Differential gene expression in coronary arteries from patients presenting with ischemic heart disease: Further evidence for the inflammatory basis of atherosclerosis

doi:10.1016/j.ahj.2004.10.025

American Heart Journal

Volume 150, Issue 3, September 2005, Pages 488-499

https://doi.org/10.1016/j.ahj.2004.10.025 Get rights and content

Background and Objective

The pathogenesis of human coronary artery disease (CAD) is likely to require the transcription of many different genes. We report here the differential gene expression profiling of human CAD using copy DNA (cDNA)/nylon array hybridization techniques.

Methods and Results

Human coronary arteries were obtained at the time of cardiac transplantation. Ten patients were transplanted for ischemic heart disease (IHD) and 5 for dilated cardiomyopathy (DCM). We generated a customized cDNA array containing 9206 clones and after hybridization of patient samples, data reduction, and refinement, identified 515 sequence-verified, differentially expressed clones. These clones represented 361 genes that were differentially expressed at significant levels between IHD and DCM arteries (t test, P < .05). Of these clones, 70% were defined genes of known function and 30% were genes of unknown function. Of the differentially expressed genes, 53.6% were up-regulated and 46.4% were down-regulated.

Hierarchical clustering was performed and several distinct functional clusters were identified, including a cluster of genes related to inflammatory mechanisms. Validation by real-time polymerase chain reaction was undertaken with 2 genes known to be up-regulated in atherosclerosis (interleukin 1β [IL-1β] and IL-8) and 2 novel genes identified by the array analysis (signal transducer and activator of transcription 6 [STAT6] and IL-1 receptor–associated kinase [IRAK]). Differential expression of IL-1β, IL-8, and STAT6 were confirmed by this method.

Immunohistochemistry of STAT6 demonstrated increased expression in vascular smooth muscle cells of IHD coronary arteries.

Conclusion

These data support the inflammatory basis of human atherosclerotic CAD and identify novel genes in atherosclerosis.

Section snippets

Tissues

Coronary arteries from patients with a diagnosis of ischemic heart disease (IHD, n = 10) and dilated cardiomyopathy (DCM, n = 5) were harvested from transplantation recipients at the time of surgery (Table I). Patients diagnosed as having DCM were free of CAD before transplantation, as assessed by coronary angiography and histological analysis using the American Heart Association (AHA) classification system.18, 19 All patients were men and white in origin.

Patient artery samples were frozen in

Patient sample hybridization

Ten IHD and 5 DCM samples from patients presenting for cardiac transplantation were hybridized to the customized cDNA nylon arrays in duplicate and the data collected. There were no apparent differences in mean age, ethnicity, diabetic status, or hyperlipidemic status of the patients in this study (Table I). The AHA pathological classification18, 19 was applied to those arteries used in the final analysis (Table I). All arteries from ischemic hearts were Stary class V or greater, whereas

Discussion

This study has used gene array methodology to perform cDNA expression profiling on whole human IHD and DCM coronary arteries. Only one other recently published study¹⁵ has used this tissue source, which was hybridized to oligonucleotide rather than cDNA arrays; our data confirm and add to this body of work. In the study described here, data reduction was stringent and quality control exacting, and these rigorous criteria reduced our total analyzable samples. However, from those samples that

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¹: These authors contributed equally to this work.

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Clinical InvestigationGeneticsDifferential gene expression in coronary arteries from patients presenting with ischemic heart disease: Further evidence for the inflammatory basis of atherosclerosis

Background and Objective

Methods and Results

Conclusion

Section snippets

Tissues

Patient sample hybridization

Discussion

Cell

J Biol Chem

Biochem Biophys Res Commun

Exp Mol Pathol

Blood

Immunity

Atherosclerosis

Nature

Altered patterns of gene expression in response to myocardial infarction

Circ Res

Conditional expression of a Gi-coupled receptor causes ventricular conduction delay and a lethal cardiomyopathy

Proc Natl Acad Sci U S A

Gene expression profile in mouse myocardium after ischemia

Physiol Genomics

Application of cDNA microarrays in determining molecular phenotype in cardiac growth, development, and response to injury

Circulation

Expression profiling reveals distinct sets of genes altered during induction and regression of cardiac hypertrophy

Proc Natl Acad Sci U S A

Overexpression of eotaxin and the CCR3 receptor in human atherosclerosis: using genomic technology to identify a potential novel pathway of vascular inflammation

Circulation

Decreased SLIM1 expression and increased gelsolin expression in failing human hearts measured by high-density oligonucleotide arrays

Circulation (Online)

Gene expression in atherosclerotic lesions of ApoE deficient mice

Mol Med

Identification of genes potentially involved in rupture of human atherosclerotic plaques

Circ Res

Gene expression profiling of apoptosis-related genes in human atherosclerosis: upregulation of death-associated proteins

Arterioscler Thromb Vasc Biol

Identification of new genes differentially expressed in coronary artery disease by expression profiling

Physiol Genomics

Gene expression in macrophage-rich inflammatory cell infiltrates in human atherosclerotic lesions as studied by laser microdissection and DNA array: overexpression of HMG-CoA reductase, colony stimulating factor receptors, CD11A/CD18 integrins, and interleukin receptors

Arterioscler Thromb Vasc Biol

Heterogeneity of gene expression in human atheroma unmasked using cDNA representational difference analysis

Physiol Genomics

A definition of initial, fatty streak, and intermediate lesions of atherosclerosis. A report from the Committee on Vascular Lesions of the Council on Arteriosclerosis, American Heart Association

Arterioscler Thromb

A definition of advanced types of atherosclerotic lesions and a histological classification of atherosclerosis. A report from the Committee on Vascular Lesions of the Council on Arteriosclerosis, American Heart Association

Circulation

1997 Annual report—advancing genomics with microarray systems

Efficient extraction of RNA from vascular tissue

Fluorescent dye–-primer cycle sequencing using unpurified PCR products as templates; development of a protocol amenable to high-throughput DNA sequencing

Nucleic Acids Res

CCR7 (EBI1) receptor down-regulation in asthma: differential gene expression in human CD4+ T lymphocytes

Q J Med

Identification of two novel diurnal genes by screening of a rat brain cDNA library

Mol Neurosci

Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations

Proc Natl Acad Sci U S A

Novel gene transcripts preferentially expressed in human muscles revealed by quantitative hybridization of a high density cDNA array

Genome Res

Clinical Investigation
Genetics
Differential gene expression in coronary arteries from patients presenting with ischemic heart disease: Further evidence for the inflammatory basis of atherosclerosis