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Volume 3 Supplement 2

30th Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2015)

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Immunotherapy generates selective pressure for acquisition of immunogenic neoantigens in escape tumors

Host immunosurveillance as a mechanism to promote tumor growth or to suppress tumor development is well studied. It is less known how immuno-selective pressure in the form of immunotherapies can instruct the immune system during this process. We hypothesized that the application of a T cell-dependent selection pressure in the form of a whole tumor vaccine would alter the immunogenic architecture in our transplantable murine melanoma model SB-3123, and generated an escape variant to test this hypothesis.

We performed whole-exome and RNA-sequencing of the tumor line SB-3123 and two fresh tumors generated by subcutaneous implantation of SB-3123 to identify mutations and to assess levels of expression. There were 349 mutations shared between the tumor line and fresh tumors, with less than 5 mutations that were unique to each sample. We then determined the stability of these mutations and created a re-derived tissue culture line from a fresh SB-3123 tumor. Remarkably, the re-derived tissue culture line retained 333 mutations in common with the prior samples and produced only 2 unique mutations.

To test the immunogenicity of SB-3123, we vaccinated mice with irradiated SB-3123 and administered a live tumor challenge two weeks after vaccination. This resulted in a profound vaccination response and mice were completely protected from tumor for over 200 days. Surprisingly, one vaccinated mouse developed a recrudesced tumor at the site of implantation 40 days after challenge, and a tumor line was created (SB-3123-esc). We asked whether SB-3123-esc represented an antigen escape variant by immunizing mice with SB-3123 and challenging with either SB-3123 or SB-3123-esc. Vaccination with SB-3123 did not protect against SB-3123-esc. We also performed sequencing on SB-3123-esc and determined that no known genes involved in antigen processing and presentation were mutated, and SB-3123-esc upregulated class I molecules at similar levels compared to SB-3123 upon IFN-γ treatment.

Our most striking results were the differences in mutational constituents between SB-3123 and SB-3123-esc. Of the nonsynonymous mutations called in the coding region, 441 were common to both tumor lines while 80 were unique to SB-3123 and 40 to SB-3123-esc. Furthermore, we were able to determine that SB-3123-esc lost 2 immunogenic neoantigens but had acquired 5. Future investigations are directed towards identifying the rejection antigen responsible for the escape phenotype of SB-3123-esc.

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This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.

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Pan, J.H., Vodnala, S., Eil, R.L. et al. Immunotherapy generates selective pressure for acquisition of immunogenic neoantigens in escape tumors. j. immunotherapy cancer 3 (Suppl 2), P68 (2015).

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