Tyrosine-protein kinase SYK-related gene signature in baseline immune cells associated with adjuvant immunotherapy-induced immune-related adverse events in melanoma.

Abstract

Immune checkpoint inhibition (ICI) shows benefits in adjuvant (AT) and neoadjuvant (NAT) melanoma treatments. However, ICI frequently induces severe immune-related adverse events (irAEs). Unlike metastatic disease, where irAEs are a clinical trade-off for treatment that improves survival, the toxicity burden from ICI in AT is a substantial clinical problem urging for irAE-predictive biomarkers. We assessed post-surgical, pre-ICI treatment peripheral CD4+ and CD8+ T cells from clinical trial patients (CheckMate-915) treated with AT nivolumab (NIVO, n=130) or ipilimumab/nivolumab (COMBO, n=82). Performing RNA-seq differential gene expression analysis we tested baseline differences associated with severe (grade 3-5) irAEs and constructed an irAE-predictive model using LASSO-regularized logistic regression. The analysis of predicted protein-protein interactions among differentially expressed genes (DEGs) in peripheral CD4+ cells revealed significant enrichment of the spleen tyrosine kinase (SYK) pathway, associated with severe irAEs in COMBO-treated patients. This gene-expression signature predicted severe-irAE COMBO patients (chi-square p-value=0.001) with 73% accuracy and was independent of disease recurrence (p=0.79). The irAE-predictive model incorporating this gene-expression signature demonstrated 82% accuracy (chi-square p-value=8.91E-06). We identified baseline gene-expression differences in key immune pathways of peripheral blood T cells from COMBO-treated patients with grade 3-5 irAEs, and defined a SYK-related gene signature correctly identifying ~60% of COMBO-treated patients with grade 3-5 irAE. This finding aligns with our previous work linking anti-CTLA-4 irAEs with a germline variant associated with high SYK expression. This gene signature may serve as a baseline biomarker of severe grade 3-5 irAE risk, which is especially important in AT.