An expression signature as an aid to the histologic classification of non-small cell lung cancer

Luc Girard, Jaime Rodriguez-Canales, Carmen Behrens, Debrah M. Thompson, Ihab W. Botros, Hao Tang, Yang Xie, Natasha Rekhtman, William D. Travis, Ignacio I. Wistuba, John D. Minna, Adi F. Gazdar

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Abstract

Purpose: Most non-small cell lung cancers (NSCLC) are now diagnosed from small specimens, and classification using standard pathology methods can be difficult. This is of clinical relevance as many therapy regimens and clinical trials are histology dependent. The purpose of this study was to develop an mRNA expression signature as an adjunct test for routine histopathologic classification of NSCLCs. Experimental Design: A microarray dataset of resected adenocarcinomas (ADC) and squamous cell carcinomas (SCC) was used as the learning set for an ADC-SCC signature. The Cancer Genome Atlas (TCGA) lung RNAseq dataset was used for validation. Another microarray dataset of ADCs and matched nonmalignant lung was used as the learning set for a tumor versus nonmalignant signature. The classifiers were selected as the most differentially expressed genes and sample classification was determined by a nearest distance approach. Results: We developed a 62-gene expression signature that contained many genes used in immunostains for NSCLC typing. It includes 42 genes that distinguish ADC from SCC and 20 genes differentiating nonmalignant lung from lung cancer. Testing of the TCGA and other public datasets resulted in high prediction accuracies (93%-95%). In addition, a prediction score was derived that correlates both with histologic grading and prognosis. We developed a practical version of the Classifier using the HTG EdgeSeq nuclease protection-based technology in combination with next-generation sequencing that can be applied to formalin-fixed paraffin-embedded (FFPE) tissues and small biopsies. Conclusions: Our RNA classifier provides an objective, quantitative method to aid in the pathologic diagnosis of lung cancer. Clin Cancer Res; 22(19); 4880-9.

Original languageEnglish (US)
Pages (from-to)4880-4889
Number of pages10
JournalClinical Cancer Research
Volume22
Issue number19
DOIs
StatePublished - Oct 1 2016

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Non-Small Cell Lung Carcinoma
Squamous Cell Carcinoma
Adenocarcinoma
Atlases
Lung
Genes
Lung Neoplasms
Neoplasms
Learning
Genome
Transcriptome
Paraffin
Formaldehyde
Histology
Research Design
Clinical Trials
RNA
Pathology
Technology
Biopsy

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

Cite this

Girard, L., Rodriguez-Canales, J., Behrens, C., Thompson, D. M., Botros, I. W., Tang, H., ... Gazdar, A. F. (2016). An expression signature as an aid to the histologic classification of non-small cell lung cancer. Clinical Cancer Research, 22(19), 4880-4889. https://doi.org/10.1158/1078-0432.CCR-15-2900

An expression signature as an aid to the histologic classification of non-small cell lung cancer. / Girard, Luc; Rodriguez-Canales, Jaime; Behrens, Carmen; Thompson, Debrah M.; Botros, Ihab W.; Tang, Hao; Xie, Yang; Rekhtman, Natasha; Travis, William D.; Wistuba, Ignacio I.; Minna, John D.; Gazdar, Adi F.

In: Clinical Cancer Research, Vol. 22, No. 19, 01.10.2016, p. 4880-4889.

Research output: Contribution to journalArticle

Girard, L, Rodriguez-Canales, J, Behrens, C, Thompson, DM, Botros, IW, Tang, H, Xie, Y, Rekhtman, N, Travis, WD, Wistuba, II, Minna, JD & Gazdar, AF 2016, 'An expression signature as an aid to the histologic classification of non-small cell lung cancer', Clinical Cancer Research, vol. 22, no. 19, pp. 4880-4889. https://doi.org/10.1158/1078-0432.CCR-15-2900
Girard, Luc ; Rodriguez-Canales, Jaime ; Behrens, Carmen ; Thompson, Debrah M. ; Botros, Ihab W. ; Tang, Hao ; Xie, Yang ; Rekhtman, Natasha ; Travis, William D. ; Wistuba, Ignacio I. ; Minna, John D. ; Gazdar, Adi F. / An expression signature as an aid to the histologic classification of non-small cell lung cancer. In: Clinical Cancer Research. 2016 ; Vol. 22, No. 19. pp. 4880-4889.
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