Biomarkers for immunotherapy. John Haanen MD PhD

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1 Biomarkers for immunotherapy John Haanen MD PhD

2 Clear value of mobilizing endogenous tumor-specific T cell responses 1. TIL therapy J. Haanen, NKI-AVL 1. Checkpoint blockade C. Robert, NEJM 2015

3 Where are we trying to get to Treat unselected patients Treat selected patients Select treatment for patients Ref. Lawrence Fong at 2016 ASCO Annual Meeting

4 Biomarker research Faeces Urine Exhaled air Melero,.., Haanen, Nat Rev Canc 2015

5 Combination therapy guided by biomarkers Melero,.., Haanen, Nat Rev Canc 2015

6 The Cancer Immunogram Describing the state of Cancer - Immune interaction Tumor foreignness Mutational load Tumor sensitivity to immune effectors MHC expression IFN-γ sensitivity General immune status Lymphocyte count Absence of inhibitory tumor metabolism LDH, glucose utilization Immune cell infiltration Intratumoral T cells Absence of soluble inhibitors IL6->CRP/ESR Absence of Checkpoints PD-L1 Blank et al. Science 2016

7 The Cancer Immunogram Tumor foreignness Mutational load Blank et al., Science 2016

8 How often does the immune system see neo-antigens in melanoma? The T cell based immune system frequently interacts with the consequences of DNA damage in human melanoma CD8 T cells: 12 pts analyzed, neo-antigen specific reactivity in 10. Not all alleles covered, exome coverage incomplete, epitope predictions imperfect CD4 T cells: 6 pts analyzed, neo-antigen specific reactivity in 5

9 Does the extent of DNA damage correlate with the clinical effects of cancer immunotherapy? Alexandrov et al, Nature 2013

10 Mutational load correlates with improved clinical benefit from CTLA-4 or PD-1 blockade Melanoma NSCLC Durable clinical benefit Non-durable benefit Van Allen et al., Science 2015 Rizvi et al., Science 2015

11 Conclusions A neo-antigen repertoire may only be common in some human cancers 1). Neo-antigen recognition is frequent in melanoma 2). Mutational load correlates with response to checkpoint blockade in a way that is consistent with a probabilistic neo-antigen lottery model Note: NO clear threshold Not (very) useful as a predictor of response for individual patients Useful to understand biology of tumor control Useful to identify tumor types that are attractive targets for immunotherapy Incentive to develop therapies that boost neo-ag. specific T cell responses

12 The Cancer Immunogram Tumor foreignness Mutational load General immune status Lymphocyte count Blank et al., Science 2016

13 General immune status lymphocyte count ipilimumab pembrolizumab Martens et al., CCR 2016 Weide et al., CCR 2016

14 Pretreatment peripheral blood T cell clonality analysis

16 Patients with clinical benefit to ipilimumab had a richer and more evenly distributed TCR repertoire Postow et al., J Immunother Cancer 2015

17 Translational research on patients treated in the Phase II IMvigor 210 Study of Atezolizumab (anti-pd-l1) in Metastatic Urothelial Carcinoma Rosenberg et al., Lancet 2016 Presented By Samuel Funt at 2016 ASCO Annual Meeting

18 Pretreatment T cell clonality in blood inversely correlated with overal survival (n=29) * Log Rank Presented by Samuel Funt, ASCO 2016

19 The Cancer Immunogram Tumor foreignness Mutational load General immune status Lymphocyte count Immune cell infiltration Intratumoral T cells Blank et al., Science 2016

20 Response to anti-pd1 is associated with baseline T cell infiltration in melanoma Tumeh et al., Nature 2014

21 Why are some tumor hot and some cold? Diffuse infiltration with CD8+ TILs in HNSCC Absence of TILs in HNSCC Keck et al., Clin Canc Res 2014

22 Higher T cell infiltration and clonality are associated with higher PD-L1 expression Presented By Samuel Funt at 2016 ASCO Annual Meeting

23 Inflamed vs non-inflamed tumoren Inflamed TILs CD8+ T cells Foreignness PD-L1 expression gene signature IFN-γ Pre-existing immunity Non-inflamed

25 Spranger et al., Nature 2015

26 Tumors with β-catenin pathway activation in non-inflamed subset Presented By Lawrence Fong at 2016 ASCO Annual Meeting

27 Loss of PTEN promotes resistance to T cell mediated immunotherapy Peng et al., Cancer Disc 2015

28 β-catenin activation and PTEN loss in non-inflamed tumors Peng et al., Cancer Disc 2015

29 Probably accounts for <10% of cold tumors

30 TIL clonality and outcome in melanoma and bladder cancer T cell repertoire assessment by TCRβ sequencing High TIL clonality associated with improved outcome

31 The Cancer Immunogram Tumor foreignness Mutational load General immune status Lymphocyte count Immune cell infiltration Intratumoral T cells Absence of Checkpoints PD-L1 Blank et al., Science 2016

33 CA : Study Design Checkmate-067: Study Design Randomized, double-blind, phase III study to compare NIVO+IPI or NIVO alone to IPI alone N=314 NIVO 1 mg/kg + IPI 3 mg/kg Q3W for 4 doses then NIVO 3 mg/kg Q2W Unresectable or Metatastic Melanoma Previously untreated 945 patients Randomize 1:1:1 Stratify by: Tumor PD-L1 expression* BRAF mutation status AJCC M stage N=316 NIVO 3 mg/kg Q2W + IPI-matched placebo Treat until progression** or unacceptable toxicity N=315 IPI 3 mg/kg Q3W for 4 doses + NIVO-matched placebo *Verified PD-L1 assay with 5% expression level was used for the stratification of patients; validated PD-L1 assay was used for efficacy analyses. **Patients could have been treated beyond progression under protocol-defined circumstances. Larkin et al., NEJM 2015

34 100 Progression-free Survival by Tumor PD-L1 Expression Tumor PD-L1 Expression Level <5% 100 Tumor PD-L1 Expression Level 5% Percentage of PFS Median PFS, months (95% CI) HR (95% CI) vs NIVO NIVO + IPI (N=210) 11.1 ( ) 0.74 ( )* NIVO (N=208) 5.3 ( ) IPI (N=202) 2.8 ( ) *Exploratory endpoint Percentage of PFS Median PFS, months (95% CI) HR (95% CI) vs. NIVO NIVO + IPI (N=212) NR (9.7 NR) 0.87 ( )* NIVO (N=218) 22.0 (8.9 NR) IPI (N=215) 3.9 ( ) *Exploratory endpoint 20 NIVO + IPI 20 NIVO + IPI 10 0 NIVO IPI NIVO IPI Number of patients at risk: NIVO + IPI NIVO IPI PFS (months) Number of patients at risk: NIVO + IPI NIVO IPI PFS (months) For the original PD-L1 PFS analysis, the descriptive hazard ratio comparing NIVO+IPI vs NIVO was 0.96, with a similar median PFS in both groups (14 months) Database lock Nov 2015

35 Response to Treatment by Tumor PD-L1 Expression* NIVO+IPI NIVO IPI PD-L1 ( 5%) PD-L1 (<5%) ORR, % (95% CI) Median Duration of Response (months) ORR, % (95% CI) Median Duration of Response (months) 72.1 ( ) 57.5 ( ) 21.3 ( ) NR 20.7 NR 54.8 ( ) 41.3 ( ) 17.8 ( ) NR Database lock Nov 2015 *Pre-treatment tumor specimens were centrally assessed by PD-L1 immunohistochemistry (using a validated BMS/Dako assay). Presented by Wolchok at ASCO 2016

36 The Cancer Immunogram Tumor foreignness Mutational load Tumor sensitivity to immune effectors MHC expression IFN-γ sensitivity General immune status Lymphocyte count Immune cell infiltration Intratumoral T cells Absence of Checkpoints PD-L1 Blank et al., Science 2016

37 Understanding tumor cell resistance to T cell attack by haploid screening Carette et al., Science 2009

38 Understanding tumor cell resistance to T cell attack by haploid screening Red => sensitive cells Green => resistant cells T cells are added Resistant cells are enriched

39 Understanding tumor cell resistance to T cell attack by haploid screening Hits obtained: IFNGR1 IFNGR2 JAK1 JAK2 STAT1 IFN inducible gene Wild WT type 2:1 1:1 0,5:1 0,25:1 0,125:1 0 Knock-out KO 2:1 1:1 0,5:1 0,25:1 0,125:1 0 IFN unrelated genes, part of the same complex.

41 Mutation in β2m gene

42 The Cancer Immunogram Tumor foreignness Mutational load Tumor sensitivity to immune effectors MHC expression IFN-γ sensitivity General immune status Lymphocyte count Absence of inhibitory tumor metabolism LDH, glucose utilization Immune cell infiltration Intratumoral T cells Absence of Checkpoints PD-L1 Blank et al., Science 2016

43 High LDH and poor survival to ipilimumab in melanoma Kelderman et al., CII 2014

44 High LDH and poor survival in melanoma treated with pembrolizumab response rate overall survival Daud et al., ASCO 2015 Weide et al., CCR 2016

45 Total population BRAF Wild-type Mutant M Stage M1c Baseline LDH ULN >ULN >2x ULN Age (yr) 65 and <75 75 PD-L1 Expression Level <5% 5% ORR in Patient Subgroups ORR (Patients) NIVO + IPI NIVO Unweighted ORR difference vs IPI (95% CI) 57.6% (314) 38.6% ( ) 43.7% (316) 24.6% ( ) 53.3% (212) 35.6% ( ) 46.8% (218) 29.1% ( ) 66.7% (102) 44.7% ( ) 36.7% (98) 14.7% ( ) 51.4% (185) 37.1% ( ) 38.9% (185) 24.6% ( ) 65.3% (199) 40.6% ( ) 51.5% (196) 26.8% ( ) 44.7% (114) 35.2% ( ) 30.4% (112) 20.8% ( ) 37.8% (37) 37.8% ( ) 21.6% (37) 21.6% ( ) 57.4% (94) 39.5% ( ) 48.1% (79) 30.1% ( ) 54.3% (35) 27.0% ( ) 43.6% (39) 16.3% ( ) 54.8% (210) 36.9% ( ) 41.3% (208) 23.5% ( ) 72.1% (68) 50.7% ( ) 57.5% (80) 36.2% ( ) ORR ipi 24.7% 9.7% 0.0% NIVO or NIVO + IPI better IPI better

46 The Cancer Immunogram Tumor foreignness Mutational load Tumor sensitivity to immune effectors MHC expression IFN-γ sensitivity General immune status Lymphocyte count Absence of inhibitory tumor metabolism LDH, glucose utilization Immune cell infiltration Intratumoral T cells Absence of soluble inhibitors IL6->CRP/ESR Absence of Checkpoints PD-L1 Blank et al., Science 2016

47 Cyclooxygenase-Dependent Tumor Growth through Evasion of Immunity CRP Zelenay et al. Cell 2015

49 Yes or no benefit to IT correlated with gene immune signature Seremet et al. J Transl Med 2016

50 Tumor microenvironment-associated biomarkers IFN gene signatures (pembrolizumab in melanoma) Signature Expanded in Validation Set<br />(While Blinded to Clinical Outcome) Presented By Antoni Ribas at 2015 ASCO Annual Meeting

51 How to use the Cancer Immunogram? Tumor foreignness Mutational load Tumor sensitivity to immune effectors MHC expression IFN-γ sensitivity General immune status Lymphocyte count Absence of inhibitory tumor metabolism LDH, glucose utilization Immune cell infiltration Intratumoral T cells Absence of soluble inhibitors IL6->CRP/ESR Absence of Checkpoints PD-L1 Blank et al., Science 2016

52 Case 1: a patient with PD-L1 positive tumor, normal LDH solution: anti-pd-1/pdl1 Tumor foreignness Mutational load Tumor sensitivity to immune effectors MHC expression IFN-γ sensitivity General immune status Lymphocyte count Absence of inhibitory tumor metabolism LDH, glucose utilization Immune cell infiltration Intratumoral T cells Absence of soluble inhibitors IL6->CRP/ESR Absence of Checkpoints PD-L1 Blank et al., Science 2016

53 Case 2: a patient with multiple unfavorable parameters possible solution: BRAFi+MEKi followed by apd-1 Tumor foreignness Mutational load Tumor sensitivity to immune effectors MHC expression IFN-γ sensitivity General immune status Lymphocyte count Absence of inhibitory tumor metabolism LDH, glucose utilization Immune cell infiltration Intratumoral T cells Absence of soluble inhibitors IL6->CRP/ESR Absence of Checkpoints PD-L1 Blank et al., Science 2016

54 Case 3: tumor with few mutations and no TIL Possible solution: adoptive T cell therapy Tumor foreignness Mutational load Tumor sensitivity to immune effectors MHC expression IFN-γ sensitivity General immune status Lymphocyte count Absence of inhibitory tumor metabolism LDH, glucose utilization Immune cell infiltration Intratumoral T cells Absence of soluble inhibitors IL6->CRP/ESR Absence of Checkpoints PD-L1 Blank et al., Science 2016

55 Case 4: a patient initially responding to PD-1 blockade Tumor foreignness Mutational load Tumor sensitivity to immune effectors MHC expression IFN-γ sensitivity General immune status Lymphocyte count Absence of inhibitory tumor metabolism LDH, glucose utilization Immune cell infiltration Intratumoral T cells Absence of soluble inhibitors IL6->CRP/ESR Absence of Checkpoints PD-L1 Blank et al., Science 2016

56 Case 4: a patient responding to PD-1 blockade Tumor foreignness Mutational load Tumor sensitivity to immune effectors MHC expression IFN-γ sensitivity General immune status Lymphocyte count Absence of inhibitory tumor metabolism LDH, glucose utilization Immune cell infiltration Intratumoral T cells Absence of soluble inhibitors IL6->CRP/ESR Absence of Checkpoints PD-L1 Blank et al., Science 2016

57 Case 4: a patient escaping from PD-1 blockade possible solution: NK cell activation? Tumor foreignness Mutational load Tumor sensitivity to immune effectors MHC expression IFN-γ sensitivity General immune status Lymphocyte count Absence of inhibitory tumor metabolism LDH, glucose utilization Immune cell infiltration Intratumoral T cells Absence of soluble inhibitors IL6->CRP/ESR Absence of Checkpoints PD-L1 Blank et al., Science 2016

58 conclusions The Cancer Immunogram is a framework to help to describe the cancer immune system interaction for individual patients and predict which aspect to target LDH (< 2x ULN) appears to be a solid biomarker of response to select melanoma patients for ipilimumab treatment Many biomarkers of response to CIT are in development. Linking all this information to create a large database will rapidly increase our understanding of immune resistance and escape.

Acknowledgements Netherlands Cancer Institute Ton Schumacher Pia Kvistborg Daniel Peeper Karin de Visser

group on Immunotherapy of Oncology (WIN-O) Geke Hospers Alfons van den Eertwegh Ellen Kapiteijn Jan Willem

Gore James Larkin MIA Sydney Georgina Long University of Tübingen Benjamin Weide University of Essen Dirk

59 Acknowledgements Netherlands Cancer Institute Ton Schumacher Pia Kvistborg Daniel Peeper Karin de Visser Christian Blank Hans van Thienen Marnix Geukes Sandra Adriaansz Henk Mallo Elsbeth van der Laan Working group on Immunotherapy of Oncology (WIN-O) Geke Hospers Alfons van den Eertwegh Ellen Kapiteijn Jan Willem de Groot Edward Fiets Rutger Kornstra Wim Kruijt Royal Marsden and Christie Hospital Paul Lorigan Martin Gore James Larkin MIA Sydney Georgina Long University of Tübingen Benjamin Weide University of Essen Dirk Schadendorf University of Regensburg Marina Kreutz Wolfgang Herr UCLA Toni Ribas Cancer Immunotherapy Dream Team

Biomarkers for immunotherapy. John Haanen MD PhD

Biomarkers for immunotherapy. John Haanen MD PhD Biomarkers for immunotherapy John Haanen MD PhD Clear value of mobilizing endogenous tumor-specific T cell responses 1. TIL therapy J. Haanen, NKI-AVL 1. Checkpoint blockade C. Robert, NEJM 2015 Where