A Gene Expression Signature That Classifies Human Atherosclerotic Plaque by Relative Inflammation Status

Abstract

Background-Atherosclerosis is a complex disease requiring improvements in diagnostic techniques and therapeutic treatments. Both improvements will be facilitated by greater exploration of the biology of atherosclerotic plaque. To this end, we carried out large-scale gene expression analysis of human atherosclerotic lesions. Methods and Results-Whole genome expression analysis of 101 plaques from patients with peripheral artery disease identified a robust gene signature (1514 genes) that is dominated by processes related to Toll-like receptor signaling, T-cell activation, cholesterol efflux, oxidative stress response, inflammatory cytokine production, vasoconstriction, and lysosomal activity. Further analysis of gene expression in microdissected carotid plaque samples revealed that this signature is differentially expressed in macrophage-rich and smooth muscle cell-containing regions. A quantitative PCR gene expression panel and inflammatory composite score were developed on the basis of the atherosclerotic plaque gene signature. When applied to serial sections of carotid plaque, the inflammatory composite score was observed to correlate with histological and morphological features related to plaque vulnerability. Conclusions-The robust mRNA expression signature identified in the present report is associated with pathological features of vulnerable atherosclerotic plaque and may be useful as a source of biomarkers and targets of novel antiatherosclerotic therapies. (Circ Cardiovasc Genet. 2011;4:595-604.)Key Words: plaque Ⅲ macrophage Ⅲ smooth muscle cell Ⅲ correlation Ⅲ coexpression A therosclerosis and its clinical sequelae, coronary heart disease, stroke, and peripheral vascular disease, represent significant medical problems. In the United States, approximately 13 million patients have diagnosed coronary heart disease, and almost 800 000 deaths in 2007 were due to cardiovascular disease or its complications. 1 Despite recent advances in pharmacological intervention, identification and prevention of processes leading to atherosclerotic plaque rupture remain incomplete. Understanding the molecular mechanisms that drive this process is a critical step toward development of therapies to slow or reverse progression of atherosclerosis. Clinical Perspective on p 604Currently, few validated targets are available for pharmacological treatment of atherosclerosis, and a limited number of diagnostic techniques can accurately predict either plaque progression or response to treatment. Gene expression microarray technology and systems biology allow comprehensive characterization of the pathological processes associated with atherosclerosis, making possible the identification of new targets to treat this disease and new diagnostic measures of disease progression. 2 To understand the underlying disease pathophysiology and gain insights into plaque biology that could facilitate the discovery of new therapies, we have undertaken gene expression profiling of human plaque. Because of its availability and documented similarity ...

Association of Neuroimmune Guidance Cue Netrin-1 and Its Chemorepulsive Receptor UNC5B With Atherosclerotic Plaque Expression Signatures and Stability in Human(s)

“…We hypothesized that dysregulation of expression of NTN1 and its receptors associate with atherosclerosis and plaque stability in vivo. Using recently published macrophage and SMC signatures, 16 we studied the expression of NTN1 and its receptors in circulating monocytes and human(s) atherosclerotic plaque samples in vivo and their potential association with plaque stability.…”

“…Therefore, these genes were selected for differential expression and correlation analyses. 16 were used in the hierarchical clustering analysis to assess whether subgroups of samples had similar marker profiles as well as whether NTN1 and UNC5B showed similar expression levels across the samples. The procedure was performed using the heatmap.2 function from the gplots R library using all 92 artery samples.…”

“…Hierarchical clustering based on the expression of the 8 inflammation and SMC marker genes 16 showed distinct separation of plaque samples from controls ( Figure 1B). Furthermore, the plaque samples from the 3 arterial beds coalesced in 2 branches of the dendrogram.…”

Sphingomyelin Phosphodiesterase Acid-like 3A (SMPDL3A) Is a Novel Nucleotide Phosphodiesterase Regulated by Cholesterol in Human Macrophages

“…We hypothesize that in the atherosclerotic lesion, densely populated with cholesterol-enriched macrophage foam cells, SMPDL3A expression will also be significantly raised. In support of this hypothesis, microarray analysis of human carotid atherosclerotic plaque tissue by other groups has indicated that SMPDL3A forms part of a gene expression signature that is indicative of inflamed foam cellrich plaque tissue (38), and SMPDL3A is the fifth most up-regulated mRNA in symptomatic (unstable) plaque tissue obtained from carotid endarterectomy patients (39). Furthermore, our re-analysis of publicly available microarray expression data using the NCBI GEO database and GEO2R tool (40) (accession number GSE21419) reveals that Smpdl3a mRNA is significantly up-regulated in laser-capture microdissected atherosclerotic plaques from apoE Ϫ/Ϫ mice, versus the adjacent healthy adventitial tissue (41,42).…”

Erratum: Inflammatory processes in cardiovascular disease: a route to targeted therapies

“…The inflammatory state of plaque macrophages was shown to be dynamically regulated as the severity of disease varied 144 . In humans, studies using LCM on surgical plaque explants has also identified genes implicated in lipid metabolism (such as FABP4 and LEP) and activation of the adipokine/peroxisome proliferator-activator receptor (PPAR) signalling pathways 145 , as well as a repertoire of inflammatory gene 'signatures' 146 , that might be important in mechanistic staging. Early findings utilizing this approach seem to corroborate observations from genome-wide association studies as well as plaque compositional changes in plaque revealed by highresolution MRI Chai, personal communication.…”