Cell Stem Cell: Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation

Recently, a new study of Wellcome Genome Campus demonstrates the power of single-cell genomics, and reveals how it can help scientists understand the early development of cells. The study found a new gene involved in the regulation of stem cells in the network, as well as new cell subsets, giving researchers an insight into pluripotent stem cells - the ability to become almost all the different types of cells. Stem cell researchers have also developed a new community resource that will help explain the future investigation. Related research results were published in a recent Cell Stem Cell.

Before stem cells are triggered to become functional cells (such as liver, heart or blood cells), they exist in a kind of "ground state." What triggered this change has a great relationship with how, when, and in what order the genes inside that cell are expressed, or turned on and off. Characterization of the gene expression at play in stem cells is essential for understanding the basic biology of health and disease.

Researchers of the Wellcome Trust Sanger Institute and EMBL's European Bioinformatics Institute (EMBL-EBI) studied the expression of thousands of genes in about 700 mouse embryonic stem cells (mESCs) with usage of single-cell RNA sequencing technology, and found a label "gene expression mix" that can characterize different cell populations. They also found that the mix determines the length of the cell cycle, that is to say, heterogeneity in gene expression across cells supports cellular behavior.

"You can take a kind of snapshot of this very dynamic process of gene expression, and infer a lot of information from it," explains Ola Kolodziejczk of EMBL-EBI and the Sanger Institute. "It's a bit like taking a picture of a crowd in Times Square at New Year's Eve from above and ordering all of the individuals by age to get a sense of their life cycle, or grouping them by clothing style to infer which party they will go onto next."

Single-cell RNA sequencing can help researchers see what makes all the cells in our body have different shapes, predict what they will do, and explore many factors contributed to their fate. In this study, the research team developed a new method to characterize how stem cell gene expression levels are changed stem cell by stem cell, between three different states.

"One really exciting thing was that we identified new genes involved in the stem-cell regulatory network, and validated our findings using the CRISPR technology," says Jong Kyoung Kim of EMBL-EBI. "That brings us closer to inferring how the whole network is put together -- and that in turn can give us insights into what keeps stem cells in a ground state and what triggers them to change."

By dissecting the noisy mix of gene expression cell by cell, the researchers discovered a rare subpopulation of cells which express a pair of marker gene (which is also the expression of the two-cell stage embryo cells). And the rare mESCs this study identified have only some of the molecular characteristics of two cellular systems, which will provide a valuable resource for early research and development.

"Our study really shows the power of single-cell transcriptomics, how it can reveal biologically relevant heterogeneity in expression that is often masked by traditional methods," says Sarah Teichmann, group leader at both EMBL-EBI and the Sanger Institute. "It adds a whole new dimension to how we find relationships between cultured cells and natural development, which is making a big difference in genomics research."