Journal Article

An experimentally validated network of nine haematopoietic transcription factors reveals mechanisms of cell state stability

Ouwehand, Willem H, Nürnberg, Sylvia T, Antoniou, Stella, Göttgens, Berthold, Wilson, Nicola K, Basilico, Silvia, Bonzanni, Nicola, Riepsaame, Joey, Hannah, Rebecca L, de Bruijn, Marella FTR, Calero-Nieto, Fernando J, Schütte, Judith, Kinston, Sarah J, Jarratt, Andrew, Moignard, Victoria, Wang, Huange, Chan, Mun Chiang

2016

Overview

Transcription factor (TF) networks determine cell-type identity by establishing and maintaining lineage-specific expression profiles, yet reconstruction of mammalian regulatory network models has been hampered by a lack of comprehensive functional validation of regulatory interactions. Here, we report comprehensive ChIP-Seq, transgenic and reporter gene experimental data that have allowed us to construct an experimentally validated regulatory network model for haematopoietic stem/progenitor cells (HSPCs). Model simulation coupled with subsequent experimental validation using single cell expression profiling revealed potential mechanisms for cell state stabilisation, and also how a leukaemogenic TF fusion protein perturbs key HSPC regulators. The approach presented here should help to improve our understanding of both normal physiological and disease processes. Blood stem cells and blood progenitor cells replenish a person’s entire blood system throughout their life and are crucial for survival. The stem cells have the potential to become any type of blood cell – including white blood cells and red blood cells – while the progenitor cells are slightly more restricted in the types of blood cell they can become. It is important to understand how the balance of cell types is maintained because, in cancers of the blood (also known as leukaemias), this organisation is lost and some cells proliferate abnormally. Almost all of a person’s cells will contain the same genetic information, but different cell types arise when different genes are switched on or off. The genes encoding proteins called transcription factors are particularly important because the proteins can control – either by activating or repressing – many other genes. Importantly, some of these genes will encode other transcription factors, meaning that these proteins essentially work together in networks. Schütte et al. have now combined extensive biochemical experiments with computational modelling to study some of the transcription factors that define blood stem cells and blood progenitor cells in mice. Firstly, nine transcription factors, which were already known to be important in blood stem cells, were thoroughly studied in mouse cells that could be grown in the laboratory. These experiments provided an overall view of which other genes these transcription factors control. Additional targeted investigations of the nine transcription factors then revealed how these proteins act in combination to activate or repress their respective activities. With this information, Schütte et al. built a computational model, which accurately reproduced how real mouse blood stem and progenitor cells behave when, for example, a transcription factor is deleted. Furthermore, the model could also predict what happens in single cells if the amounts of the transcription factors change. Lastly, Schütte et al. studied a common type of leukaemia. The model showed that the mutations that occur in this cancer change the finely tuned balance of the nine transcription factors; this may explain why leukaemia cells behave abnormally. In future these models could be extended to more transcription factors and other cell types and cancers.

• Publisher: eLife Science Publications, Ltd,eLife Sciences Publications Ltd,eLife Sciences Publications, Ltd
• Subject: Animals / Binding sites / Cell Line / Chromatin Immunoprecipitation / Computational and Systems Biology / Computer Simulation / Fusion protein / Gene expression / Gene Expression Profiling / Gene loci / Gene Regulatory Networks / Genes and Chromosomes / Genetic aspects / Genomes / Hematology / Hematopoiesis / Hematopoietic stem cells / Hematopoietic Stem Cells - physiology / Medical research / Mice / Models, Theoretical / Normal distribution / Observations / Ordinary differential equations / Physiological aspects / regulatory network / Reporter gene / Rodents / Sequence Analysis, DNA / single cell / Stem cells / Transcription factors / Transcription Factors - metabolism