ME/CFS Research: State of the Art, State of the Science

Written by Dr. Anthony Komaroff

On June 7, 2021, Drs. Lipkin and Komaroff published an article in Trends in Molecular Medicine on the state of ME/CFS research in the wake of COVID-19.

An illness like ME/CFS has been described in the medical literature for several hundred years.  Yet, when interest in the illness resurfaced in the mid-1980s, you could not find any mention of it in the major textbooks of medicine.

There were several reasons for this. First, past medical publications described the symptoms of the illness but did not report underlying biological abnormalities that might be causing those symptoms. Some doctors concluded that if no underlying biological abnormalities had been found, that the illness probably was not “real”. 

Furthermore, when doctors seeing patients with the symptoms of ME/CFS ordered the “standard” laboratory tests in the mid-1980s, the “standard” test results typically were normal. 

Unfortunately, upon receiving the normal test results some doctors told their patients that “there is nothing wrong with you.”  That was one possible conclusion.  Another possible conclusion that those doctors might have considered, but did not, was that they were ordering the wrong tests. Indeed, other tests available to them even in the mid-1980s did find abnormalities in many people with ME/CFS1.

Now, in the 21st century, we have state-of-the-art technologies for identifying underlying biological abnormalities that were unavailable (and even unimaginable) in the mid-1980s.  Most of the testing being performed by the Columbia Center for Solutions for ME/CFS employs these newer technologies.

These are some of the new technologies:

  • We now have much greater power to detect the presence of infectious agents—including previously undiscovered agents—using technologies like polymerase chain reaction (PCR). 
  • Diseases typically occur because the coordinated interaction of multiple different molecules has been disrupted. Most medical research previously measured only one or a few molecules in a blood sample. Today, we can measure literally thousands of molecules in a single sample. That means we can identify molecules that appear to be linked as part of a biological pathway. Once you identify pathways that are linked to a particular disease, the molecules in those pathways become candidates to serve as possible diagnostic tests, and also can become the basis for designing new treatments.  The Center is measuring thousands of different molecules in people with ME/CFS and in healthy control subjects.
  • The molecules the Center is measuring are not just the molecules made by our body. They also include molecules made by the microbes that live on and in our body. One of the great discoveries of the past 20 years has been the recognition that the genes of the microbes that live within us (our microbiome) produce molecules that affect our health. The Center is measuring those microbes, and the molecules they produce.
  • We can measure the structure of all the human genes as well as the microbial genes. That’s important because the purpose of a gene is to make a particular protein, and the structure of the gene determines the structure of the protein. It is the proteins that ultimately make our bodies work—that allow us to move, to see, to think. If there’s something wrong with the structure of a person’s gene, the result can be the production of a defective protein.
  • We also can measure whether a particular gene is activated to make the protein it is supposed to make. That’s important because even if the structure of a gene is perfectly fine, if the gene is not activated when it should be, it can have adverse effects on health.

That’s the remarkable state-of-the-art in biological technologies that can be deployed to study disease in 2021.  What’s the state-of-the-science, regarding ME/CFS?  I and Dr. Ian Lipkin, Director of the Center, have just published an article summarizing the state-of-the science. It was published online in late June 2021, in the journal Trends in Molecular Medicine2. As summarized in more detail in that article, we note that people with ME/CFS have:

  • Larger numbers of inflammation-causing bacteria, and smaller numbers of inflammation-fighting bacteria, in their gut, changes that correlate with symptoms;
  • Higher numbers of activated immune cells called T cells, as if the cells are fighting a battle against something;
  • Depressed function of another type of virus-fighting cell called natural killer (NK) cells;
  • Higher levels of certain chemicals (cytokines) that the immune system uses to fight battles;
  • Various autoantibodies—evidence of an autoimmune process in which the body’s immune system attacks not some foreign invader but attacks parts of the body, itself;
  • An impaired ability to make energy molecules (ATP);
  • Various abnormalities in the brain and autonomic nervous system

Finally, our recent article discusses how the growing knowledge about ME/CFS may affect our understanding of the lingering illness that can occur in people who develop COVID-19—postacute COVID-19 syndrome, or “long COVID”—and vice versa. We also propose a research agenda for both ME/CFS and postacute COVID-19 syndrome. We need to know whether the underlying biological abnormalities of ME/CFS are similar or identical to those in postacute COVID-19 syndrome.  Although we don’t yet know how many people will develop postacute COVID-19 syndrome, it is plausible that the number in the U.S. soon will match the number who already suffer from ME/CFS—as many as 2.5 million people3.

In summary, the recent article summarizes in some detail what is known about the underlying biology of ME/CFS. It also highlights the fact that understanding a disease sometimes awaits the development of new scientific technologies. The article also emphasizes why physicians should never dismiss an illness just because they don’t understand it. With dedication, new tools and an open mind, the answers are coming.

1Bates DW, Buchwald D, Lee J…Komaroff AL. Clinical laboratory test findings in patients with chronic fatigue syndrome.  Arch Intern Med 1995;155:97-103.

2Komaroff AL, Lipkin WI. Insights from myalgic encephalomyelitis/chronic fatigue syndrome may help unravel the pathogenesis of postacute COVID-19 syndrome. Trends Mol Med 2021, published online June, 2021 https://doi.org/10.1016/j.molmed.2021.06.002

3Komaroff AL, Bateman L. Will COVID-19 lead to myalgic encephalomyelitis/chronic fatigue syndrome?  Front Med 2021;7:606824. doi: 10.3389/fmed.2020.606824

Dr. Anthony Komaroff

Anthony Komaroff, MD

Editor in Chief, Harvard Health Letter

Anthony Komaroff is the Steven P. Simcox/Patrick A. Clifford/James H. Higby Professor of Medicine at Harvard Medical School, senior physician at Brigham and Women’s Hospital in Boston, and editor in chief of the Harvard Health Letter. He was director of the Division of General Medicine and Primary Care at Brigham and Women’s Hospital for 15 years, and is the founding editor of Journal Watch, a summary medical information newsletter for physicians published by the Massachusetts Medical Society/New England Journal of Medicine.

A letter from our Community Advisory Committee

Francis S. Collins, M.D., Ph.D.

Director, National Institutes of Health (NIH)

9000 Rockville Pike

Bethesda, Maryland 20892

Dear Dr. Collins,

We are a Community Advisory Committee established with the support of the NIH to advise the ME/CFS Collaborative Research Center consortium. We are housed at the Center for Solutions for ME/CFS at Columbia University. Our committee includes people living with ME/CFS, caregivers, advocates, and representatives from Solve ME/CFS Initiative, Bateman Horne Center, and #MEAction.  

We applaud the NIH’s commitment to research into Post-acute sequelae of SARS-CoV-2 infection (PASC) known as Long COVID. We also wholeheartedly support the letter sent to you by the Long COVID Alliance and join them in all their recommendations.

We believe it would be a lost opportunity to embrace the struggle of people with PASC without also embracing those with Post Viral Fatigue Syndromes and ME/CFS. It is well known that up to 80% of people who have ME/CFS develop the disease following acute infections such as SARS, Ebola and common viruses like EBV, human herpesvirus-6, enteroviruses and others – and even after parasitic and bacterial infections.

Dr. Anthony Fauci, NIAID Director, Dr. Walter Koroshetz, NINDS Director, Dr. Nina Schor, NINDS Deputy Director, and other researchers have recognized that a significant percentage of people with PASC have symptoms “strikingly similar” to ME/CFS. These include post-exertional malaise, cognitive dysfunction, pain and sleep disorders as well as POTS. Individuals with Long COVID are being diagnosed with ME/CFS. Specialist clinician researchers Dr. Anthony Komaroff and Dr. Lucinda Bateman expect the number of people with ME/CFS to at least double due to COVID-19 infections. 

Millions around the world have had their lives destroyed and held hostage by ME/CFS, while being maligned and disenfranchised in the medical and disability systems – as well as dismissed with respect to disease burden in biomedical research. They flounder in a desert of indifference, inappropriate treatment and mis-management with up to 91% undiagnosed

In 2017, you wrote that “The NIH is committed to stimulating additional research to reveal the causes of this debilitating disease. ME/CFS is such a complex condition, affecting so many body systems, that we do not know where the answers will come from.” 

There could not be a more compelling opportune moment to stimulate and expedite research into post viral illnesses. Now is the time to push post viral syndrome research alongside this tsunami of PASC illness and disability that is fast becoming a public health crisis. We should build upon the knowledge and understanding from ME/CFS research to advance research in both areas, including utilizing the knowledge of possible harms. 

Therefore, we ask that PASC research prioritize comparator control groups such as people with ME/CFS and other related post-viral illnesses and include ME/CFS researchers and clinicians in strategic planning. This will help to accelerate research and understanding of all post viral illnesses. 

We also strongly request that you, as NIH Director, be inclusive and talk about all post viral fatigue syndromes including ME/CFS and PASC together in future communications and media. In addition, please revise your 2021 blog on Long COVID to be consistent with Dr. Schor and Dr. Koroshetz’s recent public statements articulating the relationship between PASC, PVFS and ME/CFS.

This is an unprecedented time and you are in a unique position to provide leadership in unravelling PASC and associated illnesses. Millions need your support and your voice. Thank you.

Sincerely, 

The Community Advisory Committee for the NIH Collaborative Research Centers

CC:

Anthony S. Fauci, M.D., Director of National Institute of Allergy and Infectious Diseases (NIAID)

Walter J. Koroshetz, M.D., Director of National Institute of Neurological Disorders and Stroke (NINDS)

Nina Schor, M.D., Ph.D., Deputy Director, NINDS

Steven M. Holland, M.D., Director, Division of Intramural Research NIAID

Avindra Nath, M.D., Clinical Director, Division of Intramural Research NINDS

Matthew J. Fenton, Ph.D. Director, Division of Extramural Activities NIAID

Vicky Whittemore, Ph.D. Program Director NINDS

Joseph J. Breen, Ph.D., Section Chief NIAID

Amy Patterson, M.D., Deputy Director for Clinical Research and Strategic Initiatives, NHLBI 


CfS for ME/CFS Drs. Komaroff and Bateman participate in MEAction Presser

On March 25, #MEAction hosted a telepresser featuring a panel of experts uniquely positioned to speak to how long COVID is being informed by the research on myalgic encephalomyelitis / chronic fatigue syndrome (ME/CFS).

Long haulers are overwhelmingly reporting symptoms that resemble ME/CFS at six months, and researchers are expecting the number of people with ME/CFS to more than double during the pandemic, which follows the pattern of past viral outbreaks. Dr. Anthony Fauci has warned repeatedly of the risk for COVID-19 patients to develop ME/CFS.

Our panel of experts knew this was coming, and have dedicated a large part of their careers preparing for this moment. Since the beginning of the pandemic, ME/CFS researchers and clinicians expected that a worldwide viral outbreak would lead to a massive surge in chronic illnesses, including ME/CFS.

  • Dr. Lucinda Bateman, MD, founder of the Bateman Horne Center, is seeing overlapping symptoms in both her long COVID and ME/CFS patients.
  • Dr. Anthony Komaroff, MD oversees the Columbia University – Center for Solutions for ME/CFS Long-COVID study with the Bateman Horne Center. He chaired the Neurology section of the NIH Conference on Post-COVID health complications this past December. In his Frontiers article exploring how past viral outbreaks have led to surges of chronic illness, he estimates COVID-19 will double the number of people with ME/CFS.
  • NINDS Clinical Director, Dr. Avindra Nath, MD, has launched two intramural studies at the NIH to investigate long COVID, which follows on the heels of the institute’s intramural work investigating ME/CFS. Both studies are showing overlapping findings and symptoms.
  • A long hauler and person with ME/CFS will share their experiences of getting a virus and not recovering.

Links:

Read more on the connection between long COVID and ME/CFS:

Studies and articles on post-viral illness:

https://www.frontiersin.org/articles/10.3389/fmed.2020.606824/full

https://www.tandfonline.com/doi/full/10.1080/21641846.2020.1778227

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7889402/

Preprint survey on characterization of long COVID:
https://www.medrxiv.org/content/10.1101/2020.12.24.20248802v2

Read about the disease burden and historic underinvestment of ME/CFS:
https://oatext.com/Estimating-the-disease-burden-of-MECFS-in-the-United-States-and-its-relation-to-research-funding.php

Bridging the Gap: Outreach and Engagement with the ME/CFS Community

We are excited to announce the launch of the ME/CFS Collaborative Research Center’s outreach and engagement initiative led by the Center for Solutions for ME/CFS at Columbia University.

The cornerstone of this effort is the establishment of a Community Advisory Committee (CAC) to partner with the NIH Clinical Research Centers (CRCs) at Columbia University, Cornell University, The Jackson Laboratory, the Interdisciplinary Canadian Collaborative Myalgic Encephalomyelitis (ICanCME) Research Network, and the Data Management Coordinating Center at RTI International. The CAC is comprised of 14 individuals including people living with ME/CFS, caregivers, advocates, and representatives from #MEAction and Solve ME/CFS Initiative. We at the Center for Solutions for ME/CFS at Columbia University will serve as the bridge between all stakeholders by coordinating the effort.

The CAC has designated working groups based on the needs of the community as well as the Collaborative Research Centers (CRCs). The initial working groups will focus on information dissemination to address communication matters, study feasibility to aid in clinical study design, and scientific priorities to develop recommendations for future ME/CFS research pathways. The goals of the CAC will be to increase communication, research participation, and accelerate the pace of research.

To complement this work, we have also created the Center for Solutions for ME/CFS Communications Hub, which is comprised of representatives from nine network-affiliated organizations. The Hub encourages cross-promotion and amplifies the distribution of network developments and findings. Our cooperative effort ensures the timely distribution of information and significantly broadens the reach to ME/CFS stakeholders.

For more information on the launch of the ME/CFS Collaborative Research Center’s outreach and engagement initiative, tune into the NIH’s ME/CFS Working Group Call this upcoming Thursday, November 5 at 11AM ET.

Click the link below to join the webinar:

https://nih.zoomgov.com/j/1608562314?pwd=Ny92SU81SFdJV1ZTL0I1WFUwalVjdz09

Passcode: MECFS2020


Center for Solutions Community Engagement and Outreach Team

Allison Kanas

Director, Community Outreach and Engagement

Sydney Silverman

Manager, Community Outreach and Engagement

CRC Community Advisory Committee

Amy Williams

BA Occupational Therapy

Microbe Discovery Project

Person living with ME/CFS

Angela Linford

Bateman Horne Center

Cherylle McFarlane, RN

Challenged with ME/CFS

Emily Taylor

Solve M.E.

Jaime Seltzer

#MEAction

Jessie Brown-Clark

Solve M.E.

Kathi Kuehnel, J.D.

ME/CFS Caregiver

Mary Dimmock

ME/CFS Caregiver and Patient Advocate

Neal Goldberg, PhD

Dr. Nina Muirhead, BMBCh(oxon) MEd

Chair Education Group, CMRC

Forward ME, UK

Individual Living with ME/CFS

Rochelle Joslyn, PhD.

Sabrina Poirer

ICanCME Research Network

Patient Partner in Research

Individual Living with ME/CFS

Susan Taylor-Brown, MD, PhD

Individual living with ME/CFS

Tahlia Ruschioni

Bateman Horne Center

Therese Russo, MPA

ME/CFS Patient Advocate

Individual Living with ME/CFS

A Proteomics Study from the Center: Searching for the Criminal

By Dr. Anthony Komaroff

On July 21, 2020, the results of a proteomics study by the Center for Solutions for ME/CFS was published by the journal PLoS ONE.

Proteomics uses new technologies—that have become available in the last two decades—to precisely identify large numbers of proteins and measure their levels. The measurement is made in some compartment of the body: the blood, the spinal fluid, a particular organ, even within a single cell. These new technologies make it possible to take a sample from the compartment, like a small sample of blood, and to accurately measure the levels of hundreds, even thousands, of different proteins in that sample, relatively inexpensively and rapidly.

In the “old days”—way back in the 20th Century—scientists often had to be content with measuring the levels of one protein at a time. Since proteins typically interact with large numbers of other proteins and other types of molecules, you often didn’t learn much by measuring one protein at a time. A great strength of the Columbia Center for Infection and Immunity, where the Center for Solutions for ME/CFS is housed, and its collaborating facility at the University of Pennsylvania – Epigenetics Institute, is the ability to measure large numbers of molecules at the same time, and to study how they interact.

What did the latest study from the Center show? Basically, two things:

  • There appears to be a distinctive “signature” of a small group of proteins that distinguishes people with ME/CFS from healthy people;
  • The proteins involved in that “signature” are primarily involved in the immune response—particularly the response of immune cells called B cells—to infections, and the response seen in autoimmune diseases.

It is possible that the “signature” that has been found might some day become a diagnostic test for ME/CFS. A perfect diagnostic test for a disease (in this case, ME/CFS) has two essential elements:

  • It must have no “false negatives”: the test result can never be negative (“normal”) in a person who really does have the disease.
  • It must have no “false positives”: the test result can never be positive (“abnormal”) in a person who does not really have the disease.

There are very few perfect diagnostic tests in medicine, but there are many that come pretty close to perfection. For the signature that the Center’s study has identified to become a diagnostic test it will need to be tested again:

  • In larger numbers of people with ME/CFS from all over the world to determine whether the test has a very low false negative rate;
  • In large numbers of people with diseases other than ME/CFS that also can cause the hallmark symptoms of ME/CFS—fatigue, post-exertional malaise, unrefreshing sleep, cognitive impairment, orthostatic intolerance—to determine whether the test has a very low false positive rate in those diseases.

The new study is consistent with prior studies that have found abnormalities related to B cells in people with ME/CFS. B cells are white blood cells, also called lymphocytes, that are important in the response of the immune system to foreign invaders, like infectious agents. In particular, B cells ultimately lead to the production of antibodies—antibodies to fight infectious agents, and auto-antibodies that are seen in autoimmune diseases.

Does this study have implications for treatment?

The study—like most studies—seeks to identify what is going wrong in the body of people with this illness. The reason for this is not just because the answer might be interesting, but because the answer might provide a target to shoot at with a treatment.

In this case, the study may prompt scientists to test more ways to quiet overactive B cells (some past attempts have failed), particularly the production of autoantibodies. Also, if further studies can identify the antigens that the activated immune system is activated by, these results may reveal underlying toxins, infectious agents, or other foreign molecules that can themselves be targeted .

Medical researchers sometimes are called “disease detectives.” If you think of research as detective work, then the cause of a disease is the criminal. This research has not definitively found the criminal that causes ME/CFS, but the research does strongly suggest the neighborhood where the criminal is likely to be hiding.


Authors: Milivojevic M, Che X, Bateman L, Cheng A, Garcia BA, Hornig M, Huber M, Klimas NG, Lee B, Lee H, Levine S, Montoya JG, Peterson DL, Komaroff AL, Lipkin WI. Title: Plasma proteomic profiling suggests an association between antigen driven clonal B cell expansion and ME/CFS.

Journal citation: PLoS ONE 15(7): e0236148. https://doi.org/10.1371/journal.pone.0236148


Dr. Anthony Komaroff

Anthony Komaroff, MD

Editor in Chief, Harvard Health Letter

Anthony Komaroff is the Steven P. Simcox/Patrick A. Clifford/James H. Higby Professor of Medicine at Harvard Medical School, senior physician at Brigham and Women’s Hospital in Boston, and editor in chief of the Harvard Health Letter. He was director of the Division of General Medicine and Primary Care at Brigham and Women’s Hospital for 15 years, and is the founding editor of Journal Watch, a summary medical information newsletter for physicians published by the Massachusetts Medical Society/New England Journal of Medicine.

Will There Be a Post-COVID-19 Form of ME/CFS?

By Dr. Anthony Komaroff

Will some people who get COVID-19 subsequently develop ME/CFS? After all, many people with ME/CFS say that their illness began with some kind of infection: “a virus,” “a flu,” “a bad cold.” When it started, their illness didn’t feel that different from similar illnesses in the past, so no tests were done to determine what kind of infection it was. Their doctors thought there was no need, since these minor infections typically get better. Only this one didn’t get better, and the cause of the initial illness remained a mystery.

Other times, there is no mystery; the initial infection is clearly diagnosed. It might be infectious mononucleosis (“mono”), or it might be Lyme disease. The mystery then becomes why, after the clearly diagnosed illness has been treated, does the person remain sick for months and years thereafter?

Sometimes, people who develop ME/CFS—after what appears to be an infection—seem to have been part of a larger epidemic. That is, within a narrow window of time, large numbers of people in the same geographic area become sick with an illness that seems like an infection and then develop ME/CFS. Often these initial “infectious-like” illnesses are not severe, i.e. not that different from common infections. So doctors say, “it’s just something going around,” and don’t order tests. But the illness doesn’t get better.

Many such epidemics have been reported, all around the world, over the past 70 years. Organizations like the U.S. Centers for Disease Control and Prevention (CDC) have studied these apparent epidemics but often have been unable to find the cause of the initial infection1-3.

Other epidemics of more severe, clearly diagnosed infectious diseases—like SARS4, West Nile Virus5, dengue6 and Ebola virus7—can be followed by ME/CFS or a very similar illness.

So, there is abundant evidence that ME/CFS can follow either an apparently infectious illnesses of uncertain cause, or a clearly diagnosed infectious illness—including illnesses causes by viruses, bacteria, and even certain parasites.

Perhaps the best study of whether ME/CFS can develop following an infectious illness is a study supported by the CDC but conducted in a small, isolated, rural town in Australia, a town where people rarely leave to travel elsewhere. The town had one hospital, one laboratory, and a small group of doctors, making it easy to identify virtually every case of an infection that might lead to ME/CFS—and to follow people to see if they did develop ME/CFS8.

In this study, 253 individuals who developed an infection with either Epstein-Barr virus (a DNA virus), Coxiella burnetti (intracellular bacterium), or Ross River virus (an RNA virus) were followed for the next year. The study found that ME/CFS developed in 11% of the people. The strongest predictor of a “post-infective fatigue syndrome” was the severity of the initial illness, as judged both by symptoms and by laboratory test abnormalities. In other words, objective and measurable biological abnormalities predicted who would develop ME/CFS. In contrast, people with a past history of psychiatric illness were not more likely to develop ME/CFS.

It is therefore entirely plausible that some cases of ME/CFS will develop in people who get COVID-19. It is important to conduct studies that follow people with COVID-19 for several years, even after they recover, to see whether ME/CFS or other long-term complications will develop.

1.           Shelokov, A., Habel, K., Verder, E. & Welsh, W. Epidemic neuromyasthenia: an outbreak of poliomyelitislike illness in student nurses. N Engl J Med 257, 345-355 (1957).

2.           Poskanzer, D.C. et al. Epidemic neuromyasthenia: an outbreak in Punta Gorda, Florida. N Engl J Med 257, 356-364 (1957).

3.           Acheson, E.D. The clinical syndrome variously called benign myalgic encephalomyelitis, Iceland disease and epidemic neuromyasthenia. Am J Med 4, 569-595 (1959).

4.           Moldofsky, H. & Patcai, J. Chronic widespread musculoskeletal pain, fatigue, depression and disordered sleep in chronic post-SARS syndrome; a case-controlled study. BMC Neurol 11, 37 (2011).

5.           Sejvar, J.J. et al. Neurocognitive and functional outcomes in persons recovering from West Nile virus illness. J Neuropsychol 2, 477-99 (2008).

6.           Seet, R.C., Quek, A.M. & Lim, E.C. Post-infectious fatigue syndrome in dengue infection. J Clin Virol 38, 1-6 (2007).

7.           Epstein, L., Wong, K.K., Kallen, A.J. & Uyeki, T.M. Post-Ebola signs and symptoms in U.S. survivors. N Engl J Med 373, 2483-4 (2015).

8.           Hickie, I. et al. Post-infective and chronic fatigue syndromes precipitated by viral and non-viral pathogens: prospective cohort study. BMJ 333, 575-8 (2006).


Dr. Anthony Komaroff

Anthony Komaroff, MD

Editor in Chief, Harvard Health Letter

Anthony Komaroff is the Steven P. Simcox/Patrick A. Clifford/James H. Higby Professor of Medicine at Harvard Medical School, senior physician at Brigham and Women’s Hospital in Boston, and editor in chief of the Harvard Health Letter. He was director of the Division of General Medicine and Primary Care at Brigham and Women’s Hospital for 15 years, and is the founding editor of Journal Watch, a summary medical information newsletter for physicians published by the Massachusetts Medical Society/New England Journal of Medicine.

A microbe hunter turns to ME/CFS: Ian Lipkin presents at the CDC

The following is a transcript of Dr. Lipkin’s talk at the CDC in September. You can watch the full lecture here:

Transcript

21:19

This is actually how I got into this field, I was invited by Brian Mahy, who many of you will remember, and Jim Dobbins who some of you may remember, because of these reports in Japan that there were individuals who developed ME/CFS as a result. That then led to a large NIH study which found no association and Bill Switzer was a critical partner in this work and Judy Mikovits was a critical partner in this work. But in any event, we found no evidence whatsoever of XMRV being implicated. And this was a very expensive, very difficult study to do but it emphasized the importance of getting this sort of work done in a rational way.

22:30

Okay, now, for the meat of the talk, now that I’ve shown you all the tools we can bring to bear on the problem, let’s talk about ME/CFS. Right now it’s clinical diagnosis and it is a diagnosis of exclusion, so we make sure that people don’t have other intercurrent infections with hepatitis C, they don’t have hypothyroidism, they don’t have other sorts of problems. And these are data that came from what’s now known as the National Academy of Medicine. It is not a small problem, it’s something like 2 million people in the U.S. alone, and is very expensive because these people can’t work as well as requiring various types of support. The causes of the disorder are not well understood, many patients report what seems like an infectious prodrome with pharyngitis and swollen lymph nodes and feeling feverish and having night sweats and so forth.

23:17

So initially when we became involved in this, we figure this is what we’re going to do, was a standard sort of pathogen search. Now this is from the work that we did with Brian and Jim Dobbins, who are not on this paper because for reasons unclear to me, they weren’t able to do that at that time. But they really supported this work, it wouldn’t have happened otherwise. We didn’t find any evidence for Bornavirus infection, but at that point I did make one observation that I think in retrospect was prescient, and that was that these individuals, as we studied them, had high levels of antibodies to things like beta-galactosidase suggesting that they had polyclonal B cell activation.

24:04

This is really some of the very first work suggesting that there are immunological abnormalities in these patients. And this work was really done back in 1995. We now have a center for solutions for ME/CFS that’s funded by the NIH, though not as well as it should be. The clinicians are shown in yellow, Dan Peterson, Sue Levine, Cindy Bateman, and Jose Montoya has been replaced by Moneghetti, and then we have Oliver Fiehn from metabolomics. We have John Greally, who primarily focuses on transcriptomics, Tony Komaroff,who develops applications that we use for tracking patients then an admin and Columbia based core as shown here.

24:51

So what I’m going to try to do is to summarize som of the things we’ve already done. We found altered profiles for various cytokines and chemokynes in blood as well as in spinal fluid. We did these multi-center studies and so forth.

25:12

This is an example of work that we did looking at cytokine expression over the course of the illness, and what we found was that there were individuals who were caught within 6 months to a year or so of the original diagnosis, they had different cytokine profiles than did those individuals who had disease for more than 3 years, suggesting that there might be burnout, I think was the interpretation that we rendered at the time. We really don’t have an explanation for it as yet. And there were differences in levels of stickiness and chemokynes in spinal fluid and our control group here was not only normal controls but of individuals who had multiple sclerosis and you can see here now that there are various abnormalities which we’ve explained elsewhere

25:58

The center has three projects; one is broadly considered the microbiology of ME/CFS, which is essentially characterization of bacteria, viruses and fungi, and everything that we can access; feces, saliva, and blood. And the indirect measure of exposure is going to be increasingly important because we’re not really going to find anything as I’ll show you looking at direct measures based on sequencing. Metabolomic and transcriptomic studies that we’re doing with peripheral blood mononuclear cells, and then some translational aims where we look at the impact of somebody standing erect which is a problem for many of these patients, or doing some sort of an exercise test which gives them stress. One of the key features of ME/CFS is that these individuals don’t recover after exercise. And I’m going to show you some data now which I think will explain how this works.

27:02

One of the things that we’re using, which is gointo be extremely powerful, is called TruCulture and we actually began to look at drawing samples across multiple sites, their differences and levels of transcripts and proteins as a function of how things are preserved. A group at Institut Pasteur came up with a solution for this where they pull blood directly out of the patient’s arm, put it into these culture vials which can be supplemented with a variety of stimuli, in some instances they represent bacteria or viruses or fungi, and then at regular intervals, you depress this plunger, collect the supernatant, and then the cells below, you can extract and use for various sorts of things.

27:48

So this illustrates the way in which you can reduce the variability so, these are individuals who were exposed, who had cells were exposed to lipopolysaccharide and you can see how much tighter the data are, again, I don’t have a pointer, but if you look at the left there, you can see a lot of spread and as you use this other system it becomes very useful. And when you lose that sort of spread, when you get better resolution, you can find individuals that have specific genotypes and phenotypes. So that’s the approach.

28:21

So let’s talk about the fecal microbiome; so we’ve actually now done this twice, we had a pilot study that was funded by the Hutchins Family Foundation, which was 50 cases and 50 controls, and then we had a larger study funded by the NIH, which is roughly twice that. And if we look at the Venn diagram showing what comes up as being common, we find that there are 15 different bacterial types that are highly represented. You can see Ruminococcus, Clostridius species,and why is this important? Well, the Clostridius species are associated with inflammatory bowel disease, [inaudible] and so forth. And then you also have these butyrate producers that are reduced. If you have inflammation of the enteric mucosa, you have the opportunity for trafficking of molecules produced by bacteria into the systemic circulation where they can then have an impact. So that is one thing that we’re now pursuing and we do that by using metabolomics in those individuals who have ME/CFS who have irritable bowel syndrome, versus those who don’t.

29:36

Again, you can see the butyrate producers reduced, that appears to be common, but there are other bacteria which appear to be coming up as well.

29:45

We’ve looked at the salivary microbiome, there again you can find differences between cases and controls. So I don’t know that these are cause or effect, or simply epiphenomenal, but they’re at least observations and give you data that you can test in other populations. And I was meeting earlier with Beth and her team and I think, given that you have saliva, we can examine these sorts of issues. You can then ask questions about predicted metabolic pathway that might be disturbed as a function of different populations and you can see here now that the pyrimidine deoxyribonucleotides salvage, you know, is differentially infected, impacted unfortunately.

30:28

We’ve lost, you know, a lot of the information on the left side of the screen but there are inferences that you can make based upon what’s known.

30:38

We recently, and by recently I mean the day before yesterday, completed a proteomics pilot. Very, very small so it’s only 40 subjects and 40 controls, but they’re a well-matched population

30:53

And this finding has been very, very cool because what we’ve identified is that there are a number of proteins which appear to be differentially expressed in individuals who have ME/CFS. This is not to say that they all have the same cause, but if you use cancer as a paradigm for understanding this, you have multiple ways in which you can get to cancer; tumor suppressor genes, oncogenes, we think something similar is happening here.

31:23

So, I’ll give you an example on the next slide which supports the notion that at some point, there might have been an infection that resulted in an immunological trigger. And these are not bad odd ratios, you know? They’re all in excess of 3. Now what are we actually looking at here? These are proteomic studies that reveal differentially, a differential expression of immunoglobulin kappa and light chains and heavy chains, which are present at increased concentrations in individuals with ME/CFS. And you can use these immunoglobulin repertoires to try to understand.

32:13

You can actually use these then to develop biomarker diagnostics which allow you to say this individual is at risk for having ME/CFS. And it’s proving to be extremely powerful, we’ve done similar work with metagenomic analyses of feces and with metabolomics.

32:34

Metabolomics work we’ve done in collaboration with Oliver Fiehn and Dinesh Barupal at UC Davis. They again are focused really on rigor and granularity so they separately analyze biogenic amines, high and low density lipids, and primary metabolites.

32:58

Again, comparing this small group of 50 patients and 50 controls with the larger group of NIH patients, we can look for similarities and here we’re finding those as well. So there are specific abnormalities that are referent to a mitochondria, to phospholipids that are associated with ME/CFS and breakdown differently when you look at individuals who have abnormalities in the bowel and those who don’t.

33:25

So you can see here summarized, the glucosylceramide, carnitine plasmalogens, and so forth.

33:37

Now what are plasmalogens? I doubt anybody’s heard of them, but they are decreased in ME/CFS. They’ve been observed to be decreased in a variety of dementias as well and in Parkinson’s disease. So this may be some sort of marker for CNS dysfunction.

33:57

The last thing I’m going to describe for you in this respect is the epigenetics pilot that we’ve recently done. So we used a system that with bisulphite treated libraries for capturing 5.5 million methylated residues in the human genome. We restricted ourselves to those where we had good data, meaning 20x and we mapped and annotated their location within a specific genes with respect to promoters, non-coding sequences, introns and so on. And these are the results and this again, just like the proteomics work I was showing you is not yet published.

34:42

You can see that we’ve got 724 sites in almost 600 genes that met our criteria for methylation. You can see the distribution in the various regions in relationship to those genomes and this is really very interesting, so ME/CFS is marked there in blue and you can see that when we look at percentage of methylation, as you begin to look beyond [inaudible] 60-65%, you get hypermethylation in the ME/CFS group. And this just shows the data in that way. And it’s really, I think this is really some of the most promising data I’ve seen thus far, that has to do with talking about ways in which genomic modification might occur.

35:28

And there are a number of different gene circuits that have been implicated in this kind of work, it becomes, as you can see, extremely complicated. But many of these are associated with oxidative metabolism as well as with stress.

35:43

We highlight here, the ones where we see the largest changes and if anybody wants to see these data in more detail, I’ll be happy to show you.

35:54 (For animations, please refer to youtube presentation)

So I’m just going to demonstrate for you the ways in which we’re beginning to tease this apart. When we began looking at the most remarkable findings, at least to our mind, we found that they were related to iron metabolism. Now if you look at the methylation differences, you know, they’re modest, 12%, 11%, I don’t know how important that is. You then, we actually then measured RNA abundance so we created real-time PCRS so that we could actually look at the products of those methylated genes, and although no one gene is affected in a great fashion, if you sum them all, they could have a profound effect. So this is where we slip into fantasy, and I’ll show you what we think is going on.

36:42

So and this is moving into the cell, in this case we’re talking about monocytes and macrophages and somatic tissues, rather than red blood cells.

36:55

So we have our first lesion here, right? We have a lesion at the level of the clathrin coded pits. We have another lesion as these iron molecules are exiting the endosome–

37:09

You can see here now on the mitochondria, there’s an effect as it moves into mitochondria.

37:29

So in essence, what happens is you have an impact on multiple levels which should have an impact on your ability to metabolize oxygen and this could result in weakness and fatigue.

37:43

And we have to do the same thing with all of these circuits we’ve identified using all of these different methods and as we’re putting this thing together, it begins to look sort of like an anemia of chronic disease, with red blood cell damage and so forth, oxidated, stress. And this is a model that’s still in the process of being worked out.

38:04

I mentioned earlier to you the fact that we’re trying to build Serochips; this is our first Serochip which is designed to look at autoimmunity.

38:15

But more recently we’ve come up with something which is even more expensive but more exciting I think, and that is the entire human proteome complemented or supplemented by other targets that we think are important. Now in our experience, 2-5% of the patients who come through our research clinics, wind up having some evidence of persistent herpes virus infections. Some clinicals have more than others, Jose Montoya at Stanford had large numbers of those. Peterson has them as well. So, working again with this new company, Nimble Therapeutics, which has replaced NimbleGen, we have these 20 thousand odd human sequences. There are 16 mer peptides with 12 amino acid overlap.That’s not as good as what we’ve done in the past where we have 12-mers with 11 amino acid overlap,but you can see when I tell you these are arrays are $3500 each, you know, we had to make some compromises. We’ve added peptides that cover mitochondrial proteins, we have control scramble peptides which are critical for interpretation of singles, of signal, and then we have the reference proteomes of all known herpes viruses, because we’re concerned that they may be associated with persistent infection and the peptides that cover the proteomes. And then, because there’s frequently overlap with tick-borne diseases, we’ve used the refined epitope map that we’ve previously generated that allows us to do this. So we are embarking on a very expensive study that will allow us to examine, now that we haven’t found anything using direct methods, evidence that at some point these patients were also had

40:10

So one of the things that I want to highlight here is that, you know, we had the culture and Gram stain, and we had sequencing, and I think sequencing is passe, so what’s next? Right, is to examine the history of immune response so that we can make association between early life infections and [inaudible] quality and these kinds of chips, which are incredibly expensive, but hopefully it’ll come down in cost, will allow us to do this. So in summary of this part, Beth will agree, this is an important disease, it’s under studied. It’s important economically, it’s also important in terms of clinical medicine, all the things that we’ve done thus far provide biological evidence that this is a bonified illness; with cytokine, metabolomic, proteomic, epigenetic, transcriptomic differences, all consistent with some sort of an abnormal immune response oxidative stress, and a dysregulated microbiome. So we’ve come a long way. The high throughput sequencing, thus far, has not identified any one infectious agent so, although we’d hoped that we would find something, we’ve gone home empty there. But the serology will hopefully change that and the future work is going to have to focus on identifying environmental triggers of pathology in people who are genetically susceptible. And this is going to be very exciting.

41:44

I couldn’t leave without showing some movies, I’m not going to show you the movies actually though, but so Contagion, you know, Plague Inc. we helped with the game, I did some work on Bond 25 but I can’t tell you about it. I can’t even tell you if they’re still shaking and not stirring the martinis, but it should be cool. I hope it’s going to be cool anyway. If they selected one of the things I gave them. And then Utopia, which is about a flu pandemic that’s supposed to, you know, wipe out the world except for a select few maybe up here on Clifton Drive. And then Three Months, which is the story about an individual who becomes exposed to HIV and worries for 90 days, I don’t know. But you know, it’s not enough yet to pay the bills but it’s fun to work with these people.

42:42

And then the people who really do the work, who I’ve tried to identify here. And I’m happy to take questions, thank you very much.

ME/CFS Advocacy Call Highlights

The following is a summary of the trans-NIH ME/CFS working group call from March 17, 2020. For a transcript of the call please visit the NIH webpage here.


Beginning the call, Joe Breen, PhD highlighted various updates from our Collaborating Research Centers (CRC) at JAX labs, Cornell University, and our data managing site, RTI. Also in attendance were Walter Koroshetz, MD, Vicky Whittmore, PhD, and Leonard Jason, PhD.

Derya Unutmaz, MD and his group at the Jackson Laboratory reported higher levels of regulatory T cells in subjects with ME/CFS in their recently published paper. Regulatory T cells are responsible for maintaining the body’s immune response. However, deviations in T cell subsets can result in immune dysregulation and chronic activation of T cells. You can read their paper below.

Perturbation of effector and regulatory T cell subsets in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)

Maureen Hanson, PhD and her group at Cornell found distinct differences in T cell and lipid metabolism between ME/CFS cases and controls. Their data indicates possible mitochondria dysfunction in ME/CFS CD8+ T cells, observing decreased mitchondrial membrane potential and a reduction of normal glycolysis functions. You can find links to their full articles below.

Comprehensive Circulatory Metabolomics in ME/CFS Reveals Disrupted Metabolism of Acyl Lipids and Steroids

Myalgic encephalomyelitis/chronic fatigue syndrome patients exhibit altered T cell metabolism and cytokine associations

Ian Lipkin, MD and our group at The Center for Solutions for ME/CFS (CfSforMECFS) have been working on a variety of projects, one of which is looking to identify plasmic proteins in ME/CFS cases vs controls. This study confirmed that there are associations between specific immunoglobulin levels and ME/CFS. The article is pending review and will be released on our social network when it becomes available.

Other on-going studies include metagenomic analyses of saliva, blood and stool as well as our work to identify differentially expressed genes in various T cell populations.


The focus of the call was on Dr. Leonard Jason’s study, which has been widely circulated since being published in early 2020. This study examined the rates of pediatric ME/CFS cases at a community level. They concluded that 1 in 134 youth fit the criteria for ME/CFS, reporting that over 95% of these cases remain undiagnosed. Moreover, Dr. Jason and his group found that minority populations reported higher rates of ME/CFS diagnosis, which conflicts with previous research stating that this disease predominantly affects white, middle aged women. Their abstract is available here.

Our collective findings support that ME/CFS is a real, verifiable disease that impacts people from all walks of life.


Support for our work through individual donations has been pivotal to the advancement of our research. Any size donation is greatly appreciated and directly supports our mission of findings practical solutions for ME/CFS. Thank you for considering a new gift today – and envisioning the kind of impact we can make together.

You asked, we answered!

In December 2019, we asked our audience to send us questions they would want a ME/CFS expert to answer. Here are some of the questions we received from the community:

  • Can you give us any hints as to any findings you have at the moment that you are personally excited about?
  • As work progresses will you be expanding by seeking new researchers in different fields to add to your Centers team?
  • Can you clarify for people whether you are definitely using your new technology called the VirCapSeq-Vert testing in a cohort of study?
  • Will there be the possibility of any new papers being published within a year for now and can you give us any information on which studies?
  • Has your research led you to hypothesize whether auto antibodies are playing a role in ME?
  • Can Dr. Lipkin explain the relapsing/remitting nature of M.E? I was bedbound between 1994 and 1996 and then slow recovery to nearly normal until this year when I had a major relapse that has left me housebound.

To see our previous segments, navigate to the #AskOurResearchers section on our YouTube page to view them continuously.