Ngs-Based Murine Pan-Cancer Gene Expression Panel For Immunooncology And Tumor Microenvironment Studies

INTRODUCTION: Cancer is a heterogeneous disease and highly related to the immunological system. The significance of fully understanding the interactions between cancer and immunity in cancer therapeutics has been broadly noted, particularly for immunotherapies. Experimental murine models derived from a variety of biological technologies are essential preclinical model systems utilized before clinical studies. Molecular pathology techniques, such as gene expression biomarkers, are widely used to systematically profile and characterize these models. So far, however, there has been no robust and cost-effective assay designed for murine clinical immuno-oncology (I/O) research to characterize tumor-immune interactions at a gene expression level. METHODS: Marker genes were identified by combining public and in-house reference genomic data for non-tumor bearing mice as well as tumor mouse models. Oligonucleotide-based hybridization/capture techniques analogous to exome sequencing, targeting specific regions are well established on Illumina Novaseq and BGI MGIseq platforms. These methods were applied to the murine I/O panel assay, with accuracy and reproducibility verified across these two sequencing platforms. The results were further qualified using a PCR array platform. RESULTS: A mouse gene panel involving 1080 genes that encompass surface markers and transcriptomic biomarkers for the immune system, key pathways at the interface of the tumor, tumor microenvironment (TME), and immune response, as well as internal reference genes for data normalization has been established. By combining advanced NGS technologies and specific bioinformatic pipelines, we were able to detect and distinguish various immune and stromal cells involved in the complex interaction between the tumor and its microenvironment, allowing for a multifaceted characterization of disease biology and the interrogation of immune response and evasion. We validated the sensitivity, specificity, and repeatability of the panel by qPCR experiments. CONCLUSIONS: We have established a murine-I/O NGS panel involving 1080 genes to characterize tumor-immune interactions more efficiently and in a cost-effective manner for preclinical studies. This provides an enhanced insight into the TME, with high-content data that has the potential to translate more effectively to the clinic as well as for early identification of immunotherapy companion diagnostics. Citation Format: Xiaobo Chen, Jia Xue, Qixiang Li, Sheng Guo. NGS-based murine pan-cancer gene expression panel for immuno-oncology and tumor microenvironment studies [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5963.