Computational protocol: A strong host response and lack of MYC expression are characteristic for diffuse large B cell lymphoma transformed from nodular lymphocyte predominant Hodgkin lymphoma

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Protocol publication

[…] Thirty-three primary cases of LP-DLBCL were collected in a previous study []. As control 11 DLBCL classified as GCB type and 9 DLBCL classified as Non-GCB type (Hans classifier []) were included. RNA was extracted using the RNeasy FFPE Microkit (Qiagen, Hilden, Germany). Since all cases showed partially degraded RNA profiles on an Agilent Bioanalyzer (Agilent, Waldbronn, Germany), a real time polymerase chain reaction (PCR) for GAPDH was performed after cDNA synthesis from 766 ng RNA with the High-capacity cDNA Reverse Transcription Kit (Applied Biosystems, Darmstadt, Germany). Cases with GAPDH Ct values above 30 proved to show insufficient quality when hybridized on gene expression arrays. Therefore, only cases with GAPDH values below 30 were further processed. Nine of the thirty-three LP-DLBCL qualified for the study according to their GAPDH values. Of these cases, 80 ng RNA were then transcribed using the NuGEN Ovation FFPE WTA System (NUGEN, Bemmel, The Netherlands). Gene arrays 1.0 (Affymetrix, Santa Clara, USA) were hybridized over night according to manufacturer's instructions. Data were analyzed as previously described []. Gene expression data are available through the GEO database (GSE84464). The local ethics committee of Frankfurt University Hospital agreed on the study (No. 39/14). For gene expression analysis of cultured cells, RNA was extracted using the RNeasy Mini Kit (Qiagen), amplified with the NUGEN Ovation Pico WTA System V2 (NUGEN) and hybridized onto Affymetrix Gene arrays 1.0. Gene expression data are available through the GEO database (GSE84688). Gene set characterization analysis was performed using the Genomatix Pathway System (Genomatix, Munich, Germany) at default parameters, listing all canonical pathways and biological terms with a significant enrichment of the provided input genes. Gene set enrichment analysis of the host response signature by Monti et al. [] was performed according to http://software.broadinstitute.org/gsea/index.jsp [, ]. […]

Pipeline specifications

Software tools GePS, GSEA
Application Gene expression microarray analysis
Organisms Homo sapiens
Diseases Hodgkin Disease, Lymphoma, Neoplasms, Lymphoma, B-Cell