Distinct mutational landscapes characterize melanomas metastatic to different anatomical sites.
Authors: Iddawela Mahesh Y. , Kaplan Benjamin G , Greenstein Ray , Zhao Peinan , Shackleton Mark J. , Huang Richard S.P. , Andrews Miles Cameron 
Published: June 2022

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Background: Despite revolutionary advances in systemic therapies for melanoma, many patients with metastatic disease have limited treatment options and some sites of disease remain particularly challenging to control, such as brain and liver metastases. We sought to define anatomical site-specific mutational profiles of melanoma metastases from which potentially novel personalized therapeutic opportunities may be developed. Methods: Targeted exome genomic profiling was performed via the FoundationOneCDx platform and known or likely pathogenic variants retained for analysis. PD-L1 immunohistochemistry was performed with the Dako 22C3 assay with PD-L1+ defined as tumor proportion score ≥1. Tumor mutational burden (TMB)-high was defined as TMB ≥10mut/Mb. UV signature was calculated using established algorithms. Aberrations in 23 genes potentially actionable in melanoma ( BARD1, BRAF, BRCA1/2, CDKN2A, DDX3X, FANCC, HRAS, IDH1, KIT, KRAS, MAP2K1, NF1, NRAS, PALB2, PIK3CA, PPP6C, PTEN, RAC1, RAD51C/D, RB1, TP53) were compared across metastatic sites including skin, lymph node, lung, liver, and brain. Results: A total of 4918 cutaneous-type melanoma tumors was evaluated, including 2854 skin lesions (primary/metastasis) and metastases from lymph nodes (n = 858), liver (n = 194), lung (n = 342), and brain (n = 200). The commonly mutated genes were CDKN2A (2220/4918, 45.1%), BRAF (2148/4918, 43.7%), NRAS(1347/4918, 27.4%), NF1 (1038/4918, 21.1%), TP53 (1234/4918, 25.1%) and PTEN (1038/4918, 13.5%). Compared with skin lesions, metastases to the lung were enriched for variants affecting NF1 (OR 2.57, p = 8.99e-13), TP53 (OR 1.65, p = 3.04e-04) and depleted in NRAS (OR 0.49, p = 9.00e-06) and BRAF (OR 0.70, p = 1.13e-02). Lung metastases were associated with higher prevalence of UV signatures, PD-L1 positivity and high TMB. PTEN variants were enriched in both brain (OR 3.00, p = 2.38e-08) and small intestine (OR3.46, p = 6.63e-3) metastases. Brain metastases were also enriched for CDKN2A variants (OR 1.56, p = 4.50e-02). Lymph node metastases had lower rates of UV signatures, NF1 variants, or high TMB, but were associated with PD-L1 positivity. Positional analysis of variants revealed that several, including NRAS, MAP2K1, KRAS, HRAS, IDH1, RAC1, GNA11 and GNAQ were highly restricted to hotspot loci, without definite variation by metastatic site. Conversely, variants affecting CDKN2A, PTEN, TP53 and NF1 were distributed widely across the gene, with high levels of non-hotspot mutations observed in skin lesions, suggesting that such non-hotspot subclones contribute less to distant metastatic potential and are lost during disease evolution. Conclusions: We observed distinct and organ site-specific mutational patterns in patients with metastatic melanoma. These data raise the possibility of metastatic phenotype-directed therapy to improve the personalization and outcomes of treatment for this disease.