Abstract 3706: Validation of human and mouse myeloid panels on the NanoString® nCounter® Platform
Authors: Sushil Kumar, Sarah Warren, Tiziana Cotechini, Terry Medler, Christina Bailey, Joseph M. Beechem, Joseph M. Beechem, Lisa M. Coussens
Journal: Cancer Research (2017)

Abstract Introduction: The innate immune system profoundly influences cancer development as well as its response to various therapeutic approaches. Multiple myeloid cell lineages are central to the innate immune response during cancer and have been found to regulate diverse cellular processes encompassing immune suppression, angiogenesis, invasion, metastasis, and drug resistance. NanoString has collaborated with the laboratory of Prof. Lisa M. Coussens to develop research gene panels for quantitative and qualitative analysis of various myeloid subsets by evaluating relative enrichment of genes that mark recruitment and presence of select myeloid subtypes (e.g., granulocytes, dendritic cells, monocytes, macrophages, mast cells), their cell function, activation and effector status. Methods: Gene content for human and murine versions of the myeloid panels were developed from an in-house high content proteomic screen of macrophage activation (unpublished), genomic analysis of human tumor associated macrophages (unpublished), and data mining from publically available datasets featuring myeloid transcriptomes. In total, 692 genes were included in the human panel and 675 genes in the murine panel. The panels were optimized to work across a range of sample types including fresh frozen tissues, formalin-fixed paraffin-embedded (FFPE) samples, peripheral blood mononuclear cells and cell lysates. Results: To validate the panel content, we are profiling myeloid infiltrates in syngeneic murine models of mesothelioma and mammary tumorigenesis by flow cytometric analysis and the nCounter myeloid panels. Since the quality of the myeloid tumor response can skew toward adaptive immune activating (Th1) or suppressive (Th2) phenotypes, we will profile the same tumor samples with the NanoString PanCancer Immune Profiling panel to evaluate T cell activation status by gene expression and flow cytometry as well as global immune response. Finally, myeloid complexity and T cell activation status in both primary tumor and lung metastases will be evaluated by NanoString to assess regulation of adaptive immune responses by the innate compartment in distinct tumor microenvironments. Conclusions: Upon validation with these assays, the myeloid gene panels may provide insight into how the innate immune system regulates cancer development and response to therapeutic pressure. Improved characterization of the myeloid compartment may lead to greater insight into the fundamental biology of tumor-immune interactions, novel therapeutic strategies, and other applications. Citation Format: Sushil Kumar, Sarah Warren, Tiziana Cotechini, Terry Medler, Christina Bailey, Joseph M. Beechem, Joseph M. Beechem, Lisa M. Coussens. Validation of human and mouse myeloid panels on the NanoString® nCounter® Platform [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 3706. doi:10.1158/1538-7445.AM2017-3706