Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression analysis of B cell differentiation using B cell blasts and developmentally arrested plasmablasts

ABSTRACT: In vitro generated blasts from B cells deficient in prdm1 were isolated according to whether they were attempting to express Blimp1, reported by a GFP cassette knocked into the prdm1 locus After four days stimulation with CD40L, IL4 and IL5, cells were FACS sorted into GFP+ and GFP- populations, RNA extracted and gene expression analysed by microarray. Data presented in Peparzak et al, 2013, Fig 3b.

ORGANISM(S): Mus musculus

SUBMITTER: David Tarlinton

PROVIDER: E-GEOD-43213 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Mcl-1 is essential for the survival of plasma cells.

Peperzak Victor V Vikström Ingela I Walker Jennifer J Glaser Stefan P SP LePage Melanie M Coquery Christine M CM Erickson Loren D LD Fairfax Kirsten K Mackay Fabienne F Strasser Andreas A Nutt Stephen L SL Tarlinton David M DM

Nature immunology 20130203 3

The long-term survival of plasma cells is entirely dependent on signals derived from their environment. These extrinsic factors presumably induce and sustain the expression of antiapoptotic proteins of the Bcl-2 family. It is uncertain whether there is specificity among Bcl-2 family members in the survival of plasma cells and whether their expression is linked to specific extrinsic factors. We found here that deletion of the gene encoding the antiapoptotic protein Mcl-1 in plasma cells resulted ...[more]

PMID: 23377201

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Project description:Objective: To Identify gene changes in the medial tibial plateau of articular cartilage at 2, 4 and 8 weeks after destabilisation of the medial meniscus (DMM) in mice and compare our data set with previously published sets to ascertain dysregulated pathways and genes in osteoarthritis. Materials and methods: RNA was extracted from the ipsilateral and contralateral medial tibial plateaus, amplified, labelled and hybridized on Illumina WG_v2 microarrays. Results were confirmed by RT-PCR for selected genes. Results: Transcriptional analysis and network reconstruction revealed changes in extracellular matrix (ECM) and cytoskeletal genes induced by DMM. TGFalpha signalling pathway and complement and coagulation cascade genes were regulated at 2 weeks. Fibronectin (FN1) is a hub in a reconstructed network of potential protein-protein interactions at 2 weeks. Regulated genes decrease over time and by eight weeks fibromodulin (FMOD) and tenascin N (TNN) are the only dysregulated genes present in the DMM operated knees. Comparison with human and rodent published gene sets discovered genes overlapping between our array and 6 others. Conclusions: Cartilage contributes a minute percentage to the RNA extracted from the whole joint (>0.2%), yet is sensitive to changes in gene expression post-DMM. The post-DMM transcriptional reprogramming wanes over time and dissipates by 8 weeks. Common pathways between published gene sets include focal adhesion, regulation of actin cytoskeleton and TGFalpha. Common genes include Jagged 1 (Jag1), Tetraspanin 2 (Tspan2), neuroblastoma, suppression of tumourigenicity 1 (Nbl1) and N-myc downstream regulated gene 2 (Ndrg2). The concomitant genes and pathways we identify are novel and warrant further investigation as biomarkers or modulators of osteoarthritis. In total 18 samples. Each sample was a pool of the medial tibial plateau of 8 mice. Two categories (Treated and untreated) with three biological replicates each and three time points (2, 4 and 8 weeks post-surgery).

Dataset Information

Gene expression analysis of B cell differentiation using B cell blasts and developmentally arrested plasmablasts

Publications

Mcl-1 is essential for the survival of plasma cells.

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