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Single cell technology – an eye for detail

New technology is helping scientists study the secrets of single cells in more detail than ever before. Dr Roy Drissen at the  MRC Weatherall Institute for Molecular Medicine tells Sylvie Kruiniger how single cell technology has helped them discover a previously unknown stage in blood cell development which may have implications for the future of leukaemia treatment.

Dr Roy Drissen holds a microfluidic chip. Photo: martinphelps.com

 

“Before Galileo invented the telescope, we could just see Jupiter. With the telescope, we saw that Jupiter had moons. That’s what single cell technology is doing for biology: where we used to think there was only one type of cell, we can now see several.”

Professor Claus Nerlov

That’s how the group leader Professor Claus Nerlov put it. Using single cell technology, the team has rewritten the step-by-step process of how mature blood cells develop from blood progenitor cells found in bone marrow.

Progenitor cells, like stem cells, have the potential to develop into several different types of mature cell. Precisely mapping the different stages of this process could help us understand how different blood cell diseases develop, like leukaemia, ,and eventually lead to the development of better treatments.

A million to one

Before single cell technology arrived, researchers looked at populations of cells that often numbered in their thousands or millions. This meant that their characteristics had to be defined statistically by looking at the whole group and calculating their average behaviour. These profiles could hide that a sample contained distinct populations that may behave differently.

Dr Roy Drissen

“Single cell technology allows you to look at the genes being expressed by each individual cell, and that allows you to observe whether the population you’re studying is all the same, or if it contains different types of cell”, explains lead author, Dr Roy Drissen.

And single cell technology is moving fast – chips used in this study allowed for 96 cells to be individually processed at once, but researchers can now already look at 10,000 individual cells simultaneously. This means you can get more data faster, which could help us to deepen our understanding of processes within cells even more quickly.

Single cell tech in action

The group used a fluorescence-activated cell sorting machine, known as FACS, to sort a specific cell population from mouse bone marrow that was thought to contain only one type of cell. This sample could then be loaded into the microfluidic chip, and inserted into the single cell, DNA-copying machine, the Fluidigm C1. The chip allows for 96 different cell samples to be individually processed at the same time.

Close up image of the microfluidic chip that goes into the Fluidigm machine. The large holes around the edge allow the cells and reagents to be loaded into the chip by the user. These are then pumped along the channels to the microscopic capture chambers around the centre of the chip.

 

The Fluidigm machine moves the cells into separate wells in the microfluidic chip, and circulates a mild detergent through its channels to break down the cells and release their genetic material. The machine then makes multiple copies of each cell’s genetic data before ejecting the chip – with each cell carefully locked into its own chamber , along with its genetic copies. After this, the DNA from each cell type can be sequenced to reveal their unique genetic code.

The single cell technology has meant that DNA sequencing machines can work with the original cell, plus the numerous identical copies of its DNA, providing a large amount of data for analysis. In this case, when the team sequenced their cell sample, Roy found that the sample contained two different types of cell. They then discovered that these two different progenitor cell types each produced a different set of mature blood cells.

Focusing in on blood development

Claus’ group used this technology to look at a process called haematopoiesis. Haematopoiesis describes the stages that progenitor cells go through to become mature blood cells with specific functions.

“Blood consists of at least 10 different mature cell types, and they all have specific functions,” explains Roy. “Each has a limited lifespan – they die off after a couple of weeks or months. Haematopoiesis is the process where new mature cells are constantly produced from blood stem cells in the bone marrow.”

Where cancers begin

“If you look at most, if not all, blood cancers, DNA mutations in early progenitors make a cell stop differentiating. Instead of making a mature blood cell, it stays at the progenitor stage. You end up with an immature cell that just keeps multiplying.

“The blood cells we studied were thought to develop from one type of progenitor. However, when we used the single cell approach we were able to identify two different types of progenitor cell and then show that each progenitor produced a different set of mature blood cells.”

So this new understanding of the point at which different types of cell develop starts to fill a large hole in our understanding of blood and blood cancers. Currently, the main treatment for leukaemia is the drastic measure of a bone marrow transplant to replace the entire stem cell population, removing the few cells that are malfunctioning – but also destroying all the healthy stem cells at the same time. Being able to identify these problem cells earlier on and with greater precision opens up the potential of developing more targeted treatments.

A good place to start

But given that all mature human cell types develop from stem cells, and many things can go wrong in their development, why did the team chose to focus specifically on haematopoiesis? “It is a system that we already understand well,” explains Professor Adam Mead. “There were a number of tools available that complemented the new technological advances in single cell technology. This meant we could take our discoveries made using single cell technology and rapidly apply them to functional assays and understand what they mean.

Professor Adam Mead

“The idea of the Clinical Research Infrastructure initiative was to build up single cell infrastructure in Oxford.  Haematopoiesis is just the beginning; there is more work to be done for sure but in building up that knowledge we will be better equipped to explore other areas.”

According to Director of the MRC Weatherall Institute of Molecular Medicine and of the MRC Molecular Haematology Unit Professor Doug Higgs, this vast amount of single cell level data will revolutionise the field:

Professor Doug Higgs

“We will have much more data and will be able to make better analyses, as well as integrate different datasets to build a more comprehensive picture. To aid the analysis of these datasets that are increasing in size and complexity, the WIMM is using some of the funds from the MRC Clinical Research Infrastructure grant to build a new WIMM Centre for Computational Biology. We’re currently recruiting for new staff to help build a world-class facility and power new discoveries in the single cell field.”

Read the paper in Nature Immunology

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