Immune-related genes and gene sets for predicting the response to anti-programmed death 1 therapy in patients with primary or metastatic non-small cell lung cancer

Abstract

Although antibodies targeting the immune checkpoint protein programmed death-1 (PD-1) exert therapeutic effects in patients with primary or metastatic non-small cell lung cancer (NSCLC), the majority of patients exhibit partial or complete resistance to anti-PD1 treatment. Thus, the aim of the present study was to identify reliable biomarkers for predicting the response to anti-PD-1 therapy. The present study analyzed tumor specimens isolated from 24 patients (13 with primary and 11 with metastatic NSCLC) prior to treatment with approved PD1-targeting antibodies. The expression profile of 395 immune-related genes was examined using RNA immune-oncology panel sequencing. The results demonstrated that six immune-related differently expressed genes (DEGs), including HLA-F-AS1, NCF1, RORC, DMBT1, KLRF1 and IL-18, and five DEGs, including HLA-A, HLA-DPA1, TNFSF18, IFI6 and PTK7, may be used as single biomarkers for predicting the efficacy of anti-PD-1 treatment in patients with primary and with metastatic NSCLC, respectively. In addition, two DEG sets comprising either six (HLA-F-AS1, NCF1, RORC, DMBT1, KLRF and IL-18) or two (HLA-A and TNFSF18) DEGs as potential combination biomarkers for predicting the efficacy of anti-PD-1 therapy in patients with NSCLC. Patients with a calculated expression level of the DEG sets >6.501 (primary NSCLC) or >6.741 (metastatic NSCLC) may benefit from the anti-PD-1 therapy. Overall, these findings provided a basis for the identification of additional biomarkers for predicting the response to anti-PD-1 treatment.

Keywords: biomarker; gene set; non-small cell lung cancer; programmed death 1.

Figure 1.

Effective gene expression map of tumor tissues from the responding and non-responding groups. (A) Volcano plot of DEGs in patients with primary NSCLC. (B) Box plot of DEG expression levels in patients with primary NSCLC. (C) The expression levels of DEGs associated with various pathways in patients with primary NSCLC. (D) volcano map in patients with metastatic NSCLC. (E) Box plot of DEG expression levels in patients with metastatic NSCLC. (F) The expression levels of DEGs associated with various pathways in patients with metastatic NSCLC. NSCLC, non-small cell lung cancer; DEG, differentially expressed gene; HLA-F-AS1, HLA-F antisense RNA 1; NCF1, neutrophil cytosolic factor 1; RORC, RAR-related orphan receptor C; DMBT1, deleted in malignant brain tumors 1; KLRF1, killer cell lectin-like receptor F1; IL-18, interleukin-18; HLA-A, major histocompatibility complex class IA; HLA-DPA1, major histocompatibility complex class II DP α1; TNFSF18, tumor necrosis factor ligand superfamily member 18; IFI6, interferon α-inducible protein 6; PTK7, inactive tyrosine-protein kinase 7.

Figure 2.

Enrichment analysis of six differentially expressed genes from patients with primary non-small cell lung cancer. (A) Gene Ontology analysis, including biological process, cell component and molecular function. (B) Kyoto Encyclopedia of Genes and Genomes pathway analysis. (C) Reactome enrichment analysis.

Figure 3.

Enrichment analysis of five DEGs in patients with metastatic NSCLC. (A) Gene Ontology analysis, including biological process, cellular component and molecular function. (B) Kyoto Encyclopedia of Genes and Genomes analysis. (C) Reactome enrichment analysis.

Figure 4.

Associations between DEGs and PFS. (A) Associations between DEGs and PFS in patients with primary NSCLC. (B) Associations between DEGs and PFS in patients with metastatic NSCLC. DEGs, differentially expressed genes; PFS, progression-free survival; NSCLC, non-small cell lung cancer.

Figure 5.

DEG set-based prediction of the efficacy of anti-PD-1 treatment in patients with primary NSCLC. (A) Cluster analysis of the six DEGs identified in patients with primary NSCLC. (B) The expression levels of the DEG set in the responding group were significantly higher compared with those in the non-responding group. (C) Receiver operating characteristic curve was used to predict the efficacy of anti-PD-1 treatment. Patients with a DEG set expression value >6.501 benefited from anti-PD-1 therapy. PD-1, programmed death-1; NSCLC, non-small cell lung cancer; DEG, differentially expressed gene; AUC, area under the curve.

Figure 6.

DEG set-based prediction of the efficacy of anti-PD-1 treatment in patients with metastatic NSCLC. (A) Cluster analysis of the five DEGs identified in patients with metastatic NSCLC. (B) Further cluster analysis of the gene set for distinguishing patients with metastatic NSCLC. (C) The expression levels of the DEG set in the responding group were significantly higher compared with those in the non-responding group. (D) Receiver operating characteristic curve was used to predict the efficacy of anti-PD-1 treatment. Patients with a DEG set expression value >6.741 benefited from anti-PD-1 therapy. PD-1, programmed death-1; NSCLC, non-small cell lung cancer; DEG, differentially expressed gene; AUC, area under the curve.

Figure 7.

Survival analysis of patients with primary and metastatic carcinoma. (A) Among patients with primary carcinoma, high expression levels of DMBT1, KLRF1, RORC and the 6-gene set were observed in patients with longer PFS. (B) In metastatic carcinoma, patients with a longer PFS displayed high expression levels of HLA-A, TNFSF18 and the 2-gene set. PFS, progression-free survival; OS, overall survival; HLA-F-AS1, HLA-F antisense RNA 1; NCF1, neutrophil cytosolic factor 1; RORC, RAR-related orphan receptor C; DMBT1, deleted in malignant brain tumors 1; KLRF1, killer cell lectin-like receptor F1; IL-18, interleukin-18; HLA-A, major histocompatibility complex class IA; TNFSF18, tumor necrosis factor ligand superfamily member 18.