Background Immune checkpoint inhibitors (ICI) have greatly improved the treatment options for patients with metastatic melanoma. Yet, a large percentage of melanoma patients do not respond to ICIs, there is a need for biomarkers that can predict patients‘ clinical benefit thereby identifying the patient population most likely to respond. Here, we apply unbiased discovery proteomics to deeply characterize global tumor proteomes and associate proteins and pathways at baseline with clinical response to anti-PD-1 immunotherapy.

Methods Unbiased, data-independent acquisition (DIA) mass spectrometry was used to analyze Formalin Fixed Paraffin Embedded (FFPE) tumor tissue from subjects with stage IIIc-IV melanoma which were resected prior to initiation of first-line anti-PD-1 therapy. The selected samples represent two distinct clinical subgroups; those who received clinical benefit (CR or PR by RECIST criteria or OS >1 year with SD by RECIST criteria, n = 13), and those with no clinical benefit (PD by RECIST criteria or OS <1 year with SD by RECIST criteria n = 9). Previously, the sample cohort had been analyzed by a 2-hour LC-MS/MS gradient setup operated in DIA mode. In this study, all samples were analysed with a longer gradient of 4-hours which enabled the quantification of 1’000 more proteins and enabled an updated analysis with a deeper level of characterization.

Results 8’548 proteins were quantified across all samples, with 7’416 quantified on average per sample. Univariate statistical testing between groups identified 285 proteins that were significantly regulated in subjects who received clinical benefit. Through partial least squares discriminant analysis (PLS-DA) a set of 25 proteins was identified that describe the variance between the two sample groups. Ganglioside GM2 activator (GM2A) and other members of its interaction network such as HEXB, HRNR and CPPED1 were identified to be upregulated in the non-responder group.

Conclusions Global profiling of the baseline tumor proteome provides a unique characterization of melanoma tumor biology. A signature of 25 protein markers was identified as a driver of separation between responder and non-responder patients to PD-1 blockade. Among the protein markers, GM2A and its interactors, were previously shown to perturb T cell function, which might explain their enrichment in the non-responder group and provide an attractive target for improving patient response to immunotherapy.