Abstract CN07-04: Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

A single tumor is composed of malignant cells in diverse genetic and epigenetic states, and this diversity presents a significant barrier for targeted therapies. Furthermore, diverse non-malignant cells, such as immune, fibroblasts and endothelial cells shape the tumor microenvironment and are emerging as important drug targets. However, the diversity of cellular states among malignant and non-malignant cells within any tumor remains poorly understood. To begin to address these challenges we applied single-cell RNA-seq to profile >3,000 single cells isolated from 16 fresh human melanomas, and characterized distinct cell types and cell states. We found that malignant cells within the same tumor display transcriptional heterogeneity associated with multiple biological processes. In particular, subpopulations of cells in treatment-naive tumors expressed a transcriptional program associated with resistance to RAF/MEK inhibition, and these were enriched in post-relapsed samples. Among several non-malignant cell types that were identified we focused on tumor-infiltrating T-cells and identified multiple profiles of exhaustion which differed among patients and could be linked to prior immunotherapies. Finally, we used our single cell–derived profiles of cell types within melanoma to deconvolve publicly available bulk tumor profiles and infer interactions between cells in the tumor microenvironment. This work demonstrates the capacity of single cell transcriptomics to offer new insights with implications for both targeted and immune therapies and will be broadly applicable to other tumor types. Citation Format: Itay Tirosh, Benjamin Izar, Sanjay M. Prakadan, Marc H. Wadsworth II, Daniel Treacy, John J. Trombetta, Diana Lu, Asaf Rotem, Christine Lian, George Murphy, Ofir Cohen, Eli van Allen, Monica Bertagnolli, Alex Genshaft, Travis K. Hughes, Carly G. K. Ziegler, Samuel W. Kazer, Aleth Gaillard, Kellie E. Kolb, Judit Valbuena1, Charles Yoon, Orit Rozenblatt-Rosen, Alex K. Shalek, Aviv Regev and Levi Garraway. Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr CN07-04.