Background Current immune checkpoint inhibitor immunotherapy relies on the presence of a pool of pre-existing neoantigen-specific T cells that can be unsuppressed and leveraged to eliminate cancer cells. However, in many patients in many cancers, the pre-existing T cell repertoire is unable to eliminate the tumor even after immune checkpoint therapy, suggesting that a targeted neoantigen vaccination approach could improve response to immune checkpoint inhibitor therapy. Murine antigen models exist to investigate neoantigen vaccine approaches, but most current murine neoantigen models rely on OVA or viral antigens that might have very different immunogenic properties to human neoantigens. Here, we investigate the landscape of predicted neoantigens in BBN963, a syngeneic murine bladder cancer model with endogenous neoantigens generated through mouse exposure to the tobacco carcinogen BBN in their drinking water (figure 1).
Methods We used LENS to predict neoantigens in the BBN963 cell line. We performed RNAseq on the BBN963 cell line treated for 72 hours with DMSO (control) or entinostat, an HDAC inhibitor that upregulates expression of some predicted BBN963 neoantigens. We performed DNAseq on BBN963 tumors after 4 weeks of treating the mice with normal or entinostat chow to assess for immunoediting at the DNA level.1 From the list of LENS-predicted BBN963 neoantigens we assessed features of antigens with of strong immunogenic potential (strong binding affinity, low agretopicity, high binding stability, low baseline expression level), upregulated with entinostat in vitro, and immunoedited with entinostat treatment in vivo.
Results From LENS, we predicted 422 antigens from a variety of genomic sources (SNV, self-antigen, fusion event, virus, and indel). 147 of these antigens were immunoedited in vivo. A high degree of overlap existed between the neoantigens predicted by LENS from three biological replicate tumors (figure 2). Furthermore, different neoantigens are expressed by BBN963 cells in culture depending on concentration of entinostat.
Conclusions We present an endogenous neoantigen murine cancer model containing over 400 predicted neoantigens from multiple genomic sources. Some of these neoantigens have strong immunogenicity features. The BBN963 model will be invaluable in future investigation of tumor-immune evolution, immunoediting, neoantigen-specific CD8 T cell responses, and neoantigen vaccination (figure 3).
Andrew S Truong, Mi Zhou, Bhavani Krishnan, Takanobu Utsumi, Ujjawal Manocha, Kyle G Stewart, Wolfgang Beck, Tracy L Rose, Matthew I Milowsky, Xiaping He, Christof C Smith, Lisa M Bixby, Charles M Perou, Sara E Wobker, Sean T Bailey, Benjamin G Vincent, William Y Kim. Entinostat induces antitumor immune responses through immune editing of tumor neoantigens. J. Clin. Invest. 2021;131.
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