The recent Solve ME webinar “The Discovery of Target Antigens for Dysfunctional T Cells in ME/CFS and Long COVID” highlights one of the more exciting themes to emerge recently in the ME/CFS and long COVID fields – a new confidence that researchers will be able to pluck out biologically defined subsets that can be targeted with the drugs.
It will take time and considerable funding, but researchers are increasingly confident they can decipher the underlying mechanisms of these complex diseases and ultimately identify precise treatment targets.
We’re not there yet – that will take more time and resources – but the fact that multiple research groups are envisioning the day when they can you say, you have this kind of ME/CFS, and you over there have this kind, and you should be treated with X, while you should be treated by “Y” is, something that’s only recently, to my knowledge, popped up.
The ME/CFS and long COVID T-cell research groups featured in the Solve ME Webinar – which Solve has funded with its Ramsay awards – may be the first to do it. They include long-time Harvard T-cell expert Liisa Selin, PhD, the head of Translational Medicine at HiFiBiO Therapeutics, Roshan Kumar, PhD, and, more recently, a cutting-edge Harvard immunologist, Ayano Kohlgruber, PhD. These groups are seamlessly operating together – handing off one finding to the next group to deepen it.
Health Rising’s Quickie Summer Donation Drive is On!Dr. Selin, by the way, is no stranger to ME/CFS. She’s had it for 50 years and has experienced four serious episodes, the last being a reaction to a COVID-19 vaccine. She said she’s been able to come back from what she’s considered to be the living dead four times…
Roshan Kumar is also intimately acquainted with ME/CFS: his wife has had it for 20 years.
The First Step: T-cell Exhaustion
Solve ME hit the jackpot when their 2019 Ramsay award enabled Selin to snag a major NIH grant on T-cells in 2021. That, in turn, morphed into a 2023 Patient-Led Research Collaborative grant for Selin, and a 2024 grant for Roshan Kumar, Anna Gil, and Selin. Last year, Dr. Kohlgruber joined the effort. This is like the Jarred Younger story all over again: he gets a kickoff from a Solve ME grant, and goes on to score several large NIH grants for ME/CFS.
Dr. Selin’s group started a T-cell exhaustion discussion in ME/CFS that has only grown over time. They’ve found multiple lines of evidence (reduced IFN‑γ, TNF, and perforin/granzyme production) indicating that not only have the cytotoxic T-cells in these diseases become exhausted but there are fewer of them as well.
Last year, Dr. Selin reported she’d found dramatic reductions in perforin – the substance T-cells use to kill infected cells – in ME/CFS
Her idea has, over time, become a familiar one: an infection which the body failed to clear or deal with properly has left one of the big guns of the immune system – the cytotoxic T-cells – in a state of chronic activation. Cytotoxic T cells are responsible for clearing pathogens hiding inside cells. Being constantly under stress has left them exhausted, disoriented, and functioning poorly.
As any good vicious circle will do, the T-cell exhaustion only makes things worse. Having a major pathogen fighter offline could give the herpesviruses or other viruses the opportunity to reactivate. The immune system responds by trying to activate the T-cells more, leaving them more exhausted than ever. Or it’s possible that dysfunctional T-cells in ME/CFS are driving an autoimmune response. Either way these heavy hitters in our adaptive or later immune response are having problems.
An Aside – A Rich Field
Just as an aside. The ME/CFS field is rather rich in immune cells, which appear to have energy problems!
We’ve known for a long time that cytotoxic NK cells – which bear an interesting resemblance to cytotoxic T-cells – have shot their wad as well. I remember researchers speculating years ago that the T-cells in ME/CFS have the same problem. Now, thanks to Dr. Selin and others, it appears that they do.
It’s not clear whether B-cells exhibit the same exhaustion profile, but they have trouble maturing (an energy-intensive process) and clearly struggle to generate energy. Exercise seems to whack monocytes’ ability to function as well. Neutrophils also show signs of metabolic stress and impaired energy production.
One wonders where it will all end. The best evidence for immune exhaustion, though, comes from T-cells.
The Weird T-cell Population in ME/CFS
Dr. Selin found an 8-fold and a four-fold increase in ME/CFS and long COVID, respectively, in a strange bunch of T-cells called CD4/CD8 double-positive cells. T-cells are supposed to differentiate into CD4 helper and CD8 cytotoxic T-cells, but these cells haven’t; instead, they’ve become a hybrid form of both.
Dr. Selin believes they may reflect an attempt to compensate for the cytotoxic T-cell (CD8) exhaustion.
It perhaps bears noting that these cells have not matured properly, and neither have B-cells in ME/CFS patients (hmm). Whatever the reason for their increase, these CD4/CD8 double-positive cell levels have been observed in autoimmune disease, which aligns with the preponderance of these cells in females (who are at greater risk for autoimmune diseases).
The reason these T-cells may increase the risk of getting an autoimmune disease, Dr. Kumar pointed out, is that they react to more “antigens” – substances that spark an immune reaction – than other types of T-cells. At that point, this is nothing more than a statistical situation: the more antigens a T-cell reacts to, the greater the chance it may make a mistake and begin attacking the tissues in our bodies.
The Big Shift
The First Hand Off
“This finding alone tells us that pathogen or self antigen are driving the disease.” Dr. Selin
We’ll see these groups hand off their findings together in a seamless way. The first handoff – Dr. Selin to Roshan Kumar.
Here’s where it gets really interesting. Plenty of evidence indicates that immune dysregulation is present in ME/CFS, but nobody’s been able to definitively show why it’s happening or what’s driving it. Figure that out, and you might be able to get to the core of these diseases, and that’s what makes these groups’ recent work so exciting.
Dr. Selin reported that they’ve found that the rise in these abnormal T-cell levels is specifically driven by an antigen, which makes all the difference.
T-cells show up in the later stages of fighting off an infection. First, the innate immune system revs up, giving time for the T and B cells to recognize the pathogen and produce massive numbers of clones specifically designed to target and wipe it out.
These T-cells use receptors on their surface to identify infected cells. The first thing to know is that activated cytotoxic T-cells are very specific. They’re like guided missiles which are aimed at only one target. They go around inspecting other cells and if the particular receptor they’re carrying locks in, they drill a hole into the infected cell using a substance called perforin and kill it.
Or at least they’re supposed to. Dr. Selin’s work dramatically demonstrates how the very low perforin levels in cytotoxic T-cells have essentially made them impotent in diseases like ME/CFS.
Increased levels of abnormal T-cells do not, by themselves, tell us why they are present. An army of T-cells that feature the same receptors, though, indicates they’re targeting one thing – and that’s what Kumar found. Now we don’t have an undifferentiated response, we have a focused response and a potential target.
The critical T-cell expansion work
Kumar’s single-cell approach allowed him to assess the gene expression of each cell. He was able to identify a variety of abnormal T-cell states in both ME/CFS and long COVID (clusters of activated/exhausted cells, T-cells with high NF-kB signaling, T-cells promoting inflammation, and those double-positive CD4/CD8 T-cells)
Note that Kumar’s ability to find a variety of dysregulated T-cell states indicates that different T-cell problems are present in different ME/CFS and long COVID patients; i.e. while their symptoms are similar, they have fundamentally different diseases.
Every step deeper in these diseases seems to uncover yet more heterogeneity – which is what you would expect to find in these diseases. Finding a variety of dysfunctional T-cell problems is a sign that Kumar is on the right track.
Check out the T-cells with high NF-kB signaling. High NF-kB signaling is a definitive sign that the cell is in a highly activated/inflammatory state. NF-kB activation turns on the switches that allow the cells to jump into action and rapidly clone themselves in response to an invader or self-antigen.
That’s good news regarding a pathogen response, but bad news if the T-cells have begun attacking tissues. Indeed, high NF-kB activation is associated with autoimmune diseases such as rheumatoid arthritis, inflammatory bowel disease, and multiple sclerosis. Importantly, it also turns on an anti-suicide (anti-apoptotic) switch, which prevents the damaged T-cell from being purged.
Crucial Link
Dr. Kumar’s finding that the dysregulated T-cell states were characterized by specific clonotypes or T-cell clones was the crucial link that allowed the effort to expand dramatically.
Next came the crucial link. It was kind of amazing to see Kumar uncover a variety of dysregulated T-cell / disease states in ME/CFS and long COVID. If things had rested there, it would have been an important finding, but in a way, it would have been a bit superficial.
We would have added more types of T-cell dysfunction to the already abundant evidence of immune dysregulation, but, like the other immune findings, we would have been kind of stuck there without a clear pathway forward.
When Kumar found that the specific T-cell states were associated with specific T-cell clones, that potentially changed everything. That meant that the people who had the high NF-kB signaling T-cells, were been tweaked by one thing. The people with the double-positive CD4/CD8 cells had been tweaked by something else. The people with the exhausted T-cells had been tweaked by something else.
Now we’re getting to the nitty-gritty – to evidence that these dysfunctions are being driven by something and the list is not long. It’s either a pathogen or an autoimmune response. Kumar said his findings are “very strong evidence of an antigen-specific immune response,” and specificity is the holy grail here.
Not only are the T-cells in ME/CFS dysregulated in various ways, but they’re also being triggered in different ways. They could be responding to a multitude of factors: Epstein-Barr virus (EBV), HHV6 or CMV, an enterovirus, Borellia, another bacterial infection, “the” coronavirus, another coronavirus, the coronavirus vaccine, another vaccine, mold, peptides being produced by microbes in the gut, an autoimmune process, etc.
What these T-cells are getting activated by constitutes an entirely different challenge. Now it was time to hand them off to a new team member: Dr. Kohlgruber.
The Next Hand Off: Getting at Cause
“We study…the ways infectious exposures (including EBV, and potential triggers of Long COVID and ME/CFS) may initiate or amplify pathology through molecular mimicry or chronic antigen stimulation. Our goal is to understand not just that tolerance fails, but precisely where, when, and against what antigens, because that precision is what makes antigen-specific therapeutic intervention possible”. The Kohlgruber Lab
Dr. Kohlgruber has developed new techniques that are enabling researchers for the first time to understand what T-cells are reacting to.
Dr. Kohlgruber’s job is to try to figure out what’s tweaking/activating/turning on each of these dysfunctional T-cells. This work – “Decoding the antigen-specific basis of human disease” – constitutes the main goals of her Harvard lab.
Determining what a T-cell receptor (i.e. a T-cell) is actually responding to is incredibly complex and has been described as a “massive bottleneck” in immunology. Kohlbuger’s main contributions have been the development of a “high-throughput” system, which accelerates testing, and the development of something called a TCR-MAP, which is essentially an antigen discovery system.
To understand why T-cell responses, in particular, have been so difficult to map, we have to understand how T-cells work. Each T cell generates a uniquely shaped receptor that binds only one molecular target, called a peptide-MHC complex. The problem is that tens of millions of possible peptide-MHC combinations exist, and a TCR will only bind to one of them.
Finding that one has been so difficult that there’s even a name for these mysterious receptors -they’re called “orphan” TCRs. We know they’re important, we know that they’re driving disease states, but we don’t know what they’re reacting to.
Dr. Kohlgruber’s work has made it possible to search vast libraries of peptides to uncover what each dysfunctional T-cell state responds to.
Her work has changed, for instance, how we understand what’s going on in the joint inflammation that occurs in rheumatoid arthritis. In the past all we knew was that it was happening. Kohlgruber, though, was able to map the specific tissue targets and identify previously unreported autoantigens leaving the rheumatoid arthritis field with specific molecular targets to focus on.
Now that she has, courtesy of Dr. Kumar, a clean slate of dysfunctional T-cells, Dr. Kohlgrubber is using two huge “libraries” (pathogen/autoimmune) in an attempt to “deorphanize” them.
Dr. Selin was so impressed by the amount of T-cell dysregulation found that she thought multiple pathogens (which the poor T-cells have let escape) and maybe even multiple autoantigens would show up. It’s possible that one may dominate, and that would be the one to first focus on.
Moving Forward
“I think this is really important, groundbreaking work that we’re doing here, and I really hope we get support to get it to done.”
This effort has several things in its favor. The researchers (Selin, Kumar, and Kohlgruber) have strong records. Kumar’s ability to provide Kohlgrubber with already identified T-cell subsets is very helpful.
The big question is funding. Now that we have good pilot data, this research needs to be significantly scaled up. A gold-standard study that breaks the back of the T-cell problem in ME/CFS and long COVID would include uncovering dysregulated T-cell states in hundreds of patients and handing them off to Dr. Kohlburger to work her magic.
According to AI queries, we might be looking at a $10 million 5-year project for a gold-standard study. That may not happen, but it is achievable. Except for the research centers, the NIH has never, to my knowledge, supported a big effort like that. One NIH major grant opportunity (RFA) on T-cell dysregulation, though, could do the trick – and this field is way overdue for an RFA.
There are other ways. Yes, the NIH funding for ME/CFS is putrid compared to its needs, but it does fund major studies – just not a lot of them. The recent NIH ME/CFS mycotoxin grant going to Nancy Klimas’s lab and Azola’s recent blood-brain barrier ME/CFS grant will both pay out about $3 million.
Given the exciting data, one would think Selin would hopefully get an extension on her original grant, and she and Andrew Grimson of Dr. Hanson’s lab, who has seen similar T-cell clonal expansions, are submitting a joint proposal to the NIH. The PLRC, the Open Medicine Foundation, and Solve ME have all supported T-cell research and could kick in some funding. Polybio is another possible source. A big donor, of course, could make all the difference.
It would take time – 5 years – but they’re making rapid progress. Things have moved forward dramatically in the past year, and given the funding, we should expect year-by-year increases in understanding.
Once again, we see ME/CFS and Long COVID fields appear ready to take the next big leap into true precision medicine. All they need is the funding.
Health Rising Donation Drive Update
We’re committed to being there as researcher s figure out what’s going in these diseases.Thanks to everyone who has brought Health Rising almost to 50% of our goal!
We’ve been following Dr. Selin’s work on T-cells in ME/CFS and long COVID every step of the way. First, she showed they were exhausted, and that a strange group of hybrid T-cells was present. Then she added Dr. Kumar to her team, who showed that a pathogen/autoimmune process must be driving the process. Next came Dr. Kohlbruger, who is tasked with determining exactly which pathogen or autoimmune processes are at play across different patient subsets.
It’s been an exciting journey (and it’s getting more exciting). We’ll be there every step of the way. If that supports you, please support us!
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