Profiling Melanoma Heterogeneity Using Microwell RNA Cytometry

Unraveling heterogeneity of melanoma to discover new subpopulations of cells within the tumor has been fundamental to many advances in cancer biology, including identification of tumor initiating subsets and cells resisting immune-therapeutic approaches (Boiko et al., Nature 466:133-137, 2010; Civenni et al., Cancer Res 71:3098-3109, 2011; Schatton et al., Nature 451:345-349, 2008; Landsberg et al., Nature 490:412-416, 2012; Fang et al., Cancer Res 65:9328-9337, 2005). Traditionally, these discoveries were made possible due to the existence of well-characterized antibodies that enabled identification of cells homogeneous for the expression of specific cell surface antigen. However, further unwinding of heterogeneous cell populations into homogenous subsets in order to more precisely define their functional profile is limited by the availability of highly specific antibodies. Here we describe a technique capable of identifying homogeneous cell populations in heterogeneous sample based on the transcriptome profile. This approach enables semiquantitative measurement of gene expressions in hundreds to thousands of single cells in one step, paving the way to identify homogenous subpopulations of melanoma cells based on gene transcripts, independent of the availability of antibodies.