Transcriptome analysis of the ischemia-reperfused remodeling myocardium: temporal changes in inflammation and extracellular matrix. Physiol Genomics 25: 364 -374, 2006. First published March 22, 2006 doi:10.1152/physiolgenomics.00013.2006.-cDNA microarray analysis was performed to screen 15,000 genes and expressed sequence tags (ESTs) to identify changes in the ischemia-reperfused (I-R) rat myocardial transcriptome in the early (day 2) and late (day 7) inflammatory phases of acute myocardial infarction. Lists of candidate genes that were affected by I-R transiently (2 or 7 days only) or on a more sustained basis (2 and 7 days) were derived. The candidate genes represented three major functional categories: extracellular matrix, apoptosis, and inflammation. To expand on the findings from microarray studies that dealt with the two above-mentioned time points, tissues collected from days 0, 0.25, 2, 3, 5, and 7 after reperfusion were examined. Acute myocardial infarction resulted in upregulation of IL-6 and IL-18. Genes encoding extracellular matrix proteins such as types I and III collagen were upregulated in day 2, and that response progressively grew stronger until day 7 after I-R. Comparable response kinetics was exhibited by the candidate genes of the apoptosis category. Caspases-2, -3, and -8 were induced in response to acute infarction. Compared with the myocardial tissue from the sham-operated rats, tissue collected from the infarct region stained heavily positive for the presence of active caspase-3. Laser microdissection and pressure catapulting technology was applied to harvest infarct and adjacent noninfarct control tissue from a microscopically defined region in the rat myocardium. Taken together, this work presents the first evidence gained from the use of DNA microarrays to understand the molecular mechanisms implicated in the early and late inflammatory phases of the I-R heart. heart; oxygen; perceived hyperoxia; wound healing AN ACUTE MYOCARDIAL INFARCTION induces ventricular remodeling, a process that can influence ventricular functions and survival outcomes (22). Ventricular remodeling is directly implicated in postinfarction development of ventricular dilatation, a predictive sign of future congestive heart failure. Timedependent changes in ventricular architecture occur in the infarcted and noninfarcted regions, resulting in hypertrophy of the viable regions of the affected site (6). Cardiac remodeling after myocardial infarction depends on cellular responses, characterized by hypertrophy of myocytes and hyperplasia of interstitial fibroblasts (18). Animals that survive with large transmural infarctions develop heart failure without another ischemic event, as is typically seen in humans. A rat model of myocardial infarction has been extensively studied to understand the functional, structural, and molecular changes associated with clinical ischemic heart disease (23, 33). Substantial alterations in gene expression are needed to afford such profound changes within cells of the remodeling myocar...