Downregulation of the entire cellular machinery responsible for protein synthesis and mitochondria dysfunction in ME/CFS???

The preprint of (1)

Charting the Circulating Proteome in ME/CFS: Cross System Profiling and Mechanistic insights

have supplemental tabels which show increased and decreased levels of proteins in serum from ME/CFS patients. 

I selected some proteins and asked the AI ​​what it meant.

I used artificial intelligence (AI) via   https://www.google.com/  to get some answers. Don't rely on my ability to ask the right questions, and don't rely on answers from AI. But, please, be inspired to search for more information.

Me: What can be the cause of increased levels of ART4, ERP29 and SDF2L1 in serum from ME/CFS patients?

AI: Increased levels of the proteins ART4, ERP29, and SDF2L1 in the serum of ME/CFS patients are potential biomarkers that point towards underlying mechanisms of chronic inflammation, immune dysfunction, and cellular stress responses, likely triggered by a prior infection. 

The presence of these elevated proteins suggests:

• Immune System Dysregulation: ME/CFS is associated with chronic immune activation and an exaggerated innate immune response, often following a viral infection (e.g., EBV, HSV-1, or SARS-CoV-2). The elevated proteins may be part of this persistent, misdirected inflammatory signaling, possibly involving autoantibodies.
• Endoplasmic Reticulum (ER) Stress and Protein Misfolding: ERP29 is an ER-resident chaperone protein involved in the biosynthesis and trafficking of various proteins and plays a role in the ER stress response (ERS) and the unfolded protein response (UPR). Its increased level may indicate a cellular attempt to manage high levels of misfolded or aggregated proteins, potentially due to oxidative stress or impaired protein homeostasis prevalent in ME/CFS.
• Extracellular Matrix (ECM) Disruption: Research has noted disrupted extracellular matrix homeostasis in ME/CFS patients, with the release of endogenous ligands that promote inflammation. The elevated levels of ART4 and SDF2L1 might be related to this disruption, potentially as part of an ongoing tissue repair process or inflammatory signaling involving cell-cell adhesion and barrier integrity.
• Oxidative Stress: ME/CFS patients experience chronic oxidative stress, which can damage proteins and other cellular components. Increased levels of these proteins might be part of the body's response to mitigate this damage or could be a consequence of the damage itself. 

In essence, the increased levels of ART4, ERP29, and SDF2L1 are not the cause of ME/CFS itself, but rather indicators or consequences of the complex, multi-systemic pathological processes occurring in patients, primarily chronic immune activation, inflammation, and cellular stress responses originating from a potential infectious trigger

Me: The same study also showed decreased levels of EIF1AY, EIF1B. EIF2S1, EIF2S2, EIF3B, EIF4A2, EIF4B, EIF4E and EIF4G2 in serum from ME/CFS patients?

AI: The proteins with decreased levels in the serum of ME/CFS patients (EIF1AY, EIF1B, EIF2S1, EIF2S2, EIF3B, EIF4A2, EIF4B, EIF4E, and EIF4G2) are all eukaryotic translation initiation factors (eIFs). Their decreased levels suggest a significant dysfunction in the fundamental cellular process of protein synthesis and gene expression regulation. 

Function of eIF Proteins

These factors are crucial for the initiation of protein synthesis (translation): 

• EIF2S1, EIF2S2 (eIF2 subunits): These form part of the eIF2 complex, which is responsible for binding the initiator Met-tRNA to the ribosome.
• EIF3B (eIF3 subunit): eIF3 is a large complex that plays a central role in assembling the translation machinery and interacting with other factors like eIF4G.
• EIF4A2, EIF4B, EIF4E, EIF4G2 (eIF4F complex and associated factors): The eIF4F complex (eIF4E, eIF4G, eIF4A) mediates the recognition of the mRNA cap structure, unwinds mRNA secondary structures, and recruits the ribosome to the mRNA. EIF4B stimulates the helicase activity of eIF4A. EIF4G2 (DAP5) is an eIF4G homolog that can support cap-independent translation.
• EIF1AY, EIF1B: These factors are also involved in the assembly of the pre-initiation complex and scanning along the mRNA to find the start codon. 

Potential Causes for Decreased Levels in ME/CFS

The lower levels of these critical translation factors in the serum of ME/CFS patients suggest several potential underlying pathological mechanisms:

• Global Repression of Protein Synthesis: A coordinated decrease in multiple key initiation factors could lead to a general dampening or dysregulation of protein production within cells. This might be a cellular strategy to conserve energy or cope with stress, but if prolonged, it could impair normal cellular function, tissue repair, and immune responses.
• Energy Metabolism Disturbances: ME/CFS is associated with significant disturbances in energy metabolism. Protein synthesis is an energy-intensive process. A reduction in the machinery required for this process might reflect an adaptive response to chronic energy deficiency or mitochondrial dysfunction.
• Chronic Inflammation and Stress Response: Chronic inflammation and oxidative stress are central to ME/CFS pathophysiology. Inflammatory pathways (e.g., involving cytokines) can modulate translation initiation factor activity and levels as a way to control gene expression during an immune response. This downregulation might be a misdirected or persistent part of such a response.
• Circadian Rhythm Disruption: The study that likely identified these markers also found that ME/CFS serum causes a loss of coherence in cellular circadian rhythms, which regulate many biological processes including protein synthesis. The decreased eIF levels may be linked to this circadian dysregulation.
• mRNA Regulation Issues: Altered levels of these factors might impact how specific mRNAs are translated, potentially leading to an imbalance in the production of different classes of proteins (e.g., a bias towards inflammatory proteins over normal housekeeping or repair proteins). 

In summary, the decreased levels of these translation initiation factors point towards a broad disruption of the cell's ability to produce proteins efficiently and appropriately. This likely contributes to the multi-systemic symptoms of ME/CFS by impacting the function of the nervous system, immune system, and energy metabolism.

Me: The study also showed decreased levels of DARS1, DARS2, GARS1, HARS1, MARS1, SARS2 and TARS1 in the serum from ME/CFS patients. What is the realtion to decreaesed levels of translation initiation factors?

AI: The proteins DARS1, DARS2, GARS1, HARS1, MARS1, SARS2, and TARS1 are all aminoacyl-tRNA synthetases (AARSs). Their decreased levels in ME/CFS serum, in conjunction with decreased levels of translation initiation factors (eIFs), strongly suggests a coordinated and systemic downregulation of the entire cellular machinery responsible for protein synthesis.

Here is the relationship between the decreased levels of AARSs and eIFs in ME/CFS patients:

1. Functional Interdependence in Protein Synthesis

Both AARSs and eIFs are essential components of the translation process:

• AARSs' Role: Aminoacyl-tRNA synthetases are responsible for "charging" transfer RNA (tRNA) molecules with their specific amino acids (e.g., GARS1 for Glycine, HARS1 for Histidine, DARS1/2 for Aspartate). This is the crucial first step that provides the building blocks for proteins.
• eIFs' Role: Eukaryotic translation initiation factors then assemble the ribosome and mRNA to start the actual synthesis of the protein chain.

The simultaneous reduction of both sets of factors indicates a major impact on the efficiency and capacity of the cell to produce proteins. This suggests that the bottleneck in protein synthesis is not just at the initiation stage (eIFs) but also at the preparatory stage (AARSs).

2. A Coordinated Cellular Stress Response

A simultaneous decrease in multiple AARSs and eIFs is likely a cellular response to profound and chronic stress, potentially triggered by:

• Energy Depletion: Protein synthesis is one of the most energy-consuming processes in a cell. Given that ME/CFS is fundamentally linked to energy metabolism disturbances and mitochondrial dysfunction, downregulating the entire protein synthesis pathway (both AARSs and eIFs) could be an adaptive survival mechanism by cells to conserve energy under conditions of chronic low energy availability.
• Chronic Inflammation: Systemic inflammation and oxidative stress in ME/CFS can globally influence gene expression and protein stability. This simultaneous decrease may be part of an orchestrated inflammatory response that represses general cellular activities while perhaps prioritizing the production of specific stress or immune-related proteins (though overall capacity is reduced).
• Widespread Metabolic Dysregulation: The study that found these changes likely points to a systemic breakdown in metabolic homeostasis, impacting the fundamental processes that keep cells functioning correctly.

3. Impact on ME/CFS Symptoms

This broad disruption of protein synthesis machinery could directly contribute to several core symptoms of ME/CFS:

• Impaired Tissue Repair: Reduced availability of both AARSs and eIFs would hinder the body's ability to repair damaged tissues and muscle after exertion, contributing to post-exertional malaise.
• Immune Dysfunction: Proper immune function requires the rapid and efficient synthesis of antibodies, cytokines, and other immune components. A dampened translation system could compromise the immune response and resolution of infections.
• Neurological Symptoms: The brain is highly metabolically active. Impaired protein synthesis in neurons could contribute to cognitive dysfunction ("brain fog"), memory issues, and nervous system dysregulation.

In summary, the reduced levels of both AARSs and eIFs in the serum of ME/CFS patients are two sides of the same coin, highlighting a systemic and coordinated suppression of the protein synthesis machinery, likely driven by chronic energy stress and inflammation.

Me: Are you sure it is not  because the ME/CFS patients are inactive? 

AI: While physical inactivity (deconditioning) can lead to some physiological changes, it is unlikely to be the sole or primary cause of the significantly decreased levels of multiple aminoacyl-tRNA synthetases (AARSs) and translation initiation factors (eIFs) in ME/CFS patients. 

The evidence suggests that these protein changes are specific biological manifestations of the disease process itself, rather than a simple consequence of a sedentary lifestyle: 

• Distinct Pathology from Deconditioning: Studies comparing the effects of inactivity in healthy controls to the pathology in ME/CFS patients find fundamental differences. For example, muscle changes in ME/CFS are distinct from those seen in healthy, inactive individuals.
• Unique Metabolic Signatures: ME/CFS patients exhibit unique metabolic signatures that run contrary to what is typically seen with inactivity. For instance, some studies found reduced levels of branched-chain amino acids (BCAAs) in ME/CFS, whereas inactivity and obesity are generally linked to increased levels.
• Objective Measures Not Explained by Deconditioning: Research has demonstrated that core ME/CFS symptoms and physiological abnormalities, such as post-exertional malaise (PEM), impaired mitochondrial function, and abnormal cerebral blood flow during orthostatic stress, cannot be solely explained by deconditioning.
• Systemic Energy Crisis: The simultaneous downregulation of a broad range of proteins essential for the energy-intensive process of protein synthesis likely represents a coordinated "hypometabolic" or energy-saving state in the cells, a central feature of ME/CFS's energy metabolism dysfunction. Deconditioning alone does not typically lead to such a profound and specific systemic energy crisis.
• Immune System Link: The identified changes in both eIFs and AARSs are likely linked to immune system dysregulation and chronic inflammation, which are primary drivers of ME/CFS pathology. 

Inactivity is a consequence of ME/CFS symptoms (such as PEM and severe fatigue), but the unique molecular and physiological abnormalities point to a complex underlying biological illness, not just a result of being out of shape. 

Me: Now we are sure suggests that this is about  a coordinated and systemic downregulation of the entire cellular machinery responsible for protein synthesis. Can you put decreased  ME/CFS serum levels of LONP1 into the context?

AI: The decreased level of LONP1 (Lon peptidase 1, mitochondrial) in the serum of ME/CFS patients fits directly into the context of a systemic downregulation of the protein synthesis machinery (AARSs and eIFs) and points specifically to significant mitochondrial dysfunction and impaired protein quality control. 

Role of LONP1

LONP1 is a crucial, multi-functional protein primarily located in the mitochondrial matrix: 

• Protein Quality Control (Protease/Chaperone): It acts as an ATP-dependent protease and chaperone, degrading misfolded, damaged, or oxidized proteins within the mitochondria and helping new proteins fold correctly.
• Mitochondrial DNA (mtDNA) Maintenance: LONP1 binds to mtDNA and helps regulate its transcription, replication, and overall copy number.
• Metabolism Regulation: It regulates key enzymes in the tricarboxylic acid (TCA) cycle and oxidative phosphorylation (OXPHOS), essentially fine-tuning the cell's energy production processes.
• Stress Response: Its expression is normally induced by cellular stressors like oxidative stress, heat shock, and hypoxia to protect the cell. 

Relation to Decreased eIFs and AARSs

The coordinated decrease of LONP1 with eIFs and AARSs in ME/CFS serum suggests a linked and systemic issue:

• Mitochondrial-Cytosolic Link: While eIFs and AARSs operate in the cytoplasm (for general protein synthesis) and mitochondria (for mitochondrial-specific protein synthesis), a defect in one system profoundly impacts the other. LONP1 is essential for the proper folding and assembly of the 13 proteins encoded by mtDNA (which form the core of the OXPHOS complexes).
• Systemic Energy Crisis: The low levels of all these proteins point towards a broad, coordinated cellular strategy to power down energy-intensive processes, including all forms of protein production (both cytoplasmic and mitochondrial), likely in response to chronic energy deficiency or mitochondrial dysfunction.
• Accumulation of Damaged Proteins: A deficiency in LONP1's function leads to the accumulation of misfolded and aggregated proteins within the mitochondria, which are then dysfunctional. This accumulation triggers a broad integrated stress response (ISR) and can lead to apoptosis (cell death). This mitochondrial stress, in turn, likely signals the rest of the cell to downregulate general protein synthesis (eIFs and AARSs) to reduce the burden of new protein production and preserve limited energy.
• Impaired Mitochondrial Function: The lack of functional mitochondrial proteins due to both decreased synthesis (AARSs) and impaired quality control (LONP1) leads to reduced OXPHOS capacity and lower ATP production, a hallmark of ME/CFS. 

In essence, decreased LONP1 is a key piece of the puzzle that links the systemic failure of protein synthesis to core mitochondrial dysfunction and energy metabolism issues observed in ME/CFS.

Me: Can you put increased  ME/CFS serum levels of GLUD1, MRM1, NIF3L1, RIDA and UNG into the context?

Me: The increased levels of GLUD1, MRM1, NIF3L1, RIDA, and UNG in the serum of ME/CFS patients, alongside the decreased levels of protein synthesis machinery components (eIFs, AARSs, LONP1), can be put into context by highlighting a severe and chronic state of metabolic disruption, heightened mitochondrial stress, and ongoing DNA damage repair.

These proteins are predominantly located in the mitochondria and are involved in energy metabolism and genetic integrity:

• GLUD1 (Glutamate Dehydrogenase 1): A key mitochondrial enzyme that converts glutamate to alpha-ketoglutarate, linking amino acid metabolism to the TCA cycle (energy production).
• MRM1 (Mitochondrial RNA Methyltransferase 1): Involved in modifying mitochondrial ribosomal RNA, which is essential for mitochondrial protein synthesis.
• NIF3L1 (Nuclear protein interacting with the F3 region of the c-Myc promoter-like 1): A protein involved in various cellular processes including stress responses and potentially inflammation.
• RIDA (Reactive Intermediate Deaminase A): A metabolic enzyme that prevents damage from reactive metabolic intermediates (like 2-aminoacrylate), acting as a "metabolic proofreader" to protect other enzymes.
• UNG (Uracil-DNA Glycosylase): A crucial enzyme involved in DNA base excision repair, specifically removing uracil bases from DNA to prevent mutations. 

The Integrated Context

The simultaneous changes paint a picture of a cell under siege, struggling to maintain its basic functions and integrity:

• Mitochondrial Dysfunction and Stress: The presence of several increased mitochondrial proteins (GLUD1, MRM1, NIF3L1) points to a significant stress response and potential compensatory mechanisms within the mitochondria. Cells might be attempting to upregulate certain aspects of mitochondrial function or repair in response to the profound energy production defects and protein imbalances previously discussed (e.g., the Complex V inefficiency noted in some studies).
• Metabolic Crisis and Damage Control: The increased RIDA suggests the generation and accumulation of harmful, reactive metabolic byproducts, which is common in conditions with high oxidative stress and metabolic bottlenecks (like an impaired TCA cycle or glycolysis).
• Genomic Instability and Repair: The elevation of UNG highlights increased DNA damage, likely a result of the chronic oxidative stress prevalent in ME/CFS. The cell is working harder to repair its genetic material.
• Imbalance of Anabolism and Catabolism: While the machinery for general protein synthesis (anabolism) is downregulated (eIFs, AARSs), certain catabolic and stress-response proteins (like GLUD1, RIDA, UNG) are elevated, likely reflecting a shift in cellular priorities towards survival, damage control, and alternative metabolic pathways rather than normal growth and repair. 

In summary, the increased levels of these proteins are biomarkers of profound cellular distress, chronic oxidative stress, mitochondrial damage, and metabolic derangement in ME/CFS patients, all of which align with the observed decrease in general protein synthesis capacity. This complex profile reflects the body's struggle to manage a multi-systemic energy crisis and ongoing damage.

Me: The ME/CFS serum proteins mentioned in this AI thread are mostly intracelluar proteins. Is serum protein a safe way to base your answers on the function of the cells?

AI: Yes, basing conclusions on the function of cells from the presence and levels of intracellular proteins in the serum is a valid and widely used approach in medical diagnostics and research.

Here's the rationale for why this is a safe way to interpret the data:

• Intracellular Proteins as Biomarkers of Cell Damage: In healthy individuals, intracellular proteins are largely confined within the cell membrane. Their presence in the serum (extracellular space) is typically minimal. When cells are damaged, stressed, or undergo increased turnover (apoptosis or necrosis), their contents leak into the interstitial fluid and then the bloodstream. The amount of these "leaked" proteins can serve as a powerful indicator of the type and extent of cellular stress or damage occurring in the body.
• A Standard Diagnostic Principle: This concept is a fundamental principle in medicine. For example, elevated levels of liver enzymes (like ALT and AST, which are intracellular proteins) in the blood indicate liver damage, while increased troponin levels indicate heart muscle damage.
• Extracellular Vesicles (EVs): Many intracellular proteins can also be actively secreted in small packages called extracellular vesicles (EVs). These vesicles act as a form of cellular communication, carrying specific proteins that reflect the state of the parent cells to distant parts of the body. The proteomic analysis of EV cargo is a growing area of research in ME/CFS and other diseases, and these can also act as valid biomarkers.
• Systemic Reflection: The serum proteome contains proteins from almost every type of cell and tissue in the body. Alterations in this complex mixture provide a reliable "snapshot" of the overall physiological and pathological state of the organism. The coordinated changes in numerous proteins across different cellular functions (protein synthesis, mitochondrial function, DNA repair) strongly suggest a systemic, body-wide issue, not a localized or random event. 

Therefore, the observed changes in intracellular proteins in ME/CFS serum are robust evidence of systemic cellular dysfunction, supporting the biological basis of the illness. The interpretation of these findings to infer internal cellular processes is a standard scientific practice.

Me: It sounds as these patients are really ill. ME/CFS has been considered a functional disorder.  Is it outdated knowledge?

Yes, classifying ME/CFS as solely a "functional disorder" is considered outdated knowledge by the majority of the medical and scientific community [1, 2, 3].

The evidence from numerous scientific studies, including those identifying the specific protein changes we discussed (which point to profound biological dysregulation), firmly establishes ME/CFS as a complex, chronic, multi-system biomedical illness.

Here’s why the "functional disorder" label is outdated:

• Objective Biomarkers: A growing body of research has identified measurable biological abnormalities in ME/CFS patients, including those we discussed (protein level changes in AARSs, eIFs, LONP1, etc.), immune system dysfunction, mitochondrial abnormalities, brain inflammation, and autonomic nervous system dysregulation [1, 2, 3]. Functional disorders are typically defined by symptoms without clear, objective pathological findings.
• Physical, Not Psychological, Basis: The term "functional disorder" has often been associated with psychological causes or psychosomatic illness. Current research decisively shows that while psychological stress may exacerbate symptoms, the root causes of ME/CFS are physiological [2].
• Major Institutional Recognition: Key health bodies have shifted their stance.
  • The World Health Organization (WHO) classifies ME/CFS as a neurological disease (under G93.3) [1, 2].
  • The U.S. National Institutes of Health (NIH) has acknowledged it as a "serious, chronic, and complex systemic disease" and substantially increased research funding [1].
  • The U.S. Centers for Disease Control and Prevention (CDC) provides extensive information on its biomedical nature.
• The Problem with Pacing: The previous dominant treatment approach based on the "functional disorder" model, Graded Exercise Therapy (GET), often harmed patients by worsening their core symptom of post-exertional malaise (PEM), which is a key physiological feature of the disease [2, 3]. Pacing (managing energy) is now the recommended approach.
• Profound Severity: As you noted, the biological evidence points to very real and significant illness. ME/CFS can cause severe disability; many patients are housebound or even bedbound [3].

The shift in understanding is crucial for ensuring patients receive appropriate medical care, validation, and targeted biomedical research into effective treatments.

Reference:

1) Charting the Circulating Proteome in ME/CFS: Cross System Profiling and Mechanistic insights

August Hoel, Fredrik Hoel, Sissel Elisabeth Furesund Dyrstad, Henrique Chapola, Ingrid Gurvin Rekeland, Kristin Risa, Kine Alme, Kari Sørland, Karl Albert Brokstad, Hans-Peter Marti, Olav Mella, Øystein Fluge, Karl Johan Tronstad

medRxiv 2025.05.28.25328245; doi: https://doi.org/10.1101/2025.05.28.25328245

This article is a preprint and has not been peer-reviewed [what does this mean?]. It reports new medical research that has yet to be evaluated and so should not be used to guide clinical practice.

https://www.medrxiv.org/content/10.1101/2025.05.28.25328245v1