“It’s exciting to partner with you to explore one of the most baffling medical mysteries of the 21st century, chronic fatigue syndrome”


The team has grown…

The Stanford Chronic Infectious Illness Initiative led by Dr. Jose Montoya began in 2010. If they’ve been quiet lately, it’s not because they haven’t been busy. With a basketful of exciting projects, new staff members, a new advisory board and a growing biobank–not to mention Stanford’s hosting of the big IACFS/ME conference in March of next year–they’ve been busy.

“Our Initiative for infection-associated chronic illnesses is now focused on chronic fatigue syndrome”

For one thing it’s no longer the Chronic Infectious Illness Initiative; ‘chronic infectious illnesses’ have stepped down and ME/CFS is now front and center. It’s simply the Stanford Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) Initiative now.


They’ve Grown – They are substantially larger, and now list 21 people on their team including three research coordinators, three Clinical Care professionals, a neurophysiologist, a cardiologist, three immunologists, three radiologists, one research assistant, two undergrads, and two high school student volunteers.

arrow showing progress

Dr. Montoya is steadily gathering support for his ME/CFS initiative at Stanford.

They’ve Published—Three papers are out on antiviral treatment with one more being submitted for publication that looks at how men and women respond differently to antivirals.

They’ve Expanded Their Search—I don’t know about you, but hearing that a group is studying parasites (toxoplasma gondii), fungii (coccidoides immitis), and bacteria (borrelia burgdorfii) along with the usual suspects makes me feel kind of like we’re in the hands of some real experts. They didn’t mention that they’re also studying herpes simplex, a herpesvirus that’s not on any other group’s radar but which one ME/CFS theory paper suggested could be at the heart of ME/CFS.

They’ve now got an Advisory Committee—It’s a good one. It includes the former head of the Trans-NIH Working Group, Dennis Mangan, who shook the NIH up good during his short time there and promised he would stay engaged with ME/CFS after he retired. The group also has our own Dr. Lily Chu (ME/CFS patient and advocate), Stanford immunologist Mark Davis , Stanford MD and author Abraham Verghese, and others.

It couldn’t have easy establishing an ME/CFS program at one of the most highly rated medical schools in the country–they’re usually the last to fall, so to speak, with a disease like ME/CFS, but Montoya has persevered and the program is finding its legs, and is growing.

Studies Underway

Pathogen/Immune Study IA

We’ve heard a lot about the Chronic Fatigue Initiative’s big pathogen study with Mady Hornig and Ian Lipkin, but my understanding is that Montoya has his own pathogen study going. Montoya reported that all the samples have been collected and analysis has begun. If this is an entirely separate study, then we have at least four separate pathogen studies going–a kind of amazing turnaround from the pre-XMRV days when the NIH stated it would not fund pathogen studies in ME/CFS.

Now we have the monster study at the Chronic Fatigue Initiative looking at blood, saliva, tears, fecal matter, and spinal fluid; the Montoya Stanford study; and the CFIDS Association and CDC BSRI studies. Since there must be substantial overlap in the patients across the studies, if the results agree with each other the results could be validated very quickly.

Pathogen/Immune Study IB

cartoon pictures of pathogens

The Stanford Initiative goes beyond the herpesviruses usually associated with ME/CFS and is looking for fungi and bacteria as well.

The pathogen study lays the groundwork for the immune system factor study (involving cytokines, gene expression and phospho-immunoflow) to see if pathogen A is correlated with immune activation or down-regulation in patients X,Y and Z. If pathogens are found, this study will help indicate what impact they’re having, and, since a pathogen doesn’t necessarily need to be particularly harmful in order to be significant, that’s the next crucial step in the process of validating pathogen harm in ME/CFS. Nobody’s done this before that I can recall.

The study is also looking for new biomarkers that reflect improvements on medications (shades of Dr. Kogelnik’s work at the OMI). Essentially they’re trying to find out what changed in the patients that improve on antiviral and other medications. If they can do that, they may be able to find the immune system hole that’s driving the pathogen activity. Then, hopefully, they can focus on fixing that.

Aided by a DOD grant, the Montoya team is also assessing HLA antigens as well as stimulating the immune cells and determining how they respond. (A recent putative fibromyalgia biomarker suggests immune cells in that disorder are under-responding to immune stimulation.)

The Brain

Montoya will be using cutting-edge MRI techniques (not found in clinics) to identify structural changes in the brain, and MRV (magnetic resonance venography) to look at blood drainage from the brain—a fascinating topic. Several years ago Perrin, an osteopath, proposed that lymphatic drainage backing up in the brain was causing many of the symptoms in ME/CFS. Recently we saw that a Chiari malformation can disrupt fluid flow from the brain in ME/CFS-like patients, leaving it engorged with toxin-ridden blood. Now, in another first, Montoya appears to be checking out whether venous outflows are backed up in ME/CFS as well.

A qEEG study examining peak alpha frequencies hopes to establish objective biomarkers of cognitive dysfunction in ME/CFS.

The Cardiovascular System

Several studies are investigating cardiovascular aging in ME/CFS patients

Several studies are investigating cardiovascular aging in ME/CFS patients

With all the autonomic nervous system work going on elsewhere, and with Montoya hitting every other avenue he can, it’s not surprising to find him dipping his toe into cardiovascular functioning. In fact he’s dipping more than his toe in. By putting ME/CFS patients on a bike and by testing their endothelial (blood vessel) functioning, he’s assessing the ‘aging’ of a system, the cardiovascular system, that you’d really not want to age prematurely. Then again, with all the blood flow issues in ME/CFS, it might be surprisingly if it hadn’t aged. MERUK in the UK found arterial stiffening—a sign of cardiovascular ‘aging’—in ME/CFS years ago. All the study data is in and they’re analyzing the results now.

Next Up

The Montoya group will be collaborating with several others in a gene expression and immune study of Lyme patients. This, too, is unusual; most researchers focus on ME/CFS or Lyme, but Montoya’s focus on both—using the same lab tests—will be invaluable to see how people with chronic Lyme differ from those with ME/CFS. I imagine there will be significant overlaps and, if there are, that will open the door to further collaborations and interactions between the Lyme and ME/CFS fields.

A Comprehensive, Multi-System Stab at ME/CFS

A complex disorder like chronic fatigue syndrome calls for the kind multi-dimensional approach Dr. Montoya is taking

A complex disorder like chronic fatigue syndrome calls for the kind multi-dimensional approach Dr. Montoya is taking

From pathogens to the immune system, to the brain, to the cardiovascular system Montoya appears to be getting every department he can at Stanford involved with his chronic fatigue syndrome (ME/CFS) studies. Given his emphasis on infection associated patients, and his ability, hopefully, to enroll the same patients in multiple studies, we could be getting a quite comprehensive view of what’s happened to them.

If you can link pathogen presence to immune dysfunction to brain issues to cardiovascular symptoms, you can start to build a pretty convincing model of ME/CFS. There’s no telling what percentage of patients these findings will apply to, and Montoya’s been quite conservative in his estimates.

Dr. Montoya’s Stirring Chronic Fatigue Syndrome Talk at Stanford a Couple of Years Ago

From a program that, from a distance at least appeared to be struggling at one point, Montoya has built a growing team that enjoys the support of important leaders at Stanford. The Dean of the Stanford Medical School, no less, Dr. Phillip Pizzo, supports the Institute and has been integral in its development, and one of Dr. Montoya’s collaborators, Dr. Mark Davis, is the Director of the Institute for Immunity, Transplantation and Infection. Dr. Montoya appears to be steadily turning ‘the conversation’ regarding ME/CFS around at Stanford- the 2nd ranked medical school in research in the country.

Biennial educational meetings are planned, and they hope at some point to establish an in-patient clinic separate from the hospital that features capability to administer antivirals as well as complementary medicine. Things are looking up at the Stanford Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) Initiative.




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