Microarray and bioinformatics analyses of gene expression profiles in BALB/c murine macrophage polarization

Abstract

Macrophages possess the hallmark feature of plasticity, allowing them to undergo a dynamic transition between M1 and M2 polarized phenotypes. The aim of the present study was to screen for differentially-expressed genes (DEGs) that were associated with BALB/c murine macrophage polarization. The transcription profiles of three M1 and three M2 samples were obtained using microarray analysis. Based on the threshold of fold-change >2.0 and P-value <0.05, a total of 1,253 DEGs were identified, of which 696 were upregulated and 557 downregulated in M1 macrophages compared with M2 macrophages. Gene Ontology (GO) function and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed. A gene-gene interaction network of the DEGs was constructed using the Search Tool for the Retrieval of Interacting Genes database. GO annotation identified three categories: Cellular component, molecular function and biological process, with 34 and 40 enrichment terms consisting of upregulated and downregulated DEGs, respectively. GO enrichment analysis of DEGs was primarily associated with protein binding, response to stimulus, cell differentiation, and regulation of biological process. KEGG enrichment identified 15 and four pathways involving upregulated and downregulated DEGs, respectively. Signaling pathway analysis revealed that these DEGs were mainly involved in apoptosis, hypoxia-inducible factor (HIF) 1a pathway, innate immune system, tumor necrosis factor (TNF) signaling pathway, cytokine-cytokine receptor interaction, and other signal transduction pathways. Interaction network analysis indicated that genes including TNF, interleukin (IL)-6, IL-1β, suppressor of cytokine signaling 3, nitric oxide synthase 2, HIF1a may serve key roles in macrophage polarization. The present study provided new insights into the role of genes in macrophage differentiation and polarization.

IL-4/IL-13 polarization of macrophages enhances Ebola virus glycoprotein-dependent infection

“…While a large number of studies have used IL-4 and IL-13 to elicit the M2a phenotype in macrophages [31,56,57], we verified in our primary cells of interest, murine resident peritoneal macrophages (pmacs), that changes in gene expression occurred that were reflective of functional macrophage polarization following IL-4/-13 treatment. We found changes consistent with those reported by others, allowing us to confidently utilize these cytokines to induce an M2a phenotype [58,59] (S1 Fig). We next investigated the effect of these cytokines on the ability of both murine pmacs and human MDMs to support infection of rVSV/EBOV GP.…”

Effect of Polarization and Chronic Inflammation on Macrophage Expression of Heparan Sulfate Proteoglycans and Biosynthesis Enzymes

“…Using published microarray data, we analyzed expression of HS biosynthetic enzymes and core proteins in macrophages upon in vitro polarization toward an M1 or an M2 phenotype. [40][41][42][43][44][45] This meta-analysis showed that HS sulfotransferase expression was largely downregulated in M1 compared with M2 macrophages, for both human and murine macrophages ( Fig. 3).…”

“…47 It is unclear whether macrophage polarization in vitro affects HPSE1 expression, as one study on human macrophages reported increased expression 40 upon polarization with IFNγ, while murine studies reported decreased expression. 44,45 We cannot rule out differences in HPSE1 regulation in mouse and human. In addition, HPSE1 expression in other diseases does not correlate with the macrophage polarization state.…”

“…82 It is highly probable that GLCE also affects binding and signaling in macrophages, as all the characterized protein binding HS-sites contain at least one IdoA. 39 46 The expression of HS2ST1, HS3ST1, HS3ST2, and HS6ST1 is dramatically downregulated up to 12.5-fold in human and murine M1 macrophages in vitro, [40][41][42]44,45 strongly suggesting an anti-inflammatory role of O-sulfation. In line with these studies, HS2ST1, HS3ST1, HS3ST2, and HS6ST1 are also decreased up to 100-fold in macrophages from M1-driven diseases such as RA, 47,48 while their expression is increased in macrophages from more M2-associated diseases, such as asthma and COPD.…”

Computational approach to identifying universal macrophage biomarker

“…We observed that TYROBP and FCER1G both have significantly (p < 0.0001) lower standard deviation compared to the established biomarkers. However, since this dataset was part of training data for this analysis, we demonstrated this phenomena in two other independent human datasets GSE13896 (n = 170) 54 , and GSE40885 (n = 14) 35 , and three other mouse datasets GSE62420 (n = 56) 31 , GSE69607 (n = 8) 55 , and GSE81922 (n = 6) 56 . This suggests that macrophages have variable expression patterns for the established biomarkers.…”