Abstract A49: Building a comprehensive view of tumor biology in breast cancer by combining NanoString's Prosigna assay with the Pancancer Pathways, Immune Profiling, and Progression Panels
Authors: Dennis Lucas , Danaher Patrick , Eagan Maribeth , White Andrew , Elliot Nathan , Ram Namratha , Balasundaram Gayathri , Jeiranian Arthur , Kaufmann Seely , Boykin Rich , Irving Lindy , Buckingham Wesley , Ferree Sean , Bailey Christina , Beechem Joseph 
Published: May 2016

Abstract
Recent advances in molecular profiling of breast cancer have given clinicians the tools required to make better treatment decisions for patients. Building an accurate representation of the biology of a particular tumor is key for: patient selection, therapeutic monitoring, and rational combination therapy design.
The NanoString PanCancer Pathways, PanCancer Immune Profiling and PanCancer Progression Panels enable researchers to quickly analyze the expression of up to 770 genes (per panel) and construct a comprehensive view of the biology of a particular tumor. The PanCancer Pathways Panel groups genes into 13 canonical driver pathways and provides both an expression value for each gene based on digital counts of transcripts and a Pathway Score that describes the relative dysregulation of each pathway. The Immune Profiling Panel measures the expression level of target genes that are specific to immune cell types and immune cell functions. Differential expression of each gene, relative abundance of immune cell types and abundance of tumor-specific antigens can be analyzed with the Immune Profiling panel. The Progression Panel analyzes the expression level of genes within four major biological processes that are associated with tumor growth and invasiveness. Together, these panels allow holistic characterization of the biologically meaningful attributes of a tumor.
In this proof-of-concept study, we analyzed 59 FFPE primary breast tumor samples along with 10 normal breast tissues using the PanCancer panels as well as the Prosigna Gene Signature Assay. We grouped the tumor samples by intrinsic subtype and explored pathway dysregulation using the PanCancer Pathways Panel, the immune landscape using the Immune Profiling Panel and the metastatic potential of the tumor using the Progression panel. For data analysis purposes, we used NanoString's PanCancer Advanced Analysis software. In each panel's data we compared the Prosigna subtypes at the single gene and the pathway level. We measured differential expression of various genes across subtypes as well as overall changes in pathway activation and suppression. Using the Immune Profiling Panel, we further compared relative abundance of the various immune cells across subtype.
The distribution of intrinsic subtype, as determined by the Prosigna Assay, in the 59 breast tumors was as follows: 16 (27.1%) Luminal A; 20 (33.9%) Luminal B; 13 (22.0%) Her2 Enriched; and 10 (17.0%) BasalLike. PanCancer Pathways analysis of these tumor samples along with 10 normal breast tissues revealed that dysregulation of certain canonical pathways characterizes each intrinsic subtype. In BasalLike tumors, we found that genes involved in the TGF-b pathway are significantly downregulated relative to Luminal A tumors and normal breast tissues. Further analysis with the Immune Profiling Panel revealed that the relative abundance of Mast cells is reduced while that of type 2 Th (Th2) cells is increased in Basal Like tumors relative to Luminal A and normal breast tissue. These results suggest that pathways associated with angiogenesis are downregulated in Basal Like breast cancer and favor the recruitment of immune cells associated with hypoxic conditions. These results confirm findings from multiple previous studies.
In this study, we show that the NanoString PanCancer Pathways, Immune Profiling and Progression panels reveal associations between intrinsic breast cancer subtype and specific pathway dysregulation as well as related changes in the immune landscape of the tumor. We demonstrate that a comprehensive view of the biology of a tumor can be readily obtained with the NanoString platform and the PanCancer Panels.
Citation Format: Lucas Dennis, Patrick Danaher, Maribeth Eagan, Andrew White, Nathan Elliot, Namratha Ram, Gayathri Balasundaram, Arthur Jeiranian, Seely Kaufmann, Rich Boykin, Lindy Irving, Wesley Buckingham, Sean Ferree, Christina Bailey, Joseph Beechem. Building a comprehensive view of tumor biology in breast cancer by combining NanoString's Prosigna assay with the Pancancer Pathways, Immune Profiling, and Progression Panels. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research; Oct 17-20, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(2_Suppl):Abstract nr A49.