Research ArticleCancer

MHC proteins confer differential sensitivity to CTLA-4 and PD-1 blockade in untreated metastatic melanoma

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Science Translational Medicine  18 Jul 2018:
Vol. 10, Issue 450, eaar3342
DOI: 10.1126/scitranslmed.aar3342
  • Fig. 1 Summary of MHC class I and MHC class II data from the CheckMate 064 trial.

    MHC class I and MHC class II expression is shown in melanoma biopsy samples. (A) Double chromogenic IHC with antibodies targeting SOX10 (red coloration) and MHC class I (i, iii, v; brown coloration) in representative cases showing membrane staining of all SOX10+ melanoma cells (i), subset of melanoma cells (iii, scored as 50% tumor cell–positive), and no melanoma cell–positive (v; yellow arrow indicates PAX5-negative lymphocyte with positive membrane staining), or SOX10 (red coloration) and MHC class II (ii, iv, vi; brown coloration) in representative cases showing positive membrane staining MHC class II in all SOX10+ melanoma cells (ii) and no melanoma cell–positive (iv and vi; yellow arrow in iv indicates PAX5-negative lymphocyte with positive membrane staining). (B) Heat map representing the positive membrane staining of tumor cells (0 to 100%) for MHC class I (row 1) and MHC class II (row 2) proteins, the relative RNA expression of HLA-A, HLA-B, and HLA-C (rows 3 to 5, respectively), and the presence and type of alterations in HLA, B2M, STAT1, JAK2, and JAK1 genes (rows 6 to 10, respectively) for all cases (columns) with available data in the series. The threshold of 50% of tumor cells positive for MHC class I is indicated (red arrow and line). HLA, human leukocyte antigen; CN, copy number. (C to F) Kaplan-Meier estimates of overall survival (OS) by MHC class I and MHC class II expression in baseline biopsy samples according to treatment arms. OS according to expression of MHC class I is divided according to the optimum (50%) for the IPI→NIVO arm (C; P = 0.01) and the NIVO→IPI arm (D; P = 0.46). OS according to the expression of MHC class II is divided according to the optimum (1%) for the IPI→NIVO arm (E; P = 0.14) and the NIVO→IPI arm (F; P = 0.01). Patients with incomplete biomarker data are indicated (solid gray lines). Vertical dashed lines indicate the two critical time points for this analysis: 13 weeks (point of therapy switch) and 25 weeks (initiation of maintenance NIVO). The number of evaluated at-risk patients was 42 for the IPI→NIVO arm and 50 for the NIVO→IPI arm. Median OS (in months) and the HR for OS, with the 95% CIs for each, are listed below the curves. NR, not reached.

  • Fig. 2 Summary of MHC class I and MHC class II data from the CheckMate 069 trial.

    Kaplan-Meier estimates of OS by MHC class I and MHC class II expression in baseline biopsy samples according to treatment arm are shown. OS was divided according to the determined threshold for MHC class I (50%) in the (A) IPI arm (P = 0.057) and (B) NIVO + IPI arm (P = 0.66). OS was also divided according to the determined threshold for MHC class II (1%) in the (C) IPI arm (P = 0.16) and (D) NIVO + IPI arm (P = 0.25). The number of evaluated at-risk patients was 26 for the IPI arm and 63 for the NIVO + IPI arm. The median OS (in months) and the HR, with 95% CIs for each, are listed below the curves.

  • Fig. 3 Predictive value of defined gene set scores derived using RNA-seq data from baseline biopsy samples from CheckMate 064.

    (A) Gene set scores and response at week 13 for patients treated with NIVO (left) or IPI (right). (B) Gene set scores and response for the IPI→NIVO arm (left) and NIVO→IPI arm (right). (A) and (B) include gene set scores derived from a published IFN-γ signature (left box plots) (23), the top 25 differentially expressed gene transcripts for distinguishing patients according to best overall response in the NIVO→IPI arm of CheckMate 064 (middle box plots), and a curated set of 13 IFN-γ–related genes derived from the 25-gene set (right box plots). Response is divided according to progressive disease (PD) (red) or nonprogressive disease [complete response (CR), partial response (PR), or stable disease (SD); blue]. Statistical comparisons are based on one-sided Wilcoxon rank sum tests. (C) A heat map shows the relative expression of the top 25 gene transcripts differentially expressed between patients with progressive disease from those without progressive disease as best overall response (BOR) using RNA-seq data from baseline biopsy samples in the NIVO→IPI arm (P = 0.0002 to 0.01; false discovery rates, 0.14 to 0.27). Each column represents a sample. Rows represent response at week 13 (RESW13I, row 1), best overall response (BORI, row 2), and the top 25 differentially expressed transcripts grouped according to unsupervised hierarchical clustering and color-coded to indicate their relative abundance (rows 3 to 27). Gene transcripts encoding IFN-γ, markers of cells responsible for IFN-γ, transcription factors that promote IFN-γ production, or targets expressed in response to IFN-γ signaling are indicated in blue and comprise the 13 IFN-γ–related gene set. (D) Pairwise correlations using Kendall’s τ between indicated protein and transcriptional signature biomarkers across all baseline biopsy samples with available data. The empirically derived IFN-γ gene set score positively correlates with baseline melanoma MHC class II protein expression across all samples (Kendall’s pairwise correlation τ = 0.43, P < 0.001). The IFN-γ gene set score and the previously published IFN-γ signature, respectively, positively correlate with the number of tumor-associated CD3+ (P < 0.0001 and P < 0.0001), CD4+ (P = 0.0012 and P = 0.0005), and CD8+ (P < 0.0001 and P < 0.0001) T cells and with melanoma PD-L1 expression (P < 0.0001 and P < 0.0001). MHC class I protein expression more weakly positively correlates with our IFN-γ gene set (pairwise τ = 0.19, P = 0.02). N.S., not significant; #, number.

  • Fig. 4 Cell type–specific gene set scores and best overall response for patients treated sequentially with NIVO→IPI or IPI→NIVO in CheckMate 064.

    Gene set scores derived from RNA-seq data from baseline biopsy samples were divided according to a best overall response of progressive disease (red) or nonprogressive disease (complete response, partial response, or stable disease; blue) for all samples or for samples with low MHC class I expression (≤50% of cells). (A) γδ T cell gene set scores per arm. Representative image of sample stained for SOX10 (red) and TCRδ (brown) is shown with arrows indicating the presence of γδ T cells in the tumor microenvironment. (B) NK cell gene set scores per arm. Representative image of sample stained for SOX10 (red) and CD56 (brown) is shown with arrows indicating the presence of CD56+ NK cells in the tumor microenvironment. (C) IL-15 gene expression from baseline biopsy samples per arm. Statistical comparisons are based on one-sided Wilcoxon rank sum tests.

  • Table 1 Progressive disease at week 13 according to MHC class I and MHC class II thresholds in CheckMate 064.
    BiomarkerOptimal
    threshold (%)
    Number of patientsProportion with
    low biomarker
    expression and PD
    Proportion with
    high biomarker
    expression and PD
    Fisher’s exact
    P value
    In analysisLow expressionHigh expression
    IPI
      MHC class I304214281.000.640.02
      MHC class II50424110.761.000.99
    NIVO
      MHC class I305016340.440.320.53
      MHC class II15035150.460.130.05
  • Table 2 Disease progression according to defined biomarker thresholds in CheckMate 069.

    NPV, negative predictive value; PPV, positive predictive value.

    BiomarkerThreshold (%)Number of patientsProportion
    with low
    biomarker
    expression
    and PD
    Proportion
    with high
    biomarker
    expression
    and PD
    Fisher’s
    exact
    P value
    Predictive values
    (response* versus
    nonresponse)
    In analysisLow
    expression
    High
    expression
    NPV
    (95% exact CI)
    PPV
    (95% exact CI)
    IPI
      MHC class I502612140.920.430.01100%
    (74–100%)
    21%
    (5–51%)
      MHC class II12616100.750.500.2394%
    (70–99%)
    20%
    (3–56%)
    NIVO + IPI
      MHC class I506332310.310.290.9941%
    (24–59%)
    55%
    (36–73%)
      MHC class II16344190.360.160.1450%
    (35–65%)
    74%
    (49–91%)

    *Defined as complete response or partial response.

    Supplementary Materials

    • www.sciencetranslationalmedicine.org/cgi/content/full/10/450/eaar3342/DC1

      Materials and Methods

      Fig. S1. Representative IHC images.

      Fig. S2. Correlations of MHC class I IHC scores with β2M IHC scores and HLA transcripts.

      Fig. S3. Study schemas for the CheckMate 064 and CheckMate 069 trials.

      Fig. S4. Comparison of MHC class I and MHC class II expression in paired baseline and week 13 biopsy samples from CheckMate 064.

      Table S1. CheckMate 064 MHC class I and MHC class II IHC.

      Table S2. Best overall response of PD and non-PD according to optimally defined biomarker thresholds.

      Table S3. CheckMate 069 MHC class I and MHC class II IHC.

      Table S4. Genes used in the published IFN-γ signature.

      Table S5. Genes used in the NK cell and γδ T cell gene sets.

      References (5159)

    • The PDF file includes:

      • Materials and Methods
      • Fig. S1. Representative IHC images.
      • Fig. S2. Correlations of MHC class I IHC scores with β2M IHC scores and HLA transcripts.
      • Fig. S3. Study schemas for the CheckMate 064 and CheckMate 069 trials.
      • Fig. S4. Comparison of MHC class I and MHC class II expression in paired baseline and week 13 biopsy samples from CheckMate 064.
      • Legend for table S1
      • Table S2. Best overall response of PD and non-PD according to optimally defined biomarker thresholds.
      • Legend for table S3
      • Table S4. Genes used in the published IFN-γ signature.
      • Table S5. Genes used in the NK cell and γδ T cell gene sets.
      • References (5159)

      [Download PDF]

      Other Supplementary Material for this manuscript includes the following:

      • Table S1 (Microsoft Excel format). CheckMate 064 MHC class I and MHC class II IHC.
      • Table S3 (Microsoft Excel format). CheckMate 069 MHC class I and MHC class II IHC.

      [Download Tables S1 and S3]

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