Now for Something Completely Different: A microbe hunter turns to ME/CFS - Ian Lipkin presentation to CDC Sept 2019

https://www.youtube.com/watch?v=f0qvPx22F74

eta: new link

https://www.youtube.com/watch?v=SViPfk_OGGg

CDC

"Columbia University’s Ian Lipkin, MD, visited the CDC in September 2019 to present a special seminar hosted by the Division of High Consequence Pathogens and Pathology’s Chronic Viral Diseases Branch. The presentation covers his work on discovery of unknown pathogens and parallels between myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) and infectious disease and his current, and future ME/CFS research. Comments on this video are allowed in accordance with our comment policy: http://www.cdc.gov/SocialMedia/Tools/... "

 

"it’s possible to solve ME/CFS in three to five years." Ian Lipkin 2015. Well its his big year 2020.

 

Recently the Lipkin team completed a proteomics pilot study. Small study, but well matched patients from multiple sites.

They found increase or decrease of particular proteins was associated with ME/CFS.

They think ME/CFS may be a final state reachable through multiple different paths (as for example cancer).

They found immunoglobulins associated wit ME/CFS with good odd ratios (all >3).

Immunoglobulin kapp and heavy and light chains which are present at increased concentrations. Findings are consistent with clonal expansion of B cells to specific immunogens.

They're also doing plasma metabolomics (not going to list all the findings).

One of the findings were plasmalogens, which are found in particular in the brain. Known to be altered in alzheimer's disease, so this may be some marker of CNS dysfunction.

Epigenetics pilot study. He says findings are interesting and one of the most promising data. I didn't quite understand it but there appears to be a particular pattern of methylation. Many methylation and expression changes are related to oxidative metabolism as well as stress.

One of areas of interest that emerges from the findings is iron uptake and homeostasis. Various genes, taken individually are not very different, but if taken together they could have a profound effect.

He speculates that there might be a process occurring that is similar to anemia of chronic disease.

Says 2-5% of patients coming into their clinics have evidence of persistent herpesvirus infections.

Talks about a new proteomics study using a chip that can measure the whole human proteome, and stuff associated with herpesviruses and tick borne diseases.

They haven't found the cause but will continue looking at immune history. High throughput sequencing hasn't found any one infectious agent.

He finishes the talk highlighting that this is "a bona fide illness" and a serious problem for society.

There were questions from the audience.

 

He also said on the topic of herpesviruses, that some clinics have a lot more of these cases than others.

My thoughts follow:

Presumably due to regional differences and what I think is called referral patterns. Anyway according to the data presented herpes viruses appear to be a problem for some patients, but not for most. He seems interested in the topic and wants to explore it further.

 

To facilitate sharing:
https://twitter.com/user/status/1205864218286788609

 

In the Q&A Lipkin made a point to state that the NIH funded research centers only received 15-20% of the funding they were promised. This means they can only do small discovery studies.

This chip looks very interesting. It's based on a previous chip that costs $3,500 but they reconfigured it for ME/CFS and reduced the size to lower the cost, but still very expensive. Currently have 40 patient and control samples collected, want to get to 50 before starting the work.

Lipkin doubts that the pathogen answer will be found with sequencing as they have already looked quite deep that way. That's why looking at the patient samples in response to pathogens and using methods like the chip are the way to go.

Nice to see good collaboration too. Unumatz at Jackson Laboratories, another NIH funded ME research center, has found a subgroup of patients with a specific immune type. Lipkin will analyse this soubgroup of samples to see what else they have in common.

 

He didn't say what the metabolic problem they found was. They are going to publish. Probably not a real breakthrough I suspect.

And I'm guessing it's related to fatty acids and carnitine.

 

A couple of quotes I found particularly interesting... [bolding mine]

Speaking about the microbiome:

And...

 

I didn't completely follow this, but he mentioned herpes viruses a couple of times.

Later when talking about an expensive sequencing test he mentions:

Later still, when talking about developing animal models to test, he says:

I could have this wrong, but it sounds like the persistence of herpes viruses may be related to their triggering the methylation (suppression) of certain host genes which might otherwise work to eliminate these viruses. They may be looking to see if this method of persistence might be related in some way to the persistence of ME/CFS. [Just my guess based on what he said.]

 

When I asked Prof Lipkin whether his sequencing technique on blood samples would be able to detect enterovirus infections in the tissues, he said no it would not. So for any enteroviruses (and possibly other viruses) infecting the tissues of ME/CFS patients, sequencing is blind to such infections.

EDIT: unless you perform the sequencing on the tissues themselves.

 

Possible subtitle: How not to find a tissue-tropic pathogen.

 

Provided they get the funding they needed.

 

Just like nuclear fusion. 50 years ago it was 30-50 years away. Then budgets dropped and kept dropping until almost nothing and we are still 30-50 years away. A reasonable budget would be to spend annually what is spent on the whole ITER project, we are not even close to adequate fusion research funding and, surprise, have not made much progress.

Not trying generally leads to not succeeding. There are exceptions but for hard problems it almost always holds up. Here over the years not trying explains at least 90% of the failure by now, and growing over time. Ironically this is exactly what we are blamed for, that we are not magically cured by CBT because we are not trying. Because one thing you can always count on with this damned disease is that no matter the level of injury, there will always be a much larger heap of insult on top of it.

 

Apparently the video has been pulled. I hope all were able to watch it.

 

Shoot. I should have grabbed the full transcript when I was at it, but the weekend was really rough so I took a shortcut. This is all I have

I guess the above might have been slightly controversial!

Did anyone else manage to capture the full transcript?

 

I didn’t get a chance to watch, but I was very curious about the comments about a promised amount of funding. That seemed odd to me. Does anyone know what promise he’s referring to?

 

I remember that he was lobbying hard for funding before the centers were announced. I remember Ron saying a minimum of $5M a year for 5 years was really needed to support a team to do the work - and this number would approximately tie in with the 20% or so number Lipkin quoted..

Also before the centers, Lipkin used to talk about all the samples he had stored but no funding to process all of them. So I was interested yesterday to read this from @Simon M
https://twitter.com/user/status/1206552226547871744


Reading between the lines (and it's a pure guess, might be wrong) it looks like he doesn't have funding to process his own samples so is now making them available to others. Link to @Simon M post
https://www.s4me.info/threads/news-from-nih-me-cfs-webinar-october-17-2019.11766/#post-224981

I'm worried the same thing will happen to other researchers who have large bio-repositories with disease comparison but no funding as yet. As these samples age, who knows what effect that will have.

 

It’s the statement about a promise that concerns me. When the RFA stating the amount of funding was announced, Lipkin would not have even submitted a proposal. I’m concerned about promises being made behind the scenes.

 

I wondered the same thing, but it's impossible to know. Even if this discussion of funding were the reason the video was pulled, Dr. Lipkin may have been the one who asked that it be pulled.

 

CDC states Lipkin pulled the video due to it containing unpublished information
https://twitter.com/user/status/1207026488932884480