Sex-Specific Differences of Human Skeletal Muscle: A Multi-Omics Exercise Study

Identification of novel biomarkers and drug targets for frailty-related skeletal muscle aging: a multi-omics study- correspondence.

BackgroundSkeletal muscle aging is the major cause and hallmark of frailty, which poses a significant challenge to the healthcare system.AimThis study aimed to identify the potential biomarkers for the early detection and therapeutic intervention of this age-related condition.MethodsA transcriptomics-based methodology using machine learning algorithms was performed to select the biomarker genes. A predictive machine learning model for (pre-)frailty based on the transcriptomic profile of the biomarker genes was constructed and validated. The cell-type specific changes of the biomarkers during muscle aging were investigated in a single-cell RNA sequencing dataset of human skeletal muscle. Summary data-based Mendelian randomization (SMR) and Bayesian colocalization analyses were performed to identify biomarker genes with therapeutic effects on frailty-related skeletal muscle aging, and drug candidates were explored in the DSigDB database.ResultsWe identified 24 biomarker genes, most of which were discovered for the first time. The optimal predictive model showed excellent performance in the external test set. Differential expression of the biomarkers in the single-cell dataset indicated a critical role of endothelial cells modulated by the marker genes MGP and ID1 in muscle degeneration. The SMR and colocalization analyses showed causal relationships between 2 marker genes (MGP and WAC) and frailty-related muscle aging. Potential therapeutics for MGP modulation were identified in the DSigDB database.ConclusionsThis multi-omics study identified biomarkers associated with frailty-related muscle aging and provided new insights into the etiology and therapeutic targets for this age-related condition.

The expression of neutral glycosphingolipids and gangliosides has been studied in human skeletal and heart muscle using indirect immunofluorescence microscopy. Transversal and longitudinal cryosections were immunostained with specific monoclonal and polyclonal antibodies against the neural glycosphingolipids lactosylceramide, globoside, Forssman glycosphingolipid, gangliotetraosylceramide, lacto-N-neotetraosylceramide and against the gangliosides GM3(Neu5Ac) and GM1(Neu5Ac). To confirm the lipid nature of positive staining, control sections were treated with methanol and chloroform:methanol (1:1) before immunostaining. These controls were found to be either negative or strongly reduced in fluorescence intensity, suggesting that lipid bound oligosaccharides were detected. In human skeletal muscle, lactosylceramide was found to be the main neutral glycosphingolipid. Globoside was moderately expressed, lacto-N-neotetraosylceramide and gangliotetraosylceramide were minimally expressed and Forssman glycosphingolipid was not detected in human skeletal muscle. The intensities of the immunohistological stains of GM3 and GM1 correlated to the fact that GM3 is the major ganglioside in skeletal muscle whereas GM1 is expressed only weakly. In human heart muscle globoside was the major neutral glycosphingolipid. Lactosylceramide and lacto-N-neotetraosylceramide were moderately expressed, gangliotetraosylceramide was weakly expressed and the Forssman glycosphingolipid was not expressed at all in cardiac muscle. GM3 and GM1 were detected with almost identical intensity. All glycosphingolipids were present in plasma membranes as well as at the intracellular level.

Insulin-stimulated muscle glucose uptake is a key process in glycemic control. This process depends on the redistribution of glucose transporters to the surface membrane, a process which involves regulatory proteins such as TBC1D1 and TBC1D4. Accordingly, a TBC1D4 loss-of-function mutation in human skeletal muscle is associated with increased risk of type 2 diabetes, and observations from carriers of a TBC1D1 variant associate this protein to a severe obesity phenotype. Here, we identified interactors of the endogenous TBC1D4 in human skeletal muscle by an unbiased proteomics approach. We detected 76 proteins as candidate TBC1D4 interactors. The binding of 12 of these interactors were regulated by insulin, including proteins known to be involved in glucose metabolism (e.g. 14-3-3 proteins and ACTN4). TBC1D1 also co-precipitated with TBC1D4 and vice versa in both human and mouse skeletal muscle. This interaction was not regulated by insulin nor exercise in young, healthy, lean individuals. Similarly, the exercise- and insulin-regulated phosphorylation of the TBC1D1-TBC1D4 complex was intact. In contrast, we observed an altered interaction as well as compromised insulin-stimulated phospho-regulation of the TBC1D1-TBC1D4 complex in muscle of obese individuals with type 2 diabetes. Altogether, we provide a repository of TBC1D4 interactors in human and mouse skeletal muscle, which serve as potential regulators of TBC1D4 function and, thus, insulin-stimulated glucose uptake in human skeletal muscle.

Insulin-stimulated muscle glucose uptake is a key process in glycemic control. This process depends on the redistribution of glucose transporters to the surface membrane, a process that involves regulatory proteins such as TBC1D1 and TBC1D4. Accordingly, a TBC1D4 loss-of-function mutation in human skeletal muscle is associated with an increased risk of type 2 diabetes, and observations from carriers of a TBC1D1 variant associate this protein to a severe obesity phenotype. Here, we identified interactors of the endogenous TBC1D4 protein in human skeletal muscle by an unbiased proteomics approach. We detected 76 proteins as candidate TBC1D4 interactors. The binding of 12 of these interactors was regulated by insulin, including proteins known to be involved in glucose metabolism (e.g., 14-3-3 proteins and α-actinin-4 [ACTN4]). TBC1D1 also coprecipitated with TBC1D4 and vice versa in both human and mouse skeletal muscle. This interaction was not regulated by insulin or exercise in young, healthy, lean individuals. Similarly, the exercise- and insulin-regulated phosphorylation of the TBC1D1-TBC1D4 complex was intact. In contrast, we observed an altered interaction as well as compromised insulin-stimulated phosphoregulation of the TBC1D1-TBC1D4 complex in muscle of obese individuals with type 2 diabetes. Altogether, we provide a repository of TBC1D4 interactors in human and mouse skeletal muscle that serve as potential regulators of TBC1D4 function and, thus, insulin-stimulated glucose uptake in human skeletal muscle.

Insulin-stimulated muscle glucose uptake is a key process in glycemic control. This process depends on the redistribution of glucose transporters to the surface membrane, a process which involves regulatory proteins such as TBC1D1 and TBC1D4. Accordingly, a TBC1D4 loss-of-function mutation in human skeletal muscle is associated with increased risk of type 2 diabetes, and observations from carriers of a TBC1D1 variant associate this protein to a severe obesity phenotype. Here, we identified interactors of the endogenous TBC1D4 in human skeletal muscle by an unbiased proteomics approach. We detected 76 proteins as candidate TBC1D4 interactors. The binding of 12 of these interactors were regulated by insulin, including proteins known to be involved in glucose metabolism (e.g. 14-3-3 proteins and ACTN4). TBC1D1 also co-precipitated with TBC1D4 and vice versa in both human and mouse skeletal muscle. This interaction was not regulated by insulin nor exercise in young, healthy, lean individuals. Similarly, the exercise- and insulin-regulated phosphorylation of the TBC1D1-TBC1D4 complex was intact. In contrast, we observed an altered interaction as well as compromised insulin-stimulated phospho-regulation of the TBC1D1-TBC1D4 complex in muscle of obese individuals with type 2 diabetes. Altogether, we provide a repository of TBC1D4 interactors in human and mouse skeletal muscle, which serve as potential regulators of TBC1D4 function and, thus, insulin-stimulated glucose uptake in human skeletal muscle.

Decreased circulating IPA levels identify subjects with metabolic comorbidities: A multi-omics study

Genome assemblies provide a powerful basis of comparative multi-omics analyses that offer insight into parasite pathogenicity, host-parasite interactions, and invasion biology. As a unique intracellular nematode, Trichinella consists of two clades, encapsulated and non-encapsulated. Genomic correlation of the distinct differences between the two clades is still unclear. Here, we report an annotated draft reference genome of non-encapsulated Trichinella, T. pseudospiralis, and perform comparative multi-omics analyses with encapsulated T. spiralis. Genome and methylome analyses indicate that, during Trichinella evolution, the two clades of Trichinella exhibit differential expansion and methylation of parasitism-related multi-copy gene families, especially for the DNase II members of the phospholipase D superfamily and Glutathione S-transferases. Further, methylome and transcriptome analyses revealed divergent key excretory/secretory (E/S) genes between the two clades. Among these key E/S genes, TP12446 is significantly more expressed across three life stages in T. pseudospiralis. Overexpression of TP12446 in the mouse C2C12 skeletal muscle cell line could induce inhibition of myotube formation and differentiation, further indicating its key role in parasitism of T. pseudospiralis. This multi-omics study provides a foundation for further elucidation of the mechanism of nurse cell formation and immunoevasion, as well as the identification of pharmacological and diagnostic targets of trichinellosis.

Analysis of mitochondrial function in mouse and man

Telocytes in human fetal skeletal muscle interstitium during early myogenesis

Dysregulation of intramuscular triglyceride (IMTG) turnover in human skeletal muscle in sedentary and obese states leads to accumulation of lipid metabolites that contribute to skeletal muscle insulin resistance and ultimately progression to type 2 diabetes (T2D). People with T2D display low levels of IMTG turnover in comparison to insulin sensitive and trained individuals. IMTG stores are used as an energy substrate during 1 h of moderate-intensity exercise in trained individuals only and can be increased by consumption of a high fat, high calorie (HFHC) diet in sedentary and trained states. This thesis explores the metabolic and molecular regulation of proteins that regulate IMTG turnover, specifically focusing on the effects of 1) a HFHC diet and 2) a moderate-intensity exercise bout and 3) IMTG stores in different diseases states (lean, obese and T2D). Chapter 2 determined there were no sex-specific differences or main effects in functional outcomes of cardiovascular (arterial stiffness) and metabolic health (glucose tolerance and metabolic flexibility) in response to 7 days HFHC diet. Chapter 3 provides novel evidence that 7 days HFHC diet induces fibre type specific increases in IMTG stores primarily underpinned by an increase in perilipin-3 (PLIN3) protein expression and a redistribution of perilipin-2 (PLIN2) to lipid droplets (LD) storing IMTG. This occurred with no impairments in skeletal muscle insulin signalling and it is therefore proposed that increases in IMTG content assisted by PLIN2 and PLIN3 minimise the accumulation of lipid metabolites known to disrupt the insulin signalling cascade. Chapter 4 revealed that hormone sensitive lipase (HSL) preferentially redistributes to LD associated with perilipin-5 (PLIN5) following 1 h of moderate-intensity exercise. Chapter 5 developed a PLIN5 immunoprecipitation mass spectrometry protocol which identified phospholipase A2- group II, subgroup A (PA2GA) as a novel protein associated to PLIN5 in muscle from lean sedentary humans. In conclusion, this thesis presents novel data on key proteins that regulate IMTG turnover in human skeletal muscle.

International audience

Low expression of long-chain acyl-CoA dehydrogenase in human skeletal muscle

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Investigations on animal models demonstrated that changes of sialic acid (SA) expression, particularly the polymeric form, in the skeletal muscle during embryonic and post-natal development seem to be related to muscle differentiation and functionality onset. The aim of this study was to evaluate the monomeric and polymeric SA expression in human skeletal muscle during early stages of fetal development, when important morphofunctional events occur. Specimens of fetal skeletal muscle from limb, between 9 and 12 weeks of gestation (wg), were obtained from 19 pregnant women. To investigate some morphofunctional features occurring during this development period, haematoxylin-eosin staining, tunel assay and immunohistochemistry for connexin-43 (Cx43) and parvalbumin were performed. SA expression and characterization was evaluated using lectin histochemistry (MAA, SNA, PNA, SBA, DBA), associated with enzymatic and chemical treatments. Polysialic acid (PSA) expression was also evaluated using immunohistochemistry. The results showed apoptotic myotubes between 9 and 10.5 wg, disappearing from 11 wg; Cx43 was more abundant in myotubes/myoblasts between 9 and 9.5 wg, decreasing and/or disappearing from 10 wg and parvalbumin was present in myotubes between 10 and 10.5 wg. PSA was revealed in myotubes/myoblasts from 9 to 10.5 wg; from 11 wg it was reduced or disappeared. Monomeric SA appeared in myotubes/myoblasts from 10 wg, increasing successively; acetylated SA was present from 11 wg. These findings demonstrated that changes in expression of various types of SA, occurring in human fetal skeletal muscle during early development, seem to be related to some morphofunctional aspects distinctive of this organogenesis crucial period.