Development and validation of an immune checkpoint-based signature to predict prognosis in nasopharyngeal carcinoma using computational pathology analysis

Abstract

Background: Immunotherapy, especially immune checkpoint inhibition, has provided powerful tools against cancer. We aimed to detect the expression of common immune checkpoints and evaluate their prognostic values in nasopharyngeal carcinoma (NPC).

Methods: The expression of 9 immune checkpoints consistent with 13 features was detected in the training cohort (n = 208) by immunohistochemistry and quantified by computational pathology. Then, the LASSO cox regression model was used to construct an immune checkpoint-based signature (ICS), which was validated in a validation cohort containing 125 patients.

Results: High positive expression of PD-L1 and B7-H4 was observed in tumour cells (TCs), whereas PD-L1, B7-H3, B7-H4, IDO-1, VISTA, ICOS and OX40 were highly expressed in tumour-associated immune cells (TAICs). Eight of the 13 immune features were associated with patient overall survival, and an ICS classifier consisting of 5 features (B7-H3TAIC, IDO-1TAIC, VISTATAIC, ICOSTAIC, and LAG3TAIC) was established. Patients with high-risk scores in the training cohort had shorter overall (P < 0.001), disease-free (P = 0.002), and distant metastasis-free survival (P = 0.004), which were confirmed in the validation cohort. Multivariate analysis revealed that the ICS classifier was an independent prognostic factor. A combination of the ICS classifier and TNM stage had better prognostic value than the TNM stage alone. In addition, the ICS classifier was significantly associated with survivals in patients with high EBV-DNA load.

Conclusions: We determined the expression status of nine immune checkpoints consistent with 13 features in NPC and further constructed an ICS prognostic model, which might add prognostic value to the TNM staging system.

Keywords: Computational pathology analysis; EBV-DNA; Immune checkpoint-based signature; Nasopharyngeal carcinoma; Tumour-immune microenvironment.

Fig. 1

Computational pathology analysis. a Histology image analysis pipeline and validation; (b) Precision, recall and F1-score for each of the three cell classes. The scale bar represents 30 μm

Fig. 2

Kaplan-Meier curves for overall survival according to the 13 immune checkpoint features. Plots show (a) PD-L1_TC; (b) PD-L1_TAIC; (c) B7-H3_TC; (d) B7-H3_TAIC; (e) B7-H4_TC; (f) B7-H4_TAIC; (g) IDO-1_TC; (h) IDO-1_TAIC; (i) LAG3_TAIC; (j) VISTA_TAIC; (k) TIM-3_TAIC; (l) ICOS_TAIC and (m) OX40_TAIC in the training cohort. Abbreviations: TC, tumour cell; TAIC, tumour-associated immune cell; HR, hazard ratio; and CI, confidence interval

Fig. 3

Kaplan-Meier curves for overall, disease-free and distant metastasis-free survival according to the ICS. Plots show (a) overall survival, (b) disease-free survival and (c) distant metastasis-free survival in the training cohort and (d) overall survival, (e) disease-free survival and (f) distant metastasis-free survival in the validation cohort. Abbreviations: ICS, immune checkpoint-based signature; HR, hazard ratio; and CI, confidence interval

Fig. 4

Comparisons of the sensitivity and specificity for the prediction of overall, disease-free and distant metastasis-free survival by the combined ICS and TNM stage model, the TNM stage alone model, and the ICS alone model. Receiver operating characteristics (ROC) curves of (a) overall survival, (b) disease-free survival and (c) distant metastasis-free survival in the training cohort and (d) overall survival, (e) disease-free survival and (f) distant metastasis-free survival in the validation cohort. P values show the area under the ROC (AUROC) of the combined ICS and TNM stage model versus AUROCs of the TNM stage alone model or the ICS alone model

Fig. 5

Kaplan-Meier curves for overall, disease-free and distant metastasis-free survival of patients grouped by their EBV-DNA level and then stratified according to the ICS. Plots show (a) overall survival, (b) disease-free survival and (c) distant metastasis-free survival in the EBV-DNA level > 2000 copy/mL subgroup and (d) overall survival, (e) disease-free survival and (f) distant metastasis-free survival in the EBV-DNA level ≤ 2000 copy/mL subgroup. Abbreviations: ICS, immune checkpoint signature; HR, hazard ratio; and CI, confidence interval