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Genome-wide occupancy profiling of FoxO1 in human primary chondrocytes

ABSTRACT: Genome-wide occupancy profiling of FoxO1 in human primary chondrocytes

PROVIDER: PRJNA602530 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10920076.fastq.gz	Fastqsanger.gz
	SRR10920077.fastq.gz	Fastqsanger.gz
	SRR10920078.fastq.gz	Fastqsanger.gz
	SRR10920079.fastq.gz	Fastqsanger.gz
	SRR10920080.fastq.gz	Fastqsanger.gz

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Genome-wide occupancy profiling of FoxO1 in human primary chondrocytes

Project description:FoxO1 regulates extracellular matrix and circadian rhythm genes in human primary chondrocytes

2020-01-22 | GSE144026 | GEO

Genome-Wide Occupancy Profiling Reveals Critical Roles of FoxO1 in Regulating Extracellular Matrix and Circadian Rhythm Genes in Human Chondrocytes.

Project description:ObjectiveOsteoarthritis (OA) is the most common age-related joint disease. With aging and in OA, the expression of FoxO transcription factors is reduced, diminishing their chondroprotective actions. In order to elucidate the molecular mechanisms by which FoxO1 protects chondrocytes, we sought to identify the genome-wide occupancy profile of FoxO1.MethodsWe performed FoxO1 chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq) on human primary chondrocytes. ChIP-Seq data were integrated with RNA sequencing (RNA-Seq) data sets. Bioinformatics results were confirmed in primary chondrocytes that were treated with a FoxO1 inhibitor.ResultsAnalysis of FoxO1 ChIP-Seq on human primary chondrocytes showed that pathways implicated in OA pathogenesis are mainly regulated by FoxO1 binding to tissue-specific enhancers with suboptimal binding sites (20% of the peaks), while more ubiquitous FoxO1 pathways are regulated at the promoter level through interaction with its canonical binding motif (7% of the peaks). Integrating FoxO1 occupancy data with RNA-Seq data comparing OA and healthy human cartilage revealed 428 putative FoxO1 target genes that are dysregulated in OA. Pathway analysis showed enrichment for genes belonging to the senescence pathway (logP = -6.73), extracellular matrix (ECM) pathway (logP = -12.97), and circadian clock pathway (logP = -6.30), which suggests that FoxO1 dysregulation plays an important role in their abnormal expression in OA. Using an inhibitor of FoxO1, we confirmed that FoxO1 regulates these pathways in cultured human chondrocytes.ConclusionFoxO1 regulates ubiquitous and cartilage-specific genes in chondrocytes by using different mechanisms. The FoxO1 transcriptional network is a key player in regulating homeostasis, ECM, and circadian clock genes and plays an important role in the abnormal expression of these pathways observed in OA pathogenesis.

| S-EPMC7813518 | biostudies-literature

RNA-seq of Runx2 cKO primary chondrocytes.

Project description:Purpose: To demonstrate Runx2's association with organizing the extracellular matrix in primary chondrocytes. Method: RNA samples were collected from primary chondrocytes of 5-day-old Col2a1-CreERT2;Runx2fl/fl and Runx2fl/fl mice, cultured with or without IL-1beta. Results: Thirty-three genes cultured without IL-1beta and 45 genes with IL-1beta were up- or down-regulated by more than 2-fold in the Runx2 knockout in primary chondrocytes. Conclusions: Genes including collagen fibers were down-regulated in Runx2 cKO primary chondrocytes.

2021-01-21 | GSE165084 | GEO

ChIP-seq of Runx2-FLAG in primary chondrocytes.

Project description:Purpose: To demonstrate the role of Transcription factor Runx2 in primary chondrocytes with or without IL-1beta. Method: Fragmented DNA samples were collected from primary chondrocytes of 5-day-old Runx2-Biotin-FLAG-tag mice, cultured with or without IL-1beta. Results: More than 20,000 and 10,000 peaks were gained from chondrocytes without and with IL-1beta, resepectively. Conclusions: Runx2 are associated cellular process and extracellular matrics transcription in primary chondrocytes.

2021-01-21 | GSE165086 | GEO

RNA-seq of Runx2 cKO primary chondrocytes.

Project description:RNA-seq of Runx2 cKO primary chondrocytes.

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Effect of depletion of Myl3 in primary chondrocytes from mice

Project description:To investigate the function of Myl3 in in primary chondrocytes, we generated Col2a1-Cre: Myl3fl/fl (Myl3-KO) conditional knockout mice.We then performed RNA sequencing analysis with primary chondrocytes from Myl3-KO or control mice.

2023-05-16 | GSE232325 | GEO

Charaterising the surfaceome of primary equine chondrocytes

Project description:The aim of this study was to characterize the surfaceome of primary equine chondrocytes isolated from healthy joints following exposure to the pro-inflammatory cytokines interleukin-1-beta (IL-1β) and tumour necrosis factor-alpha (TNF-α). We employed combined methodology that we recently developed for investigating the surfaceome in stem cells. Membrane proteins were isolated using an aminooxy-biotinylation technique and analysed by mass spectrometry using high throughput shotgun proteomics. Amongst the 431 unique cell surface proteins identified, a high percentage of low-abundance proteins, such as ion channels, receptors and transporter molecules were detected. A high number of proteins exhibited different levels of expression following chondrocyte stimulation with pro-inflammatory cytokines. LPR-1, thrombospondin, VDAC1-2 and annexin A1 were chosen for further analysis and validation by western blotting as proteins of special interest. Our results provide, for the first time, a repository for proteomic data on differentially expressed low-abundance membrane proteins on the surface of chondrocytes in response to pro-inflammatory stimuli.

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