Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Identification of neural stem cell gene expression signatures associated with disease progression in alveolar soft part sarcoma by integrated molecular profiling [aCGH]

ABSTRACT: Alveolar soft part sarcoma (ASPS) is a soft tissue sarcoma with poor prognosis. Apart from the recurrent, non-reciprocal t(X,17)(p11.2;q25) translocation, there is little molecular evidence for the origin, initiation and progression of this cancer. We analysed 16 primary and metastatic ASPS samples to elucidate candidate molecular pathways involved in tumor pathogenesis. FISH analysis identified the ASPL-TFE3 fusion in all cases. High-resolution aCGH revealed a higher number of numerical aberrations in metastatic tumors relative to primaries, but failed to identify any consistent alterations in either group. Gene expression analysis highlighted 1,063 genes which were differentially expressed between primary and metastatic tumors. Gene set enrichment analysis identified 16 enriched genesets (p < 0.1) associated with differentially expressed genes. Notable among these were several stem cell gene expression signatures and pathways related to differentiation. In particular, the paired box transcription factor PAX6 was up-regulated in the primary tumors, along with several genes whose mouse orthologs have previously been implicated in Pax6-DNA binding during neural stem cell differentiation. In addition to suggesting a neural origin for ASPS, these results implicate transcriptional deregulation from fusion genes in the pathogenesis of ASPS, rather than extensive chromosomal instability. 15 different tumor and normal paired samples were analysed

ORGANISM(S): Homo sapiens

SUBMITTER: Ramakrishna Sompallae

PROVIDER: E-GEOD-49324 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Synovial sarcoma (SynSa) is an aggressive mesenchymal tumor, comprising approximately 10% of all soft tissue sarcomas. Over half of SynSa patients develop metastasis or local recurrence, but the underlying molecular mechanisms of the aggressive clinical behavior remain poorly characterized. Sixty four frozen tumor specimens from 54 SynSa patients were subjected to array comparative genomic hybridization (aCGH) and gene expression profiling. The examined set of tumor specimens included 16 primary tumors from untreated patients who did not develop metastasis/local recurrence (SynSa1 group), 26 primary tumors from untreated patients who developed metastases or local recurrence during follow-up (SynSa2 group), and 22 metachronous metastatic/recurrent SynSa tumors (SynSa3 group). AURKA and KIF18A, which play important roles in various mitotic events, were the two most up-regulated genes in SynSa2 and SynSa3 groups compared to the SynSa1 group. Expression profiles of SynSa2 and SynSa3 tumors did not show any significant differences. Analysis of genomic index (GI) based on aCGH profiles demonstrated that the SynSa1 group consisted of tumors with significantly less complex genomes compared to SynSa2 and SynSa3 groups. There was no significant difference in genome complexity between SynSa2 and SynSa3 tumors. Primary SynSa tumors from patients who develop metastases or local recurrence share common molecular features with metastatic/recurrent tumors. Presented data suggest that the aggressive clinical SynSa behavior is determined early in tumorigenesis and might be related to impaired regulation of mitotic mechanisms. Introduction: Synovial sarcoma (SynSa) is an aggressive mesenchymal tumor, comprising approximately 10% of all soft tissue sarcomas. Over half of SynSa patients develop metastasis or local recurrence, but the underlying molecular mechanisms of the aggressive clinical behavior remain poorly characterized. Materials and methods: Sixty four frozen tumor specimens from 54 SynSa patients were subjected to array comparative genomic hybridization (aCGH) and gene expression profiling. The examined set of tumor specimens included 16 primary tumors from untreated patients who did not develop metastasis/local recurrence (SynSa1 group), 26 primary tumors from untreated patients who developed metastases or local recurrence during follow-up (SynSa2 group), and 22 metachronous metastatic/recurrent SynSa tumors (SynSa3 group). Results: AURKA and KIF18A, which play important roles in various mitotic events, were the two most up-regulated genes in SynSa2 and SynSa3 groups compared to the SynSa1 group. Expression profiles of SynSa2 and SynSa3 tumors did not show any significant differences. Analysis of genomic index (GI) based on aCGH profiles demonstrated that the SynSa1 group consisted of tumors with significantly less complex genomes compared to SynSa2 and SynSa3 groups. There was no significant difference in genome complexity between SynSa2 and SynSa3 tumors. Conclusions: Primary SynSa tumors from patients who develop metastases or local recurrence share common molecular features with metastatic/recurrent tumors. Presented data suggest that the aggressive clinical SynSa behavior is determined early in tumorigenesis and might be related to impaired regulation of mitotic mechanisms. Genomic DNA was extracted from the frozen tumor specimens using High Pure PCR Template Preparation Kit (Roche). DNA of sufficient quality was obtained from 61 tumor specimens. Agilent SurePrint G3 Human CGH 4x180K array

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Identification of neural stem cell gene expression signatures associated with disease progression in alveolar soft part sarcoma by integrated molecular profiling [aCGH]

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