Citations

Abstract Microarray gene expression profiling has facilitated identification of molecular subtypes which can be associated with disease outcome and treatment response. However current platforms lack disease focus, potentially missing vital information contained in patient tissue samples. Moreover, a wide range of FFPE sample cohorts are available but their use is limited by the mRNA degradation inherent to the sample fixation process. By combining the Breast Cancer DSA® with powerful data analysis methodology, we reproduced the five major molecular subtypes in breast cancer based on a cohort of 107 FFPE samples. Furthermore, we showed that the established subtypes do not extend to BRCA1 and BRCA2 mutant tumours, necessitating expansion of the original breast cancer subtypes definition. Following RMA pre-processing of the 107 raw profiles, the data was transformed to overcome the association between profile quality and expression variability. If left untreated, this technical variability, often observed with FFPE tissues, can impair the study of inherent biological variations. Using the intrinsic list of 277 genes previously identified as differentiating breast cancer subtypes in fresh frozen samples [Sorlie et al., 2003], initially the sporadic samples were examined using hierarchical agglomerative clustering. All five original subtypes were identified, verifying the ability to detect subtypes in FFPE samples using the breast cancer DSA®. When the intrinsic list was applied to all 107 samples including BRCA1 and BRCA2 mutant samples, the subtypes were still distinguishable, although 31% of the mutant tumors were unclassified suggesting that specific biological processes defining BRCA1/BRCA2 mutant tumours are not captured by the original breast cancer molecular classification. We have successfully overcome the limitation imposed by FFPE sample microarray profiling by using the Breast Cancer DSA® and advanced data manipulation and exploration to reproduce molecular subtypes previously identified using fresh frozen samples. Further investigation to extend the previously identifed subtypes will progress the investigation of the heterogeneous biology underlying breast cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 326. doi:10.1158/1538-7445.AM2011-326

Abstract Introduction: Genome-wide association studies of colorectal cancer have identified 18 risk variants that explain ∼25% of the hereditable risk of colorectal cancer. These variants are located in intronic, inter-genic or gene-desert regions. To uncover whether some of these variants may have a regulatory function on the expression of near-by genes, we conducted expression quantitative trait loci (eQTL) analyses of these 18 regions. Methods: DNA and RNA were extracted from 40 fresh-frozen paired colon tumor (microsatellite stable and CpG island methylator phenotype-negative) and adjacent normal tissue samples collected by the Colon Cancer Family Registry. Whole genome gene expression assessment was performed in the tumors and adjacent normal tissue with the Affymetrix GeneChip Human Exon 1.0 ST array. Genome-wide SNP data was generated with DNA extracted from the same normal tissue samples using the Affymetrix Genome-Wide Human SNP 6.0 array. Partek software was used to compare the expression levels by genotype for each gene spanning a 2 Mb region up- and down- stream of each of the 18 established risk variants for colorectal cancer. Results: Three of the 18 risk variants (rs10795668, rs4444235, rs9929218) demonstrated significant cis-eQTLs (FDR q-values<0.05). Specifically, differential gene expression was observed in genes neighboring rs10795668 at 10p14 (ATP5C1, q=0.024), rs4444235 at 14q22.2 (DLGAP5, q=0.041), and rs9929218 at 16q22.1 (NOL3, q=0.017; DDX28, q=0.046). In particular, DLGAP5 (discs, large (Drosophila) homolog-associated protein 5) at 14q22.2 and NOL3 (nucleolar protein 3) at 16q22 are interesting candidate genes for colorectal cancer. DLGAP5 encodes for a microtubule-associated protein and functions as a mitotic regulator that has been reported to be overexpressed in colon tumors. NOL3 (nucleolar protein 3) encodes for an anti-apoptotic protein that down-regulates the expression of caspase 2 and 8, and p53. NOL3 also appears to be overexpressed in colorectal tumors. Conclusion: In summary, these findings suggest putative functional activities for three established colorectal risk variants and highlight potentially interesting candidate genes for this malignancy. If confirmed, these results may help explain the total genetic risk of the disease, as well as further our understanding of the underlying biology of colorectal cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4732. doi:10.1158/1538-7445.AM2011-4732

Background —In patients receiving intracoronary stents, stent thrombosis is reduced when ticlopidine therapy is combined with aspirin after the procedure. However, ticlopidine causes neutropenia in 1% of patients when administered for >2 weeks, and little is known about the duration that ticlopidine needs be administered to prevent stent thrombosis. Methods and Results —We analyzed 827 patients undergoing successful stent placement in 1061 coronary segments at Mayo Clinic who were treated between May 1, 1996, and October 31, 1997. Chronic warfarin therapy, cardiogenic shock, and enrollment in research protocols requiring 4 weeks of ticlopidine were exclusion criteria; ticlopidine was discontinued after 14 days in all remaining patients. The mean age of the study population was 64±11 years; 49% had suffered a prior infarction, 20% had undergone coronary artery bypass surgery, and 65% had multivessel disease. The indication for stent placement was dissection or abrupt closure in 31% of patients and suboptimal results from balloon angioplasty in 18%. Placement was elective in 51% of patients, and 10.3% of patients were treated within 12 hours of an acute myocardial infarction. Mean nominal stent size was 3.3±0.5 mm. High-pressure inflations (≥12 atm) were performed in all patients (mean, 17±4 atm). Intravascular ultrasound was used to facilitate stent placement in 8.8% of patients. Abciximab was administered to 38% of patients; 11% of patients who were at increased risk of stent thrombosis were treated with enoxaparin for 10 to 14 days. Adverse cardiovascular events in the 14 days after stent placement occurred in 11 patients (1.3%). Two patients died of nonischemic causes (sepsis and renal failure) in the 15th through 30th days after ticlopidine was stopped. However, there were no cardiovascular deaths, myocardial infarctions, coronary artery bypass operations, or repeat angioplasty procedures between the 15th and 30th days; stent thrombosis did not occur in any patient after ticlopidine had been stopped. No patient developed neutropenia, although 1.8% of the first 489 patients who were closely monitored for side effects from ticlopidine developed side effects requiring its discontinuation, and milder side effects occurred in 4.7%. Conclusions —In patients receiving intracoronary stents, the discontinuation of ticlopidine therapy 14 days after stent placement is associated with a very low frequency of stent thrombosis and other adverse events.

Background —Noninvasive assessment of diastolic filling by Doppler echocardiography provides important information about left ventricular (LV) status in selected subsets of patients. This study was designed to assess whether mitral annular velocities as assessed by tissue Doppler imaging are associated with invasive measures of diastolic LV performance and whether additional information is gained over traditional Doppler variables. Methods and Results —One hundred consecutive patients referred for cardiac catheterization underwent simultaneous Doppler interrogation. Invasive measurements of LV pressures were obtained with micromanometer-tipped catheters, and the mean LV diastolic pressure (M-LVDP) was used as a surrogate for mean left atrial pressure. Doppler signals from the mitral inflow, pulmonary venous inflow, and TDI of the mitral annulus were obtained. Isolated parameters of transmitral flow correlated with M-LVDP only when ejection fraction <50%. The ratio of mitral velocity to early diastolic velocity of the mitral annulus (E/E′) showed a better correlation with M-LVDP than did other Doppler variables for all levels of systolic function. E/E′ <8 accurately predicted normal M-LVDP, and E/E′ >15 identified increased M-LVDP. Wide variability was present in those with E/E′ of 8 to 15. A subset of those patients with E/E′ 8 to 15 could be further defined by use of other Doppler data. Conclusions —The combination of tissue Doppler imaging of the mitral annulus and mitral inflow velocity curves provides better estimates of LV filling pressures than other methods (pulmonary vein, preload reduction). However, accurate prediction of filling pressures for an individual patient requires a stepwise approach incorporating all available data.

Background —The physiological stress suffered by patients with heart failure results in an increased production of cortisol and a shift in the leukocyte differential toward a decreased percentage of lymphocytes (%L). The purpose of this study was to determine the prognostic significance of a low %L in advanced heart failure. Methods and Results —Patients evaluated in our cardiac transplantation clinic between April 1988 and July 1995 were retrospectively reviewed (n=263). Fifty-two patients were excluded because they had recent trauma, infection, surgery, myocardial infarction, corticosteroid use, or history of malignancy. In the remaining 211 patients, we used Cox proportional hazards analysis to examine the association between survival and transplant-free survival with baseline variables. Univariate analysis showed a significant association between time to death and %L ( P =.004), New York Heart Association (NYHA) class ( P =.002), and maximal oxygen uptake ( P =.05). Univariate analysis of the end point of survival free from transplantation yielded similar results. One- and 4-year survival rates for patients with a low %L (<20.3%) were 78% and 34% compared with 90% and 73% for those with a normal %L. Multivariate analysis showed NYHA class ( P <.008) and %L ( P <.01) were independent predictors of survival and survival free from cardiac transplantation. Conclusions The relative lymphocyte concentration is an inexpensive, readily available, simple prognostic marker in patients with symptomatic heart failure who do not have recent trauma, infection, surgery, myocardial infarction, corticosteroid use, or history of malignancy. It could be incorporated into clinical models to predict patient outcome and to aid in the selection of patients for cardiac transplantation.