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This paper describes the design of an early phase, prospective trial evaluating the safety and tolerability of the combination of the histone deacetylase inhibitor, entinostat, in combination with capecitabine. The study consists of two parts; an initial phase evaluating the safety of the combination in participants with metastatic breast cancer, followed by a second phase assessing the safety of the combination in participants with residual disease after neo-adjuvant chemotherapy for breast cancer. We describe the adaptation of a model-based design for identifying the maximum tolerated dose combination that efficiently moves from the initial phase in an advanced disease population to the second phase in the target population. Operating characteristics demonstrate the ability of the method to accurately predict true maximum tolerated dose combinations in a high percentage of trials with reasonable sample sizes, while treating participants at and around desirable combinations. The proposed design is a practical, early-phase, adaptive method for use with drug combination dose finding in the presence of shifting patient populations. More challenging research questions are being investigated in early-phase trials, which has created the need to implement more flexible designs that can meet the objectives of current studies, such as those exploring drug combinations while addressing patient heterogeneity. Our goal is to facilitate acceptance and application of more novel designs in contemporary early-phase studies. Keywords: Dose finding, Partial order continual reassessment method, Drug combinations, Patient heterogeneity, Early-phase

Abstract Background Breast cancer remains a leading cause of cancer death worldwide. There is evidence that immunotherapy may play a role in the eradication of residual disease. Peptide vaccines for immunotherapy are capable of durable immune memory, but vaccines alone have shown sparse clinical activity against breast cancer to date. Toll-like receptor (TLR) agonists and helper peptides are excellent adjuvants for vaccine immunotherapy and they are examined in this human clinical trial. Methods A vaccine consisting of 9 MHC class I-restricted breast cancer-associated peptides (from MAGE-A1, −A3, and -A10, CEA, NY-ESO-1, and HER2 proteins) was combined with a TLR3 agonist, poly-ICLC, along with a helper peptide derived from tetanus toxoid. The vaccine was administered on days 1, 8, 15, 36, 57, 78. CD8+ T cell responses to the vaccine were assessed by both direct and stimulated interferon gamma ELIspot assays. Results Twelve patients with breast cancer were treated: five had estrogen receptor positive disease and five were HER2 amplified. There were no dose-limiting toxicities. Toxicities were limited to Grade 1 and Grade 2 and included mild injection site reactions and flu-like symptoms, which occurred in most patients. The most common toxicities were injection site reaction/induration and fatigue, which were experienced by 100% and 92% of participants, respectively. In the stimulated ELIspot assays, peptide-specific CD8+ T cell responses were detected in 4 of 11 evaluable patients. Two patients had borderline immune responses to the vaccine. The two peptides derived from CEA were immunogenic. No difference in immune response was evident between patients receiving endocrine therapy and those not receiving endocrine therapy during the vaccine series. Conclusions Peptide vaccine administered in the adjuvant breast cancer setting was safe and feasible. The TLR3 adjuvant, poly-ICLC, plus helper peptide mixture provided modest immune stimulation. Further optimization is required for this multi-peptide vaccine/adjuvant combination. Trial registration ClinicalTrials.gov (posted 2/15/2012): NCT01532960. Registered 2/8/2012. https://clinicaltrials.gov/show/NCT01532960