Abstract 2707: NGS-based murine pan-cancer gene expression panel reveals high resolution for immuno-oncology and tumor microenvironment studies

Background: Immunotherapies have made a significant contribution in the treatment of cancer; however, the interaction between tumor, treatment and immune response remains complex. To fully understand the interactions between cancer and immunity in a tumor microenvironment (TME), experimental murine models, derived from a variety of biological technologies, are essential preclinical systems utilized before clinical studies. Next-generation sequencing (NGS) technologies have been demonstrated to be superior to microarray-based methods in assessing molecular features on omics levels. Here we describe a robust and efficient NGS-based gene expression panel to characterize murine tumor-immune interactions. Methods: We developed a murine gene expression panel (NGSmIO) with ~1100 immune-associated marker genes and immuno-oncology (I/O) signaling genes. Oligonucleotide-based hybridization/capture techniques analogous to exome sequencing, and 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. Tumor, blood and spleen tissues derived from MC38 and Hepa 1-6 tumor models with anti-PD-1 and anti-CD4 treatment were collected for both our NGS panel assay and the NanoString PanCancer Mouse IO 360™ Panel (NanoStringIO). The results were compared in parallel with historical cell cytometry, RNA-Seq (transcriptomics) and proteomics data in the same experimental conditions. Results: By systematic comparison of NGSmIO and NanoStringIO panels, we observed high correlation (mean R=0.856) and high consistency in common gene signature expression across 12 paired samples derived from different tissues and therapeutic conditions. To determine the performance of both panels, we used FACS, RNA-Seq and proteomics data in the same therapeutic conditions as previous studies for reference, and demonstrated that NanoStringIO systematically over-detects low expressed genes in different samples/conditions. Furthermore, NGSmIO detected gene expression changes under treatment, whereas NanoStringIO was unable to differentiate expression between control and treatment. Conclusions: We have established a murine-I/O NGS panel to efficiently characterize tumor-immune interactions in a robust manner for preclinical studies. Compared to the NanoStringIO panel, NGSmIO provides enhanced insight into the TME, and has the potential to both translate preclinical studies more effectively to the clinic as well as guide the design of immunotherapy companion diagnostics. Citation Format: Jia Xue, Xiaobo Chen, Henry Q. Li, Sheng Guo. NGS-based murine pan-cancer gene expression panel reveals high resolution for immuno-oncology and tumor microenvironment studies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2707.