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Lee JA, Sinkovits RS, Mock D, Rab EL, Cai J, Yang P, Saunders B, Hsueh RC, Choi S, Subramaniam S, Scheuermann RH. Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation. BMC Bioinformatics 2006; 7:237. [PMID: 16670020 PMCID: PMC1479375 DOI: 10.1186/1471-2105-7-237] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2005] [Accepted: 05/02/2006] [Indexed: 12/28/2022] Open
Abstract
Background 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. Results 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. Conclusion 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.
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Affiliation(s)
- Jamie A Lee
- Department of Pathology, Laboratory of Molecular Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Robert S Sinkovits
- San Diego Supercomputer Center, University of California, San Diego, California 92122, USA
| | - Dennis Mock
- San Diego Supercomputer Center, University of California, San Diego, California 92122, USA
| | - Eva L Rab
- Department of Pathology, Laboratory of Molecular Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jennifer Cai
- Department of Pathology, Laboratory of Molecular Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Peng Yang
- Department of Pathology, Laboratory of Molecular Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Brian Saunders
- San Diego Supercomputer Center, University of California, San Diego, California 92122, USA
| | - Robert C Hsueh
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Sangdun Choi
- Division of Biology, California Institute of Technology, Pasadena, CA, USA
| | - Shankar Subramaniam
- San Diego Supercomputer Center, University of California, San Diego, California 92122, USA
- Department of Bioengineering, University of California, San Diego, California 92122, USA
| | - Richard H Scheuermann
- Department of Pathology, Laboratory of Molecular Pathology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- San Diego Supercomputer Center, University of California, San Diego, California 92122, USA
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Raijmakers R, Egberts WV, van Venrooij WJ, Pruijn GJM. The association of the human PM/Scl-75 autoantigen with the exosome is dependent on a newly identified N terminus. J Biol Chem 2003; 278:30698-704. [PMID: 12788944 DOI: 10.1074/jbc.m302488200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The exosome is a complex of 3' --> 5' exoribonucleases that functions in a variety of cellular processes, all concerning the processing or degradation of RNA. Paradoxically, the previously described cDNA for the human autoantigenic exosome subunit PM/Scl-75 (Alderuccio, F., Chan, E. K., and Tan, E. M. (1991) J. Exp. Med. 173, 941-952) encodes a polypeptide that failed to interact with the exosome complex. Here, we describe the cloning of a more complete cDNA for PM/Scl-75 encoding 84 additional amino acids at its N terminus. We show that only the longer polypeptide is able to associate with the exosome complex. This interaction is most likely mediated by protein-protein interactions with two other exosome subunits, hRrp46p and hRrp41p, one of which was confirmed in a mammalian two-hybrid system. In addition we show that the putative nuclear localization signal present in the C-terminal region of PM/Scl-75 is sufficient, although not essential for nuclear localization of the protein. Moreover, the deletion of this element abrogated the nucleolar accumulation of PM/Scl-75, although its association with the exosome was not disturbed. This suggests that this basic element of PM/Scl-75 plays a role in targeting the exosome to the nucleolus.
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Affiliation(s)
- Reinout Raijmakers
- Department of Biochemistry, Nijmegen Center for Molecular Life Sciences, University of Nijmegen, 6525 GA Nijmegen, The Netherlands
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Stover C, Endo Y, Takahashi M, Lynch NJ, Constantinescu C, Vorup-Jensen T, Thiel S, Friedl H, Hankeln T, Hall R, Gregory S, Fujita T, Schwaeble W. The human gene for mannan-binding lectin-associated serine protease-2 (MASP-2), the effector component of the lectin route of complement activation, is part of a tightly linked gene cluster on chromosome 1p36.2-3. Genes Immun 2001; 2:119-27. [PMID: 11426320 DOI: 10.1038/sj.gene.6363745] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2000] [Accepted: 02/01/2001] [Indexed: 11/08/2022]
Abstract
The proteases of the lectin pathway of complement activation, MASP-1 and MASP-2, are encoded by two separate genes. The MASP1 gene is located on chromosome 3q27, the MASP2 gene on chromosome 1p36.23-31. The genes for the classical complement activation pathway proteases, C1r and C1s, are linked on chromosome 12p13. We have shown that the MASP2 gene encodes two gene products, the 76 kDa MASP-2 serine protease and a plasma protein of 19 kDa, termed MAp19 or sMAP. Both gene products are components of the lectin pathway activation complex. We present the complete primary structure of the human MASP2 gene and the tight cluster that this locus forms with non-complement genes. A comparison of the MASP2 gene with the previously characterised C1s gene revealed identical positions of introns separating orthologous coding sequences, underlining the hypothesis that the C1s and MASP2 genes arose by exon shuffling from one ancestral gene.
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Affiliation(s)
- C Stover
- Department of Microbiology and Immunology, University of Leicester, Leicester, UK
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