William Tillier with the assistance of Manuel Lubinus
2025.
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⚃ 6.3.1.1 Executive Summary.
⚃ 6.3.1.2 Mitochondrial pathology in IBM.
⚃ 6.3.1.3 Background on Mitochondria.
⚃ 6.3.1.4 Selected references.
.≻ Researchers see that mitochondrial dysfunction is a prominent feature of PM-Mito.
≻≻ Over 90% of PM-Mito patients go on to develop full [late stage] IBM.
≻≻ Thus, PM-Mito appears to be an eary stage of IBM.
≻ PM-Mito and IBM constitue a spectrum disease.
≻ There are several major abnormalities seen in the mitochondria of both PM-Mito and IBM.
≻≻ MtDNA copy numbers are significantly reduced [mtDNA depletion], and multiple large-scale mtDNA deletions are already evident in PM-Mito.
≻≻ The mtDNA defects are maintained throughout all stages of the disease.
≻≻ Ultrastructural abnormalities [seen] include disturbed cristae architecture and discontinuity of the mitochondrial membranes, possibly allowing a leakage of mitochondrial content into the body of the cell.
≻≻ In IBM mtDNA leaks from the mitochondria into the body of the cell and this may be a potential inflammatory trigger.
≻≻ In both PM-Mito and IBM there is activation of the canonical cGAS/STING pathway – an innate immune response [activation of the canonical cGAS/STING pathway has been linked to T-cell infiltration, and emerging research suggests it may influence the composition of T-cell subpopulations, including cells expressing KLRG1].
≻≻ The structure of individual mitochondria become abnormal, some showing a reduced length to width ratio.
≻≻ Some mitochondria become giant with highly abnormal [densely packed] cristae [folds in the inner mitochondrial membrane], seen in late stage IBM.
≻≻ Other abnormalities include elevated numbers of COX-negative and SDH-positive fibers.
≻≻ There is dysregulation of proteins and transcripts linked to the mitochondrial membranes.
≻≻ Downregulated proteins are seen – 11 of 33 downregulated proteins were linked to mitochondrial function.
≻≻ Upregulated proteins are seen – the most upregulated protein, with a 6.1-fold upregulation, was a protein located in the inner mitochondrial membrane and involved in various mitochondrial processes, including heme biosynthesis.
≻≻ Ongoing reduced mtDNA copy numbers point towards an mtDNA maintenance defect.
≻≻ Multiple mtDNA deletions and depletion may be related to the severe abnormalities of mitochondrial cristae, where mtDNA replication occurs.
≻ Mitochondrial abnormalities precede tissue remodeling and infiltration by specific T-cell subpopulations (e.g., KLRG1+) characteristic of late IBM.
≻ The initial triggers of mitochondrial dysfunction are unknown.
≻ IBM appears to be a primarily degenerative disease involving mitochondrial dysfunction with peculiar bystander or secondary (auto-) inflammatory features.
≻ In summary, “the role of mitochondria in the pathogenesis of IBM is undoubtedly both significant and complex.”
* Portions from Kleefeld et al., 2025.
≻ Abad et al., 2024: [We see a] self-sustaining loop between inflammation and mitochondrial dysfunction/oxidative stress in the [creation] of myositis.
≻ Cantó-Santos et al., 2023: In mitochondria, several characteristic fibers are displayed which are also seen in primary mitochondrial diseases and mitochondrial myopathies.
≻≻ [We now see the] systemic impact [throughout the whole body] of this disease (previously thought to be restricted to muscle) and the relevance of metabolism in IBM (which was thought to be only minor and secondary).
≻≻ It is still unclear whether these findings could guide future treatment strategies, but the implication of metabolism and oxidative stress in IBM is now undeniable.
≻≻ Metabolic dysregulation in IBM is present outside the target tissue (muscle), as seen in altered organic acids in fibroblasts and urine.
≻ D’Amato et al., 2023: This article reviews several potential treatments and concentrates on the idea of mitochondrial transplantation (MT) as a potential avenue to explore.
≻≻ Providing healthy mitochondria may be a more practical solution given the challenges of the presence of multiple and variable mtDNA mutations.
≻ De Paepe, B. 2019. Based on the cumulating evidence of mitochondrial abnormality as a disease contributor, it is therefore warranted to regard IBM as a mitochondrial disease, offering a feasible therapeutic target to be developed for this yet untreatable condition.
≻≻ Muscle of IBM patients seems to display exaggeration of normal aging-associated degenerative changes, which includes mitochondrial decline.
≻≻ We can thus conclude that, although mitochondrial alterations are not the genetic origin, they nonetheless represent an important aspect of IBM disease mechanisms and represents a druggable and valid therapeutic target.
≻ Hedberg-Oldfors et al., 2024: Detailed characterization by deep sequencing of mtDNA in muscle samples from 21 IBM patients and 10 age-matched controls was performed after whole genome sequencing with a mean depth of mtDNA coverage of 46,000x.
≻≻ Multiple large mtDNA deletions and duplications were identified in all IBM and control muscle samples.
≻≻ In general, the IBM muscles demonstrated a larger number of deletions and duplications with a mean heteroplasmy level of 10% (range 1%-35%) compared to controls (1%, range 0.2%-3%).
≻≻ There was also a small increase in the number of somatic single nucleotide variants in IBM muscle.
≻≻ More than 200 rearrangements were recurrent in at least two or more IBM muscles while 26 were found in both IBM and control muscles.
≻≻ In conclusion, deep sequencing and quantitation of mtDNA variants revealed that IBM muscles had markedly increased levels of large deletions and duplications, and there were also indications of increased somatic single nucleotide variants and reduced mtDNA copy numbers compared to age-matched controls.
≻≻ The distribution and type of variants were similar in IBM muscle and controls indicating an accelerated aging process in IBM muscle, possibly associated with chronic inflammation.
≻ Huntley et al., 2024: In this study, we investigated the association between mitochondria and TDP-43 in biopsied skeletal muscle samples from IBM patients.
≻≻ We found that IBM pathological markers TDP-43, phosphorylated TDP-43, and p62 all coexisted with intensively stained key subunits of mitochondrial oxidative phosphorylation complexes I-V in the same skeletal muscle fibers of patients with IBM.
≻≻ Further immunoblot analysis showed increased levels of TDP-43, truncated TDP-43, phosphorylated TDP-43, and p62, but decreased levels of key subunits of mitochondrial oxidative phosphorylation complexes I and III in IBM patients compared to aged matched control subjects.
≻≻ This is the first demonstration of the close association of TDP-43 accumulation with mitochondria in degenerating muscle fibers in IBM and this association may contribute to the development of mitochondrial dysfunction and pathological protein aggregates.
≻ Iu et al., 2024: sIBM muscle features major mutations in the DNA of mitochondria.
≻≻ The large-scale mitochondrial DNA deletion, aberrant protein aggregation, and slowed organelle turnover have provided mechanistic insights into the genesis of impaired mitochondria in sIBM.
≻≻ This article reviews the disease hallmarks of sIBM, the plausible contributors of mitochondrial damage in the sIBM muscle, and the immunological responses associated with mitochondrial perturbations.
≻≻ Additionally, the potential application of mitochondrial-targeted chemicals as a new treatment strategy to sIBM is explored and discussed.
≻≻ The conventional view of mitochondria solely as ATP-producing powerhouses biased our perception that defective mitochondria in IIM might only result in metabolic deficiency, thus underestimating its functional outcomes.
≻≻ Recent discoveries that highlight mitochondrial defects as inducers of immune response via pyroptosis and necroptosis in many different issues have provided new insights into the pathogenesis of IIM (Figure 1).
≻≻ Hence, it is imperative to recognize the etiological role of mitochondria and developing novel drugs that improve the mitochondrial health as a novel treatment strategy for sIBM.
≻ Kleefeld et al., 2025: [In summary,] we identified that mitochondrial dysfunction with multiple mtDNA deletions and depletion, disturbed mitochondrial ultrastructure, and defects of the inner mitochondrial membrane are features of PM-Mito and IBM, underlining the concept of an IBM-spectrum disease (IBM-SD). See here.
≻ Kummer et al., 2023: In the cell culture model of IBM, the NLRP3 inflammasome was significantly activated.
≻≻ It is reasonable to conclude that inflammasomes are a further link between inflammation and degeneration.
≻≻ The NLRP3 inflammasome is a central component of the interplay between inflammation and degeneration in IBM muscle and its model systems.
≻≻ Chronic inflammatory stimulus with IL-1ß and IFN-y results in impaired autophagy, reactive oxygen species and accumulation of ß-amyloid.
≻≻ This leads to an activation of the NLRP3 inflammasome and subsequently higher levels of IL-1ß, and a subsequent vicious cycle leading to more deposition of B-amyloid.
≻ Lindgren et al., 2024: We conclude that COX-deficient fibers in inclusion body myositis are associated with multiple mtDNA deletions.
≻≻ In IBM patients we found novel and also previously reported variants in genes of importance for mtDNA maintenance that warrants further studies.
≻ Lubinus: Mitochondrial Dysfunction: Oxidative stress and the release of mitochondrial DNA into the cytoplasm of the cell can trigger inflammasome activation.
≻≻ This damaged mitochondrial DNA might provoke an autoimmune response, leading to the production of cN1A antibodies.
≻ Naddaf, Nguyen et al., 2025: The NLRP3 inflammasome is activated in IBM, along with altered mitophagy, particularly in males. [Mitophagy removes and recycles damaged mitochondria and regulates the biogenesis of new, fully functional ones preserving healthy mitochondrial functions and activities.] [The inflammasome is part of the innate immune system, responsible for triggering inflammatory responses and cell death.] See here for more information.
≻ Naddaf, Shammas et al., 2024: Investigation of the mitochondria-centered metabolome revealed clinically significant alterations in central carbon metabolism in IBM with major differences between males and females.
≻ Oikawa et al., 2020: Bioenergetic analysis of sIBM patient myoblasts revealed impaired mitochondrial function.
≻≻ Decreased ATP production, reduced mitochondrial size and reduced mitochondrial dynamics were also observed in sIBM myoblasts.
≻≻ Cell vulnerability to oxidative stress also suggested the existence of mitochondrial dysfunction.
≻≻ Mitochonic acid-5 (MA-5) increased the cellular ATP level, reduced mitochondrial ROS, and provided protection against sIBM myoblast death.
≻ Oldfors et al., 1995: In this study enzyme histochemical analysis showed that cytochrome c oxidase (COX)-deficient muscle fibers were present at a frequency ranging from 0.5 to 5% of the muscle fibers in a series of 20 IBM patients.
≻≻ In age-matched controls, only occasional COX-deficient muscle fibers were present.
≻≻ Polymerase chain reaction (PCR) analysis of DNA extracted from muscle tissue of the IBM patients showed multiple mtDNA deletions.
≻≻ PCR analysis of isolated, single muscle fibers showed presence of mtDNA with only one type of deletion and deficiency of wild-type mtDNA in each COX-deficient muscle fiber.
≻≻ This finding was supported by results from in situ hybridization using different mtDNA probes on consecutive sections.
≻≻ A 5 kb deletion was identified in all 20 IBM patients.
≻≻ DNA sequencing of the breakpoint region showed that this deletion was the so-called “common deletion.”
≻≻ Most but not all of the investigated deletion breakpoints were flanked by direct repeats.
≻≻ COX-deficient fibers were more frequent among fibers with positive immunostaining with antibodies directed toward a regeneration marker, the Leu-19 antigen, than in the entire fiber population.
≻≻ These results show that COX deficiency in muscle fiber segments in IBM is associated with deletions of mtDNA.
≻≻ Clonal expansion of mtDNA with deletions may take place in regenerating muscle fibers following segmental necrosis.
≻ Oldfors et al., 2006: Mitochondrial changes are frequently encountered in sporadic inclusion-body myositis (s-IBM).
≻≻ Cytochrome c oxidase (COX)-deficient muscle fibers and large-scale mitochondrial DNA (mtDNA) deletions are more frequent in s-IBM than in age-matched controls.
≻≻ COX deficient muscle fibers are due to clonal expansion of mtDNA deletions and point mutations in segments of muscle fibers.
≻≻ Such segments range from 75 um to more than 1,000 um in length.
≻≻ Clonal expansion of the 4977 bp “common deletion” is a frequent cause of COX deficient muscle fiber segments, but many other deletions also occur.
≻≻ The deletion breakpoints cluster in a few regions that are similar to what is found in human mtDNA deletions in general.
≻≻ Analysis in s-IBM patients of three nuclear genes associated with multiple mtDNA deletions, POLG1, ANT1 and C10orf2, failed to demonstrate any mutations.
≻≻ In s-IBM patients with high number of COX-deficient fibers, the impaired mitochondrial function probably contribute to muscle weakness and wasting.
≻≻ Treatment that has positive effects in mitochondrial myopathies may be tried also in s-IBM.
≻ Rygiel et al., 2015: Our findings suggest that mitochondrial dysfunction has a role in sIBM progression.
≻≻ A strong correlation between the severity of inflammation, degree of mitochondrial changes and atrophy implicated existence of a mechanistic link between these three parameters.
≻≻ We propose a role for inflammatory cells in the initiation of mitochondrial DNA damage, which when accumulated, causes respiratory dysfunction, fibre atrophy and ultimately degeneration of muscle fibres.
≻ Mitochondria (singular, a mitochondrion) are structures (a type of organelle) found inside most cells.
≻ The highest numbers of mitochondria are present in organs demanding the most energy: the brain, liver and muscles.
≻ They are encased by a double wall (membrane) making them an independent structure within the cytoplasm of the cell.
≻ Although it is commonly said that the function of mitochondria are energy production, in reality, they serve many other functions.
≻≻ 1. ATP Production (Energy Generation).
≻≻≻ Mitochondria generate adenosine triphosphate (ATP)
≻≻≻ This is the primary energy source for most cellular processes.
≻≻ 2. Regulation of Cellular Metabolism.
≻≻ 3. Heat Production.
≻≻ 4. Apoptosis (Programmed Cell Death).
≻≻≻ Mitochondria control apoptotic pathways.
≻≻≻ This is vital for removing damaged or unwanted cells.
≻≻ 5. Mitochondria help regulate calcium.
≻≻≻ Cellular signaling
≻≻≻ Muscle contraction
≻≻≻ Neurotransmitter release
≻≻≻ Metabolic enzyme activity
≻≻ 6. Reactive Oxygen Species (ROS) Production & Detoxification.
≻≻≻ The electron transport chain of mitochondria produces ROS as byproducts.
≻≻≻ Mitochondria contain antioxidant enzymes to neutralize excess ROS and prevent oxidative damage.
≻≻ 7. Mitochondrial DNA and Protein Synthesis.
≻≻≻ Mitochondria have their own DNA (mtDNA) and ribosomes.
≻≻≻ They produce some of their own proteins essential for oxidative phosphorylation.
≻≻ 8. Mitochondria participate in various signaling pathways, influencing:
≻≻≻ Cell growth and differentiation
≻≻≻ Inflammation
≻≻≻ Stress responses
≻ Recent research demonstrates mitochondria can move from cell to cell. See Conroy, (2025).
⚄ 6.3.1.3.1 Structure: There are five distinct parts to a mitochondrion:
≻≻ 1. The outer mitochondrial membrane,
≻≻ 2. The intermembrane space (between the two membranes),
≻≻ 3. The inner mitochondrial membrane,
≻≻ 4. The cristae space (formed by foldings of the inner membrane), and
≻≻ 5. The matrix (space within the inner membrane), which is a fluid.
https://www.britannica.com/science/mitochondrion#/media/1/386130/17869
⚄ 6.3.1.3.2 Mitochondria are dynamic: they constantly change their structure, shape, and distribution within the cell in response to cellular needs and environmental conditions.
≻ Mitochondria undergo continuous fusion, fission, movement, and remodeling.
≻ This dynamic behavior is essential for their roles in energy production, cellular stress response, and cell signaling.
≻ Mitochondrial Fusion is when two mitochondria combine, forming a single, larger mitochondrion.
≻≻ Fusion allows mitochondria to mix their contents, which helps dilute any damaged components and optimize function.
≻≻ It also supports mitochondrial DNA (mtDNA) repair, as the sharing of mtDNA and proteins can maintain mitochondrial quality.
≻ Fission is the division of a single mitochondrion into two smaller mitochondria.
≻≻ This process is important for mitochondrial distribution across the cell, especially to regions with high energy demands.
≻≻ Fission also facilitates the removal of damaged mitochondria through mitophagy, a quality control process where dysfunctional mitochondria are degraded.
≻ The balance of fusion and fission helps the cell adapt to changing conditions.
≻≻ In low-energy situations, mitochondria may undergo fusion to maintain energy production efficiency, while in times of stress, increased fission can help isolate damaged mitochondria for degradation.
≻ Mitochondria can move around in the cell to reach areas where energy demand is highest, such as synapses in neurons or areas of active cell division.
≻≻ This mobility is crucial for maintaining cellular functions in specialized cells, like neurons and muscle cells, which have widely distributed regions with varying energy needs.
≻ Remodeling: mitochondria adapt to cellular signals that reflect the cell’s metabolic state, stress levels, or growth signals.
≻≻ For example: Increased energy demands (e.g., during exercise) prompt mitochondria to increase ATP production, expand in size, and change in number.
≻≻ Stress signals (e.g., oxidative stress or nutrient deprivation) can trigger mitochondrial fission and mitophagy to remove damaged mitochondria and minimize cellular damage.
≻ Mitochondria can increase in number (mitochondrial biogenesis) in response to high energy demands or specific signals (e.g., exercise, caloric restriction).
≻≻ This ability to multiply allows cells to adjust ATP production as needed.
⚄ 6.3.1.3.3 DNA: Mitochondria and have their own DNA (mitochondrial DNA – mtDNA – the “mitogenome”).
≻ The cell nucleus also contains some genes encoding for about 1200 proteins involved in mitochondrial structure, membrane, and the repair of mitochondrial DNA (mtDNA).
≻ mtDNA is transcribed and replicated differently than the DNA found in the nucleus – nDNA.
≻ nDNA is inherited from both mother and father – mtDNA and All of a person’s mitochondria are only inherited from the mother [During fertilization, sperm mitochondria are typically destroyed].
≻ Having their own DNA allows mitochondria to reproduce independently within the cell and produce some of their own proteins.
≻ Human mtDNA has a tiny amount of DNA – 37 genes (16,569 base pairs): 13 genes for proteins involved in the electron transport chain and ATP production, 22 for transfer RNAs (tRNAs), and 2 for ribosomal RNAs (rRNAs).
≻ Each mitochondrion can contain multiple copies of its DNA, and a typical human cell has from hundreds to thousands of mitochondria each containing from 1 to 15 molecules of mtDNA.
≻≻ So if you have 1,000 mitochondria in a cell, and each has 10 copies of mtDNA, that’s about 10,000 total mtDNA molecules per cell.
≻≻ This means there can be thousands of copies of mtDNA within a single cell.
≻ mtDNA evolves from 10 to 20 times faster than nDNA and has a less efficient damage repair system compared to nDNA.
≻≻ This makes the probability of mutation much higher in mitochondrial DNA.
≻≻ Mitochondrial disease (MD) is associated with a certain threshold of mutations in the mtDNA.
≻≻ Common mitochondrial diseases occur in the brain, skeletal muscle, heart, and eye and can occur at any age.
≻≻ Effective treatment of these diseases is challenging because of the number and variety of mutations involved.
≻≻ In practice, treatment is focused on relieving symptoms.
≻≻ Damaged mitochondria can release fragments of mitochondrial DNA (mtDNA) into the cell or into the bloodstream.
≻≻ These mtDNA fragments trigger immune responses.
⚄ 6.3.1.3.4 The endoplasmic reticulum (ER): The endoplasmic reticulum (ER) is a part of a transportation system of the cell, and has many important functions such as protein production and folding.
≻ It is a type of organelle made up of two subunits – the rough endoplasmic reticulum (RER), and smooth endoplasmic reticulum (SER).
≻ The rough endoplasmic reticulum is dotted with ribosomes, which are tiny, spherical organelles responsible for protein synthesis.
⚄ 6.3.1.3.5 Central Carbon Metabolism:
≻ This term refers to a complex network of enzymatic pathways that convert carbon-containing molecules, such as sugars and other organic compounds, into energy and precursor molecules necessary for cell growth, proliferation, and survival.
≻ Central carbon metabolism ensures that cells can efficiently use carbon sources to meet their energy and growth requirements.
≻ Several key components of central carbon metabolism take place in mitochondria where various chemical pathways produce energy necessary for cellular function.
≻ Central carbon metabolism encompasses glycolysis, the Krebs cycle (the TCA cycle), the pentose phosphate pathway (PPP), and the electron transport chain.
≻ Conventionally, the most important role for mitochondria has been seen as the generation of most of the energy needed to power the cell’s biochemical reactions.
⚄ 6.3.1.3.6 Tricarboxylic acid cycle (TAC): It is important for us to understand the vital role of mitochondria in producing energy.
ABNORMALITIES IN THIS SERIES OF CHEMICAL STEPS HAVE BEEN FOUND IN IBM.
≻ Cellular respiration is a multi-step chemical process taking place in the mitochondria through which cells transform food – carbohydrates [sugars], fats, amino acids, and oxygen – into chemical energy that cells can utilize.
≻ The process produces waste products – carbon dioxide and water, which the body gets rid of when we exhale and urinate.
≻≻ This is called aerobic respiration: glucose + oxygen → carbon dioxide + water.
≻ The energy produced is stored in a small chemical called adenosine triphosphate (ATP).
≻ START: Glycolysis is the first step in central carbon metabolism, breaking down glucose into pyruvate.
≻≻ This pyruvate is transported into the mitochondria, where it is converted into acetyl-CoA (acetyl coenzyme A), the starting molecule for the Krebs cycle.
≻≻ Step 1. In the first step of the citric acid cycle, acetyl-CoA joins with a four-carbon molecule, oxaloacetate, releasing the CoA group and forming a six-carbon molecule called citrate.
≻≻ Step 2. In the second step, citrate is converted into its isomer, isocitrate. This is actually a two-step process, involving first the removal and then the addition of a water molecule, which is why the citric acid cycle is sometimes described as having nine steps – rather than the eight listed here.
≻≻
Step 3. In the third step, isocitrate is oxidized and releases a molecule of carbon dioxide, leaving behind a five-carbon molecule – α-ketoglutarate. During this step, NAD+ is reduced to form NADH. The enzyme catalyzing this step, isocitrate dehydrogenase, is important in regulating the speed of the citric acid cycle. NADH is an important carrier of electrons.
≻≻ Step 4. The fourth step is similar to the third. In this case, it’s α-ketoglutarate that’ oxidized, reducing NAD+ to NADH and releasing a molecule of carbon dioxide in the process. The remaining four-carbon molecule picks up Coenzyme A, forming the unstable compound succinyl CoA. The enzyme catalyzing this step, α-ketoglutarate dehydrogenase, is also important in regulation of the citric acid cycle.
≻≻ Step 5. In step five, the CoA of succinyl CoA is replaced by a phosphate group, which is then transferred to ADP to make ATP. The four-carbon molecule produced in
this step is called succinate.
≻≻ Step 6. In step six, succinate is oxidized, forming another four-carbon molecule called fumarate. In this reaction, two hydrogen atoms – with their electrons – are transferred to FAD, producing FADH₂. The enzyme that carries out this step is embedded in the inner membrane of the mitochondrion, so FADH₂ can transfer its electrons directly into the electron transport chain.
≻≻ Step 7. In step seven, water is added to the four-carbon molecule fumarate, converting it into another four-carbon molecule called malate.
≻≻ Step 8. In the last step of the citric acid cycle, oxaloacetate – the starting four-carbon compound – is regenerated by oxidation of malate. Another molecule of NAD+ is reduced to NADH in the process. (Khan Academy)
⚄ 6.3.1.3.7 The pentose phosphate pathway (PPP): An anabolic pathway, responsible for generating ribose 5-phosphate and nicotinamide adenine dinucleotide phosphate (NADPH).
≻ The pentose phosphate pathway takes place in the liquid cytoplasm of the cell and produces NADPH.
≻ NADPH is involved in protecting the cell against the toxicity of reactive oxygen species (ROS) among other important roles.
≻ The PPP and the Krebs cycle work together to manage carbon flow, energy production, and biosynthetic needs.
≻ Ribose 5-phosphate is a precursor in the synthesis of nucleotides.
⚄ 6.3.1.3.8 The electron transport chain (ETC): The ETC works hand in hand with the TAC to produce energy.
≻ The ETC is made up of four protein complexes and is located in the inner mitochondrial membrane.
≻ For each turn of the TAC cycle, three molecules of NADH and one molecule of FADH₂ are produced.
≻≻ These molecules carry high-energy electrons that are transferred to the ETC.
≻≻ The transfer of electrons creates a force that powers ATP synthase to produce ATP.
≻≻ This process known as oxidative phosphorylation.
≻≻ The majority of ATP comes from oxidative phosphorylation powered by the ETC.
≻≻ The ETC also regenerates the oxidized carriers needed to sustain the TCA cycle.
⚄ 6.3.1.3.9 Mitochondrial Functions:
≻ As outlined above, in addition to supplying the cell’s energy, mitochondria are involved in other important tasks:
≻ Signalling: Mitochondria play a key role in sending signals throughout the cell that act to protect both the mitochondria and the cell.
≻≻ Stressed mitochondria transport signalling molecules to the nucleus of the cell, where they trigger an adaptive cellular response.
≻≻ Mitochondria also communicate information beyond the cell membrane to coordinate functions across various other cells, tissues and organs.
≻ Integration: Mitochondria integrate various metabolic pathways, including glycolysis, the TCA cycle, oxidative phosphorylation, and fatty acid oxidation.
≻ Creating steroid hormones: Mitochondria are the source of all steroid hormones, including the testosterone, progesterone and estrogens, as well as the stress-induced glucocorticoids that function as endocrine signals to promote stress adaptation.
≻ Stress regulation: Mitochondria are the TARGET of (and are damaged by) chronic psychological stress.
≻≻ Mitochondria also REGULATE physiology and behavior in response to psychological stress.
≻≻ Mitochondrial disruptions can impact physiological, metabolic, and transcriptional responses to psychological stress.
≻ Neuroplasticity and mental health: Mitochondrial dysfunctions cause impaired neuronal metabolism and can lead to disturbances in neuronal function, neuroplasticity, and brain circuitry.
≻≻ Mitochondria play a role in regulation of neurotransmitters.
≻≻ Studies support the role of impaired mitochondrial functions in many psychiatric and neurodegenerative diseases, including bipolar disorder, major depressive disorder, schizophrenia, psychosis and anxiety.
≻≻ Mitochondria are involved in neuronal development – synaptogenesis, synaptic development and plasticity.
≻≻ Impaired function of mitochondria leads to impaired bioenergetics, decrease of ATP production, impaired calcium homeostasis, increased production of free radicals and oxidative stress.
≻≻ Monoamine oxidase (MAO), the enzyme responsible for the metabolism of monoamine neurotransmitters, is found bound to the outer mitochondrial membrane.
≻≻ MAOs are involved in a number of psychiatric and neurological diseases, (e.g., depression) some of which can be treated with monoamine oxidase inhibitors (MAOIs) which block the action of MAOs.
≻ Regulating Cellular Metabolism: Mitochondria help control the metabolic pathways that produce or break down various biomolecules.
≻ Calcium Storage: They help regulate intracellular calcium levels, which is important for signaling processes and muscle contractions.
≻ Apoptosis (Programmed Cell Death): Mitochondria release certain proteins that can trigger apoptosis, which is a crucial process for maintaining cellular health and development.
≻ Heat Production: In some specialized cells, mitochondria can generate heat (a process known as thermogenesis) to help maintain body temperature.
⚄ 6.3.1.3.10 Mitophagy: A process that removes and recycles worn out or damaged mitochondria and regulates the creation of new, healthy ones, preserving healthy mitochondrial functions and activities.
≻≻ Mitophagy is a vital process for cellular function, and its regulation is complex and tightly controlled.
≻≻ If mitophagy does not remove defective mitochondria, they can promote inflammatory signals, which can influence systemic inflammation and contribute to diseases like type 2 diabetes, neurodegenerative diseases, and cardiovascular disorders.
⚄ 6.3.1.3.11 Inflammasome:The inflammasome is part of the innate immune system, responsible for triggering inflammatory responses and cell death.
≻≻ NLRP3 is a protein encoded by the NLRP3 gene and is a part of the inflammasome. It detects damaged cells and activates an immune response.
⚄ 6.3.1.3.12 Reactive oxygen species (ROS): ROS are continually being generated as byproducts of cellular metabolism.
≻ They play key roles in normal in cellular signaling and control several biological processes such as inflammation, proliferation, and cell death.
≻ A total of 2-3% of electrons of the electron transport chain (ETC) in mitochondria “leak.”
≻≻ Oxygen binds to the electrons and makes superoxide (an ROS) inside mitochondria.
≻≻ Superoxide then produces many other ROS and causes cell death.
≻≻ Thus, mitochondria are the most significant source of ROS production in cells.
≻ There is a delicate balance between the levels of normal ROS production and antioxidant defenses.
≻≻ Healthy cells maintain this balance and the ROS do not cause problems.
≻≻ There is growing evidence that stressed mitochondria release ROS in an effort to return to normal.
≻ This results in altered gene expression in the cell through a variety of signaling pathways.
≻≻ In particular, redox-activated proteins appear to be involved in this communication.
≻≻ All proteins supporting antioxidant reactions are encoded in the nucleus, not in the mitochondria.
≻≻ So, the communication between mitochondria and the nucleus of the cell is vital.
≻ Inflammatory mediators are significant inducers of RS production and are implicated in both the initiation and progression of OS. In turn, ROS serves in mediating immune responses.
≻≻ Most of the ROS generated during inflammation are extremely toxic and they may result in significant damage to cells by altering protein functions or generating secondary species like lipid peroxidation and glucose oxidation products.
≻ In a chronic inflammatory state, excess ROS not only results in the assembly and activation of the NLRP3 inflammasomes but will also block the process of mitophagy (Khelfi, 2024)
≻≻ Therefore, the damaged mitochondria will persist, producing more ROS, and continuing the activation of more inflammasomes. Cells containing these altered mitochondria may undergo apoptosis [cell death], which is dependent on ROS as well.
≻≻ The correlation between chronic inflammation and OS has already been confirmed in several studies and research focuses on the use of antioxidants as treatment basis for these diseases.
≻≻ See: Naddaf, Nguyen et al., 2025 below.
Khelfi, 2024.
⚄ 6.3.1.3.13 Other sources of ROS:
⚄ 6.3.1.3.14 Oxidative stress (OS): Oxidative stress occurs when there is an imbalance between the production of ROS and the cell’s ability to neutralize or detoxify the ROS with antioxidants.
≻ This imbalance causes excessive ROS levels, which can damage cellular components such as DNA, proteins, lipids, and can lead to oxidative stress and mitochondrial disfunction.
⚄ 6.3.1.3.15 The cellular stress response (“cellular stress”): Describes various molecular changes that cells experience when subjected to stressors like extreme temperatures, some viral infections, toxins, and mechanical injury.
≻ Abnormal proteins (misfolded or clumped together) can create ER stress (and thus cellular stress) leading to the UPR.
≻ Abnormal proteins can also trigger oxidative stress.
⚄ 6.3.1.3.16 The unfolded protein response (UPR): The UPR is a cellular stress response related to the endoplasmic reticulum that is activated in response to an accumulation of unfolded or misfolded proteins in the endoplasmic reticulum.
≻ Abad, C., Pinal-Fernandez, I., Guillou, C., Bourdenet, G., Drouot, L., Cosette, P., Giannini, M., Debrut, L., Jean, L., Bernard, S., Genty, D., Zoubairi, R., Remy-Jouet, I., Geny, B., Boitard, C., Mammen, A., Meyer, A., & Boyer, O. (2024). IFNλ causes mitochondrial dysfunction and oxidative stress in myositis. Nature Communications, 15(1), 5403. https://doi.org/10.1038/s41467-024-49460-1
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⚃ PM-Mito [appears to be] an IBM precursor (early IBM) within the IBM spectrum.
⚃ Both PM-Mito and IBM show mitochondrial abnormalities, suggesting mitochondrial disturbance is a critical element of IBM pathogenesis.
⚃ We found widespread mitochondrial abnormalities in both PM-Mito and IBM, illustrated by elevated numbers of COX-negative and SDH-positive fibers and prominent ultrastructural abnormalities with disorganized and concentric cristae within enlarged and dysmorphic mitochondria.
⚃ MtDNA copy numbers were significantly reduced, and multiple large-scale mtDNA deletions were already evident in PM-Mito, compared to healthy age-matched controls, similar to the IBM group.
⚃ The activation of the canonical cGAS/STING inflammatory pathway, possibly triggered by the intracellular leakage of mitochondrial DNA, was evident in PM-Mito and IBM.
⚃ Elevated levels of circulating cfmtDNA also indicated leakage of mtDNA as a likely inflammatory trigger.
⚃ In PM-Mito and IBM, these findings were accompanied by dysregulation of proteins and transcripts linked to the mitochondrial membranes.
⚃ The activation of inflammatory pathways related to mtDNA release indicates a significant role of mitochondria-associated inflammation in the pathogenesis of IBM-SD.
⚃ Thus, mitochondrial abnormalities precede tissue remodeling and infiltration by specific T-cell subpopulations (e.g., KLRG1+) characteristic of late IBM.
⚃ [More than] 90% of patients diagnosed with PM-Mito developed IBM in their later course, which was confirmed by follow-up biopsies several years apart, and proposed to include PM-Mito as an early form of IBM (eIBM) within the spectrum of IBM (IBM spectrum disease, IBM-SD).
⚃ In the present study, we hypothesized that mitochondrial dysfunction is an early feature of IBM and might be mechanistically linked to the development of autoimmunity and inflammation.
⚃ We identified that mitochondrial dysfunction, including multiple mtDNA deletions and mtDNA depletion, along with disturbed mitochondrial ultrastructure and membrane defects, is an early feature of IBM.
⚃ Activation of inflammatory pathways related to mtDNA release highlights the significant role of mitochondria-associated inflammation in IBM pathogenesis, abnormalities precede tissue remodeling and T-cell infiltration.
⚃ Our study included skeletal muscle biopsy specimens from 27 patients with PM-Mito (22 female, five male) and 27 patients with typical IBM (13 female, 14 male)
⚃ In summary, ultrastructural abnormalities of mitochondria were detected throughout all stages of the disease, including cases showing very mild signs of inflammation.
⚃ However, giant mitochondria with densely packed cristae were more abundant in typical IBM cases.
⚃ The level of mtDNA showed a statistically significant reduction in PM-Mito (7.1 ± 0.91) and typical IBM patients (6.57 ± 0.88)
⚃ The mtDNA defect is maintained throughout all stages of the disease.
⚃ mtDNA deletions arise early in the pathophysiology of the disease.
⚃ 11/33 downregulated proteins were linked to mitochondrial function, including complexes I and III of the respiratory chain, and two out of the ten most downregulated proteins were related to the inner mitochondrial membrane (SMDT1, TIMM21).
⚃ The most upregulated protein, with a 6.1-fold upregulation, was TMEM14C (Transmembrane protein 14C), a protein located in the inner mitochondrial membrane and involved in various mitochondrial processes, including heme biosynthesis.
⚃ IBM samples showed more circulating cfDNA than controls, doubling the circulating mtDNA levels (Fig. 6C).
⚃ This indicated that mtDNA release from the mitochondria is prominent in IBM and may be a potential inflammatory trigger.
⚃ The extent of mitochondrial damage did not correlate with the amount of inflammation, suggesting no causative effect [In other words, inflammation does not cause the mitochondrial damage].
⚃ ultrastructural abnormalities [seen] also included disturbed cristae architecture and discontinuity of the mitochondrial membranes, possibly allowing a leakage of mitochondrial content into the sarcoplasm.
⚃ We also detected the activation of the canonical cGAS/STING pathway throughout all stages of IBM-SD (i.e, in both PM-Mito and IBM), highlighting that the intracellular release of mitochondrial DNA, followed by activation of the innate immune response further contributes to the pathomechanism.
⚃ The role of mitochondria in the pathogenesis of IBM is undoubtedly both significant and complex.
⚃ IBM muscle is characterized by large-scale deletions in the major arc of mtDNA molecules and lower mtDNA copy numbers than healthy subjects of similar age groups.
⚃ It has been previously shown that the morphology of mitochondria in IBM myofibers is altered, with features such as shortened and enlarged cristae, membrane disruption, and a reduced mitochondrial length-to-width ratio.
⚃ We observed giant mitochondria with highly abnormal cristae, which were almost exclusively detected in IBM, but not in PM-Mito, suggesting that these ultrastructural abnormalities develop at a later stage.
⚃ Another relevant ultrastructural feature observed in this study was the disruption of mitochondrial membranes and leakage of mitochondrial content into the sarcoplasm.
⚃ The release of mtDNA and mitochondrial content into the cytosol has been described to act as mitochondrial-derived damage-associated molecular pattern (DAMP), triggering inflammatory cascades such as the cGAS/STING pathway. [activation of the canonical cGAS/STING pathway has been linked to T-cell infiltration, and emerging research suggests it may influence the composition of T-cell subpopulations, including cells expressing KLRG1]
⚃ Our data indicate that these immune phenomena might be secondary to mitochondrial dysfunction and associated inflammation in the IBM cascade.
⚃ This, in turn, could suggest that IBM can be viewed as a primarily degenerative disease with peculiar (auto-)inflammatory features.
⚃ Indeed, recently published data from mouse xenograft models pointed towards IBM being a primarily degenerative disease of skeletal muscle, in which inflammation may be a bystander or a secondary phenomenon.
⚃ However, the initial triggers of mitochondrial dysfunction in IBM remain unclear.
⚃ The reduced mtDNA copy numbers point towards an mtDNA maintenance defect.
⚃ We hypothesize that the multiple mtDNA deletions and depletion may be related to the severe abnormalities of mitochondrial cristae, where mtDNA replication occurs.
⚃ Another interesting hypothesis, derived from studies performed in the context of amyotrophic lateral sclerosis (ALS), links mitochondrial damage and the release of mtDNA to the deposition of TDP-43 in the cytosol and in mitochondria.
⚃ Indeed, TDP-43 mislocalization and sarcoplasmic deposition are characteristic, but not specific, features observed in IBM muscle.
⚃ Others and we recently demonstrated the presence of TDP-43-associated cryptic exons in IBM muscle, 2,47 pointing towards a functional impact of TDP-43 pathology.
⚃ However, we showed that the quantity of cryptic exon inclusion was relatively low in PM-Mito compared to typical IBM muscle.
⚃ This argues against a functional link between early mitochondrial dysfunction and TDP-43 deposition.
⚃ the data reported here again illustrate the considerable molecular overlap between PM-Mito and IBM, underlining the importance of considering IBM as a disease spectrum with early and late stages.
⚃ our data indicate that inflammation does not trigger mitochondrial dysfunction in a time-dependent manner but points towards mitochondrial dysfunction being an early event in disease pathogenesis.