Chris Ponting

A team led by Edinburgh University’s Professor Chris Ponting has won funding for a PhD student who would follow up and expand on remarkable recent findings made at Stanford University, where Dr Mark Davis may have pinpointed a major issue in the immune system in ME/CFS.

Last year, Davis produced strong evidence of T cell clonal expansion, similar to that seen in illnesses including multiple sclerosis and acute Lyme disease. His discovery came from a new and sophisticated way of looking at the immune system in ME/CFS, which revealed the strongest evidence yet for immune activation in this disease. These results could indicate autoimmunity or a response to infection in ME/CFS, and could point to the core problem in the disease.


Human T cell (photo: NIAID)

So if the results of the PhD work are as hoped then they could narrow down the cause of ME/CFS for some patients. The ultimate aim is for this research to form part of a concerted effort that provides affordable diagnostic tests and targets for treatment.

The PhD will be based at Ponting’s Computational and Disease Genomics lab in Edinburgh. The £90,000 cost of the PhD will be jointly funded by Action for ME and the Scottish Government’s Chief Scientist’s Office. Samples from patients will be provided by the UK ME/CFS Biobank, subject to a successful full application to the Biobank.

Ponting has drawn in impressive collaborators for this project: senior immunologist Professor Georg Höllander from Oxford University and molecular biologist Dr Lia Chappell from the prestigious Wellcome Sanger Institute. I am pleased to say that I have also been involved with this study from the outset and the successful PhD candidate will engage with more patients as the project gets underway.

The immune-system biology behind the study: T cells and their receptors

Many people have heard of B cells and the antibodies they produce; T cells are their cousins. T cells come in many forms, but the relevant ones here are called killer (CD8) T cells. These act like a security force, checking cells and killing off any that look sick because they are infected or cancerous. Much like with B cells and their antibodies, T cells are produced in countless varieties, each version specifically binding to just one molecule (called an antigen). It’s this specific binding that allows a T cell to pick off a cell infected with a particular pathogen (or affected by another problem) while avoiding collateral damage.

Because these varieties are produced randomly, most turn out to be completely useless. But all the T cells hang around, hoping to find a pathogen molecule (antigen) or tumour protein they happen to recognise, like a lock searching for the key that will open it. If a T cell finds its “key”, the T cell is activated and starts dividing to produce identical copies of itself – clones – in a process called clonal expansion. This new army of clones then heads off to target the infected or cancerous cells. And when things go awry with the immune system, T cells can end up targeting a person’s own molecules – “self” antigens – leading to autoimmunity.

Mark Davis’s study was comparing T cell clonal expansion in healthy people with that in several diseases, including multiple sclerosis (an autoimmune disease), and acute Lyme disease (an infection). At a late stage in the project, he won a grant to include samples from ME/CFS patients as well and discovered that clonal expansion in these patients was similar to that seen in these other diseases.

Measuring clonal expansion

But how do you measure clonal expansion? Every cell in a clone shares an identical T cell receptor (TCR) – the lock responsible for recognising the key of a specific molecule on the pathogen or tumour cell. So the process is to laboriously sequence the T cell receptor of every T cell and then count the matches. When a lot of T cells have matching TCRs then this means that there has been clonal expansion.

Mark Davis did this for six ME/CFS patients, and the results are shown in the figure below.

TCR Davis just mecfs

Image taken from a video of Davis’s presentation

The figure takes a little understanding, so here’s what the first pie chart shows. It’s for Patient L3-07. The white area of the chart shows that just over half of the tested cells were unique (no other cells had identical TCRs), indicating no clonal expansion for those cells. The coloured pie slices indicate the scale of clonal expansion. For example, there were two clones with more than 20 copies of the same TCR, as indicated by the two pie slices marked in red. The other coloured slices show the number of copies for clones with fewer copies.

The number underneath the chart shows that this patient’s sample contained 323 T cells.

After examining clonal expansion in ME/CFS, Davis then compared the results for ME/CFS with those for other illnesses. Examples from four patients with multiple sclerosis, ME/CFS, or a recent Lyme infection and from four healthy controls are shown below.

TCR Davis all diseases clearer

Image taken from a video of Davis’s presentation

The contrast between the disease patients – including the CFS patients – and the healthy group is striking. In the healthy individuals, about 90% of T cells are unique, with only a few expanded into clones. The ME/CFS patients look far more like patients with multiple sclerosis or Lyme. This is an astonishing result and, if replicated, could point firmly to the underlying disease process for at least some patients. It could also yield biomarkers.

Mark Davis is already trying to identify the antigen(s) that might be triggering clonal expansion, which could identify self-antigens (autoimmunity) or specific pathogens that have triggered the problem. That could pave the way to developing new treatments.

The new PhD project will use similar but improved technology. Because every cell must be sequenced separately, T cell sequencing is currently very expensive work, which effectively limits how many samples can be processed.

Dr Lia Chappell at Sanger will develop the method further in order to dramatically lower costs, allowing much bigger samples to be analysed, and the technique will be implemented by the PhD student. The goal is to sequence TCRs for 10,000 cells per patient and for many more patients. The initial target is 50 patients and 50 controls but the ultimate ambition is to eventually sequence the T cells for all samples in the UK ME/CFS Biobank, and possibly for other cohorts as well.

How the study came about

Chris Ponting is an old friend and I told him about Mark Davis’s remarkable study when I saw the video about it from last year’s Open Medicine Foundation symposium at Stanford. Chris also thought this work was exciting and important, though I hadn’t expected him to follow up on it with a research project. However, by a stroke of luck, Chris was part of a consortium at the Wellcome Sanger Institute that was looking to find a cheaper way to sequence T cell receptors. The consortium is headed by Höllander with Chappell developing the core technology and both agreed to collaborate with Chris on this new project. Chappell and Höllander are now adapting their technology to suit this new study.

Clonal expansion could be the smoking gun for what’s going wrong in ME/CFS. So if the findings of clonal expansion check out then this work could help to track down the cause of ME/CFS for at least some patients. The new technology being developed could also ultimately lead to an affordable way for doctors to measure clonal expansion, helping with diagnosis.

It’s impressive that Action for ME and the Scottish Government’s Chief Scientist’s Office are funding this important work. Replication is central to establishing robust results, and I can’t think of a more important finding to try to replicate than that of T cell clonal expansion.