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Bioinformatics approach to evaluate differential gene expression of M1/M2 macrophage phenotypes and antioxidant genes
Ricardo Fagundes da Rocha1, Marco Antônio De Bastiani, Fábio Klamt
1Laboratory of Cellular Biochemistry, Department of Biochemistry, Institute of Health Basic Sciences (ICBS), Federal University of Rio Grande do Sul (UFRGS), Rua Ramiro Barcelos - 2600, Porto Alegre, Rio Grande do Sul, 90035-003, Brazil, 00140244@ufrgs.br.
Abstract:
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.
Insights
Atherosclerosis involves increased human antioxidant genes (HAG) and M1 macrophage gene expression in advanced plaques. Macrophages from atherosclerotic subjects show higher HAG, M1, and M2 gene expression, suggesting no distinct polarization in this disease.
Area of Science:
- Cardiovascular Biology
- Immunology
- Genomics
Background:
- Atherosclerosis is a pro-inflammatory condition linked to redox imbalances.
- The roles of M1 (pro-inflammatory) and M2 (anti-inflammatory) macrophages in atherosclerosis remain unclear.
- Macrophages are key players in the development and progression of atherosclerotic plaques.
Purpose of the Study:
- To compare gene expression of human antioxidant genes (HAG) and M1/M2 macrophage markers in early versus advanced atherosclerotic plaques.
- To analyze differential gene expression in peripheral macrophages and foam cells from healthy and atherosclerotic subjects.
- To investigate macrophage polarization in the context of atherosclerosis.
Main Methods:
- Meta-analysis of public microarray datasets (GSE28829, GSE9874) from the Gene Expression Omnibus.
- Utilized STRING and Medusa for functional interaction analysis.
- Statistical analysis performed using ViaComplex and gene set enrichment analysis (GSEA).
Main Results:
- Activity of HAG and M1 gene sets significantly increased in advanced compared to early atherosclerotic plaques.
- Peripheral macrophages from atherosclerotic subjects showed increased HAG, M1, and M2 gene expression versus healthy subjects.
- Foam cells from atherosclerotic subjects showed increased M1 gene expression, but unlike cancer, no distinct M1/M2 polarization was observed.
Conclusions:
- In atherosclerosis, unlike cancer, macrophages do not exhibit distinct M1 or M2 polarization.
- Both M1 and M2 macrophage phenotypes appear to be equally induced in atherosclerosis.
- Findings provide insights into disease progression and potential therapeutic strategies.
