Bioinformatics Approach to Evaluate Differential Gene Expression of M1/M2 Macrophage Phenotypes and Antioxidant Genes in Atherosclerosis

• Published in: Cell biochemistry and biophysics 2014-11, Vol.70 (2), p.831-839
• Main Authors: da Rocha, Ricardo Fagundes, De Bastiani, Marco Antônio, Klamt, Fábio
• Format: Article
• Language: English
• Subjects: Antioxidants; Antioxidants - metabolism; Biochemistry; Bioinformatics; Biological and Medical Physics; Biomedical and Life Sciences; Biophysics; Biotechnology; Cell Biology; Computational Biology; Gene Expression Profiling; Humans; Life Sciences; Macrophages - cytology; Macrophages - metabolism; Original Paper; Pharmacology/Toxicology; Phenotype; Plaque, Atherosclerotic - genetics; Plaque, Atherosclerotic - immunology; RNA, Messenger - genetics; RNA, Messenger - metabolism; Statistical analysis
• ISSN: 1085-9195; 1559-0283
• DOI: 10.1007/s12013-014-9987-3

Atherosclerosis is a pro-inflammatory process intrinsically related to systemic redox impairments. Macrophages play a major role on disease development. The specific involvement of classically activated, M1 (pro-inflammatory), or the alternatively activated, M2 (anti-inflammatory), on plaque formation and disease progression are still not established. Thus, based on meta-data analysis of public micro-array datasets, we compared differential gene expression levels of the human antioxidant genes (HAG) and M1/M2 genes between early and advanced human atherosclerotic plaques, and among peripheric macrophages (with or without foam cells induction by oxidized low density lipoprotein, oxLDL) from healthy and atherosclerotic subjects. Two independent datasets, GSE28829 and GSE9874, were selected from gene expression omnibus ( http://www.ncbi.nlm.nih.gov/geo/ ) repository. Functional interactions were obtained with STRING ( http://string-db.org/ ) and Medusa ( http://coot.embl.de/medusa/ ). Statistical analysis was performed with ViaComplex ® ( http://lief.if.ufrgs.br/pub/biosoftwares/viacomplex/ ) and gene score enrichment analysis ( http://www.broadinstitute.org/gsea/index.jsp ). Bootstrap analysis demonstrated that the activity (expression) of HAG and M1 gene sets were significantly increased in advance compared to early atherosclerotic plaque. Increased expressions of HAG, M1, and M2 gene sets were found in peripheric macrophages from atherosclerotic subjects compared to peripheric macrophages from healthy subjects, while only M1 gene set was increased in foam cells from atherosclerotic subjects compared to foam cells from healthy subjects. However, M1 gene set was decreased in foam cells from healthy subjects compared to peripheric macrophages from healthy subjects, while no differences were found in foam cells from atherosclerotic subjects compared to peripheric macrophages from atherosclerotic subjects. Our data suggest that, different to cancer, in atherosclerosis there is no M1 or M2 polarization of macrophages. Actually, M1 and M2 phenotype are equally induced, what is an important aspect to better understand the disease progression, and can help to develop new therapeutic approaches.