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To understand how<jats:italic>Pneumocystis<\/jats:italic>inactivates alveolar macrophages, Affymetrix GeneChip<jats:sup>\u00ae<\/jats:sup>RG-U34A DNA microarrays were used to study the difference in global gene expression in alveolar macrophages from uninfected and<jats:italic>Pneumocystis carinii<\/jats:italic>-infected Sprague-Dawley rats.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Analyses of genes that were affected by<jats:italic>Pneumocystis<\/jats:italic>infection showed that many functions in the cells were affected. Antigen presentation, cell-mediated immune response, humoral immune response, and inflammatory response were most severely affected, followed by cellular movement, immune cell trafficking, immunological disease, cell-to-cell signaling and interaction, cell death, organ injury and abnormality, cell signaling, infectious disease, small molecular biochemistry, antimicrobial response, and free radical scavenging. Since rats must be immunosuppressed in order to develop<jats:italic>Pneumocystis<\/jats:italic>infection, alveolar macrophages from four rats of the same sex and age that were treated with dexamethasone for the entire eight weeks of the study period were also examined. With a filter of false-discovery rate less than 0.1 and fold change greater than 1.5, 200 genes were found to be up-regulated, and 144 genes were down-regulated by dexamethasone treatment. During<jats:italic>Pneumocystis<\/jats:italic>pneumonia, 115 genes were found to be up- and 137 were down-regulated with the same filtering criteria. The top ten genes up-regulated by<jats:italic>Pneumocystis<\/jats:italic>infection were Cxcl10, Spp1, S100A9, Rsad2, S100A8, Nos2, RT1-Bb, Lcn2, RT1-Db1, and Srgn with fold changes ranging between 12.33 and 5.34; and the top ten down-regulated ones were Lgals1, Psat1, Tbc1d23, Gsta1, Car5b, Xrcc5, Pdlim1, Alcam, Cidea, and Pkib with fold changes ranging between -4.24 and -2.25.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>In order to survive in the host,<jats:italic>Pneumocystis<\/jats:italic>organisms change the expression profile of alveolar macrophages. Results of this study revealed that<jats:italic>Pneumocystis<\/jats:italic>infection affects many cellular functions leading to reduced number and activity of alveolar macrophages during<jats:italic>Pneumocystis<\/jats:italic>pneumonia.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2180-10-103","type":"journal-article","created":{"date-parts":[[2010,4,21]],"date-time":"2010-04-21T18:16:10Z","timestamp":1271873770000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Microarray studies on effects of Pneumocystis carinii infection on global gene expression in alveolar macrophages"],"prefix":"10.1186","volume":"10","author":[{"given":"Bi-Hua","family":"Cheng","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yunlong","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoling","family":"Xuei","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chung-Ping","family":"Liao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Debao","family":"Lu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark E","family":"Lasbury","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pamela J","family":"Durant","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chao-Hung","family":"Lee","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2010,4,8]]},"reference":[{"issue":"8","key":"1059_CR1","doi-asserted-by":"publisher","first-page":"1098","DOI":"10.1086\/339548","volume":"34","author":"KA Sepkowitz","year":"2002","unstructured":"Sepkowitz KA: Opportunistic infections in patients with and patients without Acquired Immunodeficiency Syndrome. 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