CHICAGO —Single-cell RNA-sequencing can resolve the heterogeneity of both malignant and non-malignant tumor components, according to findings presented at the 2016 American Society of Clinical Oncology (ASCO) Annual Meeting.1

Current profiling technologies provide only average signals that do not reflect the intrinsic genetic phenotypic variability in heterogeneity of malignant and non-malignant cells, explained Benjamin Izar, MD, PhD, of the Broad/DFCI Center for Cancer Precision Medicine in Boston, Massachusetts. Researchers sought to apply single-cell RNA-sequencing to 4645 single cells, profiling malignant, immune, and stromal cells isolated from 19 newly-procured melanomas.

Results showed all tumors harbored dormant cells that are intrinsically resistant to RAF/MEK inhibition regardless of their bulk-RNA signature. This observation was confirmed in 6 additional pairs of pre-treatment and post-relapse biopsies of patients with melanoma who developed resistance to RAF/MEK inhibition, as well as by flow cytometry and quantitative single-cell immunofluorescence of 18 established human melanoma cell lines.

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Researchers also identified distinct patterns of the tumor microenvironment. These patters were associated with the resistant AXL-high signature, suggesting their interactions with tumor ecosystems are drivers of resistance.

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Analysis of CD8+ T cells demonstrated a strong co-expression of PD1, CTLA-4, and TIM-3 with cytotoxicity markers, such as performin 1 and granzyme B. This co-expression indicates a critical correlation of activation and exhaustion cell states. By controlling for cytotoxic T cell markers, the investigators developed a core gene signature comprising 28 genes that defined the salient exhaustion function of T cells.

“T cell profiles and salient exhaustion signature may be biomarkers for immunotherapies,” Dr Izar said.                          


  1. Izar B, Tirosh I, Prakadan S, Wadsworth M, Rotem A,  Trombetta J, et al. Implementation of single-cell genomics as a translational tool in patients with metastatic melanoma. J Clin Oncol. 2016; 34 (suppl; abstr 11503).