Haematopoiesis in a Dish: From Tissue Dynamics to Molecular Mechanisms

In an average adult, over 2 million new blood cells are generated every second, to replace red and white blood cells lost through natural turnover and/or fighting infectious diseases. This constant replenishment is mediated by so-called stem and progenitor cells, which are long-lived, can divide to amplify their numbers, and give rise to over 10 different specialised types of blood cells. This so-called process of haematopoiesis needs to be finely balanced, because under- or overproduction of blood cells can cause severe diseases such as anaemia and leukaemia.
Research at the micro-scale of individual genes and proteins has identified many regulators of haematopoiesis. It is however difficult to extrapolate from this micro-scale to the functionality of the entire blood system. Research funders have recognised this bottleneck, and therefore now prioritise research efforts aiming to connect across scales, with the expectation of accelerating both basic research as well as the drug discovery process.
Here we propose to combine the latest technologies in cell culture with molecular profiling of thousands of single cells to generate a multi-scale model of blood formation, explicitly linking the micro and macro scales across time. The proposed research will develop a platform for testing the macro-scale consequences of gene mutations found in leukaemia patients, as well as the testing of new drug candidates. Moreover, establishing this platform for blood will provide a blueprint to set up analogous research efforts for other major organs and their associated diseases.

Haematopoiesis has long served as a paradigm stem cell system. However, most of our knowledge of HSC function is based on transplantation, and therefore assesses behaviour in response to severe external stress. We have shown (unpublished data) that recently reported culture protocols for HSC expansion recapitulate a differentiation landscape highly similar to native haematopoiesis. Here we propose to complement this "haematopoiesis in a dish" model with state-of-the-art single cell genomics barcoding technology to address the following objectives:
1) Generate clonally resolved self-renewal and differentiation maps for over 1000 primary HSCs
2) Construct a quantitative model of HSC self-renewal and differentiation at single cell resolution across molecular, cellular and tissue scales
3) Define the tissue-scale dynamics of perturbed HSC function including preleukaemic mutations
The proposed studies are closely aligned with the MRC priority area "Multimodal and Multiscale Research", as we will employ time-resolved measurements that connect across the molecular, cellular and tissue scales. This will allow us to answer important questions for HSC biology and beyond, including:
1) What is the repertoire of HSC behaviours derived from clonal tracking of over 1000 primary HSCs?
2) How can we use single cell genomics to efficiently connect abstract tissue models with single cell and molecular level information?
3) How do known preleukaemic mutations affect tissue-dynamics and stem cell properties at single cell resolution, and can we validate new regulators of self-renewal and differentiation flux?
The integrated approach proposed here provides a platform for investigating normal and pathological tissue dynamics by forming explicit connections between molecular processes and tissue scale consequences. This framework will be broadly applicable, for example to interrogate tissue-scale dynamics with organoid systems that are available for a broad range of human organs.