Abstract 5556: Identification of signaling pathways active in small cell lung cancer (SCLC) compared to non-small cell lung cancer (NSCLC) by proteomic profiling
Authors: Byers Lauren Averett , Wang Jing , Yordy John , Fan You-Hong , Giri Uma , Shen Li , Wistuba Ignacio , Girard Luc , Coombes Kevin , Weinstein John , Minna John , Heymach John 
Published: February 2011

Abstract
Introduction: While there have been multiple studies identifying differences in phenotypes of small cell lung cancer (SCLC) compared to non-small cell lung cancer (NSCLC), identification of key signaling pathways that may differ and may represent new therapeutic targets for SCLC need to be specified. To this end, we have compared expression of a large number of proteins and genes involved in key cell regulatory pathways of SCLC with those in NSCLC using reverse phase protein array (RPPA) and genome-wide mRNA profiling.
Methods: 34 SCLC and 74 NSCLC cell lines that have been previously characterized for oncogenotype mutations, copy number changes, and mRNA expression profiles (using Affymetrix U133A, U133B, U133 Plus 2.0, and Illumina arrays) were grown under 10% serum, serum-starved, and serum-stimulated conditions. Cell lysates from each media condition were harvested and 176 total and phosphoproteins representing multiple signaling pathways were quantified by RPPA. Differences in protein and gene expression levels between SCLC and NSCLC lines were assessed using unsupervised hierarchical clustering, t-test, and ANOVA.
Results: Unsupervised hierarchical clustering separated SCLC from NSCLC cell lines based on their distinct protein expression patterns under all three media conditions. Two high-grade neuroendocrine NSCLC cell lines clustered with the SCLC cell lines, reflecting their SCLC-like protein expression. Using a false discovery rate of &lt;1% to identify protein markers most differentially expressed between SCLC and NSCLC, we observed high levels of proteins in DNA repair pathways (ex., PARP1, XRCC1, ATM, Chk1, 53BP1) and in apoptosis pathways (ex., Bcl-2, BIM, BAX). In contrast, MAPK pathway activity was downregulated, as reflected by low levels of phospho-ERK1/2. Among SCLC lines, an inverse correlation was observed between cKit and cMyc protein levels such that one group overexpressed cKit but had relatively lower cMyc levels, while the other group (enriched for cMyc amplification) had high cMyc and low cKit. Gene expression analysis showed similar results, with good correlation between non-phosphorylated proteins and mRNA levels among the pathways differentially expressed in SCLC.
Conclusions: Proteomic profiling identified increased DNA repair and apoptosis pathway activity and decreased MAPK pathway activity in SCLC. Among the proteins upregulated in SCLC, several have potential as therapeutic targets, such as PARP1. Although cKit over expression and cMyc amplification are both common in SCLC, we showed that they were mutually exclusive of each other at a protein expression level, reflecting the heterogeneity of SCLC and suggesting a rationale for testing targeted therapies specifically in subsets of patients whose tumors overexpress the targeted marker. Pathway activation will be further investigated in SCLC patient tumors.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 5556.