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MODELLING COMPLEX BIOLOGICAL SYSTEMS IN THE CONTEXT OF GENOMICS
                       Evry, May 21-25, 2012



On the cellular and supracellular networks
                controlling
  regulatory T cells and autoimmunity



                       Jorge Carneiro
          Instituto Gulbenkian de Ciência, Portugal
                   http://qobweb.igc.gulbenkian.pt
Quantitative Organism Biology




 Cells of multicellular organism cooperate to ensure body
development and maintenance. They do this in a collective
         distributed manner, without a global plan.

  How cells collectively generate organism’s properties?

      General principles of biological organisation

       The design and control of artificial systems
http://www.embl-heidelberg.de/digitalembryo/
How cells get along without a GPS ?
How cells get along without a GPS ?



            global information (system)
autoimmune disease and immunopathology,




                                                   2
                      2




                                                                                                                                      2
                                                                                                          2
                                                                 B                  Foxp3 represents a more specific marker than
 5RBhi alone +Foxp3/MIGR1              +MIGR1                 None          CD25-CD45RBhi alone cell-surface molecules (such as
                                                                                    currently used +Foxp3/MIGR1              +MIGR1                None
                                                                                    CD25, CD45RB, CTLA-4, and GITR), which

         Multiple                                                                   are unable to completely discriminate between
                                                                                    regulatory T cells and activated, effector, or
                                                                                    memory T cells.
          scales
                                                                    Colon
                                                                                        Mutations in the Foxp3 gene culminate in
                                                                                    the development of a fatal lymphoprolifera-
                                                                                    tive disorder associated with multiorgan pa-
                                                                                    thology both in mice and humans (12–20).
                                                                                    FOXP3 is predominantly expressed in human
                                                                                    CD25ϩCD4ϩ T cells as well (32). Further-
                                                                  Stomach           more, transduction of a mutant Foxp3 lacking
                                                                                    the forkhead domain, similar to the mutated
                                                                                    Foxp3 in scurfy mice (17), failed to confer
                                                                                    suppressive activity to CD25–CD4ϩ T cells
                                                                 Fig. 4. Prevention(fig.IBD and autoimmune gastritis by Foxp3-transduced T cells. (A) C.B-17 scid
   IBD and autoimmune gastritis by Foxp3-transduced T cells. (A) C.B-17 scid          of S7). The present results therefore sug-
 105 fresh CD25–CD45RBhighCD4ϩ cells either alone (n ϭ 6, where n is the 4 ϫ 10that mutations of thehighCD4ϩgene may alone (n ϭ 6, where n is the
                                                                 mice received gest 5 fresh CD25–CD45RB Foxp3 cells either
                                                                 derived of mice)cause squares)disorders through1.2develop- GFPϩ sorted cells derived from
 pen squares) or together with 1.2 ϫ 106 GFPϩ sorted cells number from               (open these       or together with    ϫ 106
D4ϩ cells infected with Foxp3/MIGR1 (n ϭ 7) (closed circles) or MIGR1 –(n ϭ 5) highmentalcells infected with Foxp3/MIGR1 (n ϭthe (closed circles) or MIGR1 (n ϭ 5)
                                                                 CD25 CD45RB CD4ϩ or functional abnormality of 7)
   weight is represented as the percentage of initial weight (mean Ϯ SD). Body weight is represented as the percentage of initial weight (mean Ϯ SD)
                                                                 (open circles). CD25ϩCD4ϩ T population.
                                                                                                      R
 gnificant difference, P Ͻ 0.01, Foxp3/MIGR1 versus other two groups indicate significant difference, P of T cells by Foxp3 versus other two groups by
                                                                 Astericks by           Potentially, generation Ͻ 0.01, Foxp3/MIGR1
                                                                                                                   R
   (B) Histopathology of the colon and stomach in each group and in an test. (B) Histopathology of the colon and stomach in each group and in an
                                                                 Mann-Whitney
                                                                                    transduction of naıve T cells may provide a
                                                                                                         ¨
 D mouse (None). (C) Colitis (left) and gastritis (right) were unreconstituted SCID mouse (None). (C) Colitis (left) and gastritis (right) were histologically
                                                                 histologically
  the group cotransferred with MIGR1-infected cells and one transferredTwo micepreviously unstudied therapeutic mode for cells and one transferred with
                                                                 scored. with        in the group cotransferred with MIGR1-infected
    ϩ                                                            CD25 CD45RB treatment of autoimmunedebilitation before histological examination. Results
                                                                       –
D4 cells alone died of debilitation before histological examination. Results    high
                                                                                     CD4ϩ cells alone died of and inflammatory
 are from a total of three independent experiments.              shown in (A) to (C) are from a total of three independent experiments.
                                                                                    diseases and in transplantation tolerance.

                                                1060
                    14 FEBRUARY 2003 VOL 299 SCIENCE www.sciencemag.org                                 14 FEBRUARY 2003 VOL 299 SCIENCE www.scien
autoimmune disease and immunopathology,




                                                   2
                      2




                                                                                                                                      2
                                                                                                          2
                                                                 B                  Foxp3 represents a more specific marker than
 5RBhi alone +Foxp3/MIGR1              +MIGR1                 None          CD25-CD45RBhi alone cell-surface molecules (such as
                                                                                    currently used +Foxp3/MIGR1              +MIGR1                None
                                                                                    CD25, CD45RB, CTLA-4, and GITR), which

         Multiple                                                                   are unable to completely discriminate between
                                                                                    regulatory T cells and activated, effector, or
                                                                                    memory T cells.
          scales
                                                                    Colon
                                                                                        Mutations in the Foxp3 gene culminate in
                                                                                    the development of a fatal lymphoprolifera-
                                                                                    tive disorder associated with multiorgan pa-
                                                                                    thology both in mice and humans (12–20).
                                                                                    FOXP3 is predominantly expressed in human
                                                                                    CD25ϩCD4ϩ T cells as well (32). Further-
                                                                  Stomach           more, transduction of a mutant Foxp3 lacking
                                                                                    the forkhead domain, similar to the mutated
                                                                                    Foxp3 in scurfy mice (17), failed to confer
                                                                                    suppressive activity to CD25–CD4ϩ T cells
                                                                 Fig. 4. Prevention(fig.IBD and autoimmune gastritis by Foxp3-transduced T cells. (A) C.B-17 scid
   IBD and autoimmune gastritis by Foxp3-transduced T cells. (A) C.B-17 scid          of S7). The present results therefore sug-
 105 fresh CD25–CD45RBhighCD4ϩ cells either alone (n ϭ 6, where n is the 4 ϫ 10that mutations of thehighCD4ϩgene may alone (n ϭ 6, where n is the
                                                                 mice received gest 5 fresh CD25–CD45RB Foxp3 cells either
                                                                 derived of mice)cause squares)disorders through1.2develop- GFPϩ sorted cells derived from
 pen squares) or together with 1.2 ϫ 106 GFPϩ sorted cells number from               (open these       or together with    ϫ 106
D4ϩ cells infected with Foxp3/MIGR1 (n ϭ 7) (closed circles) or MIGR1 –(n ϭ 5) highmentalcells infected with Foxp3/MIGR1 (n ϭthe (closed circles) or MIGR1 (n ϭ 5)
                                                                 CD25 CD45RB CD4ϩ or functional abnormality of 7)

                                                                 Astericks by
                                                                                                      R       Cell population dynamics
   weight is represented as the percentage of initial weight (mean Ϯ SD). Body weight is represented as the percentage of initial weight (mean Ϯ SD)
                                                                 (open circles). CD25ϩCD4ϩ T population.
 gnificant difference, P Ͻ 0.01, Foxp3/MIGR1 versus other two groups indicate significant difference, P of T cells by Foxp3 versus other two groups by
                                                                                        Potentially, generation Ͻ 0.01, Foxp3/MIGR1
                                                                                                                      (ODE)
                                                                                                                   R
   (B) Histopathology of the colon and stomach in each group and in an test. (B) Histopathology of the colon and stomach in each group and in an
                                                                 Mann-Whitney
                                                                                    transduction of naıve T cells may provide a
                                                                                                         ¨
 D mouse (None). (C) Colitis (left) and gastritis (right) were unreconstituted SCID mouse (None). (C) Colitis (left) and gastritis (right) were histologically
                                                                 histologically
  the group cotransferred with MIGR1-infected cells and one transferredTwo micepreviously unstudied therapeutic mode for cells and one transferred with
                                                                 scored. with        in the group cotransferred with MIGR1-infected
    ϩ                                                            CD25 CD45RB treatment of autoimmunedebilitation before histological examination. Results
                                                                       –
D4 cells alone died of debilitation before histological examination. Results    high
                                                                                     CD4ϩ cells alone died of and inflammatory
 are from a total of three independent experiments.              shown in (A) to (C) are from a total of three independent experiments.
                                                                                    diseases and in transplantation tolerance.

                                                1060
                    14 FEBRUARY 2003 VOL 299 SCIENCE www.sciencemag.org                                 14 FEBRUARY 2003 VOL 299 SCIENCE www.scien
autoimmune disease and immunopathology,




                                                   2
                      2




                                                                                                                                      2
                                                                                                          2
                                                                 B                  Foxp3 represents a more specific marker than
 5RBhi alone +Foxp3/MIGR1              +MIGR1                 None          CD25-CD45RBhi alone cell-surface molecules (such as
                                                                                    currently used +Foxp3/MIGR1              +MIGR1                None
                                                                                    CD25, CD45RB, CTLA-4, and GITR), which

         Multiple                                                                   are unable to completely discriminate between
                                                                                    regulatory T cells and activated, effector, or
                                                                                    memory T cells.
          scales
                                                                    Colon
                                                                                        Mutations in the Foxp3 gene culminate in
                                                                                    the development of a fatal lymphoprolifera-
                                                                                    tive disorder associated with multiorgan pa-
                                                                                    thology both in mice and humans (12–20).
                                                                                    FOXP3 is predominantly expressed in human
                                                                                    CD25ϩCD4ϩ T cells as well (32). Further-
                                                                  Stomach           more, transduction of a mutant Foxp3 lacking
                                                                                    the forkhead domain, similar to the mutated
                                                                                    Foxp3 in scurfy mice (17), failed to confer
                                                                                    suppressive activity to CD25–CD4ϩ T cells
                                                                 Fig. 4. Prevention(fig.IBD and autoimmune gastritis by Foxp3-transduced T cells. (A) C.B-17 scid
   IBD and autoimmune gastritis by Foxp3-transduced T cells. (A) C.B-17 scid          of S7). The present results therefore sug-
 105 fresh CD25–CD45RBhighCD4ϩ cells either alone (n ϭ 6, where n is the 4 ϫ 10that mutations of thehighCD4ϩgene may alone (n ϭ 6, where n is the
                                                                 mice received gest 5 fresh CD25–CD45RB Foxp3 cells either
                                                                 derived of mice)cause squares)disorders through1.2develop- GFPϩ sorted cells derived from
 pen squares) or together with 1.2 ϫ 106 GFPϩ sorted cells number from               (open these       or together with    ϫ 106
D4ϩ cells infected with Foxp3/MIGR1 (n ϭ 7) (closed circles) or MIGR1 –(n ϭ 5) highmentalcells infected with Foxp3/MIGR1 (n ϭthe (closed circles) or MIGR1 (n ϭ 5)
                                                                 CD25 CD45RB CD4ϩ or functional abnormality of 7)

                                                                 Astericks by
                                                                                                      R       Cell population dynamics
   weight is represented as the percentage of initial weight (mean Ϯ SD). Body weight is represented as the percentage of initial weight (mean Ϯ SD)
                                                                 (open circles). CD25ϩCD4ϩ T population.
 gnificant difference, P Ͻ 0.01, Foxp3/MIGR1 versus other two groups indicate significant difference, P of T cells by Foxp3 versus other two groups by
                                                                                        Potentially, generation Ͻ 0.01, Foxp3/MIGR1
                                                                                                                      (ODE)
                                                                                                                   R
   (B) Histopathology of the colon and stomach in each group and in an test. (B) Histopathology of the colon and stomach in each group and in an
                                                                 Mann-Whitney
                                                                                    transduction of naıve T cells may provide a
                                                                                                         ¨
 D mouse (None). (C) Colitis (left) and gastritis (right) were unreconstituted SCID mouse (None). (C) Colitis (left) and gastritis (right) were histologically
                                                                 histologically
  the group cotransferred with MIGR1-infected cells and one transferredTwo micepreviously unstudied therapeutic mode for cells and one transferred with
                                                                 scored. with        in the group cotransferred with MIGR1-infected
    ϩ                                                            CD25 CD45RB treatment of autoimmunedebilitation before histological examination. Results
                                                                       –
D4 cells alone died of debilitation before histological examination. Results    high
                                                                                     CD4ϩ cells alone died of and inflammatory
 are from a total of three independent experiments.              shown in (A) to (C) are from a total of three independent experiments.
                                                                                    diseases and in transplantation tolerance.

                                                1060
                    14 FEBRUARY 2003 VOL 299 SCIENCE www.sciencemag.org                                 14 FEBRUARY 2003 VOL 299 SCIENCE www.scien




                                                                                    Gene regulatory networks
                                                                                   (Logical network dynamics)
overview
Tolerance, autoimmunity, and regulatory T cells
Regulatory T cells 101

How regulatory T cells mediate tolerance ?
Modelling T cell population dynamics
Ordinary differential equations    ··························· CRM

What makes a T cell be a regulatory T cell ?
Modelling gene regulatory networks and T cell differentiation
Logical network formalism     ······················ Th cell plasticity

If regulatory T cells are plastic how can tolerance be robust ?
Multiscale modelling of cellular and supracellular networks
Agent-based stochastic simulations
What does the immune system do in the vertebrate organism?
Fighting infection
Fighting infection

Assimilating
intestinal flora
Fighting infection

Assimilating
intestinal flora




    Rejecting cancer cells
Fighting infection

Assimilating
intestinal flora




                             House keeping




    Rejecting cancer cells
Homeostasis
   Fighting infection          and Regulation

Assimilating
intestinal flora




                             House keeping




    Rejecting cancer cells
Homeostasis
   Fighting infection                                                                                  and Regulation

Assimilating
intestinal flora




                                                                                                   House keeping




    Rejecting cancer cells


       http://www.sciencemuseum.org.uk/exhibitions/lifecycle/116.asp   http://ww.grc.org/Graphics/ programs/2003/cells3.jpg
                                                                            http://www.leukemia-web.org/images/cells.jpg
Failure of homeostasis and regulation
 unleashes pathologic autoimmunity
Failure of homeostasis and regulation
 unleashes pathologic autoimmunity
    Rheumatoid arthritis




                           Type I diabetes




  Multiple sclerosis


                                               IPEX sindrome




                                         Cortesy: Magda Carneiro-Sampaio, São Paulo
From: Jean-François Bach, New England J Med
“In general, the management of human systemic
autoimmune disease is empirical and unsatisfactory. For the
most part, broadly immunosuppressive drugs, such as
corticosteroids, are used in a wide variety of severe
autoimmune and inflammatory disorders (…)”

                     – Philipe Cohen In: Fundamental Immunology (Ed. W. Paul)
Clonal selection theory
                                                      Stem Cell




Jerne, 1953
Burnet, 1957                                     G.O.D.
               Ag A




                      1   2   3   4   ...      111         112     ...   623   ...       1245    ...          n




               Ag B



                      1   2   3   4   ...      111         112     ...   623   ...       1245    ...          n




                                        111           111                         1245          1245




                                  111    111         111         111       1245    1245    1245        1245
CTL
                                        CTL
                             CTL
                    CTL                 CTL   CTL
               TH                       CTL




Antigen                                  TH
                                         TH
                                         TH
                    TH       TH         TH
                                        TH



                                    B
                                   B
          B              B          B
                                  B
                                  B
          TH
CTL
                                        CTL
                             CTL
                    CTL                 CTL   CTL
               TH                       CTL




Antigen                                  TH
                                         TH
                                         TH
                    TH       TH         TH
                                        TH



                                    B
                                   B
          B              B          B
                                  B
                                  B
          TH
CTL
                                        CTL
                             CTL
                    CTL                 CTL   CTL
               TH                       CTL




Antigen                                  TH
                                         TH
                                         TH
                    TH       TH         TH
                                        TH



                                    B
                                   B
          B              B          B
                                  B
                                  B
          TH
CTL
                                        CTL
                             CTL
                    CTL                 CTL   CTL
               TH                       CTL




Antigen                                  TH
                                         TH


                    TH
                             “Self” tolerance by deletion
                                      TH
                                         TH
                             TH
                                         TH



                                    B
                                   B
          B              B          B
                                  B
                                  B
          TH
CTL
                                        CTL
                             CTL
                    CTL                 CTL   CTL
               TH                       CTL




Antigen                                  TH
                                         TH
                                         TH
                    TH       TH         TH
                                        TH



                                    B
                                   B
          B              B          B
                                  B
                                  B
          TH
Reductionist molecular biology approach to Immunology
TOLERANCE = absence of clonal expansion = CLONAL DELETION




         Therapy of autoimmune diseases should aim at
             “deleting” autoreactive cells or clones


In the absence of clonal-specific therapies: kill them all !!!
Is there any hope ?
Tolerance is mediated by regulatory T cells
Mason-Sakaguchi




   WT
Tolerance is mediated by regulatory T cells
Mason-Sakaguchi




              CD25- CD4+ T cells
                        E E E
                    T    E T   T
                        T    T


                  (Effector T cells, TE, E)


   WT
Tolerance is mediated by regulatory T cells
Mason-Sakaguchi
                                              “empty” rag-/-



              CD25- CD4+ T cells
                        E E E
                    T    E T   T
                        T    T


                  (Effector T cells, TE, E)


   WT
Tolerance is mediated by regulatory T cells
Mason-Sakaguchi
                                              “empty” rag-/-
                                                               AID
              CD25- CD4+ T cells
                        E E E
                    T    E T   T
                        T    T


                  (Effector T cells, TE, E)


   WT
Tolerance is mediated by regulatory T cells
Mason-Sakaguchi
                                                  “empty” rag-/-
                                                                   AID
              CD25- CD4+ T cells
                          E E E
                      T    E T   T
                          T    T


                   (Effector T cells, TE, E)


   WT
              CD25+CD4+T cells
                                          R
                                  R
                          R   R               R
                          R           R
                                  R


                  (Regulatory T cells, TR, R)
Tolerance is mediated by regulatory T cells
Mason-Sakaguchi
                                                  “empty” rag-/-
                                                                   AID
              CD25- CD4+ T cells
                          E E E
                      T    E T   T
                          T    T


                   (Effector T cells, TE, E)


   WT
              CD25+CD4+T cells
                                          R
                                  R
                          R   R               R
                          R           R
                                  R


                  (Regulatory T cells, TR, R)
Tolerance is mediated by regulatory T cells
Mason-Sakaguchi
                                                  “empty” rag-/-
                                                                    AID
              CD25- CD4+ T cells
                          E E E
                      T    E T   T
                          T    T


                   (Effector T cells, TE, E)


   WT
              CD25+CD4+T cells

                          R   R
                                  R
                                          R
                                              R
                                                                   Healthy
                          R           R
                                  R


                  (Regulatory T cells, TR, R)
Tolerance is mediated by regulatory T cells
Mason-Sakaguchi
                                                  “empty” rag-/-
                                                                    AID
              CD25- CD4+ T cells
                          E E E
                      T    E T   T
                          T    T


                   (Effector T cells, TE, E)


   WT
              CD25+CD4+T cells

                          R   R
                                  R
                                          R
                                              R
                                                                   Healthy
                          R           R
                                  R


                  (Regulatory T cells, TR, R)
Tolerance is mediated by regulatory T cells
Mason-Sakaguchi
                                                  “empty” rag-/-
                                                                    AID
              CD25- CD4+ T cells
                          E E E
                      T    E T   T
                          T    T
                                                                     AID
                   (Effector T cells, TE, E)                          or
                                                                    Healthy
   WT
              CD25+CD4+T cells

                          R   R
                                  R
                                          R
                                              R
                                                                   Healthy
                          R           R
                                  R


                  (Regulatory T cells, TR, R)
Tolerance is mediated by regulatory T cells
Mason-Sakaguchi
                                                  “empty” rag-/-
                                                                    AID
              CD25- CD4+ T cells
                          E E E
                      T    E T   T
                          T    T
                                                                     AID
                   (Effector T cells, TE, E)                          or
                                                                    Healthy
   WT
              CD25+CD4+T cells

                          R   R
                                  R
                                          R
                                              R
                                                                   Healthy
                          R           R
                                  R


                  (Regulatory T cells, TR, R)
Tolerance is mediated by regulatory T cells

                                         CTL
                                         CTL
                      CTL   CTL
                                         CTL   CTL
                TH                       CTL


Self
Antigen                                  TH
                                         TH
                                         TH
                     TH                  TH
                            TH
                                         TH
               TH



                                     B
          B           B              B
                                 B
                             B
          TH                     B
TOLERANCE = absence of clonal expansion = control by regulatory T cells




         Therapy of autoimmune diseases should aim at
      stimulating autoreactive regulatory T cells or clones
… BUT …


there are many open questions
CD25+CD4+T cells
                      R
              R
      R   R               R
      R           R
              R


 (Regulatory T cells, TR, R)
What makes a T cell
be a regulatory T cell ?


                    CD25+CD4+T cells
                                           R
                                   R
                           R   R               R
                           R           R
                                   R


                      (Regulatory T cells, TR, R)
What makes a T cell
    be a regulatory T cell ?


                        CD25+CD4+T cells
                                               R
                                       R

How do they interact
                               R   R               R
                               R           R
                                       R

 with other cells ?       (Regulatory T cells, TR, R)
What makes a T cell
    be a regulatory T cell ?


                        CD25+CD4+T cells
                                               R
                                       R

How do they interact
                               R   R               R
                               R           R
                                       R

 with other cells ?       (Regulatory T cells, TR, R)


               How do they prevent
               autoimmune diseases ?
What makes a T cell
    be a regulatory T cell ?


                        CD25+CD4+T cells
                                               R
                                       R

How do they interact
                               R   R               R
                               R           R
                                       R

 with other cells ?       (Regulatory T cells, TR, R)
                                                            How do they allow
                                                       efficient immune responses ?
               How do they prevent
               autoimmune diseases ?
What makes a T cell
    be a regulatory T cell ?

                                                             How many and how
                        CD25+CD4+T cells                      diverse are they ?
                                               R
                                       R

How do they interact
                               R   R               R
                               R           R
                                       R

 with other cells ?       (Regulatory T cells, TR, R)
                                                            How do they allow
                                                       efficient immune responses ?
               How do they prevent
               autoimmune diseases ?
How does their repertoire
     What makes a T cell                       compare to that of other T
    be a regulatory T cell ?                            cells ?

                                                             How many and how
                        CD25+CD4+T cells                      diverse are they ?
                                               R
                                       R

How do they interact
                               R   R               R
                               R           R
                                       R

 with other cells ?       (Regulatory T cells, TR, R)
                                                            How do they allow
                                                       efficient immune responses ?
               How do they prevent
               autoimmune diseases ?
Balance between regulatory and effector T cell subpopulations
Is it that simple ?
Is it that simple ?


“Everything should be made as simple as possible,
                                But not simpler.”

                   Albert Einstein, XX century
http://www.medscape.com/content/2004/00/46/84/468446/468446_fig.html
http://www.medscape.com/content/2004/00/46/84/468446/468446_fig.html
http://www.sewingmachines.us/sewing-machine-636.jpg




http://www.medscape.com/content/2004/00/46/84/468446/468446_fig.html
http://www.sewingmachines.us/sewing-machine-636.jpg




                                                                      http://www.roselabiche.com/blog/index.php?2007/11
http://www.medscape.com/content/2004/00/46/84/468446/468446_fig.html
http://web.mit.edu/2.972/www/reports/sewing_machine/a-sewing_machine.gif
Cell population dynamics
J. theor. Biol. (2000) 207, 231}254
                         doi:10.1006/jtbi.2000.2169, available online at http://www.idealibrary.com on




                               Modelling T-cell-Mediated Suppression Dependent on Interactions
                                                 in Multicellular Conjugates
                                KALET LEON*-?, ROLANDO PEREZ*, AGUSTIN LAGE*
                                        D                 D                                     AND JORGE    CARNEIRO-

     MODELLING T LYMPHOCYTE LINKED SUPPRESSION                                         249
                       *Centro de ImmunolognH a Molecular, P.O. Box 16040, Habana 11600, Cuba and
                         -Instituto Gulbenkian de Ciencia, Apartado 14, 2781-901, Oeiras, Portugal
 ore than two cell types           with the alternative mechanisms of linked sup-
mechanisms can be speci- (Received on 7 February 2000, Accepted in revised form onreported 2000)
                                   pression. Overall, the modelling results 10 August
setting of the interaction         here and the whole set of observations that we
 the consequences of each          discussed would strongly favour two candidate
                          Tolerance to peripheral body antigens involves multiple mechanisms, namely T-cell-mediated
able 1). The application of
                          suppression of potentially autoimmuneare Recent in vivo and in vitro evidence indicates that
                                   mechanisms. These cells. the ones that are trans-
                          regulatory T cells suppress the response of e!ector T cells by a mechanism that requires the
 tions other than the cur-         lated by the "nal model: regulatory T cells inhibit
                          simultaneous conjugation of regulatory and e!ector T cells with the same antigen-presenting
minant tolerance can be (APC). Despite this strong requirement, it is not yet clearwhile theywhile both cells are
                          cell     the proliferation of e!ector cells what happens are
                          conjugated. Several hypotheses are discussed in the literature. Suppression may result from
  For example, it was competition of regulatory and e!ectoracells for activation resources on the APC;
                          simple nevertheless dependent on growth factor that the
  the interaction between regulatory T cellsproduce; an inhibitory signal tocells inhibit the same conjugate; or
                                   latter may deliver or regulatory e!ector T cells in the ex-
                          e!ector T cells may acquire the regulatory phenotype during their interaction with regulatory
 Ls does not involve thecells. The present article tries to further our understanding of T-cell-mediated suppression,
                          T        pansion of the population of e!ector cells because
                                   they convertnumber of multicellular conjugates of T propose the "rst general
ns between the two cells to narrow-downthe formation of to the regulatoryWe cells and APCs. Using this
                          and
                          formalism describing
                                                  the
                                                         them candidate mechanisms. phenotype.
                          formalism we derive three particularor both may be operative in of T-cell-
 resenting cell, as classi-        Either mechanism models, representing alternative mechanisms
                          mediated suppression. For each model, we make phase plane and bifurcation analysis, and
 son & O'Malley, 1987;             vivo, maybe even dependent on with the history of
                          identify their pros and cons in terms of the relationshipthe life large body of experimental
hat the APC may act as    observations on T-cell-mediated Modigliani et al.that accounting for the quantitative
                                   the e!ector cells. suppression. We argue (1996b) actually
                          details of adoptive transfers of tolerance requires models with bistable regimes in which either
nnett et al., 1998; Ridge regulatory cells or e!ectors cells dominate the steady cellsFrom this thymic conclude
                                   demonstrated that regulatory state. from analysis, we
r et al., 1998). The formal- cells actively inhibit mechanism of T-cell-mediated suppression the maintenance of the
                          that the most plausible
                          T
                                   epithelium the growth of can both suppressrequires re- regulatory
                                                     chimeras e!ector T cells, and that the that
Modelling T cell population dynamics




net growth = influx       + interaction-dependent   — death
                                 growth


     dTi
         =        i   + ↵i (T, A, m, k) · Ti            · Ti
      dt
Modelling T cell population dynamics




net growth = influx       + interaction-dependent   — death
                                 growth


     dTi
         =        i   + ↵i (T, A, m, k) · Ti            · Ti
      dt
Modelling T cell population dynamics




net growth = influx       + interaction-dependent   — death
                                 growth


     dTi
         =        i   + ↵i (T, A, m, k) · Ti            · Ti
      dt
Modelling T cell population dynamics




net growth = influx       + interaction-dependent   — death
                                 growth


     dTi
         =        i   + ↵i (T, A, m, k) · Ti            · Ti
      dt
Modelling T cell population dynamics




net growth = influx       + interaction-dependent   — death
                                 growth


     dTi
         =        i   + ↵i (T, A, m, k) · Ti            · Ti
      dt


         How to choose appropriate functional forms
                 for the interaction terms ?
Modelling T cell population dynamics

A taxonomy of putative mechanisms of cell-to-cell interaction
                                                                  R




                                                         T
                          IL-X
                                                                   R




                                                                   R




             [Leon et al. J Theor Biol 2000; Carneiro et al. Immunol Rev 2007]
Modelling T cell population dynamics

A taxonomy of putative mechanisms of cell-to-cell interaction
                                                                  R




                                                         T
                          IL-X
                                                                   R




                                                                   R




             [Leon et al. J Theor Biol 2000; Carneiro et al. Immunol Rev 2007]
Modelling T cell population dynamics

A taxonomy of putative mechanisms of cell-to-cell interaction
                                                                  R




                                                         T
                          IL-X
                                                                   R




                                                                   R


                                                                                 CRM




             [Leon et al. J Theor Biol 2000; Carneiro et al. Immunol Rev 2007]
Modelling T cell population dynamics: the crossregulation model




                      Interactive simulation
Quantitative assay for cell proliferation


+
CFSE




                Nº Cells




                                            Log FL1-H
                                  Log Intensity of CFSE staining



            [Leon et al. J.Theor.Biol. 2004]
Putting the CRM to the test


                                                                                      + anti-CD3 antibody
                            APCs


                                                                                                      Cell Cycle
                            R       R                             R       R       E
                        R               R                     R               R
                                R                                     R
                            R                                     R

B6 Thy1.2                                                                                             Analysis
                     CD25+CD4+Thy1.2+

                                                                                             3 day culture
                                        E       E                         E       E
                          E E                                   E E
                         E E E                                 E E E
                           E                E                    E            E


B6 congenic Thy1.1
                     CD25-CD4+Thy1.1+




                                                    [Carneiro et al. Immuno. Rev. 2007]
Putting the CRM to the test

                                                                                    + anti-CD3 antibody
                    APCs                                                                 Proportions                  Effector Cells               Regulatory Cells
                                                                                        Thy1.1:Thy1.2
                                                                                                                          Thy1.1                            Thy1.2
                                                                                                    Cell Cycle
                                R                       R       R           E
                    R                               R               R
                R                   R
                                                                                        Day 0     Day 3
                            R                               R
                        R                               R

                                                                                                    Analysis
       CD25+CD4+Thy1.2+




                                                                                                                           ?                                  ?
                                                                                           3 day culture
                    E
                        E E
                         E E
                         E
                                    E

                                        E
                                            E
                                                + + anti-CD3100:0 N.D.
                                                    E
                                                        E E
                                                         E E
                                                         E
                                                             antibody
                                                                E

                                                                        E
                                                                            E


                                                                                                                                                            ND
y1.1
       CD25-CD4+Thy1.1+



                                                                                         80:20     47:53
                                                                                                 Cell Cycle
            R           R                   E
        R                       R
                R
            R

                                                                                                 Analysis
.2+
                                                                                    + anti-CD3 antibody
                                                                                        50:50 24:76
            APCs                                                                      3 day culture
                            E           E
         E E
        E E E

                                                +
                                    E

                                                        + anti-CD30:100 N.D. Cycle
                                                                   antibody
          E
                                                                           Cell
            R           R                               R       R               E
        R                       R                   R                   R
                    R                                       R
                R                                       R                                                                 ND
                                                                                                           Analysis
1.1+
  CD25+CD4+Thy1.2+

                                                                                             3 day culture                     Log FL1-H / CFSE intensity
                            E                                       E
                E E                 E                   E E                 E
            E    E E                                E    E E


                                                                                                 Cell Cycle
            R
                 E
                        R
                                E
                                            E            E              E

        R                       R
                R
            R
   CD25-CD4+Thy1.1+
                                                                                                 Analysis et al. Immuno. Rev. 2007]
                                                                                                   [Carneiro
.2+
Putting the CRM to the test

                                                                                    + anti-CD3 antibody
                    APCs                                                                 Proportions                  Effector Cells               Regulatory Cells
                                                                                        Thy1.1:Thy1.2
                                                                                                                          Thy1.1                            Thy1.2
                                                                                                    Cell Cycle
                                R                       R       R           E
                    R                               R               R
                R                   R
                                                                                        Day 0     Day 3
                            R                               R
                        R                               R

                                                                                                    Analysis
       CD25+CD4+Thy1.2+




                                                                                                                                                              ?
                                                                                           3 day culture
                    E
                        E E
                         E E
                         E
                                    E

                                        E
                                            E
                                                + + anti-CD3100:0 N.D.
                                                    E
                                                        E E
                                                         E E
                                                         E
                                                             antibody
                                                                E

                                                                        E
                                                                            E


                                                                                                                                                            ND
y1.1
       CD25-CD4+Thy1.1+



                                                                                         80:20     47:53
                                                                                                 Cell Cycle
            R           R                   E
        R                       R
                R
            R

                                                                                                 Analysis
.2+
                                                                                    + anti-CD3 antibody
                                                                                        50:50 24:76
            APCs                                                                      3 day culture
                            E           E
         E E
        E E E

                                                +
                                    E

                                                        + anti-CD30:100 N.D. Cycle
                                                                   antibody
          E
                                                                           Cell
            R           R                               R       R               E
        R                       R                   R                   R
                    R                                       R
                R                                       R                                                                 ND
                                                                                                           Analysis
1.1+
  CD25+CD4+Thy1.2+

                                                                                             3 day culture                     Log FL1-H / CFSE intensity
                            E                                       E
                E E                 E                   E E                 E
            E    E E                                E    E E


                                                                                                 Cell Cycle
            R
                 E
                        R
                                E
                                            E            E              E

        R                       R
                R
            R
   CD25-CD4+Thy1.1+
                                                                                                 Analysis et al. Immuno. Rev. 2007]
                                                                                                   [Carneiro
.2+
Putting the CRM to the test

                                                                                    + anti-CD3 antibody
                    APCs                                                                 Proportions                  Effector Cells               Regulatory Cells
                                                                                        Thy1.1:Thy1.2
                                                                                                                          Thy1.1                            Thy1.2
                                                                                                    Cell Cycle
                                R                       R       R           E
                    R                               R               R
                R                   R
                                                                                        Day 0     Day 3
                            R                               R
                        R                               R

                                                                                                    Analysis
       CD25+CD4+Thy1.2+

                                                                                           3 day culture
                    E
                        E E
                         E E
                         E
                                    E

                                        E
                                            E
                                                + + anti-CD3100:0 N.D.
                                                    E
                                                        E E
                                                         E E
                                                         E
                                                             antibody
                                                                E

                                                                        E
                                                                            E


                                                                                                                                                            ND
y1.1
       CD25-CD4+Thy1.1+



                                                                                         80:20     47:53
                                                                                                 Cell Cycle
            R           R                   E
        R                       R
                R
            R

                                                                                                 Analysis
.2+
                                                                                    + anti-CD3 antibody
                                                                                        50:50 24:76
            APCs                                                                      3 day culture
                            E           E
         E E
        E E E

                                                +
                                    E

                                                        + anti-CD30:100 N.D. Cycle
                                                                   antibody
          E
                                                                           Cell
            R           R                               R       R               E
        R                       R                   R                   R
                    R                                       R
                R                                       R                                                                 ND
                                                                                                           Analysis
1.1+
  CD25+CD4+Thy1.2+

                                                                                             3 day culture                     Log FL1-H / CFSE intensity
                            E                                       E
                E E                 E                   E E                 E
            E    E E                                E    E E


                                                                                                 Cell Cycle
            R
                 E
                        R
                                E
                                            E            E              E

        R                       R
                R
            R
   CD25-CD4+Thy1.1+
                                                                                                 Analysis et al. Immuno. Rev. 2007]
                                                                                                   [Carneiro
.2+
Putting the CRM to the test

                                                                                    + anti-CD3 antibody
                    APCs                                                                 Proportions                   Effector Cells               Regulatory Cells
                                                                                        Thy1.1:Thy1.2
                                                                                                                           Thy1.1                            Thy1.2
                                                                                                    Cell Cycle
                                R                       R       R           E
                    R                               R               R
                R                   R
                                                                                        Day 0     Day 3
                            R                               R
                        R                               R

                                                                                                    Analysis
       CD25+CD4+Thy1.2+

                                                                                           3 day culture
                    E
                        E E
                         E E
                         E
                                    E

                                        E
                                            E
                                                + + anti-CD3100:0 N.D.
                                                    E
                                                        E E
                                                         E E
                                                         E
                                                             antibody
                                                                E

                                                                        E
                                                                            E


                                                                                                                                                             ND
y1.1
       CD25-CD4+Thy1.1+



                                                                                         80:20     47:53
                                                                                                 Cell Cycle
            R           R                   E
        R                       R
                R
            R

                                                                                                 Analysis
.2+
                                                                                    + anti-CD3 antibody
                                                                                        50:50 24:76



                                                                                                                            ?                                     ?
            APCs                                                                      3 day culture
                            E           E
         E E
        E E E

                                                +
                                    E

                                                        +               anti-CD30:100 N.D.
                                                                                 antibody
          E
                                                                                         Cell                  Cycle
            R           R                               R       R               E
        R                       R                   R                   R
                    R                                       R
                R                                       R                                                                  ND
                                                                                                           Analysis
1.1+
  CD25+CD4+Thy1.2+

                                                                                             3 day culture                      Log FL1-H / CFSE intensity
                            E                                       E
                E E                 E                   E E                 E
            E    E E                                E    E E


                                                                                                 Cell Cycle
            R
                 E
                        R
                                E
                                            E            E              E

        R                       R
                R
            R
   CD25-CD4+Thy1.1+
                                                                                                 Analysis et al. Immuno. Rev. 2007]
                                                                                                   [Carneiro
.2+
Putting the CRM to the test

                                                                                    + anti-CD3 antibody
                    APCs                                                                 Proportions                  Effector Cells               Regulatory Cells
                                                                                        Thy1.1:Thy1.2
                                                                                                                          Thy1.1                            Thy1.2
                                                                                                    Cell Cycle
                                R                       R       R           E
                    R                               R               R
                R                   R
                                                                                        Day 0     Day 3
                            R                               R
                        R                               R

                                                                                                    Analysis
       CD25+CD4+Thy1.2+

                                                                                           3 day culture
                    E
                        E E
                         E E
                         E
                                    E

                                        E
                                            E
                                                + + anti-CD3100:0 N.D.
                                                    E
                                                        E E
                                                         E E
                                                         E
                                                             antibody
                                                                E

                                                                        E
                                                                            E


                                                                                                                                                            ND
y1.1
       CD25-CD4+Thy1.1+



                                                                                         80:20     47:53
                                                                                                 Cell Cycle
            R           R                   E
        R                       R
                R
            R

                                                                                                 Analysis
.2+
                                                                                    + anti-CD3 antibody
                                                                                        50:50 24:76
            APCs                                                                      3 day culture
                            E           E
         E E
        E E E

                                                +
                                    E

                                                        + anti-CD30:100 N.D. Cycle
                                                                   antibody
          E
                                                                           Cell
            R           R                               R       R               E
        R                       R                   R                   R
                    R                                       R
                R                                       R                                                                 ND
                                                                                                           Analysis
1.1+
  CD25+CD4+Thy1.2+

                                                                                             3 day culture                     Log FL1-H / CFSE intensity
                            E                                       E
                E E                 E                   E E                 E
            E    E E                                E    E E


                                                                                                 Cell Cycle
            R
                 E
                        R
                                E
                                            E            E              E

        R                       R
                R
            R
   CD25-CD4+Thy1.1+
                                                                                                 Analysis et al. Immuno. Rev. 2007]
                                                                                                   [Carneiro
.2+
Putting the CRM to the test

                                                                                                                  + anti-CD3 antibody
                               APCs                                                                                                 Proportions                           Effector Cells               Regulatory Cells
                                                                                                                                   Thy1.1:Thy1.2
                                                                                                                                                                              Thy1.1                            Thy1.2
                                                                                                                                                   Cell Cycle
                                       R                                           R       R       E
                               R                                           R                   R
                           R               R
                                                                                                                                   Day 0          Day 3
                                   R                                                   R
                               R                                                   R

                                                                                                                                                   Analysis
           CD25+CD4+Thy1.2+

                                                                                                       + anti-CD3 antibody
                                                                                                                   3 day culture
           APCsE EE EE
                  E
                                           E

                                               E
                                                   E
                                                       + + anti-CD3100:0 N.D.
                                                                    antibody   E
                                                                                   E E
                                                                                    E E
                                                                                    E
                                                                                           E

                                                                                               E
                                                                                                   E


                                                                                                                                                                                                                ND
y1.1
               CD25-CD4+Thy1.1+
                                                                                                                                           Cell Cycle
                R          R  R                                                    E
           R                                           R                   R
       R               R

                                                                                                                                           + anti-CD3 antibody

                                                                                                                                                                              ?                                  ?
                   R                                               R
               R                                               R

                                                                                                                                           Analysis
CD25+CD4+Thy1.2+
                                                           APCs                                                                     80:20         47:53
                                                                                       Cell Cycle
                       R           R               E                                                                              3 day culture
                   R                   R

                                           +                           + anti-CD3 antibody
                           R




                                                                                                                                                                                   ?                                 ?
                                                                          +
                       E                                               E
               E E     R   E                                E E                E



                                                                                       Analysis Cell Cycle
           E    E E                                        E E E                                                      R       E
                E          E                               RE R            E
                                                                                                         R
                                                                                                              R
                                                                                                                          R
                                                       R                   R
                                                                   R                                              R
                                                               R                                              R

.2+
CD25-CD4+Thy1.1+
Thy1.2                                                                                                                                                             Analysis
                                           CD25+CD4+Thy1.2+                                                                          50:50        24:76
                                                                                                                          3 day culture                   3 day culture

                                                                                                                                         Cell Cycle
           R           R           EE E                        E E
                                                                       E
                                                                               E                              E E
                                                                                                                      E       E
       R           E ER                                E        E E                                       E    E E
                 R E E
                 E                                              E          E                                   E          E
               R    E                      E


                                                                                                                                         Analysis
                                                                                                                                     0:100  N.D.
ongenic Thy1.1
                                                                                                                                                                              ND
                                               CD25-CD4+Thy1.1+
+
1.1+
                                                                                                                  3 day culture                                                    Log FL1-H / CFSE intensity
                           E       E
        E E
       E E E
         E                     E



                                                                                                                                                    [Carneiro et al. Immuno. Rev. 2007]
+
Putting the CRM to the test

 Proportions              Effector Cells                Regulatory Cells
Thy1.1:Thy1.2
                              Thy1.1                             Thy1.2
Day 0   Day 3




100:0    N.D.                                                    ND




80:20   47:53




50:50   24:76




0:100    N.D.                  ND




                                    Log FL1-H / CFSE intensity




          [Carneiro et al. Immuno. Rev. 2007]
Modelling T cell population dynamics: the crossregulation model



                                                                   R




                                                            T
                           IL-X
                                                                    R




                                                                    R


                                                                                  CRM




              [Leon et al. J Theor Biol 2000; Carneiro et al. Immunol Rev 2007]
                             [Carneiro et al. Immuno. Rev. 2007]
Modelling T cell population dynamics: the crossregulation model




         Regulatory T cell populations grow as a
           function of the effector T cells they
                         suppress                                         R
                                                                           R




                    Leon et al. JTB (2000)                     R


                                                          E




                                                    E
                                                     E



                                                                                               01
                                                                                 . Imm unol 20
                                                                   iol 2 000 , J
                                                     al. J Theor B
                                              eon et                                     Thesis
                                            L                                alh  o PhD
                                                                 sis , Caram
                                                          hD The
the control of the insulin promoter. We had previously observed
Modelling T cell population dynamics: the crossregulation model
 Authorship note: Yenkel Grinberg-Bleyer and David Saadoun contributed equally to
 this work. Eliane Piaggio and Benoît L. Salomon are co–senior authors.
                                                                                                                    that HA-specific Tregs (HA-Tregs) preferentially proliferated and
                                                                                                                    expanded at days 5–7 after transfer in draining pancreatic LNs
 Conflict of interest: The authors have declared that no conflict of interest exists.                               (PLNs) of ins-HA homozygous mice (29). When we repeated the
 Citation for this article: J Clin Invest. 2010;120(12):4558–4568. doi:10.1172/JCI42945.                            experiment in ins-HA hemizygous recipients, which express lower

                                     The Journal of Clinical Investigation                      http://www.jci.org         Volume 120          Number 12           December 2010




                                                                                    Related Commentary, page 4190




                      Regulatory T cell populations grow as a
                        function of the effector T cells they
                                      suppress
                                          Yenkel Grinberg-Bleyer,1,2,3 David Saadoun,1,2,3 Audrey Baeyens,1,2,3 Fabienne Billiard,1,2,3
                                             Jérémie D. Goldstein,1,2,3 Sylvie Grégoire,1,2,3 Gaëlle H. Martin,1,2,3 Rima Elhage,1,2,3
                                             Nicolas Derian,1,2,3 Wassila Carpentier,1,4 Gilles Marodon,1,2,3 David Klatzmann,1,2,3
                                                                                                                                                                                   R
                                                                                                                                                                                   R
                                                                 Eliane Piaggio,1,2,3 and Benoît L. Salomon1,2,3
                                                              1Université   Pierre et Marie Curie — Univ Paris 06, 2CNRS UMR 7211, 3INSERM U959, Paris, France.
                                                                             4Plate-forme Post-Génomique P3S, Hôpital Pitié-Salpêtrière, Paris, France.




                                                      Leon et al. JTB (2000)
                                     CD4+CD25+Foxp3+ Tregs play a major role in prevention of autoimmune diseases. The suppressive effect of
                                     Tregs on effector T cells (Teffs), the cells that can mediate autoimmunity, has been extensively studied. How-
                                                                                                                                                                       R


                                                                                                                                   E
                                     ever, the in vivo impact of Teff activation on Tregs during autoimmunity has not been explored. In this study,
                                     we have shown that CD4     + Teff activation strongly boosts the expansion and suppressive activity of Tregs.

                                     This helper function of CD4+ T cells, which we believe to be novel, was observed in the pancreas and draining
                                     lymph nodes in mouse recipients of islet-specific Teffs and Tregs. Its physiological impact was assessed in
                                     autoimmune diabetes. When islet-specific Teffs were transferred alone, they induced diabetes. Paradoxically,
                                     when the same Teffs were cotransferred with islet-specific Tregs, they induced disease protection by boost-
                                                                                                                            E
                                     ing Treg expansion and suppressive function. RNA microarray analyses suggested that TNF family members
                                     were involved in the Teff-mediated Treg boost. In vivo experiments showed that this Treg boost was partially
                                                                                                                             E
                                     dependent on TNF but not on IL-2. This feedback regulatory loop between Teffs and Tregs may be critical to
                                     preventing or limiting the development of autoimmune diseases.

                                                                                                                    bers of mature DCs in inflamed tissues may favor the activation of
                                                                                                                                                                                                           01
                                                                                                                                                                                                   unol 20
                                  The peripheral T cell repertoire of any individual contains autoreac-             autoreactive Tregs (21–23), which would then turn on their sup-
                                  tive T cells specific for a variety of self antigens (1). Their activation        pressive activity and exert bystander suppression (24, 25).
                                                                                                                      Thus, during an autoimmune process, there is a local enrichment 00 , J
                                                                                                                                                                                             . Imm
                                  could induce an autoimmune process, eventually leading to an auto-
                                                                                                                                                                           Bi ofl 2 0
                                                                                                                    of both autoreactive Teffs and Tregs. Since heefficacy o Treg-
                                  immune disease. Severe and prolonged inflammation in a tissue may
                                                                                                                                                              J T the orbetween acti-
                                                                                                                    mediated suppression depends onal. equilibrium
                                                                                                                                            eon et the factor that could tip this                    Thesis
                                                                                                                                                                                              o PhD
                                  lead to the activation of pathological autoreactive T cells by several
                                                                                                                                           L Tregs (26), any
                                  mechanisms (2, 3). At the site of inflammation or in draining LNs,                vated Teffs and activated
                                                                                                                    balance to one side or the other could then determine thes, Ca
                                                                                                                                                                                     ramalh
                                  tissue damage results in an enhanced presentation of autoantigens
                                                                                                                                                                  hD Th esi   outcome
How does their repertoire
     What makes a T cell                       compare to that of other T
    be a regulatory T cell ?                            cells ?

                                                             How many and how
                        CD25+CD4+T cells                      diverse are they ?
                                               R
                                       R

How do they interact
                               R   R               R
                               R           R
                                       R

 with other cells ?       (Regulatory T cells, TR, R)
                                                            How do they allow
                                                       efficient immune responses ?
               How do they prevent
               autoimmune diseases ?
How does their repertoire
     What makes a T cell                       compare to that of other T
    be a regulatory T cell ?                            cells ?

                                                             How many and how
                        CD25+CD4+T cells                      diverse are they ?
                                               R
                                       R

How do they interact
                               R   R               R
                               R           R
                                       R

 with other cells ?       (Regulatory T cells, TR, R)
                                                            How do they allow
                                                       efficient immune responses ?
               How do they prevent
               autoimmune diseases ?
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difuhgdlkhjl

  • 1. MODELLING COMPLEX BIOLOGICAL SYSTEMS IN THE CONTEXT OF GENOMICS Evry, May 21-25, 2012 On the cellular and supracellular networks controlling regulatory T cells and autoimmunity Jorge Carneiro Instituto Gulbenkian de Ciência, Portugal http://qobweb.igc.gulbenkian.pt
  • 2. Quantitative Organism Biology Cells of multicellular organism cooperate to ensure body development and maintenance. They do this in a collective distributed manner, without a global plan. How cells collectively generate organism’s properties? General principles of biological organisation The design and control of artificial systems
  • 4. How cells get along without a GPS ?
  • 5. How cells get along without a GPS ? global information (system)
  • 6.
  • 7.
  • 8. autoimmune disease and immunopathology, 2 2 2 2 B Foxp3 represents a more specific marker than 5RBhi alone +Foxp3/MIGR1 +MIGR1 None CD25-CD45RBhi alone cell-surface molecules (such as currently used +Foxp3/MIGR1 +MIGR1 None CD25, CD45RB, CTLA-4, and GITR), which Multiple are unable to completely discriminate between regulatory T cells and activated, effector, or memory T cells. scales Colon Mutations in the Foxp3 gene culminate in the development of a fatal lymphoprolifera- tive disorder associated with multiorgan pa- thology both in mice and humans (12–20). FOXP3 is predominantly expressed in human CD25ϩCD4ϩ T cells as well (32). Further- Stomach more, transduction of a mutant Foxp3 lacking the forkhead domain, similar to the mutated Foxp3 in scurfy mice (17), failed to confer suppressive activity to CD25–CD4ϩ T cells Fig. 4. Prevention(fig.IBD and autoimmune gastritis by Foxp3-transduced T cells. (A) C.B-17 scid IBD and autoimmune gastritis by Foxp3-transduced T cells. (A) C.B-17 scid of S7). The present results therefore sug- 105 fresh CD25–CD45RBhighCD4ϩ cells either alone (n ϭ 6, where n is the 4 ϫ 10that mutations of thehighCD4ϩgene may alone (n ϭ 6, where n is the mice received gest 5 fresh CD25–CD45RB Foxp3 cells either derived of mice)cause squares)disorders through1.2develop- GFPϩ sorted cells derived from pen squares) or together with 1.2 ϫ 106 GFPϩ sorted cells number from (open these or together with ϫ 106 D4ϩ cells infected with Foxp3/MIGR1 (n ϭ 7) (closed circles) or MIGR1 –(n ϭ 5) highmentalcells infected with Foxp3/MIGR1 (n ϭthe (closed circles) or MIGR1 (n ϭ 5) CD25 CD45RB CD4ϩ or functional abnormality of 7) weight is represented as the percentage of initial weight (mean Ϯ SD). Body weight is represented as the percentage of initial weight (mean Ϯ SD) (open circles). CD25ϩCD4ϩ T population. R gnificant difference, P Ͻ 0.01, Foxp3/MIGR1 versus other two groups indicate significant difference, P of T cells by Foxp3 versus other two groups by Astericks by Potentially, generation Ͻ 0.01, Foxp3/MIGR1 R (B) Histopathology of the colon and stomach in each group and in an test. (B) Histopathology of the colon and stomach in each group and in an Mann-Whitney transduction of naıve T cells may provide a ¨ D mouse (None). (C) Colitis (left) and gastritis (right) were unreconstituted SCID mouse (None). (C) Colitis (left) and gastritis (right) were histologically histologically the group cotransferred with MIGR1-infected cells and one transferredTwo micepreviously unstudied therapeutic mode for cells and one transferred with scored. with in the group cotransferred with MIGR1-infected ϩ CD25 CD45RB treatment of autoimmunedebilitation before histological examination. Results – D4 cells alone died of debilitation before histological examination. Results high CD4ϩ cells alone died of and inflammatory are from a total of three independent experiments. shown in (A) to (C) are from a total of three independent experiments. diseases and in transplantation tolerance. 1060 14 FEBRUARY 2003 VOL 299 SCIENCE www.sciencemag.org 14 FEBRUARY 2003 VOL 299 SCIENCE www.scien
  • 9. autoimmune disease and immunopathology, 2 2 2 2 B Foxp3 represents a more specific marker than 5RBhi alone +Foxp3/MIGR1 +MIGR1 None CD25-CD45RBhi alone cell-surface molecules (such as currently used +Foxp3/MIGR1 +MIGR1 None CD25, CD45RB, CTLA-4, and GITR), which Multiple are unable to completely discriminate between regulatory T cells and activated, effector, or memory T cells. scales Colon Mutations in the Foxp3 gene culminate in the development of a fatal lymphoprolifera- tive disorder associated with multiorgan pa- thology both in mice and humans (12–20). FOXP3 is predominantly expressed in human CD25ϩCD4ϩ T cells as well (32). Further- Stomach more, transduction of a mutant Foxp3 lacking the forkhead domain, similar to the mutated Foxp3 in scurfy mice (17), failed to confer suppressive activity to CD25–CD4ϩ T cells Fig. 4. Prevention(fig.IBD and autoimmune gastritis by Foxp3-transduced T cells. (A) C.B-17 scid IBD and autoimmune gastritis by Foxp3-transduced T cells. (A) C.B-17 scid of S7). The present results therefore sug- 105 fresh CD25–CD45RBhighCD4ϩ cells either alone (n ϭ 6, where n is the 4 ϫ 10that mutations of thehighCD4ϩgene may alone (n ϭ 6, where n is the mice received gest 5 fresh CD25–CD45RB Foxp3 cells either derived of mice)cause squares)disorders through1.2develop- GFPϩ sorted cells derived from pen squares) or together with 1.2 ϫ 106 GFPϩ sorted cells number from (open these or together with ϫ 106 D4ϩ cells infected with Foxp3/MIGR1 (n ϭ 7) (closed circles) or MIGR1 –(n ϭ 5) highmentalcells infected with Foxp3/MIGR1 (n ϭthe (closed circles) or MIGR1 (n ϭ 5) CD25 CD45RB CD4ϩ or functional abnormality of 7) Astericks by R Cell population dynamics weight is represented as the percentage of initial weight (mean Ϯ SD). Body weight is represented as the percentage of initial weight (mean Ϯ SD) (open circles). CD25ϩCD4ϩ T population. gnificant difference, P Ͻ 0.01, Foxp3/MIGR1 versus other two groups indicate significant difference, P of T cells by Foxp3 versus other two groups by Potentially, generation Ͻ 0.01, Foxp3/MIGR1 (ODE) R (B) Histopathology of the colon and stomach in each group and in an test. (B) Histopathology of the colon and stomach in each group and in an Mann-Whitney transduction of naıve T cells may provide a ¨ D mouse (None). (C) Colitis (left) and gastritis (right) were unreconstituted SCID mouse (None). (C) Colitis (left) and gastritis (right) were histologically histologically the group cotransferred with MIGR1-infected cells and one transferredTwo micepreviously unstudied therapeutic mode for cells and one transferred with scored. with in the group cotransferred with MIGR1-infected ϩ CD25 CD45RB treatment of autoimmunedebilitation before histological examination. Results – D4 cells alone died of debilitation before histological examination. Results high CD4ϩ cells alone died of and inflammatory are from a total of three independent experiments. shown in (A) to (C) are from a total of three independent experiments. diseases and in transplantation tolerance. 1060 14 FEBRUARY 2003 VOL 299 SCIENCE www.sciencemag.org 14 FEBRUARY 2003 VOL 299 SCIENCE www.scien
  • 10. autoimmune disease and immunopathology, 2 2 2 2 B Foxp3 represents a more specific marker than 5RBhi alone +Foxp3/MIGR1 +MIGR1 None CD25-CD45RBhi alone cell-surface molecules (such as currently used +Foxp3/MIGR1 +MIGR1 None CD25, CD45RB, CTLA-4, and GITR), which Multiple are unable to completely discriminate between regulatory T cells and activated, effector, or memory T cells. scales Colon Mutations in the Foxp3 gene culminate in the development of a fatal lymphoprolifera- tive disorder associated with multiorgan pa- thology both in mice and humans (12–20). FOXP3 is predominantly expressed in human CD25ϩCD4ϩ T cells as well (32). Further- Stomach more, transduction of a mutant Foxp3 lacking the forkhead domain, similar to the mutated Foxp3 in scurfy mice (17), failed to confer suppressive activity to CD25–CD4ϩ T cells Fig. 4. Prevention(fig.IBD and autoimmune gastritis by Foxp3-transduced T cells. (A) C.B-17 scid IBD and autoimmune gastritis by Foxp3-transduced T cells. (A) C.B-17 scid of S7). The present results therefore sug- 105 fresh CD25–CD45RBhighCD4ϩ cells either alone (n ϭ 6, where n is the 4 ϫ 10that mutations of thehighCD4ϩgene may alone (n ϭ 6, where n is the mice received gest 5 fresh CD25–CD45RB Foxp3 cells either derived of mice)cause squares)disorders through1.2develop- GFPϩ sorted cells derived from pen squares) or together with 1.2 ϫ 106 GFPϩ sorted cells number from (open these or together with ϫ 106 D4ϩ cells infected with Foxp3/MIGR1 (n ϭ 7) (closed circles) or MIGR1 –(n ϭ 5) highmentalcells infected with Foxp3/MIGR1 (n ϭthe (closed circles) or MIGR1 (n ϭ 5) CD25 CD45RB CD4ϩ or functional abnormality of 7) Astericks by R Cell population dynamics weight is represented as the percentage of initial weight (mean Ϯ SD). Body weight is represented as the percentage of initial weight (mean Ϯ SD) (open circles). CD25ϩCD4ϩ T population. gnificant difference, P Ͻ 0.01, Foxp3/MIGR1 versus other two groups indicate significant difference, P of T cells by Foxp3 versus other two groups by Potentially, generation Ͻ 0.01, Foxp3/MIGR1 (ODE) R (B) Histopathology of the colon and stomach in each group and in an test. (B) Histopathology of the colon and stomach in each group and in an Mann-Whitney transduction of naıve T cells may provide a ¨ D mouse (None). (C) Colitis (left) and gastritis (right) were unreconstituted SCID mouse (None). (C) Colitis (left) and gastritis (right) were histologically histologically the group cotransferred with MIGR1-infected cells and one transferredTwo micepreviously unstudied therapeutic mode for cells and one transferred with scored. with in the group cotransferred with MIGR1-infected ϩ CD25 CD45RB treatment of autoimmunedebilitation before histological examination. Results – D4 cells alone died of debilitation before histological examination. Results high CD4ϩ cells alone died of and inflammatory are from a total of three independent experiments. shown in (A) to (C) are from a total of three independent experiments. diseases and in transplantation tolerance. 1060 14 FEBRUARY 2003 VOL 299 SCIENCE www.sciencemag.org 14 FEBRUARY 2003 VOL 299 SCIENCE www.scien Gene regulatory networks (Logical network dynamics)
  • 11. overview Tolerance, autoimmunity, and regulatory T cells Regulatory T cells 101 How regulatory T cells mediate tolerance ? Modelling T cell population dynamics Ordinary differential equations ··························· CRM What makes a T cell be a regulatory T cell ? Modelling gene regulatory networks and T cell differentiation Logical network formalism ······················ Th cell plasticity If regulatory T cells are plastic how can tolerance be robust ? Multiscale modelling of cellular and supracellular networks Agent-based stochastic simulations
  • 12.
  • 13. What does the immune system do in the vertebrate organism?
  • 14.
  • 18. Fighting infection Assimilating intestinal flora House keeping Rejecting cancer cells
  • 19. Homeostasis Fighting infection and Regulation Assimilating intestinal flora House keeping Rejecting cancer cells
  • 20. Homeostasis Fighting infection and Regulation Assimilating intestinal flora House keeping Rejecting cancer cells http://www.sciencemuseum.org.uk/exhibitions/lifecycle/116.asp http://ww.grc.org/Graphics/ programs/2003/cells3.jpg http://www.leukemia-web.org/images/cells.jpg
  • 21. Failure of homeostasis and regulation unleashes pathologic autoimmunity
  • 22. Failure of homeostasis and regulation unleashes pathologic autoimmunity Rheumatoid arthritis Type I diabetes Multiple sclerosis IPEX sindrome Cortesy: Magda Carneiro-Sampaio, São Paulo
  • 23. From: Jean-François Bach, New England J Med
  • 24. “In general, the management of human systemic autoimmune disease is empirical and unsatisfactory. For the most part, broadly immunosuppressive drugs, such as corticosteroids, are used in a wide variety of severe autoimmune and inflammatory disorders (…)” – Philipe Cohen In: Fundamental Immunology (Ed. W. Paul)
  • 25. Clonal selection theory Stem Cell Jerne, 1953 Burnet, 1957 G.O.D. Ag A 1 2 3 4 ... 111 112 ... 623 ... 1245 ... n Ag B 1 2 3 4 ... 111 112 ... 623 ... 1245 ... n 111 111 1245 1245 111 111 111 111 1245 1245 1245 1245
  • 26. CTL CTL CTL CTL CTL CTL TH CTL Antigen TH TH TH TH TH TH TH B B B B B B B TH
  • 27. CTL CTL CTL CTL CTL CTL TH CTL Antigen TH TH TH TH TH TH TH B B B B B B B TH
  • 28. CTL CTL CTL CTL CTL CTL TH CTL Antigen TH TH TH TH TH TH TH B B B B B B B TH
  • 29. CTL CTL CTL CTL CTL CTL TH CTL Antigen TH TH TH “Self” tolerance by deletion TH TH TH TH B B B B B B B TH
  • 30. CTL CTL CTL CTL CTL CTL TH CTL Antigen TH TH TH TH TH TH TH B B B B B B B TH
  • 31. Reductionist molecular biology approach to Immunology
  • 32. TOLERANCE = absence of clonal expansion = CLONAL DELETION Therapy of autoimmune diseases should aim at “deleting” autoreactive cells or clones In the absence of clonal-specific therapies: kill them all !!!
  • 33. Is there any hope ?
  • 34. Tolerance is mediated by regulatory T cells Mason-Sakaguchi WT
  • 35. Tolerance is mediated by regulatory T cells Mason-Sakaguchi CD25- CD4+ T cells E E E T E T T T T (Effector T cells, TE, E) WT
  • 36. Tolerance is mediated by regulatory T cells Mason-Sakaguchi “empty” rag-/- CD25- CD4+ T cells E E E T E T T T T (Effector T cells, TE, E) WT
  • 37. Tolerance is mediated by regulatory T cells Mason-Sakaguchi “empty” rag-/- AID CD25- CD4+ T cells E E E T E T T T T (Effector T cells, TE, E) WT
  • 38. Tolerance is mediated by regulatory T cells Mason-Sakaguchi “empty” rag-/- AID CD25- CD4+ T cells E E E T E T T T T (Effector T cells, TE, E) WT CD25+CD4+T cells R R R R R R R R (Regulatory T cells, TR, R)
  • 39. Tolerance is mediated by regulatory T cells Mason-Sakaguchi “empty” rag-/- AID CD25- CD4+ T cells E E E T E T T T T (Effector T cells, TE, E) WT CD25+CD4+T cells R R R R R R R R (Regulatory T cells, TR, R)
  • 40. Tolerance is mediated by regulatory T cells Mason-Sakaguchi “empty” rag-/- AID CD25- CD4+ T cells E E E T E T T T T (Effector T cells, TE, E) WT CD25+CD4+T cells R R R R R Healthy R R R (Regulatory T cells, TR, R)
  • 41. Tolerance is mediated by regulatory T cells Mason-Sakaguchi “empty” rag-/- AID CD25- CD4+ T cells E E E T E T T T T (Effector T cells, TE, E) WT CD25+CD4+T cells R R R R R Healthy R R R (Regulatory T cells, TR, R)
  • 42. Tolerance is mediated by regulatory T cells Mason-Sakaguchi “empty” rag-/- AID CD25- CD4+ T cells E E E T E T T T T AID (Effector T cells, TE, E) or Healthy WT CD25+CD4+T cells R R R R R Healthy R R R (Regulatory T cells, TR, R)
  • 43. Tolerance is mediated by regulatory T cells Mason-Sakaguchi “empty” rag-/- AID CD25- CD4+ T cells E E E T E T T T T AID (Effector T cells, TE, E) or Healthy WT CD25+CD4+T cells R R R R R Healthy R R R (Regulatory T cells, TR, R)
  • 44. Tolerance is mediated by regulatory T cells CTL CTL CTL CTL CTL CTL TH CTL Self Antigen TH TH TH TH TH TH TH TH B B B B B B TH B
  • 45. TOLERANCE = absence of clonal expansion = control by regulatory T cells Therapy of autoimmune diseases should aim at stimulating autoreactive regulatory T cells or clones
  • 46. … BUT … there are many open questions
  • 47. CD25+CD4+T cells R R R R R R R R (Regulatory T cells, TR, R)
  • 48. What makes a T cell be a regulatory T cell ? CD25+CD4+T cells R R R R R R R R (Regulatory T cells, TR, R)
  • 49. What makes a T cell be a regulatory T cell ? CD25+CD4+T cells R R How do they interact R R R R R R with other cells ? (Regulatory T cells, TR, R)
  • 50. What makes a T cell be a regulatory T cell ? CD25+CD4+T cells R R How do they interact R R R R R R with other cells ? (Regulatory T cells, TR, R) How do they prevent autoimmune diseases ?
  • 51. What makes a T cell be a regulatory T cell ? CD25+CD4+T cells R R How do they interact R R R R R R with other cells ? (Regulatory T cells, TR, R) How do they allow efficient immune responses ? How do they prevent autoimmune diseases ?
  • 52. What makes a T cell be a regulatory T cell ? How many and how CD25+CD4+T cells diverse are they ? R R How do they interact R R R R R R with other cells ? (Regulatory T cells, TR, R) How do they allow efficient immune responses ? How do they prevent autoimmune diseases ?
  • 53. How does their repertoire What makes a T cell compare to that of other T be a regulatory T cell ? cells ? How many and how CD25+CD4+T cells diverse are they ? R R How do they interact R R R R R R with other cells ? (Regulatory T cells, TR, R) How do they allow efficient immune responses ? How do they prevent autoimmune diseases ?
  • 54. Balance between regulatory and effector T cell subpopulations
  • 55. Is it that simple ?
  • 56. Is it that simple ? “Everything should be made as simple as possible, But not simpler.” Albert Einstein, XX century
  • 60. http://www.sewingmachines.us/sewing-machine-636.jpg http://www.roselabiche.com/blog/index.php?2007/11 http://www.medscape.com/content/2004/00/46/84/468446/468446_fig.html
  • 63. J. theor. Biol. (2000) 207, 231}254 doi:10.1006/jtbi.2000.2169, available online at http://www.idealibrary.com on Modelling T-cell-Mediated Suppression Dependent on Interactions in Multicellular Conjugates KALET LEON*-?, ROLANDO PEREZ*, AGUSTIN LAGE* D D AND JORGE CARNEIRO- MODELLING T LYMPHOCYTE LINKED SUPPRESSION 249 *Centro de ImmunolognH a Molecular, P.O. Box 16040, Habana 11600, Cuba and -Instituto Gulbenkian de Ciencia, Apartado 14, 2781-901, Oeiras, Portugal ore than two cell types with the alternative mechanisms of linked sup- mechanisms can be speci- (Received on 7 February 2000, Accepted in revised form onreported 2000) pression. Overall, the modelling results 10 August setting of the interaction here and the whole set of observations that we the consequences of each discussed would strongly favour two candidate Tolerance to peripheral body antigens involves multiple mechanisms, namely T-cell-mediated able 1). The application of suppression of potentially autoimmuneare Recent in vivo and in vitro evidence indicates that mechanisms. These cells. the ones that are trans- regulatory T cells suppress the response of e!ector T cells by a mechanism that requires the tions other than the cur- lated by the "nal model: regulatory T cells inhibit simultaneous conjugation of regulatory and e!ector T cells with the same antigen-presenting minant tolerance can be (APC). Despite this strong requirement, it is not yet clearwhile theywhile both cells are cell the proliferation of e!ector cells what happens are conjugated. Several hypotheses are discussed in the literature. Suppression may result from For example, it was competition of regulatory and e!ectoracells for activation resources on the APC; simple nevertheless dependent on growth factor that the the interaction between regulatory T cellsproduce; an inhibitory signal tocells inhibit the same conjugate; or latter may deliver or regulatory e!ector T cells in the ex- e!ector T cells may acquire the regulatory phenotype during their interaction with regulatory Ls does not involve thecells. The present article tries to further our understanding of T-cell-mediated suppression, T pansion of the population of e!ector cells because they convertnumber of multicellular conjugates of T propose the "rst general ns between the two cells to narrow-downthe formation of to the regulatoryWe cells and APCs. Using this and formalism describing the them candidate mechanisms. phenotype. formalism we derive three particularor both may be operative in of T-cell- resenting cell, as classi- Either mechanism models, representing alternative mechanisms mediated suppression. For each model, we make phase plane and bifurcation analysis, and son & O'Malley, 1987; vivo, maybe even dependent on with the history of identify their pros and cons in terms of the relationshipthe life large body of experimental hat the APC may act as observations on T-cell-mediated Modigliani et al.that accounting for the quantitative the e!ector cells. suppression. We argue (1996b) actually details of adoptive transfers of tolerance requires models with bistable regimes in which either nnett et al., 1998; Ridge regulatory cells or e!ectors cells dominate the steady cellsFrom this thymic conclude demonstrated that regulatory state. from analysis, we r et al., 1998). The formal- cells actively inhibit mechanism of T-cell-mediated suppression the maintenance of the that the most plausible T epithelium the growth of can both suppressrequires re- regulatory chimeras e!ector T cells, and that the that
  • 64. Modelling T cell population dynamics net growth = influx + interaction-dependent — death growth dTi = i + ↵i (T, A, m, k) · Ti · Ti dt
  • 65. Modelling T cell population dynamics net growth = influx + interaction-dependent — death growth dTi = i + ↵i (T, A, m, k) · Ti · Ti dt
  • 66. Modelling T cell population dynamics net growth = influx + interaction-dependent — death growth dTi = i + ↵i (T, A, m, k) · Ti · Ti dt
  • 67. Modelling T cell population dynamics net growth = influx + interaction-dependent — death growth dTi = i + ↵i (T, A, m, k) · Ti · Ti dt
  • 68. Modelling T cell population dynamics net growth = influx + interaction-dependent — death growth dTi = i + ↵i (T, A, m, k) · Ti · Ti dt How to choose appropriate functional forms for the interaction terms ?
  • 69. Modelling T cell population dynamics A taxonomy of putative mechanisms of cell-to-cell interaction R T IL-X R R [Leon et al. J Theor Biol 2000; Carneiro et al. Immunol Rev 2007]
  • 70. Modelling T cell population dynamics A taxonomy of putative mechanisms of cell-to-cell interaction R T IL-X R R [Leon et al. J Theor Biol 2000; Carneiro et al. Immunol Rev 2007]
  • 71. Modelling T cell population dynamics A taxonomy of putative mechanisms of cell-to-cell interaction R T IL-X R R CRM [Leon et al. J Theor Biol 2000; Carneiro et al. Immunol Rev 2007]
  • 72. Modelling T cell population dynamics: the crossregulation model Interactive simulation
  • 73. Quantitative assay for cell proliferation + CFSE Nº Cells Log FL1-H Log Intensity of CFSE staining [Leon et al. J.Theor.Biol. 2004]
  • 74. Putting the CRM to the test + anti-CD3 antibody APCs Cell Cycle R R R R E R R R R R R R R B6 Thy1.2 Analysis CD25+CD4+Thy1.2+ 3 day culture E E E E E E E E E E E E E E E E E E B6 congenic Thy1.1 CD25-CD4+Thy1.1+ [Carneiro et al. Immuno. Rev. 2007]
  • 75. Putting the CRM to the test + anti-CD3 antibody APCs Proportions Effector Cells Regulatory Cells Thy1.1:Thy1.2 Thy1.1 Thy1.2 Cell Cycle R R R E R R R R R Day 0 Day 3 R R R R Analysis CD25+CD4+Thy1.2+ ? ? 3 day culture E E E E E E E E E + + anti-CD3100:0 N.D. E E E E E E antibody E E E ND y1.1 CD25-CD4+Thy1.1+ 80:20 47:53 Cell Cycle R R E R R R R Analysis .2+ + anti-CD3 antibody 50:50 24:76 APCs 3 day culture E E E E E E E + E + anti-CD30:100 N.D. Cycle antibody E Cell R R R R E R R R R R R R R ND Analysis 1.1+ CD25+CD4+Thy1.2+ 3 day culture Log FL1-H / CFSE intensity E E E E E E E E E E E E E E Cell Cycle R E R E E E E R R R R CD25-CD4+Thy1.1+ Analysis et al. Immuno. Rev. 2007] [Carneiro .2+
  • 76. Putting the CRM to the test + anti-CD3 antibody APCs Proportions Effector Cells Regulatory Cells Thy1.1:Thy1.2 Thy1.1 Thy1.2 Cell Cycle R R R E R R R R R Day 0 Day 3 R R R R Analysis CD25+CD4+Thy1.2+ ? 3 day culture E E E E E E E E E + + anti-CD3100:0 N.D. E E E E E E antibody E E E ND y1.1 CD25-CD4+Thy1.1+ 80:20 47:53 Cell Cycle R R E R R R R Analysis .2+ + anti-CD3 antibody 50:50 24:76 APCs 3 day culture E E E E E E E + E + anti-CD30:100 N.D. Cycle antibody E Cell R R R R E R R R R R R R R ND Analysis 1.1+ CD25+CD4+Thy1.2+ 3 day culture Log FL1-H / CFSE intensity E E E E E E E E E E E E E E Cell Cycle R E R E E E E R R R R CD25-CD4+Thy1.1+ Analysis et al. Immuno. Rev. 2007] [Carneiro .2+
  • 77. Putting the CRM to the test + anti-CD3 antibody APCs Proportions Effector Cells Regulatory Cells Thy1.1:Thy1.2 Thy1.1 Thy1.2 Cell Cycle R R R E R R R R R Day 0 Day 3 R R R R Analysis CD25+CD4+Thy1.2+ 3 day culture E E E E E E E E E + + anti-CD3100:0 N.D. E E E E E E antibody E E E ND y1.1 CD25-CD4+Thy1.1+ 80:20 47:53 Cell Cycle R R E R R R R Analysis .2+ + anti-CD3 antibody 50:50 24:76 APCs 3 day culture E E E E E E E + E + anti-CD30:100 N.D. Cycle antibody E Cell R R R R E R R R R R R R R ND Analysis 1.1+ CD25+CD4+Thy1.2+ 3 day culture Log FL1-H / CFSE intensity E E E E E E E E E E E E E E Cell Cycle R E R E E E E R R R R CD25-CD4+Thy1.1+ Analysis et al. Immuno. Rev. 2007] [Carneiro .2+
  • 78. Putting the CRM to the test + anti-CD3 antibody APCs Proportions Effector Cells Regulatory Cells Thy1.1:Thy1.2 Thy1.1 Thy1.2 Cell Cycle R R R E R R R R R Day 0 Day 3 R R R R Analysis CD25+CD4+Thy1.2+ 3 day culture E E E E E E E E E + + anti-CD3100:0 N.D. E E E E E E antibody E E E ND y1.1 CD25-CD4+Thy1.1+ 80:20 47:53 Cell Cycle R R E R R R R Analysis .2+ + anti-CD3 antibody 50:50 24:76 ? ? APCs 3 day culture E E E E E E E + E + anti-CD30:100 N.D. antibody E Cell Cycle R R R R E R R R R R R R R ND Analysis 1.1+ CD25+CD4+Thy1.2+ 3 day culture Log FL1-H / CFSE intensity E E E E E E E E E E E E E E Cell Cycle R E R E E E E R R R R CD25-CD4+Thy1.1+ Analysis et al. Immuno. Rev. 2007] [Carneiro .2+
  • 79. Putting the CRM to the test + anti-CD3 antibody APCs Proportions Effector Cells Regulatory Cells Thy1.1:Thy1.2 Thy1.1 Thy1.2 Cell Cycle R R R E R R R R R Day 0 Day 3 R R R R Analysis CD25+CD4+Thy1.2+ 3 day culture E E E E E E E E E + + anti-CD3100:0 N.D. E E E E E E antibody E E E ND y1.1 CD25-CD4+Thy1.1+ 80:20 47:53 Cell Cycle R R E R R R R Analysis .2+ + anti-CD3 antibody 50:50 24:76 APCs 3 day culture E E E E E E E + E + anti-CD30:100 N.D. Cycle antibody E Cell R R R R E R R R R R R R R ND Analysis 1.1+ CD25+CD4+Thy1.2+ 3 day culture Log FL1-H / CFSE intensity E E E E E E E E E E E E E E Cell Cycle R E R E E E E R R R R CD25-CD4+Thy1.1+ Analysis et al. Immuno. Rev. 2007] [Carneiro .2+
  • 80. Putting the CRM to the test + anti-CD3 antibody APCs Proportions Effector Cells Regulatory Cells Thy1.1:Thy1.2 Thy1.1 Thy1.2 Cell Cycle R R R E R R R R R Day 0 Day 3 R R R R Analysis CD25+CD4+Thy1.2+ + anti-CD3 antibody 3 day culture APCsE EE EE E E E E + + anti-CD3100:0 N.D. antibody E E E E E E E E E ND y1.1 CD25-CD4+Thy1.1+ Cell Cycle R R R E R R R R R + anti-CD3 antibody ? ? R R R R Analysis CD25+CD4+Thy1.2+ APCs 80:20 47:53 Cell Cycle R R E 3 day culture R R + + anti-CD3 antibody R ? ? + E E E E R E E E E Analysis Cell Cycle E E E E E E R E E E RE R E R R R R R R R R R .2+ CD25-CD4+Thy1.1+ Thy1.2 Analysis CD25+CD4+Thy1.2+ 50:50 24:76 3 day culture 3 day culture Cell Cycle R R EE E E E E E E E E E R E ER E E E E E E R E E E E E E E R E E Analysis 0:100 N.D. ongenic Thy1.1 ND CD25-CD4+Thy1.1+ + 1.1+ 3 day culture Log FL1-H / CFSE intensity E E E E E E E E E [Carneiro et al. Immuno. Rev. 2007] +
  • 81. Putting the CRM to the test Proportions Effector Cells Regulatory Cells Thy1.1:Thy1.2 Thy1.1 Thy1.2 Day 0 Day 3 100:0 N.D. ND 80:20 47:53 50:50 24:76 0:100 N.D. ND Log FL1-H / CFSE intensity [Carneiro et al. Immuno. Rev. 2007]
  • 82. Modelling T cell population dynamics: the crossregulation model R T IL-X R R CRM [Leon et al. J Theor Biol 2000; Carneiro et al. Immunol Rev 2007] [Carneiro et al. Immuno. Rev. 2007]
  • 83. Modelling T cell population dynamics: the crossregulation model Regulatory T cell populations grow as a function of the effector T cells they suppress R R Leon et al. JTB (2000) R E E E 01 . Imm unol 20 iol 2 000 , J al. J Theor B eon et Thesis L alh o PhD sis , Caram hD The
  • 84. the control of the insulin promoter. We had previously observed Modelling T cell population dynamics: the crossregulation model Authorship note: Yenkel Grinberg-Bleyer and David Saadoun contributed equally to this work. Eliane Piaggio and Benoît L. Salomon are co–senior authors. that HA-specific Tregs (HA-Tregs) preferentially proliferated and expanded at days 5–7 after transfer in draining pancreatic LNs Conflict of interest: The authors have declared that no conflict of interest exists. (PLNs) of ins-HA homozygous mice (29). When we repeated the Citation for this article: J Clin Invest. 2010;120(12):4558–4568. doi:10.1172/JCI42945. experiment in ins-HA hemizygous recipients, which express lower The Journal of Clinical Investigation http://www.jci.org Volume 120 Number 12 December 2010 Related Commentary, page 4190 Regulatory T cell populations grow as a function of the effector T cells they suppress Yenkel Grinberg-Bleyer,1,2,3 David Saadoun,1,2,3 Audrey Baeyens,1,2,3 Fabienne Billiard,1,2,3 Jérémie D. Goldstein,1,2,3 Sylvie Grégoire,1,2,3 Gaëlle H. Martin,1,2,3 Rima Elhage,1,2,3 Nicolas Derian,1,2,3 Wassila Carpentier,1,4 Gilles Marodon,1,2,3 David Klatzmann,1,2,3 R R Eliane Piaggio,1,2,3 and Benoît L. Salomon1,2,3 1Université Pierre et Marie Curie — Univ Paris 06, 2CNRS UMR 7211, 3INSERM U959, Paris, France. 4Plate-forme Post-Génomique P3S, Hôpital Pitié-Salpêtrière, Paris, France. Leon et al. JTB (2000) CD4+CD25+Foxp3+ Tregs play a major role in prevention of autoimmune diseases. The suppressive effect of Tregs on effector T cells (Teffs), the cells that can mediate autoimmunity, has been extensively studied. How- R E ever, the in vivo impact of Teff activation on Tregs during autoimmunity has not been explored. In this study, we have shown that CD4 + Teff activation strongly boosts the expansion and suppressive activity of Tregs. This helper function of CD4+ T cells, which we believe to be novel, was observed in the pancreas and draining lymph nodes in mouse recipients of islet-specific Teffs and Tregs. Its physiological impact was assessed in autoimmune diabetes. When islet-specific Teffs were transferred alone, they induced diabetes. Paradoxically, when the same Teffs were cotransferred with islet-specific Tregs, they induced disease protection by boost- E ing Treg expansion and suppressive function. RNA microarray analyses suggested that TNF family members were involved in the Teff-mediated Treg boost. In vivo experiments showed that this Treg boost was partially E dependent on TNF but not on IL-2. This feedback regulatory loop between Teffs and Tregs may be critical to preventing or limiting the development of autoimmune diseases. bers of mature DCs in inflamed tissues may favor the activation of 01 unol 20 The peripheral T cell repertoire of any individual contains autoreac- autoreactive Tregs (21–23), which would then turn on their sup- tive T cells specific for a variety of self antigens (1). Their activation pressive activity and exert bystander suppression (24, 25). Thus, during an autoimmune process, there is a local enrichment 00 , J . Imm could induce an autoimmune process, eventually leading to an auto- Bi ofl 2 0 of both autoreactive Teffs and Tregs. Since heefficacy o Treg- immune disease. Severe and prolonged inflammation in a tissue may J T the orbetween acti- mediated suppression depends onal. equilibrium eon et the factor that could tip this Thesis o PhD lead to the activation of pathological autoreactive T cells by several L Tregs (26), any mechanisms (2, 3). At the site of inflammation or in draining LNs, vated Teffs and activated balance to one side or the other could then determine thes, Ca ramalh tissue damage results in an enhanced presentation of autoantigens hD Th esi outcome
  • 85. How does their repertoire What makes a T cell compare to that of other T be a regulatory T cell ? cells ? How many and how CD25+CD4+T cells diverse are they ? R R How do they interact R R R R R R with other cells ? (Regulatory T cells, TR, R) How do they allow efficient immune responses ? How do they prevent autoimmune diseases ?
  • 86. How does their repertoire What makes a T cell compare to that of other T be a regulatory T cell ? cells ? How many and how CD25+CD4+T cells diverse are they ? R R How do they interact R R R R R R with other cells ? (Regulatory T cells, TR, R) How do they allow efficient immune responses ? How do they prevent autoimmune diseases ?

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