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Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptional profiles of genes in the early stage of osteoclastogenesis

ABSTRACT: Osteoclast (OC) differentiation undergoes a two-step process: commitment of hematopoietic progenitor cells to tartrate-resistant acid phosphatase (TRAcP) positive OC precursors (OCPs), and fusion of OCPs into multinucleated OCs. In order to identify transcriptional profiles of genes in the transitional phase between OC commitment and fusion in OCG, AffymetrixM-BM-. Mouse Gene 1.0 ST arrays were performed on total RNA extracted from mouse (SV129/BL6 ) monocytes and pre-osteoclasts (pre-OCs), primed with macrophage colony-stimulated factor (M-CSF) or M-CSF and soluble recombinant receptor activator of NF-M-PM-:B ligand (sRANKL), respectively. The analysis identified 656 RANKL-up or down-regulated in the early stage of osteoclastogenesis. Monocytes isolated from mouse bone marrow were stimulated with M-CSF and soluble RANKL (m + r), or M-CSF alone (m).

ORGANISM(S): Mus musculus

SUBMITTER: Yongqiang Wang

PROVIDER: E-GEOD-54779 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcriptional profiles of genes in the early stage of osteoclastogenesis

Project description:Osteoclast (OC) differentiation undergoes a two-step process: commitment of hematopoietic progenitor cells to tartrate-resistant acid phosphatase (TRAcP) positive OC precursors (OCPs), and fusion of OCPs into multinucleated OCs. In order to identify transcriptional profiles of genes in the transitional phase between OC commitment and fusion in OCG, Affymetrix® Mouse Gene 1.0 ST arrays were performed on total RNA extracted from mouse (SV129/BL6 ) monocytes and pre-osteoclasts (pre-OCs), primed with macrophage colony-stimulated factor (M-CSF) or M-CSF and soluble recombinant receptor activator of NF-кB ligand (sRANKL), respectively. The analysis identified 656 RANKL-up or down-regulated in the early stage of osteoclastogenesis.

2014-02-17 | GSE54779 | GEO

The cell-based control and underlying mechanism for inflammatory bone loss

Project description:Inflammatory bone loss (IBL) is primarily caused by elevated osteoclast (OC) activity during chronic inflammation. However, the specific OC precursors (OCPs) responding to the inflammatory signals and the underlying mechanisms leading to IBL are poorly understood. We identified two OCP subsets: Ly6ChiCD11bhi inflammatory OCPs (iOCPs) specifically responsible for IBL, and homeostatic Ly6ChiCD11blo (hOCPs), not involved in IBL. Functional and proteomic characterization revealed that while the iOCPs are rare and display low osteoclastogenecity under normal conditions, they expand during chronic inflammation and generate OCs with enhanced activity. In contrast, the hOCPs are abundant and highly osteoclastogenic under normal conditions but are unresponsive to the inflammatory environment and generate OCs with low activity. We identified TNF-α and the S100A8/A9 proteins as key regulators, specifically controlling the iOCP response during chronic inflammation. Our findings offer iOCPs as new therapeutic targets and potential biomarkers to combat IBL in a wide range of inflammatory conditions.

2022-04-08 | PXD031791 | Pride

Gene expression of Dcir-/- osteoclasts induced by M-CSF and RANKL

Project description:Purpose: DCIR is an inhibitory type of C-type lectin receptor that regulates osteoclast (OC) formation and functions. This study aimed to find the genes of OCs that could be regulated through DCIR. Method: Bone marrow cells from WT and Dcir-/- mice were cultured in M-CSF for 2 days and the the cells were further cultured in M-CSF and RANKL. RNA profiles were generated by deep sequencing, in triplicate, using Illumina NovaSeq. Results: We detected xxx gense that were higher expression in Dcir-/- OCs, compared with WT OCs, with a fold change ≥1.5 and p value <0.05. Conclusion: Our data showed that Dcir deficiency in OCs changed the gene expression pattern, compared to WT OCs, which are induced by M-CSF and RANKL.

2023-06-07 | GSE223429 | GEO

Comparative genomic hybridization of Clostridium difficile strains to identify markers of different ribotypes

Project description:Clostridium difficile (C. difficile) strains belonging to PCR ribotype 027, PFGE type NAP1, REA type B1 and toxinotype III, termed NAP1/027, have been implicated in the increased frequency of outbreaks of Clostridium difficile-associated diarrhoea (CDAD) in North America and Europe. The NAP1/027 strains appears to be more virulent with an increased mortality and frequency of relapse. Current European C. difficile microarrays are designed to the first sequenced and annotated C. difficile complete genome - strain 630 (ribotype 12). A high density oligonucleotide microarray was designed to C. difficile 630 (CD630) sequence and extra probes corresponding to two PCR ribotypes O27 strains C. difficile R20291 and QCD-32g58 were also included. Comparative genomic hybridisation was used to identify markers of ribotype 027 strains and markers to identify CD630. Strains hybridised to the array included the most prevalent ribotypes found in the UK and Europe (106 and 001) as well as the emerging hypervirulent ribotype 078.

2010-07-01 | E-MTAB-162 | biostudies-arrayexpress

Monocyte Subsets with High Osteoclastogenic Potential and Their Epigenetic Regulation Orchestrated by IRF8 [RNA-Seq]

Project description:Currently, it is unclear if all monocyte subsets exhibit osteoclastogenic potential. Furthermore, the role of lineage determining TFs in regulating OC differentiation on a genome-wide scale remains poorly understood. In this study, we utilized a novel Irf8 conditional knockout (Irf8 cKO) mouse model to characterize the importance of IRF8 in OC progenitor development and epigenetic regulation of OC differentiation. We performed RNA-seq on Irf8 gWT, gKO, cWT and cKO BMMs, preosteoclasts (PreOCs), and OCs. Cells were analyzed prior to (BMMs) and 3 days (PreOCs) and 6 days (OCs) after RANKL stimulation. Here we show that greater a number of genes are significantly upregulated in Irf8 cKO OCs when compared to WT and Irf8 gKO OCs. Altogether, our data shows that Irf8 cKO mice provide more precise/reliable OC-specific transcriptomic results when compared to Irf8 gKO mice.

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The target gene investigation in osteoclats (OCs) treated with mmu-miR-5112 enriched in EVs from OCs with prostate cancer (PCa) cells [target_EV-miR-5112]

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2024-06-06 | GSE268550 | GEO

The microRNA profiles of extracellular vesicles (EVs) from osteoclasts (OCs) co-cultured with prostate cancer (PCa) cell lines [OCEVmiRNA-seq]

2024-06-06 | GSE268548 | GEO

Gene expression analysis in the zebrafish fractured scale

Project description:Bone is a connective tissue which undergoes continuous remodeling, including bone resorption and formation by osteoclasts (OCs) and osteoblasts (OBs), respectively. Recently, extracellular vesicles (EVs) are increasingly appreciated as a regulator of intercellular communication between OCs and OBs. The zebrafish scale is a thin membranous bone embedded in the skin and consists of OBs, OCs, and bone matrix, providing an elegant model to visualize OC-OB communication. Here, we developed a double-transgenic zebrafish line, trap:GFP; osterix:mCherry, which expresses GFP and mCherry under the control of the OC-specific trap (tartrate-resistant acid phosphatase) and OB-specific osterix enhancer, respectively. Utilizing this double-transgenic line, in combination with Hoechst 33342 (Hoe) staining, we isolated four distinct fractions from the scale at 1 day post-fracture by flow cytometry, GFP(–) mCh(+) Hoe(high) (OB fraction), GFP(low) mCh(+) Hoe(high) (OC precursor (pOC) fraction), GFP(high) Hoe(high) (mature OC (mOC) fraction), and mCh(+) Hoe(–) (OB-derived extracellular vesicle (EV) fraction). In this study, we have performed RNA-seq analysis using these four fractions to examine the gene expression profile of each fraction.

2020-04-29 | GSE134330 | GEO

The target gene investigation in osteoblats (OBs) treated with mmu-miR-1963 enriched in EVs from OCs with prostate cancer (PCa) cells [target_EV-miR-1963]

Project description:Bone metastatic lesions of PCa contain areas of bone destruction and formation that are directed by OCs and osteoblasts (OBs), respectively. OC-derived EVs are reported to maintain normal bone homeostasis; however, there is no study investigating the role of EVs from OCs in the presence of PCa. We identified mmu-miR-1963 enriched in EVs from OCs co-cultured with several PCa cell lines. NGS analyses were performed to investigate predicted target genes of EV-miR-1963 in OBs.

2024-06-06 | GSE268549 | GEO

TNF is a homeostatic regulator of distinct epigenetically primed human osteoclast precursors

Project description:Balanced osteoclast differentiation is crucial in maintaining skeleton health through life. Receptor activator of nuclear factor kappa-Β (RANK) is indispensable for OCs normal development in vivo and for the in vitro fusion of circulating progenitor cells into OCs. Many cytokines enhance RANK and RANK-ligand (RANK-L)-mediated differentiation of myeloid cells into OCs. In particular, tumor necrosis factor (TNF) is recognized as a potent activator and is associated with in vivo bone destruction in the context of OC dysregulation in inflammatory arthritis. Paradoxically, infiltration of monocytes into TNF rich inflammatory sites does not lead to a preponderance of osteoclasts but rather macrophages. Recent in vivo murine studies have shown how circulating myeloid precursors play a crucial role in post-natal OC differentiation and skeletal health. However, little is known about such pathways in humans. Herein we demonstrate that, unexpectedly TNF can act as a critical homeostatic regulator of human CD14+ monocyte differentiation into osteoclast by inhibiting osteoclastogenesis to favour macrophage development. In contrast, a distinct, previously unidentified human CD11c+ myeloid pre-osteoclast population is exempt from this negative regulation. In healthy humans, to control cell fate and specifically overcome OC differentiation, TNF drives epigenetic modification of the RANK promoter via a TNFR1-IKK-dependent pathway. In contrast in rheumatoid arthritis, patient-derived monocytes exhibit an altered epigenetic state that results in dysregulated TNF-mediated osteoclast homeostasis providing a pathologic consequence of failure of this pathway.

2021-03-25 | GSE152912 | GEO

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