1. Distinct baseline tissue biomarkers are associated with response to nivolumab and ipilimumab in melanoma: CheckMate 064
Scott J. Rodig,1,2 Daniel Gusenleitner,2 Donald Jackson,3 Evisa Gjini,2 Anita Giobbie-Hurder,2 Chelsea Jin,3 Han Chang,3 Scott B. Lovitch,1 Christine Horak,3 Jeffrey S. Weber,4 Margaret Ann Shipp,2 F. Stephen Hodi2
1Brigham and Women’s Hospital, Boston, MA, USA; 2Dana-Farber Cancer Institute, Boston, MA, USA; 3Bristol-Myers Squibb, Princeton, NJ, USA; 4New York University Langone Medical Center, New York, NY, USA
Abstract Number 9515

2. Introduction
Immune checkpoint inhibitors have changed the treatment landscape for patients with melanoma and other malignancies1
Response to these treatments is limited to a subset of patients, highlighting the need to better understand underlying mechanisms of response and resistance2
Major histocompatibility complex (MHC) class I and II molecules play a key role in immune recognition3; loss of these proteins is a mechanism of immune escape4
Here we evaluated whether antigen presentation machinery proteins and other baseline biomarkers predict response to nivolumab (NIVO; anti-programmed death 1 [PD-1]) and ipilimumab (IPI; anti-cytotoxic T-lymphocyte antigen 4) in the phase II study CheckMate 064
1. Postow MA et al. J Clin Oncol. 2015;33: Furness AJS et al. J Clin Cell Immunol. 2015;6: Kobayashi KS, van den Elsen PJ. Nat Rev Immunol. 2012;12: Angell TE et al. Clin Cancer Res. 2014;20:

3. CheckMate 064 Study Design
Randomized, open-label, phase II study evaluating the safety and efficacy of 2 immune checkpoint inhibitors given sequentially with planned switch
Induction Period 1
Induction Period 2
Continuation Period
NIVO 3 mg/kg Q2W x 6
IPI 3 mg/kg Q3W x 4
Cohort A
n = 70a
Randomize
NIVO 3 mg/kg Q2W 2W
IPI 3 mg/kg Q3W x 4
NIVO 3 mg/kg Q2W x 6
Cohort B
n = 70a 3W
Until PD, unacceptable toxicity, or withdrawal of consent
Week # TA 1 13 TA 25 TA
Biopsy
Biopsy
a68 patients in cohort A and 70 patients in cohort B received at least 1 dose of study drug
PD = progressive disease; Q2W = every 2 weeks; Q3W = every 3 weeks; TA = tumor assessment
Weber JS et al. Lancet Oncol. 2016;17:

4. Biomarker Assessment in All Tumor Samples at Baseline
Expression of MHC class II does not correlate with expression of MHC class I
Loss of MHC class I is also observed at the transcript level, but is rarely associated with gene mutations
MHC class II IHC %
MHC class I IHC %
All samples
HLA-C
HLA-B
HLA-A
JAK1
JAK2
STAT1
B2M
Missense HLA mutations
0% % %
IHC intensity
scaled by row max
CN gain
Missense variant
Stop gained
Normal
Missing
Mutation legend
Gene expression levels
row scaled
Disruptive inframe deletion
High
Low
CN = copy number; HLA = human leukocyte antigen

5. Overall Survival by MHC Class I
Low baseline expression of MHC class I protein by malignant cells (≤50% positive) was associated with inferior OS in cohort B (IPINIVO), but not in cohort A (NIVOIPI)
Cohort A (NIVOIPI)
Cohort B (IPINIVO)
Months
Alive (%)
100 80 60 40 20 3 6 9 12 15 18 21 24 27 30
Months
Alive (%)
100 80 60 40 20 3 6 9 12 15 18 21 24 27 30
Number at risk
Number at risk 33 32 30 29 27 26 23 18 13 3
>50 24 19 16 15 14 12 9 7 3
>50 25
≤50 17 15 12 11 9 4 3 1 12 10 6 3 2 1
≤50 17 18 17 16 14 12 10 9 2
Not evaluable/missing 25 23 22 20 18 16 11 8 2
Not evaluable/missing 28
MHC class I
>50%
≤50%
Not evaluable/ missing
Median OS, months (95% CI) NR
HR (95% CI)
0.70 (0.27, 1.81) –
P value
0.46
MHC class I
>50%
≤50%
Not evaluable/ missing
Median OS, months (95% CI)
19.1 (7.0, NR)
7.3 (2.7, 9.9)
26.1 (17.0, NR)
HR (95% CI)
0.38 (0.18, 0.82) –
P value
0.01
CI = confidence interval; HR = hazard ratio; NR = not reached

6. Overall Survival by MHC Class II
High baseline expression of MHC class II protein by malignant cells (>1% positive) was associated with improved OS in cohort A (NIVOIPI)
Cohort A (NIVOIPI)
Cohort B (IPINIVO)
Months
Alive (%)
100 80 60 40 20 3 6 9 12 15 18 21 24 27 30
Months
Alive (%)
100 80 60 40 20 3 6 9 12 15 18 21 24 27 30
Number at risk
Number at risk 15 14 13 11 9 2
>1 11 8 7 5 4 3 2
>1 ≤1 35 34 32 30 25 24 21 13 7 2 25 18 14 11 10 8 7 6 2 ≤1 31 18 17 16 14 12 10 9 2
Not evaluable/missing 25 23 22 20 18 16 11 8 2
Not evaluable/missing 28
MHC class II
>1%
≤1%
Not evaluable/ missing
Median OS, months (95% CI) NR
23.7 (17.8, NR)
HR (95% CI)
0.11 (0.02, 0.83) –
P value
0.01
MHC class II
>1%
≤1%
Not evaluable/ missing
Median OS, months (95% CI)
19.1 (7.2, NR)
8.0 (4.3, 14.1)
26.1 (17.0, NR)
HR (95% CI)
0.50 (0.20, 1.25) –
P value
0.14
CI = confidence interval; HR = hazard ratio; NR = not reached

7. Pairwise Correlation Between Biomarkers (All Samples)
A correlation was observed between TILs, tumor PD-L1, tumor MHC class II, and interferon gamma (IFN-γ) transcriptional signature, consistent with IFN-mediated inflammation
#CD4+/mm2
#CD3+/mm2
#CD8+/mm2
#PD-1/mm2
% tumor PD-L1+
IFN-γ signature
MHC class II IHC, %
Log2 mutation burden
MHC class I IHC, % 2
Count 1 -1 .5 1
Correlation
Coefficient

8. Association Between IFN-γ Signature and Progression at Week 13
A higher baseline screening pro-inflammatory IFN-γ transcriptional signature was observed in patients without disease progression at week 13 versus those with disease progression among patients treated with NIVO; no association was observed for patients treated with IPI
Cohort A
(NIVO)
Cohort B
(IPI) -2 -1 1
IFN-γ Signature Score
Baseline
Week 13
P =
P = 0.049 -2 -1 1
IFN-γ Signature Score
Baseline
Week 13
P = 0.35
P = 0.12
Visit
Overall response P NP
Visit
P values from Wilcoxon rank-sum test for P < NP. NP = CR, PR, or SD; P = PD
CR = complete response; NP = non-progression; P = progression; PD = progressive disease; PR = partial response; SD = stable disease

9. Conclusions
Different pretreatment biological characteristics of melanoma are associated with clinical response to NIVO followed by a planned switch to IPI (cohort A) and clinical response to IPI followed by a planned switch to NIVO (cohort B)
Improved outcome with initial NIVO is strongly associated with a pro- inflammatory signature enriched for IFN-γ targets
Inferior outcome with initial IPI is associated with reduction and/or loss of MHC class I protein
These data suggest that NIVO broadly activates innate and adaptive immunity, whereas IPI is reliant upon CD8/MHC class I–mediated adaptive immunity to affect clinical response