SNP array analysis on Maffucci tumours
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE26674 | GEO | 2011/07/19
SECONDARY ACCESSION(S): PRJNA142193
REPOSITORIES: GEO
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Project description:Here we have used four enchondromas and two chondrosarcomas of Maffucci patients. We also had one normal sample available for paired analysis in one of the chondrosarcoma II. We did not find any LOH or coomon copy number variation in all Maffucci enchondromas while chondrosarcomas are genetically unstable. Affymetrix SNP 6.0 array was performed using 4 EC and 2CS of Maffucci patients. Illumina expression v3 array was possible to perform using only 1 EC and 2 CS due to rarity of the disease. For SNP array, we used 29 control samples submitted previously (GSE22965) to creat baseline.
2011-07-18 | E-GEOD-26674 | biostudies-arrayexpress
Project description:We did whole genome analysis of enchondromas and chondrosarcomas of Maffucci patients. Since the disease is very rare, we had only three frozen tumour samples were available to continue with the expression array. Enchondromas of Maffucci syndrome did not show any loss of heterozygosity (LOH) or common copy number alterations (CNA) and we looked at the differentially expressed genes between Ollier high grade and Maffucci high grade tumours. There were no significant differentially expressed genes were found between these two groups. This might be due to the small sample size.
2011-07-19 | GSE26667 | GEO
Project description:We did whole genome analysis of enchondromas and chondrosarcomas of Maffucci patients. Since the disease is very rare, we had only three frozen tumour samples were available to continue with the expression array. Enchondromas of Maffucci syndrome did not show any loss of heterozygosity (LOH) or common copy number alterations (CNA) and we looked at the differentially expressed genes between Ollier high grade and Maffucci high grade tumours. There were no significant differentially expressed genes were found between these two groups. This might be due to the small sample size. We used Affymetrix SNP 6.0 array on enchondromas (n=4) and chondrosarcomas (n=2) and compared the results to a previously studied cohort of patients with Ollier disease (n = 37). We used Illumina expression array v3 chip on enchondroma (n=1) and chondrosarcomas (n=2) from Maffucci patients.
2011-07-18 | E-GEOD-26667 | biostudies-arrayexpress
Project description:Ollier disease and Maffucci syndrome are non-hereditary skeletal disorders characterized by multiple enchondromas (Ollier) combined with spindle cell hemangiomas (Maffucci). We found somatic heterozygous IDH1 mutations (R132C and R132H) in 83% of enchondromas, benign cartilage tumors, as well as in 40% of spindle cell hemangiomas, benign vascular lesions. In total, 33 of 42 (78%) patients with Ollier disease and 7 of 13 (54%) patients with Maffucci syndrome carried a mutation in at least one of their tumors. Twelve patients with multiple tumors at different locations displayed identical mutations in separate lesions. Immunohistochemical staining for the R132H IDH1 mutant protein suggested intraneoplastic as well as somatic mosaicism. IDH1 mutations were less frequent (63%) in high grade malignant cartilage tumors in Ollier disease, suggesting that IDH1 is less important for malignant transformation. IDH1 and IDH2 mutations were found in 36% of sporadic cartilage tumors and in four cell lines derived from sporadic chondrosarcomas.
2011-11-05 | GSE30354 | GEO
Project description:Ollier disease and Maffucci syndrome are non-hereditary skeletal disorders characterized by multiple enchondromas (Ollier) combined with spindle cell hemangiomas (Maffucci). We found somatic heterozygous IDH1 mutations (R132C and R132H) in 83% of enchondromas, benign cartilage tumors, as well as in 40% of spindle cell hemangiomas, benign vascular lesions. In total, 33 of 42 (78%) patients with Ollier disease and 7 of 13 (54%) patients with Maffucci syndrome carried a mutation in at least one of their tumors. Twelve patients with multiple tumors at different locations displayed identical mutations in separate lesions. Immunohistochemical staining for the R132H IDH1 mutant protein suggested intraneoplastic as well as somatic mosaicism. IDH1 mutations were less frequent (63%) in high grade malignant cartilage tumors in Ollier disease, suggesting that IDH1 is less important for malignant transformation. IDH1 and IDH2 mutations were found in 36% of sporadic cartilage tumors and in four cell lines derived from sporadic chondrosarcomas. 16 samples were analyzed in two color experiment, using normal male or female as a reference sample (gender mismatched)
2011-11-05 | E-GEOD-30354 | biostudies-arrayexpress
Project description:Chromosome 1p LOH was seen in one-third of cases. LOH events on chromosomes 11q and 1p were generally accompanied by copy number loss. The one exception was on chromosome 11p, where LOH in all 4 cases was accompanied by normal copy number or diploidy, implying uniparental disomy. Amplification of MYCN was also noted, and also, amplification of a second gene, ALK, in a single case. Keywords: SNP array analysis
2007-06-30 | GSE8333 | GEO
Project description:Chondrosarcomas, malignant cartilaginous neoplasms, are capable of transitioning to highly aggressive, metastatic, and treatment-refractory states, resulting in significant patient mortality. We aimed to uncover the transcriptional program directing such tumor progression in chondrosarcomas. Here, we conducted weighted correlation network analysis (WGCNA) to extract a characteristic gene module underlying chondrosarcoma malignancy. We identified hypoxia-inducible factor-2α (HIF-2α, encoded by EPAS1) as an upstream regulator that governs the malignancy gene module. HIF-2α was upregulated in high grade chondrosarcoma biopsies and HIF-2α gene amplification was associated with the poor prognosis of patients with chondrosarcoma. Using tumor xenograft mouse models, we demonstrated that HIF-2α confers chondrosarcomas the capacities required for tumor growth, local invasion, and metastasis. Pharmacological inhibition of HIF-2α in conjunction with the chemotherapy agents synergistically enhanced chondrosarcoma cell apoptosis and abolished malignant signatures of chondrosarcoma in mice. We expect that our insights into the pathogenesis of chondrosarcoma will provide guidelines for the development of novel molecular-targeted therapeutics for chondrosarcoma.
2020-08-21 | GSE156565 | GEO
Project description:Chondrosarcomas represent the second most common primary bone malignancy. Despite the vulnerability of chondrosarcoma cells to nicotinamide adenine dinucleotide (NAD+) depletion, targeting the NAD+ synthesis pathway remains challenging due to broad implications in biological processes. Here, we establish SIRT1 as a central mediator reinforcing the dependency of chondrosarcoma cells on NAD+ metabolism via HIF-2α-mediated transcriptional reprogramming. SIRT1 knockdown abolishes aggressive phenotypes of chondrosarcomas in orthotopically transplanted tumors in mice. Chondrosarcoma cells thrive under glucose starvation by accumulating NAD+ and subsequently activating the SIRT1–HIF-2α axis. Decoupling this link via SIRT1 inhibition unleashes apoptosis and suppresses tumor progression in conjunction with chemotherapy. Unsupervised clustering analysis identifies a high-risk chondrosarcoma patient subgroup characterized by the upregulation of NAD+ biosynthesis genes. Finally, SIRT1 inhibition abolishes HIF-2α transcriptional activity and sensitizes chondrosarcoma cells to doxorubicin-induced cytotoxicity, irrespective of underlying pathways to accumulate intracellular NAD+. We provide system-level guidelines to develop therapeutic strategies for chondrosarcomas.
2023-12-01 | GSE248490 | GEO
Project description:Mutations in the PTH1R gene were reported but these mutations are limited to a small subgroup of patients. The etiology of Ollier disease is unknown. We therefore undertook genome-wide copy number and loss of heterozygosity (LOH) analysis using Affymetrix SNP 6.0 arrays on 37 tumors of 28 Ollier patients in combination with expression array using Illumina Beadarray v3.0 for 7 tumors of 6 patients. We used Affymetrix SNP 6.0 to find out LOH and copy number alterations in Ollier tumors. To understand the genetic mechanism behind the development of enchondroma, we mainly focus on enchondromas and found alterations were validated. We used 14 enchondromas and 23 chondrosarcomas of 28 Ollier patients. We also used 30 controls (blood, saliva or frozen tissue). As controls, normal DNA derived from fresh frozen muscle tissue (n=3), peripheral blood lymphocytes (n=4) or saliva (n=4) was available for 11 Ollier patients and 3 patients with unrelated bone diseases. We used blood lymphocyte DNA from 12 healthy controls and 1 HapMap sample. We also isolated DNA from saliva for 3 of these controls to validate the use of saliva DNA in this study.
2011-08-26 | E-GEOD-22984 | biostudies-arrayexpress
Project description:Mice that develop benign cartilage lesions due to overexpression of Gli2 in chondrocytes developed lesions similar to chondrosarcomas when also deficient in p53. Gli2 overexpression and p53 deficiency had opposing effects on chondrocyte differentiation, but had additive effects negatively regulating apoptosis. Regulation of Igfbp3 expression and IGF signaling by Gli and p53 integrated their effect on apoptosis. Treatment of human chondrosarcomas or fetal mouse limbs explants with IGFBP3 or by blocking IGF increased the apoptosis rate, and mice expressing Gli2 developed substantially fewer tumors when also deficient for Igf2. IGF signaling meditated apoptosis regulates the progression to malignant chondrosarcoma. Experiment Overall Design: The CH10T1/2 cell line was stably transfected with either the R150C variant PTHR1 present in enchondromas (Hopyan, S., Gokgoz, N., Poon, R., Gensure, R. C., Yu, C., Cole, W. G., Bell, R. S., Juppner, H., Andrulis, I. L., Wunder, J. S., and Alman, B. A. (2002). A mutant PTH/PTHrP type I receptor in enchondromatosis. Nat Genet 30, 306-310) or a wild type PTHR1, as previously reported (Mau, E., Whetstone, H., Yu, C., Hopyan, S., Wunder, J. S., and Alman, B. A. (2007). PTHrP regulates growth plate chondrocyte differentiation and proliferation in a Gli3 dependent manner utilizing hedgehog ligand dependent and independent mechanisms. Dev Biol 305, 28-39). Cells were grown overnight in serum free media and treated with either 10â?? 7 M PTHrP (Bachem, King of Prussia, Pennsylvania, USA), or carrier alone for one hour. RNA was isolated from the cells CH10T1/2 cells expressing either the R150C variant PTHR1 or wild type PTHR1. RNA was converted to double-stranded cDNA using Superscript (Gibco-Invitrogen) with a T7-(dT)24 primer, which was then transcribed to biotinylated complementary RNA (cRNA) by incorporating biotin-CTP and biotin-UTP using Enzo BioArray High Yield RNA labeling kit (Enzo Diagnostics, New York, NY). The cRNA labeling and hybridizations were then performed according to Affymetrix GeneChip Protocol (Affymetrix Inc., Santa Clara, CA). The chips were scanned for fluorescence signal detection. Affymetrix - GeneChip® Mouse Genome 430A 2.0 Array was utilized.
2009-03-14 | E-GEOD-15118 | biostudies-arrayexpress