Project name: Homo sapiens

Description: To characterize the molecular origin of primary lymphomas of the central nervous system (PCNSL), 21 PCNSL of immunocompetent patients were investigated by microarray-based gene expression profiling. Comparison of the transcriptional profile of PCNSL with various normal and neoplastic B cell subsets demonstrated PCNSL (i) to display gene expression patterns most closely related to late germinal center B cells, (ii) to display a gene expression profile similar to systemic diffuse large B cell lymphomas (DLBCL), and (iii) to be in part assigned to the activated B cell-like (ABC) or the germinal center B cell-like (GCB) subtype of DLBCL.Keywords: PCNSL – DLBCL – gene expression profilingOverall design: Total RNA was extracted from tissue blocks containing > 80% tumor cells using the TRIzol reagent (Invitrogen, Carlsbad, CA) and purified using RNeasy Kit (Qiagen, Valencia, CA). Double-stranded cDNA (ds-cDNA) was generated from 5 μg of total RNA using the SuperScript Double Stranded cDNA Synthesis Kit (Invitrogen) and a poly-dT oligonucleotide that contains T7 RNA polymerase initiation site (Sigma-Proligo, St. Louis, MO). The ds-cDNA was used as template to generate biotinylated cRNA by in vitro transcription using MEGA-script T7 High Yield Transcription Kit (Ambion, Austin, TX), biotin-11-CTP, and biotin-11-UTP (Perkin Elmer, Altham, MA). The biotinylated cRNA was purified by RNAeasy Kit (Qiagen) and fragmented according to the Affymetrix protocol. 15 μg of fragmented cRNA was hybridized to HG-U95Av2 microarrays (Affymetrix, Santa Clara, CA). Gene expression values were determined by GCOS1.2 software (Affymetrix) using the global scaling option.

Data type: Transcriptome or Gene expression

Sample scope: Multiisolate

Relevance: Medical

Last updated: 2006-10-16