T helper cell type 1 response in IL-1 receptor-associated kinase (IRAK)-deficient mice. J. Exp. Med., 189, 1129–1138.
Kaufman, M., & Thomas, R. (1987). Model analysis of the bases of multistationarity in the humoral immune response. J. Theor. Biol., 129, 141–162.
Kaufman, M., Urbain, J., & Thomas, R. (1985). Towards a logical analysis of the immune response. J. Theor. Biol., 114, 527–561.
Kerr, I. M., Costa-Pereira, A. P., Lillemeier, B. F., & Strobl, B. (2003). Of JAKs, STATs, blind watchmakers, jeeps and trains. FEBS Lett., 546, 1–5.
Kestler, H. A., Wawra, C., Kracher, B., & Kühl, M. (2008). Network modeling of signal transduction: establishing the global view. BioEssays, 30, 1110–1125.
Kotenko, S. V., & Pestka, S. (2000). Jak-Stat signal transduction pathway through the eyes of cytokine class II receptor complexes. Oncogene, 19, 2557–2565.
Krebs, D. L., & Hilton, D. J. (2001). SOCS proteins: negative regulators of cytokine signaling. Stem Cells, 19, 378–387.
Laurence, A., Tato, C. M., Davidson, T. S., Kanno, Y., Chen, Z., Yao, Z., Blank, R. B., Meylan, F., Siegel, R., Hennighausen, L., Shevach, E. M., & O’Shea, J. J. (2007). Interleukin-2 signaling via STAT5 constrains T helper 17 cell generation. Immunity, 26, 371–381.
Lighvani, A. A., Frucht, D. M., Jankovic, D., Yamane, H., Aliberti, J., Hissong, B. D., Nguyen, B. V., Gadina, M., Sher, A., Paul, W. E., & O’Shea, J. J. (2001). T-bet is rapidly induced by interferon-γ in lymphoid and myeloid cells. Proc. Natl. Acad. Sci. USA, 98, 15137–15142.
Lochner, M., Peduto, L., Cherrier, M., Sawa, S., Langa, F., Varona, R., Riethmacher, D., Si-Tahar, M., Di Santo, J. P., & Eberl, G. (2008). In vivo equilibrium of proinflammatory IL−17+ and regulatory IL−10+Foxp3+RORgammat+T cells. J. Exp. Med., 205, 1381–1393.
Losman, J. A., Chen, X. P., Hilton, D., & Rothman, P. (1999). Cutting edge: SOCS-1 is a potent inhibitor of IL-4 signal transduction. J. Immunol., 162, 3770–3774.
Manu, Surkova, S., Spirov, A. V., Gursky, V. V., Janssens, H., Kim, A. R., Radulescu, O., Vanario-Alonso, C. E., Sharp, D. H., Samsonova, M., & Reinitz, J. (2009). Canalization of gene expression and domain shifts in the Drosophila blastoderm by dynamical attractors. PLoS Comput. Biol., 5, e1000303.
Mendoza, L. (2006). A network model for the control of the differentiation process in Th cells. Biosystems, 84, 101–114.
Mendoza, L., & Alvarez-Buylla, E. R. (1998). Dynamics of the genetic regulatory network for flowering in Arabidopsis thaliana. J. Theor. Biol., 193, 307–319.
Mendoza, L., & Pardo, F. (2010). A robust model to describe the differentiation of T-helper cells. Theory Biosci., 129, 283–293.
Mendoza, L., & Xenarios, I. (2006). A method for the generation of standardized qualitative dynamical systems of regulatory networks. Theor. Biol. Med. Model., 3, 13.
Medzhitov, R. (2007). Recognition of microorganisms and activation of the immune response. Nature, 449, 819–826.
Moore, K. W., de Waal Malefyt, R., Coffman, R., & O’Garra, A. (2001). Interleukin-10 and the interleukin-10 receptor. Annu. Rev. Immunol., 19, 683–765.
Mullen, A. C., High, F. A., Hutchins, A. S., Lee, H. W., Villarino, A. V., Livingston, D. M., Kung, A. L., Cereb, N., Yao, T. P., Yang, S. Y., & Reiner, S. L. (2001). Role of T-bet in commitment of TH1 cells before IL-12-dependent selection. Science, 292, 1907–1910.
Murphy, K. M., & Reiner, S. L. (2002). The lineage decisions on helper T cells. Nat. Rev. Immunol., 2, 933–944.
Naldi, A., Carneiro, J., Chaouiya, C., & Thieffry, D. (2010). Diversity and plasticity of Th cell types predicted from regulatory network modelling. PLoS Comput. Biol., 6, e1000912.
Novelli, F., D’Elios, M. M., Bernabei, P., Ozmen, L., Rigamonti, L., Almerigogna, F., Forni, G., & Del Prete, G. (1997). Expression and role in apoptosis of the alpha- and β-chains of the IFN-γ receptor in human Th1 and Th2 clones. J. Immunol., 159, 206–213.
O’Shea, J. J., & Paul, W. E. (2010). Mechanisms underlying lineage commitment and plasticity of helper CD4+ T cells. Science, 327, 1098–1102.
Osorio, F., LeibundGut-Landmann, S., Lochner, M., Lahl, K., Sparwasser, T., Eberl, G., & Reis e Sousa, C. (2008). DC activated via dectin-1 convert Treg into IL-17 producers. Eur. J. Immunol., 38, 3274–3281.
Ouyang, W., Löhning, M., Gao, Z., Assenmacher, M., Ranganath, S., Radbruch, A., & Murphy, K. M. (2000). Stat6-independent GATA-3 autoactivation directs IL-4-independent Th2 development and commitment. Immunity, 12, 27–37.
Parham, C., Chirica, M., Timans, J., Vaisberg, E., Travis, M., Cheung, J., Pflanz, S., Zhang, R., Singh, K., Vega, F., To, W., Wagner, J., O’Farrell, A. M., McClanahan, T., Zurawski, S., Hannum, C., Gorman, D., Rennick, D. M., Kastelein, D. A., de Waal Malefyt, R., & Moore, K. W. (2002). A receptor for the heterodimeric cytokine IL-23 is composed of IL-12Rβ1 and a novel cytokine receptor subunit, IL-23R. J. Immunol., 168, 5699–5708.
Park, H., Li, Z., Yang, X. O., Chang, S. H., Nurieva, R., Wang, Y. H., Wang, Y., Hood, L., Zhu, Z., Tian, Q., & Dong, C. (2005). A distinct lineage of CD4 T cells regulates tissue inflammation by producing interleukin 17. Nat. Immunol., 6, 1133–1141.
Porter, C. M., & Clipstone, N. A. (2002). Sustained NFAT signaling promotes a Th1-like pattern of gene expression in primary murine CD4+ T cells. J. Immunol., 168, 4936–4945.
Radhakrishnan, S., Cabrera, R., Schenk, E. L., Nava-Parada, P., Bell, M. P., Van Keulen, V. P., Marler, R. J., Felts, S. J., & Pease, L. R. (2008). Reprogrammed FoxP3+ T regulatory cells become IL-17+ antigen-specific autoimmune effectors in vitro and in vivo. J. Immunol., 181, 3137–3147.
Ranganath, S., & Murphy, K. M. (2001). Structure and specificity of GATA proteins in Th2 development. Mol. Cell. Biol., 21, 2716–2725.
Rigamonti, L., Ariotti, S., Losana, G., Gradini, R., Russo, M. A., Jouanguy, E., Casanova, J. L., Forni, G., & Novelli, F. (2000). Surface expression of the IFN-γR2 chain is regulated by intracellular trafficking in human T lymphocytes. J. Immunol., 164, 201–207.
Rincon, M., & Flavell, R. A. (1997). Transcription mediated by NFAT is highly inducible in effector CD4+ T helper 2 (Th2) cells but not in Th1 cells. Mol. Cell. Biol., 17, 1522–1534.
Rodríguez, A., Sosa, D., Torres, L., Molina, B., Frías, S., & Mendoza, L. (2012). A Boolean network model of the FA/BRCA pathway. Bioinformatics, 28, 858–866.
Saito, H., Morita, Y., Fujimoto, M., Narazaki, M., Naka, T., & Kishimoto, T. (2000). IFN regulatory factor-1-mediated transcriptional activation of mouse STAT-induced STAT inhibitor-1 gene promoter by IFN-γ. J. Immunol., 164, 5833–5843.
Sánchez, L., & Thieffry, D. (2003). Segmenting the fly embryo: a logical analysis of the pair-rule cross-regulatory module. J. Theor. Biol., 224, 517–537.
Sánchez, L., Chaouiya, C., & Thieffry, D. (2008). Segmenting the fly embryo: logical analysis of the role of the segment polarity cross-regulatory module. Int. J. Dev. Biol., 52, 1059–1075.
Sánchez-Corrales, Y. E., Alvarez-Buylla, E. R., & Mendoza, L. (2010). The Arabidopsis thaliana flower organ specification gene regulatory network determines a robust differentiation process. J. Theor. Biol., 264, 971–983.
Santoni, D., Pedicini, M., & Castiglione, F. (2008). Implementation of a regulatory gene network to stimulate the TH1/2 differentiation in an agent-based model of hypersensitivity reactions. Bioinformatics, 24, 1374–1380.
Schmidt-Weber, C. B., Alexander, S. I., Henault, L. E., James, L., & Lichtman, A. H. (1999). IL-4 enhances IL-10 gene expression in murine Th2 cells in the absence of TCR engagement. J. Immunol., 162, 238–244.
Shevach, E. M., DiPaolo, R. A., Andersson, J., Zhao, D. M., Stephens, G. L., & Thornton, A. M. (2006). The lifestyle of naturally occurring CD4+CD25+Foxp3+ regulatory T cells. Immunol. Rev., 212, 60–73.
Shi, Y., & Massagué, J. (2003). Mechanisms of TGF-β signaling from cell membrane to the nucleus. Cell, 113, 685–700.
Smeltz, R. B., Chen, J., Hu-Li, J., & Shevach, E. M. (2001). Regulation of interleukin (IL)-18 receptor alpha chain expression on CD4+ T cells during T helper (Th)1/Th2 differentiation: critical downregulatory role of IL-4. J. Exp. Med., 194, 143–153.
Sommer, V. H., Clemmensen, O. J., Nielsen, O., Wasik, M., Lovato, P., Brender, C., Eriksen, K. W., Woetmann, A., Kaestel, C. G., Nissen, M. H., Ropke, C., Skov, S., & Ødum, N. (2004). In vivo activation of STAT3 in cutaneous T-cell lymphoma. Evidence for an antiapoptotic function of STAT3. Leukemia, 18, 1288–1295.
Steinman, L. (2007). A brief history of TH17, the first major revision in the TH1/TH2 hypothesis of T cell-mediated tissue damage. Nat. Med., 13, 139–145.
Szabo, S. J., Dighe, A. S., Gubler, U., & Murphy, K. M. (1997). Regulation of the interleukin (IL)-12R β2 subunit expression in developing T helper 1 (Th1) and Th2 cells. J. Exp. Med., 185, 817–824.
Szabo, S. J., Kim, S. T., Costa, G. L., Zhang, X., Fathman, C. G., & Glimcher, L. H. (2000). A novel transcription factor, T-bet, directs Th1 lineage commitment. Cell, 100, 655–669.
Thierfelder, W. E., van Deursen, J. M., Yamamoto, K., Tripp, R. A., Sarawar, S. R., Carson, R. T., Sangster, M. Y., Vignali, D. A., Doherty, P. C., Grosveld, G. C., & Ihle, J. N. (1996). Requirement for Stat4 in interleukin-12-mediated responses of natural killer and T cells. Nature, 382, 171–174.
Thomas, R., & Kaufman, M. (2001a). Multistationarity, the basis of cell differentiation and memory. I. Structural conditions of multistationarity and other nontrivial behavior. Chaos, 11, 170–179.
Thomas, R., & Kaufman, M. (2001b). Multistationarity, the basis of cell differentiation and memory. II. Logical analysis of regulatory networks in terms of feedback circuits. Chaos, 11, 180–195.
Usui, T., Nishikomori, R., Kitani, A., & Strober, W. (2003). GATA-3 suppresses Th1 development by downregulation of Stat4 and not through effects on IL-12Rβ2 chain or T-bet. Immunity, 18, 415–428.
Veldhoen, M., Hocking, R. J., Atkins, C. J., Locksley, R. M., & Stockinger, B. (2006). TGFβ in the context of an inflammatory cytokine milieu supports de novo differentiation of IL-17-producing T cells. Immunity, 24, 179–189.
Wan, Y. Y., & Flavell, R. A. (2007). Regulatory T-cell functions are subverted and converted owing to attenuated Foxp3 expression. Nature, 445, 766–770.
Wan, Y. Y., & Flavell, R. A. (2009). How diverse–CD4 effector T cells and their functions. Mol. Cell. Biol., 1, 20–36.
Weaver, C. T., Harrington, L. E., Mangan, P. R., Gavrieli, M., & Murphy, K. M. (2006). Th17: An effector CD4 T cell lineage with regulatory T cell ties. Immunity, 24, 677–688.
Weinstein, N., & Mendoza, L. (2012). Building qualitative models of plant regulatory networks with SQUAD. Front. Plant Sci., 3, 72.
Williams, L. M., & Rudensky, A. Y. (2007). Maintenance of the Foxp3-dependent developmental program in mature regulatory T cells requires continued expression of Foxp3. Nat. Immunol., 8, 277–284.
Wittmann, D. M., Krumsiek, J., Saez-Rodriguez, J., Lauffenburger, D. A., Klamt, S., & Theis, F. J. (2009). Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling. BMC Syst. Biol., 3, 98.
Yang, X. O., Panopoulos, A. D., Nurieva, R., Chang, S. H., Wang, D., Watowich, S. S., & Dong, C. (2007). STAT3 regulates cytokine-mediated generation of inflammatory helper T cells. J. Biol. Chem., 282, 9358–9363.
Zhong, X., Gao, W., Degauque, N., Bai, C., Lu, Y., Kenny, J., Oukka, M., Strom, T. B., & Rothstein, T. L. (2007). Reciprocal generation of Th1/Th17 and T(reg) cells by B1 and B2 B cells. Eur. J. Immunol., 37, 2400–2404.
Zhou, L., Lopes, J. E., Chong, M. M. W., Ivanov, I. I., Min, R., Victora, G. D., Shen, Y., Du, J., Rubtsov, Y. P., Rudensky, A. Y., Ziegler, S. F., & Littman, D. R. (2008). TGF-β-induced Foxp3 inhibits TH17 cell differentiation by antagonizing RORγt function. Nature, 453, 236–240.
Zhou, L., Chong, M. M. W., & Littman, D. R. (2009). Plasticity of CD4+ T cell lineage differentiation. Immunity, 30, 646–655.
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The author wants to acknowledge the invaluable comments and suggestions to improve the present manuscript made by two anonymous referees as well as by the guest editors Dr. Claudine Chaouiya and Dr. Elisabeth Remy.
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Mendoza, L. A Virtual Culture of CD4+ T Lymphocytes. Bull Math Biol 75, 1012–1029 (2013). https://doi.org/10.1007/s11538-013-9814-9
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DOI: https://doi.org/10.1007/s11538-013-9814-9