Tag: 2025

Using the Ratio of Phosphorylated to Non-phosphorylated Forms of Stress Kinase PKR as a Potential Diagnostic Test for ME/CFS

Abstract:

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a complex illness characterized by a set of mainly neurological symptoms lasting for over 6 months. Currently, there is no definitive laboratory diagnostic test readily accessible to all clinicians and patients, and so clinical diagnosis occurs only after an exhaustive process of exclusion of all other possible causes of the varied symptoms experienced by the patient.

Here we present the development of a method that uses specific antibodies able to identify a changed ratio of phosphorylated and active protein kinase R in the peripheral blood monocyte cells (PBMCs) and neutrophil cells from a small group of ME/CFS sufferers, compared to age and sex-matched controls.

Protein kinase R (PKR) is an RNA-activated immune protein and stress kinase that has been observed to be present in its cleaved, auto-phosphorylated, and active form in past ME/CFS studies. After further validation, the activation status of PKR detected via specific antibodies in an ELISA format has potential for a simple readily accessible diagnostic tool for the early acute stage of ME/CFS illness, or as a long-term measure to evaluate the disease status.

Source: Sweetman E, Tate WP. Using the Ratio of Phosphorylated to Non-phosphorylated Forms of Stress Kinase PKR as a Potential Diagnostic Test for ME/CFS. Methods Mol Biol. 2025;2920:13-28. doi: 10.1007/978-1-0716-4498-0_2. PMID: 40372675. https://link.springer.com/protocol/10.1007/978-1-0716-4498-0_2

Using Single-Cell Raman Microspectroscopy to Profile Human Peripheral Blood Mononuclear Cells

Abstract:

A reliable, validated test would enhance our ability to treat and research chronic conditions. Early and accurate diagnosis would provide an entry point into clinical care, give access to benefits, remove the stigma associated with these conditions, and importantly, provide researchers with a fundamental tool they require to study these heterogeneous disorders.

In this chapter, we describe how Raman microspectroscopy can be utilised to study the biology of peripheral blood mononuclear cells (PBMCs) isolated from human blood samples. Using machine learning approaches, the data generated can be used to attempt to separate different patient and control groups, subgroups within a patient cohort, and identify differences in intracellular metabolites which may provide clues about disease mechanisms.

Source: Gan E, Stoker M, Guo E, Morten KJ, Xu J. Using Single-Cell Raman Microspectroscopy to Profile Human Peripheral Blood Mononuclear Cells. Methods Mol Biol. 2025;2920:29-37. doi: 10.1007/978-1-0716-4498-0_3. PMID: 40372676. https://link.springer.com/protocol/10.1007/978-1-0716-4498-0_3

MicroRNA Profiling of Blood Extracellular Vesicles in ME/CFS

Abstract:

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a chronic debilitating neuroimmune disease affecting many organs and systems which, in the absence of validated biomarkers, remains diagnosed by clinical criteria. Extracellular vesicles (EV) in blood come from practically all cells in our body and therefore may carry the disease-specific biomarkers needed for the diagnosis of ME.

This chapter presents the methodology used on a single pilot study performed to evaluate this possibility to describe a workflow for EV isolation and the analysis of the miRNAs within, which could serve to interrogate additional cohorts of ME/CFS. Among the diverse nature of EV contents miRNAs may constitute a prominent regulatory layer in the development and progress of complex diseases such as ME/CFS, and therefore their study should be further pursued.

Source:Ljungström M, Nathanson L, Oltra E. MicroRNA Profiling of Blood Extracellular Vesicles in ME/CFS. Methods Mol Biol. 2025;2920:39-55. doi: 10.1007/978-1-0716-4498-0_4. PMID: 40372677. https://link.springer.com/protocol/10.1007/978-1-0716-4498-0_4

Deep Immunophenotyping in ME/CFS Using Spectral Flow Cytometry

Abstract:

Immune dysfunction is reported to play a significant role in the etiology of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). To gain an understanding of the underlying immune abnormalities associated with this complex condition, a comprehensive approach for characterizing immune cell subsets and their inferred functional states is essential.

We developed a high-dimensional flow cytometry method that enables detailed immunophenotyping of peripheral blood mononuclear cells (PBMCs) from ME/CFS patients. By simultaneously measuring over 40 markers on individual cells within one sample, this approach provides a comprehensive assessment of immune cell subsets, incorporating effector or functional states, to enable assessment of their potential roles in disease pathogenesis.

Source: Gibson A, Chometon TQ, Damani T, Brooks AES. Deep Immunophenotyping in ME/CFS Using Spectral Flow Cytometry. Methods Mol Biol. 2025;2920:59-82. doi: 10.1007/978-1-0716-4498-0_5. PMID: 40372678. https://link.springer.com/protocol/10.1007/978-1-0716-4498-0_5

Analysis of Transient Receptor Potential Ion Channels in ME/CFS

Abstract:

This chapter provides a comprehensive overview of methodologies currently employed to study ion channels, particularly transient receptor potential melastatin 3 (TRPM3) in the context of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). Sample preparation involves the collection of whole blood, separation of peripheral blood mononuclear cells (PBMCs) via density gradient centrifugation, and isolation of natural killer (NK) cells.

Protein expression analysis utilizes flow cytometry, liquid chromatography-mass spectrometry (LC-MS), western blotting, and immunofluorescence techniques. Functional analysis focuses on calcium imaging and electrophysiology techniques to investigate ion channel responses to pharmacological stimuli.

The authors highlight that some experimental protocols included within this chapter require specialized training and equipment. In order to replicate these protocols extended training is advised, specifically when attempting electrophysiology experimentation. The use of advanced techniques for detailed analysis provides insights into ion channel function and potential implications in the pathomechanism of ME/CFS offering avenues for further research and therapeutic exploration.

Source: Eaton-Fitch N, Muraki K, Sasso EM, Magawa C, Marshall-Gradisnik S. Analysis of Transient Receptor Potential Ion Channels in ME/CFS. Methods Mol Biol. 2025;2920:83-99. doi: 10.1007/978-1-0716-4498-0_6. PMID: 40372679. https://link.springer.com/protocol/10.1007/978-1-0716-4498-0_6

Stress-Induced Changes in Immune Signatures in ME/CFS Patients Determined by Transcriptome Analysis

Abstract:

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a chronic, complex multi-organ illness characterized by unexplained debilitating fatigue and post-exertional malaise (PEM). We evaluated transcriptomic changes in peripheral blood mononuclear cells (PBMC) of ME/CFS patients undergoing an exercise challenge and explored the transcriptomic response to exercise and recovery in PBMC of ME/CFS patients, as compared to healthy controls using RNA sequencing technology. As transcriptomic changes in ME/CFS patients are still in the phase of discovery, analysis of data has to be stringent, and the most important results have to be validated by a different technology, such as real-time PCR or NanoString.

Source: Gamer J, Van Booven D, Zarnowski O, Perez M, Frank J, Pangeni RP, Collado F, Klimas NG, Oltra E, Nathanson L. Stress-Induced Changes in Immune Signatures in ME/CFS Patients Determined by Transcriptome Analysis. Methods Mol Biol. 2025;2920:103-112. doi: 10.1007/978-1-0716-4498-0_7. PMID: 40372680. https://link.springer.com/protocol/10.1007/978-1-0716-4498-0_7

Quantitative Proteomics on Immune Cells of ME/CFS Patients Using SWATH-MS

Abstract:

Proteomics is one of the “omics” disciplines that has provided molecular insights into the pathophysiology of myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). Here we describe a complete SWATH-MS workflow for the quantitative profiling of proteins extracted from peripheral mononuclear blood cells to investigate proteomic alterations in ME/CFS. This workflow covers all steps of sample preparation, data acquisition, and data analysis.

We describe the process of generating a comprehensive spectral library from a pre-fractionated peptide reference sample followed by the acquisition of DIA data sets of individual samples using a 5600+ TripleTOF mass spectrometer. Examples of both library-based and library-free data analysis pipelines are presented based on the PeakView/MarkerView software package (commercial) and DIA-NN (free) software respectively.

Source: Kumar A, Peppercorn K, Kleffmann T. Quantitative Proteomics on Immune Cells of ME/CFS Patients Using SWATH-MS. Methods Mol Biol. 2025;2920:113-140. doi: 10.1007/978-1-0716-4498-0_8. PMID: 40372681. https://link.springer.com/protocol/10.1007/978-1-0716-4498-0_8

Application of DNA Methylome Analysis to Patients with ME/CFS

Abstract:

Myalgic encephalomyelitis/chronic fatigue syndrome is a post-viral/stressor syndrome that has a complex pathophysiology reflecting multiple changes in many cell transcripts and proteins. These changes imply a change in the regulation of gene expression at the level of the DNA. A significant contributor to this is the modulation of the methylation at specific sites within regulatory regions throughout the genome that can either enhance or dampen expression depending on whether methylation is reduced or increased, respectively. DNA methylation can be analyzed by array technology or by reduced representation bisulfite sequencing (RRBS) or whole genome bisulfite sequencing (WGBS).

This chapter describes RRBS, which has been very effective at analyzing the methylation states of ME/CFS patients both in single time point studies and in longitudinal studies with individual patients, for example, following a relapse recovery cycle. Here, we describe the step-by-step experimental methodology of how RRBS has been applied to DNA samples from ME/CFS patients and the analytical platforms used to detect the methylation changes that are statistically significant between patients and health controls. It has the potential to provide molecular biomarkers for a diagnostic test or to follow the progression of the condition in patients or through relapse/recovery fluctuations that occur frequently through the ongoing course of the disease. When effective therapies become available it has the potential to monitor the effectiveness on individual patients under treatment.

Source: Peppercorn K, Edgar CD, Al Momani S, Rodger EJ, Tate WP, Chatterjee A. Application of DNA Methylome Analysis to Patients with ME/CFS. Methods Mol Biol. 2025;2920:141-160. doi: 10.1007/978-1-0716-4498-0_9. PMID: 40372682. https://link.springer.com/protocol/10.1007/978-1-0716-4498-0_9

Repeated Cardiopulmonary Exercise Testing of ME/CFS Patients

Abstract:

Post-exertional malaise is a cardinal symptom present in 95% of individuals with myalgic encephalomyelitis (ME/CFS). Repeated cardiopulmonary exercise testing has been momentous in revealing that the physiological systems of those with ME/CFS are impaired or damaged and do not respond to exercise/physical activity like those without the condition. The 24-h repeated exercise test may demonstrate a reduction in peak oxygen consumption (VO2 peak), VO2 at ventilatory threshold, power output at both peak and ventilatory threshold, along with a reduction/diminished maximal heart rate commensurate with chronotropic intolerance. In this chapter, I describe the process and methods of repeated cardiopulmonary exercise testing, used to assess exercise tolerance in individuals with ME/CFS.

Source: Hodges L. Repeated Cardiopulmonary Exercise Testing of ME/CFS Patients. Methods Mol Biol. 2025;2920:163-172. doi: 10.1007/978-1-0716-4498-0_10. PMID: 40372683. https://link.springer.com/protocol/10.1007/978-1-0716-4498-0_10

Real-Time Measurement of Mitochondrial Function and Glycolysis in Lymphoblastoid Cell Lines

Abstract:

Cells require energy in the form of ATP to function. The two main ways in which cells generate energy in mammalian cells is through glycolysis and oxidative phosphorylation (OXPHOS). Glycolysis takes place in the cytosol and involves the breakdown of glucose molecules, generating ATP and pyruvate, while OXPHOS takes place in the mitochondria and is responsible for producing the majority of ATP for the cell. A dysregulation of these cellular processes has been reported in myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). In order to understand the mechanisms of the disease, it is imperative to understand how the bioenergetic pathways are altered in ME/CFS.

Here we describe a method for measuring mitochondrial function and glycolytic function using the Agilent Seahorse Extracellular Flux Analyzer. We have optimized these assays for use in actively proliferating lymphoblastoid cell lines that are generated from blood cells. This assay measures oxygen consumption rate and extracellular acidification rates providing an overview of mitochondrial function and efficiency and glycolytic rate and capacity, respectively. These assays are performed on live, intact cells, and enable us to view different components and measurements of energy metabolism through the injection of different compounds that stimulate or inhibit various sections of these pathways. The below method details an optimized glycolysis and mitochondrial assay for 96-well plates with modifications noted for use in 24-well plates.

Source: Katsaros T, Missailidis D, Annesley SJ. Real-Time Measurement of Mitochondrial Function and Glycolysis in Lymphoblastoid Cell Lines. Methods Mol Biol. 2025;2920:173-202. doi: 10.1007/978-1-0716-4498-0_11. PMID: 40372684. https://link.springer.com/protocol/10.1007/978-1-0716-4498-0_11