Abstract 5216: Gene co-expression network analysis of small cell lung cancer (SCLC) identifies new subclasses and novel therapeutic targets including Src family kinase Fyn and Spleen Tyrosine Kinase Syk.
Authors: Udyavar Akshata R. , Hoeksema Megan D. , Clark Jonathan , Zou Yong , Li Ming , Chen Chiu-Lan (Heidi) , Eisenberg Rosana , Statnikov Alexander , Liebler Daniel C. , Field John , Shyr Yu , Estrada Lourdes , Quaranta Vito , Massion Pierre P. 
Published: August 2014

Abstract
Oncogenic mechanisms in SCLC remain poorly understood leaving this tumor with the worst prognosis among all lung cancers. Unlike other cancer types, traditional genomic approaches have been of limited success in SCLC. For instance, no patterns of prevalent mutations associated with SCLC progression or targeted therapeutics have emerged. Gene expression profiling based on differential expression have yielded potentially useful signatures in SCLC, but they have proven to be independent of each other and with minimal overlap, reducing translational potential. Nonetheless, since integrative systems biology studies of SCLC are warranted, we hypothesized that gene co-expression analyses can unveil key signaling hubs of specific networks that regulate SCLC proliferation and survival. We applied weighted gene co-expression network analysis (WGCNA) to a lung cancer patient gene expression dataset comprising of normal lung (NL), SCLC and Non-SCLC (NSCLC) such as squamous cell carcinoma and adenocarcinoma, and identified hierarchical gene networks highly specific to SCLC. The hubs of these SCLC-specific networks formed a SCLC-specific hub network (SSHN) signature that: 1) classified SCLC from NSCLC and NL on 3 independent patient and 1 cell line datasets; 2) was validated in independent RNAseq and shotgun proteomic patient datasets; 3) identified 2 SCLC subtypes with high and low SSHN expression in patients and cell lines. Three top SSHN hubs, Fyn, Syk and BRCA1, are involved in oxidative stress (OSR) and DNA damage response (DDR), respectively. At the protein level, Fyn, Syk and BRCA1 were significantly co-expressed in tissue microarrays and classified SCLC patients into 2 subtypes: High and Low Fyn/Syk/BRCA1 (F/S/B). High F/S/B staining significantly correlated with longer recurrence-free survival of patients treated with standard chemotherapy, suggesting that efficient OSR and DDR may enhance chemo response. This possibility was tested in established SCLC cell lines, which also could be separated into high vs low F/S/B groups corresponding to the clinical subtypes. High F/S/B cell lines exhibited lower proliferative rates, suggesting that OSR and DDR may still exert influence over cell cycle. Syk knockdown in these cell lines caused significant reduction in cellular viability and proliferation, as well as increased levels of Reactive Oxygen Species (ROS). Induction of oxidative stress in High F/S/B cell lines resulted in early activation of Fyn, Syk, p38, Erk and Akt. Thus, OSR may be overactive in SCLC and play a role in its natural history and response to treatment. In summary, our WGCNA combinatorial approach yielded novel insights into SCLC pathogenesis, separated two novel SCLC molecular subtypes with distinct functional OSR and DDR properties, and pointed to unsuspected potential therapeutic targets.
Citation Format: Akshata R. Udyavar, Megan D. Hoeksema, Jonathan Clark, Yong Zou, Ming Li, Chiu-Lan (Heidi) Chen, Rosana Eisenberg, Alexander Statnikov, Daniel C. Liebler, John Field, Yu Shyr, Lourdes Estrada, Vito Quaranta, Pierre P. Massion. Gene co-expression network analysis of small cell lung cancer (SCLC) identifies new subclasses and novel therapeutic targets including Src family kinase Fyn and Spleen Tyrosine Kinase Syk. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5216. doi:10.1158/1538-7445.AM2013-5216