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  • Title: Rationale and study design of the CardioGene Study: genomics of in-stent restenosis.
    Author: Ganesh SK, Skelding KA, Mehta L, O'Neill K, Joo J, Zheng G, Goldstein J, Simari R, Billings E, Geller NL, Holmes D, O'Neill WW, Nabel EG.
    Journal: Pharmacogenomics; 2004 Oct; 5(7):952-1004. PubMed ID: 15469413.
    Abstract:
    BACKGROUND AND AIMS: in-stent restenosis is a major limitation of stent therapy for atherosclerosis coronary artery disease. The CardioGene Study is an ongoing study of restenosis in bare mental stents (BMS) for the treatment of coronary artery disease. The overall goal is to understand the genetic determinants of the responses to vascular injury that result in the development of restenosis in some patients but not in others. Gene expression profiling at transcriptional and translational levels provides global assessment of gene activity after vascular injury and mechanistic insight. Furthermore, the delineation of genetic biomarkers would be of value in the clinical setting of risk-stratify patients prior to stent therapy. Prospective risk stratification would allow for the rational selection of specialized treatments against the development of in-stent restenosis (ISR), such as drug-eluting stents. SETTING: Patients are enrolled at two sites in the US with high-volume cardiac catheterization facilities: the William Beaumont Hospital in Royal Oak, MI, USA, and the Mayo Clinic in Rochester, MN, USA. STUDY DESIGN: Two complementary study designs are used to understand the molecular mechanisms of restenosis and the genetic biomarkers predictive of restenosis. First, 350 patients are enrolled prospectively at the time of stent implantation. Blood is sampled prior to stent placement and afterwards at 2 weeks and 6 months. The clinical outcome of restenosis is determined 6 and 12 months after stent placement. The primary outcome is clinical restenosis at 6 months. The major secondary outcome is clinical restenosis at 12 months. Second, a corollary case-control analysis will be carried out with the enrollment of an additional 250 cases with a history of recurrent restenosis after treatment with BMS. Controls for this analysis are derived from the prospective cohort. PATIENTS AND METHODS: Consecutive patients presenting to the cardiac catheterization laboratory are screened, informed about the study and enrolled after signing the consent form. Enrollment has been completed for the prospective cohort, and enrollment of the additional group is ongoing. A standardized questionnaire is used to collect clinical data primarily through direct patient interview to assess medical history, medication use, functional status, family history, environmental factors, and social history. Further data are abstracted from the medical charts and catheterization reports. A total of 276 clinical variables are collected per individual at baseline, and 49 variables are collected at each of the 6- and 12-month follow-up visits. A Clinical Events Committee adjudicates clinical outcomes. Blood samples are processed at each clinical enrollment site using standardized operating procedures. From each blood sample, several aliquots are prepared and stored of peripheral blood mononuclear cells, granulocytes, platelets, serum, and plasma. Additionally, a portion of each patient's leukocytes is cryopreserved for future cell-line creation. Samples are frozen and shipped to the National Heart, Lung and Blood Institute (NHLBI). Additional materials generated in the analysis of the samples at the NHLBI are frozen and stored, including isolated genomic DNA, total RNA, reverse transcribed cDNA libraries and labeled RNA hybridization mixtures used in microarray analysis. Per individual in the prospective cohort, high-quality transcript profiles of peripheral blood mononuclear cells at each time of blood sampling are obtained using Affymetrix U133A microarrays (Affymetrix, Santa Clara, CA, USA). Per chip, this yields 495,930 features per individual per time of sampling. This represents expression levels for 22,283 genes per patients oer time of blood sampling, including 14,500 well-characterized human genes. Proteomics of plasma is performed with multidimensional liquid chromatography and tandem mass spectrometry. Protein expression is examined similarly to mRNA expression as a measure of gene expression. Genotyping is performed in two manners. First, those genes showing differential expression at the levels of mRNA and protein are investigated using a candidate gene approach. Specific variants in known gene regulatory regions, such as promoters, are sought initially, as those variants may explain differences in expression level. Second, a genome-wide scan is used to identify genetic loci that are associated with ISR. Those regions identified are further examined for genes that show differential expression in the mRNA microarray profiling or proteomics investigations. These genes are finely investigated for candidate SNPs and other gene variants. Complementary genomic and proteomic approaches are expected to be robust. Integration of data sets is accomplished using a variety of informatics tools, organization of gene expression into functional pathways, and investigation of physical maps of up- and downregulated sets of genes. CONCLUSIONS: The CardioGene Study is designed to understand ISR. Global gene and protein expression profiling define molecular phenotypes of patients. Well-defined clinical phenotypes will be paired with genomic data to define analyses aimed to achieve several goals. These include determining blood gene and protein expression in patients with ISR, investigating the genetic basis of ISR, developing predictive gene and protein biomarkers, and the identification of new targets for treatment.
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