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MiRNA expression data from primary central nervous system lymphomas (PCNSL) [miRNA-4]

ABSTRACT: miRNA expression data from primary central nervous system lymphomas (PCNSL) [miRNA-4]

PROVIDER: PRJNA637440 | ENA |

REPOSITORIES: ENA

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miRNA expression data from primary central nervous system lymphomas (PCNSL)

Project description:miRNA expression data from primary central nervous system lymphomas (PCNSL)

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Array-based profiling of the lymphoma cell DNA methylome does not unequivocally distinguish primary lymphomas of the central nervous system from non-CNS diffuse large B-cell lymphomas

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The mutational landscape of primary central nervous system lymphoma (Hipo H050, A050, XD013)

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Project description:This SuperSeries is composed of the following subset Series: GSE25297: Genome-wide gene expression comparison (primary central nervous system lymphoma (PCNSL) vs normal lymph node) GSE25298: Genomic aberrations in primary central nervous system lymphoma (PCNSL) Refer to individual Series

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Project description:Purpose: Only a limited number of genetic studies have been performed in primary central nervous system lymphomas (PCNSL), partly due to the rarity of the tumors and the very limited amount of available tissue. In this report, we present the first molecular characterization of copy-number abnormalities (CNA) of newly diagnosed PCNSL by array-based comparative genomic hybridization in formalin fixed paraffin embedded (FFPE) specimens and compare the results with matched frozen tumor specimens. Experimental design: We performed array-based comparative genomic hybridization (aCGH) in FFPE tissues from PCNSL. Results were compared with matched paired frozen tumors. Results: Our analysis confirmed the good to fair quality and reliability of the data generated from limited amounts of tumoral FFPE tissue. Overall, all PCNSL cases were characterized by highly complex karyotypes with a median of 23 copy-number abnormalities (CNA) per patient (range 17-47). Overall, 20 chromosomal regions were recurrently found in more than 40% of cases. Deletions of 6p21, 6q, 9p21.3 and gain of 12q12-q24.33 were the commonest CNA. Other minimal affected regions were defined, and novel recurrent CNAs affecting single genes were identified in 3q26.32 (TBL1XR1) and 8q12.1 (TOX). Conclusions: The results obtained are encouraging. Larger archival tissue collections can now be analyzed in order to complement the still fragmented knowledge we have of the genetic basis of the PCNSL. We included samples from 7 PCNSL patients. In 6 out of these 7 PCNSL patients (cases B – G), aCGH experiments were performed in DNA samples obtained from both snap-frozen and FFPE tissues for assay quality comparative purposes. In the remaining sample (case A), only frozen sample was analyzed.

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Transcription profiling of human primary lymphomas of the central nervous system suggests PCNSL to be derived from a late germinal center B cell.

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Genome-wide gene expression comparison (primary central nervous system lymphoma (PCNSL) vs normal lymph node)

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