Human Chondrocyte Dedifferentiation Bulk RNA-Seq
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE327285 | GEO | 2026/04/14
REPOSITORIES: GEO
Similar Datasets
Project description:Objective: When primary chondrocytes are cultured in monolayer, they undergo dedifferentiation during which they lose their phenotype and their capacity to form cartilage. Dedifferentiation is an obstacle for cell therapy for cartilage degeneration. In this study, we aimed to systemically evaluate the changes in gene expression during dedifferentiation of human articular chondrocytes to identify underlying mechanisms. Methods: RNA was isolated from monolayer-cultured primary human articular chondrocytes at serial passages. Gene expression was analyzed by microarray. Based on the microarray analysis, relevant genes and pathways were identified. Their functions in chondrocyte dedifferentiation were further investigated in detail. Results: In vitro expanded human chondrocytes showed progressive changes in gene expression during dedifferentiation. Strikingly, an overall decrease in total gene expression was detected. Genes in the Wnt and BMP pathways exhibited significant changes in expression. The non-canonical rather than the canonical Wnt pathway was found to be involved in the loss of collagen II synthesis. BMP2 was able to decelerate the dedifferentiation and reinforce the maintenance of chondrocyte phenotype in monolayer culture. DNA methylation was in part responsible for the expression downregulation of a set of genes. Conclusion: Our study revealed the roles of ERK, Wnt and BMP pathways as well as DNA methylation in chondrocyte dedifferentiation in monolayer culture. RNA human chondrocytes were allowed to dedifferentiate for 8 passages. RNA was isolated at week 0, 2 ,4, 6 and 8, which was subjected to whole genome gene expression analysis.
2012-11-14 | E-GEOD-42235 | biostudies-arrayexpress
Project description:Autologous chondrocyte implantation (ACI) is an effective method to treat chronic articular cartilage injury in recent years, which requires a large number of human hyaline chondrocytes. Unfortunately, human hyaline chondrocytes often undergo dedifferentiation in vitro. Thus, it is important to elucidate the mechanism of dedifferentiation for the application of ACI technology. Long noncoding RNAs (lncRNA) play a regulatory role in gene expression in many pathological and physiological processes. However, the role of lncRNAs in human hyaline chondrocyte dedifferentiation remains unclear. The aim of this study was to investigate the expression profiles of lncRNAs in human hyaline chondrocyte dedifferentiation during in vitro culture. First, we cultured human hyaline chondrocytes in vitro and detected the expression of COL1A1, COL2A1, and SOX-9 in passage 1 (P1) and 5 (P5) chondrocytes using quantitative real-time polymerase chain reaction (qRT-PCR), immunofluorescence, and western blotting. Then, we analyzed the expression profiles of lncRNAs and mRNAs in P1 and P5 chondrocytes by microarray analysis.
2020-02-25 | GSE145817 | GEO
Project description:Objective: When primary chondrocytes are cultured in monolayer, they undergo dedifferentiation during which they lose their phenotype and their capacity to form cartilage. Dedifferentiation is an obstacle for cell therapy for cartilage degeneration. In this study, we aimed to systemically evaluate the changes in gene expression during dedifferentiation of human articular chondrocytes to identify underlying mechanisms. Methods: RNA was isolated from monolayer-cultured primary human articular chondrocytes at serial passages. Gene expression was analyzed by microarray. Based on the microarray analysis, relevant genes and pathways were identified. Their functions in chondrocyte dedifferentiation were further investigated in detail. Results: In vitro expanded human chondrocytes showed progressive changes in gene expression during dedifferentiation. Strikingly, an overall decrease in total gene expression was detected. Genes in the Wnt and BMP pathways exhibited significant changes in expression. The non-canonical rather than the canonical Wnt pathway was found to be involved in the loss of collagen II synthesis. BMP2 was able to decelerate the dedifferentiation and reinforce the maintenance of chondrocyte phenotype in monolayer culture. DNA methylation was in part responsible for the expression downregulation of a set of genes. Conclusion: Our study revealed the roles of ERK, Wnt and BMP pathways as well as DNA methylation in chondrocyte dedifferentiation in monolayer culture.
2012-11-14 | GSE42235 | GEO
Project description:Objectives: Articular cartilage damage has become a universal health burden. Despite the recent progresses in cell-based cartilage regeneration, chondrocyte dedifferentiation has compromised the clinical outcomes, which is frequently seen in chondrocyte expansion and osteoarthritis, involving functional phenotype loss. However, its concept remains elusive with unknown intermediate process and mechanisms. Here we demonstrated a time-lapse atlas of chondrocyte dedifferentiation, to provide molecular details and informative biomarkers for clinical chondrocyte evaluation. Methods: Single-cell RNA sequencing (scRNA-seq) was employed to dissect the chondrocyte dedifferentiation and identify distinct cellular subpopulations. To validate the findings, live-cell metabolic assay, high-resolution imaging and ¡°assay for transposase-accessible chromatin with high throughput sequencing¡± (ATAC-seq) were conducted. Using a chemical inhibitor BTB06584 affecting on mitochondrial F1F0ATPase, we revealed the recovery potential of early and late dedifferentiated chondrocytes. Results:Our findings shape a biphasic model consist of early and late dedifferentiation stages. Early dedifferentiated chondrocytes uniquely obtained a transient glycolytic phenotype with an activation of metabolic and anti-oxidant genes; late dedifferentiated chondrocytes exhibited ultrastructural changes including mitochondrion damages and stress-associated chromatin remodeling. Using a chemical inhibitor BTB06584, we revealed that early and late dedifferentiated chondrocytes possessed distinguished recovery potential from functional phenotype loss. BTB06584 treatment ameliorated early phenotype loss through inhibiting MAPK pathway. Notably, this two-stage transition was validated in human chondrocyte culture. An image-based approach was established for clinical utilization, to efficiently predict chondrocytes plasticity with stage-specific biomarkers. Conclusion: Thus this study lays a foundation for future clinical chondrocyte quality regulation and provides insights for deeper understanding of chondrocyte dedifferentiation.
2022-01-20 | GSE193742 | GEO
Project description:Objectives: Articular cartilage damage has become a universal health burden. Despite the recent progresses in cell-based cartilage regeneration, chondrocyte dedifferentiation has compromised the clinical outcomes, which is frequently seen in chondrocyte expansion and osteoarthritis, involving functional phenotype loss. However, its concept remains elusive with unknown intermediate process and mechanisms. Here we demonstrated a time-lapse atlas of chondrocyte dedifferentiation, to provide molecular details and informative biomarkers for clinical chondrocyte evaluation. Methods: Single-cell RNA sequencing (scRNA-seq) was employed to dissect the chondrocyte dedifferentiation and identify distinct cellular subpopulations. To validate the findings, live-cell metabolic assay, high-resolution imaging and ¡°assay for transposase-accessible chromatin with high throughput sequencing¡± (ATAC-seq) were conducted. Using a chemical inhibitor BTB06584 affecting on mitochondrial F1F0ATPase, we revealed the recovery potential of early and late dedifferentiated chondrocytes. Results:Our findings shape a biphasic model consist of early and late dedifferentiation stages. Early dedifferentiated chondrocytes uniquely obtained a transient glycolytic phenotype with an activation of metabolic and anti-oxidant genes; late dedifferentiated chondrocytes exhibited ultrastructural changes including mitochondrion damages and stress-associated chromatin remodeling. Using a chemical inhibitor BTB06584, we revealed that early and late dedifferentiated chondrocytes possessed distinguished recovery potential from functional phenotype loss. BTB06584 treatment ameliorated early phenotype loss through inhibiting MAPK pathway. Notably, this two-stage transition was validated in human chondrocyte culture. An image-based approach was established for clinical utilization, to efficiently predict chondrocytes plasticity with stage-specific biomarkers. Conclusion: Thus this study lays a foundation for future clinical chondrocyte quality regulation and provides insights for deeper understanding of chondrocyte dedifferentiation.
2022-01-20 | GSE193743 | GEO
Project description:The pathology of failure in currently used biological treatments (cell therapies and microfracture) for cartilage repair or early osteoarthritis (OA) is poorly understood. We aimed to identify a reliable panel of biological predictors, present in synovial fluid, which can be used in the preoperative setting to optimise patient selection and therapy efficacy. The-long term aim is to reduce the number of patients who progress to end-stage OA and require knee replacement by making earlier, less invasive treatments more effective. In this first stage, we have taken synovial fluid aspirates from patients undergoing autologous chondrocyte implantation (ACI) at our centre in Oswestry, UK. Synovial fluids (SFs) were obtained from 14 ACI responders (mean Lysholm improvement of 33 (17-54)) and 13 non-responders (mean Lysholm decrease of 14 (4-46)) at the two stages of surgery (cartilage harvest and chondrocyte implantation). Dynamic range compression of synovial fluids coupled with label-free quantification mass spectrometry (MS), was used in an unbiased approach to identify predictive markers of ACI success or failure and to investigate the biological pathways involved in the clinical response to ACI.
2017-07-04 | PXD005220 | Pride
Project description:Cartilage injury does not naturally repair and lead to osteoarthritis. Engineered chondrocyte sheets are readily transplantable and create neocartilage in vivo. This experiment compares global mRNA profiling of adult and juvenile chondrocyte sheets.
2025-06-30 | GSE235008 | GEO
Project description:Monolayer cultures of primary chondrocytes undergo morphological changes that have been broadly characterized as de-differentiation. Transcriptional profiling was used to evaluate changes in gene expression during this process. Articular cartilage was harvested from a single Standardbred horse; the chondrocytes were isolated and then maintained in monolayer culture for up to 14 days. Chondrocytes were collected on Day 1 and Day 14 of culture and snap frozen in liquid nitrogen. Total RNA was isolated, subjected to one round of linear RNA amplification, and then applied to an equine-specific cDNA microarray composed of 9322 elements. Three biological replicates were analyzed at each time point using a dye-swap experimental design. One hundred six transcripts were present at levels greater than or equal to five-fold higher in Day 1 chondrocytes relative to the cells collected at Day 14. Conversely, 68 transcripts were present at levels greater than or equal to five-fold higher in Day 14 chondrocytes. Northern blot hybridization validated the microarray data by confirming the down-regulation of steady state mRNA levels for type II procollagen and aggrecan core protein and the up-regulation of type I procollagen. Gene-by-gene and cluster analyses will be used to compare the process of “de-differentiation” in primary culture to the developmental stages of normal chondrocyte differentiation and to the fibrocartilage repair tissue that forms in osteoarthritic lesions. Keywords: articular cartilage, de-differentiation, horse, cDNA microarray This is a direct comparison between one and fourteen day cultured chondrocyte transcriptomes. Three sets of technical replicates were compared. For each comparison and its dye-swap, one Day 1 technical replicate was randomly compared to one Day 14 technical replicate.
2012-05-31 | E-GEOD-14255 | biostudies-arrayexpress
Project description:Background: Results obtained from our previous study using a label-free quantitation (LF) proteomic approach in which dynamic range compression was used to profile lower abundance proteins, demonstrated few proteins that were differentially abundant within the synovial fluid (SF) when comparing Autologous Chondrocyte Implantation (ACI) responders and non-responders at baseline (1). This study builds upon our previous findings by assessing higher abundance proteins within these SFs; providing a more global proteome analysis from which we can understand more fully the biology underlying ACI success or failure. Methods: Isobaric tagging for relative and absolute quantitation (iTRAQ) proteomics was used to assess SFs from ACI responders (mean Lysholm improvement of 33; n=14) and non-responders (mean Lysholm decrease of 14; n=13) at the two stages of surgery (cartilage harvest and chondrocyte implantation). Differentially abundant proteins were investigated using pathway analyses and the iTRAQ proteomic dataset was combined with our published proteomic dataset of dynamically compressed SFs, from which an interactome network model of systemic protein interactions was generated. Results: iTRAQ proteomics has confirmed our previous finding that there is a marked proteome shift in response to cartilage harvest (70 and 54 proteins demonstrating ≥2.0 fold change between Stages I and II in responders and non-responders, respectively) and has highlighted 28 proteins that were differentially abundant between responders and non-responders to ACI, that were not found in the LF study; 16 of which were altered at baseline. Two protein abundance changes (Complement C1S subcomponent and Matrix metalloproteinase 3 (MMP3), have been biochemically validated. Combination of the iTRAQ and LF proteomic datasets has generated in-depth SF proteome information that has been used to generate interactome networks representing ACI success or failure, from which functional pathways that are dysregulated in ACI non-responders have been identified. Conclusions: Several candidate biomarkers for baseline prediction of ACI outcome have been identified. A holistic overview of the SF proteome in responders and non-responders to ACI has been profiled providing a better understanding of the biological pathways underlying clinical outcome, particularly the differential response to cartilage harvest in non-responders.
2018-05-03 | PXD008321 | Pride
Project description:The purpose of this study was to understand the how the supression of H3K9me3 impacts the phenotype of chondrocytes during a monolayer expansion process which causes chondrocyte dedifferentiation. Therefore, we compared the mRNA expression profiles of chondrocytes isolated from H3K9M (inducible histone H3.3 lysine-to-methionine mutant) and H3WT (inducibly expressed wild-type H3.3) after 16 population doublings.
2023-05-03 | GSE190339 | GEO