TLR agonists polarize interferon responses in conjunction with dendritic cell vaccination in malignant glioma: a randomized phase II Trial

Abstract

In this randomized phase II clinical trial, we evaluated the effectiveness of adding the TLR agonists, poly-ICLC or resiquimod, to autologous tumor lysate-pulsed dendritic cell (ATL-DC) vaccination in patients with newly-diagnosed or recurrent WHO Grade III-IV malignant gliomas. The primary endpoints were to assess the most effective combination of vaccine and adjuvant in order to enhance the immune potency, along with safety. The combination of ATL-DC vaccination and TLR agonist was safe and found to enhance systemic immune responses, as indicated by increased interferon gene expression and changes in immune cell activation. Specifically, PD-1 expression increases on CD4+ T-cells, while CD38 and CD39 expression are reduced on CD8+ T cells, alongside an increase in monocytes. Poly-ICLC treatment amplifies the induction of interferon-induced genes in monocytes and T lymphocytes. Patients that exhibit higher interferon response gene expression demonstrate prolonged survival and delayed disease progression. These findings suggest that combining ATL-DC with poly-ICLC can induce a polarized interferon response in circulating monocytes and CD8+ T cells, which may represent an important blood biomarker for immunotherapy in this patient population.Trial Registration: ClinicalTrials.gov Identifier: NCT01204684.

Fig. 1. Combination of ATL-DC vaccine and TLR agonists results in a robust interferon pathway activation in the patient PBMCs.

A Timeline of PBMC acquisition and analysis using CyTOF and/or RNAseq. V = vaccine, D = Day. (Figure created with the help of BioRender). B Schematic of differential gene expression analysis performed on pre-treatment and post-treatment PBMCs of indicated treatment groups. Differentially expressed genes (DEGs) in TLR agonist-treated groups are compared against their changes in the placebo group to identify DEGs specific to the TLR-agonist groups. C, D Enriched gene set terms in Gene Ontology Biological Process (C) or ARCHS4 TF Coexp (D) datasets that significantly overlap with the union of DEGs from ATL-DC + poly-ICLC and ATL-DC + resiquimod groups (P values, FDR-adjusted, two-sided fisher exact test). E Differential gene expression (pre vs. post-treatment fold change, in log₂) of representative antigen presentation and IFN-related genes across treatment groups (P values, two-sided Welch t test). F Gene set enrichment score differences (pre vs. post-treatment, delta GSVA score) of representative IFN-related genesets across treatment groups (P values, two-sided Welch t test). G Heatmap of single-sample, gene set enrichment scores (GSVA) of type I and type II interferon genesets in pre-treatment, ATL-DC + placebo, ATL-DC+poly-ICLC and ATL-DC+resiquimod samples. The number of sample pairs analyzed in panels E and F are: ATL-DC+placebo, 5 pairs; ATL-DC+poly-ICLC, 8 pairs; ATL-DC+resiquimod, 8 pairs. The rectangular box in each boxplot represents the interquartile range (IQR), spanning from the first quartile (25^th percentile, bottom of box) to the third quartile (75th percentile top of box). Inside the box, the median (50th percentile) is marked. The whiskers (shown as lines extending from the box) extend to the largest and smallest non-outlier values within 1.5 times the IQR, while outliers lie beyond the whiskers.

Fig. 2. Single cell analysis reveals activation of systemic T cells and monocytes as a part of interferon pathway activation in all myeloid and lymphoid populations.

A A UMAP projection of the pre- and post-treatment PBMC sample pairs from twenty patients (placebo, n = 4 pairs; poly-ICLC, n = 9 pairs; resiquimod, n = 7 pairs). Clustering was performed with a random sampling of 5,000 cells from each patient. B Heatmap of normalized expression of all 27 cell markers within cell populations identified in the patient PBMCs. C, D Normalized expression of indicated markers in monocyte (C), or T cell populations (D) within the PBMC samples of patients from indicated treatment groups. P values, two-sided Wilcoxon rank sum test. E, UMAP projection of the PBMC-derived single cells (n = 99,590). The immune subset associated with each cluster is inferred based on the cluster’s differentially expressed transcripts. Canonical markers of known immune subsets are shown. F, G Heatmaps showing the union of recurrent DEGs computed between ATL-DC treated samples (combined with placebo, resiquimod or poly-ICLC) and pre-treatment samples in the myeloid populations (F) or lymphocyte populations (G). Shown in the heatmaps are the log fold change values of the DEGs in each cell population grouped by their treatment groups. The number of sample pairs analyzed in C and D are: ATL-DC+placebo, 4 pairs; ATL-DC+poly-ICLC, 9 pairs; ATL-DC+resiquimod, 7 pairs. The rectangular box in each boxplot represents the interquartile range (IQR), spanning from the first quartile (25th percentile, bottom of box) to the third quartile (75th percentile the top of box). Inside the box, the median (50th percentile) is marked. The whiskers (shown as lines extending from the box) extend to the largest and smallest non-outlier values within 1.5 times the IQR, while outliers lie beyond the whiskers.

Fig. 3. Combined ATL-DC vaccine and TLR agonist treatment show trends of improved tumor control and patient survival.

A–C Progression-free survival (PFS, top) and overall survival (OS, bottom) of all patients (A), patient subset with GBM (B), or grade III glioma (C) in indicated treatment groups. P values, log-rank test. D, E, Multivariate Cox proportional hazards analysis assessing the hazard ratios of tumor progression in TLR agonist treatment groups against placebo in all patients (D) or GBM subset (E) after adjusting for other clinical covariates (Tx_Group=treatment group, RecurNum=number of recurrences prior to ATL-DC treatment). In the forest plot, the squares are the hazard ratio (HR) estimates, the error bars are 95% confidence interval (CI) of the HR, the P value of each covariate is based on its Wald statistics, the P values are not adjusted. In D, the sample distribution in each covariate is Tx_Group: placebo=5, poly-ICLC = 9, resiquimod=9; Grade: III = 8, IV = 15; MGMT_methylation: True=8, False=15. In E, Tx_Group: placebo=4, poly-ICLC = 5, resiquimod=6. F, MR-computed volumes of post-treatment, recurrent tumors in indicated treatment groups. Treatment groups: Placebo (n = 5), Resiquimod (n = 8); Poly ICLC (n = 9). P values, unpaired, two-sided Wilcoxon rank sum test.

Fig. 4. IFN pathway activation is a positive predictor of survival after ATL-DC vaccine and TLR agonist therapy.

A Kaplan-Meier progression-free survival curves of all patients (left), GBM (center), and Grade III glioma subsets (right) stratified by their HALLMARK_INTERFERON_GAMMA_RESPONSE GSVA scores in their post-treatment PBMCs. P values, log-rank test. B, C Multivariate Cox proportional hazards analysis assessing hazard ratios of tumor progression in patients with high HALLMARK_INTERFERON_GAMMA_RESPONSE GSVA score in all patients (B) or GBM subset (C) after adjusting for other clinical covariates. In the forest plot, the squares are the hazard ratio (HR) estimates, the error bars are 95% confidence interval (CI) of the HR, the P value of each covariate is based on its Wald statistics, the P values are not adjusted. In B, the sample distribution in each covariate is GSVA score (post-Tx): <median=10, ≥median=11; Grade: III = 7, IV = 14; MGMT_methylation: True=7, False=14. In (C), GSVA score (post-Tx): <median=7, ≥median=7; MGMT_methylation: True=3, False=11.