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Airway epithelial gene expression in the diagnostic evaluation of smokers with suspect lung cancer

Abstract

Lung cancer is the leading cause of death from cancer in the US and the world1. The high mortality rate (80–85% within 5 years) results, in part, from a lack of effective tools to diagnose the disease at an early stage2,3,4. Given that cigarette smoke creates a field of injury throughout the airway5,6,7,8,9,10,11, we sought to determine if gene expression in histologically normal large-airway epithelial cells obtained at bronchoscopy from smokers with suspicion of lung cancer could be used as a lung cancer biomarker. Using a training set (n = 77) and gene-expression profiles from Affymetrix HG-U133A microarrays, we identified an 80-gene biomarker that distinguishes smokers with and without lung cancer. We tested the biomarker on an independent test set (n = 52), with an accuracy of 83% (80% sensitive, 84% specific), and on an additional validation set independently obtained from five medical centers (n = 35). Our biomarker had 90% sensitivity for stage 1 cancer across all subjects. Combining cytopathology of lower airway cells obtained at bronchoscopy with the biomarker yielded 95% sensitivity and a 95% negative predictive value. These findings indicate that gene expression in cytologically normal large-airway epithelial cells can serve as a lung cancer biomarker, potentially owing to a cancer-specific airway-wide response to cigarette smoke.

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Figure 1: Development and performance of an airway biomarker for lung cancer.
Figure 2: Hierarchical clustering of biomarker probeset expression in two independent test sets.
Figure 3: Principal component analysis (PCA) of airway biomarker gene expression in lung tissue samples.
Figure 4: Diagnostic utility of bronchoscopy and the gene-expression biomarker.

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Gene Expression Omnibus

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Acknowledgements

We thank C. O'Hara for histologic review of our airway epithelial cell samples; J. Warrington, J. Palma and R. Lipshutz for their support in designing and implementing this study; M. Klempner and D. Center for their review of the manuscript; F. O'Connell, J. Lundebye and the Lung Cancer Multi-Disciplinary Team at St. James's Hospital; and the doctors and nurses of the bronchoscopy service at Boston Medical Center, St. James's Hospital and Lahey Clinic. Affymetrix Inc. provided the HG-U133A arrays for these studies. This work was supported by the Doris Duke Charitable Foundation (A.S.), US National Institutes of Health/National Institute of Environmental Health Sciences (ES10377 to J.S.B.) and National Institutes of Health/ National Cancer Institute (R21CA10650 to A.S.).

Author information

Authors and Affiliations

Authors

Contributions

A.S. was responsible for the conception and design of this study and oversaw all aspects of the study including patient recruitment, experimental protocols and data analysis. J.E.B. contributed to the design of the analytic strategy and was responsible for the computational analysis of gene-expression data including preprocessing, class prediction and the connection to tumor tissue. V.S. contributed to the analysis of gene-expression and clinical data and optimization of the class prediction algorithm. K.S. was responsible for patient recruitment and for collection and analysis of clinical data on all subjects in this study. G.L. performed the microarray experiments and real-time PCR studies and was responsible for QRTPCR data analysis. F.S. performed the histologic studies of airway samples and the immunofluorescence studies. S.G. recruited subjects, collected samples and contributed to the analysis of clinical data on all subjects. Y.-M.D. was responsible for coordinating all patient recruitment and sample collection. P.C., J.B., C.L. and T.A. recruited subjects and collected samples at their respective institutions. P.S. contributed to the statistical analysis of the data. S.S. contributed to the development of the relational database. N.G. performed all microarray hybridizations. J.K. recruited subjects, collected samples and provided support in the design of the study. M.E.L. was responsible for conceptualizing many aspects of the analytic strategy and directed the computational analysis. J.S.B. was responsible for the conception and design of the study and oversaw the experimental studies and biological interpretation of the data. A.S., J.E.B., V.S., M.E.L. and J.S.B. were responsible for the writing of the manuscript and for the supplementary information.

Corresponding author

Correspondence to Avrum Spira.

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Competing interests

Affymetrix Inc. provided the HG-U133A arrays and some of the reagents for these studies.

Supplementary information

Supplementary Fig. 1

Confirmation of expression differences for selected biomarker genes by RT-PCR. (PDF 18 kb)

Supplementary Fig. 2

Inflammatory gene expression in bronchial epithelial cells. (PDF 39 kb)

Supplementary Fig. 3

Biomarker accuracy is independent of the composition of the training set. (PDF 19 kb)

Supplementary Fig. 4

Comparison of bronchoscopy cytopathology and biomarker prediction accuracies in our primary dataset by (a) cancer stage or (b) cancer subtype. (PDF 24 kb)

Supplementary Table 1

Patient demographics by dataset and cancer status. (PDF 17 kb)

Supplementary Table 2

Cell type and staging information for the 60 lung cancer patients in the n = 129 primary dataset. (PDF 11 kb)

Supplementary Table 3

Functional classification of biomarker genes. (PDF 17 kb)

Supplementary Table 4

Comparing the airway biomarker to randomized biomarkers. (PDF 16 kb)

Supplementary Table 5

Primers used for real time PCR. (PDF 14 kb)

Supplementary Methods (PDF 258 kb)

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Spira, A., Beane, J., Shah, V. et al. Airway epithelial gene expression in the diagnostic evaluation of smokers with suspect lung cancer. Nat Med 13, 361–366 (2007). https://doi.org/10.1038/nm1556

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