Mimicking Muscle Stem Cell Quiescence in Culture: Methods for Synchronization in Reversible Arrest

A Reversible Neural Stem Cell Quiescence and Activation Culture System for Metabolic Study

Stem cells in vivo can transit between quiescence and activation, two metabolically distinct states. It is increasingly appreciated that cell metabolism assumes profound roles in stem cell maintenance and tissue homeostasis. However, the lack of suitable models greatly hinders our understanding of the metabolic control of stem cell quiescence and activation. In the present study, we have utilized classical signaling pathways and developed a cell culture system to model reversible NSC quiescence and activation. Unlike activated ones, quiescent NSCs manifested distinct morphology characteristics, cell proliferation, and cell cycle properties but retained the same cell proliferation and differentiation potentials once reactivated. Further transcriptomic analysis revealed that extensive metabolic differences existed between quiescent and activated NSCs. Subsequent experimentations confirmed that NSC quiescence and activation transition was accompanied by a dramatic yet coordinated and dynamic shift in RNA metabolism, protein synthesis, and mitochondrial and autophagy activity. The present work not only showcases the broad utilities of this powerful in vitro NSC quiescence and activation culture system but also provides timely insights for the field and warrants further investigations.

Key concepts in muscle regeneration: muscle "cellular ecology" integrates a gestalt of cellular cross-talk, motility, and activity to remodel structure and restore function

This review identifies some key concepts of muscle regeneration, viewed from perspectives of classical and modern research. Early insights noted the pattern and sequence of regeneration across species was similar, regardless of the type of injury, and differed from epimorphic limb regeneration. While potential benefits of exercise for tissue repair was debated, regeneration was not presumed to deliver functional restoration, especially after ischemia-reperfusion injury; muscle could develop fibrosis and ectopic bone and fat. Standard protocols and tools were identified as necessary for tracking injury and outcomes. Current concepts vastly extend early insights. Myogenic regeneration occurs within the environment of muscle tissue. Intercellular cross-talk generates an interactive system of cellular networks that with the extracellular matrix and local, regional, and systemic influences, forms the larger gestalt of the satellite cell niche. Regenerative potential and adaptive plasticity are overlain by epigenetically regionalized responsiveness and contributions by myogenic, endothelial, and fibroadipogenic progenitors and inflammatory and metabolic processes. Muscle architecture is a living portrait of functional regulatory hierarchies, while cellular dynamics, physical activity, and muscle-tendon-bone biomechanics arbitrate regeneration. The scope of ongoing research-from molecules and exosomes to morphology and physiology-reveals compelling new concepts in muscle regeneration that will guide future discoveries for use in application to fitness, rehabilitation, and disease prevention and treatment.

mRNP granule proteins Fmrp and Dcp1a differentially regulate mRNP complexes to contribute to control of muscle stem cell quiescence and activation

Background

During skeletal muscle regeneration, satellite stem cells use distinct pathways to repair damaged myofibers or to self-renew by returning to quiescence. Cellular/mitotic quiescence employs mechanisms that promote a poised or primed state, including altered RNA turnover and translational repression. Here, we investigate the role of mRNP granule proteins Fragile X Mental Retardation Protein (Fmrp) and Decapping protein 1a (Dcp1a) in muscle stem cell quiescence and differentiation.

Methods

Using isolated single muscle fibers from adult mice, we established differential enrichment of mRNP granule proteins including Fmrp and Dcp1a in muscle stem cells vs. myofibers. We investigated muscle tissue homeostasis in adult Fmr1-/- mice, analyzing myofiber cross-sectional area in vivo and satellite cell proliferation ex vivo. We explored the molecular mechanisms of Dcp1a and Fmrp function in quiescence, proliferation and differentiation in a C2C12 culture model. Here, we used polysome profiling, imaging and RNA/protein expression analysis to establish the abundance and assembly status of mRNP granule proteins in different cellular states, and the phenotype of knockdown cells.

Results

Quiescent muscle satellite cells are enriched for puncta containing the translational repressor Fmrp, but not the mRNA decay factor Dcp1a. MuSC isolated from Fmr1^-/- mice exhibit defective proliferation, and mature myofibers show reduced cross-sectional area, suggesting a role for Fmrp in muscle homeostasis. Expression and organization of Fmrp and Dcp1a varies during primary MuSC activation on myofibers, with Fmrp puncta prominent in quiescence, but Dcp1a puncta appearing during activation/proliferation. This reciprocal expression of Fmrp and Dcp1a puncta is recapitulated in a C2C12 culture model of quiescence and activation: consistent with its role as a translational repressor, Fmrp is enriched in non-translating mRNP complexes abundant in quiescent myoblasts; Dcp1a puncta are lost in quiescence, suggesting stabilized and repressed transcripts. The function of each protein differs during proliferation; whereas Fmrp knockdown led to decreased proliferation and lower cyclin expression, Dcp1a knockdown led to increased cell proliferation and higher cyclin expression. However, knockdown of either Fmrp or Dcp1a led to compromised differentiation. We also observed cross-regulation of decay versus storage mRNP granules; knockdown of Fmrp enhances accumulation of Dcp1a puncta, whereas knockdown of Dcp1a leads to increased Fmrp in puncta.

Conclusions

Taken together, our results provide evidence that the balance of mRNA turnover versus utilization is specific for distinct cellular states.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13395-021-00270-9.

Effect of Long-Term 3D Spheroid Culture on WJ-MSC

The aim of our work was to develop a protocol enabling a derivation of mesenchymal stem/stromal cell (MSC) subpopulation with increased expression of pluripotent and neural genes. For this purpose we used a 3D spheroid culture system optimal for neural stem cells propagation. Although 2D culture conditions are typical and characteristic for MSC, under special treatment these cells can be cultured for a short time in 3D conditions. We examined the effects of prolonged 3D spheroid culture on MSC in hope to select cells with primitive features. Wharton Jelly derived MSC (WJ-MSC) were cultured in 3D neurosphere induction medium for about 20 days in vitro. Then, cells were transported to 2D conditions and confront to the initial population and population constantly cultured in 2D. 3D spheroids culture of WJ-MSC resulted in increased senescence, decreased stemness and proliferation. However long-termed 3D spheroid culture allowed for selection of cells exhibiting increased expression of early neural and SSEA4 markers what might indicate the survival of cell subpopulation with unique features.

Methods to Mimic In Vivo Muscle Cell Biology in Primary Human Myoblasts Using Quiescence as a Guidepost in Regenerative Medicine Research

Regenerative medicine research and testing of new therapeutics for muscle-related human diseases call for a deeper understanding of how human myoblasts gain and maintain quiescence in vitro versus in vivo. The more closely we can experimentally simulate the in vivo environment, the more relevance in vitro research on myoblasts will have. In this context, isolation of satellite cells from muscle tissue causes activation while myoblasts remain activated in culture, thus not simulating quiescence as in their in vivo niche. Cells synchronized for cell cycle present a good starting point for experimental intervention. In the past, myoblast quiescence has been induced using suspension culture (SuCu) and, recently, by knockout serum replacement (KOSR)-supplemented culture media. We assessed the proportion of cells in G0 and molecular regulators after combining the two quiescence-inducing approaches. Quiescence was induced in primary human myoblasts (PHMs) in vitro using KOSR-treatment for 10 days or suspension in viscous media for 2 days (SuCu), or suspension combined with KOSR-treatment for 2 days (blended method, SuCu-KOSR). Quiescence and synchronization were achieved with all three protocols (G0/G1 cell cycle arrest >90% cells). Fold-change of cell cycle controller p21 mRNA for KOSR and SuCu was 3.23 ± 0.30 and 2.86 ± 0.15, respectively. Since this was already a significant change (p < 0.05), no further change was gained with the blended method. But SuCu-KOSR significantly decreased Ki67 (p = 0.0019). Myogenic regulatory factors, Myf5 and MyoD gene expression in PHMs were much more suppressed (p = 0.0004 and p = 0.0034, respectively) in SuCu-KOSR, compared to SuCu alone. In conclusion, a homogenous pool of quiescent primary myoblasts synchronized in the G0 cell cycle phase was achieved with cells from three different donors regardless of the experimental protocol. Myogenic dedifferentiation at the level of Myogenic Regulatory Factors was greater when exposed to the blend of suspension and serum-free culture. We suggest that this blended new protocol can be considered in future biomedical research if differentiation is detected too early during myoblast expansion. This shall also inform new ways to bridge the in vitro and in vivo divides in regenerative medicine research.

Comparative nuclear matrix proteome analysis of skeletal muscle cells in different cellular states

The nuclear matrix (NuMat) serves as the structural framework for organizing and maintaining nuclear architecture, however, the mechanisms by which this non-chromatin compartment is constructed and regulated are poorly understood. This study presents a proteomic analysis of the NuMat isolated from cultured skeletal muscle cells in three distinct cellular states- proliferating myoblasts (MBs), terminally differentiated myotubes (MTs), and mitotically quiescent (G0) myoblasts. About 40% of the proteins identified were found to be common in the NuMat proteome of these morphologically and functionally distinct cell states. These proteins, termed as the "core NuMat," define the stable, conserved, structural constituent of the nucleus, with functions such as RNA splicing, cytoskeletal organization, and chromatin modification, while the remaining NuMat proteins showed cell-state specificity, consistent with a more dynamic and potentially regulatory function. Specifically, myoblast NuMat was enriched in cell cycle, DNA replication and repair proteins, myotube NuMat in muscle differentiation and muscle function proteins, while G0 NuMat was enriched in metabolic, transcription, and transport proteins. These findings offer a new perspective for a cell-state-specific role of nuclear architecture and spatial organization, integrated with diverse cellular processes, and implicate NuMat proteins in the control of the cell cycle, lineage commitment, and differentiation.

Damaged Myofiber-Derived Metabolic Enzymes Act as Activators of Muscle Satellite Cells

Muscle satellite cells are normally quiescent but are rapidly activated following muscle damage. Here, we investigated whether damaged myofibers influence the activation of satellite cells. Our findings revealed that satellite cells are directly activated by damaged-myofiber-derived factors (DMDFs). DMDFs induced satellite cells to enter the cell cycle; however, the cells stayed at the G1 phase and did not undergo S phase, and these cells were reversible to the quiescent-like state. Proteome analysis identified metabolic enzymes, including GAPDH, as DMDFs, whose recombinant proteins stimulated the activation of satellite cells. Satellite cells pre-exposed to the DMDFs demonstrated accelerated proliferation ex vivo. Treatment with recombinant GAPDH prior to muscle injury promoted expansion of the satellite cell population in vivo. Thus, our results indicate that DMDFs are not only a set of biomarkers for muscle damage, but also act as moonlighting proteins involved in satellite cell activation at the initial step of muscle regeneration.

The primary cilium dampens proliferative signaling and represses a G2/M transcriptional network in quiescent myoblasts

BACKGROUND

Reversible cell cycle arrest (quiescence/G0) is characteristic of adult stem cells and is actively controlled at multiple levels. Quiescent cells also extend a primary cilium, which functions as a signaling hub. Primary cilia have been shown to be important in multiple developmental processes, and are implicated in numerous developmental disorders. Although the association of the cilium with G0 is established, the role of the cilium in the control of the quiescence program is still poorly understood.

RESULTS

Primary cilia are dynamically regulated across different states of cell cycle exit in skeletal muscle myoblasts: quiescent myoblasts elaborate a primary cilium in vivo and in vitro, but terminally differentiated myofibers do not. Myoblasts where ciliogenesis is ablated using RNAi against a key ciliary assembly protein (IFT88) can exit the cell cycle but display an altered quiescence program and impaired self-renewal. Specifically, the G0 transcriptome in IFT88 knockdown cells is aberrantly enriched for G2/M regulators, suggesting a focused repression of this network by the cilium. Cilium-ablated cells also exhibit features of activation including enhanced activity of Wnt and mitogen signaling and elevated protein synthesis via inactivation of the translational repressor 4E-BP1.

CONCLUSIONS

Taken together, our results show that the primary cilium integrates and dampens proliferative signaling, represses translation and G2/M genes, and is integral to the establishment of the quiescence program.

Distinguishing States of Arrest: Genome-Wide Descriptions of Cellular Quiescence Using ChIP-Seq and RNA-Seq Analysis

Regenerative potential in adult stem cells is closely associated with the establishment of-and exit from-a temporary state of quiescence. Emerging evidence not only provides a rationale for the link between lineage determination programs and cell cycle regulation but also highlights the understanding of quiescence as an actively maintained cellular program, encompassing networks and mechanisms beyond mitotic inactivity or metabolic restriction. Interrogating the quiescent genome and transcriptome using deep-sequencing technologies offers an unprecedented view of the global mechanisms governing this reversibly arrested cellular state and its importance for cell identity. While many efforts have identified and isolated pure target stem cell populations from a variety of adult tissues, there is a growing appreciation that their isolation from the stem cell niche in vivo leads to activation and loss of hallmarks of quiescence. Thus, in vitro models that recapitulate the dynamic reversibly arrested stem cell state in culture and lend themselves to comparison with the activated or differentiated state are useful templates for genome-wide analysis of the quiescence network.In this chapter, we describe the methods that can be adopted for whole genome epigenomic and transcriptomic analysis of cells derived from one such established culture model where mouse myoblasts are triggered to enter or exit quiescence as homogeneous populations. The ability to synchronize myoblasts in G₀ permits insights into the genome in "deep quiescence." The culture methods for generating large populations of quiescent myoblasts in either 2D or 3D culture formats are described in detail in a previous chapter in this series (Arora et al. Methods Mol Biol 1556:283-302, 2017). Among the attractive features of this model are that genes isolated from quiescent myoblasts in culture mark satellite cells in vivo (Sachidanandan et al., J Cell Sci 115:2701-2712, 2002) providing a validation of its approximation of the molecular state of true stem cells. Here, we provide our working protocols for ChIP-seq and RNA-seq analysis, focusing on those experimental elements that require standardization for optimal analysis of chromatin and RNA from quiescent myoblasts, and permitting useful and revealing comparisons with proliferating myoblasts or differentiated myotubes.

Muscle Stem Cells: A Model System for Adult Stem Cell Biology

Skeletal muscle stem cells, originally termed satellite cells for their position adjacent to differentiated muscle fibers, are absolutely required for the process of skeletal muscle repair and regeneration. In the last decade, satellite cells have become one of the most studied adult stem cell systems and have emerged as a standard model not only in the field of stem cell-driven tissue regeneration but also in stem cell dysfunction and aging. Here, we provide background in the field and discuss recent advances in our understanding of muscle stem cell function and dysfunction, particularly in the case of aging, and the potential involvement of muscle stem cells in genetic diseases such as the muscular dystrophies.