Integration of neo-antigen vaccines and immune checkpoint therapy

Project 1 Summary Immune-checkpoint inhibitors (ICIs) are providing durable clinical responses in about 20% of cancer patients, but have minimal effect in cancers lacking intra-tumoral T cells. Approaches that turn T cell deplete cancers into ones that attract high quality T cells are needed to sensitize these unresponsive cancers to ICIs. Most tumors

have somatic mutations that encode for mutant proteins that are tumor–specific and not expressed on normal cells (termed neoantigens). Cancers with the highest mutational burdens are more likely to respond to single agent ICIs. However, most cancers, including pancreatic adenocarcinoma (PDA) have lower mutational loads,

resulting in lower antigenicity, weaker endogenous T cell repertoires, and fewer T cells infiltrating the tumor. PDAs also have an immunosuppressive tumor microenvironment (TME) consisting of suppressive monocytes, B cells and T cells that express T cell inhibitory signals and exclude T cells or suppress them within the TME.

However, we published data showing in genetically–engineered KPC mice expressing the oncoprotein mutated KRAS (mKRAS), that premalignant lesions can be prevented from progressing to PDA when a mKRAS vaccine is given with ICIs. More recently, we published in the murine Panc02 model that expresses about 50 neoantigens

similar to human PDA, that a neoantigen targeted peptide vaccine (PancVAX) consisting of a mixture of 12 peptides each 20 amino acids long emulsed in adjuvant and given with ICIs, can treat PancO2 tumor-bearing mice. Thus, in this proposal we will test the hypothesis that peptide vaccines targeting shared (mKRAS) or

personalized neoantigens will trigger high quality neoantigen–specific effector and effector memory T cells, which will become available for further activation by ICIs and result in tumor rejection. We will conduct two human clinical trials (Aims 1 and 2) to test vaccines targeting mKRAS and patient–tumor–specific neoantigens in

combination with ipilimumab and nivolumab in patients with resected and metastatic PDA, respectively. Moving from the bedside back to the bench, in Aim 3, we will further develop our novel approaches arising from our current data to enhance the immunogenicity of the neoantigen vaccines. Our new preliminary data has shown

that the inclusion of MHC Class II epitopes enhances CD8+ T cell response of our murine vaccine PancVAX (which is composed primarily of MHC Class I epitopes). We will also interrogate the otherwise immunosuppressive TME with targeted therapies that would potentially reprogram tumor-associated macrophages and stromal cells in collaboration with Projects 3 and 4. In all instances, we will assess the quality

of T cells induced by each vaccine approach in combination with immune–modulatory agents. These studies will inform future combination immunotherapy approaches for testing in Project 3 patients with PDA.