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RNA sequence of the subcutaneous microenvironment surrounding the rabbit's engineered cartilage

ABSTRACT: Purpose: To identify how axitinib stabilized the rabbit's engineered cartilage through the niche Methods: Rabbit's engineered cartilage was encapsulated in the PCL/collagen nanofibrous membrane containing no axitinib (0%-Axitinib group) or 3% axitinib (3%-Axitinib group) and implanted into nude mice. After 12 weeks of implantation, samples from the 0%-Axitinib group and 3%-Axitinib group were harvested, with the murine tissues entangled. Transcriptional profiles were generated by deep sequencing, in triplicate, using an Illumina HiSeqTM2000 machine, and filtered using Fastp software. The trimmed reads were mapped to the mouse genome (mm10, genome.UCSC.edu) using the STAR software to identify the transcriptional information in the niche of engineered cartilage. Then, the DESeq2 “counts” function of the R package was used to normalize gene expression levels based on the number of total reads of each sample. Differentially expressed genes between the 0%-Axitinib group and 3%-Axitinib group were identified as meeting the criteria of fold change ≥ 1.5 and P-value＜0.05. Lastly, we used Metascape (http://metascape.org) for gene ontology analysis. Results: Using an optimized data analysis workflow, we mapped about 20 to 30 million sequence reads per sample to the mouse genome (build mm10) and identified 20318 transcripts in the 0%-Axitinib and 3%-Axitinib groups. 837 genes were differentially expressed by more than 1.5-fold, p-value <0.05, with 313 genes downregulated and 524 genes upregulated in the 3%-Axitinib group. Gene ontology (GO) analysis revealed that the genes downregulated in the 3%-Axitinib group were mainly enriched in endothelial development, angiogenesis, and immune response. Genes upregulated in the 3%-Axitinib group were mainly enriched in response to hypoxia, Hif-1 signaling pathway, cartilage differentiation and development, and muscle structure development. Altered expression of 15 genes was further illustrated by heatmap, demonstrating the inhibited angiogenesis and improved chondrogenesis. Especially, Timp1, as a response to hypoxia, was remarkably upregulated, which also in turn inhibited the activity of matrix metalloproteinases (MMPs) and played an important role in preventing ossification. Conclusion: In this study, we proposed the first detailed transcriptional analysis of the effects of the sustainable and localized release of axitinib on the subcutaneous niche of engineered cartilage. The sustainable and localized release of axitinib created a relatively avascular, hypoxia, and low immune response niche in the 3%-Axitinib group. In this niche, Timp1 was remarkably upregulated, which inhibited the activity of MMPs and prevented endochondral ossification.

ORGANISM(S): Mus musculus

PROVIDER: GSE160825 | GEO | 2021/08/16

REPOSITORIES: GEO

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Project description:Baker2017 - The role of cytokines, MMPs and fibronectin fragments osteoarthritis This model is described in the article: Mathematical modelling of cytokines, MMPs and fibronectin fragments in osteoarthritic cartilage. Baker M, Brook BS, Owen MR. J Math Biol 2017 Feb; : Abstract: Osteoarthritis (OA) is a degenerative disease which causes pain and stiffness in joints. OA progresses through excessive degradation of joint cartilage, eventually leading to significant joint degeneration and loss of function. Cytokines, a group of cell signalling proteins, present in raised concentrations in OA joints, can be classified into pro-inflammatory and anti-inflammatory groups. They mediate cartilage degradation through several mechanisms, primarily the up-regulation of matrix metalloproteinases (MMPs), a group of collagen-degrading enzymes. In this paper we show that the interactions of cytokines within cartilage have a crucial role to play in OA progression and treatment. We develop a four-variable ordinary differential equation model for the interactions between pro- and anti-inflammatory cytokines, MMPs and fibronectin fragments (Fn-fs), a by-product of cartilage degradation and up-regulator of cytokines. We show that the model has four classes of dynamic behaviour: homoeostasis, bistable inflammation, tristable inflammation and persistent inflammation. We show that positive and negative feedbacks controlling cytokine production rates can determine either a pre-disposition to OA or initiation of OA. Further, we show that manipulation of cytokine, MMP and Fn-fs levels can be used to treat OA, but we suggest that multiple treatment targets may be essential to halt or slow disease progression. This model is hosted on BioModels Database and identified by: MODEL1704120000. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Project description:Successfully replacing damaged cartilage with tissue-engineered constructs requires integration with the host tissue and could benefit from leveraging the native tissue's intrinsic healing capacity; however, efforts are limited by a poor understanding of how cartilage repairs minor defects. Here, we investigated the conditions that foster natural cartilage tissue repair to identify strategies that might be exploited to enhance the integration of engineered/ grafted cartilage with host tissue. We damaged porcine articular cartilage explants and using a combination of pulsed SILAC-based proteomics, ultrastructural imaging, and catabolic enzyme blocking strategies reveal that integration of damaged cartilage surfaces is not driven by neo-matrix synthesis, but rather local depletion of proteoglycans. ADAMTS4 expression and activity are upregulated in injured cartilage explants, but integration could be reduced by inhibiting metalloproteinase activity with TIMP3. These observations suggest that catabolic enzyme-mediated proteoglycan depletion likely allows existing collagen fibrils to undergo cross-linking, fibrillogenesis, or entanglement, driving integration. Catabolic enzymes are often considered pathophysiological markers of osteoarthritis. Our findings suggest that damage-induced upregulation of metalloproteinase activity may be a part of a healing response that tips towards tissue destruction under pathological conditions and in osteoarthritis, but could also be harnessed in tissue engineering strategies to mediate repair. Statement of significance: Cartilage tissue engineering strategies require graft integration with the surrounding tissue; however, how the native tissue repairs minor injuries is poorly understood. We applied pulsed SILACbased proteomics, ultrastructural imaging, and catabolic enzyme blocking strategies to a porcine cartilage explant model and found that integration of damaged cartilage surfaces is driven by catabolic enzyme-mediated local depletion of proteoglycans. Although catabolic enzymes have been implicated in cartilage destruction in osteoarthritis, our findings suggest that damage-induced upregulation of metalloproteinase activity may be a part of a healing response that tips towards tissue destruction under pathological conditions. They also suggest that this natural cartilage tissue repair process could be harnessed in tissue engineering strategies to enhance the integration of engineered cartilage with host tissue.

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RNA sequence of the subcutaneous microenvironment surrounding the rabbit's engineered cartilage

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