Proteomic profiling of lung adenocarcinoma indicates heightened DNA repair, antioxidant mechanisms and identifies LASP1 as a potential negative predictor of survival

Abstract

Background: Lung cancer is the leading cause of cancer mortality in the United States. Non-small cell lung cancer accounts for 85% of all lung cancers for which adenocarcinoma is the most common histological type. Management of lung cancer is hindered by high false-positive rates due to difficulty resolving between benign and malignant tumors. Better molecular analysis comparing malignant and non-malignant tissues will provide important evidence of the underlying biology contributing to tumorigenesis.

Methods: We utilized a proteomics approach to analyze 38 malignant and non-malignant paired tissue samples obtained from current or former smokers with early stage (Stage IA/IB) lung adenocarcinoma. Statistical mixed effects modeling and orthogonal partial least squares discriminant analysis were used to identify key cancer-associated perturbations in the adenocarcinoma proteome. Identified proteins were subsequently assessed against clinicopathological variables.

Results: Top cancer-associated protein alterations were characterized by: (1) elevations in APEX1, HYOU1 and PDIA4, indicative of increased DNA repair machinery and heightened anti-oxidant defense mechanisms; (2) increased LRPPRC, STOML2, COPG1 and EPRS, suggesting altered tumor metabolism and inflammation; (3) reductions in SPTB, SPTA1 and ANK1 implying dysregulation of membrane integrity; and (4) decreased SLCA41 suggesting altered pH regulation. Increased protein levels of HYOU1, EPRS and LASP1 in NSCLC adenocarcinoma was independently validated by tissue microarray immunohistochemistry. Immunohistochemistry for HYOU1 and EPRS indicated AUCs of 0.952 and 0.841, respectively, for classifying tissue as malignant. Increased LASP1 correlated with poor overall survival (HR 3.66 per unit increase; CI 1.37-9.78; p = 0.01).

Conclusion: These results reveal distinct proteomic changes associated with early stage lung adenocarcinoma that may be useful prognostic indicators and therapeutic targets.

Keywords: Biomarker; Lung adenocarcinoma; Proteomics.

Fig. 1

Gaussian graphical model empirical network for O-PLS-DA selected top 10% discriminants between normal and tumor tissues. Edge color and width denote the direction and magnitude of partial correlations (pFDR ≤ 0.05). Node color displays the direction of the change in tumor relative to non-malignant tissue (green, decrease; red, increase; pFDR ≤ 0.05). Node inset box and whisker plots summarize differences in spectral measurements between tumor and non-malignant tissue

Fig. 2

TMA Validation of EPRS and HYOU1. a IHC scores for EPRS in TMA. b Representative IHC sections of EPRS in adenocarcinoma and control. c EPRS receiver operating characteristic (ROC) curve and statistical analysis for all 40 cases and controls using results from the LC003 TMA. d IHC scores for HYOU1 in TMA. e Representative IHC sections of HYOU1 in adenocarcinoma and control. f Receiver operating characteristic (ROC) curve for HYOU1 in TMA

Fig. 3

Association between LASP1, lymphovascular infiltration and survival. Kaplan–Meier survival curves are shown for subjects stratified presence of lymphovascular infiltration (LVI) (a) or by LASP1 protein abundance cutoff of 2.1 (b). c Multivariate Cox proportional hazard ratios are shown for LASP1 as a continuous variable and LASP1 with a cutoff of 2.1 spectral counts. Only LASP1 was a significant independent risk factor for overall survival when evaluated as a continuous variable but not at optimal x-tile derived cutoff of 2.1 spectral counts when accounting for other co-variants. d IHC scores for LASP1 in TMA. e Representative IHC sections of LASP1 in adenocarcinoma and control. f Receiver operating characteristic (ROC) Curve for LASP1 in TMA