Development and validation of blood-based diagnostic biomarkers for Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) using EpiSwitch® 3-dimensional genomic regulatory immuno-genetic profiling
Ewan Hunter, Heba Alshaker, Oliver Bundock, Cicely Weston, Shekinah Bautista, Abel Gebregzabhar, Anya Virdi, Joseph Croxford, Ann Dring, Ryan Powell, Dominik Vugrinec, Caroline Kingdon, Carol Wilson, Sarah Dowrick, Jayne Green, Alexandre Akoulitchev & Dmitri Pchejetski
Abstract
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a debilitating, multifactorial disorder characterised by profound fatigue, post-exertional malaise, cognitive impairments, and autonomic dysfunction. Despite its significant impact on quality of life, ME/CFS lacks definitive diagnostic biomarkers, complicating diagnosis and management. Recent evidence highlights potential blood tests for ME/CFS biomarkers in immunological, genetic, metabolic, and bioenergetic domains. Chromosome conformations (CCs) are potent epigenetic regulators of gene expression and cross-tissue exosome signalling. We have previously developed an epigenetic assay, EpiSwitch®, that employs an algorithm-based CCs analysis. Using EpiSwitch® technology, we have shown the presence of disease-specific CCs in peripheral blood mononuclear cells (PBMCs) of patients with amyotrophic lateral sclerosis (ALS), rheumatoid arthritis (RA), prostate and colorectal cancers, diffuse Large B-cell lymphoma and severe COVID-19. In a recent paper, we have identified a profile of systemic chromosome conformations in cancer patients reflective of the predisposition to respond to immune checkpoint inhibitors, PD-1/PD-L1 antagonists, with 85% accuracy. In this Retrospective case/control study (EPI-ME, Epigenetic Profiling Investigation in Myalgic Encephalomyelitis), we used whole blood samples retrospectively collected from n = 47 patients with severe ME/CFS and n = 61 age-matched healthy control patients to perform whole-genome 3D DNA screening for CCs correlating to ME/CFS diagnosis. We identified a 200-marker model for ME/CFS diagnosis (Episwitch®CFS test). First testing on the retrospective independent validation cohort demonstrated a strong systemic ME/CFS signal with a sensitivity of 92% and a specificity of 98%.Pathways analysis revealed several likely contributors to the pathology of ME/CFS, including interleukins, TNFα, neuroinflammatory pathways, toll-like receptor signalling and JAK/STAT. Comparison with pathways involved in the action of Rituximab and glatiramer acetate (Copaxone) (therapies with potential in ME/CFS treatment) identified IL2 as a shared pathway with clear patient clustering, indicating a possibility of a potential responder group for targeted treatment.
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Explor Neuroprot Ther. 2025;5:1004116 DOI: https://doi.org/10.37349/ent.2025.1004116
Received: April 28, 2025 Accepted: July 25, 2025 Published: October 14, 2025
Academic Editor: Vijay K. Sharma, National University of Singapore, National University Hospital, Singapore
Abstract
Aim: Post-exertional malaise (PEM) has been a challenging construct to measure, particularly with self-report instruments, which have the benefits of being less expensive and less invasive than cardiopulmonary exercise tests. Existing PEM questionnaires have often been used for diagnostic purposes and less frequently as outcome measures. Few self-report PEM measures address comprehensive PEM domains, including types of triggers, duration of symptoms, delayed symptom onset, number of symptoms, frequency and severity of symptoms, as well as whether pacing or other strategies reduce or eliminate PEM. Without characterizing these features, salient aspects of PEM would be overlooked. However, efforts to assess all these domains can be time-consuming and potentially burdensome.
Methods: The current study offers investigators a brief but comprehensive instrument of critical PEM domains, called the DePaul Symptom Questionnaire (DSQ)-PEM-2, to assess PEM. Validation data were derived from a large sample of individuals with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS).
Results: The DSQ-PEM-2 was developed using an existing dataset of individuals with ME, CFS, or both ME and CFS, allowing comprehensive coverage of key PEM domains.
Conclusions: The DSQ-PEM-2 can be used either for diagnostic purposes or as an outcome measure. The instrument’s time frames for symptom manifestation can be adapted to suit a variety of research or clinical contexts. Future validation studies need to include a healthy control group.
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Original Investigation
Effectiveness of Colchicine for the Treatment of Long COVID
A Randomized Clinical Trial
Abhinav Bassi, MPH1; Niveditha Devasenapathy, PhD, MBBS, MSc1; Shani S. Thankachen, MPH1et al
JAMA Intern Med Published Online: October 20, 2025
doi:10.1001/jamainternmed.2025.5408
Key Points
Question What is the effectiveness of 28-week oral colchicine therapy in improving functional outcomes among individuals with persistent symptoms after acute COVID-19 infection?
Findings In this randomized clinical trial including 346 adults, there was no statistically significant difference in functional capacity, respiratory function, mental states, constitutional symptoms, or inflammatory markers at 52 weeks among those treated with colchicine or placebo.
Meaning This trial provides evidence against colchicine monotherapy as a broadly effective treatment for long COVID.
Abstract
Importance Long COVID is characterized by persistent symptoms after SARS-CoV-2 infection, with inflammation playing a key role in pathogenesis. Colchicine, an established anti-inflammatory agent, may reduce these symptoms by targeting inflammatory pathways.
Objective To evaluate the superiority of colchicine over placebo in improving functional outcome at 52 weeks from baseline.
Design, Setting, and Participants This double-blind, 1:1 randomized clinical trial recruited participants with confirmed SARS-CoV-2 infection and persistent symptoms from 8 hospitals in 6 states in India between January 2022 and July 2023. Individuals were eligible if they had functional limitation (Post–COVID-19 Functional Status scale grade 2 or more) and/or elevated inflammatory markers (high-sensitivity C-reactive protein >0.20 mg/dL and/or neutrophil to lymphocyte ratio >5). Outcomes were assessed at 12, 26, and 52 weeks after randomization. Data were analyzed from January to February 2025.
Interventions Participants were randomly assigned to receive colchicine, 0.5 mg, once or twice daily, based on body weight, or placebo for 26 weeks.
Main Outcomes and Measures The primary outcome was the change in distance walked during a 6-minute walk test from baseline to 52 weeks. Secondary outcomes included changes in inflammatory markers and patient-reported outcome measures, such as quality of life, anxiety, depression, fatigue, dyspnea, measured using validated instruments.
Results Of 346 participants included in the modified intention-to-treat analysis, 209 (60.4%) were female, 137 (39.6%) were male, and the mean (SD) age was 46 (12) years. At 52 weeks, there was no difference in mean (SD) change in 6-minute walk test distance between the colchicine and placebo groups (colchicine, 35.5 [19.76] m; placebo, 29.96 [19.83] m; mean difference, 5.59 m; 95% CI, –9.00 to 20.18; P = .45). Similar null findings were seen across all predefined outcomes, except for a small, nonclinically relevant difference in the mean (SD) ratio of forced expiratory volume in 1 second to forced vital capacity (colchicine, −0.02 [0.03]; placebo, −0.06 [0.03]; mean difference, 0.04; 95% CI, 0.02 to 0.07; P = .001).
Conclusions and Relevance In this randomized clinical trial, among adults with long COVID, colchicine did not improve functional capacity, respiratory function, or inflammatory markers. These findings underscore the need to explore alternative therapeutic approaches for long COVID.
Trial Registration Clinical Trial Registry of India: CTRI/2021/11/038234
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2025 Sep 19:2025.09.18.25335914. [Version 1] doi: 10.1101/2025.09.18.25335914
The genetic architecture of fibromyalgia across 2.5 million individuals
Isabel Kerrebijn et al1,2, Author information
Copyright and License information
PMCID: PMC12458511 PMID: 41001472
The complete version history of this preprint is available at medRxiv.
Abstract
Fibromyalgia is a common and debilitating chronic pain syndrome of poorly understood etiology. Here, we conduct a multi-ancestry genome-wide association study meta-analysis across 2,563,755 individuals (54,629 cases and 2,509,126 controls) from 11 cohorts, identifying the first 26 risk loci for fibromyalgia. The strongest association was with a coding variant in HTT, the causal gene for Huntington’s disease. Gene prioritization implicated the HTT regulator GPR52, as well as diverse genes with neural roles, including CAMKV, DCC, DRD2/NCAM1, MDGA2, and CELF4. Fibromyalgia heritability was exclusively enriched within brain tissues and neural cell types. Fibromyalgia showed strong, positive genetic correlation with a wide range of chronic pain, psychiatric, and somatic disorders, including genetic correlations above 0.7 with low back pain, post-traumatic stress disorder and irritable bowel syndrome. Despite large sex differences in fibromyalgia prevalence, the genetic architecture of fibromyalgia was nearly identical between males and females. This work provides the first robust genetic evidence defining fibromyalgia as a central nervous system disorder, thereby establishing a biological framework for its complex pathophysiology and extensive clinical comorbidities.
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The Off-Label Treatment That Helps Many With Fibromyalgia
Medscape Medical News Laurie Tarkan October 29, 2025
An unlikely, decades-old drug is gaining traction as a promising off-label treatment for fibromyalgia, driven by a handful of studies and a growing number of anecdotal reports.
Low-dose naltrexone (LDN), a medication originally developed to treat substance use disorders, is said to relieve the chronic pain, fatigue, and brain fog associated with the debilitating condition that afflicts millions of Americans but is difficult to treat.
“It helps over 70% of my patients,” said Scott Zashin, MD, a Dallas-based rheumatologist, and fellow of the American College of Rheumatology. “I’d say less than 10% need to stop it because of side effects.”
Used for decades at doses of 50-100 mg to treat opioid and alcohol use disorders, the drug at that high dose binds to opioid receptors, blocking opioids from attaching to the receptors, so people don’t get that feel-good sensation from booze or drugs.
Early researchers found an unexpected result: “We noticed that when people tapered down to lower doses, their pain would also get better,” said Arya Mohabbat, MD, assistant professor at the Mayo Clinic College of Medicine and Science, Rochester, Minnesota.
Today the LDN trend is fueled primarily by success stories rather than large-scale trials.
One of those stories is Dan Kenyon, age 45, who says LDN reduced his pain by more than half. “It has helped even more with brain fog, fatigue, and sleep,” said Kenyon from Iowa, who was diagnosed in his early thirties after years of unexplained muscle soreness and fatigue.
Despite the word-of-mouth buzz, though, many doctors are not aware of it, don’t think there’s enough evidence to prescribe it, or don’t know how to prescribe it because it’s not marketed by pharmaceutical companies. Still others see LDN as a low-risk, low-cost treatment option for fibromyalgia and other chronic pain conditions — and blame lack of pharmaceutical investment for impeding its progress.
“Naltrexone is an old cheap generic medication,” said Mohabbat. “Just because you formulate it to a lower dose, it doesn’t change the patent, and they can’t charge a lot of money for it.”
How Patients in Pain Are Finding LDN
Looking back, Kenyon thinks the pain started when he was about 20. He had a physically demanding job in fire and water damage restoration, and his muscles would ache throughout the day, pain lingering into the next morning. Even after switching to less strenuous work — first running a retail store, then an online screen-printing business — his pain kept getting worse. Soon it was joined by depression and insomnia. “I got to a point where I just couldn’t motivate myself to work anymore, my sales slowed down, and I didn’t care,” Kenyon said.
At age 32, he saw a rheumatologist who diagnosed him with fibromyalgia. He tried gabapentin, but it gave him panic attacks and affected his balance. Weaning off it was so hard he was reluctant to try other medications.
Browsing an online message board, he read success stories of people on LDN. His rheumatologist said he hadn’t heard of naltrexone being used for chronic pain and wasn’t willing to prescribe it. So Kenyon dropped it.
“Things started getting more painful for me last fall, so it sparked my interest in it again,” Kenyon said. On Reddit, he learned how to get it prescribed online, purchased through a compounding pharmacy.
“I was nervous to try it but started with a very low dose and kept bumping it up every 6 or 7 days,” Kenyon said. It took about 3 months to get to 4.5 mg, which is considered an effective dose. It was working: “I have upwards of a 50% reduction in pain.”
Few Studies, Promising Results
Several studies back LDN for fibromyalgia, though most are small.
In 2013, a randomized controlled study of 31 women with fibromyalgia found that LDN offered an average 29% reduction in pain vs 18% for women on a placebo. An analysis of that data found that half the women on LDN were “much improved” or “very much improved” — compared with just 20%-30% of patients who find meaningful improvement on current fibromyalgia-approved medications, said study author Jarred Younger, PhD, director of the Neuroinflammation, Pain and Fatigue Laboratory at The University of Alabama at Birmingham.
A 2023 cohort study of LDN for pain conditions included 115 people, most having fibromyalgia. The study found that 65% reported a benefit in their pain and other symptoms. A review of nine studies found LDN effective in managing fibromyalgia symptoms, and so did a 2024 review of randomized controlled trials.
Further research shows pain improvements in other conditions, like Crohn’s disease and Long COVID.
To be sure, more research is needed. “We need a double blinded randomized trial for 12 months that looks at side effects and how people do functionally,” said Mohabbat.
“There’s still that question mark in the air,” said Younger. “Clearly it helps a lot of people, but without the study, a lot of physicians aren’t going to want to use it,” he said. But the buzz is growing. “LDN comes up in every medical conference.”
How LDN Works
LDN is thought to tamp down nerve inflammation responsible for many of the symptoms of fibromyalgia like pain, fatigue, malaise, brain fog, and flu-like symptoms. In fibromyalgia, glial cells, which support neurons, are activated, causing an inflammatory response. LDN blocks a receptor that activates glial cells, stopping the inflammatory cascade.
Like any medication, it doesn’t help everyone and won’t completely get rid of symptoms. But for those it helps, it can be life changing.
Jane Lamping, age 53, who lives in San Diego, was diagnosed with fibromyalgia in 2014, and has tried a long list of medications — among them Tramadol, Lyrica, Cymbalta, Fetzima, Mobic, gabapentin, Toradol injections. But she continued to have many flares, which left her unable to keep a job. Like many with fibromyalgia, Lamping had to carefully manage her exertion to try to prevent flares. In 2022, her doctor, who had been following the research on LDN, suggested she try it.
It reduced her pain, brain fog, and fatigue. “It has helped immensely. I do still get flares and pain cycles. But they are less frequent, and it has reduced the intensity as well,” she said. A bonus: It helped with her migraines.
A Crowd-Sourced Approach in the Absence of Robust Data
Kenyon, like many people, learned how to take LDN from online groups and shared it with his physician — a crucial step, Zashin said. “The window for optimally dosing naltrexone is very small and requires high accuracy,” said Younger. Like any medication, it carries potential risks.
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• The first big GWAS FM study scored by finding many significant regions of the genes we are born with that appear to contribute to FM. That finding, as the authors said, puts FM on a “firm biological foundation”.
- The genes highlighted in the study affect things like interneuron excitability (pain processing/subclinical seizures), hippocampal functioning (memory impairment), the kynurenine pathway (pain and others), dopamine (motivation and cognition), sleep, natural killer cell functioning (!), neuroplasticity, excitatory neurotransmission, testosterone metabolism, cognitive issues, microglial activation, neuroinflammation, lipid and mitochondrial issues.
- The study, in other words, confirmed that people with FM have a genetic predisposition to many of the biological abnormalities studies have found.
- Like ME/CFS, the genes almost wholly pointed to the brain, and, in particular, in FM, to genes that affect pain and sensory processing. Genetic variants that affect similar areas of the brain were found in both ME/CFS and FM.
- Many genes found in FM have also been found to contribute to other illnesses. This suggested to the authors that the genetic architecture found in FM constitutes a kind of “transdiagnostic” genetic vulnerability that reaches far beyond FM itself. That “vulnerability profile”, they believe, affects core neurobiological systems such as central nervous system excitability, dopaminergic/serotonergic signaling, and neuroimmune stress.
- It’s also found in diseases like ME/CFS, chronic pain conditions, IBS, PTSD, depression, and more. A ChatGPT 5.0 analysis concluded that “DecodeME’s strongest loci for ME/CFS sit exactly where you’d expect such a vulnerability to live“.
- Two genes, in particular, offer new treatment pathways for FM. Drugs for them are not available right now, but are under development and being tested.
Mestinon has done it again. Another study has shown that in the short term, Mestinon can move the needle on two factors, energy production and strength, that are in short supply in ME/CFS.
- This study assessed handgrip strength, which turns out to be quite a proxy for overall health.
- Dozens (dozens!) of large studies have found that weaker grip strength is associated with a higher risk of death from any cause. It’s more strongly predictive of cardiovascular death than high blood pressure. Reduced handgrip strength has been linked to higher rates of heart attack, stroke, type II diabetes. The list goes on and on.
- Besides keeping us stronger, our muscles play a vital role in our metabolism by regulating glucose, and the myokines they produce affect the immune system, metabolism, and the brain.
- Because inflammation, insulin resistance, oxidative stress, hormonal problems, and poor mitochondrial health can all whack the muscles, people with these problems often have poor handgrip strength.
- Given that, it’s perhaps no surprise that several studies have not only found reduced handgrip strength in ME/CFS but that it’s correlated with ME/CFS severity, and the amount of post-exertional malaise and muscle pain people with ME/CFS experience.
- The small study involved two visits. The first was done to assess handgrip strength and orthostatic intolerance at baseline, and then again hour later. During the next visit, Mestinon was administered immediately after the first handgrip strength test to assess its impact on the second handgrip strength test conducted an hour later.
- Unfortunately, the study did not break up the results by gender. (Men have much higher handgrip strengths than women.) The mean baseline handgrip strength, though, was very low (16.5 kg), and it declined during the second test an hour later.
- After taking Mestinon, though, the ME/CFS patients’ handgrip strength not only did not decline but actually increased.
- This is the second short-term study to show that Mestinon increased energy production/strength. Systrom’s earlier study showed that Mestinon increased energy production during an invasive exercise test. Mestinon, then, has scored on two important factors in ME/CFS.
- Mestinon could be doing a number of things. It could be aiding muscle recruitment during exertion. (Reduced muscle recruitment during exertion could be causing everything from mitochondrial problems, orthostatic intolerance, and low preload.) By improving autonomic nervous system activity, it could be enhancing blood flows. By improving calcium handling in the cells, it could be enhancing mitochondrial activity.
- We should know more about Mestinon and ME/CFS soon. The Open Medicine Foundation’s LIFT trial with David Systrom will not only be assessing how effective Mestinon and low dose naltrexone are, it’ll be digging deep into their pathophysiology to understand how these drugs are helping, which kinds of patients they are helping, and what pathways to focus on.
Circulating Levels of SMPDL3B Define Metabolic Endophenotypes and Subclinical Kidney Alterations in Myalgic Encephalomyelitis
Bita Rostami-Afshari Wesam Elremaly,Neil R. McGregor,Katherine Jin Kai Huang
Christopher W. Armstrong,Anita Franco,Christian Godbout,Mohamed Elbakry,Rim Abdelli
And Alain Moreau
The Open Medicine Foundation ME/CFS Collaborative Research Centre, Bio21 Molecular Science and Biochemistry Institute, University of Melbourne, Melbourne, VIC 3010, Australia
Int. J. Mol. Sci. 2025, 26(18), 8882; https://doi.org/10.3390/ijms26188882
Abstract
Myalgic Encephalomyelitis (ME) is a complex, multisystem disorder with poorly understood pathophysiological mechanisms. SMPDL3B, a membrane-associated protein expressed in renal podocytes, is essential for lipid raft integrity and glomerular barrier function. We hypothesize that reduced membrane-bound SMPDL3B may contribute to podocyte dysfunction and impaired renal physiology in ME. To investigate this, we quantified soluble SMPDL3B in plasma and urine as a surrogate marker of membrane-bound SMPDL3B status and assessed renal clearance and plasma metabolomic profiles. In a cross-sectional study of 56 ME patients and 16 matched healthy controls, ME patients exhibited significantly lower urine-to-plasma ratios of soluble SMPDL3B and reduced renal clearance, suggesting podocyte-related abnormalities. Plasma metabolomics revealed dysregulation of metabolites associated with renal impairment, including succinic acid, benzoic acid, phenyllactic acid, 1,5-anhydroglucitol, histidine, and citrate. In ME patients, plasma SMPDL3B levels inversely correlated with 1,5-anhydroglucitol concentrations and renal clearance. Multivariable modeling identified the urine-to-plasma SMPDL3B ratio as an independent predictor of clearance. Female ME patients showed more pronounced SMPDL3B alterations, reduced clearance, and greater symptom severity. Non-linear associations between soluble SMPDL3B and lipid species further suggest systemic metabolic remodeling. These findings support soluble SMPDL3B as a potential non-invasive biomarker of renal-podocyte involvement in ME, highlighting sex-specific differences that may inform future therapeutic strategies.
Keywords:
SMPDL3B; myalgic encephalomyelitis; renal clearance; metabolomics; 1,5-anhydroglucitol; sex differences; urinary biomarkers; glomerular barrier; lipid metabolism
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NPJ Metab Health Dis. 2025 Sep 3;3(1):34. doi: 10.1038/s44324-025-00079-w
Heightened innate immunity may trigger chronic inflammation, fatigue and post-exertional malaise in ME/CFS
Xiaoyu Che # 1 2, Amit Ranjan # 3, Cheng Guo 3, Keming Zhang 3, Rochelle Goldsmith 4, Susan Levine 5, Kegan J Moneghetti 6, Yali Zhai 3, Liner Ge 7, Nischay Mishra 3 8, Mady Hornig 9, Lucinda Bateman 10, Nancy G Klimas 11, Jose G Montoya 12, Daniel L Peterson 13, Sabra L Klein 14, Oliver Fiehn 15, Anthony L Komaroff 16, W Ian Lipkin 17 18 19
Affiliations Expand:PMID: 40903540 - PMCID: PMC12408823
DOI: 10.1038/s44324-025-00079-w
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is characterized by unexplained fatigue, post-exertional malaise (PEM), and cognitive dysfunction. ME/CFS patients often report a prodrome consistent with infection. We present a multi-omics analysis based on plasma metabolomic and proteomic profiling, and immune responses to microbial stimulation, before and after exercise. We report evidence of an exaggerated innate immune response after exposure to microbial antigens; impaired energy production involving the citric acid cycle, beta-oxidation of fatty acids, and urea cycle energy production from amino acids; systemic inflammation linked to lipid abnormalities; disrupted extracellular matrix homeostasis with release of endogenous ligands that promote inflammation; reduced cell-cell adhesion and associated gut dysbiosis; complement activation; redox imbalance reflected by disturbances in copper-dependent antioxidant pathways; and dysregulation of tryptophan-serotonin-kynurenine pathways. Many abnormalities were worse following exercise and correlated with the intensity of symptoms. Our findings may inform development of targeted therapeutic interventions for ME/CFS and PEM.
© 2025. The Author(s).
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Conflict of interest statement
Competing interests: The authors declare no competing interests.
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