In-depth plasma proteomics reveals increase in circulating PD-1 during anti-PD-1 immunotherapy in patients with metastatic cutaneous melanoma

Abstract

BackgroundImmune checkpoint inhibitors (ICIs) have significantly improved the outcome in metastatic cutaneous melanoma (CM). However, therapy response is limited to subgroups of patients and clinically useful predictive biomarkers are lacking.MethodsTo discover treatment-related systemic changes in plasma and potential biomarkers associated with treatment outcome, we analyzed serial plasma samples from 24 patients with metastatic CM, collected before and during ICI treatment, with mass-spectrometry-based global proteomics (high-resolution isoelectric focusing liquid chromatography–mass spectrometry (HiRIEF LC-MS/MS)) and targeted proteomics with proximity extension assays (PEAs). In addition, we analyzed plasma proteomes of 24 patients with metastatic CM treated with mitogen-activated protein kinase inhibitors (MAPKis), to pinpoint changes in protein plasma levels specific to the ICI treatment. To detect plasma proteins associated with treatment response, we performed stratified analyses in anti-programmed cell death protein 1 (anti-PD-1) responders and non-responders. In addition, we analyzed the association between protein plasma levels and progression-free survival (PFS) by Cox proportional hazards models.ResultsUnbiased HiRIEF LC-MS/MS-based proteomics showed plasma levels’ alterations related to anti-PD-1 treatment in 80 out of 1160 quantified proteins. Circulating PD-1 had the highest increase during anti-PD-1 treatment (log2-FC=2.03, p=0.0008) and in anti-PD-1 responders (log2-FC=2.09, p=0.005), but did not change in the MAPKis cohort. Targeted, antibody-based proteomics by PEA confirmed this observation. Anti-PD-1 responders had an increase in plasma proteins involved in T-cell response, neutrophil degranulation, inflammation, cell adhesion, and immune suppression. Furthermore, we discovered new associations between plasma proteins (eg, interleukin 6, interleukin 10, proline-rich acidic protein 1, desmocollin 3, C-C motif chemokine ligands 2, 3 and 4, vascular endothelial growth factor A) and PFS, which may serve as predictive biomarkers.ConclusionsWe detected an increase in circulating PD-1 during anti-PD-1 treatment, as well as diverse immune plasma proteomic signatures in anti-PD-1 responders. This study demonstrates the potential of plasma proteomics as a liquid biopsy method and in discovery of putative predictive biomarkers for anti-PD-1 treatment in metastatic CM.

Soluble immune checkpoints and T-cell subsets in blood as biomarkers for resistance to immunotherapy in melanoma patients

“…A similar finding of increased sPD1 concentrations upon anti-PD1 treatment was reported recently while profiling plasma proteomics in cutaneous melanoma patients. 28 Although the sources of sPD1 in the blood are still unknown, we found a significant negative correlation between the serum concentrations of sPD1 and PD1 expression on T cell subsets. Interestingly, we also noticed a positive correlation between sPD1 and the frequencies of LAG3 and TIM3 positive T cells analyzed at the same time points.…”

Precision Medicine and Melanoma: Multi-Omics Approaches to Monitoring the Immunotherapy Response

“…The plasma proteome is profoundly dynamic and fluctuates under the influence of several factors, such as drug treatments. The use of high-resolution isoelectric focusing liquid chromatography-mass spectrometry (HiRIEF LC-MS/MS) and antibody-based targeted proteomics with proximity extension assays (PEAs) has allowed to analyze the protein structure of blood samples from metastatic melanoma patients treated with immunotherapy and to identify plasma biomarkers [61]. For this aim, the authors of the study have used the pre-and post-treatment plasma with ICIs of 46 melanoma patients (stage IV) and have compared it with the samples of patients undergoing target therapy.…”

“…The most striking result of this screening was represented by the increase in circulating levels of PD1 only in response to anti-PD1 treatment, and in patients responding to this therapy, compared to the control group with targeted therapy. The plasmatic PD1 increase provides endogenous PDL1 inhibition in parallel with therapy-induced inhibition [61].…”

Putting Proteomics Into Immunotherapy for Glioblastoma

“…With the advantage of proteomics, the biotargets for immunotherapy and the mechanisms could be much more direct and easier to be discovered than the nucleic method. Like research in melanoma, the proteomic strategy has been a valuable platform for discovering novel biomarkers ( 63 ). Besides, the proteomics from different cells would be quite different which is even suitable for the research of heterogenetic characteristics.…”