The story of ageing, told by a single blood cell

What’s really important with single-cell sequencing is that it gives you a different perspective. We look at tissues and biological systems from the individual cell’s point of view. That helps to find novelties, really, because we have a much higher resolution within a tissue - blood, for example - or a community of microbes.

We can define the identity of each individual cell. We can look at development, track how all the stem cells in a tissue will differentiate, observe how each cell coordinates with its neighbours to make the tissue function, and learn how the cell knows its own role in this grand design. Importantly, we can investigate how this coordination process changes as we age, or in response to disease.

It really shifts the point of view, I would say, from which we look at the mechanisms that drive all biological processes. We can study development and ageing as well as diseases like cancer, for example. It's a really wide approach.

It goes down to the very key biological questions that can be applied to any biological system, from bacteria to plants and humans.

We are trying to understand how blood stem cells differentiate. What mechanisms are driving the differentiation process, and are some stem cells more primed to become a specific type of mature blood cell? Are they more prone, early on, to become one of the different cell types at the end?

I'm looking at the effect of ageing - what happens to these stem cells in the blood of an older organism.

Stem cells have the unique abilities of generating their daughter stem cells (self-renewal) as well as mature cell types (differentiation). Mature blood cells are predominantly short lived and adult hematopoietic stem cells guarantee replenishment of the mature cells during an organism’s lifespan. The delicate balance between self-renewal and differentiation properly regulates stem cell number and guarantees tissues homeostasis, function and repair. When we age this delicate balance seems to be impaired.

It's quite well known that with ageing there is a loss of function of hematopoietic stem cells, but they increase in number. So, we have more, they seem activated, we see an expansion of the stem cell, yet they lose their ability to produce a balance of multiple types of blood cells. We don't really know the mechanism driving that.

We also don't know how different stem cells actually age differently, or whether there’s a shared mechanism between all of them, and how this translates into loss of function. That's one of the questions I’m trying to answer.

Yes, definitely, because we don't really know the molecular mechanisms driving ageing, especially in the haematopoietic (or blood) stem cell. If we can find what is driving ageing, then potentially we can target that. As a very long-term application, we could be talking about some anti-ageing therapies.

But even just looking at the system and seeing what happens is really useful. Many blood system diseases are age-related. The system is ageing and the mutations are changing accordingly. Eventually this initiates disease.

If you understand how these processes work, you can look at age-related diseases from a different perspective and see if you can act at a very early stage - before the diseases are occurring - to prevent them from developing in the future.

I was previously working on next generation sequencing. I always liked molecular biology, especially genomics, and when next generation sequencing came along it was really interesting to learn the new technology.

It felt like a very natural next step because I had this experience of genomics when single-cell was starting to come out. It was the next challenge, in a way, technologically and from a biological point of view, to use my experience and my knowledge. There are just so many more things you can look at.

I actually submitted a paper this morning! So, fingers crossed. It’s really the summary of all that we've been working on - the approach to integrate short and long reads in a single-cell study. We produced a single-cell gene expression and isoform profile and applied that to study the haematopoietic system, progenitor and stem cells to see what changed during ageing.

We were able to define some marker genes that are specifically expressed in these stem cells. What was really interesting was that we observed some genes that are specifically expressed only in old stem cells, and not the young. This may have a role in driving the ageing process. They are not like the typical hematopoietic genes, so we weren't expecting to see them.

With the long-read data we also saw a different set of alternative splicing events, which seems to be cell-type specific. With ageing, we didn't observe much change in splicing itself but we did see lots of changes in long non-coding RNA [important regulatory regions of DNA that do not code for proteins, as is more commonly understood].

The most exciting observation was that old stem cells seem to express immunoglobulin, which normally is expressed solely in B cells - a type of white blood cell. That was really quite unexpected. We don't know why it’s there. At first, we thought it was perhaps an artefact or contamination but it seems to be real - which is really surprising. There's much more to follow up on!

You can read the pre-print on BioRxiv, here: https://www.biorxiv.org/content/10.1101/2020.04.06.027474v1