A Phase 1 Clinical Trial of Personalized Adoptive Cellular Therapy Targeting Myelodysplastic Syndrome (MDS) Stem Cell Neoantigens (PACTN)

Background: There are few therapeutic options for higher risk patients with myelodysplastic syndrome (MDS) who fail standard therapy, and their 2-year survival rate is approximately 15%. Here we report on a recently initiated collaborative (industry-academia) first-in-human phase 1 clinical trial to assess the safety and tolerability of a novel form of adoptive T cell immunotherapy for such patients that targets patient and disease-specific, mutation-derived neoantigens. This experimental therapy is based on the concept that a) cancer is caused by somatic mutations that may generate novel immunogenic proteins (ie, neopeptides and possible neoantigens), b) that the adaptive immune system can be trained ex vivo to recognize neopeptides as neoantigens and c) that infusion of culture-expanded, neoantigen-immunized autologous T cells may be safe and therapeutically effective.

Methods: This is an open-label, phase 1, 3+3 dose escalation trial with 3 cell doses (0.3, 1, and 3.0 × 10⁷nucleated cells/kg) in cohorts of 3 patients each (see www.clinicaltrials.gov, NCT-03258359). Eligible subjects are 18 years of age or older and will have Intermediate, High, or Very High risk MDS by the revised International Prognostic Scoring System, with at least one cytopenia, and will have failed or relapsed after 6 cycles of standard hypomethylating therapy or declined such therapy, an ECOG status 0-2, and adequate organ function. Each patient's MDS-related mutations are identified and autologous T cells are immunized ex vivo with peptides corresponding to the mutated protein(s), then expanded and suitability-tested for experimental infusion (referred to as PACTN). Importantly, the T cells must demonstrate neoantigen specificity and must kill autologous MDS stem-progenitor cells prior to qualification for infusion. Each eligible subject receives a single infusion of autologous PACTN followed by intensive monitoring for adverse events (AEs) for 4 weeks and periodic monitoring for 1 year. The primary study end-point (EP) is assessment of dose-limiting toxicity (DLT) and maximum tolerated PACTN dose (MTD). Secondary EPs include disease response 1 month after PACTN infusion, overall and progression-free survival at 6 and 12 months, and assessment of the peak abundance and persistence of the infused T cells in peripheral blood. Exploratory EPs include an assessment of the effect of PACTN infusion on the allele frequencies of the targeted and non-targeted MDS mutations in blood and marrow leukocytes.

Results: At this time, two subjects have been infused with PACTN in the first dose cohort. Neither subject had an infusion reaction, severe AE, or DLT after follow-up for 2-3 months, nor has a disease response occurred in these subjects. Of interest, the infused PACTN product in the first subject showed 59% clonal dominance by a single T cell receptor (TCR) clone that was present at only 0.002% in patient's blood prior to T cell immunization with neoantigen related peptides. Multiple additional expanded TCR clones were also identified in the infused PACTN product. The presence of a dominant TCR clone in the PACTN product enabled the assessment of the in vivo abundance and persistence of the clone after PACTN infusion. The dominant clone expanded between day 1 and day+4 after PACTN infusion to a peak frequency of 0.13%, representing a 64-fold expansion of this TCR compared with the pre-infusion sample of blood leukocytes, then decreased to 0.09% by day +8. The clone was also demonstrated in bone marrow on day +15 at a frequency of 0.03%, representing a 20-fold expansion of this TCR clone compared with the pre-infusion marrow sample. Similar studies on the second subject are in progress, and will be continued in future subjects as the clinical trial continues. Finally, our studies show that it has been possible to effectively immunize autologous T cells to patient-specific neoantigens in all patients studied with MDS (n=4) and also all patients with AML (n=3) studied to date.

Conclusion: The early results of this clinical trial support the feasibility and safety of this novel approach to adoptive T cell mediated immunotherapy for patients with higher-risk MDS and encourages continuation of the trial in the higher dose level cohorts.