Neoadjuvant cobimetinib and atezolizumab with or without vemurafenib for stage III melanoma: outcomes and the impact of the microbiome from the NeoACTIVATE trial

Abstract

Background: Neoadjuvant treatment has become standard for patients with high-risk operable stage III melanoma, but the optimal regimen is unknown. Targeted therapy approaches yield high pathological response rates, while immunotherapy regimens show favorable recurrence-free survival (RFS). NeoACTIVATE was designed to address whether a neoadjuvant combination of both targeted therapy and immunotherapy might leverage the benefits of each.

Methods: We tested neoadjuvant treatment with 12 weeks of vemurafenib, cobimetinib, and atezolizumab for patients with BRAF-mutated (BRAFm) melanoma (cohort A) and cobimetinib and atezolizumab for patients with BRAF-wild-type (BRAFwt) melanoma (cohort B), regimens which we have shown generate a substantial major pathological response. After therapeutic lymph node dissection, patients received 24 weeks of adjuvant atezolizumab. Here, we report survival outcomes and their association with biomarkers assayed among the gut microbiome and peripheral blood immune subsets.

Results: With 49 months median follow-up, the median RFS was not reached for cohort A and was 40.8 months for cohort B. At 24 months after operation, 2 of 14 cohort A patients and 4 of 13 cohort B patients had experienced distant relapse. Key findings from correlative analyses included diversity, taxonomic and functional metagenomic gut microbiome signals associated with distant metastasis-free survival at 2 years. Notably, we observed a strong correlation between low microbial arginine biosynthesis (required for T-cell activation and effector function) and early distant recurrence (p=0.0005), which correlated with taxonomic differential abundance findings. Peripheral blood immune monitoring revealed increased double-positive (CD4+CD8+) T cells in patients with early recurrence.

Conclusions: Neoadjuvant treatment with cobimetinib and atezolizumab±vemurafenib was associated with a low rate of distant metastasis in patients with high-risk stage III melanoma. Freedom from early distant metastasis was highly associated with taxonomic differences in gut microbiome structure and with functional pathway alterations known to modulate T cell immunity. Identification of predictive biomarkers will permit optimization of neoadjuvant therapy regimens for individual patients.

Trial registration number: NCT03554083.

Keywords: Immune Checkpoint Inhibitor; Immunotherapy; Neoadjuvant; Skin Cancer; Surgery.

Figure 1. CONSORT diagram. Study participation outcomes for all screened patients are shown. CONSORT, Consolidated Standards of Reporting Trials.

Figure 2. Survival outcomes. (A) Follow-up times, regional (blue triangle) and distant (red square) recurrence events, and mortality events (reverse arrowhead) for all subjects who completed a per-protocol operation and initiated adjuvant therapy. Yellow bars represent patients alive at data cut-off, gray bars represent patients who died from melanoma, and the blue bar represents a patient who died of an unrelated cause (sepsis) without melanoma recurrence. Open and closed circles denote patients with versus without a major pathological response (MPR) (≤10% viable tumor), respectively. (B) Kaplan-Meier curves were used to depict recurrence-free survival for each cohort. (C) The cumulative incidence of distant metastasis for each cohort.

Figure 3. Gut microbiome structure in association with early distant metastasis. (A) The phylum-level abundance profiles across subjects for patients with and without early distant metastasis. (B, C) Differences in α-diversity and β-diversity, respectively, by multiple measures. (D) Volcano plots identify the most significant differentially abundant taxa (x-axis: effect size in log2 fold change, y-axis: −log FDR-adjusted p value). The heatmap in (E) depicts the relative abundance of nine taxa differentially abundant between those with and without early distant metastasis at both time points. FDR, false discovery rate.

Figure 4. Gut microbiome functional pathways in association with early distant metastasis. (A) Volcano plot illustrates the most significantly differentially abundant pathways based on MaAsLin2. (B) Boxplots detail the relative expression of two key metabolic pathways with highly significant differences between patient groups.

Figure 5. Treatment-related T cell population changes. Time points indicated are baseline (prior to treatment), C1 (following one cycle of neoadjuvant therapy), C3 (following completion of neoadjuvant therapy), and C4 (after operation, prior to adjuvant therapy). (A) Individual and mean proportions of peripheral blood CD4+T cells, CD8+T cells, and CD4+CD8+ (DP) T cells as quantitated via mass cytometry by treatment cohort. Significance was defined as p<0.05 as measured by Wilcoxon’s signed rank test. (B) T cell populations by absence or presence of recurrence within 2 years, with median (middle line), IQR (box), and minimum and maximum (whiskers) indicated. Significance was determined using a linear model T-test, adjusting for treatment cohort and applying FDR correction. FDR, false discovery rate.