Lipkin finds biomarkers not bugs

September 12, 2013

The CDC PCOCA telephone broadcast on 10 September 2013, featured a lengthy presentation from Dr Ian Lipkin who revealed some stunning initial results from the study that is primarily hunting for pathogens in ME/CFS. Simon McGrath and Russell Fleming (Firestormm) review this exciting and possibly game-changing news…

Lipkin - CFI

Dr Ian Lipkin
Lead Researcher
Chronic Fatigue Initiative (CFI)
Pathogen Discovery and Pathogenesis Study

Read the full Lipkin Transcript: Here.

Dr Ian Lipkin has been a human whirlwind in ME/CFS research since he became involved a few years back, and he’s just surprised us all by announcing the first results from the world’s largest ever biomedical ME/CFS study in a public broadcast!

He started off by lowering expectations: their results thus far do not implicate a single infectious agent and they have not discovered the cause of CFS. But he then wowed the hundreds listening to the conference call by revealing they had found strong evidence for immune overstimulation, both in blood plasma and in cerebro spinal fluid; and that they were now hard at work trying to identify what could be causing these abnormalities.

The big pathogen hunt draws a blank thus far

This study is looking exhaustively for any pathogen: viral, bacterial, fungal or parasitic, to see if a chronic infection could explain ME/CFS. Many of the results are in, but so far there is no clear sign of viruses at least. It is every bit a collaborative effort, with patients provided by long-established physicians including Dr Dan Peterson and Professor Jose Montoya.

The Key Players

Lipkin began by thanking the clinicians who had provided the all-important samples. Effectively it was a roll call of America’s top ME/CFS physicians:

Professors Jose Montoya, Anthony Komaroff and Nancy Klimas; and Drs Dan Peterson, Lucinda Bateman, Sue Levine and Donna Felsenstein.

The study itself was run by Dr Mady Hornig (CFI Principal Investigator) at the Centre for Infection and Immunity at Mailman School of Public Health; where Lipkin is also based.

He went on to acknowledged the very necessary support of the Chronic Fatigue Initiative, the Evans Foundation and an anonymous donor supporting Montoya’s work.

First the researchers looked at blood plasma for 285 CFS patients and 201 controls from Jose Montoya at Stanford (these are serious numbers). They searched for genetic evidence of infection using a panel that was able to detect 20 specific bacteria, viruses or parasites; including Epstein-Barr virus, Human Herpes Virus 6, enteroviruses, Influenza A and Borrelia bacteria.

Next they used high throughput sequencing, a method that was pioneered by Lipkin and colleagues that was used to discover over 500 viruses – so they felt fairly confident that if a virus was present, then they would have found it.

But they effectively drew a blank using both methods – only 1.4% of CFS patients were found to have HHV6 infection, but so did 1% of controls.

Other findings…

Lipkin said they also found Anelloviruses in 75% of those studied in plasma samples, but it was not specific for Chronic Fatigue Syndrome (we don’t currently have separate figures for patients and controls). Anellovirus is believed to cause widespread chronic infection in the human population, but has not yet been associated to any specific disease. “I really don’t know at this point what this finding means” said Lipkin.

They also found retroviruses in 85% of the sample pools. However, Lipkin expressed caution:

“It is very difficult at this point to know whether or not this is clinically significant. And given the previous experience with retroviruses in Chronic Fatigue, I am going to be very clear in telling you – although I am reporting this at present – in Professor Montoya’s samples neither he nor we have concluded that there is a relationship to disease …if I were to place bets and speculate, I would say that this is not going to pan out.”

Window on the brain: Cerebrospinal fluid samples

Both Lipkin and Hornig were clearly excited to have had access to the 60 cerebrospinal fluid samples from Peterson, and kindly donated by his ME/CFS patients. Cerebrospinal fluid bathes our brain and spinal cord so it gives access to what goes on in the brain, a prime site of interest to researchers, but hard to access; so these spinal tap samples are precious.

However, using the same molecular techniques to track down pathogens as they had applied to Jose Montoya’s samples, Lipkin’s team again drew a blank.

At the Invest in ME conference in May, Hornig said they had  tentative findings that there might just be a novel pathogen or pathogen candidate in these samples – but it was too early to say for sure. In reply to a question yesterday, Lipkin said there is no more to report:

we do not yet have a novel pathogen nor do we have a pathogen candidate in which I would have any confidence. So at this point we have no plans to publish anything.

Nonetheless, he also said they hadn’t finished all the DNA sequencing work on these samples, so this is not yet a dead end.

Immune stimulation and biomarkers

Up to this point we’d heard a lot of very impressive negative findings, based on large, well-defined samples of patients and controls, and using powerful research techniques. But what we most wanted to hear about was positive leads – and Ian Lipkin duly obliged:

plasma and blood

Plasma is the clear fluid left when blood is separated

They took plasma from the CFI cohort of 200 very well-defined ME/CFS cases and 200 controls collected by clinicians (See ‘Key Players’ above). Then they searched for cytokines and chemokines, which are regulators and controllers of the immune system.

The big finding was a decrease in levels of Interleukin’s IL-17, IL-2, IL-8 and in TNF-alpha – all of which have a role in pro-inflammatory responses. Lipkin believes these significant differences are worth follow-up in larger cohorts to better understand what they mean.

Professor Jonathan Edwards (who is an adviser to the planned UK Rituximab trial) commented on this forum yesterday, that it was a surprise to see TNF-alpha levels decrease, and suggested it could mean that ‘inflammation’ is too crude a concept for the process.

Lipkin and colleagues also found upregulation in Leptin, a hormone that plays a key role in regulating energy uptake and use, and Serpin, a protein family with multiple roles. More obscure cytokines, and and their cousins chemokines, were also affected but Lipkin didn’t give any further detail.

Two new patient types revealed

Ian Lipkin said they found something very surprising in their data: there appear to be substantial differences in profiles between those people who have had the disease for 3 years or less and those who have had the disease for more than 3 years. And that this is important because, “it could have implications for therapy as well as for diagnosis”.

In the ‘early group’, who have been ill for less than 3 years, there seem to be a number of markers suggestive of some sort of allergy aspect. For example there are often increased numbers of eosinophils in blood, with more differences in cytokines. But while this is tentative, he was more confident in the finding the IL-17 was elevated in these ‘early’ patients, compared with reduced levels in patients ill for over three years.

Lipkin said that he thought this 3-year division could be very important and that it hadn’t been something they were looking for; but would be looked at in any future work they did.

Cerebrospinal fluid: different differences

Lipkin’s team also found differences in cerebrospinal fluid biomarkers between patients and controls. I’m not sure from what he said if there were significant differences between the ‘early’ group and patients who had been ill for more than three years. However, they did find that patients had elevated levels of the TH-2 type cytokines IL-10 and IL-13 and elevated levels of four TH-1 cytokine: IL-1 beta, TNF-alpha, IL-5, and IL-17. Lipkin said this is compatible with a profile of some particular types of response that may provide insights into immunological dysregulation in Chronic Fatigue Syndrome.

So, overall they found clear differences between patients and controls in both plasma and spinal fluid. Many immune differences have been detected before, but findings are not very consistent and none had used such a large and robustly-defined patient cohort (meeting Fukuda and Canadian criteria), or with such carefully matched controls.

HEALTH WARNING

Dr Ian Lipkin again was very clear that he did NOT recommend anyone act on these provisional findings: he doesn’t want anyone to get a spinal tap, or measure the cytokine levels and hope to modulate them with drugs based on this research: it’s too early for that.

The lost years…

Back in 1999 Ian Lipkin published his first paper on CFS, which ruled out a connection between the illness and Borna Disease Virus (one of the many viruses he’s discovered). But crucially they found evidence of polyclonal B-cell reactivity. He commented that back then:

“there was a very strong sentiment in some portions of the scientific and clinical communities – not always and not everywhere – but in some portions of the community, that this was a psychological illness. What I said was that based on our findings we had very strong evidence that people with Chronic Fatigue Syndrome were truly ill with a physical illness and they deserved a “Deep Dive” to find out why they were ill.”

He noted that was a long time ago and dryly added “I am pleased to see that people are now paying much more attention to this disorder and what we can do about it”.

What next?

“I still believe the primary cause is likely to be an infectious agent.”

Having found clear signs of cytokine abnormalities, Lipkin wants to find out what is causing these changes; he currently thinks that an ongoing stimulus is causing immune system activation which might be resulting in the symptoms we associate with the disease. And interestingly, he still believes that  infection lies at the root of it all – despite not yet finding any infections.

The team – working closely with the clinicians he’s already mentioned – plan even more extensive work on a cohort of 200 CFI patients and controls. They will further test for viruses and crucially they will also look for bacteria and fungi by sequencing ribosomal RNA (which should detect unknown bacteria and fungi, as well as known ones).

Previous infection detection

The group has looked for current pathogens in the blood and spinal fluid samples they have – and has so far drawn a blank, though there is more work underway. However, what if the trigger for ME/CFS is an earlier infection that has since been cleared: the ‘hit and run’ scenario Hornig has described? Lipkin says they are looking for “shadows” of previous infections by searching for antibodies against specific infections, rather than the infections themselves (the body will continue to produce low levels of specific antibodies years after an infection has been cleared (the basis of much immunity)).

They will use a technique called LIPS to look for antibodies against particular known infection. In addition, as in their viral sequencing work, they will use an ‘unbiased’ system (using peptide arrays) that should detect all potential viruses – or rather antibodies against them. They don’t currently have an ‘unbiased’ system that works on bacteria or fungi.

Fecal future?

What excites Ian Lipkin most is the gut microbiome, the community of micro-organisms that live in our gut – which might seem odd given his focus so far on pathogens and the immune system. However, it turns out that the microbiome can have a profound influence on the immune system and may be important in many diseases. Hornig and Lipkin have already developed techniques to study the microbiome, and have shown it could be a factor in autism and even in the severity of colon cancer.

It turns out the best way to find out what lives in the microbiome is to measure what comes out of the gut: fecal matter, or ‘poop’ to you and me. Their ME/CFS microbiome project has started, but Lipkin felt there wasn’t enough material in the first attempt at gathering samples, so things have been delayed as they switch to a new technique (the ‘special’ collection cups).

The Big Ask: “we can’t do this without you”

Microbiome research is very expensive (analysis, not sample collection), and they currently only have the funds to do 10% of what’s needed. In fact, throughout the call, Lipkin was stressing the need for more funds, because good research costs and ME/CFS is woefully underfunded: there just isn’t enough money to do the work needed. The current science budget cuts (Sequestration) in the US makes the climate even harder.

“It is probably inappropriate for me to be passing the hat, but that’s precisely what I am doing.”

He urged patients to contact their representatives in Congress, demanding more funding for ME/CFS research – pointing out that in the early days of HIV, there was little funding until patients demanded it.  He also said that if patients were able to afford it, they should invest in research themselves.

Conclusion

ME/CFS research is coming of age. Ian Lipkin has reported these early – and soon-to-be published results – from a huge study, using 285 of Jose Montoya’s patients, the 200 patients from the Chronic Fatigue Initiative, plus the 60 ‘gold-dust’ spinal fluid samples from Dan Peterson’s patients. Using state-of-the-art techniques, they have largely ruled out a role for a specific pathogen – though that work is incomplete. And they have strong evidence of ongoing immune stimulation in ME/CFS patients, with abnormalities found in both the blood and spinal fluid. The next stage involves deeper searching for bacteria and fungi, looking for ‘shadows’ of previous infections and investigating the gut microbiome. These are exciting times!

Thanks to the CDC for organizing the presentation and to Firestormm for providing a transcript of this talk, and above all to Dr Ian Lipkin for taking time out to talk to patients.

If you would like to donate to Ian Lipkin’s research, click here. In the comments box, put “for M.E/C.F.S Study” to make sure it goes to the right place.

 

Simon McGrath tweets on ME/CFS research:

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161 comments

{ 161 comments… read them below or add one }

Firestormm September 14, 2013 at 12:02 pm

The microbiome and poo

This is a gentle introduction to the microbiome and also to Jeroen Raes who quite coincidentally I was informed of by Linda Vasteenwinckel when discussing the article on Lipkin above.

Linda produces ME/CFS Evolving Science on Facebook – always my first port of call for new publications – and said of Dr Raes:

"His lab are at the forefront in gut microbiome research nowadays and are now working on Het Vlaams Darmfloraproject, the most ambitious large-scale gut microbiome project in the world.

Their first focus is on obesity, diabetes and IBD, but many ME/CFS patients have sent in samples too, and we're trying to convince them to take a closer look at those in a later stage.

But it would be fantastic to see Lipkin/Hornig's group collaborate closely with Raes' group."

I'd certainly not encountered him before and need to do some reading I think.

Thanks to Antares in NYC for posting the programme on a separate thread.​
I believe DOB is still featured on BBC2 each week – though I may be wrong as I don't have a television.​
:cool:

Legendrew September 14, 2013 at 12:11 pm


Firestormm

The microbiome and poo

This is a gentle introduction to the microbiome and also to Jeroen Raes who quite coincidentally I was informed of by Linda Vasteenwinckel when discussing the article on Lipkin above.

Linda produces ME/CFS Evolving Science on Facebook – always my first port of call for new publications – and said of Dr Raes:

I'd certainly not encountered him before and need to do some reading I think.

Thanks to Antares in NYC for posting the programme on a separate thread.

I believe DOB is still featured on BBC2 each week – though I may be wrong as I don't have a television.

:cool:

Interesting video – yet again the vagus nerve comes up. Seems to be linked to everything.

alex3619 September 14, 2013 at 2:08 pm


heapsreal

I still cant get past many of us not having chronic viral infections when most of us have low nk function, who's job it is to kill viruses. if its herpes virus or some other virus, if they cant find them then they probably havent looked in the right places or dont have the right tests.

I think they will find viruses in tissue, but those require different testing.

On the other hand, if our B cell immunity is nuts, and our T cells cranked up, and our RNase L modified and amplified, we might indeed have something like normal virus immunity. The problem is that under these conditions if we get a virus then our immune systems are getting a boot and will go into overdrive. Also I think it more likely we will get more viral infections. Its about frequency, not acute viral severity. It would be about immune severity i.e. how hard the symptoms are going to hit us, and how long it will take to recover. This point of view can be summed up in the phrase "its the immune system, not a virus".

Sparrowhawk September 14, 2013 at 2:59 pm


alex3619

I think they will find viruses in tissue, but those require different testing.

On the other hand, if our B cell immunity is nuts, and our T cells cranked up, and our RNase L modified and amplified, we might indeed have something like normal virus immunity. The problem is that under these conditions if we get a virus then our immune systems are getting a boot and will go into overdrive. Also I think it more likely we will get more viral infections. Its about frequency, not acute viral severity. It would be about immune severity i.e. how hard the symptoms are going to hit us, and how long it will take to recover. This point of view can be summed up in the phrase "its the immune system, not a virus".

So this is one of those puzzlers. For some with ME/CFS they have very overt and ongoing signs of illness like swollen lymph nodes, sore throat, headaches etc. My particular thing presented with months of pervasive dizziness as a prelude to a complete collapse with headache and the whole nine yards. But since that three month period I have literally not gotten "sick" while all of my famiy members (kids got to school and wife is a teacher) have brought home all sorts of things. That seems to jive with what some others on this board have also reported. Like the immune system is in overdrive, but while you're not getting "better" you still don't get "sick." Not complaining because if I got flu or a cold on top of this it wouldn't be pretty. But it doesn't make sense to me.

chronix September 14, 2013 at 3:09 pm

"However, they did find that patients had elevated levels of the ⁠TH-2 type⁠ cytokines IL-10 and IL-13 and elevated levels of four TH-1 cytokine: IL-1 beta, TNF-alpha, IL-5, and IL-17."

Haven't elevated cytokines been found in depression and other psychiatric conditions as well as diseases with co-morbid depression, where in the latter, cytokines are thought to play a role in the depression but not the main illness?

Can cytokine profiles serve as reliable biomarkers, and if so, will CFS be distinguishable from psychiatric disorders?

natasa778 September 14, 2013 at 3:46 pm


The big finding was a decrease in levels of Interleukin’s IL-17, IL-2, IL-8 and in TNF-alpha – all of which have a role in pro-inflammatory responses. Lipkin believes these significant differences are worth follow-up in larger cohorts to better understand what they mean.

Interesting that lowered production of these very cytokines are associated with disease progression and immunological damage in HIV patients – HIV+ long-term nonprogressors retain the ability to make these cytokines, while individuals with progressive disease start producing less of Il-17, TNF-α and IL-2 after a while…

Also interesting to read that this sudden downturn in cytokine levels happened after exactly 3.1 years in this patient
Patient maintained a stable/low viral set point for 3.1 years before control of viral replication was lost … Gradual loss of functionality was observed in these responses, characterized by early loss of IL-2 …

This paper could give us further clues on reduced IL-17 levels in chronic sufferers (also possibly linking to gut barrier breakdown)

Studies in nonhuman primate models of lentiviral infection and in HIV-infected human individuals highlight pathogenic infection to be associated with loss of Th17 cells. IL-17 serves to maintain the integrity of the mucosal barrier. Loss of Th17 cells may permit microbial translocation across the gastrointestinal mucosa and thereby promote immune activation driven by bacterial lipopolyscaacharide, which is associated with disease progression. We demonstrate that …. We demonstrate that …. reduced Treg and IL-17 numbers is a feature of chronic HIV infection

acer2000 September 14, 2013 at 4:13 pm

I will have to go back and check, but I'm fairly certain the Lyme PCR yield is in the low single digits. In this case, that would mean that if all 200-something people he was studying had proven Lyme disease, only a few would show up as positive using that method. My point is not to argue that Lyme is or isn't the cause here, its to show that for any of the hundreds of pathogens he tested for using the blood and CSF with sequencing, the negative result he got could be enough to rule out their involvement completely, or it could mean nothing – it all depends on the nature of that particular bug.

SOC September 14, 2013 at 5:19 pm

It is somewhat outdated and oversimplified to consider only the Th-1 and Th-2 branches. In fact, the Th-17 branch may be at the root of our difficulties.

From ebioscience:
[my bolding]

Th17 Cells – A New T Cell Lineage

CD4+ T helper cells are critical mediators of the cellular immune response. For many years, due to cytokine expression patterns, it was thought that CD4+ T helper cells existed as a dichotomy of lineages named Th1 and Th2. However, as these subsets were analyzed more closely, it became apparent that the T helper cell population was not limited to these two subsets. Although it has long been appreciated that IL-17 (also known as IL-17A) production by T cells is required for protection against some pathogens, in 2000 it was demonstrated that IL-17A was produced by a unique subset of T helper cells. Subsequently, it was definitively shown that T cells could differentiate into IL-17-producing cells in vitro and in vivo independently of Th1 or Th2 cell development thereby establishing Th17 cells as a unique T helper cell lineage. Functionally, Th17 cells play a role in host defense against extracellular pathogens by mediating the recruitment of neutrophils and macrophages to infected tissues. Moreover, it has become evident that aberrant regulation of Th17 cells may play a significant role in the pathogenesis of multiple inflammatory and autoimmune disorders.

SOC September 14, 2013 at 5:46 pm


Legendrew

I'd argue the point that CSF markers serve as proof of an infection, viral or otherwise, of the nervous system. They certainly hint at a form of immune dysregulation within the brain and perhaps entire central nervous system but are not even close to showing an infectious causation, certainly that could be one cause of such a dysregulation but there are numerous others to further explore too.

Also, immune dysregulation can result in multiple infections which, as in HIV infection, cause the vast majority of the negative symptoms. Such infections don't have to be continuous or acute. Recurring or reactivating infections, as well as tissue infections, are not evident 100% if the time in plasma. Finding viral particles in the blood in a population like ours may require taking blood during bad periods or crashes — just the time when most of us don't go to the doctor.

The lack of evidence of viral DNA in plasma suggests that we don't have an on-going acute infection with a known virus. That is not surprising — we've been pretty sure of that for a long time. That does not mean that such infections are not reactivating on a regular basis, chronic in tissues not yet studied, or not detectable by current methods.

As the world learned from HIV, viruses to not have to be causative for the illness to be causative for many of the symptoms of the illness. The root cause should be found in most of us, secondary infections can be many and varied.

I think (and it looks like Lipkin thinks so, too) that something is causing immune dysregulation in ME/CFS. That may be an infection that has come and gone, it could be an as yet undetected pathogen, it could be genetic, it could be something else entirely. Lipkin would like to find that something. We would like that, too. :) However, we are also concerned about finding and treating secondary infections. That may not be part of Lipkin's concern at the moment. That doesn't mean investigation of secondary infections should be abandoned.

snowathlete September 14, 2013 at 5:48 pm


acer2000

I will have to go back and check, but I'm fairly certain the Lyme PCR yield is in the low single digits. In this case, that would mean that if all 200-something people he was studying had proven Lyme disease, only a few would show up as positive using that method. My point is not to argue that Lyme is or isn't the cause here, its to show that for any of the hundreds of pathogens he tested for using the blood and CSF with sequencing, the negative result he got could be enough to rule out their involvement completely, or it could mean nothing – it all depends on the nature of that particular bug.

I'd be interested to see some data on how accurate the methods being used are and what that might mean in terms of the pathogens being looked for. I know some bacteria for instance are very hard to detect, and it's not uncommon for samples to be left to multiply in various growth mediums before they are of sufficient numbers to be detected by PCR.

Omar88 September 14, 2013 at 6:10 pm

Here's a story I love to tell but I will keep it brief. What do you do when your beloved college son gets

ME/CFS? Well, that's a problem.

What about if you are one of the richest people in the world and you also are a get it done, hard driving

Harvard business man who is a

doer? Then you do what any loving, dedicated, brilliant billionaire father would do, you fund the ME/CFS

research yourself and you.

bring answers and treatment to your very own son. It's brilliant. Done!

That's what Glenn Hutchins did, the 56 year old mega successful businessman who single handedly out

spent the entire United States government's in funding ME/CFS Research during the last three years. Glenn

has made a habit out of succeeding in life, and his Silver Lake investment firm is one of the most

successful equity firms in the world. Will he do something major for ME/CFS? That's a silly question. Of course he will!

Glenn and his son hit the same road blocks we all do when we were diagnosed with ME/CFS, so Glenn

decided to build a bridge over those blocks by ponying up close to $15 million to buy the services and

interests of the world’s BEST ME/CFS researchers, virologists, and other medical experts that all the money

in the world could buy. One of them was the brilliant and lauded virologists, Dr. Ian Lipkin, who you have

probably seen on the cover or one or another magazines. He is a virus hunter. And he's the best one in the world.

He just completed a monstrous study looking at a very large number of ME/CFS patients to see what if any

pathogens is involved in ME/CFS. He looked for everything. And his findings were surprising. Here is the

complete transcript of a large conference call on Sept. 10. The findings are fascinating and there’s a lot to

about, and I will be writing more about what they probably mean in the weeks and months ahead. There

is that much to write about.

I hope you enjoy this barrier crushing research, with its many ramifications. Isn't it great that we have this

kind of research going on even when we don't know it is? It's happening everywhere, and it's one of the

main reasons why patients will eventually have completely effective treatments and one day even the cure.

A quick note, as I would be remiss not to do this. To Glenn Hutchins, on behalf of all Chronic Fatigue

Syndrome and (the more difficult to qualify for) Myalgic Encephalomyelitis patients everywhere, thank you

very, very much.
https://www.facebook.com/photo.php?…a.10150589792146095.443635.57430136094&type=1

snowathlete September 14, 2013 at 6:28 pm


SOC

Also, immune dysregulation can result in multiple infections which, as in HIV infection, cause the vast majority of the negative symptoms. Such infections don't have to be continuous or acute. Recurring or reactivating infections, as well as tissue infections, are not evident 100% if the time in plasma. Finding viral particles in the blood in a population like ours may required taking blood during bad periods or crashes — just the time when most of us don't go to the doctor.

The lack of evidence of viral DNA in plasma suggests that we don't have an on-going acute infection with a known virus. That is not surprising — we've been pretty sure of that for a long time. That does not mean that such infections are not reactivating on a regular basis, chronic in tissues not yet studied, or not detectable by current methods.

As the world learned from HIV, viruses to not have to be causative for the illness to be causative for many of the symptoms of the illness. The root cause should be found in most of us, secondary infections can be many and varied.

I think (and it looks like Lipkin thinks so, too) that something is causing immune dysregulation in ME/CFS. That may be an infection that has come and gone, it could be an as yet undetected pathogen, it could be genetic, it could be something else entirely. Lipkin would like to find that something. We would like that, too. :) However, we are also concerned about finding and treating secondary infections. That may not be part of Lipkin's concern at the moment. That doesn't mean investigation of secondary infections should be abandoned.

Whatever that something is that triggers, and perhaps maintains that immune dysfunction, my thinking on secondary infections has changed quite a bit in the last year or so. I think with lots of different viruses having been put forward to have links with ME/CFS over the years, the view that we have a lot of coinfections has become fairly common and I used to think that myself. However, when I thought about this some more, I considered that in a disease like HIV-AIDS where you have immune deficiency and you get these secondary infections, they are quite varied and even a relatively mild pathogen can become lethal. Many of these infections are very easily identifiable – not just through testing – but through symtoms; it is usually clearly apparent that a HIV sufferer has hepatitus, tuberculosis, etc. based on symptoms alone.

Even if we had a less severe immune deficiency than HIV-AIDS, we don't get clear symptoms of secondary infections that allow identification of that secondary infection based on symtoms, as far as I can tell. To me this suggests that we don't have an immune deficiency leading to a variety of seconary infections. Perhaps none at all.

Using the common cold as an example (which it seems many of us – thought not all – don't get), If we had an immune deficiency of some kind then I'd have thought we would be more suseptible to them, not less so. So this suggests to me (and this is just my current thoughts on this and I'm very open to discussion) that as a whole, we have an up-regulated immune system not down-regulated. That isn't to say that we can't have part of our immune system that are deficient, perhaps that is likely given previously reported findings on NK-cells etc. but I think other parts of our immune system are taking up the slack by being on all the time, meaning as a whole our immune system is not deficient. This alone could explain the vast majority of our symptoms I'd have thought.

SOC September 14, 2013 at 6:57 pm


snowathlete

Many of these infections are very easily identifiable – not just through testing – but through symtoms; it is usually clearly apparent that a HIV sufferer has hepatitus, tuberculosis, etc. based on symptoms alone.

Even if we had a less severe immune deficiency than HIV-AIDS, we don't get clear symptoms of secondary infections that allow identification of that secondary infection based on symtoms, as far as I can tell. To me this suggests that we don't have an immune deficiency leading to a variety of seconary infections. Perhaps none at all.

Many of us do have symptoms of herpesvirus infections — extreme fatigue, sore throat, swollen glands, and elevated antibody titres. The problem is that doctors don't believe that herpesvirus reactivations occur in immunocompetent patients, so they declare that we cannot have those infections. The assumption there is that we are immunocompetent. I actually asked my GP if I had HIV and the symptoms and antibody titres I do, would he believe I had reactivated herpesvirus infections and prescribe antivirals. He said, "Certainly. But you don't have HIV. A healthy person's immune system prevents reactivation of herpesvirus infections, so you can't have reactivations." :rolleyes: That seems to be the ubiquitous thinking in the medical world on herpesvirus reactivations. No one said they teach science or logic in medical school.

I think there is similar thinking in other pathogens as well — everyone has them, but healthy immune systems keep them in check, so ME/CFS patients can't have them because they aren't immune-impaired. o_O Doctors like Dr Klimas and KDM, who are aware of immune dysfunction in ME/CFS, often prescribe abx and antivirals for secondary infections detected by relatively common methods.

Using the common cold as an example (which it seems many of us – thought not all – don't get), If we had an immune deficiency of some kind then I'd have thought we would be more suseptible to them, not less so. So this suggests to me (and this is just my current thoughts on this and I'm very open to discussion) that as a whole, we have an up-regulated immune system not down-regulated. That isn't to say that we can't have part of our immune system that are deficient, perhaps that is likely given previously reported findings on NK-cells etc. but I think other parts of our immune system are taking up the slack by being on all the time, meaning as a whole our immune system is not deficient. This alone could explain the vast majority of our symptoms I'd have thought.

Not all people with ME/CFS don't get colds. (Daughter and I are both fighting colds now, as a matter of fact) That seems to me to be more of a stage of the illness thing, although I could certainly be wrong. :) In my case, I went through a catching everything phase, an allergic MCS-type phase where I didn't catch common colds, and a more normal but still inclined to catch things phase.

The immune system is far more complicated than up-regulated or down-regulated. It's far from a certainty that if one part fails, another part will compensate, or that if some compensation does occurs, the immune system can maintain that abnormal condition long-term.

I don't know that all of us have the same immune abnormalities. That could explain why we have different secondary infections, and/or different immune reactions. Those different immune abnormalities may be a factor in subsets in the illness.

lansbergen September 14, 2013 at 7:26 pm


SOC

The immune system if far more complicated than up-regulated or down-regulated. It's far from a certainty that if one part fails, another part will compensate, or that if some compensation does occurs, the immune system can maintain that abnormal condition long-term..

I am convinced it will try to compensate but there is no garantee it will succeed. When one thing fails it will try something else and at one point in time it could push the right button.

Dolche September 14, 2013 at 7:44 pm

YES! IT COULD BE A COMBINATION OF OUR BAD DNA DETOX GENES AND MOLD( it's a bacteria).
I HOPE ALL CFS PATIENTS TAKE A LOOK AT WHAT FUNCTIONAL ALTERNATIVE DOCTORS THAT SPECIALIZE IN MOLD and the connection IAN LIPKIN HAVE FOUND…

A POSSIBLE BACTERIA OR FUNGI EXPOSURE! LEPTIN HORMONE! IMMUNE INFLAMATION!
Take a look at DR?SHOEMAKER AND SPANOUGLE AND FINDING ON MOLD EXPOSURE! LEPTIN! IMMUNE INFLAMMATION! AND LEAKY GUT. It would make sense mold is an epidemic 25 percent of people have poor detox pathways.

http://www.survivingmold.com/diagnosis/the-biotoxin-pathway
http://sponauglewellness.com/wellness-programs/mold-toxicity/black-mold-used-in-weaponry/

Functional medicine world meets traditional medicine (please work together!)

Rachael September 14, 2013 at 8:30 pm

I have always said that since childhood I had an immune system that was over-performing; a very good healer and few colds, flues or viruses. The day I developed severe ME/CFS over twenty-five years ago was when my over-achieving immune system crossed the line and became a full-blown autoimmune disease. The genes for (up-regulated immune function) and many triggers (viruses, bacterias, vaccines, chemicals etc) leave some of us more susceptible to develop ME/CFS.

Dolche September 14, 2013 at 9:03 pm

Interesting lipkin findings…..funny….Dr.shoemakers a functional doctor feels mold a fungi bacteria is the trigger. Some people with bad detox genes get implicated. His theory revolves mold affecting leptin in hypothalamus, leaky gut, poor ATP production,sleep problems, cytokine upregulation.
http://www.survivingmold.com/diagnosis/the-biotoxin-pathway
There is a connection . They need to talk.

Marlène September 15, 2013 at 3:53 am

I think ME is cancer of the immune system.

globalpilot September 15, 2013 at 6:25 am


Legendrew

As far as i'm aware Borrelia is an exclusionary criteria from ME anyway although I guess that depends upon which diagnostic criteria the physician is using. This extensive search is certainly worthwhile but I think it's unwise to pin hopes on this given the history pathogens have had in terms of ME research. From a personal standpoint I doubt any infectious agent lies at the heart – perhaps they simply serve to exacerbate the problem in those who have them.

I agree that even if these pathogens are hiding away in tissues there should be some evidence of the active infection. As far as i'm concerned if the pathogen is inert in these tissues there should be no symptoms so I feel that line of thought should be throw out instantly.

He only tested plasma for infection didn't he ?, and CSF ? He didn't test white blood cells. And there is activated immune system, both Th1 and Th2. I wouldn't throw out the infection impact just yet. Others are finding infections – this needs to be explained.

heapsreal September 15, 2013 at 6:34 am


globalpilot

He only tested plasma for infection didn't he ?, and CSF ? He didn't test white blood cells. And there is activated immune system, both Th1 and Th2. I wouldn't throw out the infection impact just yet. Others are finding infections – this needs to be explained.

He has stated they havent even tested serology and they think they will find some answers there, so infections are still definately in.

Snow Leopard September 15, 2013 at 7:42 am


lansbergen

I refuse to believe the immunesystem attacks self for no reason. I always have and likely always will.

Viruses may well set up the conditions for such feedback loops, such that the loops continue after the viral infection has resolved. But I don't see why the idea of an autoimmune disorder in the absence of a chronic infection is such a controversial issue.

cigana September 15, 2013 at 7:53 am

I'm confused, was TNF-alpha decreased or increased?

Snow Leopard September 15, 2013 at 8:00 am


Omar88

That's what Glenn Hutchins did, the 56 year old mega successful businessman who single handedly out

Wait, this Glenn Hutchins?

http://www.bostonglobe.com/lifestyl…nn-hutchins/tmpyyjAZoYgjzAuUsKnGCO/story.html

So when Ian Lipkin says we need to tell the government to allocate additional funds to the CDC and NIH, who is he really talking to? The guy who funded his study, the guy who plays golf with Obama, or us?

cigana September 15, 2013 at 8:13 am

What if the infection is in the tissues not blood? Like, say, borrelia or enteroviruses?

Omar88 September 15, 2013 at 9:02 am


Snow Leopard

Wait, this Glenn Hutchins?

http://www.bostonglobe.com/lifestyl…nn-hutchins/tmpyyjAZoYgjzAuUsKnGCO/story.html

So when Ian Lipkin says we need to tell the government to allocate additional funds to the CDC and NIH, who is he really talking to? The guy who funded his study, the guy who play golf with Obama, or us?

Both but a rich, good connection man with a patient sun will help us a lot !!

lansbergen September 15, 2013 at 9:13 am


Snow Leopard

But I don't see why the idea of an autoimmune disorder in the absence of a chronic infection is such a controversial issue.

There must be a reason for the immune system to attack self.

snowathlete September 15, 2013 at 9:34 am


SOC

Many of us do have symptoms of herpesvirus infections — extreme fatigue, sore throat, swollen glands, and elevated antibody titres.

Those symptoms might not be herpes though, they aren't specific. Of course if you've tested positive then perhaps it is. My point was really not to argue against herpes infection though, it was to point out that secondary infection as a result of a broad immunodeficiency is unlikely, else we'd have a plethora of infections, some with very specific, easily identifiable symptoms.

SOC

Not all people with ME/CFS don't get colds. (Daughter and I are both fighting colds now, as a matter of fact) That seems to me to be more of a stage of the illness thing, although I could certainly be wrong. :) In my case, I went through a catching everything phase, an allergic MCS-type phase where I didn't catch common colds, and a more normal but still inclined to catch things phase.

I agree. And there has to be explaination for these immune characteristics from both sets of people. I don't think a broad immunodeficiency at any stage of illness is it though, else we'd be dying more and getting those obvious symptoms from some infections. If we are more prone to certain infections as a result our our immune dysfunction then perhaps infections such as herpes which can embed in our DNA are better placed to take advantage than other infections.

SOC

The immune system is far more complicated than up-regulated or down-regulated. It's far from a certainty that if one part fails, another part will compensate, or that if some compensation does occurs, the immune system can maintain that abnormal condition long-term.

Sure, but for the purpose of discussion and given our – well, certainty my – lack of detailed immune system knowledge, it's still useful to talk in such terms I think – particularly when talking in net terms as I was.

SOC September 15, 2013 at 3:12 pm


snowathlete

My point was really not to argue against herpes infection though, it was to point out that secondary infection as a result of a broad immunodeficiency is unlikely, else we'd have a plethora of infections, some with very specific, easily identifiable symptoms.

I don't think it's as simple as that. There are certainly people with severe immune deficiencies who are susceptible to everything — think the "bubble boy" disorder. But if only part of the immune system is deficient, the person could be susceptible to a limited subset of pathogens, for example intracellular or extracellular pathogens. Also, a limited immune deficiency leaves the victim less able, but not completely unable to fight off infections.

HIV patients get different secondary infections at different stages of the illness because their immune systems can handle some infections early, but as the disease progresses their immune systems become more incapable and they get more and more infections. We could easily be in a analogous position to HIV patients in the earlier stages — more susceptible to reactivations of herpesviruses, bacterial pneumonia, staph infections, candida, malaria, TB, but not so severely impaired that we suffer from every infection that comes our way.

lansbergen September 15, 2013 at 4:03 pm


Snow Leopard

Viruses may well set up the conditions for such feedback loops, such that the loops continue after the viral infection has resolved. But I don't see why the idea of an autoimmune disorder in the absence of a chronic infection is such a controversial issue.

On the one hand it is claimed attack on self for no resean.

On the other hand it was claimed no immune response what so ever to the infection I suspect. That has changed over the years. It is now know, there are immune responses but they do not show in the useal manner.

Antares in NYC September 15, 2013 at 11:01 pm


Dolche

A POSSIBLE BACTERIA OR FUNGI EXPOSURE! LEPTIN HORMONE! IMMUNE INFLAMATION!
Take a look at DR?SHOEMAKER AND SPANOUGLE AND FINDING ON MOLD EXPOSURE! LEPTIN! IMMUNE INFLAMMATION! AND LEAKY GUT. It would make sense mold is an epidemic 25 percent of people have poor detox pathways.

http://www.survivingmold.com/diagnosis/the-biotoxin-pathway
http://sponauglewellness.com/wellness-programs/mold-toxicity/black-mold-used-in-weaponry/

Functional medicine world meets traditional medicine (please work together!)

Hi Dolche,

Have you tried Dr. Shoemaker's protocol? Do you know of anyone getting better on it?
Any ME/CFS patients that found relief with the Shoemaker protocol?
I'm really curious.

Forbin September 16, 2013 at 12:48 am


SOC said:

Not all people with ME/CFS don't get colds. (Daughter and I are both fighting colds now, as a matter of fact) That seems to me to be more of a stage of the illness thing, although I could certainly be wrong. :) In my case, I went through a catching everything phase, an allergic MCS-type phase where I didn't catch common colds, and a more normal but still inclined to catch things phase.​

I wonder if it makes sense to distinguish between “colds” and “flu.” From a symptom standpoint, influenza is more likely to involve the presence of significant fever in adults. Colds are more likely to commence with a sore throat and to involve a runny and/or stuffed up nose. Colds are generally milder than the flu.

All influenza is caused by RNA viruses of the family Orthomyxoviridae, but apparently only 10%-15% of colds are attributed to these viruses. Some 200 other viruses can cause colds.

In other words, if you were somehow very resistant to flu viruses you could still get colds, since 85%-90% of them are not caused by flu viruses.

I don’t know if such selective resistance is possible, but it would be interesting to know if CFS patients who get colds also get the flu with high fever.

[FWIW, my illness apparently commenced with a severe flu, but that was the last time I caught the flu (or a cold) for a decade.]

rosie26 September 16, 2013 at 1:57 am

Forbin

I know it may sound strange but I have never had a flu with body aches and fever in my life that I can remember until I collapsed with ME. I get heaps of colds. Anyone else never had flu until ME. ?

August59 September 16, 2013 at 4:53 am


heapsreal

Proper accurate testing as well as well defined cfs study participants could account for there inability to find viruses. Doesn't seem to be a problem for lerner Peterson klimas, as well as being able to treat and improve many of them.

I hate to sound deragotory towards some of the viral testing and I'm seriously calling BS on some of it. I don't think you can test 225 or so people with cfs/me and only come up with 4 cases of EBV and a 2 cases of HHV-6. Whether they were looking a antibody test or viral dna I'm still concerned. It's known that copy numbers for HHV-6 are very low as they just kick the shit out of you when they come rolling through. The study just a few weeks ago showing EBV is now leaving a viral copy within the host cell while it is sends a complete new copy of the virus out to infect a new cell leaving the old alive and well and still infected.

One thing that sticks out at me from the research standpoint are they using this stud to bolster their new arrays that can see 500 different viruses utilizing a high throughput system. The research should find, or at least look at the pathogens and viruses instead from a researcher perspective.

Many of these samples are 4 years old from Dr. Montoya and I imagine Dr. Peterson as well. How many times have they been thawed and re-frozen and thawed again. I'm not doubting the arrays they are using, but is this the place to be using them. As I said before I don't think a 500 virus array in a high throughput system will find HHV-6 on a very consistant basis. I'm sorry, but I find it very, very hard to believe we as patients have such high levels of EBV and HHV6 antibodies checked in a research lab for HHV-6 anyway, but they can only find four cases on their super 500 virus array on a high throughput system.

Are they looking for a cure for cfs/me or are they testing their newly develop arrays? I'm confused to say the least and not trying second guess the researchers intentions, but something don't freaking add up and I would like to know why?

Who was it that recently stated that if you look to quick it is going to get missed. It was a reference on this forum by a doctor. I hope they find something that will slow them do.

Rachael September 16, 2013 at 7:00 am

Those who are complaining about persistant colds and flues since they developed ME/CFS … are you sure that you have an infection, or are you having a reaction? Are you immune-suppressed or immune-reactive? As a long time sufferer of ME/CFS, I use to think that my symptoms, when I became extremely ill were because I had a virus or an infection (a down-regulated immune system). It was not until I began reading stories at a child daycare (germ factory), a couple of hours a day, that I realized, when I became very ill, it was not an infection or virus causing my symptoms, but that I was having a reaction (caused by an up-regulated immune system). I would become terribly congested; have a low-grade fever; sore throat; cough; suffer from headaches and extreme fatigue. By the end of the “work-week” I would feel so sick, that I use to think I had caught something from the children. The same thing would happen week, after week, but I would miraculously recover over the weekend. Eventually, I had to give up the position. As soon as I did, my problems with what I first thought was a virus or infection disappeared. I still have ME/CFS, but I am now quite aware when my symptoms become worse, I am reacting to something. I do not have a down-regulated immune system, but an up-regulated one. This knowledge has helped me to cope a with my illness.

Bob September 16, 2013 at 9:35 am

Lipkin looked in plasma and spinal fluid, but the literature that I've just looked at suggests that HHV-6 would be better detected in lymphocytes or brain tissue:

HHV-6 active infections can persist in the brain tissue long after all traces of the virus have disappeared from the blood (Caserta 2004) and can be found in large quantities in the brain tissues with barely a trace in the spinal fluid (Fotheringham 2007).

http://hhv-6foundation.org/what-is-hhv-6/epidemiology-of-hhv-6

This study, that found HHV-6 in 70% of CFS patients, detected it in lymphocytes, not plasma:
http://www.ncbi.nlm.nih.gov/pubmed/1309285

Other research has suggested that HHV-6 is found in large numbers of the general population:

In a US study of lung tissue samples, both variants were found in 67% of transplant patients and 54% of controls (Cone 1996).

http://hhv-6foundation.org/what-is-hhv-6/epidemiology-of-hhv-6

Firestormm September 16, 2013 at 9:57 am

Bob just to save me reading those papers – were they active infections that were found? Only that's what Lippers was a seeking in this first instance.

Bob September 16, 2013 at 10:41 am


Firestormm

Bob just to save me reading those papers – were they active infections that were found? Only that's what Lippers was a seeking in this first instance.

I think so, but it's only one study, and there has been plenty of conflicting HHV-6 research.
I'm not familiar with the wide range of HHV-6 research, as I've never taken a close interest in it.

Here's the results from the abstract, suggesting active infection:

Primary cell culture of lymphocytes showed active replication of HHV-6 in 79 of 113 patients (70%; CI, 61% to 78%) and in 8 of 40 controls (20%; CI, 9% to 36%) (P less than 10(-8], a finding confirmed by assays using monoclonal antibodies specific for HHV-6 proteins and by polymerase chain reaction assays specific for HHV-6 DNA.

http://www.ncbi.nlm.nih.gov/pubmed/1309285

Marco September 16, 2013 at 10:56 am

High leptin levels may be a cause for minor celebration?

Things could be worse without leptin's neuroprotective effects :

Leptin Neuroprotection in the Central Nervous System: Mechanisms and Therapeutic Potentials

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2634657/

Simon September 16, 2013 at 11:28 am


August59

I hate to sound deragotory towards some of the viral testing and I'm seriously calling BS on some of it.

Let me clarify a few points:

One thing that sticks out at me from the research standpoint are they using this stud to bolster their new arrays that can see 500 different viruses utilizing a high throughput system. The research should find, or at least look at the pathogens and viruses instead from a researcher perspective.

He says nothing in the transcript about using a 500-virus-detecting array. They screened uisng a panel of 20 viruses, bacteria and parasites. The high throughput approach, as I understand it, is unbiased ie looks for any virus based on the DNA/RNA sequence. However, Ian Lipkin did say his team had discovered over 500 viruses using this method (and you can't discover a new virus using a panel of known ones). The purpose of this stuy was not to test an array.

Many of these samples are 4 years old from Dr. Montoya and I imagine Dr. Peterson as well. How many times have they been thawed and re-frozen and thawed again.

Would be interesting to know if this had happened, or if the researchers had factored this in. I think that DNA viruses like herpes are fairly robust so would survive freezing/thawing cycles – a bigger risk is probably introducing contaminants and finding false positives.

As I said before I don't think a 500 virus array in a high throughput system will find HHV-6 on a very consistant basis. I'm sorry, but I find it very, very hard to believe we as patients have such high levels of EBV and HHV6 antibodies checked in a research lab for HHV-6 anyway, but they can only find four cases on their super 500 virus array on a high throughput system.

So far they have only reported on plasma viral studies, which will only detect viruses that are currently active. If people have dormant HHV6 and EBV (and EBV at least is prevalent but generally dormant), they won't find it in plasma. They have yet to report on the serology studies that should show up antibodies if the patient has a prior (or dormant) infection.

I note Bob study below that found high levels of HHV6 using cultured lymphocytes (rather than plasma) – but it was from 1992 and wonder if there have been a replication since? Still, it was a pretty big study.

It's quite possible that the serology work will find antibodies indicating past/dormant EBV and HHV6 infections. And I agree that it would be odd if they don't find EBV at least.

One final point. The virology work is a collaboration with Jose Montoya, an expert in HHV6 currently running a CFS pilot study treating HHV6. My guess is that Montoya would know how to detect HHV6. But maybe when the paper is published (should be soon) there will be lots of caveats about the limits of the techniques they used.

snowathlete September 16, 2013 at 1:26 pm

Is it not possible to use these techniques to look at other parts of the blood? peripheral blood mononuclear cells (PBMC) including lymphocytes, and erythrocytes which dont contain a nucleous?

alex3619 September 16, 2013 at 1:27 pm

I predict that serology will show less EBV than the general population. I suspect, based on numerous anecdotal accounts, that we lose seroconversion. So we can lose seroconversion to EBV. That means we lost the memory of how to fight EBV … those antibodies are no longer made in quantity.

In any case nearly all adults should show some serological evidence of prior EBV infection. In part that is why so many doctors have dismissed claims of EBV in CFS and ME before. Its a case of "So what? Everyone has EBV!". For patients with frequent EBV reactivation I think there should be a longtitudinal study … give blood every month or so for a year. This might show a pattern of reactivation.

One thing I think does happen is that when patients get the symptoms again, they presume its viral reactivation. I am not convinced it always is, just as I am not convinced most claims of Herxheimer reactions are really Herxheimer reactions. The symptoms are due to immunological changes, and they can have other causes. There is no substitute for confirming viral reactivation in a patient with a viral titre assay.

We still have no good way to thoroughly assess latent infections however.

alex3619 September 16, 2013 at 1:29 pm


snowathlete

Is it not possible to use these techniques to look at other parts of the blood? peripheral blood mononuclear cells (PBMC) including lymphocytes, and erythrocytes which dont contain a nucleous?

Yes, its possible. I do not know to what extent these techniques have been developed and tested though.

Whole blood assays are certainly done for some pathogens.

August59 September 16, 2013 at 4:32 pm


Simon

Let me clarify a few points:
He says nothing in the transcript about using a 500-virus-detecting array. They screened uisng a panel of 20 viruses, bacteria and parasites. The high throughput approach, as I understand it, is unbiased ie looks for any virus based on the DNA/RNA sequence. However, Ian Lipkin did say his team had discovered over 500 viruses using this method (and you can't discover a new virus using a panel of known ones). The purpose of this stuy was not to test an array.

Would be interesting to know if this had happened, or if the researchers had factored this in. I think that DNA viruses like herpes are fairly robust so would survive freezing/thawing cycles – a bigger risk is probably introducing contaminants and finding false positives.

So far they have only reported on plasma viral studies, which will only detect viruses that are currently active. If people have dormant HHV6 and EBV (and EBV at least is prevalent but generally dormant), they won't find it in plasma. They have yet to report on the serology studies that should show up antibodies if the patient has a prior (or dormant) infection.

I note Bob study below that found high levels of HHV6 using cultured lymphocytes (rather than plasma) – but it was from 1992 and wonder if there have been a replication since? Still, it was a pretty big study.

It's quite possible that the serology work will find antibodies indicating past/dormant EBV and HHV6 infections. And I agree that it would be odd if they don't find EBV at least.

One final point. The virology work is a collaboration with Jose Montoya, an expert in HHV6 currently running a CFS pilot study treating HHV6. My guess is that Montoya would know how to detect HHV6. But maybe when the paper is published (should be soon) there will be lots of caveats about the limits of the techniques they used.

Montoya does not do his own testing for HHV-6 because he does not have "something" that will let him find it with any consistency. All of his is sent out to a lab in Minnesota (I think), but he has stated that extremely hard to find because most of its time is spent in brain tissue. Montoya has also (and Lerner too) that very high levels of EBV antibodies, especially if the Early Antigen, Viral Capsid Antigen and Nuclear Antigen in the IgG form are all present well beyond normal lab values is indicative of re-activation. After the initial exposure to EBV, when you typically see IgM antibodies will never be produced again and that only IgG antibodies are produced during re-activation.

It is odd that they found a lot of retroviruses and they do terrible under a thaw and re-freeze environment.

Have the deep sequencing protocols been used yet. I missed part of the call, but I don't think it was the fecal study, but Dr. Lipkin seemed very positive on another test that they haven't done yet. I thought it had something to do with the gut, but from what I have been reading that is not part of the study? He could get samples from Dr. Chia and Dr. KDM as they both have taken some "gut" samples, but I imagine they were scrapings as I'm not sure if taking a "gut" biopsy is high on anybody's list.

Here is a link about the study that associated Leptin with fatigue severity in CFS.
http://www.ncbi.nlm.nih.gov/pubmed/23570606

Firestormm September 17, 2013 at 2:34 am


August59

Have the deep sequencing protocols been used yet. I missed part of the call, but I don't think it was the fecal study, but Dr. Lipkin seemed very positive on another test that they haven't done yet. I thought it had something to do with the gut, but from what I have been reading that is not part of the study?

If you missed aspects of the phone broadcast, you can read our full transcript from Lipkin: here (which is an attachment to our article at the head of this thread) :)

Simon September 17, 2013 at 2:59 am


August59

Montoya does not do his own testing for HHV-6 because he does not have "something" that will let him find it with any consistency. All of his is sent out to a lab in Minnesota (I think), but he has stated that extremely hard to find because most of its time is spent in brain tissue. Montoya has also (and Lerner too) that very high levels of EBV antibodies, especially if the Early Antigen, Viral Capsid Antigen and Nuclear Antigen in the IgG form are all present well beyond normal lab values is indicative of re-activation.

Thanks. That suggests that EBV is unlikely to be found in this study until they have done the serology work – and no results were given from this in Lipkin's talk.

It is odd that they found a lot of retroviruses and they do terrible under a thaw and re-freeze environment.

The retroviral sequences were reported as part of Montoya's samples. We don't know if these had been through freeze/thaw samples or not but they will be much more recent than Dan Peterson's spinal fluid samples. Also, Ian Lipkin knows a thing or two about finding retroviruses and I'm assuming that he would be well aware of the problem.

Have the deep sequencing protocols been used yet.

I'm actully not sure what the difference is between deep sequencing and high-thoughput – the latter was used in the Montoya samples:

Ian Lipkin

These same samples were studied using high throughput sequencing, which is a method that was really pioneered here – with which we have discovered over 500 viruses – so we feel fairly confident that to the extent of the technology’s capabilities at present; we would have detected everything that would have been present within these samples.

However, near the end of the call, when he is discussing the new CFI cohort (recruited via Nacny Klimas et al) he says:

Ian Lipkin

We are using a method for detection of viruses that is an unbiased approach, [which is] essentially what we refer to as high throughput sequencing. We take plasma samples, we take spinal fluid samples, we look for viruses by treating with specific enzymes that degrade host material that might otherwise interfere with sensitivity; we then extract it and then we sequence it and we look for
agents.

Anything that we find that’s suggestive of being a potential candidate, we develop a PCR assay – this is a way in which you can quantitate the presence, look for evidence of infection – and we apply those [tests] then to the larger sample-set which at this point is in excess of 400 samples/400 different patients. So this is a very large sample-set to mine by this approach.

Which to me sounds very much like what they did with Montoya's samples, so I'm a little bit confused. I did think that high-throughput and deep-sequencing involved essentially the same approach.

August59 September 17, 2013 at 3:40 am

Hopefully all this will make more sense when the final study is done and published. I'm sure we only got bits and pieces the other day.

alex3619 September 17, 2013 at 7:49 am


August59

Hopefully all this will make more sense when the final study is done and published. I'm sure we only got bits and pieces the other day.

Yes, there is no substitute for the published paper.

August59 September 17, 2013 at 12:38 pm

I know Dr. Lipkin mentioned that they were going to make house calls on some of the most severe cases of ME/CFS. He didn't happen to mention how many and if they were going to be looking for specific pathogens or cytokine malfunctions or were they going in with open eyes and look for every possible thing they can find?

cigana September 19, 2013 at 10:21 am


snowathlete
acer2000

I think the issue with sequencing blood and CSF is that some of these agents don't really inhabit either. For example, Lyme testing via PCR in blood and in CSF is specific, but has very low yield. Its mainly a tissue based infection. Some other pathogens might be the opposite. Its really hard to make hard conclusions as to what extent a pathogen is involved unless you know where it primarily lives and those tissues are sampled. So its important that they also look for the antibodies as well.

It does seem like some pathogens favour tissue but many, including Borrelia, are often enough found in the blood. If any had been missed in the patient exclusion phase then with as many subjects as this (260?) and with the best techniques available being used, you'd have thought if present then at least some cases would have been picked up, but instead we have zero. Borrelia as a cause therefore looks pretty unlikely now, though some other bacteria being responsible is yet to be ruled out as i understand it. It'll be interesting to see if they find anything, or not.

If they were chosen properly they should have had negative Borrelia blood tests already as an exclusion diagnosis. Perhaps those that get labelled "true CFS" are those that don't have borrelia or antibodies in their blood. LLMD's often say the sickest are the ones who often test negative. It would be interesting to do an antibiotic challenge.

Forbin September 21, 2013 at 1:51 am

Just some thoughts on the apparent distinction between the cytokine levels of patients who have been ill less than three years and those who have been ill longer:

If some shift if going on in this time frame, might it be related to the long standing observation that those who “recover” from ME/CFS are most likely to do so within the first five years?

I’m thinking that it might be helpful to investigate the cytokine profiles of those who have “recovered” within the first five years as well. As I recall, this is not an insignificant percentage of patients. Other than Dr. David Bell’s long term evaluation of the actual health of “recovered” patients however*, I don’t think that this group has been studied much. The feeling may be, “Why study 'healthy' people?”

My guess (and it’s only a guess) would be that the recovered patients would not have perfectly normal cytokine profiles either, but their profiles might also not be the same as the profiles of either the pre- or post-shift groups.

I’m just saying that studying the profiles of the seemingly ignored “recovered” group might add another data point and give some further insight into what is going on.

Ideally, with the new knowledge of this shift, I’d think that you would now want to follow a group of “under three year” patients so you could compare their pre- and post-shift profiles, get data from closer to when that shift happens, and also get the profiles of any of those that “recover.”

[*They were not as well as they thought they were.]

lansbergen September 21, 2013 at 3:48 am


Forbin

Ideally, with the new knowledge of this shift, I’d think that you would now want to follow a group of “under three year” patients so you could compare their pre- and post-shift profiles, get data from closer to when that shift happens, and also get the profiles of any of them that “recover.”

I agree

aimossy October 2, 2013 at 9:19 pm

I may have missed a post.
but would anyone take a wild guess at how long it will be before lipkin publishes?
miss impatient I know!
lol

Firestormm October 3, 2013 at 12:49 am


aimossy

I may have missed a post.
but would anyone take a wild guess at how long it will be before lipkin publishes?
miss impatient I know!
lol

Before the end of the year? Only a guess, I mean, hell, we are still waiting for the Norwegians to publish what they announced back in May, and which has been embargoed ever since then 'pending publication'. Drives you round the bend, doesn't it? :mad: :D

aimossy October 3, 2013 at 4:54 am

haha ABSOLUTELY. thanks for the guess!

Firestormm October 28, 2013 at 2:14 am

Morning :)

Mark was contacted by someone who noted others wanting to donate to Lipkin's work specifically and who were wondering how to do it. This was the email Mark received explaining how it can be done:

Hi there,

After reading your article – Lipkin finds Biomarkers not bugs, September 12, 2013 and noticing all the comments about where to donate, I contacted Lipkin's team to find out.

Here's the link:

https://giving.columbia.edu/giveonline/?schoolstyle=5881&alloc=12636

Perhaps this could be added to the article and to the forum thread that carried a poll and discussion on this topic:

http://forums.phoenixrising.me/inde…r-prof-lipkins-study.25213/page-4#post-399155

Thanks

Have just donated and the link goes straight through to Centre for Infection and Immunity, Lipkin Laboratory. I just put into the notes section 'for M.E/C.F.S Study'

The link has also been added to the article.

Firestormm November 6, 2013 at 9:41 am
Bob November 6, 2013 at 10:12 am

This is not directly ME related, but there was another story re gut bacteria in the news yesterday.

A strain of Lactobacillus brevis (KB290) has been found to give an immune boost to mice against a flu virus.
"The researchers noticed that the bacteria enhanced the production of not just flu-related antibodies but also the immune system molecules IFN-α."
Interesting that it boosts IFN-α (Interferon alpha.)
I haven't read the research paper yet, so I don't know how effective it's supposed to be, or what sort of immune boost it gives.
They haven't tested it in humans yet.

Scientists Prove That Special Japanese Pickle Prevents Flu Infection
http://www.scienceworldreport.com/a…anese-pickle-prevents-flu-infection-study.htm

Preventing flu: Scientists find bacteria in Japanese pickled turnips which could boost immune system
http://www.independent.co.uk/life-s…-which-could-boost-immune-system-8924768.html

Japanese Turnip Pickle has Flu-Preventing Bacteria
http://www.natureworldnews.com/arti…panese-turnip-pickle-bacteria-prevent-flu.htm

Bob November 6, 2013 at 10:18 am

I've created a new thread for the previous two posts, so that they are seen more widely on the forum:
http://forums.phoenixrising.me/inde…ritis-related-and-flu-immunity-related.26297/

Simon November 7, 2013 at 8:36 am

RE @Firestormm: Science Article: Nov 4, 2013 Gut Bacteria May Cause Rheumatoid Arthritis

The mysterious microbial world within us is beginning to reveal its secrets

New research linking gut bacteria to Rheumatoid Arthritis throws more light on the complex relationship between illness and the gut, which may yet prove key to solving ME/CFS. As this thread's blog said:

Fecal future?
What excites Ian Lipkin most is the gut microbiome, the community of micro-organisms that live in our gut – which might seem odd given his focus so far on pathogens and the immune system. However, it turns out that the microbiome can have a profound influence on the immune system and may be important in many diseases. Hornig and Lipkin have already developed techniques to study the microbiome, and have shown it could be a factor in autism and even in the severity of colon cancer.

Our gut bacteria, aka the 'microbiome', 'microbiota' or 'microflora' are becoming ever more important in our understanding of comlex long-term conditons:

eLife commentary

It has been known for decades that proper development of the immune system requires the gut microbiota, and that alterations in the repertoire of microbes are often associated with immunological disorders, in particular autoimmune diseases

The new study reported in the prestigous new open access journal eLife shows a strong link between just one bacteria and Rheumatoid Arthritis (RA): 75% of new cases of RA had Prevotella Copri bateria compared with just 21% of healthy controls. New cases are important as they are unmedicated, and drugs themselves could affect the bacterial composition of the gut.

And while the sample size was small (44 newly-diagnosed RA vs 28 healthy controls), the 21% rate of P. Copri seen in healthy controls is similar to that seen in larger population studies of bacteria, making it less likely that this is a statistical freak. Nonetheless, replication of these findings is critical.

Assuming the finding is robust, the question is what is its significance? there are 3 possibilities:

  1. Prevotella Copri plays a causal role in RA, perhaps as a trigger
  2. RA leads to changes in the gut, with the effect that Prevotella Copri increases
  3. There is a third, unknown factor that leads to both RA and higher rates of Prevotella Copri, a relationship known as co-association.

So P.Copri could be a cause of RA, or just a marker.

Clearly it can't be the cause of RA because only 75% of RA cases had P. Copri, and 21% of healthy controls had the bacterium too. However, RA is known to be a complex illness with many predisposing features so it could still play a causal role for some people, and that would be hugely significant.

Presumably this is exactly the sort of thing that Ian Lipkin is looking for in his ME/CFS microbiome study.

Background: why it's hard and expensive to study gut bacteria
Getting hold of gut bacteria is easy: 60% of the dry weight of faeces is bacteria so there is no shortage of raw material.

The much harder part is identifying all the bacteria (there are typially around 500 different species in each person's gut). The standard method for identifying bacteria has been to first culture (grow) them in the lab – but unfortunately most gut bacteria won't grow under any lab conditions.

The best current method for identifying bacteria is through their genetic material, specifically their ribosomal 16S RNA. Ribosomes are the protein-building factories of all cells, for us and bacteria included. Except bacterial ribosomes have slightly different RNA: human and all other eucaryotes have a 18S RNA while bacteria have 16S RNA, making it fairly easy to separate bacterial from human ribosomal RNA. Better still, the precise sequence of 16S RNA is different for every bacterial species, so by sequencing the 16S RNA, each species of bacteria can be identified. A similar approach can be used to work out how much of each species exists in the gut.

More information
The Human Microbiome Project was set up in 2008 to kick off systematic study of the human microbiome (note that actually the microbiome covers fungi and protozoa too, not just bacteria).

Bob November 7, 2013 at 9:27 am

Prof Edwards has also expressed some thoughts about the arthritis study:
http://forums.phoenixrising.me/inde…ximab-trial-30-july.24499/page-39#post-401745

Firestormm November 7, 2013 at 3:19 pm


Simon

RE @Firestormm: Science Article: Nov 4, 2013 Gut Bacteria May Cause Rheumatoid Arthritis

The mysterious microbial world within us is beginning to reveal its secrets

New research linking gut bacteria to Rheumatoid Arthritis throws more light on the complex relationship between illness and the gut, which may yet prove key to solving ME/CFS. As this thread's blog said:

Our gut bacteria, aka the 'microbiome', 'microbiota' or 'microflora' are becoming ever more important in our understanding of comlex long-term conditons:

The new study reported in the prestigous new open access journal eLife shows a strong link between just one bacteria and Rheumatoid Arthritis (RA): 75% of new cases of RA had Prevotella Copri bateria compared with just 21% of healthy controls. New cases are important as they are unmedicated, and drugs themselves could affect the bacterial composition of the gut.

And while the sample size was small (about 44 RA vs 28 healthy controls), the 21% rate of P. Copri seen in healthy controls is similar to that seen in larger population studies of bacteria, making it less likely that this is a statistical freak. Nonetheless, replication of these findings is critical.

Assuming the finding is robust, the key question is what is its significance? there are 3 options:

  1. Prevotella Copri plays a causal role in RA, perhaps as a trigger
  2. RA leads to changes in the gut, with the effect that Prevotella Copri increases
  3. There is a third, unknown factor that leads to both RA and higher rates of Prevotella Copri, a relationship known as co-association.

So P.Copri could be a cause of RA, or just a marker.

Clearly it can't be the cause of RA because only 75% of RA cases had P. Copri, and 21% of healthy controls had the bacterium too. However, RA is known to be a complex illness with many predisposing features so it could still play a causal role for some people, and that would be hugely significant.

Presumably this is exactly the sort of thing that Ian Lipkin is looking for in his ME/CFS microbiome study.

More information
The Human Microbiome Project was set up in 2008 to kick off systematic study of the human microbiome (this actually covers fungi and protozoa too, not just bacteria)
BBC piece on early Human Microbiome Project finds
Carl Zimmer piece in the New York Times
Learning to love our microbiomes – radio piece

The piece I cited talked about T17 cells from what I remember and without checking – because I am knackered.

Here's another piece from science that mentions T17 cells in the intestine in association with lack of sleep being a trigger for immune response and possibly leading to disease:

7 November 2013

Why Late Nights Are Bad for Your Immune System

These cells are a type of immune cell known as a T cell. They get their name from a signal they produce, called interleukin 17, which tells other T cells to increase the immune response. In normal numbers, TH17 cells, which live in the intestines, help the body fight bacterial and fungal infections. But when there are too many, the immune defense begins to cause illness rather than prevent it. Boosting NFIL3 levels in T cells growing in lab cultures resulted in fewer of them turning into TH17 cells, the researchers found, suggesting that the protein's job is to prevent T cells from going into that area of specialization. The absence of the protein, the team concluded, leads to runaway TH17 activity.

At this point, the researchers had no reason to suspect a connection to our body’s internal timekeeping system—also known as our circadian clock—which responds to daily cycles of light and dark. But as they continued to explore the connection between NFIL3 and TH17 cells, they found that some of the proteins produced by the body’s "clock genes” attach to the NFIL3 genes. What's more, cultured cells and mice whose clock genes were experimentally tampered with produced fewer TH17 cells. The researchers surmise that a key protein in the clock network binds to the NFIL3 gene to keep the production of TH17 cells synchronized with periods of light and darkness. And the team found that normal mice produce less NFIL3, and thus more TH17 cells, during the day than at night.

In a final experiment, the researchers gave the mice jet lag. "We didn't fly them anywhere," Hooper jokes. Instead, the team shifted the rodents' light/dark cycles by 6 hours every 4 days. "It would be like flying from the U.S. to Europe, India, and Japan and spending 4 days in each country," she explains. Mice with altered light cycles had nearly twice as many TH17 cells in their spleens and intestines, compared with mice having a normal day, the team reports online today in Science. The jet-lagged mice also mounted a stronger inflammatory response to irritation by an experimental chemical—a test used to gauge immune-system sensitivity that hints the animals may be more prone to inflammatory disease.

The finding adds to a growing body of research showing that a healthy pattern of light and dark, sleeping and waking, is essential to keep the immune system in balance, Hooper says. She notes that inflammation is the basis of many chronic disorders, such as heart disease, asthma, chronic pain, and many things ending in "-itis," like bursitis and dermatitis. Inflammatory conditions are more prevalent in developed countries, where people's circadian rhythms are chronically disrupted. Even people who don't work shifts or cross time zones still wake and sleep out of sync with light and darkness, Hooper says. "We all have screwed up light cycles. We stay up late, keep the lights on, look at our lit-up iPhones at 2 a.m."

About time Science and science started producing some interesting articles. It's been rather dull lately :)

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