Over one third of all cancer related deaths worldwide are caused by non-small cell lung cancer (NSCLC). Until recently, tumor histology was rarely a factor in treatment decisions. However, this paradigm is shifting with the recent emergence of molecularly targeted therapies and next-generation chemotherapies. To better define the molecular sub-types of NSCLC that associate with active therapies and to evaluate their prognostic significance in historical clinical trials, we developed a microfluidics-based multiplexed PCR platform that enables analyses of 96 gene transcripts in 96 samples using material from as little as a single biopsy slide. The multiplexed assay panel consists of Taqman assays for markers of histology, chemo-resistance, prognosis, oncogenic pathway activity, epithelial vs. mesenchymal biology, as well as NSCLC drug targets.
We report here on the development and validation of this 96-gene transcript-profiling panel. Using titrations of several lung biopsy formalin-fixed paraffin embedded (FFPE) tissues, we show that as little as 10 ng of FFPE RNA is feasible and yields robust gene expression data across all assays of the profiling panel.
Using this technology, we tested archival lung biopsy samples from multiple Phase II and III studies to assess the prevalence and potential prognostic significance of 92 endpoints in parallel. We identified several markers that were strongly associated with histology as defined by TTF1 or p63 expression. In addition, several of the these markers were also associated with longer survival regardless of therapy, and will be discussed. These data suggest that retrospective analyses of clinical trial samples using Fluidigm-based expression analysis can be used to better inform future trial design in NSCLC.
Citation Format: An D. Do, Teiko Sumiyoshi, Yulei Wang, Erica Schleifman, Yuanyuan Xiao, Barbara Klughammer, Cheryl V. Wong, Ilma Abbas, Ling Fu, Lukas C. Amler, Rajiv Raja, David S. Shames. Analysis of the prevalence and prognostic significance of 92 endpoints using high throughput multiplexed qPCR In archival tissue from multiple NSCLC trials. [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 3500. doi:10.1158/1538-7445.AM2013-3500