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Life Continues to Happen. Health Rising’s hiatus continues…

Sometimes life gets in the way…

Two botched neuters resulted in 5 trips to the emergency room, a massive surgery to save one dog’s life (thankfully successful), 3 days in intensive care, a new infection, another surgery to fix blown sutures, two early morning returns, a trailer breakdown, major dental work, and two trips to Phoenix.

Two weeks later, things are looking better. The dogs got a good report from the vet yesterday and hopefully over the next ten days or so, the cones will come off and they will be back in business.

 

Health Rising’s Quickie Summer Donation Drive is On!

Keeping up with the latest research in ME/CFS, long COVID, fibromyalgia, and allied diseases. Exploring new treatment possibilities. Learning how others have recovered. All in as thoroughly and comprehensively as we can. 

Please support Health Rising during our quickie summer donation drive. Our goal is to raise $15,000. 

 Find out more here.

Not surprisingly, my Oura ring has marked many high stress days, but I have been taking care to rest, and my sleep has been OK, and I am fine. Onto the blog!

 

The Open Medicine Foundation’s BioQuest Project

Geoff’s Narration

The GIST

 

Bioquest

BioQuest – the goal: find 5-20 molecular biomarkers for ME/CFS.

“A quantifiable biomarker is urgently required to assist in and accelerate a correct ME/CFS diagnosis. Although ME/CFS often causes severe disability, the lack of a clearly understood aetiology and corresponding diagnostic biomarker fuel a significant level of scepticism, trivialisation, marginalisation and misunderstanding of ME/CFS in wider society, including among medical personnel.” From “The search for a blood-based biomarker for Myalgic Encephalomyelitis/ Chronic Fatigue Syndrome (ME/CFS): from biochemistry to electrophysiology” Feb. 2025

My eyes widened when I looked at the Open Medicine Foundation’s Large-Scale Biomarker Project (BioQuest) study. It’s the kind of bold study that this big (in so many ways) disease and small field needs.

Big data

The big data biomarker approach. The goal: distill ME/CFS into its molecular subsets.

The BioQuest study is aimed at uncovering a holy grail in ME/CFS – biologically proven subsets in ME/CFS. This isn’t “we’re looking for biological subsets” approach; it’s a “we’re going to find, document and validate biological subsets in ME/CFS” project. The study is bigger – not just a little bigger but more like a magnitude bigger – than anything that’s been attempted before. In a field larded with 20, 30, 50, maybe 100-person studies, it’s a 1,000-person study.

It’s not just the size – it’s the scope. The OMF is throwing multiple omics assessments (metabolomics, lipodomics, proteomics, cytokines and clinical findings) at their samples in an attempt to uncover biomarkers.

It’s not easy for a poorly funded field like ME/CFS to come up with potentially game-changing studies, but by cleverly leveraging assets from other studies, the Open Medicine Foundation has found a way to do it.

THE GIST

  • unraveling

    Strong biomarkers, if they are found, could turn ME/CFS from a complicated, mysterious disorder into a series of clearer ones.

    Life continues to happen. Botched neuters, emergency surgeries, stays at the doggie ICU, early morning returns, etc., have kept Health Rising from publishing blogs. Hopefully, over the next week the dog issues will be resolved.

  • Is the Open Medicine Foundation’s BioQuest study the big biomarker study we’ve all been waiting for? At 1,000 samples strong, I think it is. The BioQuest multiphase project will used multiple omics’ analyses (metabolomics, proteomics, cytokines, etc.) in an attempt to, once and for all, find, document and validate molecular biomarkers that identify the subsets that everyone believes are present.
  • I talked with Danielle Meadows PhD about the study (see YouTube interview in the blog). The massive study has been under development and gathering funding for several years, but with the samples headed to the labs as we were speaking, it was now underway.
  • The study size dwarfs anything that has been done before. It includes 400 ME/CFS, 400 age and sex matched healthy controls, and 200 samples from multiple sclerosis, burnout syndrome, depression and long-COVID patients.
  • The study benefits by using patients that come from a large geographic area, the inclusion of fatigue, and sedentary producing diseases (multiple sclerosis, burnout syndrome, long COVID) that will allow OMF researchers to filter out biological signals caused by simply being sedentary or fatigued.
  • It hopes to produce between 5-20 molecular biomarkers (or signatures) that are able to identify distinct subsets in ME/CFS.
  • It is phase one of a three phase project. In this first phase of the project, testing the samples will occupy the rest of this year. The artificial intelligence/bioinformatic analyses that assess the data will form the most time and resource intensive part of the study and will likely last all of 2027.
  • If biomarkers are found (I would be shocked if they weren’t), the next phases of the project – verification and validation – will commence. These phases will involve testing on new sets of patients, including those with other diseases.
  • This project has the potential to be transformative. History has shown that when a field transitions from small, fragmented studies to large-scale, biomarker studies that achieve validation, the impact on the disease can be huge.
  • Blood test(s) for ME/CFS would erase stigma, validate the disease, result in quick diagnoses, make it easier to get disability insurance benefits, illuminate core factors in ME/CFS, enable researchers to target specific subsets, increase research funding, and get drug companies interested in this disease.
  • Time will tell. Biomarkers can be weak or strong. They can point to secondary or core factors. The Alzheimer’s field spent a decade in a fruitless pursuit of what turned out to be a secondary factor – amyloid beta. On the other hand, mechanistic biomarkers that define core issues can quickly lead to treatments. Lupus, for instance, had no specific treatments until biomarker studies uncovered an “interferon signature” group and the first lupus drug was developed.
  • Suddenly, we seem to be awash in ambitious studies that are attempting to get at the exact molecular drivers of this illness. The OMF’s BioQuest study, Amatica’s huge gene expression study, Precision Life’s mechanistic approach, and Liz Worthey and Camille Birch’s recent whole genome study suggest that the field is becoming more and more confident that it can, as Ian Lipkin asserted earlier this year, begin to unravel this complex disease.
  • When I asked Danielle what excited her about the ME/CFS field right now, it was no surprise to hear that it was a focus on precision medicine’s ability to identify subtypes and provide treatments for them.
  • We’re clearly light years ahead of where we were even five years ago. Seven years ago, I talked to Sadie Whittaker, Solve M.E’s Chief Scientific Officer, who came from the cancer field. She said that, above all, the ME/CFS field needed big data sets – the kind of data sets that turned breast cancer from one disease to ten diseases – and resulted in precision medicine treatments.
  • Seven years later, the OMF is embarking on the biggest data set yet, and precision medicine is becoming a kind of buzzword in ME/CFS. While we don’t have it yet, it’s no longer a pie-in-the-sky idea but something numerous research groups feel is within reach.

 

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A Talk with Danielle Meadows PhD

 

I talked with the OMF’s Vice President of Research Programs and Operations Danielle Meadows about the study. Danielle has a PhD in Biomedical Engineering and has been in the middle of an impressive array of large efforts.

She was the Senior Scientific Officer for the huge CareEvolution Platform (which the unhide Solve M.E. effort is using), she developed and executed the project plan for the mobile health platform for the NIH’s RECOVER study, was a Project Director for a Scripps Research’s Long COVID Randomized Controlled Trial, and a Project Manager of the NIH’s All of Us Research Program.

The time is ripe for a study like this. Findings from small studies that continue to cohere around general themes suggest that biological subsets are simply waiting to be found. There’s been a lot of buzz around several possible biomarkers, including a Raman spectroscopy biomarker – a DNA conformation biomarker, a biomarker in the spinal fluid, or one using flow cytometry, but these require complex and/or expensive procedures.

A Potential Blood Test for Chronic Fatigue Syndrome (ME/CFS)?

New Epigenetic Diagnostic Test For ME/CFS Wows … But Can It Hold?

The OMF, on the other hand, is looking for “a biochemical signature for ME/CFS that can be conveniently evaluated through a blood test.”; i.e. something that can easily be tested for via a standard lab.

Danielle said that creating the study design, raising funds for it, etc., has been underway at the OMF for several years. The study was announced in December 2024 and with the samples being transported to the labs has begun.

This study could not have been have happened without past efforts at the OMF Collaborative Center at Uppsala, and the Chronic Fatigue Initiative (thanks, Hitchens Foundation!) and to biobank samples, as recruiting new patients is expensive. These rigorously characterized samples from doctor-diagnosed patients include 400 people with ME/CFS, 400 healthy controls, and, as a bonus, 200 people with either multiple sclerosis, exertional malaise (burn out syndrome), clinical depression, and long COVID.

Broadscale Effort

“The important thing is if it’s a robust enough signature for ME/CFS, we’re gonna be able to see it with, you know, a panel of things. If it was one molecule, two molecules, we’d probably already have found it.” Danielle Meadows

Complex

The OMF’s broad approach – which incorporates metabolites, proteins, cytokines, etc., – strengthens the likelihood of finding verifiable biomarkers.

The OMF’s broadscale approach to measure over 10,000 proteins, metabolites, cytokines, etc., gives it a better chance to find strong biomarkers than say a single proteomic or metabolomic study.

Bringing fatiguing, sedentary producing diseases (multiple sclerosis, burn out syndrome, long COVID) into the mix also gives the study a leg up that will allow OMF researchers to filter out biological signals caused by simply being sedentary or fatigued. The study also benefits from two ME/CFS cohorts that derive from a large geographic area,

If this study follows OMF practices in other studies (that is, if it uses Somascan technology and processes the samples in highly controlled, high-throughput environment), the problem of “batch effects” that have confounded other studies will be reduced.

Five to 20 Molecular Signatures Expected

“We think we’re set up in a pretty good position, where if there’s something there to find, we’re gonna find it.” Danielle Meadows

No one expects to find a universal biomarker. The OMF expects to find from 5–20 molecular signatures. The number will depend upon how strong the signals are. Generally, researchers want to see 30-50 people with similar findings to identify a subset. That suggests that 400 ME/CFS samples could result in from 8-15 subsets – if really strong signals are found. For me, I would be very happy if the study was able to identify 3 or 4 significant subsets.

“We would not be able to conduct this study without AI. The analysis that I think we’re hoping to do is going to be hugely, hugely reliant on artificial intelligence and machine learning and all these sorts of things.” Danielle Meadows

A study of this size and complexity, not surprisingly, will take time. Danielle said the sample collation and testing will occupy the rest of this year and then AI/bio-informatics work will be the most time and resource intensive part of the study. It will likely last all of 2027. The OMF is already engaging with bioinformatics specialists to help guide the vast amount of analysis that will be needed.

Validation

Rome is not built in a day, and validating a biomarker will also take time. Biomarkers, after all, can impact everything from diagnosis, to research, to drug trials, and validating them does not happen overnight.

First, in the discovery phase, a wide net is cast to identify candidate biomarkers. Then, in the verification and validation phases, the candidates are tested in new samples and assessed against candidates from number of other diseases. The crucial step comes when outside researchers and labs validate the original findings. Once that is done – if it is done – ME/CFS is potentially off to the races.

Impact

History has shown that when a field transitions from small, fragmented studies to large-scale, biomarker studies that achieve validation, the impact on the disease can be transformative.

Biomarker key ME/CFS

Large biomarker studies have provided the key that unlocked treatments for other diseases.

The validation of the HER2/neu oncogene in breast cancer in the 1980s led to the first targeted treatment for breast cancer. Large-scale studies indicating that B-cells play a crucial role in multiple sclerosis directly led to the development of a drug, Ocrevus (ocrelizumab), that specifically targeted them. Similarly, lupus moved from a kind of wastebasket autoimmune disease to a targeted one when omics’ studies identified an “interferon Signature” which resulted in the first new lupus drug in 50 years (Benlysta) being successfully tested and approved.

On the other hand, too much faith in the beta amyloid biomarker in Alzheimer’s, which identified a secondary instead of a core factor in Alzheimer’s, resulted in a decade of failed clinical trials. It’s  possible, but probably not likely, that ME/CFS contains too many subsets (20-50) even for a 1,000 sample study to uncover.

A strong biomarker would be able to reliably distinguish ME/CFS from similar diseases (fibromyalgia, long COVID). The impact that strong, validated diagnostic biomarkers – if they are found – would have on the ME/CFS field could be immense. A mechanistic biomarker (i.e., a biomarker that directly identifies a core driver of the illness) could even quickly lead to targeted drug trials and effective treatments for a subset of patients.

“If we can identify subtypes, I think it goes a long way toward also just convincing larger pharmaceutical companies to take interest.” Danielle Meadows

  • Doctor’s Office – People with ME/CFS would get diagnosed much more quickly, and the stigma patients face in doctors’ offices would fade. Subsets that point to specific treatment options could result in quicker, more effective treatments.
  • Insurance and Disability – No more exercise tests needed to get disability? A validated finding could result in patients more quickly getting disability and insurance benefits.
  • More Effective Research Studies – Research studies today are inhibited by having to assess symptomatically similar but biologically heterogeneous cohorts of patients. Being able to target biologically defined cohorts of ME/CFS would erase the “wastebasket” theme that has so inhibited researcher interest. Increased researcher interest and funding should allow researchers to drill down on specific kinds of ME/CFS. The OMF raised money from its supporters for this study but, call me naïve, if this study is successful, I would be shocked (shocked!) if the NIH didn’t provide ample funding for follow-up studies and ultimately, clinical trials. Funding the validation studies would, hopefully, not be a problem.
  • Drug Companies Get Involved – Drug company interest (or lack of it) has been a huge hurdle. Pharmaceutical companies would feel more confident in testing their drugs. Identifying subsets would allow them to target drug trials to specific groups of patients. Ultimately prognostic biomarkers that allow them to assess how well a treatment is doing would be developed. Finding a prognostic biomarker was the breakthrough that allowed drug companies to uncover multiple drugs to stop HIV/AIDS in its tracks. It all starts with finding diagnostic biomarkers.

A Field Slowly Begins to Turn…

unraveling

Strong biomarkers, if they are found, could turn ME/CFS from a complicated, mysterious disorder into a group of clearer ones.

Even if strong, validated biomarkers are not immediately found, it’s hard to imagine this study not being very helpful. Molecular signatures that researchers can drill down on will surely pop out. At the very least, researchers will have a better understanding of ME/CFS, and better cohorts to study. Plus, further analysis of any molecular signatures found could result in validated biomarkers – it will just take more time.

I would be shocked, though, if the study didn’t ultimately result in validated biomarkers. Everything tells us that the deeper researchers dig into the molecular roots of ME/CFS, the more they find.

Suddenly, we seem to be awash in ambitious studies that are attempting to get at the exact molecular drivers of this illness. The OMF’s BioQuest study, Amatica’s huge gene expression study, Precision Life’s mechanistic approach, and Liz Worthey and Camille Birch’s recent whole genome study suggest that the field is becoming more and more confident that it can, as Ian Lipkin asserted, begin to unravel this complex disease.

PrecisionLife’s Bold Attempt to Break the Code on and Beat ME/CFS and Long COVID

When I asked Danielle what excited her about the ME/CFS field right now, it was no surprise to hear that it was a focus on precision medicine’s ability to identify subtypes and provide treatments for them.

We’re clearly light years ahead of where we were even five years ago. Seven years ago, I talked to Sadie Whittaker, Solve M.E’s Chief Scientific Officer, who came from the cancer field. She said that, above all, the ME/CFS field needed big data sets – the kind of data sets that turned breast cancer from one disease to ten diseases – and resulted in precision medicine treatments. Seven years later precision medicine is becoming a kind of buzz word in ME/CFS. While we don’t have it yet, it’s no longer a pie-in-the-sky idea but something numerous research groups feel is within reach.

Thinking Bigger and Bigger: Solve ME’s Research Director Sadie Whittaker Talks On Moving Forward on ME/CFS

What about long COVID? LIINC’s long-COVID biomarker effort called “VIPER” is underway. VIPER doesn’t have, to my knowledge, a 1,000-person study, but it is an uber-organized, large-scale effort to test possible biomarkers. Right now, the VIPER is focused on finding pathogen biomarkers, but it will, at some point, expand them. It’ll be fascinating to compare BioQuest’s and VIPER’s results.

 

Support Health Rising and Keep the Information Flowing!

Health Rising is not a 501 c (3) non-profit

 

Health Rising’s Quickie Summer Donation Drive is On!

Keeping up with the latest research in ME/CFS, long COVID, fibromyalgia, and allied diseases. Exploring new treatment possibilities. Learning how others have recovered. All in as thoroughly and comprehensively as we can. 

Please support Health Rising during our quickie summer donation drive. Our goal is to raise $15,000. 

 Find out more here.

Please support Health Rising in our Quickie Summer Donation Drive! Our goal is $15,000.Click here for more.

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