HMEC nine-condition expression profiling

Exposure to air particulate matter is associated with increased cardiovascular morbidity and mortality. One of the possible mechanisms is by promotion of atherosclerosis mediated by synergy of particulate matter chemicals and oxidized phospholipids on vascular endothelial cells. We treated human microvascular endothelial cells (HMEC) in triplicate wells with diesel exhaust particles (DEP) extract at a concentration of 5 and 25 mcg/ml, oxidized 1-palmitoyl-2-arachidonyl-sn-glycero-3-phosphorylcholine (ox-PAPC) at concentrations of 10, 20 and 40 mcg/ml or combination of DEP at 5 mcg/ml plus ox-PAPC at 10, 20 and 40 mcg/ml. The 3600 most variably expressed genes were employed to construct a weighted gene co-expression network to assess the degree of connectivity. Module enrichment analysis showed that three modules (Brown, Green and Yellow) were highly significant (p< 0.0001) in enriched genes regulated by the treatments. These three modules exhibited patterns of synergistic/additive interaction and were enriched in pathway genes relevant to vascular inflammation. The in-vivo relevance of this gene clustering analysis was established by demonstrating that liver gene expression of hypercholesterolemic mice exposed to ultrafine particles exhibited significant upregulation of similar gene pathways, as predicted by the in-vitro synergy. Keywords: Expression profiling comparison, effect of DEP vs. ox-PAPC vs. DEP plus ox-PAPC This experiment compares gene expression profiles of HMEC exposed to DEP, ox-PAPC or DEP plus ox-PAPC by Illumina HumanRef-8 v1 Expression Beadarrays. This design allowed to establish the genome wide synergistic effects of co-regulation induced by DEP and ox-PAPC.