10/3/2016. Immunotherapy of human cancer can be highly effective: TIL therapy. What T cells See on Human Cancer. Anti-PD-1. Anti-PD-1 and anti-ctla-4

Transcription

1 Immunotherapy of human cancer can be highly effective: TIL therapy Tumor-infiltrating lymphocytes (TIL) are grown from melanoma tumors Rapid Expansion Infusion of TIL + IL-2 What T cells See on Human Cancer Pia Kvistborg The Netherlands Cancer Institute ESMO course 2016 Amsterdam Patient pretreated with lymphodepleting chemotherapy - 50% response rate in trials in multiple centers (US, Israel, DK, NL) - Clinical effect at least partially mediated by CD8 T cells Clinical data N10TIL003: ongoing complete response > 4 years Immunotherapy of cancer can be highly effective: Checkpoint blockade Prior to TIL 3 wks post TIL 8 wks post TIL 12 wks post TIL Anti-PD-1 Robert et al., NEJM 2015 Anti-PD-1 and anti-ctla-4 Biopsy at wk 7 showed no viable tumor cells Combination Anti-PD-1 Anti-CTLA-4 Larkin et al., NEJM

2 What could tumor-specific T cells detect on human cancer? Mimicking how T cells see target cells How a T cell sees a target cell 1. Self antigens (to which tolerance is incomplete) Shared between patients 2. Neo-antigens, epitopes that arise as a consequence of tumor-specific mutations Truly foreign, need to be monitored on a patient-specific basis Is T cell reactivity towards neo-antigens a common property in human cancer? Mimicking how T cells see target cells Mimicking how T cells see target cells How a T cell sees a target cell How an MHC tetramer sees a T cell How an MHC tetramer sees a T cell MART-1 MHC tetramer Anti-CD8 John D Altman et al., Science, John D Altman et al., Science,

3 High throughput screening platform for antigen-specific T cells High throughput screening platform for antigen-specific T cells Rescue Peptides Rescue Peptides T cell T cell T cell Peptide 1 Peptide 2 Peptide 3 Peptide 1 Peptide 2 Peptide 3 Allows generation of 1000s of pmhc in parallel Allows generation of 1000s of pmhc in parallel Allows detection of 47 T cell responses in parallel Toebes et al. Nat. Med Bakker et al. PNAS 2008 Toebes et al. Nat. Med Bakker et al. PNAS 2008 Hadrup et al, Nat Methods 2009, Andersen et al, Nat Prot A suitable tool for analyzing patient material Analyzing the neo-antigen-specific CD8 T cell repertoire in human cancer? 10 R 2 = Generate map of tumorspecific mutations (ExomeSeq) 1 Experiment confirmation initial Experiment 2 Reproducibility and sensitivity is high MDLVLNELVISLIVESKLLE HLA-A2 HLA-B7 HLA-C2 T cell Determine which mutated genes are expressed (RNASeq) Predict epitopes for each mutation/ each HLA-allele in silico Screen for T cell recognition of mutated epitopes 3

4 Pt 002: Partial response upon anti-ctla4 treatment Analyzing the neo-antigen-specific T cell repertoire in human cancer? Aug 2010 Dec 2010 % of Non-Synonymous mutations T > A / A > T (n=1036) T > G / A > C T > C / A > G C > A / G > T C > G / G > C C > T / G > A Identify tumor-specific mutations Mutation Type Analyzing the neo-antigen-specific T cell repertoire in human cancer? Strong T cell response against an ATR S>L neo-epitope within the tumor pmhc QD 625 (ATR S>L) 3.3% pmhc PE-Cy7 (ATR S>L) Isolate tumor-infiltrating T cells Isolate tumor-infiltrating T cells Screen with MHC multimer technology Screen with MHC multimer technology Identify tumor-specific mutations Identify tumor-specific mutations Predict potential epitopes Predict potential epitopes 4

5 Increase in neo-antigen-specific T cell response under anti-ctla4 Pt 008: complete response upon TIL therapy pmhc QD 625 (ATR S>L) 3.3% pmhc PE-Cy7 (ATR S>L) Isolate tumor-infiltrating T cells Screen with MHC multimer technology Identify tumor-specific mutations Predict potential epitopes van Rooij, JCO 2013 Pt 008: complete response upon TIL therapy Pt 008: complete response upon TIL therapy TIL infusion product Peripheral blood TIL infusion product Pre-therapy D7 post TIL therapy 0.172% 0.172% 0.002% 0.010% RASSF1 R>C RASSF1 R>C 23% 23% 0.009% 54% DHX33 R>W DHX33 R>W Profound neo-antigen reactivity in TIL product Major (>5000 fold) increase in neo-antigen specific T cell reactivity upon TIL therapy 5

6 Pt 010: complete response upon TIL therapy Pt 010: complete response upon TIL therapy TIL infusion product VARS T>M MYLK G>V WDR1 N>K LRP3 T>S RBM12 S>L Isolate tumor-infiltrating T cells Screen with MHC multimer technology Identify tumor-specific mutations Predict potential epitopes Reduction in tumor Tumor burden burden Months Months post infusion post infusion of TIL of TIL Pt 010: complete response upon TIL therapy TIL infusion product VARS T>M MYLK G>V WDR1 N>K LRP3 T>S RBM12 S>L Summary of CD8 T cell analyses 12 patients analyzed, neo-antigen specific reactivity in 10 (Not all alleles covered, exome coverage incomplete, epitope predictions imperfect) CD8 T cells frequently respond to the consequence of DNA damage in human melanoma Peripheral blood Pre therapy 2 months 6 months 12 months 34 months >450 fold increase in neo-antigen specific T cell reactivity upon TIL therapy 6

7 Mutational load in human malignancies Can we expect a neo-antigen repertoire in other human cancers? 1000 CD8 T cell responses number of patients n = 10 CD4 T cell responses number of patients n = Adapted from Alexandrov et al, Nature 2013 Melanoma data set from Alexandrov, Nature 2013 with positives and negatives superimposed Can we expect a neo-antigen repertoire in other human cancers? NSCLC: Induction of neo-antigen specific T cell reactivity upon PD-1 blockade Probable Possible Questionable? Adapted from Alexandrov et al, Nature 2013 Rizvi et al, Science

8 NSCLC: Induction of neo-antigen specific T cell reactivity upon PD-1 blockade NSCLC: Induction of neo-antigen specific T cell reactivity upon PD-1 blockade pmhc multimer 2 PBMC % Tumor digest 0.134% pmhc multimer 1 Rizvi et al, Science 2015 Rizvi et al, Science 2015 Conclusions The T cell based immune system commonly responds to the consequences of DNA damage in human cancer Cancer Immunotherapy Neo-antigen specific T cell reactivity can be enhanced by different types of immunotherapies (anti-ctla-4, anti-pd-1, TIL therapy) NKI genomics core facility Arno Velds Division of Immunology Marit van Buuren Daisy Philips Dream Team MD Anderson Laszlo Radvanyi Sanger Institute Sam Behjati Mike Stratton Marlous van den Braber Sander Kelderman Mireille Toebes Chantale Bernatchez Patrick Hwu Utrecht University Can Keşmir Surgery Clinical translation Nienke van Rooij Joost van den Berg Bastiaan Nuijen Christian Blank Memorial Sloan Kettering Naiyer Rizvi Matthew Hellman Alexandra Snyder Timothy Chan Jos van der Hage John Haanen Alexander van Akkooi Michel Wouters Ton Schumacher Maartje Sier 8

9 Pt 010: complete response upon TIL therapy Pt 010: complete response upon TIL therapy Isolate tumor-infiltrating T cells TIL infusion product VARS T>M MYLK G>V WDR1 N>K BPTF P>S RBM12 S>L 26 Identify tumor-specific mutations Predict potential epitopes Screen with MHC multimer technology Reduction in tumor burden Months post infusion of TIL Pre-therapy 6M post therapy Major (500 fold) increase in neo-antigen specific T cell reactivity upon TIL therapy

10 6% 9, 10 and 11 mers Melanoma only epitopes with signature (n = 2) epitopes without signature (n = 31) 94% 8% 9 mers Melanoma only epitopes with signature (n = 1) epitopes without signature (n = 13) 92% Evidence for neo-antigen reactive CD4 T cells? Side note: Oncogene-immortalized autologous B cells versus EBV B cells Autologous hit peptides Non-autologous mutanome set Autologous hit peptide Non-autologous mutanome set Evidence for CD4 reactivity against mutant peptides True neo-antigen specific T cell response or haphazard cross reactivity? If True: Only reactivity against autologous mutanome set If True: Reactivity against mutant peptide > reactivity against parental peptide Hits drowned in background when using EBV LCL 10

11 Progression free survival P ercent p rog ressio n -free NSCLC: Mutational load and clinical outcome to antipd-1 therapy (MSKCC) Mutational load A ll sequenced tum ors M o n th s Months High Low H ig h n o n s y n o n y m o u s b u rd e n (n = 1 7 ) L o w n o n sy n o n y m o u s b u rd e n (n = 1 7 ) P ercent progression -free Smoking status S m o k in g s ta tu s M o n s Months Ever Smoker smokers (n=28) N ever smokers (n=6 ) Non-smoker 1) Inject human melanoma (NSG-mice) 2a) Inject autologous bulk T-cell product 2b) Inject autologous neo-ag enriched T-cell product 3) Monitor tumor growth Neo-antigen enriched TIL can mediate superior tumor control Mock Bulk-TIL (non-enriched) Neo-antigen enriched TIL 11