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Wnt inhibitory factor 1 (WIF1) is not silenced by DNA methylation in osteosarcoma, and instead, represents a marker of osteoblastic differentiation stage (gene expression)

ABSTRACT: The aim was to identify pathways and genes that are transcriptionally deregulated in osteosarcoma due to changes in CpG island DNA methylation. In order to identify candidates, we compared low passage cell cultures derived from a mouse model of osteosarcoma to mature osteoblasts derived by in vitro differentiation of the mouse bone marrow stromal cell line, Kusa4b10. Under cell culture osteoblastic differentiating conditions, Kusa4b10 cells acquire a mature osteoblastic phenotype (21 days). A potential role for DNA methylation in directing gene expression changes was established by integrating gene expression data with genome wide DNA methylation maps generated by methyl-DNA binding domain capture and NimbleGen promoter arrays (MBDCap-Chip).

ORGANISM(S): Mus musculus

PROVIDER: GSE46929 | GEO | 2015/07/01

SECONDARY ACCESSION(S): PRJNA203105

REPOSITORIES: GEO

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Wnt inhibitory factor 1 (WIF1) is not silenced by DNA methylation in osteosarcoma, and instead, represents a marker of osteoblastic differentiation stage (gene expression)

Project description:The aim was to identify pathways and genes that are transcriptionally deregulated in osteosarcoma due to changes in CpG island DNA methylation. In order to identify candidates, we compared low passage cell cultures derived from a mouse model of osteosarcoma to mature osteoblasts derived by in vitro differentiation of the mouse bone marrow stromal cell line, Kusa4b10. Under cell culture osteoblastic differentiating conditions, Kusa4b10 cells acquire a mature osteoblastic phenotype (21 days). A potential role for DNA methylation in directing gene expression changes was established by integrating gene expression data with genome wide DNA methylation maps generated by methyl-DNA binding domain capture and NimbleGen promoter arrays (MBDCap-Chip). 3 cell lines derived from primary tumors from p53 Rb Osterix-Cre:lox OS model, 3 Osteoblasts (differentiated Kusa4b10 cells (21 days under osteoblastic differentiation conditions)

2015-07-01 | E-GEOD-46929 | biostudies-arrayexpress

Wnt inhibitory factor 1 (WIF1) is a marker of osteoblastic differentiation stage and is not silenced by DNA methylation in osteosarcoma (methylation)

Project description:Therapeutic targeting of the Wnt pathway is of high clinical interest for treating bone loss disorders such as osteoporosis. These therapies inhibit the action of negative regulators of osteoblastic Wnt signaling. The observation that Wnt inhibitory factor 1 (WNT1) was epigenetic silencing in osteosarcoma (OS) raised concerns for such a treatment approach. In this study, genome-wide methylation profiling of OS derived from mouse models demonstrated Wif1 silencing in OS is not driven by DNA methylation. Treatment of mouse and human OS cells with methylation and HDAC inhibitors showed Wif1 was unresponsive to methylation inhibition but responded robustly to HDAC inhibition. Consistent with an HDAC dependent mechanism of silencing, the Wif1 locus in OS was characterized by low levels of acetylation and a bivalent H3K4/H3K27 trimethylation state. Wif1 expression marked late stages of normal osteoblast development and stratified OS tumours based on differentiation stage across species. Culture of human and mouse OS cells under differentiation inductive conditions increased expression of Wif1 in parallel with known osteoblast differentiation markers. Together these results demonstrate that Wif1 is not targeted for silencing by DNA methylation in OS. The reduced expression of Wif1 in OS cells is in context with their stage in differentiation. 3 cell lines derived from primary tumors from p53 Rb Osterix-Cre:lox OS model, 3 Osteoblasts (differentiated Kusa4b10 cells (21 days under osteoblastic differentiation conditions)

2015-07-01 | E-GEOD-47571 | biostudies-arrayexpress

Wnt inhibitory factor 1 (WIF1) is a marker of osteoblastic differentiation stage and is not silenced by DNA methylation in osteosarcoma (methylation)

2015-07-01 | GSE47571 | GEO

Mir-9-1 controls osteoblastic regulation of lymphopoiesis

Project description:The highly conserved MicroRNA-9 (miR-9) family consists of three members. We discovered that miR-9-1 deletion reduced mature miR-9 expression, causing 43% of the mice to display smaller size and postweaning lethality. MiR-9-1-deficient mice with growth defects experienced severe lymphopenia, but other blood cells were unaffected. The lymphopenia wasn’t due to defects in hematopoietic progenitors, as mutant bone marrow (BM) cells underwent normal lymphopoiesis after transplantation into wild-type recipients. Additionally, miR-9-1-deficient mice exhibited impaired osteoblastic bone formation, as mutant mesenchymal stem cells (MSCs) failed to differentiate into osteoblastic cells (OBs). RNA sequencing revealed reduced expression of master transcription factors for osteoblastic differentiation, Runt-related transcription factor 2 (Runx2) and Osterix (Osx), and genes related to collagen formation, extracellular matrix organization, and cell adhesion, in miR-9-1-deficient MSCs. Follistatin (Fst), an antagonist of bone morphogenetic proteins (BMPs), was found to be a direct target of miR-9-1. Its deficiency led to the up-regulation of Fst, inhibiting BMP signaling in MSCs, and reducing IL-7 and IGF-1. Thus, miR-9-1 controls osteoblastic regulation of lymphopoiesis by targeting the Fst/BMP/Smad signaling axis.

2023-08-31 | GSE239376 | GEO

Osteoblastic loss of Ezh2

Project description:Osteoblastic loss of Ezh2

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Wnt inhibitory factor 1 (WIF1) is a marker of osteoblastic differentiation stage and is not silenced by DNA methylation in osteosarcoma

Project description:Purpose: We have used microarrays to identify gene expression profiles that distinguish mouse OS cells from normal pre-osteoblast cells and mature osteoblast cells. Methods: Transcriptional profiles of three cell lines derived from tumors from Osx-Cre p53fl/fl Rbfl/fl (fibroblastic OS) mouse model, and from pre-osteoblast cells (Kusa4b10 mouse bone marrow stromal cell line) and osteoblast cells (derived by in vitro differentiation of the Kusab410 mouse bone marrow stromal cell line) were generated by microarray analysis, each in triplicate, using Affymetrix mouse Gene1.0ST arrays. Transcriptional profiles were analyzed in cell lines derived from tumors from a genetically engineered mouse model of human osteosarcoma (Osx-Cre p53fl/fl Rbfl/fl) and osteoblast cells derived from the Kusa4b10 mouse bone marrow stromal cell line, in the undifferentiated state (pre-osteoblasts) and differentiated state (osteoblasts).

2015-01-29 | E-GEOD-63939 | biostudies-arrayexpress

Genomic characterization of osteoblastic differentiation of MC-3T3E1 cells

Project description:Gene expression analysis of murine MC3T3-E1 cells induced to undergo synchronized osteoblastic differentiation in vitro. MC3T3-E1 cells were cultured in vitro for up to 28 days in the presence of 8-glycerol phosphate and ascorbic acid to induce osteoblastic differentiation. Total RNA was isolated after 2, 5, 10 and 28 days in culture to sample proliferating preosteoblasts (Day 2), growth arrested preosteoblasts (Day 5), differentiating osteoblasts (Day 10), and mature osteoblasts (Day 28). Timing of sample collection was based on direct measurements of cell number, alkaline phosphatase expression, type 1A collagen synthesis, and matrix mineralization in parallel cultures. Triplicate samples from each time point were hybridized to slide arrays printed with the Operon Mouse Oligo set, version 2.0.

2012-06-27 | E-GEOD-30393 | biostudies-arrayexpress

Gene expression comparison of pre-osteoblastic and mature osteoblastic cell populations from 5 week old and 8 week old mice, a comparison of cell populations within and between age groups

Project description:The aim of the study was to identify gene expression profiles that distinguished different stages of osteoblast commitment, and determine whether the same osteoblast cell populations from mice of different ages had distinguishable expression profiles that may indicate functional changes are apparent for the cell populations during different stages of skeletal development. Pre-osteoblastic and mature osteoblastic cells were isolated from collagenase digested bones from 5 week old and 8 week wild type C57BL6 mice by FACS based on Lin, Sca-1, CD51, and CD31 cell surface markers.

2021-08-25 | GSE82285 | GEO

Osteoblastic response in human bone marrow stromal cells

Project description:Our goal was to determine whether osteoblastic LuCaP 23.1 prostate cancer xenograft tumors can elicit an osteoblastic response at the gene expression level in human bone marrow stromal cells.

2013-12-23 | GSE48907 | GEO

Molecular profiling of functional interactions between pre-osteoblastic and breast carcinoma cells

Project description:The relationships between cancer cells and the microenvironment play a critical role in cancer growth and development. The bone stroma consists of mesenchymal stem cells (MSCs) and mature osteoblasts that promote cancer growth. Yet it is not completely understood what are the molecular processes guiding cancer cells progression to the bone. In this study, a co-culture assay and subsequent gene profiling arrays were used to compare the gene expression profile of a pre-osteoblastic cell line (MBA-15) with that of a mammary adenocarcinoma (DA3) cells. Following co-culture, cells were separated by magnetic beads based on the expression of CD326 antigen. RNA was purified and hybridized on gene expression array. The gene expression pattern changes were followed by qRT-PCR. We demonstrate that co-cultured DA3 cells express elevated levels of genes that regulate growth and responses to both hormonal stimulus and wounding, as well as reduced expression of genes related to lipid metabolism. Also, co-cultured pre-osteoblastic cells showed reduced expression of cell-junction genes. The study presents a simplified model system, composed of pre-osteoblastic and mammary cancer cells, that potentially mimics the molecular interactions in the tumor microenvironment which contribute to tumor-progression. Gene expression was studied in 2 mouse cell lines: MBA-15, a pre-osteoblastic stromal cell line, and DA3, a mammary adenocarcinomal cell line. The interaction between these 2 cell lines was also analysed by gene expression. The experiment was performed in duplicates (see Date in the Sample characteristics field).

2014-11-23 | E-GEOD-34529 | biostudies-arrayexpress

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