Table 2.
Sequence and Reactivity of Dominant T cell Clonotypes in 3713 TIL
| Infused TIL |
Pre-PBMC |
PD-1+/PD-1- CD8+ T cells (fresh tumor) |
Post 1 month |
Post 1 year |
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Rank‡ | Frequency(%) | TR-BV | CDR3b aa sequence | Autologous tumor reactivity |
Clone/TRA,TRB pair |
Antigen reactivity |
Rank | Frequency(%) | Rank | Frequency(%) | Rank | Frequency(%) | Rank | Frequency(%) |
| 1 | 4.5 | 15-1 | ATGTGGNDYEQYF | Yes | TCR T4* | CENPL | 52466 | 0.0005 | 19/481 | 1.0/0.05 | 7 | 2.8 | 8 | 1.2 |
| 2 | 3.9 | 5-6 | ASSLDRKAFF | Yes | TCR MP-1 | SRPX | ND† | <0.0001 | 86/ND | 0.24/<0.001 | 1 | 4.5 | 4 | 1.9 |
| 3 | 3.5 | 28-1 | ASSGKDREPHYEQYV | NT | Not identified | - | ND | <0.0001 | 220/ND | 0.05/<0.001 | 19 | 1.1 | 23 | 0.7 |
| 4 | 2.8 | 11-1 | ASSLIQVGYEQYF | Yes | Clone XY-51 | SRPX | 49395 | 0.0005 | 22/591 | 0.91/0.04 | 2 | 4.5 | ND | <0.0003 |
| 5 | 2.6 | 5-6 | ASSLGPVYEQYF | Yes | Clone XY-6 | SRPX | ND | <0.0001 | 10/198 | 1.6/0.01 | 3 | 4.3 | 6 | 1.6 |
| 6 | 2.6 | 10-2 | ASGGAIDTDTQYF | Yes | Clone XY-3 | SRPX | 27655 | 0.0012 | 3/963 | 3.2/0.02 | 4 | 4.1 | 7 | 1.4 |
| 7 | 2.5 | 10-2 | ASSEGHFSGNTIYF | Yes | Clone XY-38 | SRPX | ND | <0.0001 | 38/450 | 0.55/0.05 | 5 | 4.1 | 14 | 1.00 |
| 8 | 2.1 | 4-3 | ASSQDDSGAKNIQYF | No | TCR 8 | - | 45870 | 0.0006 | 507/1419 | 0.02/0.008 | 6 | 3.4 | 17 | 0.9 |
| 9 | 2.0 | 4-1 | ASSQGPLQPQHF | No | TCR 9 | - | ND | <0.0001 | 39/60 | 0.54/0.22 | 10 | 1.8 | 18 | 0.8 |
| 10 | 1.8 | 27-1 | ASSLNSGHTQYF | Yes | TCR T8-1 | HELZ2 | 15120 | 0.0017 | 2/112 | 6.5/0.15 | 9 | 2.2 | 12 | 1.0 |
| 11 | 1.7 | 28-1 | ASSPGGPGLTYEQYV | NT | Not identified | - | ND | <0.0001 | 80/1291 | 0.26/0.012 | 15 | 1.4 | 140 | 0.09 |
| 12 | 1.7 | 28-1 | ASSLSHQSSSYEQYV | NT | Not identified | - | 21157 | 0.0014 | 30/305 | 0.70/0.071 | 21 | 0.9 | 59 | 0.3 |
| 13 | 1.6 | 29-1 | SVEDRRGPFYGYTF | Yes | Clone XY52 | SEC22C | ND | <0.0001 | 41/910 | 0.53/0.024 | 17 | 1.3 | 28 | 0.5 |
| 14 | 1.6 | 5-5 | ASSLAQPNQPQHF | NT | Not identified | - | 44967 | 0.0007 | 35/40 | 0.56/0.33 | 8 | 2.7 | 9 | 1.2 |
| 15 | 1.6 | 14-1 | ASSQYAVRVGDTEAFF | NT | Not identified | - | ND | <0.0001 | 8/507 | 2.0/0.046 | 59 | 0.3 | 44 | 0.3 |
| 16 | 1.5 | 13-1 | ASSSGLAGEQFF | NT | Not identified | - | ND | <0.0001 | 211/ND | 0.056/<0.001 | 14 | 1.7 | 30 | 0.5 |
| 17 | 1.5 | 5-4 | ASSLLTEAFF | NT | Not identified | - | 5839 | 0.0027 | 1/268 | 9.7/0.079 | 22 | 0.9 | 62 | 0.3 |
| 18 | 1.4 | 7-9 | ASSHQAGALYNEQFF | Yes | TCR H1-2 | AFMID | ND | <0.0001 | 94/262 | 0.20/0.079 | 41 | 0.5 | 56 | 0.3 |
| 19 | 1.3 | 12 | ASGPRSEQFF | NT | Not identified | - | ND | <0.0001 | 529/ND | 0.012/<0.001 | 50 | 0.4 | 48 | 0.3 |
| 20 | 1.3 | 25-1 | ASLERGVSTDTQYF | NT | Not identified | - | ND | <0.0001 | ND/ND | <0.001/<0.001 | 27 | 0.7 | 29 | 0.5 |
The rearranged TR-BV region sequences of the indicated T cell populations were analyzed by deep sequencing, nucleotide sequences present at two or more copies were ranked from the highest to the lowest frequency, and amino acid sequences of the CDR3 regions determined, as described in the Materials and Methods.
^ NT – not tested
ND – not detected within the limits of the assay (0.0001% for Pre-PBMC, 0.001% for PD-1+ and PD-1− CD8+ T cells (fresh tumor), 0.0004% for Post 1 month, and 0.0003% for Post 1 year samples)
Analysis of reactivity of T cells clones and the TCRs is presented in Figure 4. Not identified indicates that T cells expressing this TR-BV sequence could not be evaluated due to the fact that a clone was not isolated and the appropriate TRAV sequence expressed by this clonotype could not be identified.