Revealing the Role of “Precocious” Dendritic Cells in Inflammatory Response

In work published in Nature, scientists at the Broad Institute and Fluidigm Corporation used the C1TM Single-Cell Auto Prep System to prepare cells for single-cell sequencing - enabling the discovery of a subpopulation of “precocious” cells expressing antiviral genes earlier than the majority of dendritic cells exposed to the same antigen. Normally, the ability to detect the actions of these  precocious expresser” cells would be lost due to averaging across many millions of cells in bulk cell studies. 

The Nature paper also highlighted the role of cellular heterogeneity and its importance in cell-to-cell  communication during an immune response. In typical studies, cells are studied together in one environment, allowing the cells to communicate and signal to one another. However, the unique properties of Fluidigm’s C1 Single-Cell Auto Prep System allowed the researchers to isolate the cells from one another to identify the specific cells expressing antiviral genes. Because these cells were isolated, the non-expressing cells did not surmount a response, indicating that cell-to-cell communication plays a critical role in promoting immune response.

In addition to the discovery of a rare subpopulation of cells, this research represented a new benchmark for sheer volume of single-cell data. The 1,774 cells represented in this paper provide one of the largest single-cell genomic datasets published to date and one of the largest mRNA sequencing datasets available anywhere.

In order to identify and characterize these rare “precocious” cells, which make up only 1% of dendritic cell populations, researchers needed to scale up to a high number of cells. To do this, they first needed to solve two key problems: how to prepare single-cell libraries for thousands of cells, and how to sequence such large sample numbers affordably.

To prepare the huge number of single-cell libraries, the researchers relied on the C1 Single-Cell Auto Prep System, which had just been introduced to the marketplace at the time these experiments began. The C1 system’s microfluidic technology enabled the researchers to rapidly and reliably isolate, process, and profile individual cells for genomic analysis. During the study, the group discovered that they could achieve stable data with single cells at less than one million reads (compared to run rates of at least 5 to 10 million reads when conducting bulk mRNA sequencing). The ability to obtain reliable data faster greatly reduced the cost of running the experiment.

The paper, "Single-cell RNA-seq reveals dynamic paracrine control of cellular variation" can be accessed below.