Transcriptional profiling of macrophages in situ in metastatic melanoma reveals localization dependent phenotypes and function

Therapeutic interventions modulating immune function at the tumor site could improve outcomes in cancer. Here we analyzed metastatic melanoma; a tumor type highly responsive to T-cell based therapies, and found that the tumor-infiltrating T cells are localized closely to CD14+ monocytes/macrophages rather than to melanoma cells. Using customized immunofluorescence-guided laser capture micro-dissection, we analyzed transcriptome of CD3+ T cells, CD14+ monocytes/macrophages and melanoma cells in non-dissociated tissue. CD14+ cells localized in tumors beds displayed specific transcriptional signature distinct from CD14+ cells that were localized in tumor stroma. When applied to TCGA cohorts, the gene module of stromal macrophages distinguished patients with significantly prolonged survival in cutaneous melanoma and as well as other cancers including uveal melanoma, bladder urothelial carcinoma and lower grade glioma. This gene module contained CD14; Ly75, a gene linked with antigen capture and regulation of tolerance and immunity; and CD2; altogether a signature of monocyte-derived dendritic cells (DCs). Thus, stromal CD14+ cell signature represents a novel candidate biomarker and targeted reprogramming of stromal macrophages to acquire DC function might offer a therapeutic opportunity for metastatic cancer. We analyzed 64 samples in total, which include 16 iCD14+, 16 sCD14+, 16 cancer cells, 8 iCD3+ and 8 sCD3+ cell samples. The samples are from 8 different patients. For CD14+ and cancer cell samples, we have 2 samples per patient. For CD3+ samples, we have 1 sample per patient. **The raw data are deposited in dbGaP (phs002564) due to patient privacy concerns**