Tumour microenvironment heterogeneity in primary and metastatic paired melanoma samples and its correlation with genetic features and prognosis

Background: The prognostic impact of tumour microenvironment (TME) heterogeneity in primary cutaneous melanomas (CM) and paired distant metastases is unclear. Few studies have explored the impact of genetic features on TME immune cell distribution. This study assessed the prognostic impact of TME heterogeneity and investigated the correlation between genetic features and TME cell composition. Methods: Demographics, treatments and outcome of melanoma patients - with paired samples - from five Italian Melanoma Intergroup (IMI) centers were collected. TME immune phenotypes and cell distribution in FFPE whole tumour sections were analyzed using 9 biomarkers (CD3, CD4, CD8, CD20, CD68, CD163, PD-1, PD-L1, FOXP3), classifying samples as desert (D), excluded (E), or inflamed (I). Additionally, genomic pathways were assessed by next-generation sequencing in both primary and paired samples. Results: TME was evaluated in 221 samples from 91 patients.The distribution of immune phenotype (I vs E/D) of CD8 + cells (p < 0.0001), CD163 + cells (p < 0.0001), CD20 + cells (p = 0.0008), CD3 + cells (p < 0.0001), CD4 + cells (p < 0.0001), CD68 + cells (p < 0.0001), PD1 + cells (p = 0.00015) significantly differed between metastatic and primary melanomas. In primary tumors, BRAFV600 status did not correlate with immune phenotypes. However, in paired metastases, it was inversely associated with infiltration of CD8 +, CD3 +, CD68 +, and CD20 + cells. Patients in the CD8 + D/E TME group had significantly shorter median survival (21 months) compared to those with at least one inflamed (I) TME sample [(58 months); HR 2.35, 95 % CI 1.28–4.32]. Conclusions: Metastatic and primary melanomas show distinct immune phenotypes. Longitudinal TME assessment predicts overall survival.