Association between gene expression profiles and clinical outcome of pemetrexed-based treatment in patients with advanced non-squamous non-small cell lung cancer: exploratory results from a phase II study

Abstract

Introduction: We report exploratory gene-expression profiling data from a single-arm Phase-II-study in patients with non-squamous (ns)NSCLC treated with pemetrexed and cisplatin. Previously disclosed results indicated a significant association of low thymidylate-synthase (TS)-expression with longer progression-free and overall survival (PFS/OS).

Methods: Treatment-naïve nsNSCLC patients (IIIB/IV) received 4 cycles of pemetrexed/cisplatin; non-progressing patients continued on pemetrexed-maintenance. Diagnostic tissue-samples were used to assess TS-expression by immunohistochemistry (IHC) and mRNA-expression array-profiling (1,030 lung cancer-specific genes). Cox proportional-hazard models were applied to explore the association between each gene and PFS/OS. Genes significantly correlated with PFS/OS were further correlated with TS-protein expression (Spearman-rank). Unsupervised clustering was applied to all evaluable samples (n = 51) for all 1,030 genes and an overlapping 870-gene subset associated with adenocarcinoma (ADC, n = 47).

Results: 51/70 tissue-samples (72.9%) were evaluable; 9 of 1,030 genes were significantly associated with PFS/OS (unadjusted p < 0.01, genes: Chromosome 16 open reading frame 89, napsin A, surfactant protein B, aquaporin 4, TRAF2- and Nck-interacting kinase, Lysophosphatidylcholine acyltransferase 1, Interleukin 1 receptor type II, NK2 homeobox 1, ABO glycosyl-transferase); expression for all except IL1R2 correlated negatively with nuclear TS-expression (statistically significant for 5/8 genes, unadjusted p<0.01). Cluster-analysis based on 1,030 genes revealed no clear trend regarding PFS/OS; the ADC-based cluster analysis identified 3 groups (n = 21/11/15) with median (95%CI) PFS of 8.1(6.9,NE)/2.4(1.2,NE)/4.4(1.2,NE) months and OS of 20.3(17.5,NE)/4.3(1.4,NE)/8.3(3.9,NE) months, respectively.

Conclusions: These exploratory gene-expression profiling results describe genes potentially linked to low TS-expression. Nine genes were significantly associated with PFS/OS but could not be differentiated as prognostic or predictive as this was a single-arm study. Although these hypotheses-generating results are interesting, they provide no evidence to change the current histology-based treatment approach with pemetrexed.

Trial registration: ClinicalTrials.gov NCT00887549.

Conflict of interest statement

Competing Interests: The study was funded by Eli Lilly and Company, the manufacturer of pemetrexed. Medical Writing Services from Trilogy Writing and Consulting were funded by Eli Lilly. The study was sponsored by Eli Lilly and Company. CVG, MD, SPM, TSN, and DF are employees at Eli Lilly and also own Eli Lilly stock. DF and MCN have received research grants for their institution from Eli Lilly. DAF and DF have been paid by Eli Lilly for consultancy. DAF, DF, and KMK have received support for travel to meetings for the study or other purposes from Eli Lilly. KMK and MCN have been provided with writing assistance, medicines, equipment, or administrative support from Eli Lilly. DAF and KMK have also received speaker honoraria from Eli Lilly. DAF has also received payment for development of educational presentations from Eli Lilly. MCN was the principal investigator of the study. DF has also received consultancy payment from Astra Zeneca, Novartis, Roche and Sanofi. KMK has received consultancy payment from Astra Zeneca, Boehringer Ingelheim, Glaxo Smith Kline, Novartis, Pfizer, and Roche. MCN has worked as consultant/advisor for or has received speaker honoraria or research grants from Abbott, Astra Zeneca, Boehringer Ingelheim, Glaxo-SmithKline, Merck Serono, Pfizer, Roche, and Synta. DF has received speaker honoraria from Sanofi and Roche. SDM was an employee of Almac Diagnostics at the time of the study and has been paid for the generation of study data. PM has no conflicts of interest to disclose. This does not alter the authors’ adherence to PLOS ONE policies on sharing data and materials.

Figures

Figure 1. Cluster analysis: Heatmap profiles of adenocarcinoma patients with microarray mRNA data (n = 47).

1a: Columns of the heatmap represent the samples with annotated cluster membership. Rows of the heatmap represent the 870 genes on the Lung Cancer-DSA microarray in common with the set of genes used by Wilkerson et al. [2012]. Additional binary profiles are plotted for the following covariates: male, adenocarcinoma yes, ECOG performance status = 1, PFS ≥5.5 months (median), OS ≥9.6 months (median), PFS time is plotted as an additional profile with added loess-smoothed curve. 1b: Binary profiles plotted for TS nucleus IHC H-score high (≥70), TS cytoplasm IHC H-score high (≥100), TS qPCR high (≥-1.3), and high expression (≥ median cutpoint) of each of the 9 genes significantly associated with both PFS and OS in the overall sample. Abbreviations: ECOG, Eastern Cooperative Oncology Group; n, number of patients; nsNSCLC, nonsquamous non-small cell lung cancer; OS, overall survival; PFS, progression-free survival; qPCR, real-time quantitative polymerase chain reaction; TS, thymidylate synthase.