Nimblegen microarrays gene expression analysis of porcine transformed MSCs and sarcomas
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ABSTRACT:
ORGANISM(S): Sus scrofa
PROVIDER: GSE78214 | GEO | 2016/02/23
SECONDARY ACCESSION(S): PRJNA312941
REPOSITORIES: GEO
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Project description:Osteosarcoma is a relatively rare solid tumour, but the most common primary bone cancer. It predominantly affects young people and is highly malignant, requiring aggressive surgical resection and cytotoxic chemotherapy. Five-year survival for patients with metastatic osteosarcoma is only around 30% 14. We report that pigs with heterozygous and homozygous inactivation of TP53 consistently develop osteosarcomas, providing a new model of osteosarcoma at human scale to understand and treat this devastating disease. Gene expression profiling and data analysis was further described in 'A porcine model of osteosarcoma' by Anja Saalfrank et al. (2016). Differential gene expression profiles of MSCs and sarcomas relative to wild type in order to identify transcriptional changes associated with the stages of porcine MSC transformation
2016-02-23 | E-GEOD-78214 | biostudies-arrayexpress
Project description:BackgroundWhile microarrays are the predominant method for gene expression profiling, probe signal variation is still an area of active research. Probe signal is sequence dependent and affected by probe-target binding strength and the competing formation of probe-probe dimers and secondary structures in probes and targets.ResultsWe demonstrate the benefits of an improved model for microarray hybridization and assess the relative contributions of the probe-target binding strength and the different competing structures. Remarkably, specific and unspecific hybridization were apparently driven by different energetic contributions: For unspecific hybridization, the melting temperature Tm was the best predictor of signal variation. For specific hybridization, however, the effective interaction energy that fully considered competing structures was twice as powerful a predictor of probe signal variation. We show that this was largely due to the effects of secondary structures in the probe and target molecules. The predictive power of the strength of these intramolecular structures was already comparable to that of the melting temperature or the free energy of the probe-target duplex.ConclusionsThis analysis illustrates the importance of considering both the effects of probe-target binding strength and the different competing structures. For specific hybridization, the secondary structures of probe and target molecules turn out to be at least as important as the probe-target binding strength for an understanding of the observed microarray signal intensities. Besides their relevance for the design of new arrays, our results demonstrate the value of improving thermodynamic models for the read-out and interpretation of microarray signals.
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Project description:To explore whether KSHV infection is a risk factor for osteosarcoma development in ethnic Uyghur population. Sarcoma specimens including tumor, adjacent normal tissues and paired blood samples were obtained from several osteosarcoma patients of Xinjiang China. Then, osteosarcoma clinical samples were subjected to analysis for the presence of the KSHV genome and proteins. Gene expression profiles of these osteosarcomas were analyzed to reveal the pathogenesis of KSHV-positive and -negative osteosarcomas.
2019-09-01 | GSE126209 | GEO
Project description:To investigate the altered patways among sarcomas and MSCs, gene expression profiles were comared among rat osteosarcoma and malignant histiocytoma (MFH) to mesenchymal stem cells (MSCs) from syngeneic origin. Several altered pathways have identified including down-regulation of Wnt, Cell adhesion, ECM interaction and up-regulation of Hedgehog, cell cycling pathways in rat sarcomas compared to MSCs. Gene expression array analysis was perfromed for the samples of rat osteosarcoma COS1NR and malignant fibrous histiocytoma MFH1NR cell lines, bothe established from chemically induced tumors in F344 rats by 4-HAQO, and rat mesenchymal stem cells freshly isolated from femur bone marrow of F344 rats.
2011-10-24 | E-GEOD-33170 | biostudies-arrayexpress
Project description:To investigate the altered patways among sarcomas and MSCs, gene expression profiles were comared among rat osteosarcoma and malignant histiocytoma (MFH) to mesenchymal stem cells (MSCs) from syngeneic origin. Several altered pathways have identified including down-regulation of Wnt, Cell adhesion, ECM interaction and up-regulation of Hedgehog, cell cycling pathways in rat sarcomas compared to MSCs.
2011-10-25 | GSE33170 | GEO
Project description:Cell lines and tumor tissues from canine osteosarcomas with accompanying survival and breed data. Comparisons of gene expression between osteosarcoma-derived cell lines and osteosarcoma tissues.
2011-09-07 | E-GEOD-27217 | biostudies-arrayexpress
Project description:BackgroundWe performed a Nimblegen intra-platform microarray comparison by assessing two categories of flax target probes (short 25-mers oligonucleotides and long 60-mers oligonucleotides) in identical conditions of target production, design, labelling, hybridization, image analyses, and data filtering. We compared technical parameters of array hybridizations, precision and accuracy as well as specific gene expression profiles.ResultsComparison of the hybridization quality, precision and accuracy of expression measurements, as well as an interpretation of differential gene expression in flax tissues were performed. Both array types yielded reproducible, accurate and comparable data that are coherent for expression measurements and identification of differentially expressed genes. 60-mers arrays gave higher hybridization efficiencies and therefore were more sensitive allowing the detection of a higher number of unigenes involved in the same biological process and/or belonging to the same multigene family.ConclusionThe two flax arrays provide a good resolution of expressed functions; however the 60-mers arrays are more sensitive and provide a more in-depth coverage of candidate genes potentially involved in different biological processes.
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Project description:Affymetrix gene expression data of 21 high-grade osteosarcomas located in the extremities.This gene expression profiling was performed in order to evaluate the expression of candidate prognostic and therapeutic targets in high-grade osteosarcoma.
2017-02-09 | GSE87437 | GEO
Project description:Conventional high-grade osteosarcoma is a primary malignant bone tumor, which is most prevalent in adolescence. Survival rates of osteosarcoma patients have not improved significantly in the last 25 years. Aiming to increase this survival rate, a variety of model systems are used to study osteosarcomagenesis and to test new therapeutic agents. Such model systems are typically generated from an osteosarcoma primary tumor, but undergo many changes due to culturing or interactions with a different host species, which may result into differences in gene expression between primary tumor cells, and tumor cells from the model system. We aimed to investigate whether gene expression profiles of osteosarcoma cell lines and xenografts are still comparable to those of the primary tumor. Osteosarcoma can be subdivided into several histological subtypes, of which osteoblastic, chondroblastic, and fibroblastic osteosarcoma are the most frequent ones. Using nearest shrunken centroids classification, we have generated an expression profile that can predict these histological subtypes in both osteosarcoma biopsies (n=66), as well as in two osteosarcoma model systems, i.e. osteosarcoma cell lines (n=13) and xenografts (n=18). Based on the preservation of mRNA expression profiles that are characteristic for the histological subtype we propose that these model systems are representative to the primary tumor from which they are derived. Genome-wide expression profiling was performed on pre-treatment diagnostic biopsies of 76 resectable high-grade osteosarcoma patients from the EuroBoNet consortium (www.eurobonet.eu). Samples with a main histological subtype (n=66) were selected for subsequent subtype analyses. Out of the EuroBoNeT panel of 19 cell lines, 13 cell lines were recorded to belong to a main histological subtype. This set of 13 cell lines contained 4 cell lines derived from fibroblastic, and 9 cell lines derived from osteoblastic osteosarcomas. The 13 osteosarcoma cell lines IOR/MOS, IOR/OS10, IOR/OS14, IOR/OS15, IOR/OS18, IOR/OS9, IOR/SARG, KPD, MG-63, MHM, OHS, OSA, and ZK-58 were maintained in RPMI 1640 (Invitrogen, Carlsbad, CA, USA) supplemented with 10% fetal calf serum and 1% Penicillin/Streptomycin (Invitrogen) as previously described (PMID: 19787792). The osteosarcoma xenograft model is described in Kresse et al. (PMID: 21713766) In short, human tumors were implanted directly from patient samples and successively passaged subcutaneously in nude mice. Eighteen different xenografts were used, of which 3 were derived from chondroblastic, and 15 from osteoblastic osteosarcomas. Osteosarcoma and xenograft tissue was handled as previously described in Buddingh, Kuijjer et al. (PMID: 21372215) Osteosarcoma cell lines were prepared as in Ottaviano et al. (PMID: 19787792) RNA isolation, synthesis of cDNA, cRNA amplification, and hybridization of cRNA onto the Illumina Human-6 v2.0 Expression BeadChips were performed as described in Buddingh, Kuijjer, et al. (PMID: 21372215) Microarray data processing and quality control were performed using the statistical language R as described in Buddingh, Kuijjer, et al. (PMID: 21372215) We performed a factorial LIMMA analysis comparing 50 osteoblastic, 9 chondroblastic, and 7 fibroblastic osteosarcomas pre-chemotherapy biopsies. Probes with Benjamini and Hochberg False discovery rate-adjusted P-values < 0.05 were considered to be significantly differentially expressed. The gene expression profile was generated on the dataset of biopsies using Bioconductor package PAMR. Internal cross-validation was performed 50 times. A threshold was selected where the error rate of the prediction profile was minimal. The minimum error rate was representative of 50 independent simulations. In order to minimize optimization bias, we validated the profile on an independent dataset of osteosarcoma biopsies (n=5), containing 1 chondroblastic osteosarcoma and 4 osteoblastic osteosarcomas. We subsequently applied the validated prediction profile to two independent datasets, the first consisting of gene expression data of osteosarcoma cell lines, the second of xenografts. Expression of the probes that composed the prediction profile was verified using a factorial LIMMA analysis, comparing chondroblastic, fibroblastic, and osteoblastic osteosarcoma biopsy samples.
2011-09-20 | E-GEOD-30699 | biostudies-arrayexpress
Project description:Three normal human osteoblast samples, acquired from PromoCell, were used as controls to compare to RNA-seq data from prepublished osteosarcoma samples (submitted to the European Bioinformatics Institute; EGAS00001000263) for the purpose of evaluating expression levels of genes identified as common insertions sites in a Sleeping Beauty screen of osteosarcomas in mice.
2015-04-06 | GSE57925 | GEO