Abstract

   Multiple sclerosis (MS), the most prevalent myelinopathy with unclear
   etiology, involves mitochondrial dysfunction that critically
   contributes to oligodendrocyte damage and neurodegeneration. Recent
   interest has surged around the role of inflammatory non-coding RNAs
   (ncRNAs) in mitochondrial function, particularly in the context of
   neurodegenerative diseases (NDs), where neuroinflammation is a hallmark
   feature. This review highlights the collection and characterization of
   mitochondrial-related ncRNAs (MRncRNAs) that have been extensively
   studied in the context of NDs. Through a literature review, we
   identified 35 MRncRNAs (23 miRNAs, 8 LncRNAs, and 4 circRNAs) across
   Parkinson’s disease (PD), Amyotrophic Lateral Sclerosis (ALS),
   Alzheimer’s disease (AD), and Huntington’s disease (HD). Notably, the
   inflammatory miRNAs miR-34a and miR-146a were commonly dysregulated in
   both PD and AD, while in HD, only a single miRNA, miR-196a, was
   identified. As expected, due to the mitochondrial nature of PD, the
   majority of MRncRNAs (9 miRNAs, 8 lncRNAs, and 3 circRNAs) were
   associated with this disorder. Further bioinformatic analysis of
   MRmiRNAs revealed that miR-124-5p, -146a-3p, and -15b-3p target
   mitochondrial genes more than others, and mRNA of pro-apoptotic protein
   BCL2L11 is the most targeted. Notably, the link between these MRncRNAs
   and mitochondrial function in MS remains unidentified. By evaluating
   upregulated MS-related ncRNAs in patients and comparing them with
   identified MRncRNAs, we found nine overlapping miRNAs (miR-15b, miR-21,
   miR-27b, miR-34a, miR-124, miR-137, miR-146a, miR-155, and miR-92a) as
   well as two shared lncRNAs, MALAT1 and HOTAIR (called MS/MRncRNAs).
   Further bioinformatic analysis of MS/MRmiRNAs revealed that the
   autophagy pathway is the most involved. Six of these miRNAs are
   significantly involved in MR diseases. Notably, miR-34a-5p showed a
   connection to oligodendrocyte mitochondria, while miR-15b targeted two
   MR hub genes, SDHC and BCL2. Moreover, several hub proteins (HIF1A,
   STAT3, MAPK1, GSK3B) targeted by these miRNAs are well-known regulators
   of inflammatory pathways and mitochondrial homeostasis: These findings
   highlight the critical roles of ncRNAs in mitochondrial dysfunction and
   neurodegeneration, emphasizing the urgent need for experimental studies
   on MRmiRNAs, particularly in the context of MS and other
   myelinopathies.

Graphical Abstract

   [38]graphic file with name 13578_2025_1438_Figa_HTML.jpg

   Keywords: Epigenetic, Demyelination, Multiple sclerosis, Mitochondria,
   Neuroinflammation

Introduction

   Neurodegenerative diseases (NDs) involve the progressive deterioration
   of neurons and neural tissues, leading to a variety of mental and
   physical impairments [[39]13, [40]165]. While common mechanisms
   contribute to neuronal loss across different NDs, each disease's unique
   pathological profile is primarily driven by specific genetic mutations
   or the toxic aggregation of certain proteins [[41]165]. Multiple
   sclerosis (MS) is a complex disease with an unknown etiology,
   unpredictable progression, and limited treatment options. Unlike
   dysmyelinating disorders (which involve abnormal myelin formation due
   to genetic mutations), MS involves the active destruction of previously
   healthy myelin by the immune system. As a prevalent myelinopathy
   disorder, MS manifests as a chronic, multifocal neuroinflammatory
   condition that leads to progressive neurodegeneration and triggers an
   autoimmune response (Mansour, [[42]62, [43]95]). The symptomatic
   pathology in MS primarily arises from the infiltration of immune cells
   targeting the myelin sheath. Oligodendrocyte precursor cells (OPCs)
   attempt to differentiate and replace damaged oligodendrocytes, but
   various factors in the MS environment can inhibit this process
   [[44]100]. This inflammatory demyelination and impaired recovery
   contribute to the formation of sclerotic plaques in the white matter of
   the brain and spinal cord. These plaques impede neurotransmission,
   causing permanent neurodegeneration and resulting in clinical
   disability [[45]169]. In recent years, it has been demonstrated that a
   common factor across various neurodegenerative conditions is
   mitochondrial dysfunction [[46]6, [47]10]. For example, mutations in
   genetic variants such as α-synuclein (SNCA), microtubule-associated
   protein tau, the glucocerebrosidase gene, Parkin (PARK2), PTEN-induced
   kinase 1 (PINK1), and multidrug resistance protein 1 are implicated in
   diseases like Alzheimer's disease (AD), Parkinson's disease (PD), and
   Huntington's disease (HD) [[48]64, [49]78]. Evidence indicates that
   mitochondrial dysfunction plays a crucial role in MS, with
   mitochondrial damage leading to energy deficits in oligodendrocytes,
   thereby impairing their function and survival. Moreover, studies have
   shown mitochondrial abnormalities in neurons of MS patients, including
   changes in enzyme activity, protein levels, transcripts, and DNA
   structure [[50]17, [51]131]. Given the crucial role of mitochondria as
   the primary power generators and metabolic hubs within cells, they need
   to be fully integrated into the cell’s regulatory and coordination
   systems to meet cellular demands. Consequently, ongoing communication
   between mitochondria and the nucleus is vital. This interaction is
   significantly mediated by both proteins and noncoding RNAs (ncRNAs),
   which work together to maintain cellular homeostasis [[52]38]. ncRNAs,
   despite not coding for proteins, regulate numerous genes at the
   transcriptional level, thereby affecting various cellular processes
   (Hanieh, [[53]7], Elham, [[54]70]). Research has underscored their
   critical roles in managing genes linked to mitochondrial integrity and
   oxidative stress in different brain pathologies [[55]22, [56]31,
   [57]91]. For example, miR-146a has been shown to influence PD by
   regulating parkin expression in mitochondria [[58]63]. In this
   manuscript, we begin by providing a broad review of the
   mitochondrial-related non-coding RNAs (MRncRNAs) across a range of NDs,
   establishing a necessary foundation for our study. We realized that
   although the crosstalk between ncRNAs and mitochondria has been
   investigated in various NDs, especially PD, research specifically
   addressing this relationship in the context of MS remains limited. We
   then extract expression patterns of MRncRNAs across human studies to
   explore their potential relevance to MS. Finally, through a comparison
   study and bioinformatic analysis, we introduced a subset of ncRNAs that
   potentially contribute to MS pathology by mediating mitochondrial
   effects, particularly in oligodendrocytes. Given the scarcity of
   comprehensive studies examining this interplay in MS, and the crucial
   role of mitochondrial integrity in oligodendrocyte survival and brain
   homeostasis, our integrated approach not only contextualizes existing
   knowledge but also introduces a promising and underexplored avenue of
   MS research. Investigating how MRncRNAs may yield valuable new insights
   into the etiology and pathogenesis of MS.

Mitochondrial dysfunction in MS

   The etiology of MS is complex, involving a range of factors including
   genetic predisposition, biological factors such as obesity, immune
   senescence, sex hormones, and the microbiome (both gut and lung).
   Environmental factors such as smoking, Epstein-Barr virus infection,
   vitamin D levels, and stress also play significant roles [[59]77,
   [60]119, [61]121]. Although no therapeutic agents can completely cure
   MS, current treatments can reduce relapse rates and, in some cases,
   delay disability progression, thereby improving patient outcomes
   [[62]12, [63]69]. The mtDNA is particularly susceptible to oxidative
   damage and exhibits higher mutation rates compared to nuclear DNA
   (nDNA). This vulnerability is likely due to the lack of protective
   histones, limited DNA repair mechanisms, and heightened exposure to ROS
   [[64]12, [65]96]. MS is categorized into three phenotypic forms:
   relapsing–remitting MS (RRMS), primary progressive MS (PPMS), and
   secondary progressive MS (SPMS). Approximately 85% of MS patients
   initially present with RRMS, characterized by alternating episodes of
   acute demyelination (relapses) and periods of neurological recovery and
   stability [[66]36, [67]129]. A study examining the mitochondrial genome
   of MS patients within an Arab population, which included 23 individuals
   with RRMS and 24 healthy controls, identified numerous variants in the
   D-loop and coding regions of mtDNA. While some variants were exclusive
   to either the patient or control group, several common variants were
   found in both cohorts. Notably, the frequency of certain common
   variants varied between patients and controls, suggesting a potential
   link to MS susceptibility. Among the unique variants found only in
   patients, 34 were missense mutations in various mtDNA-encoded genes,
   reinforcing the connection between mitochondrial genetics and MS
   [[68]3, [69]157]. Additionally, research has pointed to specific
   variations in the mitochondrial complex I gene as potentially
   associated with MS development [[70]120]. Campbell GR et al. explored
   mitochondrial respiratory chain activity and mtDNA deletions in
   individual neurons from 13 patients with SPMS. They observed
   significant mtDNA deletions in neurons, including deletions in subunits
   of complex IV. These findings indicate that neurons in MS may suffer
   from respiratory deficiencies due to extensive mtDNA deletions,
   possibly triggered by inflammation, which may represent a key
   pathogenic mechanism in MS [[71]18]. A study comparing brain tissue
   from 10 MS patients to that of healthy controls reported decreased
   activity of mitochondrial complexes I and III. Out of 119 mitochondrial
   electron transport chain-related genes analyzed, 26 showed significant
   decreases in MS samples. Mitochondrial preparations from the motor
   cortex of MS patients revealed a 61% reduction in complex I and 40% in
   complex III activity, indicating mitochondrial dysfunction and
   decreased ATP production in demyelinated axons. These findings suggest
   that reduced ATP production disrupts ion homeostasis, triggers
   Ca2^+-mediated axonal degeneration, and contributes to the progressive
   neurological disability observed in MS [[72]42, [73]151]. In parallel,
   Witte et al. suggested that mitochondrial changes might be a response
   to demyelination and inflammation. In their study of 26 MS patients,
   they assessed mitochondrial numbers and their co-localization with
   axons and astrocytes in MS lesions and normal-appearing white matter.
   The findings showed increased mitochondrial protein expression and a
   rise in mitochondrial numbers in both active and inactive lesions.
   Mitochondrial density was significantly higher in axons and astrocytes
   within active lesions compared to adjacent normal-appearing white
   matter, with a similar trend in inactive lesions. Additionally, complex
   IV activity was notably higher in MS lesions, correlating with
   up-regulated mitochondrial heat shock protein 70, which reflects
   mitochondrial involvement in the pathological processes of MS. The
   increase in mitochondrial density in MS lesions may contribute to free
   radical generation and tissue damage [[74]161, [75]162]. Another study
   investigating mitochondrial transcriptional co-factors and proteins
   involved in mitochondrial redox balance in MS examined the
   normal-appearing grey matter from the cingulate gyrus and/or frontal
   cortex of 15 MS patients and 9 control subjects. The study focused on
   peroxisome proliferator-activated receptor gamma coactivator-1α
   (PGC-1α), a critical transcription factor regulating oxidative
   phosphorylation (OxPhos) subunits and energy metabolism, as well as
   mitochondrial proteins with antioxidative properties to protect neurons
   from ROS-induced damage. Results showed a significant reduction in
   PGC-1α mRNA levels in MS patients' cortical samples. This decrease was
   associated with neuronal loss in deep cortical layers and increased ROS
   production. Reduced PGC-1α expression in MS contributes to
   mitochondrial dysfunction and neurodegeneration, highlighting its role
   in the disease's progression [[76]163]. The research also emphasizes
   that changes in the expression of nuclear factor erythroid 2-related
   factors 1 and 2 (NRF1/2), estrogen-related receptor α, and peroxisome
   proliferator-activated receptors can influence OxPhos gene expression,
   contributing to oxidative and nitrosative damage in MS. Notably,
   alterations in NRF-2 expression have been linked to impaired regulation
   of mitochondrial electron transport chain (mETC) genes and elevated ROS
   production in postmortem MS brains. Since NRF-2's DNA-binding activity
   is sensitive to redox conditions, elevated oxidative stress may impair
   its function and limit its binding to the promoters of mitochondrial
   mETC genes. This impairment may ultimately disrupt the transcription
   and production of mETC protein subunits, further exacerbating
   mitochondrial dysfunction and contributing to neurodegeneration in MS
   [[77]114, [78]116]. Other studies investigating the mitochondrial
   proteome in postmortem MS and control cortex have identified
   significant alterations in mitochondrial protein expression.
   Specifically, four proteins were found to distinguish MS from controls,
   with three of them involved in respiration: cytochrome c oxidase
   subunit 5b (COX5b), the brain-specific isozyme of creatine kinase, and
   hemoglobin β-chain. These findings highlight the critical role of
   mitochondrial dysfunction in the pathogenesis of MS, further supporting
   the hypothesis that mitochondrial alterations contribute to the
   disease's progression by affecting energy metabolism and cellular
   function in the central nervous system (CNS) [[79]14, [80]156].

Materials and methods

Searching methodology

   In this study, we employed the MeSH terms “Mitochondria and ncRNAs,”
   “Mitochondria and neurodegenerative diseases,” “ncRNAs and
   neurodegenerative diseases,” “Mitochondria and multiple sclerosis,”
   “Mitochondria and Alzheimer's diseases,” “Mitochondria and Parkinson's
   diseases,” “Mitochondria and ALS diseases,” and “Mitochondria and
   Huntington diseases” to search the PubMed and Scopus databases for
   relevant literature up to September 2024. The review focused on
   original research articles written in English that explored the role of
   ncRNAs encoded in nuclear and mitochondrial DNA in NDs. The roles of
   these ncRNAs were required to be experimentally validated. Studies that
   solely used prediction methods to determine ncRNA targets were
   excluded. During the selection process, duplicate articles were
   removed, and the remaining articles underwent thorough evaluation. Key
   details extracted from each article included the type of NDs, the
   length and name of the ncRNA, the cellular mechanisms involving ncRNAs,
   and whether these mechanisms were experimentally confirmed. Articles
   that did not meet the inclusion criteria were excluded after a
   comprehensive review of their full texts. Using an alternative search
   strategy, we queried the same databases for all reported dysregulated
   ncRNAs in MS patients and collected them for future selections.

Bioinformatic analysis of miRNAs/mRNA/protein ceRNA network

   We chose miRNAs for bioinformatic analysis because their mechanisms of
   action and epigenetic effects are clearer and simpler compared to other
   ncRNAs, such as long ncRNAs (lncRNAs) and circular RNAs (circRNAs).
   These characteristics make it easier to evaluate and predict their
   potential functions. The gene targets of miRNAs were predicted using
   the miRDB ([81]https://mirdb.org/) and TargetScan
   ([82]https://www.targetscan.org/) databases, with common gene targets
   identified for each miRNA from these databases [[83]2, [84]27].
   Additionally, the MIENTURNET database
   ([85]http://userver.bio.uniroma1.it/apps/mienturnet/) was utilized to
   find common target genes for a set of miRNAs [[86]85]. Finally, only
   common target genes related to mitochondria were reported in this
   study, reflecting our focus on this organelle. The expression of miRNAs
   in various human brain cells was verified using miRNATissueAtlas2
   ([87]https://ccb-web.cs.uni-saarland.de/tissueatlas2) [[88]73]. To
   identify direct MS-related genes targeted by miRNAs, MS-related genes
   were downloaded from the DisGeNET database (Disease ID: C0026769)
   ([89]https://disgenet.com/) and compared with miRNA target genes
   [[90]118]. Pathway enrichment analysis was performed using KEGG
   pathways via the Enrichr database
   ([91]https://maayanlab.cloud/Enrichr/) [[92]167]. Protein–protein
   interactions of miRNA target genes were verified using the STRING
   database ([93]https://string-db.org/) and analyzed with Cytoscape
   software [[94]149]. The RummaGEO tool ([95]https://rummageo.com/),
   which mines gene expression data from the GEO database, was employed to
   find relationships between target genes and gene expression in diseases
   and cells. This tool facilitates the reuse, reanalysis, and integration
   of past experiments [[96]97].

Results

ncRNAs and mitochondria crosstalk in ND

   Despite receiving less attention than protein-coding RNAs, the study of
   ncRNA function has significantly advanced across multiple fields,
   enhancing our understanding of various biological processes [[97]173].
   While approximately 80% of the genome is transcribed into RNA, only
   about 2% of these transcripts encode proteins, with the majority being
   classified as ncRNAs [[98]108, [99]173]. Numerous studies have
   identified ncRNAs within the mitochondria and highlighted their crucial
   roles in local mitochondrial protein synthesis and regulation of
   mitochondrial functions. While the import of cytoplasmic proteins into
   mitochondria is well-documented, the mechanisms facilitating the import
   of ncRNAs into mitochondria are less understood. It is hypothesized
   that a fundamental mechanism governs RNA mobilization into
   mitochondria, which relies on ATP and involves factors located in the
   mitochondrial translocase of the outer membrane (TOM). This process
   also depends on key components of the protein import pathway, including
   the TOM/translocase of the outer membrane (TIM) complexes and the
   voltage-dependent anion channel (VDAC) [[100]60, [101]127]. The
   communication between mitochondria and the nucleus involves both
   anterograde and retrograde pathways. The anterograde pathway is where
   the nucleus regulates mitochondrial gene expression and function,
   controlling processes like mitochondrial DNA transcription and protein
   synthesis. In contrast, the retrograde pathway refers to mitochondrial
   responses to nuclear signals, regulating processes such as energy
   production, calcium homeostasis, and reactive oxygen species (ROS)
   generation. The ncRNAs play crucial roles as epigenetic regulators in
   these pathways. They are involved in various cellular processes,
   including DNA replication, chromosome maintenance, transcriptional
   control, RNA processing, translation, and protein transport. These
   functions underscore the importance of ncRNAs in maintaining cellular
   homeostasis and regulating mitochondrial-nuclear communication
   [[102]51]. Growing research has enhanced our understanding of ncRNAs
   and their networks in neurodegenerative disorders, particularly through
   their impact on mitochondrial function. However, fully comprehending
   this complex interplay remains challenging [[103]173]. In NDs, several
   genes have emerged as pivotal, including leucine-rich repeat kinase 2
   (LRRK2), PINK1, PARK2, SNCA, and DJ-1 (PARK7). Proteins encoded by
   these genes are closely associated with the mitochondrial membrane,
   either directly or indirectly. Dysregulation of these genes leads to
   various mitochondrial dysfunctions, such as abnormal morphology,
   disrupted dynamics, increased ROS production, reduced membrane
   potential, impaired respiratory complex activities, and lower ATP
   levels [[104]25, [105]28, [106]134].

miRNAs and mitochondria crosstalk in NDs

   miRNAs are short, single-stranded oligonucleotides, typically 19–24
   nucleotides in length, that function as posttranslational regulators of
   gene expression [[107]179]. They can be encoded as independent
   transcriptional units or located within introns and exons of
   protein-coding genes, and at intron–exon boundaries. miRNAs play
   crucial roles in cell proliferation, differentiation, development,
   apoptosis, cell metabolism, and the pathogenesis of various diseases
   [[108]5, [109]103]. In neural stem cells, miR-137 has been shown to
   influence mitochondrial dynamics by downregulating MEF2A, thereby
   reducing PGC1α transcription. Interestingly, miR-137 also promotes
   mitochondrial biogenesis through a PGC1α-independent mechanism by
   upregulating NRF2 and TFAM expression, ultimately enhancing
   mitochondrial content and function [[110]23]. Moreover, mitochondrial
   dysfunction is known to trigger the production of ROS and the release
   of pro-inflammatory signals such as mitochondrial DNA and cytochrome c,
   suggesting that certain miRNAs may play a key role in mediating
   neuroinflammatory responses. Among them, miR-15b has been shown to
   negatively regulate stress-induced SIRT4 expression. Suppression of
   miR-15b leads to reduced mitochondrial membrane potential and elevated
   ROS production through a SIRT4-dependent mechanism, indicating its role
   in protecting against senescence-associated mitochondrial dysfunction.
   Interestingly, decreased levels of miR-15b have also been reported in
   the peripheral blood of ALS patients. While direct evidence in ALS is
   lacking, the combination of these findings suggests that upregulation
   of miR-15b might help counteract stress-induced SIRT4 expression and
   potentially mitigate mitochondrial dysfunction in ALS as well [[111]81,
   [112]86]. A comprehensive list of 35 experimentally validated MRncRNAs
   upregulated in NDs is provided in Table [113]1, while 16 downregulated
   ncRNAs are detailed in Table A of the supplementary material. Below is
   a summary of select miRNAs with particularly strong associations with
   mitochondrial functions.

Table 1.

   Summary of 35 experimentally confirmed upregulated ncRNAs involved in
   mitochondrial function/dysfunction in neurodegenerative disease
   Disease ncRNAs Targets (translational value) Study nature References