bims-musmir Biomed News
on microRNAs in muscle
Issue of 2025–06–22
twelve papers selected by
Katarzyna Agnieszka Goljanek-Whysall, University of Galway



  1. FASEB J. 2025 Jun 30. 39(12): e70609
      In addition to the canonical metabolism-regulating function, Adenosine monophosphate-activated protein kinase (AMPK) has noncanonical functions, in which AMPK spatiotemporally phosphorylates specific sets of substrates. Recently, we identified LSMEM2, a novel substrate of AMPK in the heart. LSMEM2 is a membrane protein localized at the intercalated disc (ICD), whose function is currently under investigation. Interestingly, LSMEM2 is also expressed in the skeletal muscles. As skeletal muscles lack a homophilic intercellular junction corresponding to the ICD in the heart, predicting the role of LSMEM2 in skeletal muscles is difficult. In this study, we identified that LSMEM2 is expressed in skeletal muscles, specifically at the neuromuscular junction (NMJ). LSMEM2-knockout mice showed no histological abnormalities, suggesting that LSMEM2 is not essential for skeletal muscle development. The overexpression of full-length wild-type or C-del mutant of LSMEM2 led to the tubular aggregate formation with functional abnormality in male mice. RNA sequence analysis revealed that the gene sets of mitochondrial oxidative phosphorylation and vesicle-mediated transport are enriched in LSMEM2 overexpression. Furthermore, histological analysis demonstrated the accumulation of swollen subsarcolemmal mitochondria in LSMEM2-overexpressing skeletal muscles. The study findings suggest that LSMEM2 may play a role in the pathogenesis of skeletal muscle diseases.
    Keywords:  intercalated disc (ICD); membrane protein; neuromuscular junction (NMJ); skeletal muscle diseases; subsarcolemmal mitochondria; tubular aggregate
    DOI:  https://doi.org/10.1096/fj.202402152R
  2. Life Sci Alliance. 2025 Sep;pii: e202403082. [Epub ahead of print]8(9):
      Mitochondrial gene expression regulation is required for the biogenesis of oxidative phosphorylation (OXPHOS) complexes, yet the spatial organization of mitochondrial RNAs (mt-RNAs) remains unknown. Here, we investigated the spatial distribution of mt-RNAs during various cellular stresses using single-molecule RNA-FISH. We discovered that transcription inhibition leads to the formation of distinct RNA granules within mitochondria, which we term inhibition granules. These structures differ from canonical mitochondrial RNA granules and form in response to multiple transcription arrest conditions, including ethidium bromide treatment, specific inhibition or stalling of the mitochondrial RNA polymerase, and depletion of the SUV3 helicase. Inhibition granules appear to stabilize certain mt-mRNAs during prolonged transcription inhibition. This phenomenon coincides with an imbalance in OXPHOS complex expression, where mitochondrial-encoded transcripts decrease while nuclear-encoded subunits remain stable. We found that cells recover from transcription inhibition via resolving the granules, restarting transcription, and repopulating the mitochondrial network with mt-mRNAs within hours. We suggest that inhibition granules may act as a reservoir to help overcome OXPHOS imbalance during recovery from transcription arrest.
    DOI:  https://doi.org/10.26508/lsa.202403082
  3. Aging Dis. 2025 Jun 07.
      Sarcopenic obesity (SO), a geriatric syndrome characterized by the coexistence of progressive skeletal muscle atrophy and excessive adipose tissue accumulation, represents a growing public health challenge associated with aging populations. While multifactorial pathogenesis involves chronic inflammation, hormonal changes, and mitochondrial dysfunction, sedentary lifestyles and aging remain primary modifiable and non-modifiable risk factors, respectively. Mechanistically, exercise exerts dual therapeutic effects: (1) hypertrophy of type II muscle fibers through IGF-1/Akt/mTORC1 signaling activation, and (2) enhanced lipid β-oxidation via AMPK/PGC1α axis stimulation, thereby mitigating both sarcopenia and adiposity. The autophagy-lysosome system, a conserved cellular quality-control mechanism, orchestrates organelle turnover and nutrient recycling through three distinct pathways: macroautophagic, chaperone-mediated autophagy, and mitophagy. In SO, impaired proteolytic and lipolytic processes converge to induce autophagic flux blockade, manifested by accumulated p62/SQSTM1 and reduced LC3-II/LC3-I ratio. Targeting the AMPK/mTOR signaling nexus, which senses cellular energy status, emerges as a strategic intervention. Exercise-mediated ATP depletion activates AMPK while suppressing mTORC1, thereby synchronously inducing autophagy initiation (ULK1 phosphorylation) and lysosomal biogenesis (TFEB nuclear translocation). This metabolic reprogramming ultimately restores proteostasis and lipid homeostasis in myocytes and adipocytes.
    DOI:  https://doi.org/10.14336/AD.2025.0419
  4. Sci Rep. 2025 Jun 20. 15(1): 20176
      Muscle loss in critically ill patients, particularly during prolonged ICU stays, poses significant challenges to recovery and long-term outcomes. ICU-acquired weakness (ICUAW) manifests as severe muscle depletion, correlating with illness severity and hospitalization duration. This study aims to characterize long-term muscle loss trajectories in ICU patients with acute respiratory distress syndrome (ARDS) due to COVID-19 and severe acute pancreatitis (AP) and to explore contributing factors to elevated muscle decay. Retrospective cohort study including 154 ICU patients, 100 individuals suffering from AP and 54 from COVID-19 ARDS, who underwent a minimum of three CT scans during hospitalization, totaling 988 assessments. Sequential segmentation of psoas muscle area (PMA) was performed, and relative muscle loss per day for the entire monitoring period, as well as for the interval between each consecutive scan, was calculated. Bivariate and multivariate linear regression analyses were conducted to identify and evaluate the factors contributing to muscle loss. ICU patients experienced an average PMA decline of 46.0%, with a reduction of 41.8% observed in COVID-19 patients and 48.2% in AP patients. Notably, the long-term daily PMA loss was significantly greater in COVID-19 patients (1.88%) compared to AP patients (0.98%; p < 0.001). Linear regression analysis identified disease entity (p < 0.001), length of hospitalization (p < 0.001), and obesity as significant contributors to daily muscle deterioration. Patients admitted to the ICU for COVID-19 and severe AP can experience extreme muscle decay, reaching up to 48.2%. While decay rates vary considerably, COVID-19 patients experienced nearly twice the daily muscle loss compared to AP patients. Key factors contributing to muscle decay included disease entity, hospitalization duration, and obesity. These findings highlight the distinct impact of the underlying disease on muscle deterioration and emphasize the heightened risk for obese patients and those undergoing extended hospitalization.
    Keywords:  Acute pancreatitis; Artificial intelligence; COVID-19; Computed tomography; Critical care; Muscle wasting
    DOI:  https://doi.org/10.1038/s41598-025-05912-2
  5. iScience. 2025 Jun 20. 28(6): 112648
      Amyotrophic lateral sclerosis (ALS) is the most common and fatal motor neuron disease. Approximately 90% of ALS patients exhibit pathology of the master RNA regulator, transactive response DNA binding protein (TDP-43). Despite the prevalence TDP-43 pathology in ALS motor neurons, recent findings suggest immune dysfunction is a determinant of disease progression in patients. Whether TDP-43 aggregates elicit immune responses remains underexplored. In this study, we demonstrate that TDP-43 aggregates are internalized by antigen-presenting cell populations, cause vesicle rupture, and drive innate and adaptive immune cell activation by way of antigen presentation. Using a multiplex imaging platform, we observed enrichment of activated microglia/macrophages in ALS white matter that correlated with phosphorylated TDP-43 accumulation, CD8 T cell infiltration, and major histocompatibility complex expression. Taken together, this study sheds light on a novel cellular response to TDP-43 aggregates through an immunological lens.
    Keywords:  Immunity; Neuroscience; Omics
    DOI:  https://doi.org/10.1016/j.isci.2025.112648
  6. Basic Res Cardiol. 2025 Jun 19.
      NLRX1 is the only NOD-like innate immune receptor that localises to mitochondria. We previously demonstrated that NLRX1 deletion increased infarct size in isolated mouse hearts subjected to ischemia-reperfusion injury (IRI); however, underlying mechanisms are yet to be identified. Given the crucial role played by mitochondria in cardiac IRI, we here hypothesise that NLRX1 affects key mechanisms of cardiac IRI. Cardiac IRI was evaluated in isolated C57BL/6J (WT) and NLRX1 knock out (KO) mouse hearts. The following known modulators of IRI were explored in isolated hearts, isolated mitochondria; or permeabilised cardiac fibres: 1) mTOR/RISK/autophagy regulation, 2) AMPK and mitochondrial energy production, and 3) mitochondrial permeability transition pore (mPTP) opening. NLRX1 deletion increased IRI, and cardiac NLRX1 was decreased after IRI in mouse and pig hearts. NLRX1 ablation caused decreased mTOR and RISK pathway (Akt, ERK, and S6K) activation following IR, without affecting autophagy/inflammation/oxidative stress markers. The RISK activator Urocortin dissipated NLRX1 effects on mTOR, RISK pathway and IRI, indicating that increased cardiac IRI with NLRX1 deletion is, at least partly, due to impaired RISK activation. The energy sensor AMPK was activated in NLRX1 KO hearts, possibly due to slowed mitochondrial respiratory responses (impaired mitochondrial permeability) towards palmitoylcarnitine in permeabilised cardiac fibres. NLRX1 deletion completely abolished calcium-induced mPTP opening, and cyclosporine A (CsA) effects on mPTP, both before and after IR, and was associated with increased mitochondrial calcium content after IR. Mitochondrial sub-fractionation studies localised NLRX1 to the inner mitochondrial membrane. NLRX1 deletion associated with decreased phosphorylation of mitochondrial Got2, Cx43, Myl2, Ndufb7 and MICOS10. The mPTP inhibitor CsA abolished IRI differences between KO and WT hearts, suggesting that the permanent closure of mPTP due to NLRX1 deletion contributed to the increased IR sensitivity of NLRX1 KO hearts. This is the first demonstration that the mitochondrial NLRX1 is a novel factor required for mPTP opening and contributes to cardioprotection against acute IRI through RISK pathway activation and prevention of permanent mPTP closure.
    Keywords:  AMPK; I/R injury; Mitochondria; Mitochondrial transition pore opening; NLRX1; RISK pathway
    DOI:  https://doi.org/10.1007/s00395-025-01124-x
  7. Exp Neurol. 2025 Jun 12. pii: S0014-4886(25)00212-2. [Epub ahead of print]392 115348
       BACKGROUND AND AIMS: Chronic nerve compression (CNC) impacts over one million Americans annually, causing substantial functional and economic burdens. Despite its prevalence, the translational relevance of murine CNC models is limited by the use of young animals and a lack of studies investigating post-decompression recovery. This study aims to characterize CNC in aged mice compared to young mice and assess nerve and muscle recovery following surgical release in aged animals.
    METHODS: Young (20-week) and aged (67-week) male C57BL/6 J mice underwent 16 weeks of sciatic nerve compression. A subset of aged mice received surgical decompression, followed by a 4-week recovery. Electrophysiological, histological, and molecular analyses were performed on nerve and muscle tissues to evaluate changes induced by CNC and decompression.
    RESULTS: CNC induced demyelination in both young and aged mice, with aged mice exhibiting greater axonal atrophy. Young mice muscle demonstrated increased expression of atrophic and fibrotic markers such as Atrogin1, MuRF1, and α-SMA. Conversely, we observed increased expression of MyoD and MyoG myogenic markers in aged mice muscle, correlating with increased average muscle fiber cross-sectional area. In aged mice, surgical release restored electrophysiological parameters, normalized histological features, and reversed molecular gene adaptations.
    CONCLUSION: The molecular and structural responses to CNC in affected muscle differ with age, with aged mice demonstrating a shift from atrophic to myogenic pathways compared to young mice. Surgical release effectively mitigates CNC-induced deficits, emphasizing its therapeutic value. This study highlights the importance of age-appropriate models for understanding CNC pathophysiology and recovery dynamics.
    Keywords:  Animal model; Carpal tunnel syndrome; Chronic nerve compression; Entrapment neuropathy; Peripheral nerve; Surgical release
    DOI:  https://doi.org/10.1016/j.expneurol.2025.115348
  8. Circ Heart Fail. 2025 Jun 19. e012512
       BACKGROUND: Heart failure with preserved ejection fraction (HFpEF) is a systemic process with contributions from peripheral factors, including skeletal muscle (SM). Age-associated SM loss and impaired energy metabolism occur without heart failure, but the relative importance of changes in SM quantity versus metabolic quality in patients with HFpEF for exercise intolerance (EI) or outcomes has not been studied. We hypothesized that EI and subsequent clinical outcomes across the adult lifespan in patients with HFpEF are related to impaired SM energy metabolism rather than age-associated SM loss.
    METHODS: Patients with HFpEF (n=64; aged 34-86 years) with left ventricular ejection fraction ≥50% were stratified by age in a prospective study. They underwent 3T magnetic resonance imaging to measure calf muscle quantity and 31P magnetic resonance spectroscopy to measure muscle high-energy phosphate metabolism during plantar flexion exercise.
    RESULTS: Older patients with HFpEF exhibited more severe EI, less calf muscle, faster exercise-induced high-energy phosphate decline, and worse SM energetics at fatigue than younger patients. EI correlated closely with muscle metabolic quality, not quantity. Neither magnetic resonance imaging exercise time, 6-minute walk distance, nor peak oxygen uptake at cardiopulmonary exercise testing on cardiopulmonary bicycle exercise testing correlated with calf SM area. In contrast, the 6-minute walk distance and peak oxygen uptake at cardiopulmonary exercise testing were inversely related to rapid exercise-induced high-energy phosphate decline and worse SM energetic profile at fatigue. Rapid exercise-induced high-energy phosphate decline and lower ATP at fatigue were associated with increased cardiovascular death and heart failure hospitalizations in univariate analysis over a median of 39.3 months.
    CONCLUSIONS: EI in older patients with HFpEF is closely linked to age-associated abnormalities in SM energy metabolism, namely, rapid exercise-induced energetic decline and worse energetic profile at fatigue, and not SM quantity. Abnormal SM energy metabolism is associated with worse outcomes in patients with HFpEF in unadjusted analysis. These findings support SM energy metabolism as a barometer of systemic HFpEF severity and the pursuit of new SM metabolic modulators to reduce disabling EI and possibly adverse outcomes in patients with HFpEF.
    Keywords:  aging; heart failure; hospitalization; magnetic resonance imaging; metabolism
    DOI:  https://doi.org/10.1161/CIRCHEARTFAILURE.124.012512
  9. J Virol. 2025 Jun 18. e0091425
      Altered gene regulation downstream of infection has been linked to devastating cancers and neurological diseases, highlighting the importance of understanding viral:host gene interactions. Historically, approaches based on bioinformatic binding prediction showed that host microRNAs (miRNAs) can target and regulate viral genes to impact viral replication and pathogenesis. More recently, Argonaute cross-linking and immunoprecipitation (AGO-CLIP) and advancements incorporating a miRNA:target RNA ligation step (AGO-CLIP + ligation) enable a global view of miRNA interactions with target cellular and viral transcripts. These genome-wide approaches paired with RNA sequencing reveal that miRNA binding to viral transcripts can not only act conventionally to regulate viral replication but can also act to reduce miRNA targeting of host genes with resulting de-repression of host target genes and downstream biological impacts. Viruses with accumulated evidence of miRNA sequestration are selected as examples for review and include hepatitis C virus (HCV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and respiratory syncytial virus (RSV). The significant impact of target de-repression on host cellular biology warrants a broader investigation of this mechanism. In this mini-review, we examine examples of crosstalk between host miRNAs and viral transcripts and highlight the advance and potential of analyses from AGO-CLIP + ligation with RNA-seq for expanding the identification of global miRNA:viral target interactions and interrogating the biological impacts of host miRNA sequestering and target de-repression. Host target de-repression by miRNA:viral target interactions could shed light on antiviral therapeutic candidates to aid in mitigating consequences such as malignancies and neurodegeneration.
    Keywords:  AGO; AGO-CLIP; Argonaute; CLEAR-CLIP; HCV; RNA-seq; miRNA; microRNA; viruses
    DOI:  https://doi.org/10.1128/jvi.00914-25
  10. FASEB J. 2025 Jun 30. 39(12): e70746
      Brain atrophy is a common feature of neurodegenerative disorders, including Alzheimer's disease, Parkinson's disease, multiple sclerosis, and more recently SARS-CoV-2 infection for which the neuroinflammatory mechanism is not fully understood. Nevertheless, neuroinflammation and CD8 T cell accumulation is frequently observed in postmortem brain tissue of patients with neurodegeneration. We therefore developed a murine model of brain atrophy using the Theiler's murine encephalomyelitis virus (TMEV) infection model of multiple sclerosis. We employ single major histocompatibility complex (MHC) class I molecule conditional knockout mice generated by our program to analyze the contribution of immune cell infiltration and onset of atrophy. TMEV infected C57BL/6 mice that singularly express H-2Kb or H-2Db were evaluated. TMEV infection of these mice resulted in ventricular atrophy at 14 d.p.i. However, H-2Db expressing mice presented with significantly greater and continuous ventricular atrophy compared to H-2Kb expressing mice and MHC class I knockout control mice. Flow cytometric analysis revealed H-2Db expressing mice had greater brain infiltrating CD8 T cell responses at 7 and 28 dpi which correlated with the extent of ventricular atrophy. Meanwhile, H-2Kb and MHC class I knockout mice also had distinct positive correlations with ventricular atrophy and global neuroinflammation in general. These findings support the role of immune cell infiltration into the CNS as a putative mechanism of ventricular atrophy following TMEV infection, with the progressive enlargement of ventricular atrophy observed in H-2Db mice being associated with the presence of long-lived memory CD8 T cells residing in the brain.
    Keywords:  CD8 T cell; MHC class I molecule; brain atrophy; mouse model; multiple sclerosis; neurodegeneration; neuroinflammation; neurotropic virus
    DOI:  https://doi.org/10.1096/fj.202501045R
  11. PLoS One. 2025 ;20(6): e0325813
       BACKGROUND: The incidence and mortality of sepsis in the intensive care unit (ICU) remain persistently high. This study primarily investigates the risk factors associated with the 90-day mortality in sepsis patients.
    METHOD: This retrospective study included 123 sepsis patients admitted to a hospital in China from January 2015 to December 2018, clinical and abdominal CT data were compared between survivors and non-survivors, logistic regression and Cox regression analyses were performed on the abdominal CT data, Finally, survival curves for different skeletal muscle indices were analyzed using the Kaplan-Meier (K-M) method.
    RESULT: In the abdominal CT scan data, significant differences were observed between survivors and non-survivors in skeletal muscle density (SMD), skeletal muscle area (SMA), skeletal muscle index (SMI), and subcutaneous adipose tissue area (SAT); Cox regression analysis revealed that higher skeletal muscle density (SMD) (HR = 0.953; 95% CI = 0.923-0.984; p = 0.003), skeletal muscle area (SMA) (HR = 0.986; 95% CI = 0.976-0.997; p = 0.011), and skeletal muscle index (SMI) (HR = 0.951; 95% CI = 0.917-0.985; p = 0.005) were significantly associated with lower 90-day mortality compared to non-survivors. Finally, the Kaplan-Meier (K-M) curves demonstrated differences in survival based on the median skeletal muscle index (SMI).
    CONCLUSION: Body composition parameters assessed by abdominal CT scans are highly associated with 90-day mortality in ICU patients with sepsis. Among them, SMD, SMA, and SMI are valuable prognostic factors.
    DOI:  https://doi.org/10.1371/journal.pone.0325813
  12. Free Radic Biol Med. 2025 Jun 15. pii: S0891-5849(25)00761-0. [Epub ahead of print]238 1-16
      Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by selective motor neuron death. Dysregulated energy metabolism is implicated in ALS pathogenesis, yet the role of pyruvate kinase M2 (PKM2), a key glycolytic enzyme, remains elusive. Here, we demonstrated that PKM2 expression was upregulated in the spinal neurons of SOD1G93A mice during early stages of disease. Pharmacological inhibition of PKM2 with compound 3k (C3k) shortened survival times, exacerbated motor deficits, and amplified mitochondrial oxidative stress and neuronal apoptosis in mice with ALS. Mechanistically, PKM2 mitigated mitochondrial dysfunction via its enzymatic activity, promoting lactate metabolism to reduce reactive oxygen species (ROS) accumulation. Concurrently, nuclear PKM2 directly bound to the Nrf2 promoter, enhancing Nrf2 transcription to strengthen antioxidant defenses. Our findings unveil PKM2 as a multifunctional neuroprotectant in ALS, offering novel therapeutic directions through metabolic and transcriptional modulation.
    Keywords:  ALS; Apoptosis; Nrf2; Oxidative stress; PKM2
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2025.06.012