Analysis of Broad Melanoma Proteomic Dataset Associates Prior Treatments with Response to Immunotherapy.

Introduction: Melanoma is one of the most immunogenic tumors, due to its high mutational burden. The most prevalent mutation in melanoma is an activating mutation in BRAF, which can be targeted therapeutically by selective kinase inhibitors. Despite the high initial response to BRAF inhibitors, its durability is limited due to acquired resistance. The combination of tumor aggressiveness, high mortality, BRAF inhibitor resistance and high immunogenicity made melanoma a prime target for immunotherapy. Despite the great success of immunotherapy, still only a subset of patients responds to these treatments. Aiming to understand resistance mechanisms, we performed a proteomic analysis of responders and non-responders to immunotherapy, in order to associate the proteomic profiles with patient clinical parameters and BRAF status.

Materials and methods: The proteomic data is based on a former dataset of formalin-fixed paraffin-embedded (FFPE) tissues from 185 metastatic melanoma patients, before treatment with tumor infiltrating lymphocytes (TIL), anti-CTLA4 or anti-PD1. Quantitative proteomic analysis was performed by high-resolution LC-MS/MS analysis followed by computational analysis.

Results and discussion: Based on the clinical data, we examined the differences between tumor samples from patients with mutant BRAF which previously received treatment with RAF/MEK inhibitors, in comparison to samples with mutant BRAF from patients that did not receive this treatment and Wild type (WT) samples. We saw that the BRAF mutant untreated group has a significantly higher response to immunotherapy compared to WT or to prior treated samples. In sequential proteomic analysis, we found a significant elevation in mitochondria-related annotations, such as OXPHOS and TCA cycle pathways in the treated group. In the untreated group, we saw higher levels of proteins involved in cell movement and ECM, and in proteins connected to the innate and adaptive immune system.

Conclusion: Altogether, our results revealed an association between prior treatments and immunotherapy response and suggests mechanisms of treatment resistance.