3.1. Protein aggregation
Protein aggregation represents the main degenerative feature of sIBM. Protein misfolding/unfolding was initially discovered with the detection of cytoplasmic congophilic deposits indicating the presence of amyloid inclusions [
44]. This observation was followed by the identification of Aβ protein, tau, and ubiquitin in the aggregates [
45,
46,
47,
48,
49]. Aβ peptides, mainly Aβ40 and Abβ42, are produced from AβPP through sequential proteolytic cleavage by the β-secretases β-site of the APP cleaving enzyme 1 and 2 (BACE1 and BACE2) and the γ-secretase complex [
50]. It has been shown that among the different forms of Aβ proteins, the more cytotoxic Aβ42 is predominantly aggregated in sIBM muscle fibers and occurs in the form of oligomers [
51]. Increased plasma Aβ42 was also reported in patients with sIBM [
52]. Moreover, the proteases involved in AβPP processing were found to be significantly increased and/or accumulated in sIBM [
49,
51,
53,
54,
55]. Phosphorylated tau has also been detected in cytoplasmic aggregates where it was found to colocalize with kinases involved in its phosphorylation such as extracellular signal-regulated kinase (ERK), cyclin-dependent kinase 5 (CDK5), glycogen synthase kinase 3β (GSK-3β), and casein kinase 1 [
56,
57,
58,
59,
60,
61].
The detection of Aβ and p-tau have initially received a lot of attention due to their already known involvement in Alzheimer’s disease. Nevertheless, over decades, several other proteins have been found as abnormally accumulated in the cytoplasm of sIBM muscle fibers in the form of aggregates/inclusions, and many of them are linked to different neurodegenerative disorders. These include proteins prone to unfold/misfold such as α-synuclein, presenilin 1, and prion, proteins involved in endoplasmic reticulum (ER) stress (GRP78 and GRP94) and oxidative/nitrative stress (nitrotyrosine, NOS and SOD1), protein-folding homeostasis (heath shock proteins, 26S proteasome components, ubiquitin, p62/ SQSTM1), and RNA metabolism (RNA polymerase II, FUS, TDP-43, VCP, c-Jun, NFkB hnRNPA1, hnRNPA2/B1, hnRNPC1/C2 and hnRNPH) [
8,
62,
63,
64].
Even though the list of proteins that are abnormally accumulated in sIBM aggregates has been growing over the years, the pathogenic events that drive the abnormal cytoplasmic localization and aggregation of these proteins as well as their relationship with the immune component of sIBM still remain unknown. A combination of processes likely contributes to the protein aggregation: these include increased protein translation and specific posttranslational modification, impaired protein disposal via ubiquitin proteasome system (UPS) and autophagy pathway, and altered cellular environment due, for example, to oxidative stress and aged milieu that promote damage and misfolding/unfolding of proteins and interfere with protein quality control systems [
40].
3.2. Impairment of ubiquitin proteasome system (UPS) and autophagy
In the cell, several events can trigger protein misfolding such as protein mutation, harsh cellular environment and metabolic stress [
65,
66]. Misfolded proteins can have deleterious consequences for the cells due to the loss of specific function/s or the acquisition of toxic activities and the tendency to form insoluble aggregates [
65,
66]. Cells are equipped with protein quality control mechanisms that aim to maintain protein homeostasis (or proteostasis) by refolding, degrading, or segregating misfolded proteins [
65,
66]. Molecular chaperons constitute a group of proteins that bind to unstructured proteins including nascent polypeptides on ribosomes and abnormally exposed hydrophobic regions, to prevent protein misfolding and facilitated the acquisition of correct protein conformation [
67]. A few studies are reported in the literature that suggest a possible alteration of molecular chaperones in sIBM [
68,
69]. HSP70 immunopositive inclusions have been observed in sIBM muscle [
68]. Specifically, HSP70 immunoreactivity was found to colocalized with Aβ and p-tau signal mostly in vacuolated muscle fibers. It has also been found that HSP70 protein is upregulated in sIBM muscles and co-immunoprecipitates with Aβ [
68]. This observation has been interpreted as a possible role of HSP70 in Aβ folding, although it cannot be excluded that this interaction is the result of unspecific binding due to protein unfolding/misfolding. αB-crystallin (αBC), a member of the small heat shock protein family, has also be found accumulated in sIBM muscle fibers and in other muscle diseases [
69,
70]. Evidence for the association between αBC with AβPP and Aβ oligomers have been shown both in sIBM muscle and in AβPP-overexpressing cultured human muscle fibers. It has been proposed that the binding of αBC to Aβ oligomers might hinder the segregation Aβ oligomers into non-toxic aggregates and, therefore, prolong their toxic effects [
68,
70].
Failure of molecular chaperones to assist protein folding results in the presence of unfolded/misfolded proteins in the cell that can have toxic and harmful effects. In addition, other types of protein damages resulting, for example, by oxidation, accumulation of proteins in insoluble aggregates can be cytotoxic. Therefore, unfolded/misfolded, damaged, and aggregated proteins need to be eliminated to avoid, or minimize, cellular toxicity. Two major systems are responsible for protein degradation, namely the ubiquitin proteasome system (UPS) and the autophagy pathway. Alterations in both processes have been described in sIBM and considered important players in pathogenesis of the disease [
40].
The UPS consists of multiple components that act synergistically to remove aberrant proteins [
71]. E1 ubiquitin-activating enzyme, E2 ubiquitin-conjugating enzymes, and E3 ubiquitin-protein ligases act sequentially to tag proteins that need to be eliminated with multi-ubiquitin chains [
71]. Shuttle factors are then responsible for the delivery of ubiquitinated proteins to the 26S proteasome, the molecular machine responsible for the degradation [
71]. The 26S proteasome is multiprotein complex composed of a 20S catalytic subunit and one or two 19S regulatory subunits [
71]. The regulatory complex unfolds the ubiquitin-conjugated proteins so that they can enter the 20S core where they are subjected to different proteolytic activities of various subunits of the 20S core [
71]. Abnormalities in the UPS in sIBM is supported by the increased expression and accumulation of 26S proteasome subunits and decreased activity of proteasomal proteolytic enzymes [
72,
73]. The impairment of the UPS is also supported by the observation that multiprotein aggregates in sIBM have features of aggresome, an extreme form of protein aggregates [
74]. Aggresome formation is a protective mechanism activated under chronic UPS inhibition that aims to sequester misfolded proteins to prevent their possible toxic effects and eliminate them through autophagy [
67].
Autophagy is an intracellular catabolic pathway through which components that cannot be degraded by the UPS, such as part of the cytoplasm, protein aggregates, malfunctioning organelles, or invading pathogens, are eliminated and recycled by the cell [
75]. These components are first segregated in double lipid bilayer structures known as autophagosomes and then delivered to lysosomes to be degraded by lysosomal hydrolases into macromolecules such as aminoacidic, nucleotides, and sugars that can be reused by the cell [
75]. Autophagy allows the elimination of damaged components and the maintenance of the proper number of functional organelles. Furthermore, the cell can exploit autophagy to self-digest some of its structure to survive under conditions of low nutrient and stress [
75]. Several studies have provided evidence that impairment of autophagy contributes to the accumulation of proteins in the form of aggregates in muscle fibers of patients with sIBM. A histological hallmark of sIBM is the presence of cytoplasmic vacuoles. The autophagic nature of these vacuoles is supported by their positivity for acid phosphatase and other lysosomal enzyme as wells as by their content consisting of membranous debris that could arise from remnants of impaired organelles [
76,
77]. The first indication of a possible involvement of autophagy in sIBM muscles came from the detection of increased mRNA or protein levels of some lysosome proteins including M6PR, clathrin and hApg5 and hApg12 in sIBM muscles [
77]. Later, Atg8/LC3 positive autophagic vacuoles containing AβPP and Aβ were detected in muscle fibers from sIBM patients [
78]. These AβPP/Aβ and Atg8/LC3 double-positive vacuoles were almost exclusively detected in degenerating muscle fibers and occurred in a subset of muscle fibers expressing major histocompatibility complex (MHC) class II and surrounded by CD4
+and CD8
+ T cells. This finding indicates a possible involvement of autophagy in generation of antigens for MHC presentation to invading T cells [
78]. Other factors involved in autophagy have been found to be altered in sIBM muscles. Increased transcript and protein levels of p62/SQSTM1, a factor involved in targeting ubiquitinated proteins for proteasomal and lysosomal degradation, were detected in sIBM muscle and found to colocalize with p-tau positive inclusions. Based on the increase of p62 that occurs following pharmacological inhibition of proteasomal or lysosomal protein degradation, it has been proposed that defective protein degradation through these two processes might participate in sIBM pathology [
79]. In support to this scenario, a decrease in the activity of the lysosomal enzymes cathepsin D and B was found in sIBM muscles [
76].
Micro-tubule-associated protein 1 light chain 3B (LC3) is detected, under normal conditions, in the cytoplasm as LC3I form. After induction of autophagy, LC3I is conjugated to phosphatidylethanolamine to generated LC3II which is relocated to autophagosomes and autolysosomes and is therefore considered a marker of autophagy [
80]. LC3II and a decreased ratio of phosophorylated p70S6 kinase to total p70S6 kinase were considered an indication of autophagy induction in sIBM muscles [
76]. According to this interpretation, the accumulation of LC3II and its binding partner p62 in sIBM muscle fibers could be the result of increased autophagosome formation [
81].
Like p62/SQSTM1, NBR1 is another carrier protein involved in the transport of ubiquitinated proteins for autophagic degradation. It has been found that NBR1 protein is increased and accumulated in sIBM muscle in aggregates immunopositive to p62, ubiquitin, and phosphorylated tau [
82].
Increased expression levels of the autophagy markers Beclin 1, ATG5 and LC3 and of the endosomal marker clathrin were detected in sIBM muscle and attributed to increased autophagosomal and endosomal structure due to increased autophagosome formation and/or to impaired late steps of the autophagy pathway [
83]. It has also been shown that Beclin 1 associates with p-tau in the sarcoplasm of s-IBM myofibers and that lymphocytes preferentially surround Beclin 1 fibers [
83].
An upregulation of components of the chaperone-mediated autophagy (CMA), a form of lysosomal pathway responsible for the degradation of proteins carrying the KFERQ motif, have been reported in sIBM muscle [
84]. Hsc70, involved in the recognition and binding of protein carrying the KFERQ motif, and LAMP2A, which binds Hsc70-chargo protein complex at the level of the lysosome, unfolds and transfers target proteins within the lysosome, are both increased in sIBM muscle [
84]. Interestingly, α-synuclein, which contains a KFERQ motif and is a CMA substrate, was found to be physically associated with LAMP2A and Hsc70 [
84]. These observations might indicate that CMA is induced in sIBM muscle to remove misfolded proteins and avoid the formation of insoluble protein aggregates. However, since these proteins are targeted to defective lysosomal structure, as suggested by the decreased lysosomal enzyme activity, they are not properly cleared but accumulated in aggregates [
84].
Overall, these studies support that impaired proteostasis occurs in sIBM and contributes to protein accumulation by reducing protein disposal and recycling.
3.3. Endoplasmic reticulum (ER) stress and Unfolded Protein Response (UPR)
The endoplasmic reticulum (ER) plays a critical role in the processing, folding, posttranslational modification, and exporting of newly synthesized proteins into the secretory pathway [
85,
86]. Under certain conditions, ER protein folding capacity become saturated and unfolded/misfolded proteins accumulate in the ER lumen compromising the ER homeostasis, a state referred as ER stress [
85,
86]. In attempt to cope with unfolded/misfolded protein loading, cell triggers a set of signaling pathways, collectively known as the unfolded protein response (UPR), that ultimately regulate gene expression to increase ER abundance and protein folding machinery and to repress protein synthesis [
85,
86]. UPR involves three major signaling pathways, each of which is activated by specific ER stress sensor proteins that reside in the ER membrane such as ATF6 (activating transcription factor 6), IRE1 (inositol requiring enzyme 1) and PERK (double-stranded RNA-activated protein kinases (PKR)-like ER kinase) [
85,
86]. An additional pathway to relieve ER stress is the ER-associated degradation (ERAD) by which unfolded/misfolded proteins undergo retrotranslocation into the cytosol to be degraded by UPS [
86].
ER stress, UPR activation, and ERAD induction have been documented in muscle fibers of sIBM patients highlighting the significant role of ER stress in the pathogenesis of sIBM. Increased expression of several ER chaperones including calnexin, calreticulin, BiP/GRP78, GRP94, and ERp72 have been found in muscle specimens of patients with sIBM [
87]. Furthermore, both in sIBM muscle and in the AβPP-overexpressing cultured human muscle fibers, those chaperones physically interact with Aβ suggesting their possible role in Aβ folding process and/or in Aβ protein clearance [
87]. The presence of the processed ATF6 N-terminal fragment, which mediates the upregulation of UPR target genes including BiP/GRP78, the production of the alternative spliced form of XBP1, which leads to the transcriptional activation of chaperones and folding proteins involved in ERAD, the increased expression of ATF4 protein, and the augmented levels of CHOP mRNA, which is regulated by the oligomerization of PERK and subsequent phosphorylation of the transcription factor eIF2α, were detected in muscle biopsies of sIBM patients, suggesting that all the three main UPR pathways are activated in sIBM [
88].
Many other proteins implicated in ER stress have also been found to be altered in sIBM muscle. Upregulation at mRNA and protein level of Herp (homocysteine-induced ER protein), an ER stress-inducible protein normally localized to the ER membrane, and its focal accumulation in the cytoplasm of affected fibers together with Aβ, the ER chaperone BiP/GRP78, and the 20S β2 proteasome subunit was detected in muscle of patients with sIBM [
89]. Furthermore, Herp was found to be overexpressed both at mRNA and protein level in ER stress-induced cultured human muscle fibers, where the protein presented a diffuse staining, and increased at protein level in proteasome-inhibited cultured human muscle fibers, where it forms cytoplasmic aggregates [
89]. These observations led the authors to speculate that the increased expression of HERP is induced in sIBM muscle fibers by both ER stress and proteasome inhibition to stimulate the ER folding capacity and misfolded protein removal [
89].
In cultured human muscle fiber ER stress has been demonstrated to regulate the expression of MstnPP (myostatin precursor protein) via the transcription factor NF-κB that become activated during UPR [
90]. In skeletal muscle MstnPP is posttranslationally processed primarily into myostatin (Mstn), a member of the transforming growth factor beta (TGF-β) superfamily that negatively regulates muscle development and growth. Increased expression of MstnPP, at both the mRNA and protein levels, was observed in muscle of patients with sIBM [
91,
92]. Myostatin dimer were detected in sIBM muscle and found to colocalize and physically interacts with Aβ/AβPP [
91,
92]. These findings led to the hypothesis that an aberrant aggregation of MstnPP/Mstn contribute to muscle fiber atrophy and weakness in patients with sIBM.
3.4. Mitochondrial abnormalities
Mitochondrial alterations have been widely described in muscle of patients with sIBM. These alterations include mitochondrial proliferation, COX-negative fibers, and mitochondrial DNA (mtDNA) changes, and occur with a greater extent and frequency in sIBM patients compared to healthy aged-matched controls [
93].
Mitochondria proliferation is detectable by the modified Gomori trichrome stain which highlights the accumulation of abnormal mitochondria (red stain) in the subsarcolemmal region of the muscle fibers that look overall irregular in shape and are, therefore, referred as “ragged red fibers” (RRFs). In patients with sIBM, RRFs represent 1% of the total fibers whereas in the elderly RRFs occur with a frequency of about 0.3% [
93]. Accumulations of mitochondria might represent a compensatory response to the impaired functionalities of these organelles. Increased percentage of COX negative fibers in sIBM patients compared to healthy aged-matched controls has been reported in several studies [
94,
95]. Reported frequencies of COX negative fibers ranges between 0.5% to 5% of total fibers in sIBM muscles whereas they are only occasionally observed in healthy subjects with similar age [
94]. Impaired oxidative phosphorylation (OXPHOS) has been further supported by biochemical studies that detected a 30% decreased in COX activity, confirming the COX deficit observed by histological analysis [
95].
An impairment of mitochondrial function has been detected also in primary myoblasts isolated from patients with sIBM. sIBM primary myoblasts displayed reduced oxygen consumption rate (OCR) and intracellular ATP, but increased extracellular acidification rate (ECAR), compared to normal myoblasts, indicating the activation of glycolysis to compensate for the reduced oxidative phosphorylation [
96].
Abnormalities in the expression of some of the mitochondrial respiratory complexes has been observed in sIBM muscles. A reduction in the protein levels of complex I, III, and, with more variability, complex IV, that are partly encoded by mtDNA, was documented in sIBM muscle supporting a functional alteration of the respiratory chain [
97].
Mitochondrial function is tightly linked to mitochondrial dynamics and morphology. Abnormalities in mitochondria structure have also been observed by ultrastructural analysis on sIBM muscles [
94,
96]. Structural alterations include mitochondria enlargement, loss of cristae, and paracrystalline inclusions [
94,
96]. Some of these structural abnormalities might results from disturbances of the mitochondrial dynamics occurring in sIBM muscle. Alteration of the expression of mitofusins (Mfn), which control fusion of the outer mitochondrial membrane, and of optic atrophy 1 (OPA1), which regulates fusion of the inner mitochondrial membrane, have been found in sIBM and contribute to the abnormalities of the mitochondrial network [
95]. A decrease in Opa1 and Drp1 mRNA levels were reported in sIBM patient myoblasts compared with normal control myoblasts, whereas the expression levels of mitofusin 1 (Mfn1) and mitofusin 2 (Mfn2) were found to be unchanged [
96]. Time-lapse imaging of mitochondria revealed a decreased mitochondrial mobility in primary myoblasts obtained from sIBM patients compared to myoblasts from healthy subjects [
96]. Alterations in mitochondrial biogenesis in sIBM is suggested by the altered expression of important regulators of this process [
93,
98]. The non-coding microRNAs (miRNAs) miR-133 is markedly reduced in sIBM whereas gene expression of peroxisome proliferator-activated receptor γ coactivator-1α (PGC-1α) is increased in sIBM compared to control muscles [
93,
98]. Interestingly, metabolomics studies performed on peripheral blood revealed that patients with sIBM share metabolic changes with subjects affected by primary mitochondrial myopathies [
99]. Notably, a greater degree of lymphocytic and macrophage infiltration has been observed in sIBM muscle fibers with more respiratory chain dysfunction. A strong positive correlation between the degree of inflammation, mitochondrial changes and atrophy has been found, suggesting that the mitochondrial dysfunctions have a role in sIBM progression [
100].
As part of mitochondrial pathology, a remarkable mtDNA depletion and the presence of mtDNA alterations have been found in sIBM [
42,
94,
96,
97,
101,
102]. mtDNA deletions have been detected in muscle from sIBM patients with different techniques [
94,
101]. PCR and Southern blot analysis detected the occurrence of multiple mtDNA deletions in muscle tissue of IBM patients [
94,
101]. In situ hybridization using different mtDNA probes revealed that deleted mtDNA accumulates in COX deficient muscle fibers in patients with sIBM [
94]. PCR analysis performed on isolated single muscle fibers have detected mtDNA with only one type of deletion in each COX-deficient muscle fiber, suggesting that clonal expansion of deleted mtDNA might occurs in each COX negative fiber [
101]. The 4977 bp “common deletion”, which deletes between nucleotides 8,470 and 13,447 of the human mtDNA, is frequently detected COX deficient fibers in sIBM muscles [
42,
101]. This mutation leads to the loss all or part of the genes encoding four subunits of complex I, one subunit of complex IV, two subunits of complex V and five tRNA genes and, as expected, has a major impact on mitochondrial functionality [
103].
Recently, deep sequencing of mtDNA by whole genome sequencing (WGS) has led to the identification of somatic mtDNA variants (deletions, duplications, and single nucleotide variants) [
97] An increase of all these mtDNA alterations has been found in sIBM muscle compared to age-matched controls [
97]. mtDNA copy numbers was also increased in muscle samples from sIBM patients, as reported in other studies [
96,
97]. Novel variants in nuclear genes involved in mtDNA maintenance have been found in sIBM. New variants of POLG and C10orf2 and a significantly higher frequency of an RRM2B variant were reported in IBM patients, suggesting that alterations in mechanisms involved in mtDNA maintenance might contribute to the disease [
41].
3.5. Oxidative stress
The possible causative role of oxidative and nitrative stress in sIBM pathogenesis was first proposed by Askanas and Engel [
104]. Nitric oxide (NO) is a short-lived free radical which plays a significant physiological role in different biological processes including vasodilation, antimicrobial activity of activated macrophages, transcriptional and post-transcriptional regulation of genes [
105]. NO generation is catalyzed by three distinct isoforms of nitric oxide synthase (NOS): endothelial (eNOS), neuronal (nNOS) and inducible (iNOS) [
106]. Nitric oxide (NO) can react with superoxide, a biologically relevant reactive oxygen species (ROS), to generate peroxynitrite, an highly reactive nitrogen species (RNS), which in turn leads to the conversion of tyrosine to 3-nitrotyrosine (3-NT), either free or part of a polypeptide chain [
105]. The nitration of tyrosine can compromise the functional and/or structural integrity of target proteins [
105]. The occurrence of nitrative stress in sIBM is supported by the abnormal accumulation of nitrotyrosine and of two NOS isoforms, nNOS and iNOS, in vacuolated fibers of sIBM muscle [
107].
Since superoxide can be toxic, mammalian cells contain an enzymatic protective system against ROS-mediated damage which mainly include manganese superoxide dismutase (MnSOD) and copper-zinc superoxide dismutase (CuZnSOD). MnSOD, located in the mitochondria, and CuZnSOD, located in the cytoplasm, are scavenging enzymes that transform superoxide anions into hydrogen peroxide [
108]. MnSOD and CuZnSOD were found to be increased and accumulated in vacuolated muscle fibers of patients with sBM but while MnSOD colocalized with nitrotyrosine and occasionally with p-tau, CuZnSOD was associated with ubiquitin suggesting that the two enzymes could have a different role in fiber protection [
109,
110]. It has been therefore hypothesized that while MnSOD exerts a protective effect in muscle fibers against the oxidative and nitrative stress, CuZnSOD participates in ubiquitination and clearance of inclusions in affected fibers [
109,
110]. Oxidative stress could also act as a key upstream trigger of AβPP overexpression in sIBM muscle through the upregulation of transcription factor NF-kB and redox factor-1 (Ref-1) [
107,
111].
Other factors that exert a protective function against the harmful effects of oxidative stress have been found in sIBM muscle. Increased mRNA and protein levels of insulin-like growth factor I (IGF-I), a pleiotropic growth factor with endocrine, paracrine and autocrine functions, and members of one of two main IGF-I signaling pathways, namely phosphoinositide-3-kinase (PI3K) and Akt, were detected in affected but not regenerating muscle fibers containing Aβ inclusions [
112]. Based on the upregulation of IGF-I mRNA and protein that occurs in primary muscle cultures treated with Aβ(25-35) peptide, it has been postulated that IGF-I overexpression represent a protective response in vulnerable fibers to Aβ toxicity and that oxidative stress could play an important role in leading to increased expression of IGF-I [
112]. DJ-1 is a small ubiquitously expressed protein that dimerizes under physiological conditions and plays several cellular functions including antioxidant response, chaperone activity, autophagy regulation, mitochondrial homeostasis, transcription regulation and neuroinflammation reduction [
113]. DJ-1 was reported to be increased at both mRNA and protein level and highly oxidized in muscle of patients with sIBM [
114]. It has also been shown that DJ protein forms cytoplasmic aggregates only in a small percentage of abnormal muscle fibers and is overexpressed as a 46 kDa dimer in addition to the 23 kDa monomer in the soluble fraction of sIBM muscle while the mitochondrial-enriched fraction contains only monomer. These observations have been interpreted as a possible role of DJ-1 in counteracting oxidative stress and mitochondria dysfunction in abnormal muscle fibers [
114].
It is conceivable that multiple mechanisms can lead to generation of ROS/RNS and oxidative/nitrative stress in sIBM, one potential explanation is that mitochondrial dysfunction documented in muscle of sIBM patients causes increased ROS production with consequent oxidative stress and cellular damage.