Supplementary Table 1: Clinical characteristics of LUD00-0018 cohort; Supplementary Table 2. Patient characteristics; Supplementary Table 3: Adverse events; Supplementary Figure 1: Ex vivo frequencies of circulating Melan-A-specific CD8 T cell following peptide vaccinations; Supplementary Figure 2: Ex vivo characteriza9on of tumor--�specific CD8 stem cell--�like memory T cells before and after peptide vaccination; Supplementary Figure 3: Gating strategy for functional analyses following recognition of T2 target cells pulsed with native/EAA peptide; Supplementary Figure 4: Impact of peptide vaccinations on tumor antigen-specific CD8 T cell differentiation; Supplementary Figure 5: Gating strategy for single cell sorting of tumor-specific CD8 T cells following early and late native/EAA peptide vaccination time-points; Supplementary Figure 6: Ex vivo TRBV repertoire diversity and clonotype frequency of Melan-A-specific CD8 T cell subsets at early time-points after peptide vaccination.
Funding
Swiss National Center of Competence in Research
Swiss National Science Foundation
Swiss Cancer Research
SwissTransMed
Wilhelm Sander-Foundation
Cancer Research Institute
Ludwig Cancer Research
Cancer Vaccine Collaborative
Atlantic Philanthropies
Canadian Institutes of Health Research
ARTICLE ABSTRACT
Purpose: Patients with cancer benefit increasingly from T-cell–based therapies, such as adoptive T-cell transfer, checkpoint blockade, or vaccination. We have previously shown that serial vaccinations with Melan-AMART-126-35 peptide, CpG-B, and incomplete Freund adjuvant (IFA) generated robust tumor-specific CD8 T-cell responses in patients with melanoma. Here, we describe the detailed kinetics of early- and long-term establishment of T-cell frequency, differentiation (into memory and effector cells), polyfunctionality, and clonotype repertoire induced by vaccination.Experimental Design: Twenty-nine patients with melanoma were treated with multiple monthly subcutaneous vaccinations consisting of CpG-B, and either the native/EAA (n = 13) or the analogue/ELA (n = 16) Melan-AMART-126-35 peptide emulsified in IFA. Phenotypes and functionality of circulating Melan-A–specific CD8 T cells were assessed directly ex vivo by multiparameter flow cytometry, and TCR clonotypes were determined ex vivo by mRNA transcript analyses of individually sorted cells.Results: Our results highlight the determining impact of the initial vaccine injections on the rapid and strong induction of differentiated effector T cells in both patient cohorts. Moreover, long-term polyfunctional effector T-cell responses were associated with expansion of stem cell–like memory T cells over time along vaccination. Dominant TCR clonotypes emerged early and persisted throughout the entire period of observation. Interestingly, one highly dominant clonotype was found shared between memory and effector subsets.Conclusions: Peptide/CpG-B/IFA vaccination induced powerful long-term T-cell responses with robust effector cells and stem cell-like memory cells. These results support the further development of CpG-B–based cancer vaccines, either alone or as specific component of combination therapies. Clin Cancer Res; 23(13); 3285–96. ©2016 AACR.
