An Immune-Related Gene Pair Index Predicts Clinical Response and Survival Outcome of Immune Checkpoint Inhibitors in Melanoma

Abstract

The durable responses and favorable long-term outcomes are limited to a proportion of advanced melanoma patients treated with immune checkpoint inhibitors (ICI). Considering the critical role of antitumor immunity status in the regulation of ICI therapy responsiveness, we focused on the immune-related gene profiles and aimed to develop an individualized immune signature for predicting the benefit of ICI therapy. During the discovery phase, we integrated three published datasets of metastatic melanoma treated with anti-PD-1 (n = 120) and established an immune-related gene pair index (IRGPI) for patient classification. The IRGPI was constructed based on 31 immune-related gene pairs (IRGPs) consisting of 51 immune-related genes (IRGs). The ROC curve analysis was performed to evaluate the predictive accuracy of IRGPI with AUC = 0.854. Then, we retrospectively collected one anti-PD-1 therapy dataset of metastatic melanoma (n = 55) from Peking University Cancer Hospital (PUCH) and performed the whole-transcriptome RNA sequencing. Combined with another published dataset of metastatic melanoma received anti-CTLA-4 (VanAllen15; n = 42), we further validated the prediction accuracy of IRGPI for ICI therapy in two datasets (PUCH and VanAllen15) with AUCs of 0.737 and 0.767, respectively. Notably, the survival analyses revealed that higher IRGPI conferred poor survival outcomes in both the discovery and validation datasets. Moreover, correlation analyses of IRGPI with the immune cell infiltration and biological functions indicated that IRGPI may be an indicator of the immune status of the tumor microenvironment (TME). These findings demonstrated that IRGPI might serve as a novel marker for treating of melanoma with ICI, which needs to be validated in prospective clinical trials.

Keywords: immune checkpoint inhibitor (ICI); immune infiltration; immune-related gene pair index (IRGPI); melanoma; prediction.

Figure 1

The flowchart showing the scheme of this study.

Figure 2

Construction and evaluation of IRGPI in the discovery cohort. (A) A heatmap of the identified 31 IRGPs with corresponding IRGPI groups. (B) ROC curve for the predictive performance of IRGPI. (C) The rate of durable clinical response for patients with high and low IRGPI scores. (D) Kaplan-Meier plots of overall survival segregated by IRGPI score with cut-off points selected according to the Youden index. (E) Waterfall plot of IRGPI for distinct clinical response groups. IRGPI, immune-related gene pair index; IRGPs, immune-related gene pairs; ROC, receiver operating characteristic; AUC, area under curve; CI, confidence interval.

Figure 3

Validation the performance of IRGPI in two cohorts. (A, B) ROC curves for the predictive performance of IRGPI in VanAllen15 and PUCH cohorts, respectively. (C, D) The rate of durable clinical response for patients with high and low IRGPI scores in VanAllen15 and PUCH cohorts, respectively. (E, F) Kaplan-Meier plots of overall survival segregated by IRGPI score with cut-off points selected according to the Youden index in VanAllen15 and PUCH cohorts, respectively. IRGPI, immune-related gene pair index; ROC, receiver operating characteristic; AUC, area under curve; CI, confidence interval.

Figure 4

Comparison of immune microenvironment characteristics according to IRGPI status. (A, B) ESTIMATE algorithm revealed the ImmuneScore and ESTIMATEScore between IRGPI-high and IRGPI-low groups. (C) Evaluation of 22 immune cell infiltrating using the CIBERSORT method. (D) GSEA plots of immune-related pathways in comparison between IRGPI-high and IRGPI-low groups. IRGPI, immune-related gene pair index; GSEA, gene set enrichment analysis. *P < 0.05, **P < 0.01, ***P < 0.001.

Figure 5

Association of IRGPI to other potential biomarkers in melanoma. (A) Comparison of tumor mutation burden level according to IRGPI status. (B) Correlation of IRGPI to immune inhibitory receptors, including PDCD1, CTLA4, LAG3, HAVCR2, TIGIT. (C) The profile of HLA member expression levels between IRGPI-high and IRGPI-low groups. (D) Box plot of the immune-related signatures in comparison of the IRGPI-high and IRGPI-low groups. IRGPI, immune-related gene pair index; HLA, human leukocyte antigen; IFN, interferon; Teff, effective T cells; TLS, tertiary lymphoid structure. *P < 0.05, ***P < 0.001.