8%) (Fig. 3A, Supporting Information INCB024360 Fig. 2A) and BAL (44.5%) (data not shown) in 4/5 A7 transgenics. Earlier experiments established that a “public” TCRβ repertoire was consistently detected in wt B6 DbNPVβ8.3+CD8+ populations 14, 15. Loss of this Vβ8.3

bias in the DbNPCD8+ T cells from A7 mice suggests that either the public DbNPVβ8.3+ clonotypes require pairing with one or more DbNP366-specific Vαs for optimal recognition, or that there are structural constrains that limit pairing with the KbOVA257-specific Vα2 chain. However, this did not reflect any overall incapacity of naïve Vβ8.3+CD8+ T cells to pair with at least some Vα2+ TCR, as analysis of naïve CD8+ T cells in B6 mice showed that an average of 8.26±0.35% of Vβ8.3 CD8+ T cells are Vα2+ (Supporting Information Fig. 3). Similar to the restricted and public nature of wt DbNPVβ8.3+ T cells, CH5424802 analysis of the subdominant Vβ4+DbNPCD8+ sets in B6 mice showed a profile of restricted TCRβ repertoire diversity, with several clonotypes being found repeatedly in different individuals 24. Is this also the case for DbNPCD8+ T cells generated from the A7 transgenics? Analysis of 237 CDR3β sequences from seven mice showed that an average of 2.14±1.46 DbNP366-specific Vβ4 clonotypes were detected per mouse (Table 1). Sequencing established a profile of

predominant Jβ1S6 usage, a long CDR3β loop of 12 aa and identified two clonotypes (Table 1A) that were detected previously in the wt B6 SQDRRNSYNSPL and SQDRRSSYNSPL 24. The public DbNPVβ4+CD8+ clonotype SQDRRNSYNSPL found in all B6 mice (Table 1B) was detected in 3/7 A7 transgenics. The Vβ4+DbNPCD8+ cells elicited by influenza virus infection of A7 mice thus display broadly the same TCRβ characteristics as those from the B6 controls 24. Taken together, the Thalidomide DbNPCD8+ T cells generated in the A7 transgenics utilize TCRβ clonotypes that are also found within the subdominant Vβ4+ set from normal mice. Following influenza infection of B6 mice, the DbPACD8+ set displays a strong Vβ7 bias 13. This profile of Vβ7 preference was maintained for the DbPACD8+ T cells in A7 transgenics (Fig. 3B). Similar

to the 53.7% of wt DbPACD8+ T cells that utilize Vβ7 25, the A7 DbPACD8+ set showed preferential usage of Vβ7 (Fig. 3B, Supporting Information Fig. 2B) for those recovered from the spleen (51.2%) and BAL (71.9%, data not shown). A strong Vβ9 bias was also observed in two of the A7 mice (Supporting Information Fig. 2B), suggesting alternate pairing with the OVA257-specific Vα2 for a proportion of the DbPACD8+ T cells. Subsequent analysis of CDR3β sequences for 264 DbPAVβ7+CD8+ T cells from six A7 transgenics established that there is a pattern of limited TCRβ diversity, with an average of 5.3±3.4 clonotypes detected per mouse (Table 2) in contrast to the much broader TCRβ repertoire (20.6±3.8) characteristic of the B6 controls 13, 17. Many of the TCRβ clonotypes identified in the A7 (9/37) had been detected in the B6 mice.