The Myotube Analyzer: how to assess myogenic features in muscle stem cells

SEPO-FI: Deep-learning based software to calculate fusion index of muscle cells

The fusion index is a critical metric for quantitatively assessing the transformation of in vitro muscle cells into myotubes in the biological and medical fields. Traditional methods for calculating this index manually involve the labor-intensive counting of numerous muscle cell nuclei in images, which necessitates determining whether each nucleus is located inside or outside the myotubes, leading to significant inter-observer variation. To address these challenges, this study proposes a three-stage process that integrates the strengths of pattern recognition and deep-learning to automatically calculate the fusion index. The experimental results demonstrate that the proposed process achieves significantly higher performance in cell nuclei detection and classification, with an F1-score of 0.953, whereas traditional object detection methods achieve less than 0.5. In addition, the fusion index obtained using the proposed method is closely aligned with the human-assessed values, showing minimal discrepancy and strong agreement with human evaluations. This process is incorporated into the development of "SEPO-FI" as public software, automating cell detection and classification to enable effective fusion index calculation and broaden access to this methodology within the scientific community.

Quantitative analysis of the dexamethasone side effect on human-derived young and aged skeletal muscle by myotube and nuclei segmentation using deep learning

MOTIVATION

Skeletal muscle cells (skMCs) combine together to create long, multi-nucleated structures called myotubes. By studying the size, length, and number of nuclei in these myotubes, we can gain a deeper understanding of skeletal muscle development. However, human experimenters may often derive unreliable results owing to the unusual shape of the myotube, which causes significant measurement variability.

RESULTS

We propose a new method for quantitative analysis of the dexamethasone side effect on human-derived young and aged skeletal muscle by simultaneous myotube and nuclei segmentation using deep learning combined with post-processing techniques. The deep learning model outputs myotube semantic segmentation, nuclei semantic segmentation, and nuclei center, and post-processing applies a watershed algorithm to accurately distinguish overlapped nuclei and identify myotube branches through skeletonization. To evaluate the performance of the model, the myotube diameter and the number of nuclei were calculated from the generated segmented images and compared with the results calculated by human experimenters. In particular, the proposed model produced outstanding outcomes when comparing human-derived primary young and aged skMCs treated with dexamethasone. The proposed standardized and consistent automated image segmentation system for myotubes is expected to help streamline the drug-development process for skeletal muscle diseases.

AVAILABILITY AND IMPLEMENTATION

The code and the data are available at https://github.com/tdn02007/QA-skMCs-Seg.

The circular RNA circNFIX regulates MEF2C expression in muscle satellite cells in spastic cerebral palsy

Cerebral palsy (CP) is a pediatric onset disorder with poorly understood molecular causes and progression, making early diagnosis difficult. Circular RNAs are regulatory RNAs that show promise as biomarkers in various diseases but the role of circular RNAs in CP is beginning to be understood. This study identified the role of circNFIX in regulating the expression of myocyte-specific enhancer factor 2C (MEF2C), an important transcription factor for sarcomere development. We found that circNFIX is downregulated in the muscle cells of individuals with CP, and its localization shifts toward the nucleus as visualized using single-molecule resolution imaging. The decreased expression of circNFIX, MEF2C, and MEF2C targets persisted throughout myoblasts to myotubes differentiation, and in the skeletal muscle tissue. Bioinformatic and experimental validation confirmed that circNFIX acts as a sponge for miR373-3p, a microRNA that represses MEF2C translation. In normal muscle, circNFIX derepresses MEF2C translation by sponging miR373-3p, allowing for normal sarcomere generation. In CP, reduced circNFIX expression results in loss of miRNA sponging, leading to lower MEF2C expression and downregulation of sarcomere genes, potentially causing shortened and dysfunctional muscle fibers. Knockdown (KD) of circNFIX reduced myogenic capacity of myoblasts to fuse and form myotubes similar to CP cells evident from the lower fusion index in CP and KD as compared to control myotubes. This is the first study reporting reduction of MEF2C in CP and single-molecule resolution imaging of circNFIX's subcellular distribution and its role in CP, suggesting circNFIX as a potential therapeutic target and biomarker for early CP diagnosis.

MyoFInDer: An AI-Based Tool for Myotube Fusion Index Determination

The fusion index is a key indicator for quantifying the differentiation of a myoblast population, which is often calculated manually. In addition to being time-consuming, manual quantification is also error prone and subjective. Several software tools have been proposed for addressing these limitations but suffer from various drawbacks, including unintuitive interfaces and limited performance. In this study, we describe MyoFInDer, a Python-based program for the automated computation of the fusion index of skeletal muscle. At the core of MyoFInDer is a powerful artificial intelligence-based image segmentation model. MyoFInDer also determines the total nuclei count and the percentage of stained area and allows for manual verification and correction. MyoFInDer can reliably determine the fusion index, with a high correlation to manual counting. Compared with other tools, MyoFInDer stands out as it minimizes the interoperator variability, minimizes process time and displays the best correlation to manual counting. Therefore, it is a suitable choice for calculating fusion index in an automated way, and gives researchers access to the high performance and flexibility of a modern artificial intelligence model. As a free and open-source project, MyoFInDer can be modified or extended to meet specific needs.

The myokine FGF21 associates with enhanced survival in ALS and mitigates stress-induced cytotoxicity

Amyotrophic lateral sclerosis (ALS) is an age-related and fatal neurodegenerative disease characterized by progressive muscle weakness. There is marked heterogeneity in clinical presentation, progression, and pathophysiology with only modest treatments to slow disease progression. Molecular markers that provide insight into this heterogeneity are crucial for clinical management and identification of new therapeutic targets. In a prior muscle miRNA sequencing investigation, we identified altered FGF pathways in ALS muscle, leading us to investigate FGF21. We analyzed human ALS muscle biopsy samples and found a large increase in FGF21 expression with localization to atrophic myofibers and surrounding endomysium. A concomitant increase in FGF21 was detected in ALS spinal cords which correlated with muscle levels. FGF21 was increased in the SOD1G93A mouse beginning in presymptomatic stages. In parallel, there was dysregulation of the co-receptor, β-Klotho. Plasma FGF21 levels were increased and high levels correlated with slower disease progression, prolonged survival, and increased body mass index. In NSC-34 motor neurons and C2C12 muscle cells expressing SOD1G93A or exposed to oxidative stress, ectopic FGF21 mitigated loss of cell viability. In summary, FGF21 is a novel biomarker in ALS that correlates with slower disease progression and exerts trophic effects under conditions of cellular stress.

CCL2 signaling promotes skeletal muscle wasting in non-tumor and breast tumor models

Despite advancements in treatment, approximately 25% of patients with breast cancer experience long-term skeletal muscle wasting (SMW), which limits mobility, reduces drug tolerance and adversely impacts survival. By understanding the underlying molecular mechanisms of SMW, we may be able to develop new strategies to alleviate this condition and improve the lives of patients with breast cancer. Chemokines are small soluble factors that regulate homing of immune cells to tissues during inflammation. In breast cancers, overexpression of C-C chemokine ligand 2 (CCL2) correlates with unfavorable prognosis. Elevated levels of CCL2 in peripheral blood indicate possible systemic effects of this chemokine in patients with breast cancer. Here, we investigated the role of CCL2 signaling on SMW in tumor and non-tumor contexts. In vitro, increasing concentrations of CCL2 inhibited myoblast and myotube function through C-C chemokine receptor 2 (CCR2)-dependent mechanisms involving JNK, SMAD3 and AMPK signaling. In healthy mice, delivery of recombinant CCL2 protein promoted SMW in a dose-dependent manner. In vivo knockdown of breast tumor-derived CCL2 partially protected against SMW. Overall, chronic, upregulated CCL2-CCR2 signaling positively regulates SMW, with implications for therapeutic targeting.

Generation of Mature Toxoplasma gondii Bradyzoites in Human Immortalized Myogenic KD3 Cells

Toxoplasma gondii is a zoonotic protozoan parasite and one of the most successful foodborne pathogens. Upon infection and dissemination, the parasites convert into the persisting, chronic form called bradyzoites, which reside within cysts in muscle and brain tissue. Despite their importance, bradyzoites remain difficult to investigate directly, owing to limited in vitro models. In addition, the need for new drugs targeting the chronic stage, which is underlined by the lack of eradicating treatment options, remains difficult to address since in vitro access to drug-tolerant bradyzoites remains limited. We recently published the use of a human myotube-based bradyzoite cell culture system and demonstrated its applicability to investigate the biology of T. gondii bradyzoites. Encysted parasites can be functionally matured during long-term cultivation in these immortalized cells and possess many in vivo-like features, including pepsin resistance, oral infectivity, and antifolate resistance. In addition, the system is scalable, enabling experimental approaches that rely on large numbers, such as metabolomics. In short, we detail the cultivation of terminally differentiated human myotubes and their subsequent infection with tachyzoites, which then mature to encysted bradyzoites within four weeks at ambient CO2 levels. We also discuss critical aspects of the procedure and suggest improvements. Key features • This protocol describes a scalable human myotube-based in vitro system capable of generating encysted bradyzoites featuring in vivo hallmarks. • Bradyzoite differentiation is facilitated through CO2 depletion but without additional artificial stress factors like alkaline pH. • Functional maturation occurs over four weeks.

Hypoxia promotes proliferation and inhibits myogenesis in broiler satellite cells

Breast muscle myopathies in broilers compromise meat quality and continue to plague the poultry industry. Broiler breast muscle myopathies are characterized by impaired satellite cell (SC)-mediated repair, and localized tissue hypoxia and dysregulation of oxygen homeostasis have been implicated as contributing factors. The present study was designed to test the hypothesis that hypoxia disrupts the ability of SC to differentiate and form myotubes, both of which are key components of myofiber repair, and to determine the extent to which effects are reversed by restoration of oxygen tension. Primary SC were isolated from pectoralis major of young (5 d) Cobb 700 chicks and maintained in growth conditions or induced to differentiate under normoxic (20% O2) or hypoxic (1% O2) conditions for up to 48 h. Hypoxia enhanced SC proliferation while inhibiting myogenic potential, with decreased fusion index and suppressed myotube formation. Reoxygenation after hypoxia partially reversed effects on both proliferation and myogenesis. Western blotting showed that hypoxia diminished myogenin expression, activated AMPK, upregulated proliferation markers, and increased molecular signaling of cellular stress. Hypoxia also promoted accumulation of lipid droplets in myotubes. Targeted RNAseq identified numerous differentially expressed genes across differentiation under hypoxia, including several genes that have been associated with myopathies in vivo. Altogether, these data demonstrate localized hypoxia may influence SC behavior in ways that disrupt muscle repair and promote the formation of myopathies in broilers.

Exploring the Potential of Olive Flounder Processing By-Products as a Source of Functional Ingredients for Muscle Enhancement

Olive flounder (OF) is a widely aqua-cultivated and recognized socioeconomic resource in Korea. However, more than 50% of by-products are generated when processing one OF, and there is no proper way to utilize them. With rising awareness and interest in eco-friendly bio-materialization recycling, this research investigates the potential of enzymatic hydrolysis of OF by-products (OFB) to produce functional ingredients. Various enzymatic hydrolysates of OFB (OFBEs) were generated using 11 commercial enzymes. Among them, Prozyme 2000P-assisted OFBE (OFBP) exhibited the highest protein content and yield, as well as low molecularization. The muscle regenerative potential of OFBEs was evaluated using C2C12 myoblasts, revealing that OFBP positively regulated myoblast differentiation. In an in vitro Dex-induced myotube atrophy model, OFBP protected against muscle atrophy and restored myotube differentiation and Dex-induced reactive oxygen species (ROS) production. Furthermore, zebrafish treated with OFBEs showed improved locomotor activity and body weight, with OFBP exhibiting outstanding restoration in the Dex-induced muscle atrophy zebrafish in vivo model. In conclusion, OFBEs, particularly OFBP, produce hydrolysates with enhanced physiological usability and muscle regenerative potential. Further research on its industrial application and mechanistic insights is needed to realize its potential as a high-quality protein food ingredient derived from OF processing by-products.

Resident muscle stem cell myogenic characteristics in postnatal muscle growth impairments in children with cerebral palsy

Children with cerebral palsy (CP), a perinatal brain alteration, have impaired postnatal muscle growth, with some muscles developing contractures. Functionally, children are either able to walk or primarily use wheelchairs. Satellite cells are muscle stem cells (MuSCs) required for postnatal development and source of myonuclei. Only MuSC abundance has been previously reported in contractured muscles, with myogenic characteristics assessed only in vitro. We investigated whether MuSC myogenic, myonuclear, and myofiber characteristics in situ differ between contractured and noncontractured muscles, across functional levels, and compared with typically developing (TD) children with musculoskeletal injury. Open muscle biopsies were obtained from 36 children (30 CP, 6 TD) during surgery; contracture correction for adductors or gastrocnemius, or from vastus lateralis [bony surgery in CP, anterior cruciate ligament (ACL) repair in TD]. Muscle cross sections were immunohistochemically labeled for MuSC abundance, activation, proliferation, nuclei, myofiber borders, type-1 fibers, and collagen content in serial sections. Although MuSC abundance was greater in contractured muscles, primarily in type-1 fibers, their myogenic characteristics (activation, proliferation) were lower compared with noncontractured muscles. Overall, MuSC abundance, activation, and proliferation appear to be associated with collagen content. Myonuclear number was similar between all muscles, but only in contractured muscles were there associations between myonuclear number, MuSC abundance, and fiber cross-sectional area. Puzzlingly, MuSC characteristics were similar between ambulatory and nonambulatory children. Noncontractured muscles in children with CP had a lower MuSC abundance compared with TD-ACL injured children, but similar myogenic characteristics. Contractured muscles may have an intrinsic deficiency in developmental progression for postnatal MuSC pool establishment, needed for lifelong efficient growth and repair.

Morphological and Molecular Responses of Lateolabrax maculatus Skeletal Muscle Cells to Different Temperatures

Temperature strongly modulates muscle development and growth in ectothermic teleosts; however, the underlying mechanisms remain largely unknown. In this study, primary cultures of skeletal muscle cells of Lateolabrax maculatus were conducted and reared at different temperatures (21, 25, and 28 °C) in both the proliferation and differentiation stages. CCK-8, EdU, wound scratch and nuclear fusion index assays revealed that the proliferation, myogenic differentiation, and migration processes of skeletal muscle cells were significantly accelerated as the temperature raises. Based on the GO, GSEA, and WGCNA, higher temperature (28 °C) induced genes involved in HSF1 activation, DNA replication, and ECM organization processes at the proliferation stage, as well as HSF1 activation, calcium activity regulation, myogenic differentiation, and myoblast fusion, and sarcomere assembly processes at the differentiation stage. In contrast, lower temperature (21 °C) increased the expression levels of genes associated with DNA damage, DNA repair and apoptosis processes at the proliferation stage, and cytokine signaling and neutrophil degranulation processes at the differentiation stage. Additionally, we screened several hub genes regulating myogenesis processes. Our results could facilitate the understanding of the regulatory mechanism of temperature on fish skeletal muscle growth and further contribute to utilizing rational management strategies and promoting organism growth and development.