Melanoma study with RNA-Seq data on dbGaP (8 participants)

phs002564 — Transcriptional Profiling of Macrophages In Situ in Metastatic Melanoma    Reveals Localization-Dependent Phenotypes and Function

<p>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 novel immunofluorescence-guided laser capture micro-dissection, we analyzed transcriptomes of CD3+ T cells, CD14+ monocytes/macrophages and melanoma cells in non-dissociated tissue. CD14+ cells localized in tumors beds displayed specific transcriptional signatures distinct from CD14+ cells that were localized in tumor stroma.</p><p></p><div>The 8 distinct metastatic melanoma samples are from the Cooperative Human Tissue Network (CHTN). 64 RNA-seq files are available from 16 intraCD14+, 16 stromaCD14+, 16 cancer cells, 8 intraCD3+ and 8 stromaCD3+ cells. 2 LCM harvests were completed for the CD14+ and cancer cells on two sections of the samples. One harvest was done for the CD3+ samples.</div><div><br></div><div>The processed data (TPM/raw counts tables) are available on GEO under <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE180124">GSE180124</a>. </div><p></p>