Unknown,Transcriptomics,Genomics,Proteomics

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Comparison of enchondromas with controls (growth plate and cartilage)

ABSTRACT: Ollier disease is a rare, non-hereditary disorder which is characterized by the presence of multiple enchondromas (EC), benign cartilaginous neoplasms arising within the medulla of the bone, with an asymmetric distribution. The risk of malignant transformation towards central chondrosarcoma (CS) is increased up to 35%. The etiology of Ollier disease is unknown. We therefore undertook genome-wide expression profiling using Illumina Beadarray v3.0 for 7 enchondromas of 6 patients and compared them with controls in order to find differentially expressed genes in these benign tumors. The goal of this study was to find differentially expressed genes between enchondromas, a benign cartilage forming tumor occuring in the metaphyses of bone, and controls. We have used samples of normal growth plate and articular cartilage as the controls. Seven enchondromas were compared to two growth plate and four cartilage samples.

ORGANISM(S): Homo sapiens

SUBMITTER: Twinkal Pansuriya

PROVIDER: E-GEOD-22855 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Ollier disease and Maffucci syndrome are non-hereditary skeletal disorderscharacterized by multiple enchondromas (Ollier disease) combined with spindle cellhemangiomas (Maffucci syndrome). Somatic heterozygous IDH1 (R132C and R132H) orIDH2 (R172S) mutations were found in 87% of enchondromas, benign cartilage tumors,as well as in 70% of spindle cell hemangiomas, benign vascular lesions. In total, 35 of 43(81%) patients with Ollier disease and 10 of 13 (77%) patients with Maffucci syndromecarried IDH1 (98%) or rarely IDH2 (2%) mutations in their tumors. Fourteen patientswith multiple tumors at different anatomic locations displayed identical mutations inseparate lesions. Since in other tumor types the presence of an IDH1 mutation is strongly associated withhypermethylation 26, 27, we assessed whether there was a difference in methylation patternof enchondromas with (n = 8) and without (n = 4) IDH1 mutations detactable at Sangersequencing. Methylation and expressionprofiling showed that IDH1 mutations in cartilage tumors are associated withhypermethylation and downregulation of the expression of several genes. Total 12 samples which includes 8 enchondromas with IDH1 mutation (4 Ollier enchondromas, 2 Maffucci enchondromas and 2 solitary enchondromas) and 4 enchondromas (1 Ollier enchondroma, 3 solitary enchondromas) without IDH1 or IDH2 mutations were used. Of these 4 enchondromas without IDH1 mutation, one had R132G IDH1 mutated cells present in the subpopulation, below the threshold level of Sanger sequencing. Bisulfite treatment was performed using EZ DNA Methylation™ Kit (ZymoResearch, Orange, CA). Bisulphite converted DNA was then hybridized to IlluminaHumanMethylation27 BeadChip (Illumina Inc., San Diego, CA) by followingmanufacturer’s instructions. Infinium Unsupervised clustering analysis was performed 25 using the Ward’s clustering algorithm based on Euclidian distance. The 2000 most variable CpG sites (excluding those on the X and Y chromosomes) were used in the clustering analysis.

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Comparison of enchondromas with controls (growth plate and cartilage)

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