Collaborating Investigator: Jeffrey Weber, M.D., Ph.D
Affiliation: NYU Langone Medical Center

Funding Source: DOD
Grant Number: RM1CA150630
Project Period: 09/01/16-08/31/19
Project Status: New

Significance

In this proposal, we wish to demonstrate the feasibility of identifying and expanding neoantigen-specific T cells for adoptive transfer following PD-1 blockade, in order to show that the majority of patients can have melanoma neoantigen-specific T cells expanded from their peripheral blood. We also aim to optimize ex vivo conditions for expansion of functionally and phenotypically optimal T cells for transfer using analysis of T cell function, TCR diversity and affinity to identify optimal neoantigen-specific T cell populations that will allow us to design truly personalized immunotherapeutics in future studies. This is highly clinically significant and represents an outstanding translational project. The work described is quite novel in that for the first time we propose to use peripheral blood cells from patients treated with a PD-1 antibody that we have found are enriched for antigen specific T cells. Our preliminary data suggest that in the tumor and in the periphery, clonality of increased and cells within the tumor can be found in the peripheral blood at low levels. We will expand these infrequent clones with the use of artificial antigen presenting cells, a truly innovative approach to expanding rare T cells within the periphery.

Approach

In aim 1, we propose to subject available frozen tumors from twenty melanoma patients from which we have matching peripheral blood mononuclear cells to whole exome sequencing and RNA Seq analysis to define neo-antigens using established software algorithms. In aim 2, we propose to expand optimal PD-1 blockade-inducing neoantigen-specific T cells for adoptive transfer. As part of this Collaborative Project with TR&D#1, effector cells will then be rapidly expanded after exposure to neo-antigen peptide-pulsed nanoparticle-based aAPC that express anti CD28 and HLA on their surface, using all 20 peptides in separate aliquots. The concentration of peptides pulsed onto the aAPC will be varied by a factor of 100 around 1 micromolar to test the peptide concentration that results in the best yield of antigen specific T cells. We will establish the feasibility of expanding neo-antigen specific T cells from at least 20 patients with melanoma using available peripheral blood cells taken after PD-1 blockade from a previous clinical trial with nivolumab. The feasibility of this process will be defined at several levels. First, we wish to be able to show that at least 2 of the top 20 predicted binding peptides can be pulsed onto aAPC and generate T cell populations that recognize HLA matched melanoma cell lines.

The second level of feasibility involves expansion of the resulting T cells. Feasibility would be defined as expansion of T cells that are predominantly (more than 75%) CD8 positive at least 1000-fold in a 2-week period using peptide pulsed aAPC obtained through this Collaborative Project from at three quarters of patients tested. Optimal conditions of aAPC concentration and ratio to PBMC, peptide concentration for pulsing, and cytokine concentration will be identified that primarily promote expansion of a central memorylike phenotype of CCR7+, CD45RA- CD8+ T cells. Subsequent conditions will be selected that allow the expansion of cells that retain high effector functions, including proliferation, IFN production and granzyme mobilization.

Push-Pull relationship:

The Schneck lab has expertise in the synthesis of and development of nanoparticle based aAPC and their use in expansion of cognate CD8+ T cell populations in vitro from healthy donors. The Weber lab has access to melanoma patients treated with nivolumab and has ongoing participation in immunotherapy clinical trials. Together, the Schneck and Weber labs have the ability to optimize in vitro stimulation of neo-antigen-specific T cells on clinically-relevant patient samples. The push-pull relationship will entail engineering aAPC optimal for the expansion of neo-antigen specific CD8+ T cells in a clinical setting of patients on immunotherapy. The push-pull relationship will entail tailoring signal 2 and ligand density on aAPC to optimize expansion/detection of responses in clinical settings.