Alterations of LKB1 and KRAS and risk of brain metastasis: comprehensive characterization by mutation analysis, copy number, and gene expression in non-small-cell lung carcinoma

Abstract

Background: Brain metastases are one of the most malignant complications of lung cancer and constitute a significant cause of cancer related morbidity and mortality worldwide. Recent years of investigation suggested a role of LKB1 in NSCLC development and progression, in synergy with KRAS alteration. In this study, we systematically analyzed how LKB1 and KRAS alteration, measured by mutation, gene expression (GE) and copy number (CN), are associated with brain metastasis in NSCLC.

Materials and methods: Patients treated at University of North Carolina Hospital from 1990 to 2009 with NSCLC provided frozen, surgically extracted tumors for analysis. GE was measured using Agilent 44,000 custom-designed arrays, CN was assessed by Affymetrix GeneChip Human Mapping 250K Sty Array or the Genome-Wide Human SNP Array 6.0 and gene mutation was detected using ABI sequencing. Integrated analysis was conducted to assess the relationship between these genetic markers and brain metastasis. A model was proposed for brain metastasis prediction using these genetic measurements.

Results: 17 of the 174 patients developed brain metastasis. LKB1 wild type tumors had significantly higher LKB1 CN (p<0.001) and GE (p=0.002) than the LKB1 mutant group. KRAS wild type tumors had significantly lower KRAS GE (p<0.001) and lower CN, although the latter failed to be significant (p=0.295). Lower LKB1 CN (p=0.039) and KRAS mutation (p=0.007) were significantly associated with more brain metastasis. The predictive model based on nodal (N) stage, patient age, LKB1 CN and KRAS mutation had a good prediction accuracy, with area under the ROC curve of 0.832 (p<0.001).

Conclusion: LKB1 CN in combination with KRAS mutation predicted brain metastasis in NSCLC.

Keywords: Brain Metastasis; KRAS; LKB1; NSCLC; Prognostic model.

Conflict of interest statement

Conflict of Interest Statement: D. Neil Hayes and N. Zhao hold a provisional patent on the predictive model of brain metastasis.

Copyright © 2014 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Figures

Figure 1

Correlation between LKB1 gene expression and copy number measurement. Panel A: LKB1 wild type group had significantly higher gene expression. Panel B: LKB1 GE and CN were positively correlated. Panel C: Wild type group had significantly higher CN. CN for each marker was calculated as log2 intensity ratio between tumor samples and normal samples using CRMA_v2 [17]. GE microarray was preprocessed by Loess normalization and GE values are unit-less values.

Figure 2

Correlation between KRAS gene expression and copy number measurement.. Panel A: KRAS wild type samples had a significantly lower gene expression. Panel B: KRAS expression and copy number were positively correlated. Panel C: Wild type group had significantly lower copy number. CN for each marker was calculated as log2 intensity ratio between tumor samples and normal samples using CRMA_v2 [17]. GE microarray was preprocessed by Loess normalization and GE values are unit-less values.

Figure 3

ROC curve for the multivariant predictive model. Predictors in this model include LKB1 CN, KRAS mutation, patients’ age at diagnosis and nodal stage. P values were generated by testing the hypothesis that area under the cuver (AUC) is 0.5.