Gene Expression: A Snapshot of Stem Cell Development

The power of single-cell genomics is demonstrated in new research from the Wellcome Genome Campus, revealing how it could help scientists understand early development of cells. The study found new genes involved in stem cell regulatory networks and new subpopulations of cells, giving insights into stem cell pluripotency – the ability to develop into almost all different types of cell. The researchers also developed new resources for the stem-cell community, which will help interpret future investigations.

Stem cells exist in a 'ground' state before something triggers them to develop into functional cells such as liver, heart or blood cells. What sparks that change has a lot to do with how, when and in what order the genes inside that cell are expressed, or turned on and off. Characterising the gene expression at play in stem cells is essential to understanding the fundamental biology of health and disease. It can also help in detecting genetic factors that figure into a person's response to a medicine.

Researchers at the Wellcome Trust Sanger Institute and European Bioinformatics Institute (EMBL-EBI) used single-cell RNA sequencing technology to study the expression of thousands of genes in around 700 mouse Embryonic Stem Cells (mESCs), and found there is a signature 'gene expression mix' that characterises different cell populations. They also found this mix determines the length of the cell cycle. In other words, heterogeneity in gene expression across cells underpins cellular behaviour.

"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, a first author from the Sanger Institute and EMBL-EBI."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 helps researchers see what makes all the cells in our bodies take on different shapes, predict what they might do and explore the many elements that contribute to their fates. In this study, the team developed novel approaches to characterise how gene expression levels vary, stem cell by stem cell, in 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 uncovered a rare subpopulation of cells that express a couple of marker genes also expressed by cells at the two-cell stage of the embryo, which are able to develop into any cell type ('totipotent'). While the rare mESCs identified in this study only share some molecular features of the two-cell system, they will provide valuable resources to the study of early development.