High resolution genomic analysis of sporadic breast cancer using array-based comparative genomic hybridization

INTRODUCTION: Genomic aberrations in the form of subchromosomal DNA copy number changes are a hallmark of epithelial cancers, including breast cancer. The goal of the present study was to analyze such aberrations in breast cancer at high resolution. METHODS: We employed high-resolution array comparative genomic hybridization with 4,134 bacterial artificial chromosomes that cover the genome at 0.9 megabase resolution to analyze 47 primary breast tumors and 18 breast cancer cell lines. RESULTS: Common amplicons included 8q24.3 (amplified in 79% of tumors, with 5/47 exhibiting high level amplification), 1q32.1 and 16p13.3 (amplified in 66% and 57% of tumors, respectively). Moreover, we found several positive correlations between specific amplicons from different chromosomes, suggesting the existence of cooperating genetic loci. Queried by gene, the most frequently amplified kinase was PTK2 (79% of tumors), whereas the most frequently lost kinase was PTK2B (hemizygous loss in 34% of tumors). Amplification of ERBB2 as measured by comparative genomic hybridization (CGH) correlated closely with ERBB2 DNA and RNA levels measured by quantitative PCR as well as with ERBB2 protein levels. The overall frequency of recurrent losses was lower, with no region lost in more than 50% of tumors; the most frequently lost tumor suppressor gene was RB1 (hemizygous loss in 26% of tumors). Finally, we find that specific copy number changes in cell lines closely mimicked those in primary tumors, with an overall Pearson correlation coefficient of 0.843 for gains and 0.734 for losses. CONCLUSION: High resolution CGH analysis of breast cancer reveals several regions where DNA copy number is commonly gained or lost, that non-random correlations between specific amplicons exist, and that specific genetic alterations are maintained in breast cancer cell lines despite repeat passage in tissue culture. These observations suggest that genes within these regions are critical to the malignant phenotype and may thus serve as future therapeutic targets

Characterization of adjacent breast tumors using oligonucleotide microarrays

BACKGROUND: Current methodology often cannot distinguish second primary breast cancers from multifocal disease, a potentially important distinction for clinical management. In the present study we evaluated the use of oligonucleotide-based microarray analysis in determining the clonality of tumors by comparing gene expression profiles. METHOD: Total RNA was extracted from two tumors with no apparent physical connection that were located in the right breast of an 87-year-old woman diagnosed with invasive ductal carcinoma (IDC). The RNA was hybridized to the Affymetrix Human Genome U95A Gene Chip(®) (12,500 known human genes) and analyzed using the Gene Chip Analysis Suite(®) 3.3 (Affymetrix, Inc, Santa Clara, CA, USA) and JMPIN(®) 3.2.6 (SAS Institute, Inc, Cary, NC, USA). Gene expression profiles of tumors from five additional patients were compared in order to evaluate the heterogeneity in gene expression between tumors with similar clinical characteristics. RESULTS: The adjacent breast tumors had a pairwise correlation coefficient of 0.987, and were essentially indistinguishable by microarray analysis. Analysis of gene expression profiles from different individuals, however, generated a pairwise correlation coefficient of 0.710. CONCLUSION: Transcriptional profiling may be a useful diagnostic tool for determining tumor clonality and heterogeneity, and may ultimately impact on therapeutic decision making

Managing high dose oxytocin via a standardized protocol: An institutional experience *********

ABSTRACT Aims: Oxytocin has been on the Institute for Safe Medication Practices (ISMP) high alert medication list since 2007. This raises concern over the safety of oxytocin, especially in higher dose regimens. However, expediting delivery using high dose oxytocin would facilitate care for more patients by decreasing length of hospitalization. Drawing off the experience from the aviation industry, standardized protocols have been shown to increase both safety and efficiency. A high dose, standardized oxytocin protocol may expedite labor without sacrificing patient safety. We evaluated the impact of a high dose oxytocin protocol for labor induction with a hypothesis that length of hospitalization would decrease without adverse obstetrical or maternal outcomes. We further hypothesized that education regarding the use of high dose oxytocin would increase nursing compliance with the protocol. Methods: A retrospective cohort study involving 277 obstetric patients >35 weeks gestation who received oxytocin before protocol and 109 patients after protocol for induction / augmentation of labor. Oxytocin orders were standardized into a "low" and "high" dose protocol. Educational sessions were held to explain the safety and efficacy of these regimens. Obstetric interventions, outcomes, and nursing compliance with oxytocin orders were evaluated before and after standardization. Results: A comparison of intra-partum interventions and outcomes at the time of delivery showed no difference in the rate of occurrence in the before or after protocol implementation (p >0.05). While the overall percentage of patients receiving the high dose oxytocin protocol as ordered improved from 52.8% before protocol implementation to 66.7% after implantation, this difference was not significant (p >0.05). The high dose protocol (6x6) was the only treatment where the patients did not always get oxytocin administered as ordered. The rate of maternal infectious morbidity was reduced almost by half after protocol standardization (5.8% before versus 2.8% after). However, this was not statistically significant (p = 0.21). A significant barrier to implementation of the high dose protocol was nursing compliance with the standard orders (47% before protocol/33% after protocol). Upon further questioning, it was identified this was due to nursing concerns about possible adverse side effects in high risks obstetrical patients. Conclusion: We found no significant difference between the low and high dose protocols as far as the outcome/intervention parameters studied. Nursing compliance proved to be a barrier to implementation of the high dose protocol

HOXA9 regulates BRCA1 expression to modulate human breast tumor phenotype

Breast cancer 1, early onset (BRCA1) expression is often reduced in sporadic breast tumors, even in the absence of BRCA1 genetic modifications, but the molecular basis for this is unknown. In this study, we identified homeobox A9 (HOXA9) as a gene frequently downregulated in human breast cancers and tumor cell lines and noted that reduced HOXA9 transcript levels associated with tumor aggression, metastasis, and patient mortality. Experiments revealed that loss of HOXA9 promoted mammary epithelial cell growth and survival and perturbed tissue morphogenesis. Restoring HOXA9 expression repressed growth and survival and inhibited the malignant phenotype of breast cancer cells in culture and in a xenograft mouse model. Molecular studies showed that HOXA9 restricted breast tumor behavior by directly modulating the expression of BRCA1. Indeed, ectopic expression of wild-type BRCA1 phenocopied the tumor suppressor function of HOXA9, and reducing BRCA1 levels or function inhibited the antitumor activity of HOXA9. Consistently, HOXA9 expression correlated with BRCA1 in clinical specimens and with tumor aggression in patients lacking estrogen receptor/progesterone receptor expression in their breast tissue. These findings indicate that HOXA9 restricts breast tumor aggression by modulating expression of the tumor suppressor gene BRCA1, which we believe provides an explanation for the loss of BRCA1 expression in sporadic breast tumors in the absence of BRCA1 genetic modifications