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tel-00827710, version 1 - 29 May 2013 1) Current techniques (a) Limiting dilutions analysis For many years, limiting dilution analysis was the standard method used to determine the frequency of antigen-specific T cells in a particular model. The main limitations of this approach were the requirement for exogenous stimulation and expansion, which introduced potential bias and significant inter-assay variability. (b) Tetramer staining The generation of MHC-I tetrameric complexes, originally described by Altman and Davis, represents what has been proven to be a major technical advance for the study of the antigen- specific T cell responses (Altman et al., 1996). MHC tetramers are reagents that carry 4 MHC class I-peptide complexes and, thus, have the ability to interact with multiple TCRs at the surface of a single CD8 + T cell. Fluorescent labeling of tetramers has allowed the identification of antigen-specific T lymphocytes based on the avidity of their TCR. By combining this method with other antibody-based staining protocols (surface markers or intracellular cytokines), it is now possible to phenotypically and functionally characterize the antigen-specific T cell response. Nevertheless, there remains one important technical limitation: the limit of detection is relatively high – for tetramer staining, only one cell in 10 4 can be observed, which does not permit the direct detection of rare antigen-specific populations such as circulating naïve antigen-specific T cells (Figure 13). (c) ELISPOT and intracellular staining Both ELISPOT and intracellular staining techniques allow the functional characterization of the T cell populations of interest. These assays are based on the ability of antigen-specific T cells to secrete cytokines upon short, in vitro restimulation with cognate peptide. Such approaches are capable of distinguishing lymphocytes possessing the capacity to secrete a given cytokine at the time of the assay, indicating the extend of prior T cell priming; however this response corresponds only to a fraction of the antigen-specific population. 72

tel-00827710, version 1 - 29 May 2013 Figure 13. Limit of detection of established techniques for studying the T cell response in vivo. (d) Adoptive transfer of TCR-transgenic CD8 T cells Some antigens induce a low level T cell response, which is not consistently detectable by the techniques just described. Another approach was developed to study the T cells that are specific for a given epitope, even in the case that the response is not robust. To address this and develop a technique that would allow for these instances, mice that were transgenic for a given TCR were generated. In these mice, the vast majority of the CD8 + T cells are specific for the same epitope. These mice were then crossed to Rag-deficient mice, ensuring that all T cells were specific for this epitope. In this way, various numbers of antigen-specific T cells can be transferred into naïve mice, allowing for easier detection by artificially increasing the precursor frequency. The transfer of TCR-transgenic T cells has been extensively used to model the endogenous response in combination with tetramer and intracellular staining. Another benefit of this approach is the possibility to label transgenic T cells prior to their transfer in order to follow them in vivo. Moreover, it is also possible to transfer TCR- transgenic T cells that are deleted for specific genes to further dissect the mechanisms of the T cell response. Some years ago, several groups demonstrated that adoptive transfer experiments using large numbers of specific T cells can actually modify the outcome of the immune response under examination (Marzo et al., 2005). It was then realized and acknowledged that the transfer of non-physiologic numbers of TCR-transgenic T cells does not accurately mimic the endogenous response, which poses a severe limitation on the interpretation of studies using this strategy. Specifically, Badovinac and colleagues performed experiments transferring graded numbers of TCR-transgenic T cells and showed that high initial precursor frequencies actually limited the expansion of effector cells (Badovinac et al., 2007). They concluded that Page 73 of 256

tel-00827710, version 1 - 29 May 2013<br />

Figure 13. Limit of d<strong>et</strong>ection of established techniques for studying the T cell response in vivo.<br />

(d) Adoptive transfer of TCR-transgenic CD8 T cells<br />

Some antigens induce a low level T cell response, which is not consistently d<strong>et</strong>ectable by the<br />

techniques just <strong>de</strong>scribed. Another approach was <strong>de</strong>veloped to study the T cells that are<br />

specific for a given epitope, even in the case that the response is not robust. To address this<br />

and <strong>de</strong>velop a technique that would allow for these instances, mice that were transgenic for a<br />

given TCR were generated. In these mice, the vast majority of the CD8 + T cells are specific<br />

for the same epitope. These mice were then crossed to Rag-<strong>de</strong>ficient mice, ensuring that all T<br />

cells were specific for this epitope. In this way, various numbers of antigen-specific T cells<br />

can be transferred into naïve mice, allowing for easier d<strong>et</strong>ection by artificially increasing the<br />

precursor frequency. The transfer of TCR-transgenic T cells has been extensively used to<br />

mo<strong>de</strong>l the endogenous response in combination with t<strong>et</strong>ramer and intracellular staining.<br />

Another benefit of this approach is the possibility to label transgenic T cells prior to their<br />

transfer in or<strong>de</strong>r to follow them in vivo. Moreover, it is also possible to transfer TCR-<br />

transgenic T cells that are <strong>de</strong>l<strong>et</strong>ed for specific genes to further dissect the mechanisms of the T<br />

cell response.<br />

Some years ago, several groups <strong>de</strong>monstrated that adoptive transfer experiments using large<br />

numbers of specific T cells can actually modify the outcome of the immune response un<strong>de</strong>r<br />

examination (Marzo <strong>et</strong> al., 2005). It was then realized and acknowledged that the transfer of<br />

non-physiologic numbers of TCR-transgenic T cells does not accurately mimic the<br />

endogenous response, which poses a severe limitation on the interpr<strong>et</strong>ation of studies using<br />

this strategy. Specifically, Badovinac and colleagues performed experiments transferring<br />

gra<strong>de</strong>d numbers of TCR-transgenic T cells and showed that high initial precursor frequencies<br />

actually limited the expansion of effector cells (Badovinac <strong>et</strong> al., 2007). They conclu<strong>de</strong>d that<br />

Page 73 of 256

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