Exploring Genomic Biomarkers for Pembrolizumab Response: A Real-World Approach and Patient Similarity Network Analysis Reveal DNA Response and Repair Gene Mutations as a Signature

Abstract

Purpose: Single-agent immune checkpoint inhibitor (IO) therapy is the standard for non-oncogene-addicted advanced non-small cell lung cancer (aNSCLC) with PD-L1 tumor proportion score ≥ 50%. Smoking-induced harm generates high tumor mutation burden (H-TMB) in smoking patients (S-pts), while never-smoking patients (NS-pts) typically have low TMB (L-TMB) and are unresponsive to IO. However, the molecular characterization of NS-pts with H-TMB remains unclear. Experimental design: Clinical data of 142 aNSCLC patients with PD-L1 ≥ 50% treated with first line pembrolizumab were retrospectively collected. Next-generation sequencing was performed using the FoundationOne^®CDx assay to correlate genomic alterations with clinical characteristics and response outcomes. Detected mutations were classified into eleven main pathways and enrichment analysis identified patient subgroups based on mutated pathways. Additionally, a patient similarity network was constructed to analyze molecular characterization. Results were validated using data from 853 aNSCLC patients in POPLAR and OAK trials. Results: Among the patients, S-pts had higher TMB than NS-pts. Interestingly, 11 (8%) NS-pts exhibited H-TMB and were enriched in β-catenin/Wnt and DDR pathway mutations. DDR pathway mutations were confirmed to be enriched in NS-pts with H-TMB using data from POPLAR and OAK trials. In the real-world cohort, the NS/H-TMB subgroup with DDR pathway mutations demonstrated improved IO outcome. Patient similarity network analysis confirmed the clustering of NS/H-TMB patients with DDR mutations and their association with improved overall survival in both the real-world cohort and the trials. Conclusions: The DDR signature has a potential role as an additional generator of H-TMB in NS-pts. This subgroup of IO-responsive NS-pts may have better prognosis. Our findings suggest that DDR-based mutational profiling may help identify NS-pts who could benefit from IO therapy.

Keywords: DNA damage response and repair; immunotherapy; network analysis; never-smoker; non-small cell lung cancer.

Figure 1

TMB values according to the smoking status population of the real-world aNSCLC patient cohort (142 pts). The violin plots depict the TMB values (Mut/Mb) in S-pts (111) and NS-pts (31). Median values are indicated as red dashes.

Figure 2

Clinical responses to pembrolizumab in H-TMB patients identified according to smoking status (S- vs. NS-patients): Kaplan-Meier curves for overall survival (OS) (panel A) and bar diagram showing ORR values (panel B).

Figure 3

(A) Patient similarity network of the never-smoking cohort. Nodes color codes for the TMB level: orange for TMB > 10 Mut/Mb, yellow for TMB ≤ 10 Mut/Mb. (B) Kruskal–Wallis test results on the effect of TMB. (C) The four identified communities are shown with the associated mutated pathways profile: bar diagrams of the percentage of patients characterized by at least one mutation in each of the analyzed pathways (1-Cell cycle-pathway, 2-Hippo pathway, 3-Myc pathway, 4-Notch pathway, 5-Oxidative stress/Nrf2 pathway, 6-PI3K pathway, 7-RTK/RAS/MAP pathway, 8-TGF beta pathway, 9-p53 pathway, 10-beta-catenin/Wnt pathway, and 11-DDR pathway).

Figure 4

(A) Patient similarity network of the smoking cohort. Nodes color codes for the TMB level: orange for TMB > 10 Mut/Mb, yellow for TMB ≤ 10 Mut/Mb. (B) Kruskal–Wallis test results on the effect of TMB. (C) The four identified communities are shown with the associated mutated pathways profile: bar diagrams of the percentage of patients characterized by at least one mutation in each of the analyzed pathways (1-Cell cycle-pathway, 2-Hippo pathway, 3-Myc pathway, 4-Notch pathway, 5-Oxidative stress/Nrf2 pathway, 6-PI3K pathway, 7-RTK/RAS/MAP pathway, 8-TGF beta pathway, 9-p53 pathway, 10-beta-catenin/Wnt pathway, and 11-DDR pathway).

Figure 5

Mutated pathways profile of the OAK/POPLAR NS community (panel A) correlated with the mutational profile of the real-world NS C1 (panel B): Spearman correlation, ρ = 0.727. The bar diagrams show the percentage of patients characterized by at least one mutation in each of the analyzed pathways (1—Cell cycle-pathway, 2—Hippo pathway, 3—Myc pathway, 4—Notch pathway, 5—Oxidative stress/Nrf2 pathway, 6—PI3K pathway, 7—RTK/RAS/MAP pathway, 8—TGF-β pathway, 9—p53 pathway, 10—β-catenin/Wnt pathway, and 11—DDR pathway). In the network community representation, nodes represent the patients and their color codes for the TMB level: orange for TMB > 10 Mut/Mb, yellow for TMB ≤ 10 Mut/Mb.