Abstract 3983: A cross comparison of technologies for the detection of immune system related gene expression signatures in clinical FFPE samples of metastatic prostate cancer patients
Authors: Kruse Kimberly , Lo Fang Yin , Fleming Ryan , Chung Douglas , Satele Vickie , Maassel Lindsey , Saloranta Tuuli , Golez Inah , Tahir Saman , Dow Sally , Anderson Evan , Chee Spencer , Venkatramanan Raghavee , Anderson Steve , Nelson Peter S. , Morrissey Colm , Madan Anup , Austin Sharon , Howard Kellie 
Published: July 2017

The success of immunotherapy for the treatment of metastatic cancers relies on the prediction and identification of potential neo-antigens. In recent years expression levels of these neo-antigens along with other immune system related genes have been evaluated in an effort to better understand response rates for immunotherapy in various cancers. Gene expression levels can be assessed by numerous techniques including hybridization-based or direct sequencing technologies. Two platforms-HTG Molecular and NanoString nCounter have been utilized to profile changes in gene expression and offer unique advantages for analyzing challenging specimens such as formalin-fixed paraffin embedded (FFPE) tissues. The NanoString nCounter platform utilizes hybridized fluorescent probes targeted against genes of interest for a non-amplified measurement of gene expression. Several studies have been shown that the NanoString platform has good sensitivity, specificity, and reproducibility for the assessment of gene expression levels from FFPE samples. The HTG platform is relatively new and also uses a hybridization based method to enrich genes of interest without first isolating RNA. To determine the robustness of the HTG platform, we profiled a set of 30 metastatic prostate cancer samples using the HTG Molecular EdgeSeq Immuno-Oncology Assay. In these experiments, we found that expression data obtained by using both extracted RNA and lysate from FFPE slides was highly reproducible (Spearman coefficient &gt; 0.85). In addition, the expression profile of targeted genes obtained by using different slides from the same blocks was also highly correlated (Spearman coefficient &gt; 0.90). Our experiments also showed a high correlation between gene expressions profiles obtained by HTG, the NanoString PanCancer Immune Profiling panel and RNA-Seq from the same set of 30 metastatic prostate cancer samples. Further analysis to evaluate and compare the sensitivity of different platforms is being performed and results of these will be presented.

Citation Format: Kimberly Kruse, Fang Yin Lo, Ryan Fleming, Douglas Chung, Vickie Satele, Lindsey Maassel, Tuuli Saloranta, Inah Golez, Saman Tahir, Sally Dow, Evan Anderson, Spencer Chee, Raghavee Venkatramanan, Steve Anderson, Peter S. Nelson, Colm Morrissey, Anup Madan, Sharon Austin, Kellie Howard. A cross comparison of technologies for the detection of immune system related gene expression signatures in clinical FFPE samples of metastatic prostate cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3983. doi:10.1158/1538-7445.AM2017-3983