A Transcriptome Sequencing Study on Genome-Wide Gene Expression Differences of 3D Cultured Chondrocytes in Hydrogel Scaffolds with Different Gel Density

Genome-wide analysis for nanofiber induced global gene expression profile: A study in MC3T3-E1 cells by RNA-Seq

Nanofibers are one of the attractive biomaterials that can provide unique environments to direct cell behaviors. However, how nanofiber structure affects the global gene expression of laden cells remains unclear. Herein, high-throughput mRNA sequencing (RNA-seq) is applied to analyze the transcriptome of the MC3T3-E1 cells (a model osteoblast cell line) cultured on electrospun nanofibers. The cell-adhesive poly(L-lactide) nanofibers and membranes are developed by the mussel-inspired coating of gelatin-dopamine conjugate under H₂O₂-mediated oxidation. The MC3T3-E1 cells cultured on nanofibers exhibit elongated morphology and increased proliferation compared with those on membranes. The differences in global gene expression profiles are determined by RNA-seq, in which 905 differentially expressed genes (DEGs) are identified. Significantly, the DEGs related to cytoskeleton, promotion of cell cycle progression, cell adhesion, and cell proliferation, are higher expressed in the cells on nanofibers, while the DEGs involved in cell-cycle arrest and osteoblast mineralization are up-regulated in the cells on membranes. This study elucidates the roles of nanofiber structure in affecting gene expression of laden cells at the whole transcriptome level, and it will lay the foundation for understanding nanofiber-guided cell behaviors.

A transcriptome sequencing study on the effect of macro-pores in hydrogel scaffolds on global gene expression of laden human cartilage chondrocytes

The macro-porous hydrogel scaffolds can not only enhance the proliferation of laden chondrocytes but also favor the deposition of hyaline cartilaginous extracellular matrix, however, the underlying molecular mechanism is still unclear. Herein, the global gene expression of human cartilage chondrocytes (HCCs) encapsulated in traditional hydrogel (Gel) constructs and micro-cavitary gel (MCG) constructs are investigated by using high-throughput RNA sequencing (RNA-seq). The differentially expressed genes (DEGs) between the HCCs cultured in Gel and MCG constructs have been identified via bioinformatics analysis. Significantly, the DEGs that promote cell proliferation (e.g. POSTN, MKI67, KIF20A) or neo-cartilage formation (e.g. COL2, ASPN, COMP, FMOD, FN1), are more highly expressed in MCG constructs than in Gel constructs, while the expressions of the DEGs associated with chondrocyte hypertrophy (e.g. EGR1, IBSP) are upregulated in Gel constructs. The expression of representative DEGs is verified at both mRNA and protein levels. Besides, cellular viability and morphology as well as the enriched signaling pathway of DEGs are studied in detail. These results of this work may provide data for functional tissue engineering of cartilage.

Application of Alginate Hydrogels for Next-Generation Articular Cartilage Regeneration

The articular cartilage has insufficient intrinsic healing abilities, and articular cartilage injuries often progress to osteoarthritis. Alginate-based scaffolds are attractive biomaterials for cartilage repair and regeneration, allowing for the delivery of cells and therapeutic drugs and gene sequences. In light of the heterogeneity of findings reporting the benefits of using alginate for cartilage regeneration, a better understanding of alginate-based systems is needed in order to improve the approaches aiming to enhance cartilage regeneration with this compound. This review provides an in-depth evaluation of the literature, focusing on the manipulation of alginate as a tool to support the processes involved in cartilage healing in order to demonstrate how such a material, used as a direct compound or combined with cell and gene therapy and with scaffold-guided gene transfer procedures, may assist cartilage regeneration in an optimal manner for future applications in patients.

Polystyrene nanoparticles induced neurodevelopmental toxicity in Caenorhabditis elegans through regulation of dpy-5 and rol-6

Micro- and nano- polystyrene particles have been widely detected in environment, posing potential threats to human health. This study was designed to evaluate the neurodevelopmental toxicity of polystyrene nanoparticles (NPs) in Caenorhabditis elegans (C. elegans), to screen crucial genes and investigate the underlying mechanism. In wild-type C. elegans, polystyrene NPs (diameter 50 nm) could concentration-dependently induce significant inhibition in body length, survival rate, head thrashes, and body bending, accompanying with increase of reactive oxygen species (ROS) production, lipofuscin accumulation, and apoptosis and decrease of dopamine (DA) contents. Moreover, pink-1 mutant was demonstrated to alleviate the locomotion disorders and oxidative damage induced by polystyrene NPs, indicating involvement of pink-1 in the polystyrene NPs-induced neurotoxicity. RNA sequencing results revealed 89 up-regulated and 56 down-regulated differently expressed genes (DEGs) response to polystyrene NPs (100 μg/L) exposure. Gene Ontology (GO) enrichment analysis revealed that predominant enriched DEGs were correlated with biological function of cuticle development and molting cycle. Furthermore, mutant strains test showed that the neurodevelopmental toxicity and oxidative stress responses induced by 50 nm polystyrene NPs were regulated by dpy-5 and rol-6. In general, polystyrene NPs induced obvious neurodevelopmental toxicity in C. elegans through oxidative damage and dopamine reduction. Crucial genes dpy-5 and rol-6 might participate in polystyrene NPs-induced neurodevelopmental toxicity through regulation on synthesis and deposition of cuticle collagen.

Three-dimensional (3D) hydrogel serves as a platform to identify potential markers of chondrocyte dedifferentiation by combining RNA sequencing

Dedifferentiation of chondrocyte greatly restricts its function and application, however, it is poorly understood except a small number of canonical markers. The non-cell-adhesive property endows polysaccharide hydrogel with the ability to maintain chondrocyte phenotype, which can serve as a platform to identify new molecular markers and therapeutic targets of chondrocyte dedifferentiation. In this study, the high-throughput RNA sequencing (RNA-seq) was first performed on articular chondrocytes at primary (P0) and passage 1 (P1) stages to explore the global alteration of gene expression along with chondrocyte dedifferentiation. Significantly, several potential marker genes, such as PFKFB3, KDM6B, had been identified via comparatively analyzing their expression in P0 and P1 chondrocytes as well as in 3D constructs (i.e. chondrocyte-laden alginate hydrogel and HA-MA hydrogel) at both mRNA and protein level. Besides, the changes in cellular morphology and enriched pathway of differentially expressed genes during chondrocyte dedifferentiation was studied in detail. This study developed the use of hydrogel as a platform to investigate chondrocyte dedifferentiation; the results provided new molecular markers and potential therapeutic targets of chondrocyte dedifferentiation.