ME/CFS Research Review

Simon McGrath explores the big biomedical stories

Tag: Lipkin

The heart of ME/CFS? Lipkin’s Collaborative probes the impact of exertion

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The hallmark symptom of ME/CFS is post-exertional malaise (PEM), a prolonged, grim and disproportionate response to exertion. While Dr W. Ian Lipkin’s NIH-funded Collaborative – the Center for Solutions for ME/CFS – is focusing primarily on how problems in patients’ gut microbiomes might drive the disease, his team is also probing deeply what happens when patients exert themselves.​ Lipkin says that the exertion studies are so important that the Collaborative will devote a third of its research resources to them.

When I spoke to Lipkin about the Collaborative’s work, he also said he was very hopeful that there would be real progress for patients within five years. More on this later in the blog.

Exertion studies

The Collaborative has a simple idea for exploring PEM: use two different exertion tests that should provoke symptoms in patients and then see what happens, both to how patients feel and to their biology.

If biological changes, such as those to cytokines, ramp up along with symptoms then it’s more likely that the biological changes are directly related to the illness and should give clues as to their role. Any insights into the nature of PEM could lead to a much better understanding of ME/CFS.

bike-CPET-FFifty patients and controls will undergo a single maximal exercise test, a sure-fire way to provoke PEM. Patients’ symptoms will be measured before the test and then 24 hours, 48 hours and one week after the test. Crucially, researchers will collect blood, saliva and stool (poop) samples on two occasions: before the test, and 24 hours later.

The other, gentler exertion test, called LEAN, simply involves patients leaning against a wall for ten minutes. This test is designed to induce orthostatic intolerance – the development of symptoms when standing upright that ease when lying down – which is a common problem in ME/CFS.

Symptoms (including brain fog, tested using a special phone app) will be measured just before the test and at three time-points afterward. Researchers will also check blood pressure and take other clinical measures both before and immediately after the test.

The researchers running the Collaborative’s immune study will apply transcriptomics (which examines gene expression) and metabolomics to blood samples from both the exertion tests. And this should reveal any biological changes as symptoms kick off.

Patients and samples

The basis of any good study is to have samples from a large group of robustly diagnosed patients. The Collaborative already has such samples for the microbiome/immune work that was discussed in Part 1 of this blog and is assembling a new cohort of patients and controls for the additional work. This is necessary because many of the patients who provided samples for the earlier projects aren’t available for the exertion studies and other work discussed here.

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Dr Komaroff

Dr Anthony Komaroff will head the team overseeing this work, and that team will also run the exertion tests. Patients will come from the clinics of expert physicians Drs Susan Levine, Jose Montoya, Dan Peterson and Cindy Bateman – some of the finest ME/CFS clinicians in the US. They will recruit 100 patients and 100 controls.

Dr Dana March, Assistant Professor of Epidemiology at Columbia University, is a key part of the team and their projects, which include mining existing patient data for insights, and creating a new app.

A new bioresource to power future research

With this work the project is also creating a “bioresource” of well-defined patients and of samples taken both before and after exercise. Lipkin says that researchers from both inside and outside the Collaborative can draw on the bioresource to power a new wave of studies.

Lipkin said that the Collaborative itself would like to make more use of the samples: for example, running epigenomics and proteomic profiling of the exertion-study blood samples, and analysing the stool samples, work that would have allowed his team to have the same data on these patients as for the microbiome study. As yet, he doesn’t have funds for this work.

The MyME/CFS app

app, iphoneThe Collaborative have more in store for this cohort of patients. Working with a tech company, they will create an app for patients that will help both patients and the clinicians to track the illness for an extended period.

The app will collect information in real-time from patients, covering their symptoms, activities, events in their lives, including other illnesses and any treatments they are trying. This detailed history could help identify what might be causing any setbacks, relapses or even improvements.

Komaroff has said that using technology like this will allow researchers to collect much more comprehensive information much more cheaply than was possible before. Work is already under way, and the team have started by asking patients what they really want from the app.

Mining data for insights

Lipkin has data from several previous studies that all used the same group of patients. The team will combine the data from these studies into one unified database, creating a rich seam of biological, clinical and survey data on a single set of patients. The team will then mine the combined data, looking in particular for patient subtypes and for risk factors.

For example, subtypes might be based on how the illness started, symptom clusters, gender, types of other illness patients have had or how long people have been ill. Risk factors could include previously having a different disease. The idea is that the data will talk.

The team will also bring together and mine data from studies that used the same measures, but not necessarily the same patients. This could also help reveal subtypes and risk factors.

Bringing it all together

One of the most exciting things about this project is the wealth of data the Collaborative will have on every patient they study. For the first group of patients, this means the detailed molecular profiling of the microbiome and the immune system – including antibodies to “self” and to past infections – coupled with rich clinical data.

For the second, newly recruited cohort of patients, the Collaborative will have data on their molecular and physiological responses to exertion, along with clinical data, plus the same data on antibodies as the first group of patients – and the data tracking patients’ health in relation to a whole collection of factors.

Combining results from such different sources will provide researchers with a deep and rich source of data that will dramatically increase their chances of finding what’s going wrong in ME/CFS.

With so much new data to explore, it’s possible that Lipkin’s group will be able to identify any subtypes of patients, regardless of findings from the data-mining of existing studies.

The crystal ball

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Dr W Ian Lipkin

I asked Lipkin how he thought things might look at the end of the five-year NIH funding for the Collaborative’s research program.

He was bullish about the prospects for significant progress. He made a comparison with the situation with cancer treatment 20 years ago.

He believes that in ME/CFS, as with cancer, a group of similar-looking patients will prove to have different causes or triggers for their illness but will share a final common pathway: “ME/CFS”.  As with cancer, he expects they will find the specific cause of ME/CFS for some groups of patients quite quickly – the low-hanging fruit.

On the other hand, Lipkin believes it may prove much harder to find causes for ME/CFS in other patients – the fruit higher up the tree.

precision medicine

Precision medicine: targeting treatments by patient subtype

Lipkin is aiming for precision medicine, where doctors try to establish each patient’s exact problem so that it can be treated in the most effective way. If for example, the microbiome is abnormal, there are already plausible treatments available, such as probiotics, antibiotics or antivirals that could have a profound impact on illness. Other patients may have abnormalities in immune system or mitochondrial function that will require the development of specific drugs or genetic therapies.

Lipkin said that he hoped that the Collaborative network could be starting clinical trials in three years’ time – assuming that results support that next step. He stressed that these trials should be as rigorous as those used for other diseases. To avoid bias in interpretation of results the trials should be blinded so that neither the patient nor the researcher knows whether the patient is receiving a specific treatment. And adverse events – patient harms – should be tracked by a data safety monitoring board.

Lipkin noted that his team and others are already working across the US and internationally to share ideas, expertise, data, samples and other resources. He asked me to assure the community that we have reached an inflection point in the history of ME/CFS research and wanted to specifically thank the community for its support.

In some ways, his programme of research represents a voyage of discovery, and Lipkin’s not sure what he’ll find. The Collaborative will set off in the most promising directions with the tools and the samples but will change course, if necessary, based on the results, following the evidence to see where it leads.

Whatever the final course taken, the goal remains the same. In a recent NIH briefing-call to patients, Lipkin stated the aim of the Center for Solutions for ME/CFS simply and clearly: to find “real solutions for real people so that we can make it possible for people to become active again.”

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The microbiome hypothesis: Lipkin’s collaborative, part 1

Image credits: Exercise test, © Can Stock Photo / 4774344sean; Dr Komaroff, his Twitter profile; App, Pixabay; Dr Lipkin, Center for Infection & Immunity; Precision medicine, National Cancer Institute.

The microbiome hypothesis: Lipkin’s collaborative, part 1

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Dr W. Ian Lipkin

A gut reaction is the problem in ME/CFS – that’s the main idea being pursued by Dr W. Ian Lipkin of the Center for Infection and Immunity at Columbia University. He believes that the body’s response to changes in the gut could be what’s driving ME/CFS for at least some patients.

Lipkin’s collaborative group, the Center for Solutions for ME/CFS, will test this theory as part of a $9.6 million, five-year research programme, which Lipkin was good enough to discuss with me via phone and email.

This huge research programme, which is funded by the National Institutes of Health (NIH), is made up of three main projects. This blog looks at the first two, which will use high-tech approaches to see if changes in the gut are causing changes in the body, particularly in the immune system. The third project, which looks at the biological response to exertion in ME/CFS, will be covered in the next blog.

Evidence from research supports the idea that gut problems could lead to ill health. Inside the gut, trillions of microbes – viruses, bacteria and fungi – form an ecosystem. Some are hitching a free ride, but many are useful, crowding out harmful microbes, helping us to digest our food or providing essential nutrients such as vitamin K.

A short video introduction to the microbiome from NPR

But sometimes the ecosystem can get out of balance, with too many of particular types of microbes or too few. This “dysbiosis” can play an important role in conditions such as inflammatory bowel disease.

This is where Lipkin comes in. He suspects dysbiosis as a possible cause for ME/CFS and sees two main possible mechanisms leading to disease. One could be through the metabolites produced by an unhealthy microbial ecosystem. Metabolites are small molecules that are a core part of the chemical processes that sustain life, and undesirable ones from microbes could enter the bloodstream from the gut.

Lipkin told me that these metabolites could be creating ME/CFS symptoms by, for instance, altering mitochondrial activity and so causing fatigue, or even affecting the brain, which could lead to brain fog and other cognitive problems.

The microbiome and the immune system: it’s complicated

A second way that Lipkin believes that dysbiosis could cause ME/CFS is via the immune system. Recent research on microbial numbers indicates that there are roughly as many microbes in the gut as there are cells in the human body. That represents a serious threat of infection and requires a delicate balancing act for the immune system, dealing with dangerous pathogens without starting an inflammatory war.  A fired-up immune system can lead to both fatigue and cognitive problems in many illnesses.

However, it’s a two-way relationship between the immune system and the microbiome. For instance, some gut bacteria produce the metabolite butyrate that stimulates certain types of T cells, helping to maintain the peace.

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Microbiome dysbiosis might drive ME/CFS via the immune system.

So there are at least two possible ways that the microbiome could be driving ME/CFS in at least some patients: microbiome metabolites that enter the blood could directly cause fatigue and cognitive problems; or more complex interactions between the microbiome and the immune system could lead to similar problems. But is either of these possibilities actually happening?

Dr Ian Lipkin is a good scientist to have on your case. He has probably discovered more viruses than anyone else. The Chinese government hired him to deal with the 2003 SARS outbreak. And he’s pioneered new technology throughout his career, most recently with a new way of detecting just about any human virus in a patient using a small chip. Versions of that technology will be used in this study.

Project 1: Mapping the microbiome

Lipkin has been working on the gut microbiome in ME/CFS for some time (see this recent paper, for example). Now, in this first collaborative project, he and his colleagues aim to find out if some or all ME/CFS patients have dysbiosis in the gut, by comparing patients with healthy controls.

Gut microbiome computer

Bacteria, fungi and viruses make up the gut microbiota.

All the microbes of the microbial ecosystem are technically known as the microbiota, but are usually referred to as simply the microbiome – the collection of all the genes that make up all the organisms. Surprisingly, it’s easier to find out the microbial make-up of the gut by analysing this huge set of genes – the microbiome – rather than by studying individual organisms.

Lipkin and colleagues will take this approach, using DNA sequencing and analysis of the microbiome to create microbial maps for all 107 patients and 97 healthy controls in the study.

The team will use a range of high-tech approaches to map the microbiome in a more sophisticated way than has been done before for ME/CFS, to provide the most accurate data possible. The resulting microbial maps will reveal if some or all patients have an off-balance microbiome that could be causing their illness – and the research team are looking at the viruses and fungi in the microbiome, not just the bacteria.

In addition, the team’s deep-sequencing method will provide insights into what genes are present in the whole microbiome, and how those genes might then affect a patient’s biology.

Project 2: Total molecular mapping of the immune system

Microb-Immune-p1,2The next – and critical – step in Lipkin’s research programme will be to link any changes in patients’ microbiomes observed in Project 1 to changes in their immune systems, and this is the goal of Project 2.

Lipkin will be using “omics” technology – a big data approach – to probe the working of immune cells in many different ways.

Omics offers a huge advantage over more traditional approaches in which, for example, researchers would have looked at the level of a single protein in a sample, such as the level of haemoglobin in blood. But with a protein omics approach, called proteomics, researchers look at a huge number of proteins in the sample – here the sample is all the immune cells that make up the white blood cells.

This broad omics approach can reveal far more about what’s going on in the immune cells than just looking at one or a few proteins.

Lipkin’s team hope to find differences between the immune cell proteins in patients and those of healthy controls, and that could reveal what’s gone wrong in ME/CFS.

The real bite of this study is that it won’t just use proteomics; it’s also using epigenomics to probe gene regulation, transcriptomics to see which genes are active, and metabolomics to probe which cellular chemical reactions are taking place.

These four omics approaches cover almost all fundamental levels of a cell’s molecular biology, providing a detailed map of activity in immune cells. This should give researchers extraordinary insight into the problems in the biology of ME/CFS patients.

Most processes in a cell begin with genes, the cell’s instructions written into its DNA. Genomics – the first and best known omics – looks at these instructions. But this study will instead use epigenomics, which looks at a level of broad gene regulation carried out by epigenetic tags. These tags are added to either sections of DNA or their scaffolding proteins and switch sets of genes on or off. Differences in regulation of genes between patients and controls revealed by epigenomics work could give clues about where problems arise for patients. So epigenomics provides the first level of information, as shown in the figure below.

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Genes themselves do nothing until their DNA is transcribed (copied) into a similar molecule called RNA in a process known as gene expression. All the RNA transcripts in the sample are known as the transcriptome, and most of it consists of messenger RNA (mRNA), which tells cells which proteins to make. Other types of RNA can play a number of roles in the cell. Previous ME/CFS studies have looked at gene expression by looking for a large number of prespecified mRNAs, but not all of them. Transcriptomics offers a more comprehensive approach to understanding which genes are active in a cell.

The third level of omics is proteomics, which looks at the proteins. Proteins are the body’s ‘doing’ molecules, such as antibodies, cell receptors and enzymes.

The final level is metabolomics, looking at metabolites, such as glucose and some amino acids. Metabolites are key molecules in the chemistry of life: for example, they make up the energy cycle in the mitochondria – where Professor Ron Davis and others have identified abnormalities in ME/CFS patients.

So a cell’s DNA gets regulated, in part, by epigenetic tags (looked at by epigenomics) and is transcribed by RNA (looked at by transcriptomics) to make proteins (looked at by proteomics). Then enzymes, which are a type of protein, catalyse reactions involving metabolites (looked at by metabolomics).

Using omics to look at these four different levels of immune cells’ molecular biology – genes, RNA, proteins and metabolites – hugely improves the odds of findings where the problem lies.

Lipkin told me that you can start by finding an issue with a metabolite and then “swim upstream” to see if that problem is driven by a change in proteins, in RNA or in gene regulation. Similarly, you can swim downstream if you find an issue with broad gene regulation – does it make a difference to RNA, proteins and/or metabolites?

To make this aspect of Project 2 happen, Lipkin has recruited an impressive roster of omics experts to his collaborative, namely Dr John Greally for the epigenomics and transcriptomics work, Dr Ben Garcia for the proteomics, and Dr Oliver Fiehn, who leads one of the largest metabolomics labs in the world, to analyse metabolites. All of them are relatively new to ME/CFS and will bring fresh perspectives.

Probing antibodies for signs of autoimmunity and infection

In addition to the microbiome and related immune work, Lipkin’s team will also use elegant new technology that he developed to look for  potential autoimmune problems and past infections that might have triggered the illness.

The approach focuses on antibodies, which bind very specifically to just one antigen – antigens are fragments of proteins, such as part of a virus’s protein coat, that trigger an immune response in the body. The antibody is like a specific lock that binds to just one antigen key.

Bunch-of-keys

“Antigen keys” could unlock antibody secrets.

The new technology essentially offers up a huge bunch of antigen keys (actually fragments of antigens called epitopes) and detects which one fits. If the antigen key is a protein from a pathogen, such as a flu virus, that indicates that the body has fought off an infection, possibly one that triggered ME/CFS. On the other hand, if the key is part of a “self” protein, that could be a sign of an autoimmune disease. Researchers will focus on any differences between patients and healthy controls.

And there’s more. The team will use additional technology – based on Lipkin’s high-tech way of detecting just about any human virus – to check the gut, saliva and blood for fungal or bacterial infections.

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With these three approaches – a high-tech dive into the microbiome, linking changes in the microbiome to changes in the immune system at all molecular levels, and a search for what patients’ antibodies respond to – Lipkin’s investigation of what’s going on in ME/CFS patients is impressive. He hopes that this combination of depth and breadth will help to unlock ME/CFS.

One final point: Lipkin is not alone in thinking that problems with the microbiome might be driving ME/CFS via the immune system. Dr Derya Unutmaz is pursuing the same idea with his own collaborative. The main difference between the two researchers’ approaches is that while Lipkin has a more molecular focus, Unutmaz is focusing more on the different cells of the immune system, such as T cells and their subtypes. [Update:  Unutmaz and Lipkin have announced a collaboration – both will apply their techniques to the same patients to give the deepest possible profiling of immune cells.]

Part 2: The heart of ME/CFS? Lipkin’s Collaborative probes the impact of exertion

The blog also features Lipkin’s bullish views on the future for ME/CFS.

Image credits: Dr Lipkin, Center for Infection & Immunity; Microbiome, source unknown (please contact me if it is yours); Immune cells, © Can Stock Photo / Kateryna_Kon; Metabolite & protein molecules, also Can Stock; Dr Fiehn, UC Davis;

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