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Ian Lipkin: Three to Five Years* to Solve Chronic Fatigue Syndrome (ME/CFS)

December 26, 2015

Ian Lipkin flew to Lake Tahoe this December to fundraise for work he’s doing with the Simmaron Research Foundation. In a talk covering his virus hunting career, the threat of pathogens to humanity, and his work with chronic fatigue syndrome (ME/CFS), he dropped a bombshell: he stated that he believes it’s possible to solve ME/CFS in three to five years. 

On that hopeful note, let’s learn more about Dr. Lipkin, his work, and his collaborations with Simmaron.

Dr. Peterson’s Introduction

Lipkin’s Columbia Center for Infection and Immunity (CII) has established close ties with the Simmaron Research Foundation. Only a couple of months before, his chief collaborator, Mady Hornig (and Simmaron Scientific Advisory Board member) had given a talk.  Now Ian Lipkin was here.

Dr. Peterson started his introduction of Ian Lipkin by noting that he’d known him since they crossed paths in the 1980’s when Dr. Peterson sent him patients suffering from HIV/AIDS.

Lipkin has changed the ways researchers identify pathogens

Lipkin has changed the ways researchers identify pathogens

Ian Lipkin began a new era in pathogen detection when he became the first researcher to isolate a virus (Borna disease virus) using genetics.  He identified the West Nile Virus that had throw New York City into a panic, developed technologies to identify SARS and then hand carried 10,000 test kits to Beijing at the height of the outbreak. He most recently discovered a highly dangerous virus that recently jumped into humans called MERS (Middle Eastern Respiratory Syndrome Coronavirus).

Lipkin has pioneered many technological breakthroughs in finding pathogens including the use of MassTag-PCR, the GreeneChip Diagnostic, and High Throughput Sequencing. His latest breakthrough is the development of a new screening technique that enhances researchers ability to find viruses 10,000 fold.

Called the top virus hunter in the world, Ian Lipkin runs the Center for Infection and Immunity at Columbia, and is the director of the Center for Research in Diagnostics and Discovery (CRDD) at the NIH. He also worked closely with Steven Soderbergh on his film Contagion.

Ian Lipkin Talks

Who says brilliant scientists can’t be a hoot to listen to as well? Ian Lipkin’s presentation was both enlightening and at times hilarious. Exhibiting a wry sense of humor, Lipkin poked fun at himself and virtually everyone around him.

The last time he was in Lake Tahoe, he said, was in 1984 and he hearkened back to the HIV/AIDS patients Dr. Peterson sent him in the early 1980’s.

“When you come to a fork in the road – take it!”

He stated the guiding principle in the search for pathogens could be summed up by the great Yogi Berra’s adage “When you come to a fork in the road – take it!”.

HIV/AIDS was the beginning of many changes. Even after the medical community knew it was being passed in the blood it still took them 2 1/2 years to find it. (In a Discover interview,  Lipkin noted that he ran the first clinic in San Francisco that would treat HIV/AIDS (then called GRID) patients with neurological problems. Note an iconoclastic element to Lipkin that showed up early in his career: he was willing to see patients others wouldn’t. Check out Lipkin’s fascinating story of how HIV/AIDS lead to him to study infectious diseases.)

Lipkin-chronic-fatigue-syndrome

Lipkin first showed a willingness to support underserved groups early in the HIV/AIDS epidemic

Lipkin then worked on a virus which demonstrated the effects a persistent viral infection can have on the central nervous system.

Next, in another story with possible overtones for chronic fatigue syndrome (ME/CFS), he investigated patients who’d come down with what appeared to be a mysterious psychiatric disorder. It took him two years but using a new method involving genetic cloning he uncovered the Borna disease virus. It was the first virus discovered using genetic means.

The Borna virus discovery was a game-changer for pathogen community. Jump forward thirty years(after it took the medical community almost three years to find HIV, and viruses are being discovered using molecular means every week. The Center for Infection and Immunity itself discovered 700 new viruses from 2009-2015.

Lipkin was aware of and interested in ME/CFS in the eighties but there was no money. In 1999 he and Britta Evangaard found no evidence of the Borna disease virus in ME/CFS. From there we jump forward to 2010 when NIH Director Francis Collins tasked Lipkin to determine if a retrovirus, XMRV, was causing ME/CFS. XMRV turned out to be a laboratory artifact, and the paper was retracted – something Lipkin said was not all that unusual in science. (He emphasized that he and Dr. Peterson were very careful to put out studies that would stand the test of time.)

The XMRV discovery tanked but proved to be a boon for ME/CFS by heightening the attention around it. Lipkin had kept an eye on ME/CFS for years and after being hired by the Chronic Fatigue Initiative to take it on, he was back in a big way.

In the next portion of his talk he turned to viruses and humans.

Viruses and Humans

How are most viruses getting into humans? From animals. After it’s jump from primates to humans, HIV is, of course, the most familiar example, but viruses are also escaping from bats, birds, pigs, rodents, insects and even camels into humans.

A sea change in the viral field occurred in 1999 when a mosquito-borne virus – the West Nile Virus – had the audacity to attack the residents of the New York City. Lipkin shifted his work from the West to East coasts to search for the virus and ultimately identified it. As the outbreak spread, it got the attention of Senator Joesph Lieberman who sponsored the first big initiative to learn how viruses spread from animals to humans. Politicians, Lipkin noted, can be important allies.

Infections

Most pathogens have yet to be identified by humans.

New York City may be an ideal transit stop for new viruses. Twenty-one million passengers traveling to and from 72 countries pass through New York city airports every year. Animal products including bushmeat – all potentially contaminated with nasty viruses – pour into New York City regularly.

Many more viruses are undiscovered than have been discovered. A survey of one species of bats found fifty-five viruses, fifty of which were new to science. Lipkin estimated 320,000 viruses were still unknown and they’re bumping up against humans all the time. Lipkin next demonstrated how quickly they can jump from animals into humans.

Bats –  Called to investigate an ill Saudi Arabian man (with four wives), he uncovered a new virus called MERS (Middle East Respiratory Syndrome) similar to those found in bats. (Asked if there were any bats in the area, he was told no. The next video showed bats flying every which way in the area :)). If the bats weren’t biting the humans, though, how was the bat virus jumping into people?

Lipkin found MERS was present in about 75% of the camels in the country. Further research indicated that MERS jumped into camels in the 1990’s, and then rapidly escaped into humans around 2010.

MERS

Since its escape into humans around 2010 MERS has spread to 26 countries.

MERS is not particularly easy to transmit but once it gets transmitted, watch out. Death rates are high. It took just one Saudi Arabian to spread MERS to South Korea this year where it killed several dozen people, put several thousand others into quarantine and basically threw the country into a panic. Schools were closed, tourists stopped coming, and parts of the economy slumped as South Korea fought off the virus. It has since been found in 26 countries. It’s the kind of virus that keeps public health officials up at night.

It’s not surprising that Lipkin is wary of pathogens. He noted that he rarely shakes hands but darting a glance at Dr. Peterson said he’d made an exception that evening.

(If you haven’t seen Steven Soderbergh film “Contagion” and can handle apocalyptic scenario’s you might want to give it a try. Lipkin consulted extensively on the movie which involved a worst-case scenario of a virus wiping out much of humanity. The film was praised for its scientific accuracy. (Spoiler alert – we do survive in the end :)).

Ticks –  Coming closer to home Lipkin believes chronic Lyme patients who are not recovering from antibiotics may have gotten another infection from the ticks. He found that over 70% of the Ixodes scapularis ticks associated with Lyme disease carried at least one pathogen and 30% carried more than one in New York. Last year he identified a rhabdovirus (Long Island tick rhabdovirus) new not just to ticks but to science itself. A small survey suggested that 15% of residents may carry antibodies to the virus.

Rats- Lipkin’s  study of New York City’s second most common resident – rats – revealed they carried an amazing array of pathogens including Escherichia coli, Clostridium difficile, and Salmonella enterica, Bartonella spp., Streptobacillus moniliformis, Leptospira interrogans, and Seoul hantavirus.

In one of his many asides (did you know he loves Sinatra?) Lipkin referred to the hamburger and French fries lunch that he and Peterson  usually have. (“Do as we say not as we do” he said). How does Lipkin reportedly like his meat? “Burn it” he tells the waiter. The man is taking no chances – he knows too much.

Infection and Disease

timing-infections-lipkin

The timing of an infection is just one of many factors that determine the effects it will have.

A pathogen is just one of the players, however, in a vast swirl of factors which ultimately determines whether one is going to have a chronic illness. Timing, for instance, is a key factor.

If you expose a mouse to a pathogen at one stage of pregnancy, it’ll stop moving around its cage. If you expose the same mouse to the same pathogen later in pregnancy, it will run round and around its cage unceasingly.

A large autism study underscored the complex role timing plays in humans. The 120,000 person autism birth cohort study found that if a mother comes down with a fever after the first trimester, her chances of giving birth to a son with autism go up three-fold.  If she treats the fever with acetaminophen, her chances of giving birth to an autistic child drop significantly.  If she takes acetaminophen for any other problem than a fever, her risk of giving birth to an autistic child goes up again.

Three to Five Years – An ME/CFS Timeline

How does all this relate to ME/CFS? Likpin cited the findings of their work to date.

  • The suspected pathogens don’t appear to be the problem (the CII is reportedly looking further at herpesviruses.)
  • Evidence suggests altered microbiomes (gut flora) are present
  • Striking differences in immune expression between shorter and longer duration patients suggest profound immune changes have occurred
  • Preliminary evidence suggests that levels “X” and “Y” metabolites and, at least, one immune protein are significantly altered in ME/CFS. (Lipkin embargoed this information pending publication of the paper. One of them is a shocker.)

Lipkin emphasized, though, that ME/CFS is not a one-size fits all disease. For instance, it’s possible that fungi may be a problem for some patients. That’s an intriguing idea given the recent fungi funding in Alzheimer’s disease published in Nature.

Lipkin timeline chronic fatigue syndrome

Lipkin’s timeline for solving ME/CFS given enough resources – a mere three to five years.

Then Lipkin made his bold declaration “We’re going to solve this in three to five years”. It came with a significant proviso “provided the resources are made available” but indicated that he believes ME/CFS is a mystery that can be cracked fairly quickly.  That sounds really fast, but Lipkin’s time-frame is not that far off from Ronald Davis’s 5-10 year time-frame (provided he gets the resources as well.) (or Dr. Montoya’s).

These eminent researchers believe that given the technology present today we could understand ME/CFS fairly quickly – if enough resources were brought to bear.  Lipkin pointed to a slate of researchers in his lab working on ME/CFS to signify the major shift he’s seen happen in just the last couple of years. He said “I couldn’t have gotten them five years ago”.

He highlighted two places the patient community can make an impact:

  • Funding Pilot Studies –   The community can fund pilot studies which can be turned into big grants
  • Advocacy – Lipkin is a savvy researcher. He knows how the NIH works, and once again he emphasized the need for the ME/CFS community to push harder legislatively – to talk to their representatives in the House of Representatives, in particular – and get them to push the NIH for more funding.

Lipkin’s Bucket List

Ian Lipkin has clearly developed a special relationship with ME/CFS, Dr. Peterson, the Simmaron Research Institute. He hadn’t been in the Lake Tahoe area for decades, yet he and two of his assistants had flown across the country to support the Simmaron Research Institute’s spinal fluid work. He was even shaking hands.

lipkin bucket list chronic fatigue

Lipkin’s Bucket List contains two items: solving ME/CFS is one of them.

I shook my head – not for the first time – about Ian Lipkin. How had we gotten so lucky? Lipkin oversees the work of 65 researchers in the U.S. and 150 more across the globe. The New York Times reported that on any given day his lab had 140 viral research projects underway. The head of the National Institute of Allergy and Infectious Disease, Anthony Fauci said, “Lipkin really stands out from the crowd.”

Yet, here he was in the Lake Tahoe area in mid-December exhorting the audience to support an important Simmaron study that he believed needed funding.

What had driven the “The World’s Most Celebrated Virus Hunter” to take on our disease? I asked his assistants. They told me that Ian Lipkin wants to do two things more than anything else before he retires: he wants to solve ME/CFS, and he wants to solve autism. We’re on his bucket list.

That floored me even more (:)) so I asked – but, but…..doesn’t  he care what other people think about this neglected disease? That question left them almost gasping for breath. After they had been able to calm down, they assured me: no Ian Lipkin doesn’t care.

The Simmaron Research Foundation’s Next Spinal Fluid Study

Lipkin was at the event to support the Simmaron Research Institute’s next spinal fluid study. The results of the first one – the most extensive spinal fluid study ever done in ME/CFS – were eye-opening. Using Dr. Peterson’s suggestion to separate atypical from typical ME/CFS patients, and focusing on patients with a longer duration illness, they’d found evidence of an immune dysregulation almost equal to that found in MS. The difference was that instead of being raised, the cytokine levels were reduced in ME/CFS.

That finding surely left a big smile on Lipkin’s and Hornig’s faces.  Earlier they’d found evidence of a profound reduction in immune functioning in the blood of later-duration ME/CFS patients.  Now a similar reduction was showing up in their spinal fluid. These unprecedented findings suggested they were uncovering system-wide problems.

No wonder Lipkin was eager to begin a new and larger spinal fluid study: it’s part of achieving his bucket list.

SR_Donate_6.9.14_1

Triple Your Support! – Between now and Dec 31 triple your support for Ian Lipkin’s work with the Simmaron Research Foundation (SRF). A generous donor is offering to match $2 for every $1 donated before Dec 31. The funds will support the SRF’s collaborations with Drs. Ian Lipkin and Mady Hornig at Columbia University.

 

Major Study Suggests Early Immune Activation May Drive Chronic Fatigue Syndrome

“This study delivers what has eluded us for so long: unequivocal evidence of immunological dysfunction in ME/CFS and diagnostic biomarkers for disease” W. Ian Lipkin

big me-cfs study

Big study – big results

Distinct plasma immune signatures in ME/CFS are present early in the illness. Hornig. M. Monotoya, J, Levine, S., Felsenstein, D., Bateman, L, Gottshalk, G….Likpin. L. Sci Adv 27 Feb. 2015.

It’s a major study indeed – the first, I believe, to come out of the Hutchins Foundation’s Chronic Fatigue Initiative and the media is picking it up quickly. The Hutchins Foundation doesn’t mess around. They’re putting $10 million into researching chronic fatigue syndrome. They do big rigorous studies with top researchers.

This study with its carefully selected patients from across the country was loaded with ME/CFS expertise. Besides Mady Hornig and Ian Lipkin of Columbia, Dr. Montoya, Dr. Peterson, Dr. Klimas, Dr. Bateman, Dr. Levine and Dr. Komaroff were listed as co-authors.

The Simmaron Research Foundation and Dr. Peterson provided samples for this study. One of  Simmaron goals is to provide samples and data from well-characterized patients to major researchers and institutions.

It’s Biological

“These immune signatures represent the first robust physical evidence that ME/CFS is a biological illness as opposed to a psychological disorder, and the first evidence that the disease has distinct stages.” Columbia University Press Release

Once again we see claims made that finally, finally we have proof that ME/CFS is a biological illness. (The head of the CDC said something similar regarding their study about ten years ago at a National Press Club event.) This time the claim is a bit different, however. This time they have not just evidence but “robust” evidence that ME/CFS is a biological illness.

If the study size is any indicator of robustness – and in a well-designed study it is – their evidence is robust, indeed.

It’s So Big!

This wasn’t just a big study – it was a huge study containing almost 650 patients and healthy controls (298 ME/CFS patients and 348 healthy controls).  (A similarly large study is underway at Stanford).

All the patients met both the Fukuda and Canadian Consensus Criteria.

The study wasn’t just big in size – the 51 immune factors it measured meant it was deep as well, and  leptin was one of the immune factors measured.

Different But Not Substantive

The study started off on a bit of a downer. Differences in immune factors between the ME/CFS patients and the healthy controls were present, but not “substantive”.

Note, however, almost all the immune factors are lowered – not increased –  in the chronic fatigue syndrome patients. We’ll come to a reason for that later.

  •  Pro-inflammatory – IL171A (p<.0043), CXLC10 (p<.04), TNF-B (p<.0028), Il-6 (p<.04), sFasL (p<.01)
  •  Anti-inflammatory – Il-10 (p<.024), CSF1 (p<.025)

The one immune factor moderately  increased in ME/CFS was leptin (p<.03).

That didn’t mean many in the group hadn’t experienced profound immune alterations, though. They had – earlier…

Hit and Run

“The immunopathology of ME/CFS is not static” the authors.

Further analyses uncovered something the authors freely admitted surprised them. The ME/CFS patient’s immune measures didn’t differ by triggering factor or age or even by sex – they differed by time.

chronic fatigue syndrome early immune findings

The key factor for the immune system – was time

Alterations in over half the immune measures found (combined with some very, very low probability factors that the results weren’t correct)  (p< >0002-.0008) indicated that “substantive” differences in immune functioning had existed at one point in time.  The short duration patients showed signs of intense immune activation not found in the other groups.

Both the pro and anti-inflammatory sides of the immune system were on high alert early on in ME/CFS.

Immune Differences Between Short-term ME/CFS patients and Healthy Controls:

  • • Increased levels in ME/CFS: IL1A, IL1B, IL-6, IL-12, IL-17a, Il-17f, IL-8, TNF-a, sFasL, TRAIL, IFN-y, CCL2, TGFa, CSF, resistin, CCL-11, CSF2, IL1RA, IL-13.
    • Reduced Levels in ME/CFS – PDGFBB, CD40L

Cytokine results have been spotty in ME/CFS and that’s been a problem.   A few up or down regulated cytokines just don’t raise many eyebrows in the research world. They’re looking for evidence of broad immune alteration – and here it is. I don’t think anybody has seen this kind of sweeping immune activation in ME/CFS before.

Viral Fighter Stands Out

A logistic regression suggested that IFN-y played a particularly significant role in the immune system activation. Produced mostly by natural killer and cytotoxic T-cells – two cells with similar problems in ME/CFS – IFN-y is both an immune stimulator and pathogen inhibitor. (Microglia are big IFN-y producers in the central nervous system).

The IFN-y findings suggest either a pathogen attack or an autoimmune shift may be triggering the immune upregulation seen early in the disease.

infection chronic fatigue syndrome

Bug alert! The early immune findings were consonant with a pathogen attack.

High IFN-y levels are associated with Th2 dominance in the immune system and an increased risk of autoimmune processes. Post-viral fatigue has been associated with high IFN-y levels, and alterations in the IFN-y gene have been associated with increased fatigue following infection as well.

IFN-y also showed up in Broderick’s small study examining 16 cytokine levels in adolescents in the first two years after coming down with infectious mononucleosis. Four cytokines IL-8, Il-23, IL-5 and IL-2 were significantly altered or nearly significantly altered.

IFN-y levels were not increased but a computer model suggested it and four other cytokines constituted an immune signature that differentiated people who came down with ME/FS after IM and those who recovered.

Mady Hornig on the Study

IL-5 levels were significantly decreased in ME/CFS patients but IL-5 did not, interestingly enough, make it into the computer model. Further analysis indicated that IL-5 levels were significantly correlated with Il-23 and IFN-y: two cytokines that did make into the model. These cytokines were essentially analogues for IL-5 in the body.

THE Pathway???

IFN-y also accelerates tryptophan degradation by activating the indoleamine-2,3 deoxygenase enzyme in the kynurenine pathway – Mady Hornig’s favorite pathway. That pathway produces neurotoxic substances that increase production of the excitatory neurotransmitter glutamate that some researchers believe is in play in both fibromyalgia and ME/CFS. Andrew Miller of Emory University has earmarked the kynurenine pathway in ME/CFS.

kynurenine pathway chronic fatigue

Could the kynurenine pathway be it for ME/CFS?

Cognitive problems and mood changes have been associated with up-r egulation of the kynurenine pathway in diseases ranging from Alzheimer’s to depression. In fact, disruption of the one part or other of the kynurenine pathway occurs in many neurological and psychological disorders.

The authors were confident enough to hypothesize that lesions produced by high IFN-y levels early in the disease are producing the cognitive slowing and depression found in ME/CFS. Andrew Lloyd of the Dubbo project has been suggesting for years that high cytokine loads early in the disease process had disrupted brain functioning, but nobody has gotten this specific before. Now Hornig and Lipkin et. al are proposing a specific mechanism for that: IFN-y produced lesions.

“We propose that IFN-y mediated lesions in kynurenine metabolism may culminate in the depression and psychomotor tardiness (slowed information processing) that contribute to disability in some patients with ME/CFS”.

That kynurenine pathway gets more intriguing when we consider that IFN-y activation and tryptophan degradation has been associated with chronic Epstein-Barr virus infection. Epstein-Barr virus is often associated with infectious mononucleosis – a common trigger of ME/CFS.

CD40L

CD40L appears to be another early key immune factor. A clear driver of immune functioning in the healthy controls and longer-term ME/CFS patients, CD40l was found to be reduced and strangely disengaged from the immune system in shorter-term ME/CFS patients.

A B-cell maturation regulator, deficiencies in CD40L are associated with recurrent infections and unexplained cognitive issues and CD40 deficient mice exhibit major immune deficiencies. Citing the Fluge/Mella Rituximab study the authors suggested the collapse of this immune factor   early in this disease could be important.

Nice Fit

One scenario proposed by this study – natural killer and cytotoxic T-cells pumping out IFN-y early in the disease only to collapse later on–appears to fill in some holes that smaller studies would have missed. If this study is representative maybe 20% of the patients in any study have probably had ME/CFS for three years or less. That would mean that the typical low NK dysfunction will show up but the up-regulation early in the disease the authors believe may be contributing to that doesn’t.

Flipping the Switch

That suggests that somewhere around the 3rd year of illness major immune shift occurs. The immune system flips from being hyperactive not to being normal but to being somewhat under active.

Dr. Hornig described a condition of immune system burnout:

“It appears that ME/CFS patients are flush with cytokines until around the three-year mark, at which point the immune system shows evidence of exhaustion and cytokine levels drop.”

primed for burnout cfs

Does the immune system get burned out in longer duration ME/CFS patients?

There’s something very right about “immune exhaustion” being associated with this disease The fact that many cytokines  increased in the early stages of ME/CFS are  decreased in the later stages suggests a kind of burnout process is occurring.

Poor natural killer cell functioning in ME/CFS is often described as a type of immune system “burnout” and evidence is emerging of similar cytotoxic T-cell problems as well.

Leptin Again

It’s hard for me parse how leptin showed up in this study. The only immune factor increased in the whole ME/CFS group vs the controls, leptin was highlighted in one network analysis of early duration patients and showed up moderately in two others. The authors noted that it was tightly correlated with most of the immune factors later in the disease but not early.

Another cytokine called PDGFBB appeared to be the main driver of the immune reductions later in the disease.

Hit and Run

That suggests the disease has in some way moved on from the immune system. The authors of the paper didn’t have a great explanation for why people remained ill after their immune system activation had died down or had become decreased. If Younger’s findings pan out perhaps the lone elevated immune marker – leptin – found is enough.

hit and run me/cfs

The findings suggested ME/CFS is a hit and run disease.

A email to Jarred Younger gave a quick answer  and a warning that it was not based on a close reading of the paper. He suggested systemic inflammation may drive ME/CFS early on but sensitized microglia and astrocytes in the central nervous system drive it in its later stages. Because we don’t have good ways to test central nervous system inflammation at that point the disease mostly becomes invisible to testing afterwards.

In fact, the authors tantalizingly noted because ME/CFS appears at least in part to be a central nervous disorder cerebral spinal fluid may very well be a better medium to investigate than peripheral blood. That could suggest we’re due some more important findings in a couple of weeks when the Simmaron Research Foundation/Chronic Fatigue Initiative CSF study is published.

The High Cytokine Longer Duration Patients

The study doesn’t make any mention of longer duration patients ME/CFS patients with high cytokine levels. Anecdotal reports from patients indicate they are definitely out there, but this study – involving many quite ill patients being seen at ME/CFS practitioners – suggests that they probably constitute a relatively small subset of patients.

Conclusion

“We now have evidence confirming what millions of people with this disease already know, that ME/CFS isn’t psychological,” Mady Hornig, MD

This large study presents what appears to be almost novel finding in medicine: distinct before and after stages early in a chronic illness. In the early stages of ME/CFS (first 3 years) a distinct and impressive immune activation is present that is followed by modest immune deactivation.

The early immune activation is highly suggested of an infection or some other immune altering process.

The study may ultimately open up possibilities for treating patients with recent onset but provides no possible treatment options at this point for patients who have been sick longer. The  more modest immune deactivation found later in the disease suggests that the core causes of the disease are either found elsewhere or were not illuminated by the study.

A major question facing researchers now is finding ways to translate this hit and run immune activation or viral infection into long lasting central nervous system problems. Microglia sensitized by chronic immune activation/kynurenine pathway activity is one possible answer.

Ian Lipkin’s statement that they hope to find important answers in their microbiome study suggests he believes a permanently altered microbiome  could provide an answer to that question.

“The question we are trying to address in a parallel microbiome project is what triggers this dysfunction.”Ian Lipkin

The authors statement that cerebral spinal fluid may provide a better medium for understanding this disease could mean we’re in for some interesting findings in a couple of weeks.  The Simmaron Research Foundations rare  and extensive trove of cerebral spinal fluid samples from ME/CFS patients provided the foundation for that study.

Stay tuned!

Foremost Virus Hunter Finds Biomarkers, Few Viruses in Big Chronic Fatigue Syndrome Study

Dr.Ian Lipkin collaborated with Dr. Peterson, Dr. Klimas, Dr. Bateman and others

A Surprise Presentation

We will publish data very soon on biomarkers of cytokines. Our evidence now suggests there is ongoing stimulus to the immune system. Dr. Ian Lipkin

You don’t usually get study results in talks like the one put on by  the CDC yesterday but this time Dr. Ian Lipkin spilled the beans on the results from the big pathogen studies sponsored by the Chronic Fatigue Initiative (n=200) and Dr. Montoya (400).  (From notes taken on the talk)

Virus Study Results Revealed

SR Facebook logo new

The Simmaron Foundation provided a rare resource: sixty cerebral spinal fluid samples

Viruses have always been the elephant in the room in ME/CFS; everybody has wondered about them but until the Chronic Fatigue Initiative came along, few major studies had been done.  This landmark  study, using the one of the top virus hunters in the world and epidemiologist  Mady Hornig, and containing hundreds of patients from ME/CFS specialists (Dr. Peterson, Klimas, Montoya, Levine, etc.) from across the country, sets a benchmark for pathogen research in ME/CFS.

A special feature of the study involved Simmaron Research’s spinal fluid samples. Called a ‘unique resource’ earlier by Dr. Mady Hornig, these samples allowed the researchers to get as close to the brain – long thought to be a key area in chronic fatigue syndrome – as they could.  And the spinal fluid results were spectacular.

The Studies

virus cartoon

This study funded by the CFI, using top labs, and involving hundreds of people with ME/CFS, is a benchmark in ME/CFS research.

The studies looked at both pathogen presence and  the immune response in hundreds of people with chronic fatigue syndrome.

Pathogens

  • First Phase – Screens for 18 specific pathogens already implicated in ME/CFS (herpesviruses, HTLV, enteroviruses, West Nile Virus, etc.) were done on blood from Montoya’s patients and the CFI’s group (Dr’s Peterson, Klimas, Bateman, Levine, etc.).  Dr. Lipkin was looking for the virus, not a indication it was present, but the virus itself. Any finding of a virus in the blood would indicate it was active.  The same screen was done on Dr. Peterson’s sixty spinal fluid samples.
  • Second Phase – The second phase involved sequencing all the DNA/RNA in the blood to identify  known and unknown viruses. Dr. Lipkin’s lab has been able to identify hundreds of novel viruses using this technique.
  • Third Phase – Any finds in the second phase are confirmed/denied by more accurate testing.

Immune Response

A ‘multiplexed immunoassay’ looked at 50 proteins associated with immune activation/inflammation and oxidative stress.

Active Viruses Strike Out

Four of the 285 ME/CFS blood  samples tested positive for HHV-6B.  One of the sixty spinal fluid samples tested positive for a virus (HHV-6B).  None of the other viruses commonly associated with ME/CFS (Epstein Barr-Virus, enteroviruses, the cytomegalovirus, etc.) commonly associated with ME/CFS showed up in the first pathogen screen.

The high throughput screening designed to look for any viruses including novel viruses drew a blank as well. Dr. Lipkin was confident in his results stating his lab had found over 500 new viruses using this technique.

Infections

Lipkin’s search for 18 viruses and for novel viruses in hundreds of people with chronic fatigue syndrome largely turned up empty

The  news – that fewer than 2% of patients  with infectious onset – tested positive for viruses in the blood was stunning but not without precedent.  Dr. Unger reported earlier that  the first stage of the CDC’s BSRI pathogen study  drew a blank.  A spinal fluid study also turned up no viruses, and PCR analyses done by the Dubbo group were unable to find evidence of a virus in their post-infectious cohort.

With two large sample sets turning up negative in the lab of one of  most acclaimed virus hunters on the planet, it’s probably safe to say that the hunt for an virus in the blood of people with ME/CFS is over.

(Lipkin did report 85% of pooled samples possibly showed evidence of a retrovirus but believes they will not be related to CFS. He also dismissed earlier rumors that a novel infectious agent had been found.)

Infectious Agent Still Proposed

That doesn’t mean an infectious agent is not involved. In  fact, Dr. Lipkin stated he didn’t doubt that an infectious agent was involved.  He didn’t say where and he didn’t say it was still present.  His allusion to the importance of finding evidence of a past infection (“researching the shadows”) suggested  he could  be leaning to the ‘hit and run’ hypothesis where a pathogen sweeps in, does its damage, and then gets removed by the immune system.

The Dubbo studies’ finding that high cytokine levels early in the infection were strongly associated with getting ME/CFS later on suggested an overactive immune system may have a blown a few fuses somewhere.

On the other hand, Dr. Lipkin specifically alluded to an ‘agent’ driving the immune activation he found in both the blood and spinal fluid of ME/CFS patients (but not the healthy controls).

Localized Infections Still Appear to Be a Possibility

Dr. Lipkin didn’t discuss this possibility. The blood is the most convenient place to search for an virus and active viruses usually do travel through the blood but central nervous system or localized infections may not show up in the blood or the spinal fluid.

Some evidence of localized infections in the gastrointestinal tract has been found in ME/CFS. A De Merileir team found evidence of HHV-6, EBV and parvovirus B-19 in 15-40% of gut biopsies. Eighty-two percent of stomach biopsies tested positive for a protein associated with enteroviruses in Dr. Chia’s 2008 study. Dr. Chia reports enteroviruses are found much more readily in the stomach than the blood (but he is able to find it in the blood). No enterviruses were found in the present study.

Vanelzakker proposes that a localized vagal nerve infection is causing the symptoms in ME/CFS.  It’s not clear what these results mean for Dr. Lerner’s theory that an aborted EBV infection is spilling viral  proteins into the blood that are sparking an immune result.

The Three Year Breakpoint 

Data suggests there may be substantial differences in biomarkers in people with less than 3 years of disease and those with more than 3 years of disease. Dr. Lipkin

subsets

Two recent research findings suggest the immune systems of people with recent onset and longer duration ME.CFS are significantly different.

Echoing similar recent findings from the Broderick/ Klimas team at NSU, Dr. Lipkin stated the immune system in ‘newbies’  (patients with recent onset), and patients with a longer case of  ME/CFS was different.  Dr. Lipkin’s ability to independently differentiate ‘newer’ from ‘older’ patients using  cytokine results is pivotal, and points to the central and progressive role the immune may play in this disorder.

With Broderick suggesting that two distinct illnesses emerge over time, and Lipkin proposing treatment options should reflect illness duration, it was clear these changes were significant indeed.

Natelson, on very different track, is finding changes over time as well with more POTS in his adolescents and a different kind of orthostatic intolerance in older patients.  Studies are underway to understand why this might be so.

An Early Allergic Response

Allergy is not usually mentioned in association with ME/CFS but eosinophils and other markers suggested to Dr. Lipkin that  the allergic response was enhanced in ME/CFS early on. The cast of immune characters Lipkin’s biomarker search fleshed out was refreshingly familiar with IL-17, IL-2, IL-8 and TNF-a leading the list.

IL-17

Levels of Il-17 were raised in recent onset ME/CFS patients. Lipkin suggested immunomoculators able to bring IL-17 levels down might be a treatment option at some point.

No mention, interestingly, was made of autoimmunity, but Lipkin, pointing at the high IL-17 levels in the newbies,  embraced the idea (only after further validation) of using immunomodulators in some ME/CFS patients  to turn down the fire in the immune system.  Immunomodulators exist now, he said, that can bring that IL-17 cytokine  down.  (He stressed, however, that there is not enough research to start using them on patients.)

The spinal fluid, interestingly enough, showed a very different pattern. It showed a consistent profile of immunological dysregulation in CFS, regardless of duration of illness. Dr. Lipkin identified increased IL-10 and IL-13 levels suggesting enhanced Th2 activation and increased IL-1B, IL-5 and IL-17 suggesting Th1 (proinflammatory) activation. Dr. Lipkin was obviously intrigued by the differences in cytokine findings between spinal fluid and blood.

A Focus on the Gut

I think the gut microbiome is going to be where the action is (in chronic fatigue syndrome). Dr. Ian Lipkin

Lipkin’s prime focus at this point is the gut and fecal matter. He  believes the gut microbiome is going to play a, perhaps the key role in ME/CFS.

The Hornig/Lipkin team has had considerable experience with the gut microbiome. They’ve been successful  finding gut abnormalities in autism, a disorder that shares some intriguing commonalities with ME/CFS, including low natural killer cell functioning.  Noting that the gut can modulate immune functioning, not just in the gut, but across the body he asserted the gut is going to be ‘where the action is’ in ME/CFS.

gut picture

Lipkin believes ‘the action’ in ME/CFS is going to take place in the gut microbiome (flora)

Unfortunately, the fecal samples originally collected didn’t provide enough material for analysis so they’re restarting that part of the study.

Even more unfortunately, characterizing the bacteria in fecal matter is extremely expensive and with Lipkin, with just 10% of the money needed to do the job, evidenced considerable frustration at having his hands tied  by lack of money.

Stating that he was not pointing fingers, he then proceeded to point  them everywhere:  at federal politics of funding, at NIH budget cuts, and at the paucity of research funding in our field. As at his last public talk, he urged patients to get active and enlist their congressman in  their cause.  Oddly enough, he also said Dr. Fauci, long considered a kind of ME/CFS nemesis by patients, was supportive of more work in this area.

Reiterating his belief that chronic fatigue syndrome has pathophysiological roots, Lipkin noted his history with it. Dr. Lipkin’s 1999 ME/CFS  study did not find the virus he was researching but it did find a great deal of immune (polyclonal B-cell) activation, a pattern that was recently repeated when he didn’t find XMRV but was impressed by the evidence of immune activation he did find.

Next Up

Lipkin, in close collaboration with his ME/CFS experts, Dr. Peterson, Dr. Montoya. Dr. Klimas, Dr. Komaroff, etc. is following these results with deep sequencing of samples, completion of fecal matter analysis and larger studies to confirm and deepen the understanding of cytokines as biomarkers. Protein analysis was not mentioned but it was part of the original project. Tracking down evidence of past infection was also on the agenda.

Conclusion

The Chronic Fatigue Initiative’s pathogen study set a benchmark for rigor and size in the ME/CFS research field, not the least because of Dr. Lipkin’s leadership. Surprisingly few viruses were found in the blood of ME/CFS patients, yet Lipkin asserted that an infectious agent was likely driving the immune activation he found in the blood and spinal samples.  Cytokine analyses of the blood suggested a different pattern of immune dysregulation was present in  newer onset patients (<3 years) and patients with a longer duration of illness.

Dr. Lipkin believes the “primary cause is likely to be an infectious agent” and the gut microbiome is where ‘the action’ will be in ME/CFS.