Transcriptomic profiling of splenic B lymphomas spontaneously developed in B cell-specific TRAF3-deficient mice

Abstract

TRAF3, a critical regulator of B cell survival, was recently recognized as a tumor suppressor gene in B lymphocytes. Specific deletion of TRAF3 from B lymphocytes leads to spontaneous development of marginal zone lymphomas (MZL) or B1 lymphomas in mice. To identify novel oncogenes and tumor suppressive genes involved in malignant transformation of TRAF3-deficient B cells, we performed a microarray analysis to identify genes differentially expressed in TRAF3−/− mouse splenic B lymphomas. We have identified 160 up-regulated genes and 244 down-regulated genes in TRAF3−/−B lymphomas as compared to littermate control splenocytes. Here we describe the samples, quality control assessment, as well as the data analysis methods in detail for the transcriptomic profiling study. Data are archived at NIH GEO with accession number GSE48818.

Targeting TRAF3 Downstream Signaling Pathways in B cell Neoplasms

“…To identify such secondary oncogenic alterations and to discover new therapeutic targets for the treatment of B cell neoplasms, we performed global gene expression profiling of TRAF3 −/− mouse B lymphomas by transcriptomic microarray analysis [ 52 , 53 ]. Our results of the microarray analysis identified 160 up-regulated genes and 244 down-regulated genes in TRAF3 −/− B lymphomas as compared to TRAF3-sufficient littermate control spleens (cut-off fold of changes: 2-fold up or down, p < 0.05) (NCBI GEO accession number: GSE48818) [ 52 , 53 ]. From the 160 up-regulated genes, we selected 13 genes for further verification by quantitative real time PCR using TaqMan gene expression assay kits.…”