Identification of Mutations Related to Cisplatin-Resistance and Prognosis of Patients With Lung Adenocarcinoma

Abstract

Background: Lung adenocarcinoma (LUAD) is the most common histologic type of non-small cell lung cancer (NSCLC; approximately 60%), and platinum-based chemotherapy is the cornerstone of the treatment for patients with LUAD. However, a considerable number of patients experience tumor recurrence after developing cisplatin (cis-diamminedichloroplatinum(II) or CDDP) resistance. Therefore, it is particularly important to screen primary CDDP-resistant LUAD patient populations, which can maximize the clinical benefits for these patients. Methods: Data for 61 LUAD cell lines were downloaded from the Genomics of Drug Sensitivity in Cancer (GDSC) database to screen for mutations related to CDDP susceptibility, and we conducted whole-exome sequencing (WES) of tumors from 45 LUAD patients from Zhujiang Hospital of Southern Medical University. Subsequently, the clinical prognostic value of these mutations was verified by using The Cancer Genome Atlas (TCGA)-LUAD cohort and our cohort (n = 45). Results: Based on drug sensitivity data for the GDSC-LUAD cell lines and survival analysis of the cohorts TCGA-LUAD and Local-LUAD, we found only one gene (GREB1) with mutations related to decreased CDDP sensitivity as well as worse overall survival (OS) and progression-free survival (PFS) [OS: log-rank p = 0.038, hazard ratio (HR; 95% confidence interval (95% CI)): 2.19 (0.73-6.55); PFS: log-rank p = 0.001; HR: 4.65, 95% CI: 1.18-18.37]. The GREB1-mutant (GREB1-MT) group had a higher frequency of gene mutations. Additionally, gene set enrichment analysis (GSEA) and single-sample GSEA (ssGSEA) suggested reduced accumulation of intracellular drugs in the GREB1-MT group, in addition to increased drug efflux and enhanced DNA damage repair and intracellular detoxification. Conclusion: This study found that GREB1 mutations may mediate the primary resistance and clinical prognosis of LUAD patients undergoing treatment with CDDP. Further functional analysis showed that GREB1 mutations are related to the known mechanism of CDDP resistance. These results suggest that GREB1 mutations are potential biomarkers for screening of CDDP resistance among LUAD patients.

Keywords: chemotherapy; cisplatin; lung adenocarcinoma; mutation; resistance.

FIGURE 1

(A) The workflow of the bioinformatics analysis. (B) The IC50 distribution for CDDP by tissue type. (C) Scatter plot of the IC50 distribution for CDDP in sixty-one LUAD cell lines. IC50, half maximal inhibitory concentration; LUAD, lung adenocarcinoma.

FIGURE 2

(A) IC50 values for CDDP in GDSC-LUAD cell lines with or without GREB1 mutations. (B) Regarding OS, the Kaplan-Meier method revealed GREB1 mutations (green) and wild-type GREB1 (orange) for the dataset of 494 patients with LUAD (TCGA database). (C) Regarding PFS, the Kaplan-Meier method revealed GREB1 mutations (green) and wild-type GREB1 (orange) in the dataset of 45 patients with LUAD (Local-LUAD cohort). IC50, half maximal inhibitory concentration; CDDP, cis-diamminedichloroplatinum(II); GDSC, Genomics of Drug Sensitivity in Cancer; LUAD, lung adenocarcinoma; OS, overall survival; TCGA, The Cancer Genome Atlas; PFS, progression-free survival.

FIGURE 3

Genomic alterations in LUAD. (A) Sixty-one LUAD cell lines are arranged according to their GREB1 mutation status, from left (with GREB1 mutations) to right (without GREB1 mutations). Gene alterations in the LUAD cell line are annotated for each sample according to the color panel below the image. Tumor samples from TCGA-LUAD (B) and Local-LUAD (C) are arranged according to their GREB1 mutation status, from left (with GREB1 mutations) to right (without GREB1 mutations). Alterations in TCGA-LUAD candidate genes are annotated for each sample according to the color panel below the image. Clinical information for each candidate gene is plotted in the top panel. ****p < 0.0001; ***p < 0.001; **p < 0.01; *p < 0.05 (Fisher’s exact test). LUAD, lung adenocarcinoma; TCGA, The Cancer Genome Atlas.

FIGURE 4

Transcriptome traits in GDSC-LUAD cell lines with or without GREB1 mutations. (A–C) GSEA of hallmark gene sets downloaded from the MSigDB database. All transcripts were ranked by log2 (fold change) between the GREB1-MT and GREB1-WT LUAD cell lines. Each run was performed with 1,000 permutations. GDSC, Genomics of Drug Sensitivity in Cancer; LUAD, lung adenocarcinoma; GSEA, gene set enrichment analysis; MT, mutant; WT, wild-type.

FIGURE 5

Transcriptome traits in the TCGA-LUAD cohort with or without GREB1 mutations. (A–D) GSEA of hallmark gene sets downloaded from the MSigDB database. All transcripts were ranked by log2 (fold change) between GREB1-MT and GREB1-WT LUAD patients. Each run was performed with 1,000 permutations. (E) Correlation between the single-sample GSEA enrichment score and IC50 values of 55 LUAD cell lines in GDSC (Spearman method). GSEA, gene set enrichment analysis; MT, mutant; WT, wild-type; LUAD, lung adenocarcinoma; IC50, half maximal inhibitory concentration; GDSC, Genomics of Drug Sensitivity in Cancer.

FIGURE 6

Potential mechanism of GREB1 mutations mediating the resistance of CDDP in LUAD. CDDP, cis-diamminedichloroplatinum(II); LUAD, lung adenocarcinoma.