bims-musmir 2024-12-15 papers

NAR Mol Med. 2024 Oct;1(4): ugae016

Network-based modelling reveals cell-type enriched patterns of non-coding RNA regulation during human skeletal muscle remodelling.

Jonathan C Mcleod, Changhyun Lim, Tanner Stokes, Jalil-Ahmad Sharif, Vagif Zeynalli, Lucas Wiens, Alysha C D'Souza, Lauren Colenso-Semple, James McKendry, Robert W Morton, Cameron J Mitchell, Sara Y Oikawa, Claes Wahlestedt, J Paul Chapple, Chris McGlory, James A Timmons, Stuart M Phillips.

A majority of human genes produce non-protein-coding RNA (ncRNA), and some have roles in development and disease. Neither ncRNA nor human skeletal muscle is ideally studied using short-read sequencing, so we used a customized RNA pipeline and network modelling to study cell-type specific ncRNA responses during muscle growth at scale. We completed five human resistance-training studies (n = 144 subjects), identifying 61% who successfully accrued muscle-mass. We produced 288 transcriptome-wide profiles and found 110 ncRNAs linked to muscle growth in vivo, while a transcriptome-driven network model demonstrated interactions via a number of discrete functional pathways and single-cell types. This analysis included established hypertrophy-related ncRNAs, including CYTOR-which was leukocyte-associated (false discovery rate [FDR] = 4.9 × 10-7). Novel hypertrophy-linked ncRNAs included PPP1CB-DT (myofibril assembly genes, FDR = 8.15 × 10-8), and EEF1A1P24 and TMSB4XP8 (vascular remodelling and angiogenesis genes, FDR = 2.77 × 10-5). We also discovered that hypertrophy lncRNA MYREM shows a specific myonuclear expression pattern in vivo. Our multi-layered analyses established that single-cell-associated ncRNA are identifiable from bulk muscle transcriptomic data and that hypertrophy-linked ncRNA genes mediate their association with muscle growth via multiple cell types and a set of interacting pathways.

DOI: https://doi.org/10.1093/narmme/ugae016

Brain Behav Immun. 2024 Dec 11. pii: S0889-1591(24)00739-6. [Epub ahead of print]

GDF15-GFRAL signaling drives weight loss and lipid metabolism in mouse model of amyotrophic lateral sclerosis.

Germana Cocozza, Ludovica Maria Busdraghi, Giuseppina Chece, Antonio Menini, Marco Ceccanti, Laura Libonati, Chiara Cambieri, Francesco Fiorentino, Dante Rotili, Ferdinando Scavizzi, Marcello Raspa, Eleonora Aronica, Maurizio Inghilleri, Stefano Garofalo, Cristina Limatola.

Weight loss is a common early sign in amyotrophic lateral sclerosis (ALS) patients and negatively correlates with survival. In different cancers and metabolic disorders, high levels of serum growth differentiation factor 15 (GDF15) contribute to a decrease of food intake and body weight, acting through GDNF family receptor alpha-like (GFRAL). Here we report that GDF15 is highly expressed in the peripheral blood of ALS patients and in the hSOD1G93A mouse model and that GFRAL is upregulated in the brainstem of hSOD1G93A mice. We demonstrate that the localized GFRAL silencing by shRNA in the area postrema/nucleus tractus solitarius of hSOD1G93A mice induces weight gain, reduces adipose tissue wasting, ameliorates the motor function and muscle atrophy and prolongs the survival time. We report that microglial cells could be involved in mediating these effects because their depletion with PLX5622 reduces brainstem GDF15 expression, weight loss and the expression of lipolytic genes in adipose tissue. Altogether these results reveal a key role of GDF15-GFRAL signaling in regulating weight loss and the alteration of and lipid metabolism in the early phases of ALS.

Keywords: Adipose tissue; Feeding behaviour; GDF15; GFRAL; Microglia; Neurodegenerative disease

DOI: https://doi.org/10.1016/j.bbi.2024.12.010

Free Radic Biol Med. 2024 Dec 04. pii: S0891-5849(24)01097-9. [Epub ahead of print]227 395-406

Peroxiredoxin 2 mediates redox-stimulated adaptations to oxidative phosphorylation induced by contractile activity in human skeletal muscle myotubes.

Robert A Heaton, Sam Tm Ball, Caroline A Staunton, Vincent Mouly, Samantha W Jones, Anne McArdle, Malcolm J Jackson.

Skeletal muscle generates superoxide during contractions, which is converted to hydrogen peroxide (H2O2). H2O2 has been proposed to activate signalling pathways and transcription factors that regulate adaptive responses to exercise, but the concentration required to oxidize and activate key redox-sensitive signalling proteins in vitro is much higher than the typical intracellular levels seen in muscle after exercise. We hypothesized that 2-Cys-peroxiredoxins (PRDX), which rapidly oxidize in the presence of physiological concentrations of H2O2, serve as intermediary signalling molecules and play a crucial role in activating adaptive pathways following muscle contractions. This study has examined the human muscle myotube responses to contractile activity, or exposure to low extracellular concentrations (2.5-5 μM) of H2O2 and whether knock down of muscle PRDX2 alters the differential gene expression (DEG) that results from these stresses. Exposure of human skeletal muscle myotubes to a 15 min period of aerobic electrically stimulated isometric contractions or 5 μM H2O2 induced substantial changes in DEG with modification of many genes associated with adaptations of skeletal muscle to contractile activity. Common DEG in these conditions included upregulation of genes associated with increased mitochondrial oxidative phosphorylation, including COX1, COX2, COX3 and ATP6. In myotubes with PRDX2 knock down (94 % decrease in PRDX2 mRNA), the upregulation of genes associated with increased mitochondrial oxidative phosphorylation was abolished following contractile activity or exposure to H2O2. These data indicate that a common effect of contractile activity and exposure to "physiological" levels of H2O2 in human myotubes is to increase the expression of multiple genes associated with increased mitochondrial oxidative phosphorylation. Furthermore, these effects were abolished in PRDX2 knock down myotubes indicating that adaptations to upregulate multiple genes related to increased mitochondrial capacity in human muscle myotubes in response to exercise is both redox regulated and requires PRDX2 as an essential mediator of the effects of H2O2.

DOI: https://doi.org/10.1016/j.freeradbiomed.2024.11.053

Diabetologia. 2024 Dec 13.

Genetic variation in the RETN promoter, accompanied by latent sarcopenic obesity, led to insulin resistance in a Japanese cohort: the Toon Genome Study.

Yosuke Ikeda, Ryoichi Kawamura, Yasuharu Tabara, Koutatsu Maruyama, Daisuke Shiokawa, Misaki Takakado, Toshimi Hadate, Yasunori Takata, Jun Ohashi, Isao Saito, Yoshihiro Ogawa, Haruhiko Osawa.

AIMS/HYPOTHESIS: Resistin, inducing insulin resistance, is elevated in the sera of individuals with the G-A haplotype at c.-420 C>G (rs1862513) and c.-358 G>A (rs3219175). This haplotype is associated with visceral obesity and low grip strength. To elucidate the hidden relationship between the G-A haplotype and insulin resistance, integration of specific phenotypes defined by body composition and 75 g OGTT would be a promising strategy.
METHODS: The 803 Japanese participants (average age: 62 years), attending annual medical checkups, were evaluated every 5 years. Participants were categorised by skeletal muscle mass, visceral fat score and OGTT results. Hierarchical clustering was performed using body composition and glucose metabolism parameters. Whole blood cells from participants homozygous for the G-A or C-G haplotype (n=25 and 33, respectively), matched for age, sex and BMI, using propensity score matching, were used for RNA-seq, pathway analysis and RT-PCR.
RESULTS: Multivariate analysis showed that individuals with the G-A haplotype, when accompanied by latent skeletal muscle loss and visceral obesity (latent sarcopenic obesity), presented a pronounced deterioration in insulin resistance over a 5 year period. Cluster 2, identified using hierarchical clustering, was characterised by low skeletal muscle mass, visceral obesity and insulin resistance. This cluster, with the G-A haplotype, demonstrated deterioration in insulin resistance. RNA-seq and RT-PCR revealed altered expression of mitophagy-related genes in whole blood cells of the G-A homozygotes.
CONCLUSIONS/INTERPRETATION: The G-A haplotype, accompanied by latent low skeletal muscle mass and visceral obesity, led to the deterioration of insulin resistance over a 5 year period in this cohort, possibly through the altered expression of mitophagy-related genes.

Keywords: Insulin resistance; Mitophagy; OGTT; Resistin; SNP; Skeletal muscle mass; Visceral fat score

DOI: https://doi.org/10.1007/s00125-024-06322-1

Autophagy. 2024 Dec 12. 1-16

Inhibition of the PI3K-AKT-MTORC1 axis reduces the burden of the m.3243A>G mtDNA mutation by promoting mitophagy and improving mitochondrial function.

Chih-Yao Chung, Kritarth Singh, Preethi Sheshadri, Gabriel E Valdebenito, Anitta R Chacko, María Alicia Costa Besada, Xiao Fei Liang, Lida Kabir, Robert D S Pitceathly, Gyorgy Szabadkai, Michael R Duchen.

Mitochondrial DNA (mtDNA) encodes genes essential for oxidative phosphorylation. The m.3243A>G mutation causes severe disease, including myopathy, lactic acidosis and stroke-like episodes (MELAS) and is the most common pathogenic mtDNA mutation in humans. We have previously shown that the mutation is associated with constitutive activation of the PI3K-AKT-MTORC1 axis. Inhibition of this pathway in patient fibroblasts reduced the mutant load, rescued mitochondrial bioenergetic function and reduced glucose dependence. We have now investigated the mechanisms that select against the mutant mtDNA under these conditions. Basal macroautophagy/autophagy and lysosomal degradation of mitochondria were suppressed in the mutant cells. Pharmacological inhibition of any step of the PI3K-AKT-MTORC1 pathway activated mitophagy and progressively reduced m.3243A>G mutant load over weeks. Inhibition of autophagy with bafilomycin A1 or chloroquine prevented the reduction in mutant load, suggesting that mitophagy was necessary to remove the mutant mtDNA. Inhibition of the pathway was associated with metabolic remodeling - mitochondrial membrane potential and respiratory rate improved even before a measurable fall in mutant load and proved crucial for mitophagy. Thus, maladaptive activation of the PI3K-AKT-MTORC1 axis and impaired autophagy play a major role in shaping the presentation and progression of disease caused by the m.3243A>G mutation. Our findings highlight a potential therapeutic target for this otherwise intractable disease.Abbreviation: ΔΨm: mitochondrial membrane potential; 2DG: 2-deoxy-D-glucose; ANOVA: analysis of variance; ARMS-qPCR: amplification-refractory mutation system quantitative polymerase chain reaction; Baf A1: bafilomycin A1; BSA: bovine serum albumin; CQ: chloroquine; Cybrid: cytoplasmic hybrid; CYCS: cytochrome c, somatic; DCA: dichloroacetic acid; DMEM: Dulbecco's modified Eagle's medium; DMSO: dimethylsulfoxide; EGFP: enhanced green fluorescent protein; LC3B-I: carboxy terminus cleaved microtubule-associated protein 1 light chain 3 beta; LC3B-II: lipidated microtubule-associated protein 1 light chain 3 beta; LY: LY290042; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MELAS: mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes; MFC: mitochondrial fragmentation count; mt-Keima: mitochondrial-targeted mKeima; mtDNA: mitochondrial DNA/mitochondrial genome; MTOR: mechanistic target of rapamycin kinase; MTORC1: MTOR complex 1; OA: oligomycin+antimycin A; OxPhos: oxidative phosphorylation; DPBS: Dulbecco's phosphate-buffered saline; PPARGC1A/PGC-1α: PPARG coactivator 1 alpha; PPARGC1B/PGC-1β: PPARG coactivator 1 beta; PI3K: phosphoinositide 3-kinase; PINK1: PTEN induced kinase 1; qPCR: quantitative polymerase chain reaction; RNA-seq: RNA sequencing; RP: rapamycin; SQSTM1/p62: sequestosome 1; TEM: transmission electron microscopy; WT: wild-type.

Keywords: PI3K-AKT-MTORC1; m.3243A>G; mitochondria; mitophagy; mtDNA mutations; nutrient signaling

DOI: https://doi.org/10.1080/15548627.2024.2437908

CNS Neurosci Ther. 2024 Dec;30(12): e70130

The Circadian Clock Gene Bmal1 Regulates Microglial Pyroptosis After Spinal Cord Injury via NF-κB/MMP9.

Dachuan Li, Siyang Liu, Xiao Lu, Zhaoyang Gong, Hongli Wang, Xinlei Xia, Feizhou Lu, Jianyuan Jiang, Yuxuan Zhang, Guangyu Xu, Fei Zou, Xiaosheng Ma.

BACKGROUND: The treatment of spinal cord injury (SCI) is usually ineffective, because neuroinflammatory secondary injury is an important cause of the continuous development of spinal cord injury, and microglial pyroptosis is an important step of neuroinflammation. Recently, Bmal1, a core component of circadian clock genes (CCGs), has been shown to play a regulatory role in various tissues and cells. However, it is still unclear whether Bmal1 regulates microglial pyroptosis after SCI.
METHODS: In this study, we established an in vivo mouse model of SCI using Bmal1 knockout (KO) mice and wild-type (WT) mice, and lipopolysaccharide (LPS)-induced pyroptosis in BV2 cells as an in vitro model. A series of molecular and histological methods were used to detect the level of pyroptosis and explore the regulatory mechanism in vivo and in vitro respectively.
RESULTS: Both in vitro and in vivo results showed that Bmal1 inhibited NLRP3 inflammasome activation and microglial pyroptosis after SCI. Further analysis showed that Bmal1 inhibited pyroptosis-related proteins (NLRP3, Caspase-1, ASC, GSDMD-N) and reduced the release of IL-18 and IL-1β by inhibiting the NF-κB /MMP9 pathway. It was important that NF-κB was identified as a transcription factor that promotes the expression of MMP9, which in turn regulates microglial pyroptosis after SCI.
CONCLUSIONS: Our study initially identified that Bmal1 regulates the NF-κB /MMP9 pathway to reduce microglial pyroptosis and thereby reduce secondary spinal cord injury, providing a new promising therapeutic target for SCI.

Keywords: Bmal1; MMP9; NF‐κB; pyroptosis; spinal cord injury

DOI: https://doi.org/10.1111/cns.70130