Interview: Ian Lipkin’s Million Dollar Appeal for Microbiome Study

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Simon McGrath recently secured an interview with the world famous Dr Ian Lipkin – a scientist who continues to believe that ME/CFS has a physical cause – to discover more about his plans for a major study of the gut microbiome and to find out why he's asking the patient community for its support…


Dr W. Ian Lipkin has demonstrated a clear commitment to ME/CFS research. First came his study looking at Borna virus in the 1990′s, and then the landmark study that ruled out XMRV as a cause, and most recently we have heard about the huge pathogen and immune study – a vast collaboration with many key clinicians and researchers, including Dr Dan Peterson and Professor Jose Montoya.

That research had already found clear signs of immune activation in patients and, when I spoke to him, Lipkin was clearly excited about the very latest results to emerge from the study - I wish I could reveal more, but a paper has just been submitted and details are embargoed until publication.

Lipkin believes that immune activation may be responsible for driving the symptoms associated with ME/CFS. And that the immune activation and could itself be triggered by bugs, not in the blood, but found in the vast ecosystem of bacteria, viruses and fungi, that constitute the gut microbiome.

However, he doesn’t have the funds to pursue this research and so he’s appealing to the patient community for the one million dollars he needs to get the work done. The payoff? A better understanding of the illness and the possibility of new treatments.

Dr Lipkin on ME/CFS

Lipkin made a splash in the world of ME/CFS when he led the XMRV study that both disproved its role in the illness and also managed to unite the patient community. At the press conference for that study he said his first brush with CFS was a large study in the 1990s that demonstrated no connection between the Borna virus (one of many viruses he’s discovered) and CFS. But he stressed that their findings in the same study of B-cell activation in CFS patients was a clear sign that this was not a psychosomatic disorder. The findings in his new study have only confirmed his views:

“There is no question in my mind that this is a physical disorder. The fact that we haven‘t been smart enough or invested enough in it to sort that, doesn’t mean that this is anything else.”

The smoking gun

The immune activation he’s found could explain fatigue – it’s almost a universal symptom of infections like flu, and is actually a consequence of immune activation rather than caused by pathogens themselves.

The same could be true of other ME/CFS symptoms including disturbed sleep and brain dysfunction which again are typical symptoms of immune activation.

Lipkin is eager to build on this work. He believes the immune activation is a smoking gun and now wants to track down who or what pulled the trigger.

“I am more keen than ever … to see if we can identify the trigger”
- all quotes are from Dr Lipkin

There are several credible places to look for the culprits triggering the activation. One is white blood cells: some viruses could be hiding out in cells and so wouldn’t have been found by the initial search in the blood plasma – and Lipkin already has a white blood cell study lined up.

However, his attention is particularly focused on the microbiome, the large ecosystem of bugs that live on our skin and within our ‘inner tube‘ that leads from mouth to bottom.

There are at least one trillion bugs in the gut microbiome – and there are more immune cells in the gut than anywhere else: it’s a great place to hunt for bugs that might be triggering immune activation.

Microbiome problems are increasingly being linked to serious illness. The most striking example is the superbug Clostridium Difficile (C. diff), which has become a major problem in hospitals. C. diff lives in most of our guts harmlessly at low levels, but it can take over (particularly if ‘good’ bacteria are killed off) – causing diarrhoea and even death. Happily, doctors have discovered that severe C. diff cases can be treated relatively easily by restoring the microbiome; unhappily, this involves a faecal transplant.

The potential to treat disease by restoring the microbiome is one reason this area of research is attracting so much attention. This recent article explains more about the microbiome, how it might link to ME/CFS and looks at other research being performed.

“If the answer were simple, it would be done by now”

Irritable Bowel Disease is another example – here inflammation is believed to result from changes in the microbiome. Lipkin’s team have just been studying women in sub-saharan Africa and found that certain bacteria in the vaginal microbiome increase the risk of HIV infection. Lipkin thinks the gut microbiome could be playing a similarly important role in ME/CFS:

“By analogy with animals and human situations, we see that different populations of fungi, bacteria and viruses in the colon can have an impact on the immune system and give rise to cytokine activation which could cause the symptom complexes we see in ME/CFS”

in other words:

changes in microbiome > immune activation > symptoms of ME/CFS

I asked Lipkin if this meant particular bugs causing inflammation and he said that is certainly possible. But, he added, another route to illness is that an overgrowth of ‘’bad’’ bacteria could form a film, preventing ‘’good’’ bacteria from interacting positively with the immune system (see this article for more) – an indirect way of causing immune dysfunction.

The exact role that microorganisms in the gut play in health and in the development of disease is complex and still being determined. There are many plausible hypotheses, says Lipkin, and only research can show which (if any) are right.

If the microbiome is the cause, is it treatable?

If the microbiome is the cause (or a cause, or even a contributor) of ME/CFS, it might be relatively easy to treat, perhaps with probiotics, restriction diets, drugs, or even faecal transplants.

Cause or effect?
Of course, the first step in this process is demonstrating a strong link between the microbiome and ME/CFS. If one is found then the next step is to look for evidence it plays a causal role: i.e. do microbiome changes cause immune dysfunction, as opposed to being a consequence of or simply associated with immune dysfunction?

Lipkin says one option is to use an animal model: the idea would be to introduce the microbes suspected of triggering ME/CFS into the gut microbiome of animals, to see if this leads to similar symptoms and immune activation as seen in humans. Something that has been used to study Metabolic syndrome.

Personalised medicine
If there is evidence of a causal role, Lipkin says they would look to establish clinical trials of treatments that could include probiotics, antibiotics followed by prebiotics, restriction diets and possibly even faecal transplants. He believes that there would not be a single microbiome cause of the illness, but different types – potentially fungal, bacterial and viral problems causing three separate types of immune dysfunction.

Lipkin calls these different types ‘endophenotypes’ and it could lead to personalised medicine, where the particular treatment depends on the specific form of the illness. There will be endophenotypes beyond those in the gut, such as genetics endophenotypes, and it is highly unlikely that the microbiome would account for all forms of ME/CFS – but this approach could tackle a very substantial proportion of cases.

The study breakdown

Lipkin’s proposed study will look at all three trees of life: bacteria, fungi and viruses in the microbiome of 100 patients and 100 controls recruited for a previous NIH study. It will cost a cool million dollars:

1. Sample collection: $150,000
Collection of faecal (and blood) samples from patients, including checking the initial ME/CFS diagnosis remains valid and shipping chilled samples back to the labs at Columbia.

2. Faecal Microbiome sequencing and Analysis: $317,000
- Separate, purify and perform high-throughput sequencing of viruses, fungi and bacteria
- Complete sequencing of viruses; partial sequencing to identify bacteria (using 16S rRNA) and fungi (using ITS, the ‘fungal barcode’)
- Generate microbiome profile for each patient, one each for bacteria, fungi and viruses​

Comparison of patient and control microbiomes: bacteria, fungi and viruses that differ in prevalence between CFS subjects and controls will be considered candidates for contributing to either health or disease.

3. Development of highly-accurate real-time PCR assays to confirm findings and levels of microbes: $328,000
This will quantify how much there is of each bug of interest (the main high throughput sequencing approach gives an indication of quantity but is less accurate than real-time PCR).

It’s possible, that the most important thing isn’t the presence or absence of a microbe, but the amount of it – as with C.Difficile. These assays will also be used to check that key microbes haven’t been missed in any patient or controls who were negative for them in initial sequencing, as PCR assays are far more sensitive than high-throughput sequencing.

4. Cytokine analysis: $86,000
The study will again measure cytokines in blood and undertake data analysis to see if there is an association between cytokine profiles and immune profiles. It would then provide strong evidence of an important relationship between the microbiome and immune dysfunction – the hypothesis driving this study. Sophisticated analysis will be required on the vast amount of data generated by microbiome and cytokine profiling; happily, Lipkin’s Center for Infection and Immunity have a team of biostatisticians dedicated to such work.

5. Development of antibody tests for important bugs identified by the microbiome work: $249,000
It could be a few individual species or particular groups of microbes, but antibody tests will be developed by Lipkin’s lab to allow much easier testing to see if the same problems in this sample are found in the wider patient population.

As well as guiding treatments, the PCR assays and antibody tests developed here could both provide a diagnostic test for ME/CFS.

Lipkin’s record



Featured in the New York Times, described by Discovery magazine as the world’s foremost virus hunter, and consultant to a successful Hollywood movie, Dr W. Ian Lipkin has a higher profile than most researchers. But this profile is built on a stellar scientific reputation.

He’s discovered more viruses than anyone else. He’s part of the World Health Organization (WHO) diagnostic discovery and surveillance programme designed to catch pandemics as they arise. And the Chinese recruited him play a leading role in their fight against SARS.

Amongst other things he is John Snow Professor of Epidemiology and Director, Center for Infection and Immunity at Columbia University. Full biography.

He is passionate about communicating science to a wider audience but is insistent the science is right.

Lipkin only agreed to consult on Contagion, a movie about the terrifying potential of epidemics, because of director Steven Soderbergh’s desire to make a film that was true to the science – having turned down offers to advise on several movies with somewhat wilder plots.

When Lipkin was shown a near-final version of the film he threw up his hands at the scene near the climax where a scientist injects herself in the leg with the new vaccine, through her tights – a poor practice that could easily introduce an infection.

This might seem a small detail given everything else the film had right, but Lipkin was adamant it had to go: cue a $100,000 reshoot.

This near-obsession with getting things right is a Lipkin hallmark. The very first point he made to me about this study, before discussing any details, was the need for real, robust findings – because there have been too many false dawns in this field.

At the end of the interview he emphasised the need of crisp, rigorous data. Whatever the findings from this new study – positive or even negative, we should be able to rely on them.​


Scientist in a hurry for answers

Dr Lipkin is a scientist in a hurry for answers. That’s true both in his work trying to stop a new pandemic in its tracks, and in his work on ME/CFS.

He wants to follow up as many promising leads as possible, as soon as possible – rather than waiting for the results of a single study before planning a new one if the first draws a blank.

That’s why he set up a huge study looking for specific pathogens such as EBV, but also used deep sequencing alongside that to search for any other pathogen, known or unknown.

He’s looked in blood plasma for pathogens but is also about to look for them in white blood cells too.

He set the study up to look at immune markers including cytokines as well as for pathogens – and the significant findings of immune activation show the value of backing more than one horse.

On top of all this, Lipkin has invested in a gene expression study using samples from the same study, with results expected shortly that could throw up new leads in epigenetics and genomics.

Dr Lipkin has committed a huge amount of his 60-strong institution’s time to pursuing numerous studies, all aiming to uncover what’s really going on in ME/CFS

Too much, too soon?
However, it may be that the NIH is not in such a hurry as it has declined to fund the study at this time.

But then the NIH has only ever committed relatively small amounts of funding to ME/CFS – around $5 million a year, compared with around $115 annually for MS and $284m for Asthma.

Its funding record firmly suggests the NIH’s priorities lie elsewhere.

So, as Lipkin says, “we are stuck”. It’s possible that the NIH will fund this work in the future, and possible they won’t.

The question is, do we want to wait?

“We are already well behind where we should be”

Dr Lipkin has now appealed to patients to fund his latest study that aims to hunt in the gut microbiome for the ‘trigger’ of the immune activation his study found in ME/CFS. And he needs a cool million dollars to pay for the study outlined above.

Actually, the study comes to a bit over a million dollars (see above) - $1.13 million, to which another $140,000 of costs for maintaining the high-tech equipment used and general lab costs making $1.27 million in total. However, the initial target has been set at $1 million.

In his CDC telecast to patients last September, Lipkin explained the microbiome project was being held up by this lack of funds, and urged patients to contact their representatives in Congress.

He also appealed directly to patients who could afford to do so, to invest in research:

“it may not be appropriate to pass the hat, but that is exactly what I am doing”

How long will it take for the results? “Within a year”, said Lipkin

The man is in a hurry, and the study is all set up and ready to go – once funding is available.

“As long as I can do it, I will do it. I‘m eager to start, I‘m optimistic it will bear fruit, it‘s not just an academic exercise, it could lead to treatment”
When I mentioned to Dr Mady Hornig, the Principal Investigator on this study, that I was interviewing Dr Lipkin she added: “Terrific – we need the resources to get this done”.

Crowdsourcing: Together we can make it happen

I do think we are very lucky to have Dr Lipkin on our case and believe that we should back his new study, which will be performed at his Center for Infection and Immunity, Columbia University – the world’s largest and most advanced academic center in microbe discovery, identification and diagnosis.

“Why don‘t we crowdsource this, we are all losing valuable time in our lives?”
Vanessa Li, Phoenix Rising member and fundraiser

ME/CFS patient, Vanessa Li, responded to Lipkin’’s call last year, by contacting his office and suggesting crowdsourcing in a similar way to MEandYou, which through the efforts of Dr Maria Gjerpe had raised an astonishing $0.5 million towards the Norwegian Rituximab trial in 90 days.

Lipkin was a physician in San Francisco at the start of the AIDS epidemic and commented how, when the government was reluctant to pay, much of the important early work was funded by private donors so he’s very open to this possibility. He continued to seek funds for his work from institutions, but as that hasn’t worked he is now asking patients if they can make the study happen - and has given this interview to launch the million dollar appeal.

Donate to the the ME/CFS microbiome study
I have just donated and hope many other patients will do too. Just click on the button below and follow the instructions. The option is to donate to CFS research, but in the next page you can add ‘special instructions’ such as ‘for the microbiome study’.

We need only for every US patient to donate $1. Or one in ten patients to donate $10.


If people want to do more to help – and this is a big target – they can help to promote this crowdsourcing initiative at this new group, or email Vanessa Li. I will give her the last word:

The CDC says there are more than one million ME/CFS patients today in the US alone. There is no reason why, if every patient were made aware of Dr. Lipkin’s appeal and donated $1, that we should fail to raise the $1 million. An esteemed researcher doing high-caliber work is taking a serious interest in finding out the cause of our desperately under-researched illness. Now is the time to act!​

Simon McGrath tweets on ME/CFS research:


Phoenix Rising is a registered 501 c.(3) non profit. We support ME/CFS and NEID patients through rigorous reporting, reliable information, effective advocacy and the provision of online services which empower patients and help them to cope with their isolation.

There are many ways you can help Phoenix Rising to continue its work. If you feel able to offer your time and talent, we could really use some more authors, proof-readers, fundraisers, technicians etc. and we’d love to expand our Board of Directors. So, if you think you can help then please contact Mark through the Forum.

And don’t forget: you can always support our efforts at no cost to yourself as you shop online! To find out more, visit Phoenix Rising’s Donate page by clicking the button below.


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Comments

Center for Infection and Immunity posted Simon´s article on their facebook page. Maybe we can "like" it or post some comments to show our interest and support. Here you can find it:
https://www.facebook.com/CII.Columbia
Here it is (thanks Tuha): https://www.facebook.com/CII.Columbia/posts/10202414687581465?stream_ref=10
Canary film: https://www.facebook.com/canaryfilm/posts/361930483944691?stream_ref=10
And if anyone'd like to add me on FB just 'cause that's one more channel of communication and it's easier to share things, feel free to add me; please just tell me whether you're from PR or we have mutual friends or whatever so I can approve you faster: https://www.facebook.com/Rom5hope
 
@MeSci I just wanted to say I'm aware of your fears; I'm not oblivious to them. However I'm not up to scratch on the science frankly and I'm in no position to argue with you about whether the microbiome of a human could be successfully replicated in an animal (or if that work would even show anything). However I'm not sure but I think I pleaded to Simon and Sasha to answer you, and I think they did. I hope their replies were at least satisfactory to you.
My educated guess as to whether a pathogenic human microbiome would produce useful information relevant to humans is no. It appears likely to me that even a healthy human microbiome would cause illness in a different species, just as a healthy monkey/rat/mouse/pig/dog/horse microbiome would probably cause illness in a human.

With Lipkin's reputation and apparent expertise and intelligence I am surprised that he would even seriously consider such research, unless it were to satisfy regulatory authorities prior to clinical trials.
 
My educated guess as to whether a pathogenic human microbiome would produce useful information relevant to humans is no. It appears likely to me that even a healthy human microbiome would cause illness in a different species, just as a healthy monkey/rat/mouse/pig/dog/horse microbiome would probably cause illness in a human.

With Lipkin's reputation and apparent expertise and intelligence I am surprised that he would even seriously consider such research, unless it were to satisfy regulatory authorities prior to clinical trials.
But, like I said earlier, an animal model plays no part at all in the research that we're being asked to fund now. This $1 million project is to determine whether there's an association between particular pathogens in the gut and having ME. We need to know if that's the case, just as we needed to know whether XMRV was associated with having ME. That's what started the whole cascade of enormous, unprecedented interest in our condition over the last few years: apparent evidence of the link between a specific pathogen and having ME. Even though that didn't pan out, it caused all these new scientists to notice our disease and get involved. Once we've established a firm association between ME and a pathogen (or pathological process), we're in business and that's when more and more scientists will leap on the bandwagon.

We desperately need this study.
 
My educated guess as to whether a pathogenic human microbiome would produce useful information relevant to humans is no. It appears likely to me that even a healthy human microbiome would cause illness in a different species, just as a healthy monkey/rat/mouse/pig/dog/horse microbiome would probably cause illness in a human.

With Lipkin's reputation and apparent expertise and intelligence I am surprised that he would even seriously consider such research, unless it were to satisfy regulatory authorities prior to clinical trials.
You make a lot of good points and I agree that replicating a human microbiome in another species (whether it be healthy or the unbalanced one Lipkin is hypothesising) is a very difficult task and is likely to be for the most part unhelpful, it is however only suggested as a possible route to go and I don't think much will be done with it even if it ends up being looked at. I think we may be blowing this small suggestion out of the water, certainly this study is not worth overlooking because a small potential part of it may or may not use an animal model - which may actually be of use as there is little work done to date trying to replicate human gut microbiome in animals and we could learn something that may even aid further studies in the future. As a firm advocate of the leaky gut hypothesis i'd have thought this study would be something you'd think is worthwhile, I know I myself like to pick out the problems in studies that I think are promising in hope that the problems can be ironed out.
 
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I totally support @MeSci's right to raise her heart-felt concerns about research using an animal model.
We can promote the study, and fundraise, while acknowledging and accepting people's concerns.

But just to be clear, this study does not incorporate any animal testing.
The only reference to animals in @Simon's article is the following:
Lipkin says one option is to use an animal model: the idea would be to introduce the microbes suspected of triggering ME/CFS into the gut microbiome of animals, to see if this leads to similar symptoms and immune activation as seen in humans.
 
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Re: Concerns raised or questions asked.

We will be contacting Columbia and seeking more information to hopefully provide some more reassurance where necessary. The replies will be posted, or a further article will be generated, as soon as we can.

It is only Day Three and the Group is really only bedding down. We just need a bit more time to hand-over from the Content Team to the Group and then to work back through the comments, here and elsewhere. Hopefully, many questions have been addressed, but outstanding ones will be raised as will concerns.
 
I have just read the proposed study carefully. I think is a very elaborated and intelligence way to approach and perform a good trial, to try to find out a possible microbial cause (or at least implicated factors) for ME/CFS. I hope it can be finally done.

One of the main goals is to find the "bad guys", right? Well, I think we know some of them very well, and other not that much, but in any case, they should contribute to the possible success of the study. I am talking about the "old guys" (EBV, CMV, HHV6...), the "old and now more famous guys" (Borrelia, Batonella, Chlamydia, enteroviruses...), and of course, he's talking about these bugs probably be hidden in the WBCs... Well, I want to remember that Dr. Kenny De Meirleir et al found plasmacitoid dendritic cells (specific macrophages of the gut) expressing HERVs (Human Endoretroviruses), and probably guilty for an excessive and improper immune activation leading to CFS symptoms--for these cells to do so, they must interact with some of the guys I mentioned before!!!!

So.. I think a lot of work has been made so far, and it is time to put it all together. I root for this study, hoping it counts with the evidence available up to date.

Best!
Sergio
 
Wow. This thread has quickly become the latest hot topic. And rightly so.

But even after the guilty bug is found, what type of treatment would be likely to eliminate it?

Antibiotics, antivirals, herbs, supplements as well as a cohort of alternative medicine has already been self-administered empirically by many PWCFS.

What could be left that has not been tried yet....
 
I totally support @MeSci's right to raise her heart-felt concerns about research using an animal model.
We can promote the study while acknowledging and accepting people's concerns.

But just to be clear, this study does not incorporate any animal testing.
The only reference to animals in @Simon's article is the following:
I don't want to hijack this thread or cause any confusion, so have started what I hope will be a series of blogposts (time permitting) on important species differences relating to this line of research. The first one is here. You are welcome to leave constructive comments there.

I fully acknowledge and applaud Lipkin's proposed initial research, for which he seeks funding, as stated earlier. It was just undermined for me by that suggested proposed follow-up research, the quote re which I posted with its preceding paragraph earlier in this thread.
 
Wow. This thread has quickly become the latest hot topic. And rightly so.

But even after the guilty bug is found, what type of treatment would be likely to eliminate it?

Antibiotics, antivirals, herbs, supplements as well as a cohort of alternative medicine has already been self-administered empirically by many PWCFS.

What could be left that has not been tried yet....
It's hard for anyone to draw conclusions from individuals with our binbag diagnosis dosing themselves with all sorts of different stuff for different periods of time with all sorts of confounding factors and without those patients knowing what bugs they were going after. Targetted therapy with a rationale based on specific testing would be a very different matter.
 
We are working on it. The pressure will most likely need to come from Congress and of course a more unified voice from the ME/CFS community. :woot: More to follow on this plan very soon . . . :nerd: Lots of :hug: working on this as we speak. ;)
Has Dr. Lipkin applied for a NIH grant for this work and been denied? Because If I write to the NIH or congress etc.. and ask for them to back this research project, the first thing they are going to say is he needs to apply for a grant. We need some way for him to get money with out having to go through the grant process. Like when the CDC hired him for the XMRV issue or how the NIH coughed up a million dollars for the IOM mess.
 
As somebody who brought up the idea of crowdfunding for CFS research as a way to raise money for CFS research, I'm not happy about Lipkin coming to patients for money.

My original concept for crowd funding was to fully vet the research projects through a crowd sourced web review before funding anything. This would include a full disclosure on how the studies were designed and who is doing what. A full review would allow full input from all the experts before a dime was spent. Everybody's name would be on it with a clear vision and goals.

Additionally, crowd funding was intended to fund guys Like Rich Van K and other independent people who are not boxed in or associated with politics.

Crowd funding truley independent people outside the "establishment" with clear goals and much input from everybody was the goal.

Crowdfunding is a way to change funding, if done correctly. It provides a unique opportunity to fully vet a project. To select the best project, and to insure money is used correctly with accountability. Most importantly; to have an independent study that produces something useful for the community. Tangible and usable results.
 
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Hello @Jarod

Like I said to @Jon_Tradicionali and @Daffodil, members are free to donate or not to donate to Columbia whether it be for financial reasons (like @Bob said) or because they have doubts and queries about the study. I am compiling an email to Columbia that contains all these questions and as much as anyone would like them resolved as fast and as unequivocally as possible.

When I was helping (in a very small way) Simon put the article together I asked around for people's opinions on researching the microbiome for ME and heard from many De Meirleir patients and others who complained that funds should be given to their researchers, not Lipkin. My immediate gut reaction was (if you'll excuse the pun): well if you feel this strognly about it, why don't you try to organise a campaign for him? As should be obvious, even the person with the least experience or knowledge of these things (me) can initiate such a campaign--it's just that I need tons of help.

I am also a little confused as to why you think any results that Lipkin sees researching the microbiome would not be "tangible and usable" even if other points that you made are valid; but perhaps I'll let others jump in here.
 
I am happy to report that I just received an email from Columbia that says that yesterday (2/11/14) 66 gifts were received for the microbiome study for a total of $5,312. Thank you so much, everyone!! :balloons::balloons::balloons:
 
Can people be aware that in the special instructions box you have to type in

for the microbiome study’.

I didn't see this until after I'd donated:(