immunotherapies with TCR sequencing EACR25 symposium Noel F.C.C. de - PowerPoint PPT Presentation

Fingerprinting immune responses and improving immunotherapies with TCR sequencing EACR25 symposium Noel F.C.C. de Miranda Immunogenetics Lab HLA II - neoantigen – TCR Deng L et al . Nat Immunol 2017 1 Insert > Header & footer 4-Jul-18

Antigen presentation and T cell recognition 2 4-Jul-18

Antigen presentation and T cell recognition HLA-A*02:01 HLA-A*11:01 3 4-Jul-18

Antigen presentation and T cell recognition Reinherz, E.L, et al . Science. 1999 Hennecke & Wiley Cell 2001 4 4-Jul-18

Mutation burden and response to checkpoint blockade DNA repair defects UV damage Smoking damage Higher probability of Neo-antigen presentation And T cell recogition Yarchoan M, et al. NEJM 2017 5 4-Jul-18

TCR diversity – V(D)J recombination Turner et al . NatRev Immunol 2006 6 4-Jul-18

CDR regions – T cell molecular barcodes >300 bp (RNA) 400 bp read-length Hennecke & Wiley Cell 2001 7 4-Jul-18

Sjoerd van der Burg Els Verdegaal 8 4-Jul-18

Adoptive T-cell transfer in melanoma 9 4-Jul-18

Stage IV melanoma patient AB MLTC T cell reactivity Exome sequencing 10 4-Jul-18

Stage IV melanoma patient AB MLTC 04.01 TIL 04.01 TIL 08.01 TIL 12.07 TIL 12.09 11 4-Jul-18

Stage IV melanoma patient AB 12.09 tumor tissue 04.01 tumor tissue 08.01 tumor tissue SEPT2 R300C MLTC 04.01 TIL 04.01 TIL 08.01 TIL 12.07 TIL 12.09 12 4-Jul-18

Stage IV melanoma patient AB Gene expression MLTC 04.01 TIL 12.07 13 4-Jul-18

Stage IV melanoma patient AB Was tumor immunoediting and response to therapy driven by the ACT treatment? Ion AmpliSeq Immune Repertoire Assay 14 4-Jul-18

Stage IV melanoma patient AB MLTC 04.01 TIL 04.01 TIL 08.01 TIL 12.07 TIL 12.09 15 4-Jul-18

TIL 04.01 Clones: 11118, Shannon diversity: 10,7217, Clone evenness: 0,7977 16 4-Jul-18

MLTC 04.01 Clones: 2716; Shannon diversity: 8,4940; Clone evenness: 0,7446 17 4-Jul-18

Matchmaking – CDR 3 sequences TIL 04.01 Variable Joining CDR3 AA CDR3 NT Diversity Frequency TRBV9 TRBJ1-1 ASHGQGVGEAF GCCAGCCACGGACAGGGGGTTGGTGAAGCTTTC TRBD1 0.050681 TRBV29-1 TRBJ2-1 SVAGGRAGEQF AGCGTTGCTGGCGGGAGGGCCGGTGAGCAGTTC TRBD2 0.02175 TRBV5-6 TRBJ2-3 ASSTQSGVTQY GCCAGCAGCACCCAGAGCGGGGTTACGCAGTAT TRBD2 0.013705 TRBV6-6 TRBJ2-3 ASTQARGTDTQY GCCAGCACTCAGGCCCGTGGCACAGATACGCAGTAT 0.011479 TRBV12-4 TRBJ2-1 ASSLAGSIDEQF GCCAGCAGTTTAGCGGGTTCCATTGATGAGCAGTTC TRBD2 0.011431 TRBV3-1 TRBJ2-1 ASSQGLDSYNEQF GCCAGCAGCCAAGGACTTGACTCCTACAATGAGCAGTTC TRBD2 0.010884 TRBV7-6 TRBJ2-2 ASSPPGPGTGELF GCCAGCAGCCCGCCGGGGCCTGGCACCGGGGAGCTGTTT TRBD1 0.010861 TRBV12-3 TRBJ2-5 ASSLGRAGWETQY GCCAGCAGTTTAGGTCGAGCGGGGTGGGAGACCCAGTAC TRBD2 0.008158 TRBV7-2 TRBJ1-2 ASSLADLANYGYT GCCAGCAGCTTAGCGGATCTAGCTAACTATGGCTACACC TRBD2 0.007764 386 clones in common with MLTC 04.01 (3.5% of clones, 23% of reads) TRBV3-1 TRBJ2-4 ASSPRTTPTWNIQY GCCAGCAGCCCAAGGACTACGCCGACCTGGAACATTCAGTAC TRBD2 0.006712 TRBV5-4 TRBJ1-1 ASSTDRNTEAF GCCAGCAGCACCGACAGGAACACTGAAGCTTTC TRBD1 0.006612 TRBV9 TRBJ2-7 ASSMTGLGNEQY GCCAGCAGCATGACAGGTCTGGGCAACGAGCAGTAC TRBD1 0.006181 TRBV2 TRBJ2-1 ASSGRRHEQF GCCAGCAGTGGTAGAAGGCATGAGCAGTTC 0.006084 TRBV7-7 TRBJ2-7 ASSPGTNEFYEQY GCCAGCAGCCCCGGGACTAATGAATTTTACGAGCAGTAC TRBD2 0.005142 TRBV4-1 TRBJ2-7 ASSQEIRRQSSYEQY GCCAGCAGCCAAGAAATTAGGAGACAGAGCTCCTACGAGCAGTAC TRBD1 0.004753 TRBV7-9 TRBJ2-3 ASRGLAVSNTQY GCCAGCAGGGGACTGGCGGTTTCAAATACGCAGTAT TRBD1 0.00448 TRBV29-1 TRBJ2-7 SVAPRGGSYEQY AGCGTCGCACCGCGTGGGGGCTCCTACGAGCAGTAC TRBD1 0.004417 TRBV6-4 TRBJ2-2 ASSDSRGRDTGELF GCCAGCAGTGACTCGAGAGGGAGAGACACCGGGGAGCTGTTT TRBD2 0.00438 TRBV6-1 TRBJ2-1 ASREYGEQF GCCAGCAGGGAATATGGTGAGCAGTTC 0.004191 TRBV12-4 TRBJ1-2 ASSLPGGPGYT GCCAGCAGTTTACCCGGAGGACCTGGCTACACC TRBD2 0.004183 TRBV20-1 TRBJ1-1 SASSSDRPNTEAF AGTGCTAGTAGTAGCGACAGGCCGAACACTGAAGCTTTC TRBD1 0.003886 TRBV13 TRBJ2-7 ASSLAPGLAAEQY GCCAGCAGCTTAGCCCCGGGACTAGCAGCCGAGCAGTAC TRBD2 0.003881 18 4-Jul-18

TIL 04.01 vs MLTC 04.01 TIL 04.01 386 clones in common with MLTC 04.01 (3.5% of clones, 23% of reads) MLTC 04.01 386 clones in common with TIL 04.01 (14% of clones, 37% of reads) 19 4-Jul-18

TIL12.07 and TIL12.09 TIL 12.07 Clones: 591, Shannon diversity: 2,3160, Clone evenness: 0,3078 TIL 12.09 Clones: 3898, Shannon diversity: 6,9033, Clone evenness: 0,5787 20 4-Jul-18

TIL12.07 and TIL12.09 TIL 12.07 0.07% 0.4% 95 clones in common with MLTC 04.01 (16% of clones, 86% of reads!!!) TIL 12.09 0.2% 0.1% 0.06% 0.04% 0.3% 226 clones in common with MLTC 04.01 (5.8% of clones, 45% of reads!!!) 21 4-Jul-18

Adapting immunotherapeutic interventions based on TCR profiling TIL 12.07 12.07 TIL 12.09 TIL 12.07 22 4-Jul-18

More or less diversity? TIL 12.07 TIL 04.01 23 4-Jul-18

T cell repertoire before/during checkpoint blockade TIL 12.07 24 4-Jul-18

Acknowledgments TIL 12.07 Pathology, LUMC: Ruud van der Breggen Dina Ruano Medical Oncology, LUMC: Sjoerd van der Burg Els Verdegaal Marten Visser 25 4-Jul-18