Serum extracellular vesicle RNA profiles in long COVID: insights from exercise-induced gene modulation, 2026, Asghar Abbasi et al

[Mij]

Abstract

The Persistence of SARS-CoV-2 in tissues has been proposed as a driver of prolonged symptoms in long COVID. Pulmonary rehabilitation with exercise training is a well-established intervention for improving symptoms, functional capacity, and inflammation in chronic cardiorespiratory diseases. To investigate whether long COVID is associated with persistent viral or immune-related signals, we analyzed the long RNA profile of circulating extracellular vesicles (EVs) to determine the presence of virus-related transcripts and assess changes in response to exercise training.

Fourteen adults with long COVID participated in this single-center pilot clinical trial and completed a 10-week aerobic exercise training program (twenty 1.5 h sessions). Serum-derived EV RNA profiles were analyzed via sequencing at rest (T0) and peak cardiopulmonary exercise testing (T1), before (V2) and after (V24) exercise training. Differentially expressed genes (DEGs) were identified (q < 0.05), and pathway activation analysis was performed. Serum EVs carried diverse RNA species, including protein-coding RNAs, long non-coding RNAs, short non-coding RNAs, and pseudogenes, with no virus-related RNAs detected. No significant DEGs were identified at rest between pre- and post-training, nor in response to acute exercise at pre-training.

However, following training, 53 DEGs were found at peak exercise (V24T1) compared to rest (V24T0), including three upregulated genes (ANK3, FTO, FCN1) and 50 downregulated genes (TOP 5: MYL9, NRGN, H2AC6, MAP3K7CL, B2M). These genes were primarily involved in inflammation and metabolism. Pathway analysis revealed significant regulation of 100 pathways at post-training compared to pre training, predominantly inactivated, including pathways involved in inflammation (STAT3 signaling) and metabolism (O-linked glycosylation).

Acute exercise and exercise training modulated EV-associated gene expression in long COVID, primarily through transcriptional downregulation. Suppression of inflammation- and immune-related genes post-training highlights potential molecular mechanisms underlying symptom improvement and identifies candidate biomarkers of recovery biology in long COVID.

Importantly, while exercise training did not substantially alter EV RNA content at rest, it enhanced the body’s ability to mount a dynamic EV-mediated molecular response during exertion, reflecting improved physiological adaptability.
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[forestglip]

Without any healthy controls, I don't see how we can have any idea that any of this is specific to long COVID, and not just an effect of exercise.

 

[Utsikt]

No traces of covid:

To determine if any DEGs were associated with the SARS-CoV-2 virus, the SARS-CoV-2 reference genome was included in the mapping and annotation for each sample. No transcripts mapping the SARS-CoV-2 genome were identified in any of the samples.

In the present study we did not detect any SARS-CoV-2 related RNA in serum EVs across all time points.

They mention your concern, @forestglip, but seem to ignore it in the rest of the text.

This could be considered the first study linking exercise-induced EV RNA profiles to physiological adaptations in long COVID patients. However, because this study was a single-arm design without a control group, we cannot distinguish the effects of exercise training from spontaneous recovery or the passage of time. Nonetheless, these findings warrant further mechanistic investigation in controlled studies.

It doesn’t seem to dawn on them that pwLC don’t need improved physical fitness, they need less symptoms in general. They keep going on and on about all of these benefits of exercise, but there is not a single mention of the patient’s actual symptoms or how you can’t even know if exercise helped them.

This is all we get about symptoms at baseline, and nothing after.

14 subjects completed exercise training, and their demographics are presented in Table 1. Participating subjects were older (53.5 y ± 11.6), primarily male (57%), and obese (BMI 32.5 ± 8.4). The primary symptoms were brain fog (100%), fatigue (86%), post exertional malaise (57%), exercise intolerance (46%), and dyspnea (36%).

 

[SNT Gatchaman]

I thought this was an interesting passage.

While 53 genes were differentially regulated in the EVs in response to acute exercise after exercise training, there were no changes in EV RNA profiles at rest (baseline) from pre- to post-training. The lack of DEGs in EV RNA profiles at baseline between pre- and post-training may indicate that the effects of exercise training on circulating EV cargo are context-dependent and may only be uncovered under physiological stress, such as during acute exercise. This suggests that exercise training may not substantially alter resting EV RNA content but rather enhances the body’s ability to elicit a dynamic EV-mediated molecular response when challenged. Such findings align with the concept that exercise training improved physiological adaptability, which may not be detectable under resting conditions but becomes evident during exertion.

Signals relating to mitochondria, metabolism, rho GTPases, neutrophils (granzyme, NETs), myosin, neurogranin (synapses again) and HDAC —

Furthermore, after training, the response to acute exercise (V24T1 vs V24T0) was predominantly characterized by pathway inactivation, with 52 significantly regulated pathways (based on 718 regulated genes, p < 0.05), including 8 activated and 44 strongly inactivated pathways.

The top activated pathways included Mitochondrial Dysfunction (z-score = 3), Parkinson’s Signaling Pathway (z-score = 2.887), Granzyme A Signaling (z-score = 2.646), RHOGDI Signaling (z-score = 2.236), and HER-2 Signaling in Breast Cancer (z-score = 2).

Conversely, pathways related to mitochondrial function, metabolism, and the immune system were predominantly inactivated at peak exercise after training. Among these, the top five inactivated pathways were tRNA Processing in the Mitochondrion (z-score = − 4.123), rRNA Processing (z-score = − 3.873), Mitochondrial RNA Degradation (z-score = − 3.873), Neutrophil Extracellular Trap Signaling (z-score = − 3.464), and Oxidative Phosphorylation (z-score = − 3.464).

MYL9 (Myosin Light Chain 9), one of the most significantly downregulated genes, encodes a surface molecule expressed on activated T cells that serves as a ligand for CD69, a marker of activated immune cells. The interaction between MYL9 and CD69 is essential for the migration of activated T cells into inflammatory lesions and the induction of immune-driven diseases. Moreover, MYL9 has been implicated in microthrombi formation in SARS-CoV-2-induced lung vasculitis, where its elevation correlates with disease severity.

Another strongly downregulated gene, NRGN (Neurogranin), encodes a protein primarily expressed in the brain, which plays a role in synaptic plasticity and neuroinflammation. […] Other downregulated genes further support the hypothesis that exercise training modulates the immune response to acute exercise in long COVID. H2AC6, a histone variant, interacts with histone deacetylase 6 (HDAC6), a key inflammatory regulator, while B2M (Beta-2-Microglobulin) is essential for antigen presentation via MHC class I molecules.

Lectin and ficolin get a mention —

Additionally, dopaminergic signaling (Parkinson’s Signaling Pathway), immune system activation and inflammation (STAT3 pathway and C-type lectin receptors), and vesicle formation and transport (COPII-mediated vesicle transport) were also significantly inactivated. Notably, 21 (e.g., STAT3, SAPK/JNK, PDGF, and C-type lectin receptor pathways) of the 44 inactivated pathways were directly or indirectly linked to inflammation, suggesting that their inactivation in response to acute exercise after exercise training may represent a beneficial immune-regulatory response.

Three differentially expressed genes- ANK3, FTO, and FCN1- were significantly upregulated in circulating EVs of long COVID patients at peak exercise after training. […] While ANK3 and FTO help maintain axon initial segment and neuronal excitability (in neurons) and involved in cell signaling, possibly immune synapse formation, and RNA metabolism, especially energy balance (in other cells) […]. Similarly, FCN1, a key component of innate immunity, activates the lectin pathway of the complement system to promote microbial clearance.

Since Long COVID is frequently associated with neurological symptoms (e.g., brain fog), increased ANK2, FTO and FCN1 in EVs during acute exercise after training may suggest enhanced neuronal remodeling and vesicle-mediated signaling (ANK3), improved metabolic regulation and RNA turnover (FTO), and a shift toward controlled immune activation and resolution pathways (FCN1).