Graham lab discovers human gut stem cells' "wiggle" behaviour: Cell Reports

Zoe Leech Posted in Publications 07 August 2014

Until now, little was known about how intestinal stem cells (iSCs) behave in the human gut; previous work has focused on mouse models and we have not been able to be sure of how this translates to humans.

A new study by Dr Trevor Graham in our Centre for Tumour Biology is the first to reveal how human iSCs divide and maintain crypt structures in the colon. Dr Graham said:

“Unearthing how stem cells behave within the human bowel is a big step forward for stem cell research. Until now, stem cell research was mostly conducted in mice or involved taking the stem cells out of their natural environment, thus distorting their usual behaviour.”

They have found that the physical location of iSCs – the stem cell niche – is a competitive space where iSC numbers are tightly controlled. This control is compromised in the early stages of tumour development, and suggests iSCs are involved in the development of bowel cancer.


Crypts in the human colon.
Source: Nephron, Wikimedia Commons

What’s special about stem cells?

Stem cells are self-renewing; their role is to maintain a tissue in the body that needs regular replacement – this includes but is not limited to the bowel, the skin and the bone marrow. In the bowel, cells are arranged in structures called crypts that absorb water and nutrients passing through this section of the digestive system.

Understanding how iSCs behave is vital in taking steps to prevent carcinogenesis in the bowel; stem cells are long-lived, unlike the daughter cells they produce that are sloughed off as part of their normal function in the gut. iSCs are the cells that are able to accumulate mutations and therefore likely to be responsible for initiating cancer.

Building this understanding could help us find ways to block the development of bowel cancer, as well as managing and possibly treating or curing unhealthy bowels – for example in cases of chronic inflammatory disease, which is also a cancer risk.

How do you go about tracking what you can’t follow?

What the group wanted to find out was how do human iSCs behave - in the same way as mouse iSCs (so we can keep using those models) or in a different way? How can we follow human SCs around when we cannot observe them in real-time?

For the last 1-2 decades, SC research has used traditional mouse models and methods of tracking SC behaviour that are impractical for working out what happens in people. Therefore Dr Graham’s group, which specialises in computational biology, created a “mathematical toolkit” to look at samples of human tissue and work out iSC behavioural patterns within it.

The group was able to study samples of human bowel that were removed in a standard procedure called polypectomy, which is used to reduce colon cancer risk in people with bowel growths called polyps. In this procedure, some surrounding normal tissue is also removed, so the group could look at the stem cells in those normal crypts as well as pre-cancerous areas.

Scott Robinson ripples

Ripples. Source: “Constructive interference”,
Scott Robinson, Wikimedia Commons

A toolkit to study the passing of time

While this tissue provides only a snapshot in time, the cells contain a record of their origin in their mitochondrial DNA (mtDNA). Dr Graham’s lab chose a mutation in a gene called cytochrome c oxidase (CCO), known to occur occasionally, as cells can either have this enzyme (CCO+) or lack it once the mutation occurs (CCO-).

Once the mutation occurs it is not undone, so even though they could not observe the moment the mutation happened, they could see CCO- daughter cells of the mutated stem cells along the crypt lengths by taking serial sections along the tissue and checking for the presence of the enzyme.

Dr Graham suggested the analogy of ripples on water; we can look at them and work out where they started if we know how water works. Using previous research on cell movement in crypts, the group created a mathematical model to look at these “clones” (cells that have arisen from a stem cell; like a family) in the colon.

It wiggles

They have affectionately dubbed this study “the wiggle paper” due how this change in stem cell activity over time looks if it is represented graphically. They found that the clones formed a “ribbon” along the crypt, whose width varies over time, representing how active the stem cells have been in dividing and producing daughter cells over time – as those cells move along the crypt, the width of the ribbon changes.

 GrahamPaperWiggle 2  From the paper: gut lumen represented at the top of the diagram and iSC niche at the bottom. CCO- cells are represented by blue areas and normal (WT) CCO+ cells in black.

The more active the stem cells, the wider the blue “clonal ribbon” – knowing the speed of cell movement up the crypt towards the lumen means we can infer stem cell divisions over time using these “wiggle” values.

This process is comparable to what has been found in mouse intestines previously, meaning what we learned from them is applicable to us; that the models are valid.

Dr Graham said:

“We now want to use the methods developed in this study to understand how stem cells behave inside bowel cancer, so we can increase our understanding of how bowel cancer grows.

This will hopefully shed more light on how we can prevent bowel cancer – the fourth most common cancer in the UK. We are positive this research lays important foundations for future bowel cancer prevention work, as well as prevention work in other cancers.”

Their work was not restricted to the stem cell dynamics; they also studied the crypts as a whole, whose evolution in the human gut has also not been previously described. Using their mathematical “toolkit” to study stem cell behaviour, the group looked at how often crypts divided in normal and cancerous tissue.

They found that normal gut crypts divide once every few decades – once or twice in a lifetime, about half as often as previously thought. The divisions happened much more frequently in adenomas (benign tumours) suggesting that crypt division is a driving factor in colon carcinogenesis, and that mutations in the known tumour suppressor gene called APC, mutated in many colon cancers, is often the cause of changes to both stem cell and crypt behaviour.

Dr Marnix Jansen, histopathologist and co-author of the paper, said:

“This study was made possible through the involvement of patients either diagnosed with bowel cancer or born with a tendency to develop bowel cancer. Only by investigating tissues taken directly from patients could we study how bowel cancers develop.

Our work underlines the importance of patient involvement in scientific research if we areto tackle bowel cancer and help the greatest number of people”

Importantly, this new “toolkit” can also be applied to other human stem cell niches, including the skin, prostate, lung and breast, contributing to our understanding of these cancer types as well.

The study was supported by Cancer Research UK (AMB, NAW) the Medical Research Council (BC, SACM), the Engineering and Physical Sciences Research Council (AGF), Microsoft Research Ltd (AGF), the National Institute
for Health Research University College London Hospitals Biomedical Research Centre (MRJ), the Dutch Cancer Research Foundation (MJ) and the Wellcome Trust (BDS)


Quantification of crypt and stem cell evolution in the normal and neoplastic human colon
A Baker, B Cereser, S Melton, AG Fletcher, M Rodriguez-Justo, PJ Tadrous, A Humphries, G Elia, SAC McDonald, NA Wright, BD Simons, M Jansen, TA Graham. Cell Reports (2014) DOI:

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