Abstract A013: Biomarker development for cancer immuno-oncology/immunotherapy: Simultaneous digital counting of nucleic acids and proteins at 800-plex
Authors: Beechem Joseph , Manrao Liz , Ross Marty , Demirkan Gokhan , Filanoski Brian , Birditt Brian , Ngouenet Celine , Bailey Christina , Dennis Lucas , Pekker Irena , Meredith Gavin , Kim Dae , Giess Gary 
Published: May 2016

Abstract
The ability of mutated cells to give rise to pathological cancer relies upon the capability of these cells to interact with the immune system and ultimately evade immune recognition, suppress immune activity, and persist in a chronically inflamed environment. There is a clear need for new technologies capable of monitoring these crucial tumor immune-system interactions. The importance of measuring non-DNA markers (e.g., mRNA and proteins) becomes crucial in immuno-oncology (IO), since transcriptional reprogramming, cell-signaling, tumor microenvironment, and protein-protein interactions dominate the immune response. Combining multiple data types together into a single correlated analysis, however, is very difficult, due to the drastically different methodologies utilized for measurement. New developments in multiple biomarker-class optical barcode counting significantly reduce this problem. Recent work from the Weissleder-lab [1] has shown how optical barcode technology can be utilized for multiplexed digital counting of proteins, and be combined with simultaneous digital counting of nucleic-acids on a single platform. NanoString has expanded upon this original work and developed a cancer immune-profiling technology that simultaneously measures 770 mRNA's (unique signatures for 24 infiltrating immune cell types plus extensive immune-signaling pathways) plus 30 key IO proteins (including PD-1, PD-L1, PD-L2, CTLA4, OX40) using small amounts of clinically relevant samples (~ 50,000 PBMCs for mRNA+protein, 1 or 2, 5um slices for mRNA alone). This technology (RNA:Protein) is forming the basis for multi-year collaborations between NanoString and both MD Anderson (Houston TX) and the Cancer Immunotherapy Trials Network (CITN) to discover unique multi-analyte-type (mRNA + protein) biomarker signatures to guide cancer immunotherapy. NanoString gene expression profiling has also been highlighted by Merck (poster # 6017, ASCO 2015) as a method to select patients that will benefit from anti-PD1 based therapy (Keytruda). This technology is also being expanded to work on multi-analyte detection completely from FFPE slices. Several examples of the utilization of RNA:Protein immune-profiling technology to develop biomarker signatures will be presented.
Reference:
[1] Ullal et al. Science Translational Medicine 6:219 (Jan 15 2014)
Citation Format: Joseph Beechem, Liz Manrao, Marty Ross, Gokhan Demirkan, Brian Filanoski, Brian Birditt, Celine Ngouenet, Christina Bailey, Lucas Dennis, Irena Pekker, Gavin Meredith, Dae Kim, Gary Giess. Biomarker development for cancer immuno-oncology/immunotherapy: Simultaneous digital counting of nucleic acids and proteins at 800-plex. [abstract]. In: Proceedings of the CRI-CIMT-EATI-AACR Inaugural International Cancer Immunotherapy Conference: Translating Science into Survival; September 16-19, 2015; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(1 Suppl):Abstract nr A013.