Pancreatic ductal adenocarcinoma (PDAC) remains highly lethal and has poor immunogenicity, warranting the use of vaccines to guide and recruit the immune response. Building on prior efforts to achieve clinical immunotherapeutic responses against PDAC, we conducted a phase II study (NCT03190265) that combined attenuated mesothelin (MSLN)-secreting listeria vaccine (CRS-207) and GM-CSF-secreting allogeneic whole-cell vaccine (GVAX) along with checkpoint inhibition. Patients with metastatic PDAC who progressed on chemotherapy were enrolled in one of two treatment arms in a randomized fashion. CRS-207 was given with anti-PD-1 (nivolumab) and anti-CTLA4 (ipilimumab) with (arm A) or without (arm B) GVAX. The primary endpoint was the objective response rate (ORR), and the secondary endpoint was safety. Fifty-seven patients received at least one dose of treatment, with two partial responses (4% ORR), in both arm B. The response rates were not significantly different between the two arms. Related grade ≥3 adverse events were seen in 39 (68%) patients, including 33 events attributed to CRS-207. Mass cytometry analysis of serially obtained biospecimens demonstrated treatment-induced promotion of T-cell memory and infiltration into the tumor microenvironment (TME). Peptide-specific T-cell expansions in vitro, followed by T-cell receptor sequencing, revealed clones specific to MSLN and mutant KRAS within the tumor. Accompanying these antitumor T-cell responses was significant enrichment of myeloid cells. High myeloid and regulatory T-cell signatures correlated with poor responses. We conclude that GVAX/CRS-207 plus nivolumab and ipilimumab successfully generates and expands T-cell clones specific to MSLN and mutant KRAS within the PDAC TME, but immunotherapy-induced myeloid cell enrichment remains a barrier to greater efficacy. See related article by Sidiropoulos et al., p. 399.

Comparison of CAF gene expression in monoculture and coculture

CyTOF profiling of T cells in the peripheral blood

Combination vaccine and checkpoint inhibitor therapy has previously demonstrated immunologic responses in patients with pancreatic ductal adenocarcinoma (PDAC), although with limited efficacy. An urgent need to augment responses has warranted a deeper understanding of how each treatment modality contributes to the overall inflammatory response. Serial blood samples from patients with PDAC treated with GVAX, CRS-207, anti-CTLA-4, and/or anti-PD-1 therapies were profiled using two mass cytometry panels. Generating 260 cytometric profiles from 64 unique patients allowed us to create an annotated PDAC immunotherapy atlas. Analysis of this atlas revealed that although GVAX alone did not significantly alter T-cell relative frequencies, it induced T-cell activation and upregulated checkpoint expression. Adding anti-PD-1 blockade to GVAX further enhanced T-cell activation, whereas adding anti-CTLA-4 distinctly enhanced memory formation. Vaccine-mediated effects were similar, but GVAX promoted plasmacytoid dendritic cells more than CRS-207. Derived phenotypic patterns could also be projected onto tumor imaging data, underscoring the potential for discoveries relating treatment-induced peripheral signatures to changes in the tumor microenvironment. See related article by Bever et al., p. 411.

Representative images of immune, stromal, and architectural markers in the IMC panel

Pancreatic ductal adenocarcinoma (PDAC) carries an extremely poor prognosis, in part resulting from cellular heterogeneity that supports overall tumorigenicity. Cancer-associated fibroblasts (CAF) are key determinants of PDAC biology and response to systemic therapy, and multiple CAF subtypes have been defined. However, defining the effects of patient-specific CAF heterogeneity and plasticity on tumor cell behavior is required to better characterize the role of CAFs in PDAC. In this study, we used multiomic analyses to characterize the tumor microenvironment (TME) in tumors from patients undergoing curative-intent surgery for PDAC. In these same patients, matched tumor organoid and CAF lines were established to functionally validate the impact of CAFs on the tumor cells. CAFs promoted epithelial-mesenchymal transition and a switch in tumor cell classification from classical to basal subtype. Furthermore, CAF-specific interleukin 8 functioned as a modulator of tumor cell subtype. Finally, neighborhood relationships between tumor cells and T cell subsets were defined, demonstrating a distinct spatial coordination among CAF and tumor cell subtypes. Overall, this study provides data supporting CAF signaling as a regulator of the cellular and behavioral heterogeneity in the PDAC TME. These findings can be used to explore rational approaches to improve therapies for this difficult-to-treat disease. SIGNIFICANCE:Multidimensional analyses highlight the diverse role of cancer-associated fibroblasts in influencing cells in the tumor microenvironment and provide a platform for evaluating emerging therapeutic approaches and studying mechanisms dictating tumor behavior.

Supplementary Figure 4. Effects of GVAX on T helper cells and myeloid cells. Impact of anti–PD-1 therapy (αPD1) when added to GVAX on T cells.

IMC subset analysis of T cell relationship to tumor cells and CAFs

In this phase I study, we test a pooled synthetic long peptide vaccine targeting the six KRAS mutations (G12V, G12A, G12R, G12C, G12D, G13D) with ipilimumab and nivolumab in resected pancreatic adenocarcinoma. Co-primary endpoints include safety and maximal percent change of IFNγ-producing mutant KRAS T cell responses in the blood within 17 weeks. Secondary endpoints include disease-free survival, overall survival, and maximal percent change of IFNγ-producing mutant KRAS T cell responses at any time after vaccination. Vaccine-related adverse events are grade 1-2. 11/12 and 10/12 patients generate a significant increase in average T cell response to 6 mutant KRAS antigens and tumor-specific response, respectively. Immunophenotyping demonstrate Th1 CD4 central memory and effector memory T cells, and CD8 effector memory T cells at a lower frequency. The vaccine also generates cross-reactive T cells that recognize more than one mutant KRAS antigen. These findings support the safety and diverse anti-tumor immunity of mutant KRAS vaccines (NCT04117087).

Motivation:The Functional Expansion of Specific T cell (FEST)-based assays combine short-term peptide stimulation with TCR sequencing to identify clonotypes that expand in response to specific antigens. These approaches have proven invaluable for detecting neoantigen-specific T cell responses, guiding vaccine development, and assessing checkpoint blockade efficacy. However, variability introduced by biological and technical replicates poses challenges for reproducibility and interpretation, and existing computational tools do not address replicate-level analysis in these assays. Results:We developed replicateFest, a computational framework implemented as an R package and Shiny web application, to analyze FEST-based TCR-seq data with and without replicates. replicateFest applies Fisher's exact test for non-replicate datasets and negative binomial modeling for replicate experiments, returning adjusted p-values and odds ratios to identify clonotypes significantly expanded in antigen-stimulated conditions. The framework distinguishes FEST-expanded clonotypes (relative to a no-antigen control) and FEST-positive clonotypes (expanded compared to all other conditions). Validation using synthetic datasets confirmed accurate detection of antigen-specific clonotypes. Application to published HIV-1 epitope stimulation data reproduced original findings and demonstrated replicateFest's utility for reproducibility assessment and quality control. Availability and Implementation:replicateFest is freely available under the Apache-2.0 license as an R package at https://github.com/OncologyQS/replicateFest and as an interactive Shiny application at http://www.stat-apps.onc.jhmi.edu/FEST/.

Coculture setup and deconstruction.

Cells analyzed per patient and subset nearest neighbor analysis by treatment status and at increased radii

Quantification of N-cadherin and Krt17 surface expression on organoids with and without coculture

Proteome profiler from CAF conditioned media

Representative plots of annotated single cells delineated by IMC workflow

Supplementary Data File S1: NCT00727441 PatternMarkers