Tag: stem cells

Heart, human, diagram. Caption: Wellcome Images
Sanger Science

A breath of fresh air for oxygen-starved tissue

22 June, 2015
By Dr Rameen Shakur

The artificial membrane opens brand new research avenues in cardiology. Credit: Wellcome Images

The artificial membrane opens brand new research avenues in cardiology.
Credit: Wellcome Images

Sudden, vigorous exercise can cause a bit of a burn. We’ve all been there: chasing after a bus, a train, a dog or a personal best on the running track and we feel our chest tighten uncomfortably. This is hypoxia; it’s your heart telling you that its tissue is being starved of oxygen.

Patients with heart disease experience hypoxia regularly. With so little oxygen getting into the depths of the heart tissue, cells can die off, worsening a patient’s symptoms. Current clinical management by cardiologists like me has been to use drugs or interventions, such as stents in the arteries of heart. Now, chemists I am working with have discovered and used a new artificial substance that provides more oxygen for cells.

In this approach, developed at the University of Bristol, the oxygen-carrying protein myoglobin is attached to chemical components on the membrane of cells. The artificial membrane, known as a polymer-surfactant conjugate, provides a reservoir of oxygen that prevents hypoxia. My colleagues and I at the Wellcome Trust Sanger Institute and the Laboratory of Regenerative Medicine, University of Cambridge analysed the way this membrane affects stem cells and are now looking at how they effect heart muscle cells, and found that it might be able to change the way cells behave, without all the trouble of altering their genetic code.

Laboratory tests, where the membrane was applied to human stem cells shows very encouraging results. When genetic expression analysis was performed, researchers found significant down regulation (reduced activity) in the genes known to be responsible for causing hypoxia. This effect lasted in the cells for at least seven to 14 days.

The treatment is currently being tested on other cells and needs to be tested in live models before we can think about experimental clinical trials. There is a need for caution but there’s plenty of cause for optimism: this technique opens brand new research avenues in cardiology. The membrane may work in other tissues as well, presenting us with a whole new batch of possible therapeutic uses.

Innovation like this is impossible without collaboration. A team including chemists, stem cell biologists, genetic researchers and clinicians had to come together and share their expertise to get this idea off the ground. Let’s hope this continues and that we see more fresh eyes and fresh ideas transforming the way we treat heart conditions.

This is a real practical example of a successful translational project, taking basic science work and utilising it for the benefit of clinical medicine, to really have an impact on patient care and management. It is gratifying to work with so many dedicated scientists who share a common goal to improve the treatment options for patients with heart disease.

Rameen Shakur is a cardiologist at the Laboratory for Regenerative Medicine, Department of Surgery, School of Clinical Medicine, University of Cambridge, and a clinical researcher at the Wellcome Trust Sanger Institute.


  • Armstrong JP, Shakur R, et al. (2015). Artificial membrane-binding proteins stimulate oxygenation of stem cells during engineering of large cartilage tissue. Nature CommunicationsDOI:10.1038/ncomms8405

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Credit: Wellcome Library, London
Sanger Science

Answering age-old questions

09 March 2015
By Tamir Chandra and Philip Ewels

What is cellular senescence? Credit: Designed by Freepik

What is cellular senescence? Credit: Icons from Freepik.com

The reason for mankind’s ageing has fascinated scientists for generations and, over the years, many theories have emerged in an effort to explain it. A central question within these studies is the nature of ageing; is it unavoidable programming in our body or simply an effect of wear and tear?

Short-lived vertebrates such as the turquoise killifish, whose average life-span is six months, seem to suggest that ageing may be partly predefined by a programme written into our DNA.

One theory of cellular ageing predicts that as mammals mature we accumulate increasing numbers of ageing cells, known as senescent cells, within our organs. These cells stop dividing and no longer perform their original function; as their number increases, the ability of that organ system to do its job is restricted.

The same mechanism might also affect stem-cell populations, decreasing our regenerative potential as we exhaust our stem-cell pool. It’s thought that this could be one of several cellular ageing mechanisms that contribute to the effects of ageing we observe.

People have approached the phenomenon of cellular ageing in a variety of contexts. Some studies use isolated cells from older individuals or children suffering premature ageing syndromes as a model. Other groups have observed that cells isolated from healthy young individuals stop dividing after a certain number of cell divisions (replicative senescence) or after exposing the cells to certain cellular stresses (oncogenic stimulus and stress-induced senescence).

While these models agree on a number of details, there are also areas where they contradict one another. One particular point of dispute is the qualitative change of heterochromatin, the most condensed part of the genome.

The tightly packed DNA that forms heterochromatin seems to open up in cellular models of the premature ageing disorder Hutchinson-Gilford Progeria Syndrome. However, heterochromatin appears to tighten up in stress-induced senescence, culminating in a chromatin structure called senescence associated heterochromatic foci.

We initiated our study to understand senescence associated heterochromatic foci function, a phenomenon that has been observed in different forms of stress-induced senescence and to a lesser extent in replicative senescence. Senescence associated heterochromatic foci can be easily detected using a DNA stain and a microscope and the prominence of these foci suggests a change in the nuclear architecture in senescent cells.

Before our project, there had been a lack of functional understanding of this phenomenon and we used a recently developed method to map the architecture of the genome, hoping that a structural understanding of senescence associated heterochromatic foci would suggest possible functions of this process.

Initially, we were disappointed; the general changes we observed did not fit in with what we previously thought about stress-induced senescent chromatin and senescence associated heterochromatic foci formation. We expected a tightening or increase of heterochromatic domains; instead, we found a relaxation of these domains.

Stepping back from our initial research question, we realised that our findings might provide an explanation of the perceived difference between Hutchinson-Gilford Progeria Syndrome and stress-induced models of cellular ageing: the role of heterochromatin. This was made possible through directly mapping the physical contacts, regions of DNA that are touching because the chromatin structures are folded or coiled over one another.

Now, our data indicated that we may be able to align the behaviour of these domains in both conditions, suggesting a common mechanism for both models of cellular ageing. Finally, our findings may suggest that we should focus our future efforts on understanding the early events of cellular senescence chromatin changes.

Tamir Chandra is a Postdoctoral Fellow at the Wellcome Trust Sanger Institute. He works with Wolf Reik at the Babraham and Sanger Institutes on the nuclear biology of cellular ageing, with implications for cancer and ageing. Tamir has a long standing interest in senescence biology and did his PhD at the Cancer Research UK Institute in Cambridge with Masashi Narita on chromatin dynamics in senescent cells.

Philip Ewels is a bioinformatician at National Genomics Infrastructure at the Science for Life Laboratory in Stockholm, Sweden. Previously he worked with Wolf Reik at the Babraham Institute in Cambridge. His core interests are in the field of epigenetics, with particular emphasis on bisulfite sequencing, HiC data analysis and systems approaches to data analysis. You can find out more at his site: http://phil.ewels.co.uk/


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Sanger Science

Do stem cells have memory?

14 August 2014
By Daniel Gaffney and Foad Rouhani

iPS colonies. Credit: Foad Rouhani

iPS colonies. Credit: Foad Rouhani

Human induced pluripotent stem cells (hIPSCs) can be created from skin, blood or other tissues, and can be differentiated into any cell in the human body. Because they can be easily derived from pretty much anyone, hIPSCs have enormous potential for personalised medicine and the study of disease.

However, for reasons we don’t really understand, hIPSCs are highly variable in the lab: some cell lines are almost impossible to work with, but others are relatively trouble-free. One potential problem might be that hIPSCs remember their origins, the skin or blood cells they were originally derived from, long after they’ve been reprogrammed, a phenomenon some people have called “epigenetic memory”.

On the other hand, genetic differences between people also influence the behaviour and character of cells. Although it’s often overlooked, different cell lines probably vary simply because they’re derived from different people.

We wanted to understand whether hIPSC “memory” could really explain some of the variability we see between cell lines and how important this effect was relative to the effects of genetic differences between people. We made hIPSCs in controlled experimental conditions from two different types of skin cells, and blood derived from healthy donors. A key feature of our experiment was that we were able to get multiple tissue types from the same people, allowing us to disentangle the effects of genetics from other experimental factors.

The major result of our paper is that, although epigenetic memory may exist, its effects on hIPSCs look less influential than the effects of normal genetic differences between healthy people. In other words, on average, hIPSCs derived from two different tissues in the same person are more similar than hIPSCs derived from the same tissue in two unrelated people. We did find a handful of genes that showed some evidence of epigenetic memory, but none of these appeared to be the “master regulators”, that can drastically alter every aspect of a cell’s behaviour and morphology.

The results of our study have a few consequences we think are important. The first is that the impact of an entire genome’s worth of genetic differences can’t be ignored when studying, for example, the consequences of an individual mutation. In the future, hIPSCs are likely to be a vital research tool in understanding the functions of disease causing mutations. When faced with the choice of making lots of hIPSC lines from a single individual, or one hIPSC line from lots of individuals, we think that in most experimental scenarios the latter option is the right one. At the Sanger Institute, we’re currently involved in a large project, the Human Induced Pluripotent Stem Cells Initiative, to generate hIPSCs from a large number of healthy people, to provide exactly this type of resource for the research community.

A second point is that the effects of epigenetic memory seem to be pretty modest. This is important because it’s sometimes not possible to ensure that all cell types in a study have all been derived in exactly the same way. Our study suggests that hIPSCs derived from different tissues are comparable although, as always, this should be done cautiously. It also important to point out that our study can’t say really whether epigenetic memory exists or not.

Finally, an intriguing possibility is that some important differences in hIPSC behavior, such as better differentiation into certain cell types, might be driven by genetic differences. Although for the moment this is speculation, analysis of the data generated by the HIPSCI project will give us much better insights into this question. By identifying what causes variation in iPS cells we can design more efficient differentiation protocols and be better able to generate clinically useful cells for treating patients.

Daniel Gaffney is a junior group leader in Computational Genomics at the Wellcome Trust Sanger Institute. His group works on understanding how mutations affect the regulation of gene expression.

Foad Rouhani is a former clinical PhD student under the supervision of Allan Bradley. His research focussed on genetic and transcriptional variations following reprogramming of cells into induced pluripotent stem cells.


  • Rouhani,F et al (2014). Genetic Background Drives Transcriptional Variation in Human Induced Pluripotent Stem Cells. PLOS Genetics. DOI: 10.1371/journal.pgen.1004432

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Colin Barker and his Colinator Colony Picking Robot
Sanger Life

Colin’s Colony Collecting “Colinator” minimises mindless monotony

Colin Barker and his Colinator Colony Picking Robot

Colin Barker with ‘The Colinator’ colony picking robot. Credit: Genome Research Limited

18 July 2012

Written by Colin Barker

I’m an engineer at the Sanger Institute and I’m often asked to work with scientists to find new ways to make research techniques faster, more efficient and, sometimes, a whole lot less boring.

About two years ago, Bill Skarnes (who leads the stem cell team) asked me to build a robot to help with the colony picking process. It is a dull and monotonous task that is also labour intensive and highly repetitive – an ideal process to be given to a robot. The team works with colonies of stem cells that are grown for a few days and then need to be identified, isolated and separated in the space of just 24-48 hours. This need to separate out the colonies is a major bottleneck in the research process.

So that I could create a robot that will mimic the way the researchers work in the most appropriate fashion, I sat in the laboratory clean rooms observing the researchers in action. I rapidly realised that this was a highly skilled and delicate operation and that a robot would never be able to fully replace the researchers’ expertise. Knowing which colonies to pick, and which to leave, is a skill that is best left to the scientists.

However, I knew that if I could automate the rest of the process I could help bring benefit in several ways. My robot would relieve RSI caused by repeated pipetting to aspirate and separate colonies, remove the eye strain of peering down a microscope, and save valuable time by freeing researchers to do other, more creative, tasks. The challenge was set.

I worked closely with Wendy Bushell from the ES Cell Mutagenesis team to design ‘The Colinator’ – a robot that accurately picks 96 colonies in under 14 minutes, to an accuracy of less than the width of a human hair. It uses an image detection system to highlight colonies on screen for the researcher to choose. Once the best colonies have been chosen, the Colinator gently slices, slides and lifts each colony away from the plate using a syringe needle with an accuracy and reliability of close to 100 per cent. The picked colony is then dispensed into a well, and the needle is washed clean before returning to pick another one. Not only does the robot enable researchers to continue with other tasks, but the gentle picking process keeps the colonies intact and increases the cells’ ability to grow and thrive.

The Colinator will soon be working full time in the Sanger Institute laboratories, but the story doesn’t end there. We are now working with a commercial partner to turn the Colinator into a line of machines that can be used in labs around the world to free researchers from monotonous colony picking tasks. Watch this space, as they say.

Colin Barker is an engineer at the Wellcome Trust Sanger Institute… more

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