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1 Cardiovascular Genome Unit, Department of Medicine
2 Department of Anesthesiology, Brigham and Women’s Hospital, Harvard Medical School, Boston 02115
3 Division of Cardiovascular Medicine, Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
4 Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts
5 Cardiology Branch, National Heart, Lung, and Blood Institute, Bethesda, Maryland
6 Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada
Despite similar clinical endpoints, heart failure resulting from dilated cardiomyopathy (DCM) or hypertrophic cardiomyopathy (HCM) appears to develop through different remodeling and molecular pathways. Current understanding of heart failure has been facilitated by microarray technology. We constructed an in-house spotted cDNA microarray using 10,272 unique clones from various cardiovascular cDNA libraries sequenced and annotated in our laboratory. RNA samples were obtained from left ventricular tissues of precardiac transplantation DCM and HCM patients and were hybridized against normal adult heart reference RNA. After filtering, differentially expressed genes were determined using novel analyzing software. We demonstrated that normalization for cDNA microarray data is slide-dependent and nonlinear. The feasibility of this model was validated by quantitative real-time reverse transcription-PCR, and the accuracy rate depended on the fold change and statistical significance level. Our results showed that 192 genes were highly expressed in both DCM and HCM (e.g., atrial natriuretic peptide, CD59, decorin, elongation factor 2, and heat shock protein 90), and 51 genes were downregulated in both conditions (e.g., elastin, sarcoplasmic/endoplasmic reticulum Ca2+-ATPase). We also identified several genes differentially expressed between DCM and HCM (e.g., 
B-crystallin, antagonizer of myc transcriptional activity, ß-dystrobrevin, calsequestrin, lipocortin, and lumican). Microarray technology provides us with a genomic approach to explore the genetic markers and molecular mechanisms leading to heart failure.
cDNA microarray; normalization; real-time reverse transcription-polymerase chain reaction
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