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The story of ageing, told by a single blood cell

Dr Laura Mincarelli works at the cutting edge of single-cell technology, isolating individual blood stem and progenitor cells to understand how we age. What she discovers could one day help us to prevent ageing. In the short term, she is helping to transform our understanding of biology - one cell at a time.

Dr Laura Mincarelli works at the cutting edge of single-cell technology, isolating individual blood stem and progenitor cells to understand how we age. What she discovers could one day help us to prevent ageing. In the short term, she is helping to transform our understanding of biology - one cell at a time.

Mincarelli, a postdoc in Iain Macaulay’s single-cell genomics group at EI, spoke to us about stem cells, how they develop and age, and why that’s important for human health and fundamental biological research.

Dr Laura Mincarelli pictured in the single cell labs at EI

Image: Dr Laura Mincarelli pictured in the single cell labs at EI

Why is single-cell sequencing important?

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.

Stem cells, the focus of Laura's work provides great insight into human health.

Image: Close up image of stem cells

What are you working on at the moment?

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.

What sort of technology does this require?

Another cool thing about single-cell genomics is that there’s a lot of technology development going on. I'm developing novel technology, which integrates a short-read DNA-sequencing platform, like the Illumina, with a long-read platform, such as the PacBio.

The goal is to look at gene expression: how genes change and whether they are turned down or upregulated at different time points. I’m also looking at splicing and how this is regulated to get a more comprehensive picture of what's going on at the molecular level. Regulation is related to cell function, tissue homeostasis and consequently organism health.

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

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Can this help us better understand ageing?

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.

The science of ageing is benefiting from a different perspective, thanks to single-cell sequencing

Image: An elderly man's hands clasped together showing wrinkles in the skin.

How did you get into single-cell genomics?

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.

What's the best thing about working with the EI single-cell genomics team?

I really like that I have access to a lot of very impressive infrastructure. There really is everything you need for each step: from collecting your sample to sequencing and data analysis.

You learn to work on every step and this gives you a lot of flexibility. You can play with the technology and get feedback, go back to your sample, and you learn a lot.

Single-cell genomics platforms at Earlham Institute in Norwich

Contact our expert single-cell genomics team today to discuss a project.

Single-cell isolation platforms:

  • 10X Chromium: High-throughput single-cell sequencing protocols for 3’ and 5’ single-cell RNA-seq, ATAC-seq, CITE-seq and multi-omic profiling
  • BD FACSMelody & BD FACSAria Fusion: Cell sorting and sample collection for downstream genomic analysis
  • Leica LMD7 Laser Microdissection microscope: Isolation of single-cells or microbiopsy from tissue sections
  • Cellenion cellenONE F1.4: Cell sorting and imaging compatible with very large and very small cells

Single-cell sequencing protocols supported by our Genomics Services team:

  • Single-cell RNA sequencing : Full-length single-cell RNA-seq using Smart-seq2
  • Single-cell DNA sequencing: Whole Genome Amplification using Single-cell Multiple Displacement Amplification or Picoplex
  • G&T-seq: Parallel genome and transcriptome sequencing of the same single cell

Want to discuss a project? Get in touch via:

business.development@earlham.ac.uk

Have you got any publications and exciting findings in the pipeline?

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

Open quote marks

I have access to a lot of very impressive infrastructure. There really is everything you need for each step: from collecting your sample to sequencing and data analysis.

Closing quote marks

How do you see the future of single cell genomics?

This is a very big question as there are so many applications and technology developments.

I would say a key area would be multi-omics. Looking at the genome, the transcriptome, the epigenome, and even the proteome from the same single cell. The information we can get out of the multi-omics data is really impressive. There are some technological challenges there so that's definitely one of the areas that will develop more.

And then we have long reads, of course, and spatial transcriptomics [a new technology which allows us to analyse single-cell thin layers of tissue]. This is really exciting because it gives us an extra layer of information. You can see how cells are organised in the tissue, how they talk to their neighbour and so on. If we can define that, it'd be really cool.

In the long term, there are projects working on the clinical application of single-cell genomics. There is a project called LifeTime, a European collaboration, which is working on a single-cell genomics index and how you can use that to better define disease for personalised medicine.

For example, my colleague Silvia Ogbede is working on a Cancer Research UK funded project to analyse a cancer patient's derived organoids [cells extracted from the tumour of a patient and grown in the lab] at the single-cell level, before and after cells are exposed to different treatments. The main goals are to understand the evolution of the tumour, its resistance to therapy and ultimately tailor a personalised treatment for the patients.

Peter Bickerton

Article author

Peter Bickerton

Scientific Communications & Outreach Manager

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