27P Gene Ontology Enrichment Analysis of Peripheral CD3+CD4+T Cells Predicts the Immune-Mediated Behavior of Melanoma

Melanoma, from its early stages, has a natural propensity to spread, that is regulated via constant immune counteraction. Unleashing adaptive immunity via ICIs has improved melanoma prognosis, but not all patients behave similarly under immunotherapy. Some relapse in the first few months of immunotherapy, while others experience durable disease control, even after discontinuation of ICIs. In order to identify any cellular/molecular signature in the peripheral blood that could predict primary immune escape, we examined 100 consecutive patients with stage III or IV melanoma who were scheduled to start ICIs. A multiparameter flow cytometry was used to detect differences in immune subpopulations, gating them by standard conjugated antibodies and mRNA was extracted after sorting of CD3+CD4+T-cells. A gene ontology (GO) enrichment analysis was performed to recognize which specific genes and key pathways are upregulated in stage III and IV melanoma and between long responders (>36 months) and early progressors(<6 months) to ICIs. Although circulating immune cells did not differ numerically in patients with stage III and IV melanoma as well as in responders and non-responders to ICIs, transcriptomic analysis of CD3+CD4+T-cells from 24 selected patients showed that 189 genes were upregulated in stage IV vs. 92 in stage III; while 101 genes were upregulated in early progressors vs. 47 in long responders. These differentially expressed genes (e.g., HLA-DRB5, BCL3, TRIM37, NCAM1, FGFR1) were functionally implicated in distinct cellular pathways that were particularly activated in these two settings. In fact, biological GO pathways of adaptive immunity, negative regulation of DNA-binding transcription factor activity, and lipid metabolism were significantly more upregulated in stage IV compared to stage III melanoma; while phosphorylation of CD3 and TCR chains, PD-1 and IFN signaling were more activated in early progressors compared to long responders to ICIs. Extrapolating the rules of intra-tumoral plasticity to the blood, specific epigenetically altered pathways in the peripheral CD3+CD4+T-cells may differentiate the melanoma evolution from stage III to IV and drive the resistance to ICIs.