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Murine syngeneic tumor models are critical to novel immuno-based therapy development, but the molecular and immunologic features of these models are still not clearly defined. The translational relevance of differences between the models is not fully understood, impeding appropriate preclinical model selection for target validation, and ultimately hindering drug development. Across a panel of commonly used murine syngeneic tumor models, we showed variable responsiveness to immunotherapies. We used array comparative genomic hybridization, whole-exome sequencing, exon microarray analysis, and flow cytometry to extensively characterize these models, which revealed striking differences that may underlie these contrasting response profiles. We identified strong differential gene expression in immune-related pathways and changes in immune cell–specific genes that suggested differences in tumor immune infiltrates between models. Further investigation using flow cytometry showed differences in both the composition and magnitude of the tumor immune infiltrates, identifying models that harbor “inflamed” and “non-inflamed” tumor immune infiltrate phenotypes. We also found that immunosuppressive cell types predominated in syngeneic mouse tumor models that did not respond to immune-checkpoint blockade, whereas cytotoxic effector immune cells were enriched in responsive models. A cytotoxic cell–rich tumor immune infiltrate has been correlated with increased efficacy of immunotherapies in the clinic, and these differences could underlie the varying response profiles to immunotherapy between the syngeneic models. This characterization highlighted the importance of extensive profiling and will enable investigators to select appropriate models to interrogate the activity of immunotherapies as well as combinations with targeted therapies in vivo. Cancer Immunol Res; 5(1); 29–41. ©2016 AACR.

Supplementary Figure S1: Summary of experiments Supplementary Figure S2: Gating strategy Supplementary Figure S3:Profiling by array CGH, whole-exome and targeted sequencing Supplementary Figure S4: Comparison of mutational profiles of murine syngeneic tumor cell lines and TCGA patient tumors Supplementary Figure S5: Differentially-expressed gene-sets in lymph node and spleen Supplementary Table S1: Cell line details Supplementary Table S2: Copy Number Variation Supplementary Table S3: List of 64 genes investigated by targeted sequencing Supplementary Table S4: Fluorescent antibodies used Supplementary Methods: Linear mixed-effect model

Supplementary dataset containing raw data from targeted sequencing, whole exome sequencing, array CGH and transcriptomic analysis