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tel-00827710, version 1 - 29 May 2013 tag. This approach allows you to work with the same multimer labeled in different colors, thus improving specificity of the assay (see Note 14) and permits multiplexing different specificities in the same tube (see Notes 16 and 22). Note that regardless of the source, high-quality monomers are important, with monomer purity impacting multimerization. Moreover, the choice of streptavidin reagent is critical, and it is recommended to purchase high-quality streptavidin conjugated to bright fluorochromes. 7. When using MHC multimers, it is recommended to choose an appropriate method to validate the specificity of tetramer-stained cells. Positive controls will be multimers targeting abundant populations of CD8 T cells. For human, EBV BMLF1 280-288 or Influenza A-M1 58-66 can be used as a positive control. For mice, the strategy will be to stain splenocytes from a TCR-transgenic mouse with the corresponding multimer (CD8 OT-I T cells that are specific for H2-K b -SIINFEKL complexes stained with H2-K b -SIINFEKL multimer for instance). It will help you to establish the assay and ensure that enrichment is sufficient for detection of rare cells. Concerning naïve cells in humans, MART1 26-35(Leu27) is a good choice, as it will also be a useful reference for establishing gating parameters for naïve vs. memory populations [30]. Negative control tetramers can be employed to help establish the assay, although there is the potential to observe CD8 + T cells with the capacity to bind any MHCI, including self-antigens. An alternative option is the evaluation of background staining based on the non-specific labeling of CD4 + T cells. That said, recent work has suggested that even this interaction might be of physiologic relevance [28]. More definitive controls are also important, such as assessment of TCR CDR3-variable region usage skewing, peptide-induced TCR downregulation and, after cell sorting, TCR sequences analysis or TCR genes transfer into immortalized cell lines to show that the specificity can be reconstituted [8]. 8. Biotinylated monomers may be stored for months at -80°C. Stability testing is recommended. In contrast, multimers are less stable, should be stored at 4 o C and ideally should be used within 4 weeks. Best is even to multimerize the amount you will need for each experiment one day before. 9. The use of a « Dump channel » is essential as it excludes cells that bind non-selectively to the MHC multimer reagents. Its composition has to be reviewed in the context of the experimental aims. For 220

tel-00827710, version 1 - 29 May 2013 example, CD56 is useful for exclusion of NK cells in human samples when evaluating naive cell repertoires, but should be used with caution when studying human memory or activated T cell populations as some cells express CD56 and would thus be lost in the gating strategy. Similarly, it can be useful to add anti-CD33 and anti-CD34 antibodies when studying T cell populations present in bone-marrow populations. As indicated above, we deliberately do not included CD4 as we use the staining of this population as an assessment of background, but this can be added when multiple free channels are needed for complex multicolor experiments. In the same way, the Dump channel must to be chosen carefully for mouse experiments: some markers, such as CD11c, may in fact upregulate on activated T cells. 10. Addition of a viability marker is necessary in order to avoid non-specific background staining on dead cells. While this may be omitted in some instances in which fresh blood is utilized, it should be noted that the enrichment columns have an affinity for dead cells. Ideally, select a viability dye in the same channel as the Dump channel – thus keeping the maximum number of channels free for phenotypic characterization. 11. At least four fluorescent channels are necessary for careful assessment of enriched T cells: (i) a Dump channel; (ii) CD3 staining for gating on T cells; (iii) CD8 staining for gating of CD8 + T cells; and the multimer-conjugated label for the specificity of interest. This can be extended when differently labeled multimers are included in the same experiment (for reducing non-specific binding in the assay and/or for multiplexing enrichment). Anti-CD3 can eventually be omitted if you really need a maximum of free channels for phenotypic characterization. Additional channels that are available will depend upon the technical specifications of the cytometer and antibodies will be chosen depending on the experimental questions being evaluated. Note that it is crucial to stain with multimers prior to washing and staining with other Abs, especially for CD8 and CD4, as some clones have been shown to influence multimer staining [31]. 12. As cells will be fixed to perform intracellular staining, DAPI cannot be used as a viability marker. We therefore recommend the use of a fixable live/dead cell marker such as Aqua. Note that Aqua labeling has to be done in azide-free buffer. Page 221 of 256

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

example, CD56 is useful for exclusion of NK cells in human samples when evaluating naive cell<br />

repertoires, but should be used with caution when studying human memory or activated T cell<br />

populations as some cells express CD56 and would thus be lost in the gating strategy. Similarly, it<br />

can be useful to add anti-CD33 and anti-CD34 antibodies when studying T cell populations present<br />

in bone-marrow populations. As indicated above, we <strong>de</strong>liberately do not inclu<strong>de</strong>d CD4 as we use<br />

the staining of this population as an assessment of background, but this can be ad<strong>de</strong>d when multiple<br />

free channels are nee<strong>de</strong>d for complex multicolor experiments. In the same way, the Dump channel<br />

must to be chosen carefully for mouse experiments: some markers, such as CD11c, may in fact<br />

upregulate on activated T cells.<br />

10. Addition of a viability marker is necessary in or<strong>de</strong>r to avoid non-specific background staining on<br />

<strong>de</strong>ad cells. While this may be omitted in some instances in which fresh blood is utilized, it should<br />

be noted that the enrichment columns have an affinity for <strong>de</strong>ad cells. I<strong>de</strong>ally, select a viability dye<br />

in the same channel as the Dump channel – thus keeping the maximum number of channels free for<br />

phenotypic characterization.<br />

11. At least four fluorescent channels are necessary for careful assessment of enriched T cells: (i) a<br />

Dump channel; (ii) CD3 staining for gating on T cells; (iii) CD8 staining for gating of CD8 + T<br />

cells; and the multimer-conjugated label for the specificity of interest. This can be exten<strong>de</strong>d when<br />

differently labeled multimers are inclu<strong>de</strong>d in the same experiment (for reducing non-specific<br />

binding in the assay and/or for multiplexing enrichment). Anti-CD3 can eventually be omitted if<br />

you really need a maximum of free channels for phenotypic characterization. Additional channels<br />

that are available will <strong>de</strong>pend upon the technical specifications of the cytom<strong>et</strong>er and antibodies will<br />

be chosen <strong>de</strong>pending on the experimental questions being evaluated. Note that it is crucial to stain<br />

with multimers prior to washing and staining with other Abs, especially for CD8 and CD4, as some<br />

clones have been shown to influence multimer staining [31].<br />

12. As cells will be fixed to perform intracellular staining, DAPI cannot be used as a viability marker.<br />

We therefore recommend the use of a fixable live/<strong>de</strong>ad cell marker such as Aqua. Note that Aqua<br />

labeling has to be done in azi<strong>de</strong>-free buffer.<br />

Page 221 of 256

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