Single-cell RNA-seq to Decipher Complex Immune Responses
Roberto Spreafico, Kurt Wong, Rathi Ryan, Ariel Schwartz and Sean Stevens
Synthetic Genomics Inc, 11149 North Torrey Pines Rd, La Jolla, CA, 92037
Since its inception, transcriptome-wide RNA sequencing (RNA-seq) has become the tool of choice to measure and understand gene expression programs, quickly replacing microarrays thanks to its superior technical features, from wider dynamic range to unbiased detection of novel transcripts. However, bulk RNA-seq quantifies average gene expression levels in a cell population. In certain fields, such as developmental, neuro- and immuno-biology, the heterogeneity of cell populations is typically high, limiting the insight provided by average measurements. To understand heterogeneous biological systems, distributions (rather than averages) of gene expression levels across a population of cells are needed, and can be obtained using single-cell techniques.
With its roots in the 1970s, flow cytometry is perhaps the most mature single-cell technology, with a throughput of thousands of cells analyzed per minute. However, it relies on high-quality antibodies, and multiplexing is limited to 14-18 gene products. Mass cytometry has increased multiplexing capabilities to 50+ gene products, but this remains far from getting a full picture of the entire set of mRNA or protein abundances in a cell. The recent introduction of single-cell RNA-seq (scRNA-seq), and particularly of its most promising implementation, Drop-seq, holds promise to disentangle the complexity of whole transcriptomes in thousands of cells.
Using the 10x Genomics platform, we are developing strategies to decipher the heterogeneity of immune responses. In pilot experiments, we focused on responses of NK cells, lymphocytes belonging to the innate arm of the immune system. Due to their stochastic expression of activating and inhibitory receptors, NK cells are extremely diverse, making them well suited to understand advantages and limitations of scRNA-seq over bulk techniques. Novel insights in NK cell responses would bring benefit to a wide range of human diseases and conditions, from cancer through transplantation to autoimmunity.