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Variability in synovial inflammation in rheumatoid arthritis investigated by microarray technology

In recent years microarray technology has been used increasingly to acquire knowledge about the pathogenic processes involved in rheumatoid arthritis. The present study investigated variations in gene expression in synovial tissues within and between patients with rheumatoid arthritis. This was done...

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Autores principales: Lindberg, Johan, af Klint, Erik, Ulfgren, Ann-Kristin, Stark, André, Andersson, Tove, Nilsson, Peter, Klareskog, Lars, Lundeberg, Joakim
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1526587/
https://www.ncbi.nlm.nih.gov/pubmed/16507157
http://dx.doi.org/10.1186/ar1903
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author Lindberg, Johan
af Klint, Erik
Ulfgren, Ann-Kristin
Stark, André
Andersson, Tove
Nilsson, Peter
Klareskog, Lars
Lundeberg, Joakim
author_facet Lindberg, Johan
af Klint, Erik
Ulfgren, Ann-Kristin
Stark, André
Andersson, Tove
Nilsson, Peter
Klareskog, Lars
Lundeberg, Joakim
author_sort Lindberg, Johan
collection PubMed
description In recent years microarray technology has been used increasingly to acquire knowledge about the pathogenic processes involved in rheumatoid arthritis. The present study investigated variations in gene expression in synovial tissues within and between patients with rheumatoid arthritis. This was done by applying microarray technology on multiple synovial biopsies obtained from the same knee joints. In this way the relative levels of intra-patient and inter-patient variation could be assessed. The biopsies were obtained from 13 different patients: 7 by orthopedic surgery and 6 by rheumatic arthroscopy. The data show that levels of heterogeneity varied substantially between the biopsies, because the number of genes found to be differentially expressed between pairs of biopsies from the same knee ranged from 6 to 2,133. Both arthroscopic and orthopedic biopsies were examined, allowing us to compare the two sampling methods. We found that the average number of differentially expressed genes between biopsies from the same patient was about three times larger in orthopedic than in arthroscopic biopsies. Using a parallel analysis of the tissues by immunohistochemistry, we also identified orthopedic biopsies that were unsuitable for gene expression analysis of synovial inflammation due to sampling of non-inflamed parts of the tissue. Removing these biopsies reduced the average number of differentially expressed genes between the orthopedic biopsies from 455 to 171, in comparison with 143 for the arthroscopic biopsies. Hierarchical clustering analysis showed that the remaining orthopedic and arthroscopic biopsies had gene expression signatures that were unique for each patient, apparently reflecting patient variation rather than tissue heterogeneity. Subsets of genes found to vary between biopsies were investigated for overrepresentation of biological processes by using gene ontology. This revealed representative 'themes' likely to vary between synovial biopsies affected by inflammatory disease.
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spelling pubmed-15265872006-08-04 Variability in synovial inflammation in rheumatoid arthritis investigated by microarray technology Lindberg, Johan af Klint, Erik Ulfgren, Ann-Kristin Stark, André Andersson, Tove Nilsson, Peter Klareskog, Lars Lundeberg, Joakim Arthritis Res Ther Research Article In recent years microarray technology has been used increasingly to acquire knowledge about the pathogenic processes involved in rheumatoid arthritis. The present study investigated variations in gene expression in synovial tissues within and between patients with rheumatoid arthritis. This was done by applying microarray technology on multiple synovial biopsies obtained from the same knee joints. In this way the relative levels of intra-patient and inter-patient variation could be assessed. The biopsies were obtained from 13 different patients: 7 by orthopedic surgery and 6 by rheumatic arthroscopy. The data show that levels of heterogeneity varied substantially between the biopsies, because the number of genes found to be differentially expressed between pairs of biopsies from the same knee ranged from 6 to 2,133. Both arthroscopic and orthopedic biopsies were examined, allowing us to compare the two sampling methods. We found that the average number of differentially expressed genes between biopsies from the same patient was about three times larger in orthopedic than in arthroscopic biopsies. Using a parallel analysis of the tissues by immunohistochemistry, we also identified orthopedic biopsies that were unsuitable for gene expression analysis of synovial inflammation due to sampling of non-inflamed parts of the tissue. Removing these biopsies reduced the average number of differentially expressed genes between the orthopedic biopsies from 455 to 171, in comparison with 143 for the arthroscopic biopsies. Hierarchical clustering analysis showed that the remaining orthopedic and arthroscopic biopsies had gene expression signatures that were unique for each patient, apparently reflecting patient variation rather than tissue heterogeneity. Subsets of genes found to vary between biopsies were investigated for overrepresentation of biological processes by using gene ontology. This revealed representative 'themes' likely to vary between synovial biopsies affected by inflammatory disease. BioMed Central 2006 2006-02-16 /pmc/articles/PMC1526587/ /pubmed/16507157 http://dx.doi.org/10.1186/ar1903 Text en Copyright © 2006 Lindberg et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Lindberg, Johan
af Klint, Erik
Ulfgren, Ann-Kristin
Stark, André
Andersson, Tove
Nilsson, Peter
Klareskog, Lars
Lundeberg, Joakim
Variability in synovial inflammation in rheumatoid arthritis investigated by microarray technology
title Variability in synovial inflammation in rheumatoid arthritis investigated by microarray technology
title_full Variability in synovial inflammation in rheumatoid arthritis investigated by microarray technology
title_fullStr Variability in synovial inflammation in rheumatoid arthritis investigated by microarray technology
title_full_unstemmed Variability in synovial inflammation in rheumatoid arthritis investigated by microarray technology
title_short Variability in synovial inflammation in rheumatoid arthritis investigated by microarray technology
title_sort variability in synovial inflammation in rheumatoid arthritis investigated by microarray technology
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1526587/
https://www.ncbi.nlm.nih.gov/pubmed/16507157
http://dx.doi.org/10.1186/ar1903
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