Muscle Transcriptome Research Articles

Characteristic Muscle Quality Parameters of Male Largemouth Bass (Micropterus salmoides) Distinguished from Female and Physiological Variations Revealed by Transcriptome Profiling

Male largemouth bass (Micropterus salmoides) are often overlooked because females grow faster. We explored the value of male largemouth bass by comparing muscle nutrition, texture, and transcriptomes between males and females. Females grew faster than males (p < 0.05) because of lipid accumulation. Male fish muscles had higher contents of serine, valine, methionine, arginine, nervonic acid, and α-linolenic acid (p < 0.05), and female fish muscles had higher contents of aspartic acid, glycine, cysteine, leucine, palmitic acid, docosahexaenoic acid, and 11,14,17-eicosatrienoic acid (p < 0.05). Male muscles had a higher concentration of collagen fibers and greater shear force, indicative of a chewier texture. Male muscles had a lighter color, suggesting that they were less susceptible to oxidation and deterioration. Transcriptomic analyses revealed upregulation of lpl, sadb, dgat2, bhmt, tecrb, and hsd3b7, encoding components of amino acid and fatty acid metabolism; and upregulation of akt2, src, and kras, encoding crucial regulators of cellular immunity and homeostasis, in male muscles. Immunity-related pathways, including apoptosis, ErbB signaling, and cellular senescence, were enriched in male fish muscles, indicating heightened immune function. The muscles of male fish have a unique profile and distinctive advantages in terms of nutrition, flavor, texture, and transcriptional regulation.

Blood-based biomarkers for early frailty are sex-specific: validation of a combined in silico prediction and data-driven approach.

Frailty is characterized by loss of physical function and is preferably diagnosed at an early stage (e.g., during pre-frailty). Unfortunately, sensitive tools that can aid early detection are lacking. Blood-based biomarkers, reflecting pathophysiological adaptations before physical symptoms become apparent, could be such tools. We identified candidate biomarkers using a mechanism-based computational approach which integrates a priori defined database-derived clinical biomarkers and skeletal muscle transcriptome data. Identified candidate biomarkers were used as input for a sex-specific correlation analysis, using individual gene expression data from female (n = 24) and male (n = 28) older adults (all 75 + years, ranging from fit to pre-frail) and three frailty-related physical parameters. Male and female groups were matched based on age, BMI, and Fried frailty index. The best correlating candidate biomarkers were evaluated, and selected biomarkers were measured in serum. In females, myostatin and galectin-1 and, in males, cathepsin B and thrombospondin-4 serum levels were significantly different between the physically weakest and fittest participants (all p < 0.05). Logistic regression confirmed the added value of these biomarkers in conjunction with age and BMI to predict whether the subjects belonged to the weaker or fittest group (AUC = 0.80 in females and AUC = 0.83 in males). In conclusion, both in silico and in vivo analyses revealed the sex-specificity of candidate biomarkers, and we identified a selection of potential biomarkers which could be used in a biomarker panel for early detection of frailty. Further investigation is needed to confirm these leads for early detection of frailty.

Identification and characterization of tissue-specific genes in response to handling stress in topmouth culter (Culter alburnus) kidney, liver and muscle tissues

Topmouth culter (Culter alburnus) is an important freshwater economic fish in China. However, external stress often triggers strong reactions, resulting in low survival rates and reduced productivity. The absence of stress-related genes has significantly limited our understanding of stress response in this fish. Therefore, 85,846,206 high-quality reads were acquired from kidney, liver and muscle cDNA libraries of topmouth culter using illumina sequencing technology in this study. Comparative analysis revealed that 3,158; 409 and 1,952 unigenes were specifically expressed in the kidney, liver and muscle transcriptome, respectively. Additionally, 83 crucial tissue-specific genes were identified within three stress-related GO terms: response to stimulus (GO:0050896), response to stress (GO:0006950) and response to hypoxia (GO:0001666). From these, 18 tissue-specific genes were further isolated. During the short-term stress experiment (two repeated handling stress, including chasing 2 min and netting out of water for 30s), significant changes were observed in the cortisol levels of both the treatment and recovery groups. Furthermore, notable changes were noted in the expression of LCP2, PTK2b and P-selectin genes in the kidney; FABP1, IGFBP1 and CYP4V2 genes in the liver; and MYH10, Myogenin 2 and Toponin C genes in the muscle of topmouth culter in the treatment and recovery groups (P &lt; 0.05). The tissue-specific transcriptome profiles generated in this study offer valuable insights into the molecular and functional mechanisms associated with stress response in topmouth culter. We characterizated genes related to stress response in tissues such as the kidney, liver and muscle, these findings offer novel insights into stress research in fish. We can further explore the breeding of strains with enhanced stress resistance and promote the healthy development of topmouth culter industry.

Exploring the molecular basis of efficient feed utilization in low residual feed intake slow-growing ducks based on breast muscle transcriptome

Residual feed intake (RFI) has recently gained attention as a key indicator of feed efficiency in poultry. In this study, 800 slow-growing ducks with similar initial body weights were reared in an experimental facility until they were culled at 42 d of age. Thirty high RFI (HRFI) and 30 low RFI (LRFI) birds were selected to evaluate their growth performance, carcass characteristics, and muscle development. Transcriptome and weighted gene co-expression correlation network analyses of pectoral muscles were conducted on six LRFI and six HRFI ducks. The results revealed that selecting for LRFI significantly reduced feed consumption (P < 0.05) and improved feed efficiency without affecting the growth performance, slaughter rate, or meat quality of ducks (P > 0.05). Moreover, compared with HRFI ducks, LRFI ducks had a lower pectoral muscle fat content (P < 0.05), larger muscle fiber diameter and area (P < 0.05), and lower muscle fiber density (P < 0.05). There were significant differences in gene expression between LRFI and HRFI ducks, with 102 upregulated and 258 downregulated genes, which were enriched in the PPAR signaling pathway, adipocytokine signaling pathway, actin cytoskeleton regulation, ECM-receptor interaction, and focal adhesion. The expression of genes associated with fat and energy metabolism, including ACSL6, PCK1, APOC3, HMGCS2, PRKAG3, and G6PC1, was downregulated in LRFI ducks, and weighted gene co-expression correlation network analysis identified PRKAG3 as a hub gene. Our findings indicate that reduced mitochondrial energy metabolism may contribute to the RFI of slow-growing ducks, with PRKAG3 playing a pivotal role in this biological process. These findings provide novel insights into the molecular changes underlying RFI variation in slow-growing ducks.

Increased rumen Prevotella enhances BCAA synthesis, leading to synergistically increased skeletal muscle in myostatin-knockout cattle

Myostatin (MSTN) is a negative regulator of muscle growth, and its relationship with the gut microbiota is not well understood. In this study, we observed increase muscle area and branched-chain amino acids (BCAAs), an energy source of muscle, in myostatin knockout (MSTN-KO) cattle. To explore the link between increased BCAAs and rumen microbiota, we performed metagenomic sequencing, metabolome analysis of rumen fluid, and muscle transcriptomics. MSTN-KO cattle showed a significant increase in the phylum Bacteroidota (formerly Bacteroidetes), particularly the genus Prevotella (P = 3.12e-04). Within this genus, Prevotella_sp._CAG:732, Prevotella_sp._MSX73, and Prevotella_sp._MA2016 showed significant upregulation of genes related to BCAA synthesis. Functional enrichment analysis indicated enrichment of BCAA synthesis-related pathways in both rumen metagenomes and metabolomes. Additionally, muscle transcriptomics indicated enrichment in muscle fiber and amino acid metabolism, with upregulation of solute carrier family genes, enhancing BCAA transport. These findings suggest that elevated rumen Prevotella in MSTN-KO cattle, combined with MSTN deletion, synergistically improves muscle growth through enhanced BCAA synthesis and transport.

Full-length transcriptome sequencing of the longissimus dorsi muscle of yak and cattle-yak using nanopore technology

Short-read RNA sequencing has been used to sequence the transcriptome of the skeletal muscle of yak and cattle-yak; however, full-length transcripts cannot be obtained and alternative splicing (AS) events cannot be inferred using this sequencing approach. Here, we used Oxford Nanopore Technologies (ONT) full-length sequencing to sequence the transcriptome of the longissimus dorsi of yak and cattle-yak. A total of 20,323 novel genes and 172,870 novel transcripts were identified, and 159,700 novel transcripts were successfully annotated. A total of 157,812 AS events, 58,073 simple sequence repeats, 57,468 complete open reading frames, 2296 transcription factors, and 20,404 lncRNAs were detected. Differentially expressed transcripts (DETs) in the longissimus dorsi muscle of yak and cattle-yak were involved in the MAPK and JAK-STAT signaling pathways related to muscle development and growth. Protein–protein interaction analysis of DETs suggested that TNNI2 might make a major contribution to differences in muscle growth and meat quality traits between yak and cattle-yak. The results have enriched the transcriptome data of dorsal muscles, providing new ideas for the study of transcriptional regulation processes, and also providing useful information for the production of higher yields of yak meat.

Effects of High-Dose Vitamin D3 Supplementation on Pig Performance, Vitamin D Content in Meat, and Muscle Transcriptome in Pigs.

Vitamin D is known for its role in calcium homeostasis, bone health, and immune function. Recent research has explored its effects on muscle functionality and meat quality in pigs. This study examined high-dose vitamin D3 supplementation in pigs, focusing on growth, blood and tissue vitamin D3 levels, and muscle transcriptome changes. Thirty pigs were divided into three groups, given different amounts of oral supplementation: control, 5000 IU/kg and 10,000 IU/kg vitamin D3. Biochemical and haematological blood parameters, vitamin D content in blood and muscle, and kidney calcium content were evaluated. RNA-seq and qPCR analysed muscle transcriptome changes, while gene set enrichment analysis (GSEA) identified gene expression enrichments. Results showed that 5000 IU/kg vitamin D3 supplementation altered blood parameters like platelet anisocytosis and glucose levels but did not affect body weight, weight gain, or feed intake. Kidney calcium content increased with supplementation. The muscle (longissimus dorsi) vitamin D content increased, suggesting the potential for biofortified pork, although still not optimal as a dietary vitamin D source. Transcriptome analysis revealed minimal gene expression changes, with only the interferon-gamma receptor 2 (IFNGR2) gene differentially expressed at the highest dose. GSEA indicated enrichment in ATP metabolic processes and electron transport chain genes in the 5000 IU/kg group, and immune system, cholesterol, steroid, and fatty acid metabolism genes in the 10,000 IU/kg group. Despite literature suggesting a role for vitamin D in muscle gene expression and growth improvement, this study found its effects limited.

Transcriptional profiling of the M. complexus in naked neck chickens suggest a direct pleiotropic effect of GDF7 on feathering and reduced hatchability

BackgroundThe locus for naked neck (Na) in chickens reduces feather coverage and leads to increased heat dissipation from the body surface resulting in better adaptability to hot conditions. However, the Na gene is linked to significantly lower hatchability due to an increased late embryonic mortality. It has been argued that the causative gene GDF7 may have a direct pleiotropic effect on hatchability via its effect on muscle development. Thus, the study presented here analyses the transcriptome of the hatching muscle (M. complexus) and shows how GDF7 impacts development leading to reduced hatching rates in Na chickens.ResultsUsing 12 chicken embryos (6 x wildtype (Wt) and 6 x Na) RNA was extracted from the M. complexus of each embryo and sequenced. The resulting differential expression analyses led to the discovery of 461 differentially expressed (DE) genes in the M. complexus of the experimental group. Among those, 77 genes were of uncertain function (LOC symbols), with 31 were classified as uncharacterised. The regulation of a number of pathways involved in normal embryonic development, were found to be negatively influenced by the Na genotype. Further pathways involved in cell-cell adhesion, cell signalling pathways, and amino acid (AA) metabolism/transport were also observed. GDF7 (alias BMP12), whose localised overexpression in the neck skin causes the Na/Na phenotype, was significantly overexpressed in the M. complexus of Na/Na embryos, and shows a significant increase in the number of binding sites for the transcription factor PITX2 was also observed.ConclusionIn Na chickens, GDF7 is under the control of a mutated cis-regulatory element, whose actions are known to suppress the development and distribution of feathers through the sensitizing action of retinoic acid. In this study, a number of DE genes with over 10 retinoic acid response elements (RAREs) in close proximity were observed, indicating changes to the retinol metabolism. With the understanding that the Na/Na mutation leads to increased retinoic acid activity, this indicates a high likelihood of GDF7 excerpting a direct pleiotropic effect, not just in the observed reduction in feather patterning, but also impacting the development of the M.complexus, and consequently leading to the reduced hatchability observed in birds with the Na/Na genotype.Furthermore, the enrichment of PITX2 binding sites in proximity to DE genes in the M. complexus, also indicates that muscle development is still ongoing in Na embryos. This suggests that the M. complexus is not yet fully developed, further increasing the potential for late embryonic mortality in Na chicks at hatching.

Transcriptomic evidence for atopic dermatitis as a systemic disease in NC/Nga mice

BackgroundIn the current study, we evaluated whether atopic dermatitis (AD) affects the entire body rather than being limited to skin barrier damage and inflammation. We hypothesized that medium-term exposure of distant organs to systemic inflammatory cytokines in sub-chronic inflammatory skin diseases has detrimental effects on distant tissues.ResultsOur findings demonstrated the dysregulation of genes and pathways associated with inflammation and the skin barrier, as well as genes and pathways involved in muscle development that respond to chemicals or stress in muscle tissues, all of which were reversed by hydrocortisone (Hc) administration. The expression of Ces1d showed significant differences during disease onset and after treatment in both skin and skeletal muscle, suggesting that Ces1d is likely responsible for the alleviation of subchronic AD.ConclusionsUsing NC/Nga mice with AD-like symptoms, we compared the transcriptomes of the skeletal muscle (a tissue that is relatively distant from the skin) with those of the skin (the lesion induction site) before and after disease induction, after which Hc was administered. Although further study is needed to better understand the effects of Ces1d on AD, skeletal muscle was associated with AD pathogenesis, and AD-like symptoms appeared to affect the body in a systemic manner. Given the importance of evidence-based medicine and the development of precision medicine, our findings provide insights into the mechanisms of AD onset and progression.

Comparative analysis of acute eccentric contraction-induced changes to the skeletal muscle transcriptome in young and aged mice and humans.

Adaptations to skeletal muscle following resistance exercise are due in part to changes to the skeletal muscle transcriptome. While transcriptional changes in response to resistance exercise occur in young and aged muscle, aging alters this response. Rodent models have served great utility in defining regulatory factors that underscore the influence of mechanical load and aging on changes to skeletal muscle phenotype. Unilateral eccentric contractions in young and aged rodents are widely used to model resistance exercise in humans. However, the extent to which unilateral eccentric contractions in young and aged rodents mimics the transcriptional response in humans remains unknown. We re-analyzed two publicly available RNA sequencing datasets from young and aged mice and humans that were subjected to acute eccentric contractions to define key similarities and differences to the muscle transcriptional response following this exercise modality. The effect of aging on the number of contraction-sensitive genes, the distribution patterns of those genes into unique/common categories, and the cellular pathways associated with the differentially expressed genes (DEGs) were similar in mice and humans. However, there was little overlap between species when comparing specific contraction-sensitive DEGs within the same age group. There were strong intraspecies relationships for the common transcription factors predicted to influence the contraction-sensitive gene sets, whereas interspecies relationships were weak. Overall, these data demonstrate key similarities between mice and humans for the contraction-induced changes to the muscle transcriptome, but we posit species-specific responses exist and should be taken into consideration when attempting to translate rodent eccentric exercise models.

Contractile regulation of the glucocorticoid-sensitive transcriptome in young and aged skeletal muscle.

Elevated glucocorticoids alter the skeletal muscle transcriptome to induce a myopathy characterized by muscle atrophy, muscle weakness, and decreased metabolic function. These effects are more likely to occur and be more severe in aged muscles. Resistance exercise can blunt the development of glucocorticoid myopathy in young muscle, but the potential to oppose the signals initiating myopathy in aged muscle is unknown. To answer this, young (4-mo-old) and aged (24-to 25-mo-old) male C57BL/6 mice were randomized to receive either an intraperitoneal (IP) injection of dexamethasone (DEX; 2 mg/kg) or saline as a control. Two hours postinjections, the tibialis anterior (TA) muscles of mice were subjected to unilateral high-force contractions. Muscles were harvested 4 h later. The glucocorticoid- and contraction-sensitive genes were determined by RNA sequencing. The number of glucocorticoid-sensitive genes was similar between young and aged muscle. Contractions opposed changes to more glucocorticoid-sensitive genes in aged muscle, with this outcome primarily occurring when hormone levels were elevated. Glucocorticoid-sensitive gene programs opposed by contractions were primarily related to metabolism in young mice and muscle size regulation and inflammation in aged mice. In silico analysis implied peroxisome proliferator-activated receptor gamma-1 (PPARG) contributed to the contraction-induced opposition of glucocorticoid-sensitive genes in aged muscle. Increasing PPARG expression in the TA of aged mice using adeno-associated virus serotype 9 partially counteracted the glucocorticoid-induced reduction in runt-related transcription factor 1 (Runx1) mRNA content, recapitulating the effects observed by contractions. Overall, these data contribute to our understanding of the contractile regulation of the glucocorticoid transcriptome in aged skeletal muscle.NEW & NOTEWORTHY We establish the extent to which muscle contractions oppose changes to the glucocorticoid-sensitive transcriptome in both young and aged muscle. We also identify peroxisome proliferator-activated receptor gamma (PPARG) as a transcription factor likely contributing to contraction-induced opposition to the glucocorticoid transcriptome in aged muscle. Overall, these data contribute to our understanding of the contractile regulation of the glucocorticoid transcriptome.

Aquo-ethanolic extract of Lilii Bulbus attenuates dexamethasone-induced muscle loss and enhances muscle strength in experimental mice

Traditionally, Lilium lancifolium bulb is known for its ability to nourish yin, nourish the lungs, clear the heart, soothe coughs, reduce irritability, and calm the mind. In Oriental Medicine, it is categorized as a tonic remedy for alleviating symptoms of fatigue and enhancing the strength of bones and muscles.In this study, we aimed to validate the effectiveness of the aquo-ethanolic extract of Lilli Bulbus (LBE) in a dexamethasone (DEX)-induced muscle atrophy model, both in vitro and in vivo, and elucidate its mechanism of action through muscle transcriptome analysis. The effects of LBE on the viability and myotube density of C2C12 myoblasts and differentiated C2C12 myotubes with and without DEX treatment were investigated. LBE pretreatment protected C2C12 myoblast cells and increased the muscle density of C2C12 myotubes in response to DEX. LBE showed potent free radical scavenging activities in cell-free biochemical assays as well as antioxidant activity in C2C12 myoblasts. LBE also exhibited protective effects in an experimental animal model of DEX-induced muscle atrophy, showing muscular function and motor coordination recovery. Transcriptomic analysis of three different muscle tissues from mice with DEX-induced muscle atrophy showed that the regulation of the extracellular matrix was perturbed by glucocorticoid treatment, and this perturbation was reversed by LBE treatment.Collectively, LBE alleviated skeletal muscle loss and maintained muscle function from the chronic toxicity of DEX by protecting muscle cells from various stressful conditions, as well as DEX itself, inhibiting muscle protein degradation, and preserving the muscle tissue microenvironment.

Behavioural Monitoring Underlines Habituation to Repeated Stressor Stimuli in Farmed Gilthead Sea Bream (Sparus aurata) Reared at a High Stocking Density.

A confinement stress test with 75% tank space reduction and behavioural monitoring through tri-axial accelerometers externally attached to the operculum was designed. This procedure was validated by demonstrating the less pronounced stress response in gilthead sea bream than in European sea bass (950-1200 g). Our study aimed to assess habituation to high stocking densities with such procedure in gilthead sea bream. Animals (420-450 g) were reared (June-August) in a flow-through system at two stocking densities (CTRL: 10-15 kg/m3; HD: 18-24 kg/m3), with natural photoperiod and temperature (21-29 °C), and oxygen levels at 5.2-4.2 (CTRL) and 4.2-3.2 ppm (HD). At the end, blood and muscle were sampled for haematology and transcriptomic analyses, and external tissue damage was assessed by image-based scoring. Four days later, fish underwent a 45 min confinement stress test over two consecutive days. HD fish showed reduced feed intake, growth rates and haematopoietic activity. Muscle transcriptome changes indicated a shift from systemic to local growth regulation and a primed muscle regeneration over protein accretion in HD animals with slight external injuries. After stress testing, HD fish exhibited a decreased recovery time in activity and respiration rates, which was shorter after a second stressor exposure, confirming habituation to high densities.

Screening of hub genes for sepsis-induced myopathy by weighted gene co-expression network analysis and protein-protein interaction network construction

Sepsis-induced myopathy is one of the serious complications of sepsis, which severely affects the respiratory and peripheral motor systems of patients, reduces their quality of life, and jeopardizes their lives, as evidenced by muscle atrophy, loss of strength, and impaired regeneration after injury. The pathogenesis of sepsis-induced myopathy is complex, mainly including cytokine action, enhances free radical production in muscle, increases muscle protein hydrolysis, and decreases skeletal muscle protein synthesis, etc. The above mechanisms have been demonstrated in existing studies. However, it is still unclear how the overall pattern of gene co-expression affects the pathological process of sepsis-induced myopathy. Therefore, we intend to identify hub genes and signaling pathways. Weighted gene co-expression network analysis was our main approach to study gene expression profiles: skeletal muscle transcriptome in ICU patients with sepsis-induced multi-organ failure (GSE13205). After data pre-processing, about 15,181 genes were used to identify 13 co-expression modules. Then, 16 genes (FEM1B, KLHDC3, GPX3, NIFK, GNL2, EBNA1BP2, PES1, FBP2, PFKP, BYSL, HEATR1, WDR75, TBL3, and WDR43) were selected as the hub genes including 3 up-regulated genes and 13 down-regulated genes. Then, Gene Set Enrichment Analysis was performed to show that the hub genes were closely associated with skeletal muscle dysfunction, necrotic and apoptotic skeletal myoblasts, and apoptosis in sepsis-induced myopathy. Overall, 16 candidate biomarkers were certified as reliable features for more in-depth exploration of sepsis-induced myopathy in basic and clinical studies.

Multi-omics reveals the molecular mechanisms of rapid growth in distant hybrid fish

Distant hybridization usually results in heterosis. In previous studies, we obtained an improved fish (WR-II, 2n = 100) with rapid growth through distant hybridization. To investigate the molecular mechanisms underlying the rapid growth of WR-II, the intestinal structure, microbiome and metabolome of the gut and the transcriptome of muscle were compared between WR-II and its parents (WCC and RCC, 2n = 100). The results revealed that WR-II had more intestinal folds, and the height, width and goblet cell density of the intestinal folds were greater than those of its parents. The absolute abundances of the probiotics Ralstonia and Salinivibrio were significantly greater in WR-II than in the parents (p < 0.05), and the probiotic Cupriavidus was found in only WR-II. A total of 481 and 718 differentially abundant metabolites (DMs) were identified in WR-II vs. WCC and WR-II vs. RCC, respectively. These DMs were enriched mainly in pathways related to metabolism, protein synthesis and development, such as fumaric acid, sphingosine, betaine and 5′-adenylic acid (AMP). A total of 5680 and 11,795 differentially expressed genes (DEGs) were identified in WR-II vs. WCC and WR-II vs. RCC, respectively. These DEGs were enriched mainly in pathways related to protein synthesis and substance metabolism. Growth-related genes such as irs1, irs2, foxo1, igf1r, and akt were upregulated in WR-II. Multi-omics analysis revealed that Salinivibrio can promote the level of AMP, which then regulates the expression of irs1 and foxo1, thus promoting the growth of WR-II. This study revealed the mechanism of rapid growth of WR-II from the probiotics, metabolites and genes, which provides evidence for the molecular mechanism of heterosis.

Comparative Transcriptome Analysis of Bovine, Porcine, and Sheep Muscle Using Interpretable Machine Learning Models.

The growth and development of muscle tissue play a pivotal role in the economic value and quality of meat in agricultural animals, garnering close attention from breeders and researchers. The quality and palatability of muscle tissue directly determine the market competitiveness of meat products and the satisfaction of consumers. Therefore, a profound understanding and management of muscle growth is essential for enhancing the overall economic efficiency and product quality of the meat industry. Despite this, systematic research on muscle development-related genes across different species still needs to be improved. This study addresses this gap through extensive cross-species muscle transcriptome analysis, combined with interpretable machine learning models. Utilizing a comprehensive dataset of 275 publicly available transcriptomes derived from porcine, bovine, and ovine muscle tissues, encompassing samples from ten distinct muscle types such as the semimembranosus and longissimus dorsi, this study analyzes 113 porcine (n = 113), 94 bovine (n = 94), and 68 ovine (n = 68) specimens. We employed nine machine learning models, such as Support Vector Classifier (SVC) and Support Vector Machine (SVM). Applying the SHapley Additive exPlanations (SHAP) method, we analyzed the muscle transcriptome data of cattle, pigs, and sheep. The optimal model, adaptive boosting (AdaBoost), identified key genes potentially influencing muscle growth and development across the three species, termed SHAP genes. Among these, 41 genes (including NANOG, ADAMTS8, LHX3, and TLR9) were consistently expressed in all three species, designated as homologous genes. Specific candidate genes for cattle included SLC47A1, IGSF1, IRF4, EIF3F, CGAS, ZSWIM9, RROB1, and ABHD18; for pigs, DRP2 and COL12A1; and for sheep, only COL10A1. Through the analysis of SHAP genes utilizing Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, relevant pathways such as ether lipid metabolism, cortisol synthesis and secretion, and calcium signaling pathways have been identified, revealing their pivotal roles in muscle growth and development.

Knockout of &lt;i&gt;Hsp70&lt;/i&gt; genes modulates age-related transcriptomic changes in leg muscles, reduces locomotion speed and lifespan of &lt;i&gt;Drosophila melanogaster&lt;/i&gt;

The study investigated the effect of knockout of six Hsp70 genes (orthologues of the mammalian genes Hspa1a, Hspa1b, Hspa2 and Hspa8) on age-related changes in gene expression in the legs of Drosophila melanogaster, which contain predominantly skeletal muscle bundles. For this, the leg transcriptomic profile was examined in males of the w1118 control line and the Hsp70– line on the 7th, 23rd and 47th days of life. In w1118 flies, an age-related decrease in the locomotion (climbing) speed (a marker of functional state and endurance) was accompanied by a pronounced change in the transcriptomic profile of the leg skeletal muscles, which is conservative in nature. In Hsp70– flies, the median lifespan was shorter and the locomotion speed was significantly lower compare to the control; at the same time, complex changes in the age-related dynamics of the skeletal muscle transcriptome were observed. Mass spectrometry-based quantitative proteomic showed that 47-day-old Hsp70– flies, compared with w1118, demonstrated multidirectional changes in the content of key enzymes of glucose metabolism and fat oxidation (glycolysis, pentose phosphate pathway, Krebs cycle, beta-oxidation and oxidative phosphorylation). Such dysregulation may be associated with a compensatory increase in the expression of other genes encoding chaperones (small Hsp, Hsp40, 60, and 70), which regulate specific sets of target proteins. Taken together, our data show that knockout of six Hsp70 genes slightly reduces the median lifespan of flies, but significantly reduces the locomotion speed, which may be associated with complex changes in the transcriptome of the leg skeletal muscles and with multidirectional changes in the content of key enzymes of energy metabolism.

7138 Testosterone Modulation of Muscle Transcriptome Profile During Intensive Lifestyle Intervention in Older Men With Obesity and Hypogonadism

Abstract Disclosure: V. Viola: None. T. Samanta: None. M. Duremdes Nava: None. A. Celli: None. R.C. Villareal: None. N.H. Nguyen: None. G. Colleluori: None. Y. Barnouin: None. N. Napoli: None. C. Qualls: None. B.A. Kaipparettu: None. D.T. Villareal: None. Background: We reported that testosterone replacement added to lifestyle therapy can mitigate weight loss-induced reduction of muscle mass and bone mineral density (BMD) in older men with obesity and hypogonadism (Barnouin et al., J Clin Endocrinol Metab, 2021). Objective: To investigate the molecular mechanisms underlying the mitigation of muscle and BMD loss in response to testosterone replacement therapy during intensive lifestyle intervention in this at-risk population. Materials and Methods: Among the 83 older (≥ 65 y) men with obesity (BMI ≥ 30 kg/m2) and hypogonadism (early AM testosterone persistently &amp;lt;300 ng/dl) associated with frailty (PPT score ≤ 31) who were randomized into 26-week lifestyle therapy plus testosterone (LT+Test) or placebo (LT+Pbo), 38 underwent serial muscle biopsies for the muscle transcriptomics substudy. Results: Despite a similar 9% weight loss, lean body mass and thigh muscle volume decreased less in LT+Test than LT+Pbo (both -2% vs -4%, respectively; p=0.04). Hip BMD was preserved in LT+Test compared with LT+Pbo (0.4% vs -1.1%; p=0.03). Muscle strength increased similarly in LT+Test and LT+Pbo (23% vs 24%; p=0.95). Total testosterone increased more in LT+Test than LT+Pbo (133% vs 32%; p=0.01). Based on Next Generation Sequencing, of the 39,160 and 39,115 genes detected in LT+Test and LT+Pbo, respectively, 151 genes were differentially expressed (DEGs) in LT+Test and 114 in LT+Pbo group. Gene Ontology enrichment analyses revealed that in the LT+Test group, just four muscle-related terms (muscle organ development, muscle organ morphogenesis, regulation of skeletal muscle contraction, muscle atrophy) were downregulated, and one term (muscle system process) was upregulated while in the LT+Pbo, nine terms related to muscle (muscle system process, muscle tissue development, muscle organ development, skeletal muscle tissue development, skeletal muscle organ development, skeletal muscle cell differentiation, muscle organ morphogenesis, response to stimuli involved in regulation of muscle adaptation, muscle atrophy), and one term related to bone (bone mineralization involved in bone maturation) were downregulated. Notably, muscle system process was upregulated in the LT+Test but downregulated in the LT+Pbo. The RT-PCR analyses showed that LT+Test resulted in a higher expression of MYOD1 (p=0.02) and WNT4 (p= 0.08), key genes involved in muscle and bone metabolism, respectively, compared to LT+Pbo. Furthermore, we observed significantly higher mRNA expression of MYBPH (p=0.01), SCN3B (p=0.02), and DSC2 (p=0.01), genes involved in the muscle system process, in response to LT+Test compared to LT+Pbo. Conclusion: The addition of testosterone replacement to lifestyle therapy mitigates the weight loss-induced reduction of muscle mass and BMD via countering the weight loss-induced downregulation of genes involved in muscle and bone anabolism. Presentation: 6/2/2024

Profiling muscle transcriptome in mice exposed to microgravity using gene set enrichment analysis

Space exploration’s advancement toward long-duration missions prompts intensified research on physiological effects. Despite adaptive physiological stability in some variables, persistent changes affect genome integrity, immune response, and cognitive function. Our study, utilizing multi-omics data from GeneLab, provides crucial insights investigating muscle atrophy during space mission. Leveraging NASA GeneLab’s data resources, we apply systems biology-based analyses, facilitating comprehensive understanding and enabling meta-analysis. Through transcriptomics, we establish a reference profile of biological processes underlying muscle atrophy, crucial for intervention development. We emphasize the often-overlooked role of glycosylation in muscle atrophy. Our research sheds light on fundamental molecular mechanisms, bridging gaps between space research and terrestrial conditions. This study underscores the importance of interdisciplinary collaboration and data-sharing initiatives like GeneLab in advancing space medicine research.

Prenatal and progressive coenzyme Q10 administration to mitigate muscle dysfunction in mitochondrial disease.

ADCK genesencode aarF domain-containing mitochondrial kinases involved in coenzyme Q (CoQ) biosynthesis and regulation. Haploinsufficiency of ADCK2 in humans leads to adult-onset physical incapacity with reduced mitochondrial CoQ levels in skeletal muscle, resulting in mitochondrial myopathy and alterations in fatty acid β-oxidation. The sole current treatment for CoQ deficiencies is oral administration of CoQ10, which causes only partial recovery with postnatal treatment, underscoring the importance of early diagnosis for successful intervention. We used Adck2 heterozygous mice to examine the influence of this gene on muscle structure, function and regeneration throughout development, growth and ageing. This investigation involved techniques including immunohistochemistry, analysis of CoQ levels, mitochondrial respiratory content, muscle transcriptome analysis and functional tests. We demonstrated that Adck2 heterozygous mice exhibit defects from embryonic development, particularly in skeletal muscle (1102 genes deregulated). Adck2 heterozygous embryos were 7% smaller in size and displayed signs of delayed development. Prenatal administration of CoQ10 could mitigate these embryonic defects. Heterozygous Adck2 mice also showed a decrease in myogenic cell differentiation, with more severe consequences in 'aged' mice (41.63% smaller) (P<0.01). Consequently, heterozygous Adck2 mice displayed accelerated muscle wasting associated with ageing in muscle structure (P<0.05), muscle function (less grip strength capacity) (P<0.001) and muscle mitochondrial respiration (P<0.001). Furthermore, progressive CoQ10 administration conferred protective effects on mitochondrial function (P<0.0001) and skeletal muscle (P<0.05). Our work uncovered novel aspects of CoQ deficiencies, revealing defects during embryonic development in mammals for the first time. Additionally, we identified the gradual establishment and progression of the deleterious Adck2 mouse phenotype. Importantly, CoQ10 supplementation demonstrated a protective effect when initiated during development.