140 Illumina probes corresponding to138 unique genes differentially expressed in regressing (R) vs. progressing (P) cutaneous metastases based on whole genome microarray analysis (fold change magnitude {greater than or equal to}1.7, p value {less than or equal to}0.05 )
Funding
Melanoma Research Alliance
Bloomberg~Kimmel Institute
Barney Family Foundation
Melanoma of Delaware
Laverna Hahn Charitable Trust
National Cancer Institute
Memorial Sloan-Kettering Cancer Center
Starr Cancer Consortium
Pershing Square Sohn Cancer Research Foundation
Immunogenomics and Precision Oncology Platform
Center for Molecular Oncology
ARTICLE ABSTRACT
Purpose: To explore factors associated with response and resistance to anti–PD-1 therapy, we analyzed multiple disease sites at autopsy in a patient with widely metastatic melanoma who had a heterogeneous response.Materials and Methods: Twenty-six melanoma specimens (four premortem, 22 postmortem) were subjected to whole exome sequencing. Candidate immunologic markers and gene expression were assessed in 10 cutaneous metastases showing response or progression during therapy.Results: The melanoma was driven by biallelic inactivation of NF1. All lesions had highly concordant mutational profiles and copy number alterations, indicating linear clonal evolution. Expression of candidate immunologic markers was similar in responding and progressing lesions. However, progressing cutaneous metastases were associated with overexpression of genes associated with extracellular matrix and neutrophil function.Conclusions: Although mutational and immunologic differences have been proposed as the primary determinants of heterogeneous response/resistance to targeted therapies and immunotherapies, respectively, differential lesional gene expression profiles may also dictate anti–PD-1 outcomes. Clin Cancer Res; 23(12); 3168–80. ©2017 AACR.See related commentary by Wilmott et al., p. 2921
