Association of Tumor Microenvironment T-cell Repertoire and Mutational Load with Clinical Outcome after Sequential Checkpoint Blockade in Melanoma - PubMed (original) (raw)

Association of Tumor Microenvironment T-cell Repertoire and Mutational Load with Clinical Outcome after Sequential Checkpoint Blockade in Melanoma

Erik Yusko et al. Cancer Immunol Res. 2019 Mar.

Abstract

To understand prognostic factors for outcome between differentially sequenced nivolumab and ipilimumab in a randomized phase II trial, we measured T-cell infiltration and PD-L1 by IHC, T-cell repertoire metrics, and mutational load within the tumor. We used next-generation sequencing (NGS) and assessed the association of those parameters with response and overall survival. Immunosequencing of the T-cell receptor β-chain locus (TCRβ) from DNA of 91 pretreatment tumor samples and an additional 22 pairs of matched pre- and posttreatment samples from patients who received nivolumab followed by ipilimumab (nivo/ipi), or the reverse (ipi/nivo), was performed to measure T-cell clonality and fraction. Mutational and neoantigen load were also assessed by NGS in 82 of the 91 patients. Tumors were stained using IHC for PD-L1+ and CD8+ T cells. Pretreatment tumor TCR clonality and neoantigen load were marginally associated with best response with nivo/ipi (P = 0.04 and 0.05, respectively), but not with ipi/nivo. Amalgamated pretreatment mutational load and tumor T-cell fraction were significantly associated with best response with nivo/ipi (P = 0.002). Pretreatment PD-L1 staining intensity and CD8+ T-cell counts were correlated with T-cell fraction and clonality, but not mutational or neoantigen load. Patients with increased T-cell fraction posttreatment at week 13 had a 30-fold increased likelihood of survival (P = 0.002). Mutational and neoantigen load, and T-cell infiltrate within the tumor, were associated with outcome of sequential checkpoint inhibition using nivolumab then ipilimumab, but not when ipilimumab was administered before nivolumab.

©2019 American Association for Cancer Research.

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Figures

Fig 1.

Fig 1.

Mutational burden and neoantigen load versus clinical benefit in arm A (nivo/ipi). (A) Mutational burden (P = 0.06, n = 30). (B) Neoantigen load (P = 0.05, n = 30) for all patients calculated as described in Patients and Methods is shown on a log scale on the ordinate, and benefit defined as complete and partial response as well as stable disease (CR + PR) versus stable plus progressive disease (SD+PD) shown on the abscissa. The box plots show median (horizontal middle line), the interquartile range (IQR) (shaded box region), and the minimum and maximum (lines extended above and below the box). P values were obtained from a Mann–Whitney U Test.

Fig 2.

Fig 2.

Pretreatment TIL clonality in tumor samples of arm A, and pretreatment T-cell fraction in tumor samples from both arms A and B, correlated with clinical benefit (P = 0.04 with N = 30 and P = 0.02 with N = 89, respectively). (A) Pretreatment T-cell clonality. (B) T-cell fraction calculated as described in Patients and Methods is shown on a linear scale on the ordinate with response (CR + PR) versus non-response (SD + PD) shown on the abscissa. P values are determined from a Mann–Whitney U Test.

Fig 3.

Fig 3.

Mutation, T-cell fraction, and TIL clonality in pretreatment tumors predict clinical benefit in arm A. (A) ROC curves generated from an exhaustive leave-one-out cross-validation (LOOCV) procedure with a trivariate model (red line) with mutation, T-cell fraction, and TIL clonality compared to a univariate model (black line) employing PD-L1 expression. (B) Outcome of the multivariate logistic regression model, which included data from 34 patients. (C) Outcome of the univariate logistic regression model, including data from 30 patients. Two-dimensional projections of the TIL clonality and mutation burden in (D), T-cell fraction and mutational burden in (E), and T-cell fraction and mutation burden in (F). The color of the point or circle indicates clinical benefit, with closed circles indicating patients correctly classified and open circles indicating patients incorrectly classified in the LOOCV procedure.

Fig 4.

Fig 4.

Increased on-treatment TIL clonality and T-cell fraction in tumor samples correlate with clinical benefit (P = 0.002, OR = 30). Changes in TIL clonality and T-cell fraction were determined by subtracting values determined at baseline from those determined in week 13 biopsies. P value was obtained from a Fisher’s exact test of CR/PR versus SD/PD comparing the top right quadrant to the remaining three quadrants.

Fig 5.

Fig 5.

Overall survival curves for patients in arm A (30) with high T-cell fraction and mutational burden shown in orange, high T-cell fraction and low mutational burden in blue and low T-cell fraction and mutational burden in brown. High versus low was determined by the medians for each parameter.

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