Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

GDF5 variant with superior healing capacity

ABSTRACT: Seventy-two female Sprague-Dawley rats underwent a 5 mm critical-sized femoral segmental defect followed by stabilization with a custom-made unilateral external fixator. Following femoral defect generation, absorbable type I bovine collagen sponges were loaded either with 50 ug GDF5wt or 50 ug GDF5N445T, dissolved in dilution buffer (10 mM HCl), and placed into the defect. The control group was treated with collagen sponges soaked with dilution buffer. For analysis of the early healing phase, 48 rats (n = 4 rats/group & time point) were sacrificed at day 3, 5, 7 and 14 post-operation and the callus tissue between the two inner pins was harvested and immediately flash frozen in liquid nitrogen for RNA extraction. Tissue was subsequently pulverized and total RNA was isolated using Trifast reagent and RNeasy Mini Kit. The total RNA from 3 animals per group and time point were pooled prior to hybridization on an Affymetrix GeneChip Rat Gene 1.0 ST Array.

ORGANISM(S): Rattus norvegicus

SUBMITTER: Claus Ott

PROVIDER: E-MTAB-2249 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

Improved bone defect healing by a superagonistic GDF5 variant derived from a patient with multiple synostoses syndrome.

Degenkolbe Elisa E Schwarz Carolin C Ott Claus-Eric CE König Jana J Schmidt-Bleek Katharina K Ellinghaus Agnes A Schmidt Tanja T Lienau Jasmin J Plöger Frank F Mundlos Stefan S Duda Georg N GN Willie Bettina M BM Seemann Petra P

Bone 20141224

Multiple synostoses syndrome 2 (SYNS2) is a rare genetic disease characterized by multiple fusions of the joints of the extremities, like phalangeal joints, carpal and tarsal joints or the knee and elbows. SYNS2 is caused by point mutations in the Growth and Differentiation Factor 5 (GDF5), which plays an essential role during skeletal development and regeneration. We selected one of the SYNS2-causing GDF5 mutations, p.N445T, which is known to destabilize the interaction with the Bone Morphogene ...[more]

PMID: 25543012

Similar Datasets

Project description:The steriod-induced necrosis of femoral head(SINFH) is a serious clinical problem and the underlying mechanism of this disease remains unknown. As its etiology and pathogenesis are not clear, there hasn’t been an effective treatment yet. In-depth studies on its pathogenesis will provide important information for the prevention and treatment of this devastated disease. Animal model researches are helpful to a better understanding of its etiology and pathogenesis, to early diagnosis and treatments and provide the basis for clinical treatment It has been proved that the occurrence of SINFH is related to gene itself and its polymorphism. These studies, in which only one or a few genes were investigated, could not provide a comprehensive understanding to the pathogenesis of SINFH. We used microarrays to compare the gene expression profile of SINFH rats with that of normal rats and identified gene expression changes between SINFH rats and normal rats. Adult healthy male Wistar rats(body weight 200±10g) were randomly divided into control and experimental groups. All the rats were given injection of E. coli endotoxin at a dose of 20μg/kg body weight into abdominal cavity for two times with a 24 hour interval. 24 hours after the second administration of E. coli endotoxin, methylprednisolone 40mg/kg was administered into the left gluteus muscle of experimental group rats for three times with a 24 hour interval. Rats were then killed 6 weeks after steroid administration. In experiment, immediately after death the left femoral heads were isolated. Femoral heads were used for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain the gene expression profile of SINFH rats and that of normal rats in order to identified gene expression changes between SINFH rats and normal rats by comparing the gene expression profile of SINFH rats with that of normal rats. To that end, we have established the gene expression profiles of normal and SINFH disease of rat femoral head and found out differentially expressed genes.

Project description:Enhanced understanding of differential gene expression and biological pathways associated with distinct phases of intramembranous bone regeneration following femoral marrow ablation surgery will improve future advancements regarding osseointegration of joint replacement implants, biomaterials design, and bone tissue engineering. A rat femoral marrow ablation model was performed and genome-wide microarray data were obtained from samples at 1, 3, 5, 7, 10, 14, 28, and 56 days post-ablation, with intact bones serving as controls at Day 0. Bayesian model-based clustering produced eight distinct groups amongst 9,062 significant gene probe sets based on similar temporal expression profiles, which were further categorized into three major temporal classes of increased, variable, and decreased expression. Differential biological processes and pathways associated with each major temporal group were identified, and significantly expressed genes involved were visually represented by heat maps. It was determined that the increased expression group exclusively contains genes involved in pathways for matrix metalloproteinases (MMPs), Wnt signaling, TGF-Î² signaling, and inflammatory pathway. Only the variable expression group contains genes associated with glycolysis and gluconeogenesis, Notch Signaling Pathway, natural killer cell mediated cytotoxicity, and B cell receptor signaling pathway, among others. The decreased group exclusively consists of genes involved in heme biosynthesis, p53 signaling pathway, and hematopoietic cell lineage. Significant biological pathways and transcription factors expressed at each time point post-ablation were also identified. These data present the first temporal gene expression profiling analysis of the rat genome during intramembranous bone regeneration induced by femoral marrow ablation. In an Institutional Animal Care and Use Committee (IACUC) approved study, 27 adult male rats (Sprague Dawley, 400-425 g) were divided into nine groups: intact control (0 day), and 1, 3, 5, 7, 10, 14, 28, and 56 days post marrow ablation. Twenty-four animals received unilateral femoral ablation. At each time point, animals were killed in a carbon dioxide chamber, and whole femurs were harvested and denuded of soft tissue. For three samples per time point, both the distal and proximal ends of the femurs were cut off in order to exclude the epiphyses and growth plate regions. Diaphyseal marrow tissue and cells from the mid-shaft were flushed out using TrizolÂ®. Extracted RNA was homoginized and was prepared for hybridization. For each of the three samples per time point, gene expression was analyzed with GeneChipÂ® Rat Genome 230 2.0 Arrays (Affymetrix, Santa Clara, CA).

Dataset Information

GDF5 variant with superior healing capacity

Publications

Improved bone defect healing by a superagonistic GDF5 variant derived from a patient with multiple synostoses syndrome.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure