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Open Access Highly Accessed Research article

Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation

Jamie A Lee1, Robert S Sinkovits3, Dennis Mock3, Eva L Rab1, Jennifer Cai1, Peng Yang1, Brian Saunders3, Robert C Hsueh2, Sangdun Choi5, Shankar Subramaniam34, Richard H Scheuermann13* and in collaboration with the Alliance for Cellular Signaling

Author Affiliations

1 Department of Pathology, Laboratory of Molecular Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA

2 Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA

3 San Diego Supercomputer Center, University of California, San Diego, California 92122, USA

4 Department of Bioengineering, University of California, San Diego, California 92122, USA

5 Division of Biology, California Institute of Technology, Pasadena, CA, USA

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BMC Bioinformatics 2006, 7:237  doi:10.1186/1471-2105-7-237

Published: 2 May 2006



Activation of naïve B lymphocytes by extracellular ligands, e.g. antigen, lipopolysaccharide (LPS) and CD40 ligand, induces a combination of common and ligand-specific phenotypic changes through complex signal transduction pathways. For example, although all three of these ligands induce proliferation, only stimulation through the B cell antigen receptor (BCR) induces apoptosis in resting splenic B cells. In order to define the common and unique biological responses to ligand stimulation, we compared the gene expression changes induced in normal primary B cells by a panel of ligands using cDNA microarrays and a statistical approach, CLASSIFI (Cluster Assignment for Biological Inference), which identifies significant co-clustering of genes with similar Gene Ontology™ annotation.


CLASSIFI analysis revealed an overrepresentation of genes involved in ion and vesicle transport, including multiple components of the proton pump, in the BCR-specific gene cluster, suggesting that activation of antigen processing and presentation pathways is a major biological response to antigen receptor stimulation. Proton pump components that were not included in the initial microarray data set were also upregulated in response to BCR stimulation in follow up experiments. MHC Class II expression was found to be maintained specifically in response to BCR stimulation. Furthermore, ligand-specific internalization of the BCR, a first step in B cell antigen processing and presentation, was demonstrated.


These observations provide experimental validation of the computational approach implemented in CLASSIFI, demonstrating that CLASSIFI-based gene expression cluster analysis is an effective data mining tool to identify biological processes that correlate with the experimental conditional variables. Furthermore, this analysis has identified at least thirty-eight candidate components of the B cell antigen processing and presentation pathway and sets the stage for future studies focused on a better understanding of the components involved in and unique to B cell antigen processing and presentation.