Dr Ian Lipkin's $1.27m gut microbiome study - crowdfunding campaign - news and updates

[leokitten]

Also, if I haven't already said this earlier in the thread it's very likely that the decision to fund this grant as an interim R56 came from the top, from the OD. Given the timing we've discussed I doubt that my letter, Brian's WP letter, and Ron Davis's letter to Francis Collins contributed to this decision as these were sent in July. I believe the IOM and NIH P2P reports likely had the most impact on the OD.

 

[Sidereal]

Let's hope the pilot/interim data they generate from the funds that they got are interesting enough to facilitate a more hypothesis-driven application next time.

 

[waiting]

All may not be lost.

Leokitten pointed out here that an R56 NIH grant was awarded (rather than the usual R01).

http://grants.nih.gov/grants/funding/r56.htm

Any biomedical research funding is excellent, but I'm still not clear on why Drs Lipkin & Hornig have to revise their original application in the first place?

As you said, the data they collect will hopefully allow them to write a more hypothesis-driven grant.

However, if the current funding (partly) covers data collection, they will need funding for analysis before they can generate hypotheses.

I wonder what feedback they received from the NIH to their original application. It would be interesting to read those, especially now that we've read the comments Dr. Davis received on his.

 

[aimossy]

@waiting from the MDP information - the NIH wanted more time points of collection as the microbiome can change due to diet. @Simon that is correct isn't it? My brain is on the nasty side of functional right now.

"The not so great news is that the NIH only funded them for a single year, not the five years Columbia requested, for collection only, and the money doesn’t nearly cover the patient recruitment and sample collection costs. In fact, they felt it was important to take into account microbiome changes over time as this may give valuable insight; hence the expansion from two timepoints to four timepoints of collection over the one year period."

 

[Bob]

Dr Mady Hornig presents an overview of her ongoing research at the Center for Infection and Immunity at Columbia University.

"The Invisible"
"A conference on severe ME/CFS and the way forward."
The National Society for ME patients (RME).
Sweden. Oct 2015.
Horning. Petersen. Jason. Sköndal.
Videos now available from conference:
http://www.rme.nu/node/513

"De osynliga"
"En konferens om svår ME/CFS och vägen framåt"
Riksföreningen för ME-patienter (RME)
Stockholm & Göteborg. oktober 2015.
Horning. Petersen. Jason. Sköndal.
Filmer från konferensen:
http://www.rme.nu/node/513

 

[msf]

I don´t understand how top researchers can conflate ´pathogen´ and ´virus.´

 

[adreno]

Pathogen

noun
MEDICINE
plural noun: pathogens

1. a bacterium, virus, or other microorganism that can cause disease.

 

[msf]

Sorry, I mispoke, I meant equate, not conflate.

 

[msf]

I don´t understand how they can treat ´pathogen´ and ´virus´ as synonyms?

Someone want to help me with my English?

 

[Bob]

@msf, you are right that 'pathogen' does not equate to 'virus'. But, as you know, a virus is a pathogen. (Your English seems perfectly fine. Better than mine, and I am English.)

 

[msf]

Haha, I´m English too, and an English teacher to boot. I will just blame brainfog.

 

[Bob]

I'm deeply impressed by the extent of the research program that Mady has outlined. They are doing a very thorough search for pathogens and antibodies. They're also looking for autoantibodies and all the other stuff that we've discussed before (e.g. metabolomics, proteomics) looking at various tissues and microbiomes. There's also talk of creating the foundations of a "Center of Excellence in ME" (note, it's 'ME' not 'CFS') as part of the NIH grant that they've received. But no details about it. If there's something to be found, these people seem to be throwing all their tools at it. And Mady confirms that they're using their new technique (VirCapSeq-VERT) that can detect every known vertebrate virus - all 1.7m of them! They're also looking for antibodies to all 1.7m viruses.

 

[Bob]

It's refreshing to hear about some science after all the recent PACE stuff.

I'll post some brief notes about the video tomorrow.

www.youtube.com/watch?v=bAbK8B6Mu1Y

 

[SOC]

It's refreshing to hear about some science after all the recent PACE stuff.

I'll post some brief notes about the video tomorrow.

www.youtube.com/watch?v=bAbK8B6Mu1Y

The degree to which they are trying to manage confounding factors with very carefully matched controls is impressive. It makes the PACE trial (gold standard/evidence-based, yeah right ) with it's lack of blinding and controls look like pre-school research.

 

[Sidereal]

www.youtube.com/watch?v=bAbK8B6Mu1Y

Great stuff.

 

[BurnA]

It's refreshing to hear about some science after all the recent PACE stuff.

I'll post some brief notes about the video tomorrow.

www.youtube.com/watch?v=bAbK8B6Mu1Y

I am sure with all the research taking place now and in the next few years a lot more will be known by 2020. I think the endless debate about autoimmune or chronic infection will be over by then. Who knows both might exist.

I have a feeling that despite the poor history of research in this disease a breakthrough will occur soon and when it does it will have a snowball effect.

I wish I could fast forward time a few years to see what they find.

 

[Bob]

Some notes etc., from the Sweden presentation.

Here are some very brief notes from the video. There is so much more within the video, so i've just picked out some bits of information that caught my eye. There is plenty more.

Dr Hornig outlines a comprehensive ME/CFS research program, seeking pathogens, antibodies, auto-antibodies & immune markers. There is also proteomics and metabolomics.

Dr Hornig confirms her team is using their new research tool (VirCapSeq-VERT) that can detect every known vertebrate virus - all 1.7m of them! If you'd like to read more about the tool, then click here.

Dr Hornig's team are searching for auto-antibodies in ME/CFS patients.

Dr Hornig is looking for antibodies to all known vertebrate viruses. All 1.7m viruses!

Dr Hornig explains that pathogens may retreat from blood, so antibodies can be useful signs of past or present infection. i.e. If virus has retreated to an organ system & no longer circulating in blood, then antibodies can be useful signs of infection.

Dr Hornig mentions that they hope to set foundations for a "Center of Excellence in ME" as part of NIH grant.

Dr Hornig says her team have a gene expression study to be published soon, as part of their #MECFS research program.

There is also discussion of cytokines, potential research involving cytokine targetting drugs, and plenty more.

In a separate post-conference discussion video (see here), Dr Hornig also discusses mitochondria dysfunction, and also the potential of probiotic therapy and faecal transplant therapy.

In the post-conference discussion, Dr Hornig says: "Mitochondrial defects can occur as a post-infectious type of phenomenon. And i think that's worthy also of pursuing[...]mitochondrial DNA studies as well."

Dr Lipkin's & Dr Hornig's huge ME/CFS research program is not fully funded.
All donations are gratefully received: www.bit.ly/DonateToDrLipkin

All our thanks to all our friends & supporters who continue to support Dr Lipkin's & Dr Hornig's research program. We can't thank you enough.

Below is a transcription of a small section of Dr Hornig's presentation which starts at 8.28 in the video.
There is plenty more info within the video, and i've just picked out a small extract that describes a very narrow part of the overall research program.

8.28 in video.

In addition, we are also used to, in trying to figure out what's going on with a chronic disorder, to add in the host response and to do that through a variety of techniques, looking at the RNA level, through RNAseq or microRNA approaches, to look at the abundance of the transcripts produced by various genes. We have data that are about to come out in that regard and these may tell us something, not only about which genes are expressed, but can also be informative as to what types of gene variance may exist in the population. We know many immune response genes may be a link in other disorders to vulnerability to infection agents or to have an untoward or prolonged course after an infection. So we're very eager to look there in terms of gene expression but also trying to detect the variance in the genes that may be involved which could help us for earlier detection.

I'll be speaking to you about our immune marker analyses; We are still analysing the longitudinal data, but we're also beginning to use immune profiling to look for antibodies, may be to pieces of viruses or bacteria or fungi, that lead to an autoimmune type of response.

And Recently in Norway, as well as other groups, have found that there is some suggestion that there may be auto-antibodies to receptors that are involved in the beta adrenergic system, in control of blood pressure and pulse and autonomic nervous system responses. It's just recently been detected in ME.

And indeed as Dr Peterson alluded to, Rituximab is a B-cell depleting agent, is used not only in cancer situations but also used in auto-immune diseases. The safety and efficacy needs to be determined in the clinical trials but it does look promising and suggests that there could be an auto-immune subset, of disease. And we need to try to understand who that subset is and whether they have genetic factors perhaps; immune response genes that are involved as well as certain pathogens that may kick the process off.

 

[lauluce]

THANKS FOR THIS INFO! could you tell me if this study described in your post is already funded and wen will it star? I'm sure it´s on the tread but I really can´t read it now, my mind is barelly respondig. Thank you...

Some notes etc., from the Sweden presentation.

View attachment 13713

Here are some very brief notes from the video. There is so much more within the video, so i've just picked out some bits of information that caught my eye. There is plenty more.

Dr Hornig outlines a comprehensive ME/CFS research program, seeking pathogens, auto-antibodies & immune markers.

Dr Hornig confirms her team is using their new research tool (VirCapSeq-VERT) that can detect every known vertebrate virus - all 1.7m of them! If you'd like to read more about the tool, then click here.

Dr Hornig's team are searching for auto-antibodies in ME/CFS patients.

Dr Hornig is looking for antibodies to all known vertebrate viruses. All 1.7m viruses!

Dr Hornig explains that pathogens may retreat from blood, so antibodies can be useful signs of past or present infection. i.e. If virus has retreated to an organ system & no longer circulating in blood, then antibodies can be useful signs of infection.

Dr Hornig mentions that they hope to set foundations for a "Center of Excellence in ME" as part of NIH grant.

Dr Hornig says her team have a gene expression study to be published soon, as part of their #MECFS research program.

There is also discussion of cytokines, potential research involving cytokine targetting drugs, and plenty more.

In a separate post-conference discussion video (see here), Dr Hornig also discusses mitochondria dysfunction, and also the potential of probiotic therapy and faecal transplant therapy.

In the post-conference discussion, Dr Hornig says: "Mitochondrial defects can occur as a post-infectious type of phenomenon. And i think that's worthy also of pursuing[...]mitochondrial DNA studies as well."


View attachment 13714




View attachment 13715


Below is a transcription of a small section of Dr Hornig's presentation which starts at 8.28 in the video.
There is plenty more info within the video, and i've just picked out a small extract that describes a very narrow part of the overall research program.

 

[Bob]

THANKS FOR THIS INFO! could you tell me if this study described in your post is already funded and wen will it star? I'm sure it´s on the tread but I really can´t read it now, my mind is barelly respondig. Thank you...

Hi lauluce, Mady was discussing her entire research program, so my post describes a number of studies. Some studies are underway and some are just getting started. If u look at the second image in my post, it lists a number of studies that are part of the program.

 

[Sasha]

And Recently in Norway, as well as other groups, have found that there is some suggestion that there may be auto-antibodies to receptors that are involved in the beta adrenergic system, in control of blood pressure and pulse and autonomic nervous system responses. It's just recently been detected in ME.

Just wondering if there's a summary of this studies somewhere - some indication of how solid a finding this is.